Changes between Initial Version and Version 1 of Ticket #15628


Ignore:
Timestamp:
Jul 18, 2024, 10:01:29 AM (17 months ago)
Author:
Eric Pettersen
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #15628

    • Property Component Unassigned → Window Toolkit
    • Property Owner set to Tom Goddard
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → assigned
    • Property Summary ChimeraX bug report submission → Crash changing Mac display configuration

  • Ticket #15628 – Description

    initial v1  
    6565  "threads" : 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    1479     "uuid" : "25b2f3eb-07b4-3cb9-9457-2c26210c27c8",
    1480     "path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
    1481     "name" : "libsystem_pthread.dylib"
    1482   },
    1483   {
    1484     "source" : "P",
    1485     "arch" : "x86_64",
    1486     "base" : 140703372247040,
    1487     "size" : 557048,
    1488     "uuid" : "93fb3816-608b-33af-83d2-209b4bd673ad",
    1489     "path" : "\/usr\/lib\/system\/libsystem_c.dylib",
    1490     "name" : "libsystem_c.dylib"
    1491   },
    1492   {
    1493     "source" : "P",
    1494     "arch" : "x86_64",
    1495     "base" : 140703373840384,
    1496     "size" : 45048,
    1497     "uuid" : "acde8386-eb3f-36f2-bc5e-069cc59d079c",
    1498     "path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
    1499     "name" : "libsystem_platform.dylib"
    1500   },
    1501   {
    1502     "size" : 0,
    1503     "source" : "A",
    1504     "base" : 0,
    1505     "uuid" : "00000000-0000-0000-0000-000000000000"
    1506   },
    1507   {
    1508     "source" : "P",
    1509     "arch" : "x86_64",
    1510     "base" : 140703464718336,
    1511     "CFBundleShortVersionString" : "1.600.0",
    1512     "CFBundleIdentifier" : "com.apple.SkyLight",
    1513     "size" : 4595703,
    1514     "uuid" : "c85f48c7-7d13-316b-a28b-cfbd2693b663",
    1515     "path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
    1516     "name" : "SkyLight"
    1517   },
    1518   {
    1519     "source" : "P",
    1520     "arch" : "x86_64",
    1521     "base" : 140703371943936,
    1522     "size" : 290802,
    1523     "uuid" : "511b909b-7a60-3295-9981-a508477c7893",
    1524     "path" : "\/usr\/lib\/system\/libdispatch.dylib",
    1525     "name" : "libdispatch.dylib"
    1526   },
    1527   {
    1528     "source" : "P",
    1529     "arch" : "x86_64h",
    1530     "base" : 140703374061568,
    1531     "CFBundleShortVersionString" : "6.9",
    1532     "CFBundleIdentifier" : "com.apple.CoreFoundation",
    1533     "size" : 4829181,
    1534     "uuid" : "59d4644f-7aa6-3767-80ab-73d7a388a4ff",
    1535     "path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
    1536     "name" : "CoreFoundation",
    1537     "CFBundleVersion" : "2503.1"
    1538   },
    1539   {
    1540     "source" : "P",
    1541     "arch" : "x86_64",
    1542     "base" : 140703552733184,
    1543     "CFBundleShortVersionString" : "2.1.1",
    1544     "CFBundleIdentifier" : "com.apple.HIToolbox",
    1545     "size" : 2732020,
    1546     "uuid" : "de4aeb8b-676c-3a36-9364-1cdee78a3b41",
    1547     "path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
    1548     "name" : "HIToolbox"
    1549   },
    1550   {
    1551     "source" : "P",
    1552     "arch" : "x86_64",
    1553     "base" : 140703431389184,
    1554     "CFBundleShortVersionString" : "6.9",
    1555     "CFBundleIdentifier" : "com.apple.AppKit",
    1556     "size" : 21164019,
    1557     "uuid" : "33ecd3dc-c895-35e2-a1fd-c1761b155964",
    1558     "path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
    1559     "name" : "AppKit",
    1560     "CFBundleVersion" : "2487.60.105"
    1561   },
    1562   {
    1563     "source" : "P",
    1564     "arch" : "x86_64",
    1565     "base" : 140703369920512,
    1566     "size" : 592800,
    1567     "uuid" : "baa6f02e-dff3-3562-8c99-ea2820c91ad9",
    1568     "path" : "\/usr\/lib\/dyld",
    1569     "name" : "dyld"
    1570   },
    1571   {
    1572     "source" : "P",
    1573     "arch" : "x86_64",
    1574     "base" : 140703372804096,
    1575     "size" : 503796,
    1576     "uuid" : "e443af07-488b-3b1b-83ae-31bd883e6ef1",
    1577     "path" : "\/usr\/lib\/libc++.1.dylib",
    1578     "name" : "libc++.1.dylib"
    1579   }
    1580 ],
     67[deleted to fit within ticket size limits],
    158168  "sharedCache" : {
    158269  "base" : 140703369224192,
    … …  
    29961483 
    29971484
    2998 > hide sel cartoons
    2999 
    3000 > select #1.6/B
    3001 
    3002 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    3003 
    3004 > show sel cartoons
    3005 
    3006 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    3007 
    3008 Chain information for AF3 E2 1-352.pdb #29 
    3009 --- 
    3010 Chain | Description 
    3011 B | No description available 
    3012  
    3013 
    3014 > matchmaker #29 to #1.6 & sel
    3015 
    3016 Parameters 
    3017 --- 
    3018 Chain pairing | bb 
    3019 Alignment algorithm | Needleman-Wunsch 
    3020 Similarity matrix | BLOSUM-62 
    3021 SS fraction | 0.3 
    3022 Gap open (HH/SS/other) | 18/18/6 
    3023 Gap extend | 1 
    3024 SS matrix |  |  | H | S | O 
    3025 ---|---|---|--- 
    3026 H | 6 | -9 | -6 
    3027 S |  | 6 | -6 
    3028 O |  |  | 4 
    3029 Iteration cutoff | 2 
    3030  
    3031 Matchmaker 3j0c.pdb1, chain B (#1.6) with AF3 E2 1-352.pdb, chain B (#29),
    3032 sequence alignment score = 583.7 
    3033 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    3034 5.933) 
    3035  
    3036 
    3037 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    3038 
    3039 Chain information for AF3 E2 353-438.pdb #30 
    3040 --- 
    3041 Chain | Description 
    3042 B | No description available 
    3043  
    3044 
    3045 > matchmaker #30 to #1.6 & sel
    3046 
    3047 Parameters 
    3048 --- 
    3049 Chain pairing | bb 
    3050 Alignment algorithm | Needleman-Wunsch 
    3051 Similarity matrix | BLOSUM-62 
    3052 SS fraction | 0.3 
    3053 Gap open (HH/SS/other) | 18/18/6 
    3054 Gap extend | 1 
    3055 SS matrix |  |  | H | S | O 
    3056 ---|---|---|--- 
    3057 H | 6 | -9 | -6 
    3058 S |  | 6 | -6 
    3059 O |  |  | 4 
    3060 Iteration cutoff | 2 
    3061  
    3062 Matchmaker 3j0c.pdb1, chain B (#1.6) with AF3 E2 353-438.pdb, chain B (#30),
    3063 sequence alignment score = 333.4 
    3064 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    3065 8.411) 
    3066  
    3067 
    3068 > hide sel cartoons
    3069 
    3070 > select #1.6/C
    3071 
    3072 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    3073 
    3074 > show sel cartoons
    3075 
    3076 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    3077 
    3078 Chain information for AF3 CA.pdb #31 
    3079 --- 
    3080 Chain | Description 
    3081 A | No description available 
    3082  
    3083 
    3084 > matchmaker #31 to #1.6 & sel
    3085 
    3086 Parameters 
    3087 --- 
    3088 Chain pairing | bb 
    3089 Alignment algorithm | Needleman-Wunsch 
    3090 Similarity matrix | BLOSUM-62 
    3091 SS fraction | 0.3 
    3092 Gap open (HH/SS/other) | 18/18/6 
    3093 Gap extend | 1 
    3094 SS matrix |  |  | H | S | O 
    3095 ---|---|---|--- 
    3096 H | 6 | -9 | -6 
    3097 S |  | 6 | -6 
    3098 O |  |  | 4 
    3099 Iteration cutoff | 2 
    3100  
    3101 Matchmaker 3j0c.pdb1, chain C (#1.6) with AF3 CA.pdb, chain A (#31), sequence
    3102 alignment score = 328.1 
    3103 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    3104 2.714) 
    3105  
    3106 
    3107 > hide sel cartoons
    3108 
    3109 > color #27 dodgerblue
    3110 
    3111 > color #28 dodgerblue
    3112 
    3113 > color #29 #00b305ff
    3114 
    3115 > color #30 #00b305ff
    3116 
    3117 > color #31 #f15839ff
    3118 
    3119 > select #1.7/A
    3120 
    3121 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    3122 
    3123 > show sel cartoons
    3124 
    3125 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    3126 
    3127 Chain information for AF3 E1 1-421.pdb #32 
    3128 --- 
    3129 Chain | Description 
    3130 A | No description available 
    3131  
    3132 
    3133 > matchmaker #32 to #1.7 & sel
    3134 
    3135 Parameters 
    3136 --- 
    3137 Chain pairing | bb 
    3138 Alignment algorithm | Needleman-Wunsch 
    3139 Similarity matrix | BLOSUM-62 
    3140 SS fraction | 0.3 
    3141 Gap open (HH/SS/other) | 18/18/6 
    3142 Gap extend | 1 
    3143 SS matrix |  |  | H | S | O 
    3144 ---|---|---|--- 
    3145 H | 6 | -9 | -6 
    3146 S |  | 6 | -6 
    3147 O |  |  | 4 
    3148 Iteration cutoff | 2 
    3149  
    3150 Matchmaker 3j0c.pdb1, chain A (#1.7) with AF3 E1 1-421.pdb, chain A (#32),
    3151 sequence alignment score = 1060.7 
    3152 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    3153 3.020) 
    3154  
    3155 
    3156 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    3157 
    3158 Chain information for AF3 E1 422-461.pdb #33 
    3159 --- 
    3160 Chain | Description 
    3161 A | No description available 
    3162  
    3163 
    3164 > matchmaker #33 to #1.7 & sel
    3165 
    3166 Parameters 
    3167 --- 
    3168 Chain pairing | bb 
    3169 Alignment algorithm | Needleman-Wunsch 
    3170 Similarity matrix | BLOSUM-62 
    3171 SS fraction | 0.3 
    3172 Gap open (HH/SS/other) | 18/18/6 
    3173 Gap extend | 1 
    3174 SS matrix |  |  | H | S | O 
    3175 ---|---|---|--- 
    3176 H | 6 | -9 | -6 
    3177 S |  | 6 | -6 
    3178 O |  |  | 4 
    3179 Iteration cutoff | 2 
    3180  
    3181 Matchmaker 3j0c.pdb1, chain A (#1.7) with AF3 E1 422-461.pdb, chain A (#33),
    3182 sequence alignment score = 626.9 
    3183 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    3184 2.775) 
    3185  
    3186 
    3187 > hide sel cartoons
    3188 
    3189 > select #1.7/B
    3190 
    3191 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    3192 
    3193 > show sel cartoons
    3194 
    3195 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    3196 
    3197 Chain information for AF3 E2 1-352.pdb #34 
    3198 --- 
    3199 Chain | Description 
    3200 B | No description available 
    3201  
    3202 
    3203 > matchmaker #34 to #1.7 & sel
    3204 
    3205 Parameters 
    3206 --- 
    3207 Chain pairing | bb 
    3208 Alignment algorithm | Needleman-Wunsch 
    3209 Similarity matrix | BLOSUM-62 
    3210 SS fraction | 0.3 
    3211 Gap open (HH/SS/other) | 18/18/6 
    3212 Gap extend | 1 
    3213 SS matrix |  |  | H | S | O 
    3214 ---|---|---|--- 
    3215 H | 6 | -9 | -6 
    3216 S |  | 6 | -6 
    3217 O |  |  | 4 
    3218 Iteration cutoff | 2 
    3219  
    3220 Matchmaker 3j0c.pdb1, chain B (#1.7) with AF3 E2 1-352.pdb, chain B (#34),
    3221 sequence alignment score = 583.7 
    3222 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    3223 5.933) 
    3224  
    3225 
    3226 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    3227 
    3228 Chain information for AF3 E2 353-438.pdb #35 
    3229 --- 
    3230 Chain | Description 
    3231 B | No description available 
    3232  
    3233 
    3234 > matchmaker #35 to #1.7 & sel
    3235 
    3236 Parameters 
    3237 --- 
    3238 Chain pairing | bb 
    3239 Alignment algorithm | Needleman-Wunsch 
    3240 Similarity matrix | BLOSUM-62 
    3241 SS fraction | 0.3 
    3242 Gap open (HH/SS/other) | 18/18/6 
    3243 Gap extend | 1 
    3244 SS matrix |  |  | H | S | O 
    3245 ---|---|---|--- 
    3246 H | 6 | -9 | -6 
    3247 S |  | 6 | -6 
    3248 O |  |  | 4 
    3249 Iteration cutoff | 2 
    3250  
    3251 Matchmaker 3j0c.pdb1, chain B (#1.7) with AF3 E2 353-438.pdb, chain B (#35),
    3252 sequence alignment score = 333.4 
    3253 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    3254 8.411) 
    3255  
    3256 
    3257 > hide sel cartoons
    3258 
    3259 > select #1.7/C
    3260 
    3261 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    3262 
    3263 > show sel cartoons
    3264 
    3265 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    3266 
    3267 Chain information for AF3 CA.pdb #36 
    3268 --- 
    3269 Chain | Description 
    3270 A | No description available 
    3271  
    3272 
    3273 > matchmaker #36 to #1.7 & sel
    3274 
    3275 Parameters 
    3276 --- 
    3277 Chain pairing | bb 
    3278 Alignment algorithm | Needleman-Wunsch 
    3279 Similarity matrix | BLOSUM-62 
    3280 SS fraction | 0.3 
    3281 Gap open (HH/SS/other) | 18/18/6 
    3282 Gap extend | 1 
    3283 SS matrix |  |  | H | S | O 
    3284 ---|---|---|--- 
    3285 H | 6 | -9 | -6 
    3286 S |  | 6 | -6 
    3287 O |  |  | 4 
    3288 Iteration cutoff | 2 
    3289  
    3290 Matchmaker 3j0c.pdb1, chain C (#1.7) with AF3 CA.pdb, chain A (#36), sequence
    3291 alignment score = 328.1 
    3292 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    3293 2.714) 
    3294  
    3295 
    3296 > hide sel cartoons
    3297 
    3298 > hide #32 models
    3299 
    3300 > color #32 dodgerblue
    3301 
    3302 > color #33 dodgerblue
    3303 
    3304 > color #34 #00b305ff
    3305 
    3306 > color #35 #00b305ff
    3307 
    3308 > color #36 #f15839ff
    3309 
    3310 > select #1.8/A
    3311 
    3312 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    3313 
    3314 > show sel cartoons
    3315 
    3316 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    3317 
    3318 Chain information for AF3 E1 1-421.pdb #37 
    3319 --- 
    3320 Chain | Description 
    3321 A | No description available 
    3322  
    3323 
    3324 > matchmaker #37 to #1.8 & sel
    3325 
    3326 Parameters 
    3327 --- 
    3328 Chain pairing | bb 
    3329 Alignment algorithm | Needleman-Wunsch 
    3330 Similarity matrix | BLOSUM-62 
    3331 SS fraction | 0.3 
    3332 Gap open (HH/SS/other) | 18/18/6 
    3333 Gap extend | 1 
    3334 SS matrix |  |  | H | S | O 
    3335 ---|---|---|--- 
    3336 H | 6 | -9 | -6 
    3337 S |  | 6 | -6 
    3338 O |  |  | 4 
    3339 Iteration cutoff | 2 
    3340  
    3341 Matchmaker 3j0c.pdb1, chain A (#1.8) with AF3 E1 1-421.pdb, chain A (#37),
    3342 sequence alignment score = 1060.7 
    3343 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    3344 3.020) 
    3345  
    3346 
    3347 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    3348 
    3349 Chain information for AF3 E1 422-461.pdb #38 
    3350 --- 
    3351 Chain | Description 
    3352 A | No description available 
    3353  
    3354 
    3355 > matchmaker #38 to #1.8 & sel
    3356 
    3357 Parameters 
    3358 --- 
    3359 Chain pairing | bb 
    3360 Alignment algorithm | Needleman-Wunsch 
    3361 Similarity matrix | BLOSUM-62 
    3362 SS fraction | 0.3 
    3363 Gap open (HH/SS/other) | 18/18/6 
    3364 Gap extend | 1 
    3365 SS matrix |  |  | H | S | O 
    3366 ---|---|---|--- 
    3367 H | 6 | -9 | -6 
    3368 S |  | 6 | -6 
    3369 O |  |  | 4 
    3370 Iteration cutoff | 2 
    3371  
    3372 Matchmaker 3j0c.pdb1, chain A (#1.8) with AF3 E1 422-461.pdb, chain A (#38),
    3373 sequence alignment score = 626.9 
    3374 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    3375 2.775) 
    3376  
    3377 
    3378 > hide sel cartoons
    3379 
    3380 > select #1.8/B
    3381 
    3382 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    3383 
    3384 > show sel cartoons
    3385 
    3386 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    3387 
    3388 Chain information for AF3 E2 1-352.pdb #39 
    3389 --- 
    3390 Chain | Description 
    3391 B | No description available 
    3392  
    3393 
    3394 > matchmaker #39 to #1.8 & sel
    3395 
    3396 Parameters 
    3397 --- 
    3398 Chain pairing | bb 
    3399 Alignment algorithm | Needleman-Wunsch 
    3400 Similarity matrix | BLOSUM-62 
    3401 SS fraction | 0.3 
    3402 Gap open (HH/SS/other) | 18/18/6 
    3403 Gap extend | 1 
    3404 SS matrix |  |  | H | S | O 
    3405 ---|---|---|--- 
    3406 H | 6 | -9 | -6 
    3407 S |  | 6 | -6 
    3408 O |  |  | 4 
    3409 Iteration cutoff | 2 
    3410  
    3411 Matchmaker 3j0c.pdb1, chain B (#1.8) with AF3 E2 1-352.pdb, chain B (#39),
    3412 sequence alignment score = 583.7 
    3413 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    3414 5.933) 
    3415  
    3416 
    3417 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    3418 
    3419 Chain information for AF3 E2 353-438.pdb #40 
    3420 --- 
    3421 Chain | Description 
    3422 B | No description available 
    3423  
    3424 
    3425 > matchmaker #40 to #1.8 & sel
    3426 
    3427 Parameters 
    3428 --- 
    3429 Chain pairing | bb 
    3430 Alignment algorithm | Needleman-Wunsch 
    3431 Similarity matrix | BLOSUM-62 
    3432 SS fraction | 0.3 
    3433 Gap open (HH/SS/other) | 18/18/6 
    3434 Gap extend | 1 
    3435 SS matrix |  |  | H | S | O 
    3436 ---|---|---|--- 
    3437 H | 6 | -9 | -6 
    3438 S |  | 6 | -6 
    3439 O |  |  | 4 
    3440 Iteration cutoff | 2 
    3441  
    3442 Matchmaker 3j0c.pdb1, chain B (#1.8) with AF3 E2 353-438.pdb, chain B (#40),
    3443 sequence alignment score = 333.4 
    3444 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    3445 8.411) 
    3446  
    3447 
    3448 > hide sel cartoons
    3449 
    3450 [Repeated 1 time(s)]
    3451 
    3452 > select #1.8/C
    3453 
    3454 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    3455 
    3456 > show sel cartoons
    3457 
    3458 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    3459 
    3460 Chain information for AF3 CA.pdb #41 
    3461 --- 
    3462 Chain | Description 
    3463 A | No description available 
    3464  
    3465 
    3466 > matchmaker #41 to #1.8 & sel
    3467 
    3468 Parameters 
    3469 --- 
    3470 Chain pairing | bb 
    3471 Alignment algorithm | Needleman-Wunsch 
    3472 Similarity matrix | BLOSUM-62 
    3473 SS fraction | 0.3 
    3474 Gap open (HH/SS/other) | 18/18/6 
    3475 Gap extend | 1 
    3476 SS matrix |  |  | H | S | O 
    3477 ---|---|---|--- 
    3478 H | 6 | -9 | -6 
    3479 S |  | 6 | -6 
    3480 O |  |  | 4 
    3481 Iteration cutoff | 2 
    3482  
    3483 Matchmaker 3j0c.pdb1, chain C (#1.8) with AF3 CA.pdb, chain A (#41), sequence
    3484 alignment score = 328.1 
    3485 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    3486 2.714) 
    3487  
    3488 
    3489 > hide sel cartoons
    3490 
    3491 > show #32 models
    3492 
    3493 > color #37 dodgerblue
    3494 
    3495 > color #38 dodgerblue
    3496 
    3497 > color #39 #00b305ff
    3498 
    3499 > color #40 #00b305ff
    3500 
    3501 > color #41 #f15839ff
    3502 
    3503 > select #1.9/A
    3504 
    3505 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    3506 
    3507 > show sel cartoons
    3508 
    3509 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    3510 
    3511 Chain information for AF3 E1 1-421.pdb #42 
    3512 --- 
    3513 Chain | Description 
    3514 A | No description available 
    3515  
    3516 
    3517 > matchmaker #42 to #1.8 & sel
    3518 
    3519 No 'to' model specified 
    3520 
    3521 > matchmaker #42 to #1.9 & sel
    3522 
    3523 Parameters 
    3524 --- 
    3525 Chain pairing | bb 
    3526 Alignment algorithm | Needleman-Wunsch 
    3527 Similarity matrix | BLOSUM-62 
    3528 SS fraction | 0.3 
    3529 Gap open (HH/SS/other) | 18/18/6 
    3530 Gap extend | 1 
    3531 SS matrix |  |  | H | S | O 
    3532 ---|---|---|--- 
    3533 H | 6 | -9 | -6 
    3534 S |  | 6 | -6 
    3535 O |  |  | 4 
    3536 Iteration cutoff | 2 
    3537  
    3538 Matchmaker 3j0c.pdb1, chain A (#1.9) with AF3 E1 1-421.pdb, chain A (#42),
    3539 sequence alignment score = 1060.7 
    3540 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    3541 3.020) 
    3542  
    3543 
    3544 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    3545 
    3546 Chain information for AF3 E1 422-461.pdb #43 
    3547 --- 
    3548 Chain | Description 
    3549 A | No description available 
    3550  
    3551 
    3552 > matchmaker #43 to #1.9 & sel
    3553 
    3554 Parameters 
    3555 --- 
    3556 Chain pairing | bb 
    3557 Alignment algorithm | Needleman-Wunsch 
    3558 Similarity matrix | BLOSUM-62 
    3559 SS fraction | 0.3 
    3560 Gap open (HH/SS/other) | 18/18/6 
    3561 Gap extend | 1 
    3562 SS matrix |  |  | H | S | O 
    3563 ---|---|---|--- 
    3564 H | 6 | -9 | -6 
    3565 S |  | 6 | -6 
    3566 O |  |  | 4 
    3567 Iteration cutoff | 2 
    3568  
    3569 Matchmaker 3j0c.pdb1, chain A (#1.9) with AF3 E1 422-461.pdb, chain A (#43),
    3570 sequence alignment score = 626.9 
    3571 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    3572 2.775) 
    3573  
    3574 
    3575 > hide sel cartoons
    3576 
    3577 > select #1.9/B
    3578 
    3579 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    3580 
    3581 > show sel cartoons
    3582 
    3583 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    3584 
    3585 Chain information for AF3 E2 1-352.pdb #44 
    3586 --- 
    3587 Chain | Description 
    3588 B | No description available 
    3589  
    3590 
    3591 > matchmaker #44 to #1.9 & sel
    3592 
    3593 Parameters 
    3594 --- 
    3595 Chain pairing | bb 
    3596 Alignment algorithm | Needleman-Wunsch 
    3597 Similarity matrix | BLOSUM-62 
    3598 SS fraction | 0.3 
    3599 Gap open (HH/SS/other) | 18/18/6 
    3600 Gap extend | 1 
    3601 SS matrix |  |  | H | S | O 
    3602 ---|---|---|--- 
    3603 H | 6 | -9 | -6 
    3604 S |  | 6 | -6 
    3605 O |  |  | 4 
    3606 Iteration cutoff | 2 
    3607  
    3608 Matchmaker 3j0c.pdb1, chain B (#1.9) with AF3 E2 1-352.pdb, chain B (#44),
    3609 sequence alignment score = 583.7 
    3610 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    3611 5.933) 
    3612  
    3613 
    3614 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    3615 
    3616 Chain information for AF3 E2 353-438.pdb #45 
    3617 --- 
    3618 Chain | Description 
    3619 B | No description available 
    3620  
    3621 
    3622 > matchmaker #45 to #1.9 & sel
    3623 
    3624 Parameters 
    3625 --- 
    3626 Chain pairing | bb 
    3627 Alignment algorithm | Needleman-Wunsch 
    3628 Similarity matrix | BLOSUM-62 
    3629 SS fraction | 0.3 
    3630 Gap open (HH/SS/other) | 18/18/6 
    3631 Gap extend | 1 
    3632 SS matrix |  |  | H | S | O 
    3633 ---|---|---|--- 
    3634 H | 6 | -9 | -6 
    3635 S |  | 6 | -6 
    3636 O |  |  | 4 
    3637 Iteration cutoff | 2 
    3638  
    3639 Matchmaker 3j0c.pdb1, chain B (#1.9) with AF3 E2 353-438.pdb, chain B (#45),
    3640 sequence alignment score = 322.6 
    3641 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    3642 8.411) 
    3643  
    3644 
    3645 > hide sel cartoons
    3646 
    3647 > select #1.9/C
    3648 
    3649 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    3650 
    3651 > show sel cartoons
    3652 
    3653 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    3654 
    3655 Chain information for AF3 CA.pdb #46 
    3656 --- 
    3657 Chain | Description 
    3658 A | No description available 
    3659  
    3660 
    3661 > matchmaker #46 to #1.9 & sel
    3662 
    3663 Parameters 
    3664 --- 
    3665 Chain pairing | bb 
    3666 Alignment algorithm | Needleman-Wunsch 
    3667 Similarity matrix | BLOSUM-62 
    3668 SS fraction | 0.3 
    3669 Gap open (HH/SS/other) | 18/18/6 
    3670 Gap extend | 1 
    3671 SS matrix |  |  | H | S | O 
    3672 ---|---|---|--- 
    3673 H | 6 | -9 | -6 
    3674 S |  | 6 | -6 
    3675 O |  |  | 4 
    3676 Iteration cutoff | 2 
    3677  
    3678 Matchmaker 3j0c.pdb1, chain C (#1.9) with AF3 CA.pdb, chain A (#46), sequence
    3679 alignment score = 328.1 
    3680 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    3681 2.714) 
    3682  
    3683 
    3684 > hide sel cartoons
    3685 
    3686 > hide #42 models
    3687 
    3688 > show #42 models
    3689 
    3690 > color #42 dodgerblue
    3691 
    3692 > color #43 dodgerblue
    3693 
    3694 > color #44 #00b305ff
    3695 
    3696 > color #45 #00b305ff
    3697 
    3698 > color #46 #f15839ff
    3699 
    3700 > select #1.10/A
    3701 
    3702 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    3703 
    3704 > show sel cartoons
    3705 
    3706 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    3707 
    3708 Chain information for AF3 E1 1-421.pdb #47 
    3709 --- 
    3710 Chain | Description 
    3711 A | No description available 
    3712  
    3713 
    3714 > matchmaker #47 to #1.10 & sel
    3715 
    3716 Parameters 
    3717 --- 
    3718 Chain pairing | bb 
    3719 Alignment algorithm | Needleman-Wunsch 
    3720 Similarity matrix | BLOSUM-62 
    3721 SS fraction | 0.3 
    3722 Gap open (HH/SS/other) | 18/18/6 
    3723 Gap extend | 1 
    3724 SS matrix |  |  | H | S | O 
    3725 ---|---|---|--- 
    3726 H | 6 | -9 | -6 
    3727 S |  | 6 | -6 
    3728 O |  |  | 4 
    3729 Iteration cutoff | 2 
    3730  
    3731 Matchmaker 3j0c.pdb1, chain A (#1.10) with AF3 E1 1-421.pdb, chain A (#47),
    3732 sequence alignment score = 1060.7 
    3733 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    3734 3.020) 
    3735  
    3736 
    3737 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    3738 
    3739 Chain information for AF3 E1 422-461.pdb #48 
    3740 --- 
    3741 Chain | Description 
    3742 A | No description available 
    3743  
    3744 
    3745 > matchmaker #47 to #1.10 & sel
    3746 
    3747 Parameters 
    3748 --- 
    3749 Chain pairing | bb 
    3750 Alignment algorithm | Needleman-Wunsch 
    3751 Similarity matrix | BLOSUM-62 
    3752 SS fraction | 0.3 
    3753 Gap open (HH/SS/other) | 18/18/6 
    3754 Gap extend | 1 
    3755 SS matrix |  |  | H | S | O 
    3756 ---|---|---|--- 
    3757 H | 6 | -9 | -6 
    3758 S |  | 6 | -6 
    3759 O |  |  | 4 
    3760 Iteration cutoff | 2 
    3761  
    3762 Matchmaker 3j0c.pdb1, chain A (#1.10) with AF3 E1 1-421.pdb, chain A (#47),
    3763 sequence alignment score = 1060.7 
    3764 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    3765 3.020) 
    3766  
    3767 
    3768 > matchmaker #47 to #1.10 & sel
    3769 
    3770 Parameters 
    3771 --- 
    3772 Chain pairing | bb 
    3773 Alignment algorithm | Needleman-Wunsch 
    3774 Similarity matrix | BLOSUM-62 
    3775 SS fraction | 0.3 
    3776 Gap open (HH/SS/other) | 18/18/6 
    3777 Gap extend | 1 
    3778 SS matrix |  |  | H | S | O 
    3779 ---|---|---|--- 
    3780 H | 6 | -9 | -6 
    3781 S |  | 6 | -6 
    3782 O |  |  | 4 
    3783 Iteration cutoff | 2 
    3784  
    3785 Matchmaker 3j0c.pdb1, chain A (#1.10) with AF3 E1 1-421.pdb, chain A (#47),
    3786 sequence alignment score = 1060.7 
    3787 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    3788 3.020) 
    3789  
    3790 
    3791 > matchmaker #48 to #1.10 & sel
    3792 
    3793 Parameters 
    3794 --- 
    3795 Chain pairing | bb 
    3796 Alignment algorithm | Needleman-Wunsch 
    3797 Similarity matrix | BLOSUM-62 
    3798 SS fraction | 0.3 
    3799 Gap open (HH/SS/other) | 18/18/6 
    3800 Gap extend | 1 
    3801 SS matrix |  |  | H | S | O 
    3802 ---|---|---|--- 
    3803 H | 6 | -9 | -6 
    3804 S |  | 6 | -6 
    3805 O |  |  | 4 
    3806 Iteration cutoff | 2 
    3807  
    3808 Matchmaker 3j0c.pdb1, chain A (#1.10) with AF3 E1 422-461.pdb, chain A (#48),
    3809 sequence alignment score = 626.9 
    3810 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    3811 2.776) 
    3812  
    3813 
    3814 > hide sel cartoons
    3815 
    3816 > select #1.10/B
    3817 
    3818 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    3819 
    3820 > show sel cartoons
    3821 
    3822 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    3823 
    3824 Chain information for AF3 E2 1-352.pdb #49 
    3825 --- 
    3826 Chain | Description 
    3827 B | No description available 
    3828  
    3829 
    3830 > matchmaker #49 to #1.10 & sel
    3831 
    3832 Parameters 
    3833 --- 
    3834 Chain pairing | bb 
    3835 Alignment algorithm | Needleman-Wunsch 
    3836 Similarity matrix | BLOSUM-62 
    3837 SS fraction | 0.3 
    3838 Gap open (HH/SS/other) | 18/18/6 
    3839 Gap extend | 1 
    3840 SS matrix |  |  | H | S | O 
    3841 ---|---|---|--- 
    3842 H | 6 | -9 | -6 
    3843 S |  | 6 | -6 
    3844 O |  |  | 4 
    3845 Iteration cutoff | 2 
    3846  
    3847 Matchmaker 3j0c.pdb1, chain B (#1.10) with AF3 E2 1-352.pdb, chain B (#49),
    3848 sequence alignment score = 583.7 
    3849 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    3850 5.933) 
    3851  
    3852 
    3853 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    3854 
    3855 Chain information for AF3 E2 353-438.pdb #50 
    3856 --- 
    3857 Chain | Description 
    3858 B | No description available 
    3859  
    3860 
    3861 > matchmaker #50 to #1.10 & sel
    3862 
    3863 Parameters 
    3864 --- 
    3865 Chain pairing | bb 
    3866 Alignment algorithm | Needleman-Wunsch 
    3867 Similarity matrix | BLOSUM-62 
    3868 SS fraction | 0.3 
    3869 Gap open (HH/SS/other) | 18/18/6 
    3870 Gap extend | 1 
    3871 SS matrix |  |  | H | S | O 
    3872 ---|---|---|--- 
    3873 H | 6 | -9 | -6 
    3874 S |  | 6 | -6 
    3875 O |  |  | 4 
    3876 Iteration cutoff | 2 
    3877  
    3878 Matchmaker 3j0c.pdb1, chain B (#1.10) with AF3 E2 353-438.pdb, chain B (#50),
    3879 sequence alignment score = 322.6 
    3880 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    3881 8.411) 
    3882  
    3883 
    3884 > hide sel cartoons
    3885 
    3886 > select #1.10/C
    3887 
    3888 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    3889 
    3890 > show sel cartoons
    3891 
    3892 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    3893 
    3894 Chain information for AF3 CA.pdb #51 
    3895 --- 
    3896 Chain | Description 
    3897 A | No description available 
    3898  
    3899 
    3900 > matchmaker #51 to #1.10 & sel
    3901 
    3902 Parameters 
    3903 --- 
    3904 Chain pairing | bb 
    3905 Alignment algorithm | Needleman-Wunsch 
    3906 Similarity matrix | BLOSUM-62 
    3907 SS fraction | 0.3 
    3908 Gap open (HH/SS/other) | 18/18/6 
    3909 Gap extend | 1 
    3910 SS matrix |  |  | H | S | O 
    3911 ---|---|---|--- 
    3912 H | 6 | -9 | -6 
    3913 S |  | 6 | -6 
    3914 O |  |  | 4 
    3915 Iteration cutoff | 2 
    3916  
    3917 Matchmaker 3j0c.pdb1, chain C (#1.10) with AF3 CA.pdb, chain A (#51), sequence
    3918 alignment score = 328.1 
    3919 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    3920 2.714) 
    3921  
    3922 
    3923 > hide sel cartoons
    3924 
    3925 > color #47 dodgerblue
    3926 
    3927 > color #48 dodgerblue
    3928 
    3929 > color #49 #00b305ff
    3930 
    3931 > color #50 #00b305ff
    3932 
    3933 > color #51 #f15839ff
    3934 
    3935 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    3936 
    3937 > select #1.11/A
    3938 
    3939 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    3940 
    3941 > show sel cartoons
    3942 
    3943 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    3944 
    3945 Chain information for AF3 E1 1-421.pdb #52 
    3946 --- 
    3947 Chain | Description 
    3948 A | No description available 
    3949  
    3950 
    3951 > matchmaker #52 to #1.11 & sel
    3952 
    3953 Parameters 
    3954 --- 
    3955 Chain pairing | bb 
    3956 Alignment algorithm | Needleman-Wunsch 
    3957 Similarity matrix | BLOSUM-62 
    3958 SS fraction | 0.3 
    3959 Gap open (HH/SS/other) | 18/18/6 
    3960 Gap extend | 1 
    3961 SS matrix |  |  | H | S | O 
    3962 ---|---|---|--- 
    3963 H | 6 | -9 | -6 
    3964 S |  | 6 | -6 
    3965 O |  |  | 4 
    3966 Iteration cutoff | 2 
    3967  
    3968 Matchmaker 3j0c.pdb1, chain A (#1.11) with AF3 E1 1-421.pdb, chain A (#52),
    3969 sequence alignment score = 1060.7 
    3970 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    3971 3.020) 
    3972  
    3973 
    3974 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    3975 
    3976 Chain information for AF3 E1 422-461.pdb #53 
    3977 --- 
    3978 Chain | Description 
    3979 A | No description available 
    3980  
    3981 
    3982 > matchmaker #53 to #1.11 & sel
    3983 
    3984 Parameters 
    3985 --- 
    3986 Chain pairing | bb 
    3987 Alignment algorithm | Needleman-Wunsch 
    3988 Similarity matrix | BLOSUM-62 
    3989 SS fraction | 0.3 
    3990 Gap open (HH/SS/other) | 18/18/6 
    3991 Gap extend | 1 
    3992 SS matrix |  |  | H | S | O 
    3993 ---|---|---|--- 
    3994 H | 6 | -9 | -6 
    3995 S |  | 6 | -6 
    3996 O |  |  | 4 
    3997 Iteration cutoff | 2 
    3998  
    3999 Matchmaker 3j0c.pdb1, chain A (#1.11) with AF3 E1 422-461.pdb, chain A (#53),
    4000 sequence alignment score = 626.9 
    4001 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    4002 2.776) 
    4003  
    4004 
    4005 > hide sel cartoons
    4006 
    4007 > select #1.11/B
    4008 
    4009 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    4010 
    4011 > show sel cartoons
    4012 
    4013 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    4014 
    4015 Chain information for AF3 E2 1-352.pdb #54 
    4016 --- 
    4017 Chain | Description 
    4018 B | No description available 
    4019  
    4020 
    4021 > matchmaker #54 to #1.11 & sel
    4022 
    4023 Parameters 
    4024 --- 
    4025 Chain pairing | bb 
    4026 Alignment algorithm | Needleman-Wunsch 
    4027 Similarity matrix | BLOSUM-62 
    4028 SS fraction | 0.3 
    4029 Gap open (HH/SS/other) | 18/18/6 
    4030 Gap extend | 1 
    4031 SS matrix |  |  | H | S | O 
    4032 ---|---|---|--- 
    4033 H | 6 | -9 | -6 
    4034 S |  | 6 | -6 
    4035 O |  |  | 4 
    4036 Iteration cutoff | 2 
    4037  
    4038 Matchmaker 3j0c.pdb1, chain B (#1.11) with AF3 E2 1-352.pdb, chain B (#54),
    4039 sequence alignment score = 583.7 
    4040 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    4041 5.933) 
    4042  
    4043 
    4044 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    4045 
    4046 Chain information for AF3 E2 353-438.pdb #55 
    4047 --- 
    4048 Chain | Description 
    4049 B | No description available 
    4050  
    4051 
    4052 > matchmaker #55 to #1.11 & sel
    4053 
    4054 Parameters 
    4055 --- 
    4056 Chain pairing | bb 
    4057 Alignment algorithm | Needleman-Wunsch 
    4058 Similarity matrix | BLOSUM-62 
    4059 SS fraction | 0.3 
    4060 Gap open (HH/SS/other) | 18/18/6 
    4061 Gap extend | 1 
    4062 SS matrix |  |  | H | S | O 
    4063 ---|---|---|--- 
    4064 H | 6 | -9 | -6 
    4065 S |  | 6 | -6 
    4066 O |  |  | 4 
    4067 Iteration cutoff | 2 
    4068  
    4069 Matchmaker 3j0c.pdb1, chain B (#1.11) with AF3 E2 353-438.pdb, chain B (#55),
    4070 sequence alignment score = 333.4 
    4071 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    4072 8.411) 
    4073  
    4074 
    4075 > hide sel cartoons
    4076 
    4077 > select #1.11/C
    4078 
    4079 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    4080 
    4081 > show sel cartoons
    4082 
    4083 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    4084 
    4085 Chain information for AF3 CA.pdb #56 
    4086 --- 
    4087 Chain | Description 
    4088 A | No description available 
    4089  
    4090 
    4091 > matchmaker #56 to #1.11 & sel
    4092 
    4093 Parameters 
    4094 --- 
    4095 Chain pairing | bb 
    4096 Alignment algorithm | Needleman-Wunsch 
    4097 Similarity matrix | BLOSUM-62 
    4098 SS fraction | 0.3 
    4099 Gap open (HH/SS/other) | 18/18/6 
    4100 Gap extend | 1 
    4101 SS matrix |  |  | H | S | O 
    4102 ---|---|---|--- 
    4103 H | 6 | -9 | -6 
    4104 S |  | 6 | -6 
    4105 O |  |  | 4 
    4106 Iteration cutoff | 2 
    4107  
    4108 Matchmaker 3j0c.pdb1, chain C (#1.11) with AF3 CA.pdb, chain A (#56), sequence
    4109 alignment score = 328.1 
    4110 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    4111 2.714) 
    4112  
    4113 
    4114 > hide sel cartoons
    4115 
    4116 > color #52 dodgerblue
    4117 
    4118 > color #53 dodgerblue
    4119 
    4120 > color #54 #00b305ff
    4121 
    4122 > color #55 #00b305ff
    4123 
    4124 > color #56 #f15839ff
    4125 
    4126 > select #1.12/A
    4127 
    4128 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    4129 
    4130 > show sel cartoons
    4131 
    4132 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    4133 
    4134 Chain information for AF3 E1 1-421.pdb #57 
    4135 --- 
    4136 Chain | Description 
    4137 A | No description available 
    4138  
    4139 
    4140 > matchmaker #57 to #1.12 & sel
    4141 
    4142 Parameters 
    4143 --- 
    4144 Chain pairing | bb 
    4145 Alignment algorithm | Needleman-Wunsch 
    4146 Similarity matrix | BLOSUM-62 
    4147 SS fraction | 0.3 
    4148 Gap open (HH/SS/other) | 18/18/6 
    4149 Gap extend | 1 
    4150 SS matrix |  |  | H | S | O 
    4151 ---|---|---|--- 
    4152 H | 6 | -9 | -6 
    4153 S |  | 6 | -6 
    4154 O |  |  | 4 
    4155 Iteration cutoff | 2 
    4156  
    4157 Matchmaker 3j0c.pdb1, chain A (#1.12) with AF3 E1 1-421.pdb, chain A (#57),
    4158 sequence alignment score = 1060.7 
    4159 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    4160 3.020) 
    4161  
    4162 
    4163 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    4164 
    4165 Chain information for AF3 E1 422-461.pdb #58 
    4166 --- 
    4167 Chain | Description 
    4168 A | No description available 
    4169  
    4170 
    4171 > matchmaker #58 to #1.12 & sel
    4172 
    4173 Parameters 
    4174 --- 
    4175 Chain pairing | bb 
    4176 Alignment algorithm | Needleman-Wunsch 
    4177 Similarity matrix | BLOSUM-62 
    4178 SS fraction | 0.3 
    4179 Gap open (HH/SS/other) | 18/18/6 
    4180 Gap extend | 1 
    4181 SS matrix |  |  | H | S | O 
    4182 ---|---|---|--- 
    4183 H | 6 | -9 | -6 
    4184 S |  | 6 | -6 
    4185 O |  |  | 4 
    4186 Iteration cutoff | 2 
    4187  
    4188 Matchmaker 3j0c.pdb1, chain A (#1.12) with AF3 E1 422-461.pdb, chain A (#58),
    4189 sequence alignment score = 626.9 
    4190 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    4191 2.776) 
    4192  
    4193 
    4194 > hide sel cartoons
    4195 
    4196 > select #1.12/B
    4197 
    4198 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    4199 
    4200 > show sel cartoons
    4201 
    4202 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    4203 
    4204 Chain information for AF3 E2 1-352.pdb #59 
    4205 --- 
    4206 Chain | Description 
    4207 B | No description available 
    4208  
    4209 
    4210 > matchmaker #59 to #1.12 & sel
    4211 
    4212 Parameters 
    4213 --- 
    4214 Chain pairing | bb 
    4215 Alignment algorithm | Needleman-Wunsch 
    4216 Similarity matrix | BLOSUM-62 
    4217 SS fraction | 0.3 
    4218 Gap open (HH/SS/other) | 18/18/6 
    4219 Gap extend | 1 
    4220 SS matrix |  |  | H | S | O 
    4221 ---|---|---|--- 
    4222 H | 6 | -9 | -6 
    4223 S |  | 6 | -6 
    4224 O |  |  | 4 
    4225 Iteration cutoff | 2 
    4226  
    4227 Matchmaker 3j0c.pdb1, chain B (#1.12) with AF3 E2 1-352.pdb, chain B (#59),
    4228 sequence alignment score = 583.7 
    4229 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    4230 5.933) 
    4231  
    4232 
    4233 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    4234 
    4235 Chain information for AF3 E2 353-438.pdb #60 
    4236 --- 
    4237 Chain | Description 
    4238 B | No description available 
    4239  
    4240 
    4241 > matchmaker #60 to #1.12 & sel
    4242 
    4243 Parameters 
    4244 --- 
    4245 Chain pairing | bb 
    4246 Alignment algorithm | Needleman-Wunsch 
    4247 Similarity matrix | BLOSUM-62 
    4248 SS fraction | 0.3 
    4249 Gap open (HH/SS/other) | 18/18/6 
    4250 Gap extend | 1 
    4251 SS matrix |  |  | H | S | O 
    4252 ---|---|---|--- 
    4253 H | 6 | -9 | -6 
    4254 S |  | 6 | -6 
    4255 O |  |  | 4 
    4256 Iteration cutoff | 2 
    4257  
    4258 Matchmaker 3j0c.pdb1, chain B (#1.12) with AF3 E2 353-438.pdb, chain B (#60),
    4259 sequence alignment score = 333.4 
    4260 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    4261 8.411) 
    4262  
    4263 
    4264 > hide sel cartoons
    4265 
    4266 > select #1.12/C
    4267 
    4268 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    4269 
    4270 > show sel cartoons
    4271 
    4272 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    4273 
    4274 Chain information for AF3 CA.pdb #61 
    4275 --- 
    4276 Chain | Description 
    4277 A | No description available 
    4278  
    4279 
    4280 > matchmaker #61 to #1.12 & sel
    4281 
    4282 Parameters 
    4283 --- 
    4284 Chain pairing | bb 
    4285 Alignment algorithm | Needleman-Wunsch 
    4286 Similarity matrix | BLOSUM-62 
    4287 SS fraction | 0.3 
    4288 Gap open (HH/SS/other) | 18/18/6 
    4289 Gap extend | 1 
    4290 SS matrix |  |  | H | S | O 
    4291 ---|---|---|--- 
    4292 H | 6 | -9 | -6 
    4293 S |  | 6 | -6 
    4294 O |  |  | 4 
    4295 Iteration cutoff | 2 
    4296  
    4297 Matchmaker 3j0c.pdb1, chain C (#1.12) with AF3 CA.pdb, chain A (#61), sequence
    4298 alignment score = 328.1 
    4299 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    4300 2.714) 
    4301  
    4302 
    4303 > hide sel cartoons
    4304 
    4305 > hide #57 models
    4306 
    4307 > show #57 models
    4308 
    4309 > color #57 dodgerblue
    4310 
    4311 > color #58 dodgerblue
    4312 
    4313 > color #59 #00b305ff
    4314 
    4315 > color #60 #00b305ff
    4316 
    4317 > color #61 #f15839ff
    4318 
    4319 > select #1.13/A
    4320 
    4321 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    4322 
    4323 > show sel cartoons
    4324 
    4325 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    4326 
    4327 Chain information for AF3 E1 1-421.pdb #62 
    4328 --- 
    4329 Chain | Description 
    4330 A | No description available 
    4331  
    4332 
    4333 > matchmaker #62 to #1.12 & sel
    4334 
    4335 No 'to' model specified 
    4336 
    4337 > matchmaker #62 to #1.13 & sel
    4338 
    4339 Parameters 
    4340 --- 
    4341 Chain pairing | bb 
    4342 Alignment algorithm | Needleman-Wunsch 
    4343 Similarity matrix | BLOSUM-62 
    4344 SS fraction | 0.3 
    4345 Gap open (HH/SS/other) | 18/18/6 
    4346 Gap extend | 1 
    4347 SS matrix |  |  | H | S | O 
    4348 ---|---|---|--- 
    4349 H | 6 | -9 | -6 
    4350 S |  | 6 | -6 
    4351 O |  |  | 4 
    4352 Iteration cutoff | 2 
    4353  
    4354 Matchmaker 3j0c.pdb1, chain A (#1.13) with AF3 E1 1-421.pdb, chain A (#62),
    4355 sequence alignment score = 1060.7 
    4356 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    4357 3.020) 
    4358  
    4359 
    4360 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    4361 
    4362 Chain information for AF3 E1 422-461.pdb #63 
    4363 --- 
    4364 Chain | Description 
    4365 A | No description available 
    4366  
    4367 
    4368 > matchmaker #63 to #1.13 & sel
    4369 
    4370 Parameters 
    4371 --- 
    4372 Chain pairing | bb 
    4373 Alignment algorithm | Needleman-Wunsch 
    4374 Similarity matrix | BLOSUM-62 
    4375 SS fraction | 0.3 
    4376 Gap open (HH/SS/other) | 18/18/6 
    4377 Gap extend | 1 
    4378 SS matrix |  |  | H | S | O 
    4379 ---|---|---|--- 
    4380 H | 6 | -9 | -6 
    4381 S |  | 6 | -6 
    4382 O |  |  | 4 
    4383 Iteration cutoff | 2 
    4384  
    4385 Matchmaker 3j0c.pdb1, chain A (#1.13) with AF3 E1 422-461.pdb, chain A (#63),
    4386 sequence alignment score = 626.9 
    4387 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    4388 2.775) 
    4389  
    4390 
    4391 > hide sel cartoons
    4392 
    4393 > select #1.13/B
    4394 
    4395 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    4396 
    4397 > show sel cartoons
    4398 
    4399 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    4400 
    4401 Chain information for AF3 E2 1-352.pdb #64 
    4402 --- 
    4403 Chain | Description 
    4404 B | No description available 
    4405  
    4406 
    4407 > matchmaker #64 to #1.13 & sel
    4408 
    4409 Parameters 
    4410 --- 
    4411 Chain pairing | bb 
    4412 Alignment algorithm | Needleman-Wunsch 
    4413 Similarity matrix | BLOSUM-62 
    4414 SS fraction | 0.3 
    4415 Gap open (HH/SS/other) | 18/18/6 
    4416 Gap extend | 1 
    4417 SS matrix |  |  | H | S | O 
    4418 ---|---|---|--- 
    4419 H | 6 | -9 | -6 
    4420 S |  | 6 | -6 
    4421 O |  |  | 4 
    4422 Iteration cutoff | 2 
    4423  
    4424 Matchmaker 3j0c.pdb1, chain B (#1.13) with AF3 E2 1-352.pdb, chain B (#64),
    4425 sequence alignment score = 583.7 
    4426 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    4427 5.933) 
    4428  
    4429 
    4430 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    4431 
    4432 Chain information for AF3 E2 353-438.pdb #65 
    4433 --- 
    4434 Chain | Description 
    4435 B | No description available 
    4436  
    4437 
    4438 > matchmaker #65 to #1.13 & sel
    4439 
    4440 Parameters 
    4441 --- 
    4442 Chain pairing | bb 
    4443 Alignment algorithm | Needleman-Wunsch 
    4444 Similarity matrix | BLOSUM-62 
    4445 SS fraction | 0.3 
    4446 Gap open (HH/SS/other) | 18/18/6 
    4447 Gap extend | 1 
    4448 SS matrix |  |  | H | S | O 
    4449 ---|---|---|--- 
    4450 H | 6 | -9 | -6 
    4451 S |  | 6 | -6 
    4452 O |  |  | 4 
    4453 Iteration cutoff | 2 
    4454  
    4455 Matchmaker 3j0c.pdb1, chain B (#1.13) with AF3 E2 353-438.pdb, chain B (#65),
    4456 sequence alignment score = 322.6 
    4457 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    4458 8.411) 
    4459  
    4460 
    4461 > select #1.13/C
    4462 
    4463 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    4464 
    4465 > show sel cartoons
    4466 
    4467 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    4468 
    4469 Chain information for AF3 CA.pdb #66 
    4470 --- 
    4471 Chain | Description 
    4472 A | No description available 
    4473  
    4474 
    4475 > matchmaker #66 to #1.13 & sel
    4476 
    4477 Parameters 
    4478 --- 
    4479 Chain pairing | bb 
    4480 Alignment algorithm | Needleman-Wunsch 
    4481 Similarity matrix | BLOSUM-62 
    4482 SS fraction | 0.3 
    4483 Gap open (HH/SS/other) | 18/18/6 
    4484 Gap extend | 1 
    4485 SS matrix |  |  | H | S | O 
    4486 ---|---|---|--- 
    4487 H | 6 | -9 | -6 
    4488 S |  | 6 | -6 
    4489 O |  |  | 4 
    4490 Iteration cutoff | 2 
    4491  
    4492 Matchmaker 3j0c.pdb1, chain C (#1.13) with AF3 CA.pdb, chain A (#66), sequence
    4493 alignment score = 328.1 
    4494 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    4495 2.714) 
    4496  
    4497 
    4498 > hide sel cartoons
    4499 
    4500 > select #1.13/B
    4501 
    4502 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    4503 
    4504 > hide sel cartoons
    4505 
    4506 > color #62 dodgerblue
    4507 
    4508 > color #63 dodgerblue
    4509 
    4510 > color #64 #00b305ff
    4511 
    4512 > color #65 #00b305ff
    4513 
    4514 > color #66 #f15839ff
    4515 
    4516 > select #1.14/A
    4517 
    4518 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    4519 
    4520 > show sel cartoons
    4521 
    4522 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    4523 
    4524 Chain information for AF3 E1 1-421.pdb #67 
    4525 --- 
    4526 Chain | Description 
    4527 A | No description available 
    4528  
    4529 
    4530 > matchmaker #67 to #1.13 & sel
    4531 
    4532 No 'to' model specified 
    4533 
    4534 > matchmaker #67 to #1.14 & sel
    4535 
    4536 Parameters 
    4537 --- 
    4538 Chain pairing | bb 
    4539 Alignment algorithm | Needleman-Wunsch 
    4540 Similarity matrix | BLOSUM-62 
    4541 SS fraction | 0.3 
    4542 Gap open (HH/SS/other) | 18/18/6 
    4543 Gap extend | 1 
    4544 SS matrix |  |  | H | S | O 
    4545 ---|---|---|--- 
    4546 H | 6 | -9 | -6 
    4547 S |  | 6 | -6 
    4548 O |  |  | 4 
    4549 Iteration cutoff | 2 
    4550  
    4551 Matchmaker 3j0c.pdb1, chain A (#1.14) with AF3 E1 1-421.pdb, chain A (#67),
    4552 sequence alignment score = 1060.7 
    4553 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    4554 3.020) 
    4555  
    4556 
    4557 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    4558 
    4559 Chain information for AF3 E1 422-461.pdb #68 
    4560 --- 
    4561 Chain | Description 
    4562 A | No description available 
    4563  
    4564 
    4565 > matchmaker #68 to #1.14 & sel
    4566 
    4567 Parameters 
    4568 --- 
    4569 Chain pairing | bb 
    4570 Alignment algorithm | Needleman-Wunsch 
    4571 Similarity matrix | BLOSUM-62 
    4572 SS fraction | 0.3 
    4573 Gap open (HH/SS/other) | 18/18/6 
    4574 Gap extend | 1 
    4575 SS matrix |  |  | H | S | O 
    4576 ---|---|---|--- 
    4577 H | 6 | -9 | -6 
    4578 S |  | 6 | -6 
    4579 O |  |  | 4 
    4580 Iteration cutoff | 2 
    4581  
    4582 Matchmaker 3j0c.pdb1, chain A (#1.14) with AF3 E1 422-461.pdb, chain A (#68),
    4583 sequence alignment score = 626.9 
    4584 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    4585 2.775) 
    4586  
    4587 
    4588 > hide sel cartoons
    4589 
    4590 > select #1.14/B
    4591 
    4592 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    4593 
    4594 > show sel cartoons
    4595 
    4596 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    4597 
    4598 Chain information for AF3 E2 1-352.pdb #69 
    4599 --- 
    4600 Chain | Description 
    4601 B | No description available 
    4602  
    4603 
    4604 > matchmaker #69 to #1.14 & sel
    4605 
    4606 Parameters 
    4607 --- 
    4608 Chain pairing | bb 
    4609 Alignment algorithm | Needleman-Wunsch 
    4610 Similarity matrix | BLOSUM-62 
    4611 SS fraction | 0.3 
    4612 Gap open (HH/SS/other) | 18/18/6 
    4613 Gap extend | 1 
    4614 SS matrix |  |  | H | S | O 
    4615 ---|---|---|--- 
    4616 H | 6 | -9 | -6 
    4617 S |  | 6 | -6 
    4618 O |  |  | 4 
    4619 Iteration cutoff | 2 
    4620  
    4621 Matchmaker 3j0c.pdb1, chain B (#1.14) with AF3 E2 1-352.pdb, chain B (#69),
    4622 sequence alignment score = 583.7 
    4623 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    4624 5.933) 
    4625  
    4626 
    4627 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    4628 
    4629 Chain information for AF3 E2 353-438.pdb #70 
    4630 --- 
    4631 Chain | Description 
    4632 B | No description available 
    4633  
    4634 
    4635 > matchmaker #70 to #1.14 & sel
    4636 
    4637 Parameters 
    4638 --- 
    4639 Chain pairing | bb 
    4640 Alignment algorithm | Needleman-Wunsch 
    4641 Similarity matrix | BLOSUM-62 
    4642 SS fraction | 0.3 
    4643 Gap open (HH/SS/other) | 18/18/6 
    4644 Gap extend | 1 
    4645 SS matrix |  |  | H | S | O 
    4646 ---|---|---|--- 
    4647 H | 6 | -9 | -6 
    4648 S |  | 6 | -6 
    4649 O |  |  | 4 
    4650 Iteration cutoff | 2 
    4651  
    4652 Matchmaker 3j0c.pdb1, chain B (#1.14) with AF3 E2 353-438.pdb, chain B (#70),
    4653 sequence alignment score = 322.6 
    4654 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    4655 8.411) 
    4656  
    4657 
    4658 > hide sel cartoons
    4659 
    4660 > select #1.14/C
    4661 
    4662 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    4663 
    4664 > show sel cartoons
    4665 
    4666 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    4667 
    4668 Chain information for AF3 CA.pdb #71 
    4669 --- 
    4670 Chain | Description 
    4671 A | No description available 
    4672  
    4673 
    4674 > matchmaker #71 to #1.14 & sel
    4675 
    4676 Parameters 
    4677 --- 
    4678 Chain pairing | bb 
    4679 Alignment algorithm | Needleman-Wunsch 
    4680 Similarity matrix | BLOSUM-62 
    4681 SS fraction | 0.3 
    4682 Gap open (HH/SS/other) | 18/18/6 
    4683 Gap extend | 1 
    4684 SS matrix |  |  | H | S | O 
    4685 ---|---|---|--- 
    4686 H | 6 | -9 | -6 
    4687 S |  | 6 | -6 
    4688 O |  |  | 4 
    4689 Iteration cutoff | 2 
    4690  
    4691 Matchmaker 3j0c.pdb1, chain C (#1.14) with AF3 CA.pdb, chain A (#71), sequence
    4692 alignment score = 328.1 
    4693 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    4694 2.714) 
    4695  
    4696 
    4697 > hide sel cartoons
    4698 
    4699 > color #67 dodgerblue
    4700 
    4701 > color #68 dodgerblue
    4702 
    4703 > color #69 #00b305ff
    4704 
    4705 > color #70 #00b305ff
    4706 
    4707 > color #71 #f15839ff
    4708 
    4709 > select #1.15/A
    4710 
    4711 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    4712 
    4713 > show sel cartoons
    4714 
    4715 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    4716 
    4717 Chain information for AF3 E1 1-421.pdb #72 
    4718 --- 
    4719 Chain | Description 
    4720 A | No description available 
    4721  
    4722 
    4723 > matchmaker #72 to #1.15 & sel
    4724 
    4725 Parameters 
    4726 --- 
    4727 Chain pairing | bb 
    4728 Alignment algorithm | Needleman-Wunsch 
    4729 Similarity matrix | BLOSUM-62 
    4730 SS fraction | 0.3 
    4731 Gap open (HH/SS/other) | 18/18/6 
    4732 Gap extend | 1 
    4733 SS matrix |  |  | H | S | O 
    4734 ---|---|---|--- 
    4735 H | 6 | -9 | -6 
    4736 S |  | 6 | -6 
    4737 O |  |  | 4 
    4738 Iteration cutoff | 2 
    4739  
    4740 Matchmaker 3j0c.pdb1, chain A (#1.15) with AF3 E1 1-421.pdb, chain A (#72),
    4741 sequence alignment score = 1060.7 
    4742 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    4743 3.020) 
    4744  
    4745 
    4746 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    4747 
    4748 Chain information for AF3 E1 422-461.pdb #73 
    4749 --- 
    4750 Chain | Description 
    4751 A | No description available 
    4752  
    4753 
    4754 > matchmaker #73 to #1.15 & sel
    4755 
    4756 Parameters 
    4757 --- 
    4758 Chain pairing | bb 
    4759 Alignment algorithm | Needleman-Wunsch 
    4760 Similarity matrix | BLOSUM-62 
    4761 SS fraction | 0.3 
    4762 Gap open (HH/SS/other) | 18/18/6 
    4763 Gap extend | 1 
    4764 SS matrix |  |  | H | S | O 
    4765 ---|---|---|--- 
    4766 H | 6 | -9 | -6 
    4767 S |  | 6 | -6 
    4768 O |  |  | 4 
    4769 Iteration cutoff | 2 
    4770  
    4771 Matchmaker 3j0c.pdb1, chain A (#1.15) with AF3 E1 422-461.pdb, chain A (#73),
    4772 sequence alignment score = 626.9 
    4773 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    4774 2.776) 
    4775  
    4776 
    4777 > hide sel cartoons
    4778 
    4779 > select #1.15/B
    4780 
    4781 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    4782 
    4783 > show sel cartoons
    4784 
    4785 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    4786 
    4787 Chain information for AF3 E2 1-352.pdb #74 
    4788 --- 
    4789 Chain | Description 
    4790 B | No description available 
    4791  
    4792 
    4793 > matchmaker #74 to #1.15 & sel
    4794 
    4795 Parameters 
    4796 --- 
    4797 Chain pairing | bb 
    4798 Alignment algorithm | Needleman-Wunsch 
    4799 Similarity matrix | BLOSUM-62 
    4800 SS fraction | 0.3 
    4801 Gap open (HH/SS/other) | 18/18/6 
    4802 Gap extend | 1 
    4803 SS matrix |  |  | H | S | O 
    4804 ---|---|---|--- 
    4805 H | 6 | -9 | -6 
    4806 S |  | 6 | -6 
    4807 O |  |  | 4 
    4808 Iteration cutoff | 2 
    4809  
    4810 Matchmaker 3j0c.pdb1, chain B (#1.15) with AF3 E2 1-352.pdb, chain B (#74),
    4811 sequence alignment score = 583.7 
    4812 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    4813 5.933) 
    4814  
    4815 
    4816 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    4817 
    4818 Chain information for AF3 E2 353-438.pdb #75 
    4819 --- 
    4820 Chain | Description 
    4821 B | No description available 
    4822  
    4823 
    4824 > matchmaker #75 to #1.15 & sel
    4825 
    4826 Parameters 
    4827 --- 
    4828 Chain pairing | bb 
    4829 Alignment algorithm | Needleman-Wunsch 
    4830 Similarity matrix | BLOSUM-62 
    4831 SS fraction | 0.3 
    4832 Gap open (HH/SS/other) | 18/18/6 
    4833 Gap extend | 1 
    4834 SS matrix |  |  | H | S | O 
    4835 ---|---|---|--- 
    4836 H | 6 | -9 | -6 
    4837 S |  | 6 | -6 
    4838 O |  |  | 4 
    4839 Iteration cutoff | 2 
    4840  
    4841 Matchmaker 3j0c.pdb1, chain B (#1.15) with AF3 E2 353-438.pdb, chain B (#75),
    4842 sequence alignment score = 333.4 
    4843 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    4844 8.411) 
    4845  
    4846 
    4847 > hide sel cartoons
    4848 
    4849 > select #1.15/C
    4850 
    4851 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    4852 
    4853 > show sel cartoons
    4854 
    4855 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    4856 
    4857 Chain information for AF3 CA.pdb #76 
    4858 --- 
    4859 Chain | Description 
    4860 A | No description available 
    4861  
    4862 
    4863 > matchmaker #76 to #1.15 & sel
    4864 
    4865 Parameters 
    4866 --- 
    4867 Chain pairing | bb 
    4868 Alignment algorithm | Needleman-Wunsch 
    4869 Similarity matrix | BLOSUM-62 
    4870 SS fraction | 0.3 
    4871 Gap open (HH/SS/other) | 18/18/6 
    4872 Gap extend | 1 
    4873 SS matrix |  |  | H | S | O 
    4874 ---|---|---|--- 
    4875 H | 6 | -9 | -6 
    4876 S |  | 6 | -6 
    4877 O |  |  | 4 
    4878 Iteration cutoff | 2 
    4879  
    4880 Matchmaker 3j0c.pdb1, chain C (#1.15) with AF3 CA.pdb, chain A (#76), sequence
    4881 alignment score = 328.1 
    4882 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    4883 2.714) 
    4884  
    4885 
    4886 > hide sel cartoons
    4887 
    4888 > color #72 dodgerblue
    4889 
    4890 > color #73 dodgerblue
    4891 
    4892 > color #74 #00b305ff
    4893 
    4894 > color #75 #00b305ff
    4895 
    4896 > color #76 #f15839ff
    4897 
    4898 > select #1.16/A
    4899 
    4900 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    4901 
    4902 > show sel cartoons
    4903 
    4904 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    4905 
    4906 Chain information for AF3 E1 1-421.pdb #77 
    4907 --- 
    4908 Chain | Description 
    4909 A | No description available 
    4910  
    4911 
    4912 > matchmaker #77 to #1.16 & sel
    4913 
    4914 Parameters 
    4915 --- 
    4916 Chain pairing | bb 
    4917 Alignment algorithm | Needleman-Wunsch 
    4918 Similarity matrix | BLOSUM-62 
    4919 SS fraction | 0.3 
    4920 Gap open (HH/SS/other) | 18/18/6 
    4921 Gap extend | 1 
    4922 SS matrix |  |  | H | S | O 
    4923 ---|---|---|--- 
    4924 H | 6 | -9 | -6 
    4925 S |  | 6 | -6 
    4926 O |  |  | 4 
    4927 Iteration cutoff | 2 
    4928  
    4929 Matchmaker 3j0c.pdb1, chain A (#1.16) with AF3 E1 1-421.pdb, chain A (#77),
    4930 sequence alignment score = 1060.7 
    4931 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    4932 3.020) 
    4933  
    4934 
    4935 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    4936 
    4937 Chain information for AF3 E1 422-461.pdb #78 
    4938 --- 
    4939 Chain | Description 
    4940 A | No description available 
    4941  
    4942 
    4943 > matchmaker #78 to #1.16 & sel
    4944 
    4945 Parameters 
    4946 --- 
    4947 Chain pairing | bb 
    4948 Alignment algorithm | Needleman-Wunsch 
    4949 Similarity matrix | BLOSUM-62 
    4950 SS fraction | 0.3 
    4951 Gap open (HH/SS/other) | 18/18/6 
    4952 Gap extend | 1 
    4953 SS matrix |  |  | H | S | O 
    4954 ---|---|---|--- 
    4955 H | 6 | -9 | -6 
    4956 S |  | 6 | -6 
    4957 O |  |  | 4 
    4958 Iteration cutoff | 2 
    4959  
    4960 Matchmaker 3j0c.pdb1, chain A (#1.16) with AF3 E1 422-461.pdb, chain A (#78),
    4961 sequence alignment score = 626.9 
    4962 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    4963 2.775) 
    4964  
    4965 
    4966 > hide sel cartoons
    4967 
    4968 > select #1.16/B
    4969 
    4970 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    4971 
    4972 > show sel cartoons
    4973 
    4974 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    4975 
    4976 Chain information for AF3 E2 1-352.pdb #79 
    4977 --- 
    4978 Chain | Description 
    4979 B | No description available 
    4980  
    4981 
    4982 > matchmaker #79 to #1.16 & sel
    4983 
    4984 Parameters 
    4985 --- 
    4986 Chain pairing | bb 
    4987 Alignment algorithm | Needleman-Wunsch 
    4988 Similarity matrix | BLOSUM-62 
    4989 SS fraction | 0.3 
    4990 Gap open (HH/SS/other) | 18/18/6 
    4991 Gap extend | 1 
    4992 SS matrix |  |  | H | S | O 
    4993 ---|---|---|--- 
    4994 H | 6 | -9 | -6 
    4995 S |  | 6 | -6 
    4996 O |  |  | 4 
    4997 Iteration cutoff | 2 
    4998  
    4999 Matchmaker 3j0c.pdb1, chain B (#1.16) with AF3 E2 1-352.pdb, chain B (#79),
    5000 sequence alignment score = 583.7 
    5001 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    5002 5.933) 
    5003  
    5004 
    5005 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    5006 
    5007 Chain information for AF3 E2 353-438.pdb #80 
    5008 --- 
    5009 Chain | Description 
    5010 B | No description available 
    5011  
    5012 
    5013 > matchmaker #80 to #1.16 & sel
    5014 
    5015 Parameters 
    5016 --- 
    5017 Chain pairing | bb 
    5018 Alignment algorithm | Needleman-Wunsch 
    5019 Similarity matrix | BLOSUM-62 
    5020 SS fraction | 0.3 
    5021 Gap open (HH/SS/other) | 18/18/6 
    5022 Gap extend | 1 
    5023 SS matrix |  |  | H | S | O 
    5024 ---|---|---|--- 
    5025 H | 6 | -9 | -6 
    5026 S |  | 6 | -6 
    5027 O |  |  | 4 
    5028 Iteration cutoff | 2 
    5029  
    5030 Matchmaker 3j0c.pdb1, chain B (#1.16) with AF3 E2 353-438.pdb, chain B (#80),
    5031 sequence alignment score = 322.6 
    5032 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    5033 8.411) 
    5034  
    5035 
    5036 > hide sel cartoons
    5037 
    5038 > select #1.16/C
    5039 
    5040 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    5041 
    5042 > show sel cartoons
    5043 
    5044 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    5045 
    5046 Chain information for AF3 CA.pdb #81 
    5047 --- 
    5048 Chain | Description 
    5049 A | No description available 
    5050  
    5051 
    5052 > matchmaker #81 to #1.16 & sel
    5053 
    5054 Parameters 
    5055 --- 
    5056 Chain pairing | bb 
    5057 Alignment algorithm | Needleman-Wunsch 
    5058 Similarity matrix | BLOSUM-62 
    5059 SS fraction | 0.3 
    5060 Gap open (HH/SS/other) | 18/18/6 
    5061 Gap extend | 1 
    5062 SS matrix |  |  | H | S | O 
    5063 ---|---|---|--- 
    5064 H | 6 | -9 | -6 
    5065 S |  | 6 | -6 
    5066 O |  |  | 4 
    5067 Iteration cutoff | 2 
    5068  
    5069 Matchmaker 3j0c.pdb1, chain C (#1.16) with AF3 CA.pdb, chain A (#81), sequence
    5070 alignment score = 328.1 
    5071 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    5072 2.714) 
    5073  
    5074 
    5075 > hide sel cartoons
    5076 
    5077 > color #77 dodgerblue
    5078 
    5079 > color #78 dodgerblue
    5080 
    5081 > color #79 #00b305ff
    5082 
    5083 > color #80 #00b305ff
    5084 
    5085 > color #81 #f15839ff
    5086 
    5087 > select #1.17/A
    5088 
    5089 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    5090 
    5091 > show sel cartoons
    5092 
    5093 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    5094 
    5095 Chain information for AF3 E1 1-421.pdb #82 
    5096 --- 
    5097 Chain | Description 
    5098 A | No description available 
    5099  
    5100 
    5101 > matchmaker #82 to #1.17 & sel
    5102 
    5103 Parameters 
    5104 --- 
    5105 Chain pairing | bb 
    5106 Alignment algorithm | Needleman-Wunsch 
    5107 Similarity matrix | BLOSUM-62 
    5108 SS fraction | 0.3 
    5109 Gap open (HH/SS/other) | 18/18/6 
    5110 Gap extend | 1 
    5111 SS matrix |  |  | H | S | O 
    5112 ---|---|---|--- 
    5113 H | 6 | -9 | -6 
    5114 S |  | 6 | -6 
    5115 O |  |  | 4 
    5116 Iteration cutoff | 2 
    5117  
    5118 Matchmaker 3j0c.pdb1, chain A (#1.17) with AF3 E1 1-421.pdb, chain A (#82),
    5119 sequence alignment score = 1060.7 
    5120 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    5121 3.020) 
    5122  
    5123 
    5124 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    5125 
    5126 Chain information for AF3 E1 422-461.pdb #83 
    5127 --- 
    5128 Chain | Description 
    5129 A | No description available 
    5130  
    5131 
    5132 > matchmaker #83 to #1.17 & sel
    5133 
    5134 Parameters 
    5135 --- 
    5136 Chain pairing | bb 
    5137 Alignment algorithm | Needleman-Wunsch 
    5138 Similarity matrix | BLOSUM-62 
    5139 SS fraction | 0.3 
    5140 Gap open (HH/SS/other) | 18/18/6 
    5141 Gap extend | 1 
    5142 SS matrix |  |  | H | S | O 
    5143 ---|---|---|--- 
    5144 H | 6 | -9 | -6 
    5145 S |  | 6 | -6 
    5146 O |  |  | 4 
    5147 Iteration cutoff | 2 
    5148  
    5149 Matchmaker 3j0c.pdb1, chain A (#1.17) with AF3 E1 422-461.pdb, chain A (#83),
    5150 sequence alignment score = 626.9 
    5151 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    5152 2.776) 
    5153  
    5154 
    5155 > hide sel cartoons
    5156 
    5157 > select #1.17/B
    5158 
    5159 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    5160 
    5161 > show sel cartoons
    5162 
    5163 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    5164 
    5165 Chain information for AF3 E2 1-352.pdb #84 
    5166 --- 
    5167 Chain | Description 
    5168 B | No description available 
    5169  
    5170 
    5171 > matchmaker #84 to #1.17 & sel
    5172 
    5173 Parameters 
    5174 --- 
    5175 Chain pairing | bb 
    5176 Alignment algorithm | Needleman-Wunsch 
    5177 Similarity matrix | BLOSUM-62 
    5178 SS fraction | 0.3 
    5179 Gap open (HH/SS/other) | 18/18/6 
    5180 Gap extend | 1 
    5181 SS matrix |  |  | H | S | O 
    5182 ---|---|---|--- 
    5183 H | 6 | -9 | -6 
    5184 S |  | 6 | -6 
    5185 O |  |  | 4 
    5186 Iteration cutoff | 2 
    5187  
    5188 Matchmaker 3j0c.pdb1, chain B (#1.17) with AF3 E2 1-352.pdb, chain B (#84),
    5189 sequence alignment score = 583.7 
    5190 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    5191 5.933) 
    5192  
    5193 
    5194 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    5195 
    5196 Chain information for AF3 E2 353-438.pdb #85 
    5197 --- 
    5198 Chain | Description 
    5199 B | No description available 
    5200  
    5201 
    5202 > matchmaker #85 to #1.17 & sel
    5203 
    5204 Parameters 
    5205 --- 
    5206 Chain pairing | bb 
    5207 Alignment algorithm | Needleman-Wunsch 
    5208 Similarity matrix | BLOSUM-62 
    5209 SS fraction | 0.3 
    5210 Gap open (HH/SS/other) | 18/18/6 
    5211 Gap extend | 1 
    5212 SS matrix |  |  | H | S | O 
    5213 ---|---|---|--- 
    5214 H | 6 | -9 | -6 
    5215 S |  | 6 | -6 
    5216 O |  |  | 4 
    5217 Iteration cutoff | 2 
    5218  
    5219 Matchmaker 3j0c.pdb1, chain B (#1.17) with AF3 E2 353-438.pdb, chain B (#85),
    5220 sequence alignment score = 322.6 
    5221 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    5222 8.411) 
    5223  
    5224 
    5225 > hide sel cartoons
    5226 
    5227 > select #1.17/C
    5228 
    5229 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    5230 
    5231 > show sel cartoons
    5232 
    5233 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    5234 
    5235 Chain information for AF3 CA.pdb #86 
    5236 --- 
    5237 Chain | Description 
    5238 A | No description available 
    5239  
    5240 
    5241 > matchmaker #86 to #1.17 & sel
    5242 
    5243 Parameters 
    5244 --- 
    5245 Chain pairing | bb 
    5246 Alignment algorithm | Needleman-Wunsch 
    5247 Similarity matrix | BLOSUM-62 
    5248 SS fraction | 0.3 
    5249 Gap open (HH/SS/other) | 18/18/6 
    5250 Gap extend | 1 
    5251 SS matrix |  |  | H | S | O 
    5252 ---|---|---|--- 
    5253 H | 6 | -9 | -6 
    5254 S |  | 6 | -6 
    5255 O |  |  | 4 
    5256 Iteration cutoff | 2 
    5257  
    5258 Matchmaker 3j0c.pdb1, chain C (#1.17) with AF3 CA.pdb, chain A (#86), sequence
    5259 alignment score = 328.1 
    5260 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    5261 2.714) 
    5262  
    5263 
    5264 > hide sel cartoons
    5265 
    5266 > color #82 dodgerblue
    5267 
    5268 > color #83 dodgerblue
    5269 
    5270 > color #84 #00b305ff
    5271 
    5272 > color #85 #00b305ff
    5273 
    5274 > color #86 #f15839ff
    5275 
    5276 > select #1.18/A
    5277 
    5278 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    5279 
    5280 > show sel cartoons
    5281 
    5282 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    5283 
    5284 Chain information for AF3 E1 1-421.pdb #87 
    5285 --- 
    5286 Chain | Description 
    5287 A | No description available 
    5288  
    5289 
    5290 > matchmaker #87 to #1.18 & sel
    5291 
    5292 Parameters 
    5293 --- 
    5294 Chain pairing | bb 
    5295 Alignment algorithm | Needleman-Wunsch 
    5296 Similarity matrix | BLOSUM-62 
    5297 SS fraction | 0.3 
    5298 Gap open (HH/SS/other) | 18/18/6 
    5299 Gap extend | 1 
    5300 SS matrix |  |  | H | S | O 
    5301 ---|---|---|--- 
    5302 H | 6 | -9 | -6 
    5303 S |  | 6 | -6 
    5304 O |  |  | 4 
    5305 Iteration cutoff | 2 
    5306  
    5307 Matchmaker 3j0c.pdb1, chain A (#1.18) with AF3 E1 1-421.pdb, chain A (#87),
    5308 sequence alignment score = 1060.7 
    5309 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    5310 3.020) 
    5311  
    5312 
    5313 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    5314 
    5315 Chain information for AF3 E1 422-461.pdb #88 
    5316 --- 
    5317 Chain | Description 
    5318 A | No description available 
    5319  
    5320 
    5321 > matchmaker #88 to #1.18 & sel
    5322 
    5323 Parameters 
    5324 --- 
    5325 Chain pairing | bb 
    5326 Alignment algorithm | Needleman-Wunsch 
    5327 Similarity matrix | BLOSUM-62 
    5328 SS fraction | 0.3 
    5329 Gap open (HH/SS/other) | 18/18/6 
    5330 Gap extend | 1 
    5331 SS matrix |  |  | H | S | O 
    5332 ---|---|---|--- 
    5333 H | 6 | -9 | -6 
    5334 S |  | 6 | -6 
    5335 O |  |  | 4 
    5336 Iteration cutoff | 2 
    5337  
    5338 Matchmaker 3j0c.pdb1, chain A (#1.18) with AF3 E1 422-461.pdb, chain A (#88),
    5339 sequence alignment score = 626.9 
    5340 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    5341 2.776) 
    5342  
    5343 
    5344 > hide sel cartoons
    5345 
    5346 > select #1.18/B
    5347 
    5348 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    5349 
    5350 > show sel cartoons
    5351 
    5352 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    5353 
    5354 Chain information for AF3 E2 1-352.pdb #89 
    5355 --- 
    5356 Chain | Description 
    5357 B | No description available 
    5358  
    5359 
    5360 > matchmaker #89 to #1.18 & sel
    5361 
    5362 Parameters 
    5363 --- 
    5364 Chain pairing | bb 
    5365 Alignment algorithm | Needleman-Wunsch 
    5366 Similarity matrix | BLOSUM-62 
    5367 SS fraction | 0.3 
    5368 Gap open (HH/SS/other) | 18/18/6 
    5369 Gap extend | 1 
    5370 SS matrix |  |  | H | S | O 
    5371 ---|---|---|--- 
    5372 H | 6 | -9 | -6 
    5373 S |  | 6 | -6 
    5374 O |  |  | 4 
    5375 Iteration cutoff | 2 
    5376  
    5377 Matchmaker 3j0c.pdb1, chain B (#1.18) with AF3 E2 1-352.pdb, chain B (#89),
    5378 sequence alignment score = 583.7 
    5379 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    5380 5.933) 
    5381  
    5382 
    5383 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    5384 
    5385 Chain information for AF3 E2 353-438.pdb #90 
    5386 --- 
    5387 Chain | Description 
    5388 B | No description available 
    5389  
    5390 
    5391 > matchmaker #90 to #1.18 & sel
    5392 
    5393 Parameters 
    5394 --- 
    5395 Chain pairing | bb 
    5396 Alignment algorithm | Needleman-Wunsch 
    5397 Similarity matrix | BLOSUM-62 
    5398 SS fraction | 0.3 
    5399 Gap open (HH/SS/other) | 18/18/6 
    5400 Gap extend | 1 
    5401 SS matrix |  |  | H | S | O 
    5402 ---|---|---|--- 
    5403 H | 6 | -9 | -6 
    5404 S |  | 6 | -6 
    5405 O |  |  | 4 
    5406 Iteration cutoff | 2 
    5407  
    5408 Matchmaker 3j0c.pdb1, chain B (#1.18) with AF3 E2 353-438.pdb, chain B (#90),
    5409 sequence alignment score = 333.4 
    5410 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    5411 8.411) 
    5412  
    5413 
    5414 > hide sel cartoons
    5415 
    5416 > select #1.18/C
    5417 
    5418 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    5419 
    5420 > show sel cartoons
    5421 
    5422 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    5423 
    5424 Chain information for AF3 CA.pdb #91 
    5425 --- 
    5426 Chain | Description 
    5427 A | No description available 
    5428  
    5429 
    5430 > matchmaker #91 to #1.18 & sel
    5431 
    5432 Parameters 
    5433 --- 
    5434 Chain pairing | bb 
    5435 Alignment algorithm | Needleman-Wunsch 
    5436 Similarity matrix | BLOSUM-62 
    5437 SS fraction | 0.3 
    5438 Gap open (HH/SS/other) | 18/18/6 
    5439 Gap extend | 1 
    5440 SS matrix |  |  | H | S | O 
    5441 ---|---|---|--- 
    5442 H | 6 | -9 | -6 
    5443 S |  | 6 | -6 
    5444 O |  |  | 4 
    5445 Iteration cutoff | 2 
    5446  
    5447 Matchmaker 3j0c.pdb1, chain C (#1.18) with AF3 CA.pdb, chain A (#91), sequence
    5448 alignment score = 328.1 
    5449 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    5450 2.714) 
    5451  
    5452 
    5453 > hide sel cartoons
    5454 
    5455 > color #87 dodgerblue
    5456 
    5457 > color #88 dodgerblue
    5458 
    5459 > color #89 #00b305ff
    5460 
    5461 > color #90 #00b305ff
    5462 
    5463 > color #91 #f15839ff
    5464 
    5465 > select #1.19/A
    5466 
    5467 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    5468 
    5469 > show sel cartoons
    5470 
    5471 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    5472 
    5473 Chain information for AF3 E1 1-421.pdb #92 
    5474 --- 
    5475 Chain | Description 
    5476 A | No description available 
    5477  
    5478 
    5479 > matchmaker #92 to #1.19 & sel
    5480 
    5481 Parameters 
    5482 --- 
    5483 Chain pairing | bb 
    5484 Alignment algorithm | Needleman-Wunsch 
    5485 Similarity matrix | BLOSUM-62 
    5486 SS fraction | 0.3 
    5487 Gap open (HH/SS/other) | 18/18/6 
    5488 Gap extend | 1 
    5489 SS matrix |  |  | H | S | O 
    5490 ---|---|---|--- 
    5491 H | 6 | -9 | -6 
    5492 S |  | 6 | -6 
    5493 O |  |  | 4 
    5494 Iteration cutoff | 2 
    5495  
    5496 Matchmaker 3j0c.pdb1, chain A (#1.19) with AF3 E1 1-421.pdb, chain A (#92),
    5497 sequence alignment score = 1060.7 
    5498 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    5499 3.020) 
    5500  
    5501 
    5502 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    5503 
    5504 Chain information for AF3 E1 422-461.pdb #93 
    5505 --- 
    5506 Chain | Description 
    5507 A | No description available 
    5508  
    5509 
    5510 > matchmaker #93 to #1.19 & sel
    5511 
    5512 Parameters 
    5513 --- 
    5514 Chain pairing | bb 
    5515 Alignment algorithm | Needleman-Wunsch 
    5516 Similarity matrix | BLOSUM-62 
    5517 SS fraction | 0.3 
    5518 Gap open (HH/SS/other) | 18/18/6 
    5519 Gap extend | 1 
    5520 SS matrix |  |  | H | S | O 
    5521 ---|---|---|--- 
    5522 H | 6 | -9 | -6 
    5523 S |  | 6 | -6 
    5524 O |  |  | 4 
    5525 Iteration cutoff | 2 
    5526  
    5527 Matchmaker 3j0c.pdb1, chain A (#1.19) with AF3 E1 422-461.pdb, chain A (#93),
    5528 sequence alignment score = 626.9 
    5529 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    5530 2.775) 
    5531  
    5532 
    5533 > hide sel cartoons
    5534 
    5535 > select #1.19/B
    5536 
    5537 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    5538 
    5539 > show sel cartoons
    5540 
    5541 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    5542 
    5543 Chain information for AF3 E2 1-352.pdb #94 
    5544 --- 
    5545 Chain | Description 
    5546 B | No description available 
    5547  
    5548 
    5549 > matchmaker #94 to #1.19 & sel
    5550 
    5551 Parameters 
    5552 --- 
    5553 Chain pairing | bb 
    5554 Alignment algorithm | Needleman-Wunsch 
    5555 Similarity matrix | BLOSUM-62 
    5556 SS fraction | 0.3 
    5557 Gap open (HH/SS/other) | 18/18/6 
    5558 Gap extend | 1 
    5559 SS matrix |  |  | H | S | O 
    5560 ---|---|---|--- 
    5561 H | 6 | -9 | -6 
    5562 S |  | 6 | -6 
    5563 O |  |  | 4 
    5564 Iteration cutoff | 2 
    5565  
    5566 Matchmaker 3j0c.pdb1, chain B (#1.19) with AF3 E2 1-352.pdb, chain B (#94),
    5567 sequence alignment score = 583.7 
    5568 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    5569 5.933) 
    5570  
    5571 
    5572 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    5573 
    5574 Chain information for AF3 E2 353-438.pdb #95 
    5575 --- 
    5576 Chain | Description 
    5577 B | No description available 
    5578  
    5579 
    5580 > matchmaker #95 to #1.19 & sel
    5581 
    5582 Parameters 
    5583 --- 
    5584 Chain pairing | bb 
    5585 Alignment algorithm | Needleman-Wunsch 
    5586 Similarity matrix | BLOSUM-62 
    5587 SS fraction | 0.3 
    5588 Gap open (HH/SS/other) | 18/18/6 
    5589 Gap extend | 1 
    5590 SS matrix |  |  | H | S | O 
    5591 ---|---|---|--- 
    5592 H | 6 | -9 | -6 
    5593 S |  | 6 | -6 
    5594 O |  |  | 4 
    5595 Iteration cutoff | 2 
    5596  
    5597 Matchmaker 3j0c.pdb1, chain B (#1.19) with AF3 E2 353-438.pdb, chain B (#95),
    5598 sequence alignment score = 322.6 
    5599 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    5600 8.411) 
    5601  
    5602 
    5603 > hide sel cartoons
    5604 
    5605 > select #1.19/C
    5606 
    5607 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    5608 
    5609 > show sel cartoons
    5610 
    5611 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    5612 
    5613 Chain information for AF3 CA.pdb #96 
    5614 --- 
    5615 Chain | Description 
    5616 A | No description available 
    5617  
    5618 
    5619 > matchmaker #96 to #1.19 & sel
    5620 
    5621 Parameters 
    5622 --- 
    5623 Chain pairing | bb 
    5624 Alignment algorithm | Needleman-Wunsch 
    5625 Similarity matrix | BLOSUM-62 
    5626 SS fraction | 0.3 
    5627 Gap open (HH/SS/other) | 18/18/6 
    5628 Gap extend | 1 
    5629 SS matrix |  |  | H | S | O 
    5630 ---|---|---|--- 
    5631 H | 6 | -9 | -6 
    5632 S |  | 6 | -6 
    5633 O |  |  | 4 
    5634 Iteration cutoff | 2 
    5635  
    5636 Matchmaker 3j0c.pdb1, chain C (#1.19) with AF3 CA.pdb, chain A (#96), sequence
    5637 alignment score = 328.1 
    5638 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    5639 2.714) 
    5640  
    5641 
    5642 > hide sel cartoons
    5643 
    5644 > color #92 dodgerblue
    5645 
    5646 > color #93 dodgerblue
    5647 
    5648 > color #94 dodgerblue
    5649 
    5650 > color #94 #00b305ff
    5651 
    5652 > color #95 #00b305ff
    5653 
    5654 > color #96 #f15839ff
    5655 
    5656 > select #1.20/A
    5657 
    5658 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    5659 
    5660 > show sel cartoons
    5661 
    5662 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    5663 
    5664 Chain information for AF3 E1 1-421.pdb #97 
    5665 --- 
    5666 Chain | Description 
    5667 A | No description available 
    5668  
    5669 
    5670 > matchmaker #97 to #1.20 & sel
    5671 
    5672 Parameters 
    5673 --- 
    5674 Chain pairing | bb 
    5675 Alignment algorithm | Needleman-Wunsch 
    5676 Similarity matrix | BLOSUM-62 
    5677 SS fraction | 0.3 
    5678 Gap open (HH/SS/other) | 18/18/6 
    5679 Gap extend | 1 
    5680 SS matrix |  |  | H | S | O 
    5681 ---|---|---|--- 
    5682 H | 6 | -9 | -6 
    5683 S |  | 6 | -6 
    5684 O |  |  | 4 
    5685 Iteration cutoff | 2 
    5686  
    5687 Matchmaker 3j0c.pdb1, chain A (#1.20) with AF3 E1 1-421.pdb, chain A (#97),
    5688 sequence alignment score = 1060.7 
    5689 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    5690 3.020) 
    5691  
    5692 
    5693 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    5694 
    5695 Chain information for AF3 E1 422-461.pdb #98 
    5696 --- 
    5697 Chain | Description 
    5698 A | No description available 
    5699  
    5700 
    5701 > matchmaker #98 to #1.20 & sel
    5702 
    5703 Parameters 
    5704 --- 
    5705 Chain pairing | bb 
    5706 Alignment algorithm | Needleman-Wunsch 
    5707 Similarity matrix | BLOSUM-62 
    5708 SS fraction | 0.3 
    5709 Gap open (HH/SS/other) | 18/18/6 
    5710 Gap extend | 1 
    5711 SS matrix |  |  | H | S | O 
    5712 ---|---|---|--- 
    5713 H | 6 | -9 | -6 
    5714 S |  | 6 | -6 
    5715 O |  |  | 4 
    5716 Iteration cutoff | 2 
    5717  
    5718 Matchmaker 3j0c.pdb1, chain A (#1.20) with AF3 E1 422-461.pdb, chain A (#98),
    5719 sequence alignment score = 626.9 
    5720 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    5721 2.775) 
    5722  
    5723 
    5724 > hide sel cartoons
    5725 
    5726 > select #1.20/B
    5727 
    5728 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    5729 
    5730 > show sel cartoons
    5731 
    5732 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    5733 
    5734 Chain information for AF3 E2 1-352.pdb #99 
    5735 --- 
    5736 Chain | Description 
    5737 B | No description available 
    5738  
    5739 
    5740 > matchmaker #99 to #1.20 & sel
    5741 
    5742 Parameters 
    5743 --- 
    5744 Chain pairing | bb 
    5745 Alignment algorithm | Needleman-Wunsch 
    5746 Similarity matrix | BLOSUM-62 
    5747 SS fraction | 0.3 
    5748 Gap open (HH/SS/other) | 18/18/6 
    5749 Gap extend | 1 
    5750 SS matrix |  |  | H | S | O 
    5751 ---|---|---|--- 
    5752 H | 6 | -9 | -6 
    5753 S |  | 6 | -6 
    5754 O |  |  | 4 
    5755 Iteration cutoff | 2 
    5756  
    5757 Matchmaker 3j0c.pdb1, chain B (#1.20) with AF3 E2 1-352.pdb, chain B (#99),
    5758 sequence alignment score = 583.7 
    5759 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    5760 5.933) 
    5761  
    5762 
    5763 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    5764 
    5765 Chain information for AF3 E2 353-438.pdb #100 
    5766 --- 
    5767 Chain | Description 
    5768 B | No description available 
    5769  
    5770 
    5771 > matchmaker #100 to #1.20 & sel
    5772 
    5773 Parameters 
    5774 --- 
    5775 Chain pairing | bb 
    5776 Alignment algorithm | Needleman-Wunsch 
    5777 Similarity matrix | BLOSUM-62 
    5778 SS fraction | 0.3 
    5779 Gap open (HH/SS/other) | 18/18/6 
    5780 Gap extend | 1 
    5781 SS matrix |  |  | H | S | O 
    5782 ---|---|---|--- 
    5783 H | 6 | -9 | -6 
    5784 S |  | 6 | -6 
    5785 O |  |  | 4 
    5786 Iteration cutoff | 2 
    5787  
    5788 Matchmaker 3j0c.pdb1, chain B (#1.20) with AF3 E2 353-438.pdb, chain B (#100),
    5789 sequence alignment score = 322.6 
    5790 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    5791 8.411) 
    5792  
    5793 
    5794 > hide sel cartoons
    5795 
    5796 > select #1.20/C
    5797 
    5798 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    5799 
    5800 > show sel cartoons
    5801 
    5802 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    5803 
    5804 Chain information for AF3 CA.pdb #101 
    5805 --- 
    5806 Chain | Description 
    5807 A | No description available 
    5808  
    5809 
    5810 > matchmaker #101 to #1.20 & sel
    5811 
    5812 Parameters 
    5813 --- 
    5814 Chain pairing | bb 
    5815 Alignment algorithm | Needleman-Wunsch 
    5816 Similarity matrix | BLOSUM-62 
    5817 SS fraction | 0.3 
    5818 Gap open (HH/SS/other) | 18/18/6 
    5819 Gap extend | 1 
    5820 SS matrix |  |  | H | S | O 
    5821 ---|---|---|--- 
    5822 H | 6 | -9 | -6 
    5823 S |  | 6 | -6 
    5824 O |  |  | 4 
    5825 Iteration cutoff | 2 
    5826  
    5827 Matchmaker 3j0c.pdb1, chain C (#1.20) with AF3 CA.pdb, chain A (#101),
    5828 sequence alignment score = 328.1 
    5829 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    5830 2.714) 
    5831  
    5832 
    5833 > hide sel cartoons
    5834 
    5835 > color #97 dodgerblue
    5836 
    5837 > color #98 dodgerblue
    5838 
    5839 > color #99 #00b305ff
    5840 
    5841 > color #100 #00b305ff
    5842 
    5843 > color #101 #f15839ff
    5844 
    5845 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    5846 
    5847 > select #1.21/A
    5848 
    5849 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    5850 
    5851 > show sel cartoons
    5852 
    5853 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    5854 
    5855 Chain information for AF3 E1 1-421.pdb #102 
    5856 --- 
    5857 Chain | Description 
    5858 A | No description available 
    5859  
    5860 
    5861 > matchmaker #102 to #1.21 & sel
    5862 
    5863 Parameters 
    5864 --- 
    5865 Chain pairing | bb 
    5866 Alignment algorithm | Needleman-Wunsch 
    5867 Similarity matrix | BLOSUM-62 
    5868 SS fraction | 0.3 
    5869 Gap open (HH/SS/other) | 18/18/6 
    5870 Gap extend | 1 
    5871 SS matrix |  |  | H | S | O 
    5872 ---|---|---|--- 
    5873 H | 6 | -9 | -6 
    5874 S |  | 6 | -6 
    5875 O |  |  | 4 
    5876 Iteration cutoff | 2 
    5877  
    5878 Matchmaker 3j0c.pdb1, chain A (#1.21) with AF3 E1 1-421.pdb, chain A (#102),
    5879 sequence alignment score = 1060.7 
    5880 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    5881 3.020) 
    5882  
    5883 
    5884 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    5885 
    5886 Chain information for AF3 E1 422-461.pdb #103 
    5887 --- 
    5888 Chain | Description 
    5889 A | No description available 
    5890  
    5891 
    5892 > matchmaker #103 to #1.21 & sel
    5893 
    5894 Parameters 
    5895 --- 
    5896 Chain pairing | bb 
    5897 Alignment algorithm | Needleman-Wunsch 
    5898 Similarity matrix | BLOSUM-62 
    5899 SS fraction | 0.3 
    5900 Gap open (HH/SS/other) | 18/18/6 
    5901 Gap extend | 1 
    5902 SS matrix |  |  | H | S | O 
    5903 ---|---|---|--- 
    5904 H | 6 | -9 | -6 
    5905 S |  | 6 | -6 
    5906 O |  |  | 4 
    5907 Iteration cutoff | 2 
    5908  
    5909 Matchmaker 3j0c.pdb1, chain A (#1.21) with AF3 E1 422-461.pdb, chain A (#103),
    5910 sequence alignment score = 626.9 
    5911 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    5912 2.775) 
    5913  
    5914 
    5915 > hide sel cartoons
    5916 
    5917 > select #1.21/B
    5918 
    5919 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    5920 
    5921 > show sel cartoons
    5922 
    5923 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    5924 
    5925 Chain information for AF3 E2 1-352.pdb #104 
    5926 --- 
    5927 Chain | Description 
    5928 B | No description available 
    5929  
    5930 
    5931 > matchmaker #104 to #1.21 & sel
    5932 
    5933 Parameters 
    5934 --- 
    5935 Chain pairing | bb 
    5936 Alignment algorithm | Needleman-Wunsch 
    5937 Similarity matrix | BLOSUM-62 
    5938 SS fraction | 0.3 
    5939 Gap open (HH/SS/other) | 18/18/6 
    5940 Gap extend | 1 
    5941 SS matrix |  |  | H | S | O 
    5942 ---|---|---|--- 
    5943 H | 6 | -9 | -6 
    5944 S |  | 6 | -6 
    5945 O |  |  | 4 
    5946 Iteration cutoff | 2 
    5947  
    5948 Matchmaker 3j0c.pdb1, chain B (#1.21) with AF3 E2 1-352.pdb, chain B (#104),
    5949 sequence alignment score = 583.7 
    5950 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    5951 5.933) 
    5952  
    5953 
    5954 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    5955 
    5956 Chain information for AF3 E2 353-438.pdb #105 
    5957 --- 
    5958 Chain | Description 
    5959 B | No description available 
    5960  
    5961 
    5962 > matchmaker #105 to #1.21 & sel
    5963 
    5964 Parameters 
    5965 --- 
    5966 Chain pairing | bb 
    5967 Alignment algorithm | Needleman-Wunsch 
    5968 Similarity matrix | BLOSUM-62 
    5969 SS fraction | 0.3 
    5970 Gap open (HH/SS/other) | 18/18/6 
    5971 Gap extend | 1 
    5972 SS matrix |  |  | H | S | O 
    5973 ---|---|---|--- 
    5974 H | 6 | -9 | -6 
    5975 S |  | 6 | -6 
    5976 O |  |  | 4 
    5977 Iteration cutoff | 2 
    5978  
    5979 Matchmaker 3j0c.pdb1, chain B (#1.21) with AF3 E2 353-438.pdb, chain B (#105),
    5980 sequence alignment score = 322.6 
    5981 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    5982 8.411) 
    5983  
    5984 
    5985 > hide sel cartoons
    5986 
    5987 > select #1.21/C
    5988 
    5989 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    5990 
    5991 > show sel cartoons
    5992 
    5993 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    5994 
    5995 Chain information for AF3 CA.pdb #106 
    5996 --- 
    5997 Chain | Description 
    5998 A | No description available 
    5999  
    6000 
    6001 > matchmaker #106 to #1.21 & sel
    6002 
    6003 Parameters 
    6004 --- 
    6005 Chain pairing | bb 
    6006 Alignment algorithm | Needleman-Wunsch 
    6007 Similarity matrix | BLOSUM-62 
    6008 SS fraction | 0.3 
    6009 Gap open (HH/SS/other) | 18/18/6 
    6010 Gap extend | 1 
    6011 SS matrix |  |  | H | S | O 
    6012 ---|---|---|--- 
    6013 H | 6 | -9 | -6 
    6014 S |  | 6 | -6 
    6015 O |  |  | 4 
    6016 Iteration cutoff | 2 
    6017  
    6018 Matchmaker 3j0c.pdb1, chain C (#1.21) with AF3 CA.pdb, chain A (#106),
    6019 sequence alignment score = 328.1 
    6020 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    6021 2.714) 
    6022  
    6023 
    6024 > hide sel cartoons
    6025 
    6026 > color #102 dodgerblue
    6027 
    6028 > color #103 dodgerblue
    6029 
    6030 > color #104 #00b305ff
    6031 
    6032 > color #105 #00b305ff
    6033 
    6034 > color #106 #f15839ff
    6035 
    6036 > select #1.22/A
    6037 
    6038 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    6039 
    6040 > show sel cartoons
    6041 
    6042 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    6043 
    6044 Chain information for AF3 E1 1-421.pdb #107 
    6045 --- 
    6046 Chain | Description 
    6047 A | No description available 
    6048  
    6049 
    6050 > matchmaker #107 to #1.22 & sel
    6051 
    6052 Parameters 
    6053 --- 
    6054 Chain pairing | bb 
    6055 Alignment algorithm | Needleman-Wunsch 
    6056 Similarity matrix | BLOSUM-62 
    6057 SS fraction | 0.3 
    6058 Gap open (HH/SS/other) | 18/18/6 
    6059 Gap extend | 1 
    6060 SS matrix |  |  | H | S | O 
    6061 ---|---|---|--- 
    6062 H | 6 | -9 | -6 
    6063 S |  | 6 | -6 
    6064 O |  |  | 4 
    6065 Iteration cutoff | 2 
    6066  
    6067 Matchmaker 3j0c.pdb1, chain A (#1.22) with AF3 E1 1-421.pdb, chain A (#107),
    6068 sequence alignment score = 1060.7 
    6069 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    6070 3.020) 
    6071  
    6072 
    6073 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    6074 
    6075 Chain information for AF3 E1 422-461.pdb #108 
    6076 --- 
    6077 Chain | Description 
    6078 A | No description available 
    6079  
    6080 
    6081 > matchmaker #108 to #1.22 & sel
    6082 
    6083 Parameters 
    6084 --- 
    6085 Chain pairing | bb 
    6086 Alignment algorithm | Needleman-Wunsch 
    6087 Similarity matrix | BLOSUM-62 
    6088 SS fraction | 0.3 
    6089 Gap open (HH/SS/other) | 18/18/6 
    6090 Gap extend | 1 
    6091 SS matrix |  |  | H | S | O 
    6092 ---|---|---|--- 
    6093 H | 6 | -9 | -6 
    6094 S |  | 6 | -6 
    6095 O |  |  | 4 
    6096 Iteration cutoff | 2 
    6097  
    6098 Matchmaker 3j0c.pdb1, chain A (#1.22) with AF3 E1 422-461.pdb, chain A (#108),
    6099 sequence alignment score = 626.9 
    6100 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    6101 2.776) 
    6102  
    6103 
    6104 > hide sel cartoons
    6105 
    6106 > select #1.22/B
    6107 
    6108 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    6109 
    6110 > show sel cartoons
    6111 
    6112 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    6113 
    6114 Chain information for AF3 E2 1-352.pdb #109 
    6115 --- 
    6116 Chain | Description 
    6117 B | No description available 
    6118  
    6119 
    6120 > matchmaker #109 to #1.22 & sel
    6121 
    6122 Parameters 
    6123 --- 
    6124 Chain pairing | bb 
    6125 Alignment algorithm | Needleman-Wunsch 
    6126 Similarity matrix | BLOSUM-62 
    6127 SS fraction | 0.3 
    6128 Gap open (HH/SS/other) | 18/18/6 
    6129 Gap extend | 1 
    6130 SS matrix |  |  | H | S | O 
    6131 ---|---|---|--- 
    6132 H | 6 | -9 | -6 
    6133 S |  | 6 | -6 
    6134 O |  |  | 4 
    6135 Iteration cutoff | 2 
    6136  
    6137 Matchmaker 3j0c.pdb1, chain B (#1.22) with AF3 E2 1-352.pdb, chain B (#109),
    6138 sequence alignment score = 583.7 
    6139 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    6140 5.933) 
    6141  
    6142 
    6143 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    6144 
    6145 Chain information for AF3 E2 353-438.pdb #110 
    6146 --- 
    6147 Chain | Description 
    6148 B | No description available 
    6149  
    6150 
    6151 > matchmaker #110 to #1.22 & sel
    6152 
    6153 Parameters 
    6154 --- 
    6155 Chain pairing | bb 
    6156 Alignment algorithm | Needleman-Wunsch 
    6157 Similarity matrix | BLOSUM-62 
    6158 SS fraction | 0.3 
    6159 Gap open (HH/SS/other) | 18/18/6 
    6160 Gap extend | 1 
    6161 SS matrix |  |  | H | S | O 
    6162 ---|---|---|--- 
    6163 H | 6 | -9 | -6 
    6164 S |  | 6 | -6 
    6165 O |  |  | 4 
    6166 Iteration cutoff | 2 
    6167  
    6168 Matchmaker 3j0c.pdb1, chain B (#1.22) with AF3 E2 353-438.pdb, chain B (#110),
    6169 sequence alignment score = 322.6 
    6170 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    6171 8.411) 
    6172  
    6173 
    6174 > hide sel cartoons
    6175 
    6176 > select #1.22/C
    6177 
    6178 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    6179 
    6180 > show sel cartoons
    6181 
    6182 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    6183 
    6184 Chain information for AF3 CA.pdb #111 
    6185 --- 
    6186 Chain | Description 
    6187 A | No description available 
    6188  
    6189 
    6190 > matchmaker #111 to #1.22 & sel
    6191 
    6192 Parameters 
    6193 --- 
    6194 Chain pairing | bb 
    6195 Alignment algorithm | Needleman-Wunsch 
    6196 Similarity matrix | BLOSUM-62 
    6197 SS fraction | 0.3 
    6198 Gap open (HH/SS/other) | 18/18/6 
    6199 Gap extend | 1 
    6200 SS matrix |  |  | H | S | O 
    6201 ---|---|---|--- 
    6202 H | 6 | -9 | -6 
    6203 S |  | 6 | -6 
    6204 O |  |  | 4 
    6205 Iteration cutoff | 2 
    6206  
    6207 Matchmaker 3j0c.pdb1, chain C (#1.22) with AF3 CA.pdb, chain A (#111),
    6208 sequence alignment score = 328.1 
    6209 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    6210 2.714) 
    6211  
    6212 
    6213 > hide sel cartoons
    6214 
    6215 > color #107 dodgerblue
    6216 
    6217 > color #108 dodgerblue
    6218 
    6219 > color #109 #00b305ff
    6220 
    6221 > color #110 #00b305ff
    6222 
    6223 > color #111 #f15839ff
    6224 
    6225 > select #1.23/A
    6226 
    6227 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    6228 
    6229 > show sel cartoons
    6230 
    6231 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    6232 
    6233 Chain information for AF3 E1 1-421.pdb #112 
    6234 --- 
    6235 Chain | Description 
    6236 A | No description available 
    6237  
    6238 
    6239 > matchmaker #112 to #1.23 & sel
    6240 
    6241 Parameters 
    6242 --- 
    6243 Chain pairing | bb 
    6244 Alignment algorithm | Needleman-Wunsch 
    6245 Similarity matrix | BLOSUM-62 
    6246 SS fraction | 0.3 
    6247 Gap open (HH/SS/other) | 18/18/6 
    6248 Gap extend | 1 
    6249 SS matrix |  |  | H | S | O 
    6250 ---|---|---|--- 
    6251 H | 6 | -9 | -6 
    6252 S |  | 6 | -6 
    6253 O |  |  | 4 
    6254 Iteration cutoff | 2 
    6255  
    6256 Matchmaker 3j0c.pdb1, chain A (#1.23) with AF3 E1 1-421.pdb, chain A (#112),
    6257 sequence alignment score = 1060.7 
    6258 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    6259 3.020) 
    6260  
    6261 
    6262 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    6263 
    6264 Chain information for AF3 E1 422-461.pdb #113 
    6265 --- 
    6266 Chain | Description 
    6267 A | No description available 
    6268  
    6269 
    6270 > matchmaker #113 to #1.23 & sel
    6271 
    6272 Parameters 
    6273 --- 
    6274 Chain pairing | bb 
    6275 Alignment algorithm | Needleman-Wunsch 
    6276 Similarity matrix | BLOSUM-62 
    6277 SS fraction | 0.3 
    6278 Gap open (HH/SS/other) | 18/18/6 
    6279 Gap extend | 1 
    6280 SS matrix |  |  | H | S | O 
    6281 ---|---|---|--- 
    6282 H | 6 | -9 | -6 
    6283 S |  | 6 | -6 
    6284 O |  |  | 4 
    6285 Iteration cutoff | 2 
    6286  
    6287 Matchmaker 3j0c.pdb1, chain A (#1.23) with AF3 E1 422-461.pdb, chain A (#113),
    6288 sequence alignment score = 626.9 
    6289 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    6290 2.776) 
    6291  
    6292 
    6293 > hide sel cartoons
    6294 
    6295 [Repeated 1 time(s)]
    6296 
    6297 > select #1.23/B
    6298 
    6299 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    6300 
    6301 > show sel cartoons
    6302 
    6303 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    6304 
    6305 Chain information for AF3 E2 1-352.pdb #114 
    6306 --- 
    6307 Chain | Description 
    6308 B | No description available 
    6309  
    6310 
    6311 > matchmaker #114 to #1.23 & sel
    6312 
    6313 Parameters 
    6314 --- 
    6315 Chain pairing | bb 
    6316 Alignment algorithm | Needleman-Wunsch 
    6317 Similarity matrix | BLOSUM-62 
    6318 SS fraction | 0.3 
    6319 Gap open (HH/SS/other) | 18/18/6 
    6320 Gap extend | 1 
    6321 SS matrix |  |  | H | S | O 
    6322 ---|---|---|--- 
    6323 H | 6 | -9 | -6 
    6324 S |  | 6 | -6 
    6325 O |  |  | 4 
    6326 Iteration cutoff | 2 
    6327  
    6328 Matchmaker 3j0c.pdb1, chain B (#1.23) with AF3 E2 1-352.pdb, chain B (#114),
    6329 sequence alignment score = 583.7 
    6330 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    6331 5.933) 
    6332  
    6333 
    6334 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    6335 
    6336 Chain information for AF3 E2 353-438.pdb #115 
    6337 --- 
    6338 Chain | Description 
    6339 B | No description available 
    6340  
    6341 
    6342 > matchmaker #115 to #1.23 & sel
    6343 
    6344 Parameters 
    6345 --- 
    6346 Chain pairing | bb 
    6347 Alignment algorithm | Needleman-Wunsch 
    6348 Similarity matrix | BLOSUM-62 
    6349 SS fraction | 0.3 
    6350 Gap open (HH/SS/other) | 18/18/6 
    6351 Gap extend | 1 
    6352 SS matrix |  |  | H | S | O 
    6353 ---|---|---|--- 
    6354 H | 6 | -9 | -6 
    6355 S |  | 6 | -6 
    6356 O |  |  | 4 
    6357 Iteration cutoff | 2 
    6358  
    6359 Matchmaker 3j0c.pdb1, chain B (#1.23) with AF3 E2 353-438.pdb, chain B (#115),
    6360 sequence alignment score = 333.4 
    6361 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    6362 8.411) 
    6363  
    6364 
    6365 > hide sel cartoons
    6366 
    6367 > select #1.23/C
    6368 
    6369 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    6370 
    6371 > show sel cartoons
    6372 
    6373 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    6374 
    6375 Chain information for AF3 CA.pdb #116 
    6376 --- 
    6377 Chain | Description 
    6378 A | No description available 
    6379  
    6380 
    6381 > matchmaker #116 to #1.23 & sel
    6382 
    6383 Parameters 
    6384 --- 
    6385 Chain pairing | bb 
    6386 Alignment algorithm | Needleman-Wunsch 
    6387 Similarity matrix | BLOSUM-62 
    6388 SS fraction | 0.3 
    6389 Gap open (HH/SS/other) | 18/18/6 
    6390 Gap extend | 1 
    6391 SS matrix |  |  | H | S | O 
    6392 ---|---|---|--- 
    6393 H | 6 | -9 | -6 
    6394 S |  | 6 | -6 
    6395 O |  |  | 4 
    6396 Iteration cutoff | 2 
    6397  
    6398 Matchmaker 3j0c.pdb1, chain C (#1.23) with AF3 CA.pdb, chain A (#116),
    6399 sequence alignment score = 328.1 
    6400 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    6401 2.714) 
    6402  
    6403 
    6404 > hide sel cartoons
    6405 
    6406 > color #112 dodgerblue
    6407 
    6408 > color #113 dodgerblue
    6409 
    6410 > color #114 #00b305ff
    6411 
    6412 > color #115 #00b305ff
    6413 
    6414 > color #116 #f15839ff
    6415 
    6416 > select #1.24/A
    6417 
    6418 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    6419 
    6420 > show sel cartoons
    6421 
    6422 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    6423 
    6424 Chain information for AF3 E1 1-421.pdb #117 
    6425 --- 
    6426 Chain | Description 
    6427 A | No description available 
    6428  
    6429 
    6430 > matchmaker #117 to #1.24 & sel
    6431 
    6432 Parameters 
    6433 --- 
    6434 Chain pairing | bb 
    6435 Alignment algorithm | Needleman-Wunsch 
    6436 Similarity matrix | BLOSUM-62 
    6437 SS fraction | 0.3 
    6438 Gap open (HH/SS/other) | 18/18/6 
    6439 Gap extend | 1 
    6440 SS matrix |  |  | H | S | O 
    6441 ---|---|---|--- 
    6442 H | 6 | -9 | -6 
    6443 S |  | 6 | -6 
    6444 O |  |  | 4 
    6445 Iteration cutoff | 2 
    6446  
    6447 Matchmaker 3j0c.pdb1, chain A (#1.24) with AF3 E1 1-421.pdb, chain A (#117),
    6448 sequence alignment score = 1060.7 
    6449 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    6450 3.020) 
    6451  
    6452 
    6453 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    6454 
    6455 Chain information for AF3 E1 422-461.pdb #118 
    6456 --- 
    6457 Chain | Description 
    6458 A | No description available 
    6459  
    6460 
    6461 > matchmaker #118 to #1.24 & sel
    6462 
    6463 Parameters 
    6464 --- 
    6465 Chain pairing | bb 
    6466 Alignment algorithm | Needleman-Wunsch 
    6467 Similarity matrix | BLOSUM-62 
    6468 SS fraction | 0.3 
    6469 Gap open (HH/SS/other) | 18/18/6 
    6470 Gap extend | 1 
    6471 SS matrix |  |  | H | S | O 
    6472 ---|---|---|--- 
    6473 H | 6 | -9 | -6 
    6474 S |  | 6 | -6 
    6475 O |  |  | 4 
    6476 Iteration cutoff | 2 
    6477  
    6478 Matchmaker 3j0c.pdb1, chain A (#1.24) with AF3 E1 422-461.pdb, chain A (#118),
    6479 sequence alignment score = 626.9 
    6480 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    6481 2.775) 
    6482  
    6483 
    6484 > hide sel cartoons
    6485 
    6486 > select #1.24/B
    6487 
    6488 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    6489 
    6490 > show sel cartoons
    6491 
    6492 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    6493 
    6494 Chain information for AF3 E2 1-352.pdb #119 
    6495 --- 
    6496 Chain | Description 
    6497 B | No description available 
    6498  
    6499 
    6500 > matchmaker #119 to #1.24 & sel
    6501 
    6502 Parameters 
    6503 --- 
    6504 Chain pairing | bb 
    6505 Alignment algorithm | Needleman-Wunsch 
    6506 Similarity matrix | BLOSUM-62 
    6507 SS fraction | 0.3 
    6508 Gap open (HH/SS/other) | 18/18/6 
    6509 Gap extend | 1 
    6510 SS matrix |  |  | H | S | O 
    6511 ---|---|---|--- 
    6512 H | 6 | -9 | -6 
    6513 S |  | 6 | -6 
    6514 O |  |  | 4 
    6515 Iteration cutoff | 2 
    6516  
    6517 Matchmaker 3j0c.pdb1, chain B (#1.24) with AF3 E2 1-352.pdb, chain B (#119),
    6518 sequence alignment score = 583.7 
    6519 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    6520 5.933) 
    6521  
    6522 
    6523 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    6524 
    6525 Chain information for AF3 E2 353-438.pdb #120 
    6526 --- 
    6527 Chain | Description 
    6528 B | No description available 
    6529  
    6530 
    6531 > matchmaker #120 to #1.24 & sel
    6532 
    6533 Parameters 
    6534 --- 
    6535 Chain pairing | bb 
    6536 Alignment algorithm | Needleman-Wunsch 
    6537 Similarity matrix | BLOSUM-62 
    6538 SS fraction | 0.3 
    6539 Gap open (HH/SS/other) | 18/18/6 
    6540 Gap extend | 1 
    6541 SS matrix |  |  | H | S | O 
    6542 ---|---|---|--- 
    6543 H | 6 | -9 | -6 
    6544 S |  | 6 | -6 
    6545 O |  |  | 4 
    6546 Iteration cutoff | 2 
    6547  
    6548 Matchmaker 3j0c.pdb1, chain B (#1.24) with AF3 E2 353-438.pdb, chain B (#120),
    6549 sequence alignment score = 333.4 
    6550 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    6551 8.411) 
    6552  
    6553 
    6554 > hide sel cartoons
    6555 
    6556 > select #1.24/C
    6557 
    6558 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    6559 
    6560 > show sel cartoons
    6561 
    6562 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    6563 
    6564 Chain information for AF3 CA.pdb #121 
    6565 --- 
    6566 Chain | Description 
    6567 A | No description available 
    6568  
    6569 
    6570 > matchmaker #121 to #1.24 & sel
    6571 
    6572 Parameters 
    6573 --- 
    6574 Chain pairing | bb 
    6575 Alignment algorithm | Needleman-Wunsch 
    6576 Similarity matrix | BLOSUM-62 
    6577 SS fraction | 0.3 
    6578 Gap open (HH/SS/other) | 18/18/6 
    6579 Gap extend | 1 
    6580 SS matrix |  |  | H | S | O 
    6581 ---|---|---|--- 
    6582 H | 6 | -9 | -6 
    6583 S |  | 6 | -6 
    6584 O |  |  | 4 
    6585 Iteration cutoff | 2 
    6586  
    6587 Matchmaker 3j0c.pdb1, chain C (#1.24) with AF3 CA.pdb, chain A (#121),
    6588 sequence alignment score = 328.1 
    6589 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    6590 2.714) 
    6591  
    6592 
    6593 > hide sel cartoons
    6594 
    6595 > color #117 dodgerblue
    6596 
    6597 > color #118 dodgerblue
    6598 
    6599 > color #119 #00b305ff
    6600 
    6601 > color #120 #00b305ff
    6602 
    6603 > color #121 #f15839ff
    6604 
    6605 > select #1.25/A
    6606 
    6607 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    6608 
    6609 > show sel cartoons
    6610 
    6611 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    6612 
    6613 Chain information for AF3 E1 1-421.pdb #122 
    6614 --- 
    6615 Chain | Description 
    6616 A | No description available 
    6617  
    6618 
    6619 > matchmaker #122 to #1.25 & sel
    6620 
    6621 Parameters 
    6622 --- 
    6623 Chain pairing | bb 
    6624 Alignment algorithm | Needleman-Wunsch 
    6625 Similarity matrix | BLOSUM-62 
    6626 SS fraction | 0.3 
    6627 Gap open (HH/SS/other) | 18/18/6 
    6628 Gap extend | 1 
    6629 SS matrix |  |  | H | S | O 
    6630 ---|---|---|--- 
    6631 H | 6 | -9 | -6 
    6632 S |  | 6 | -6 
    6633 O |  |  | 4 
    6634 Iteration cutoff | 2 
    6635  
    6636 Matchmaker 3j0c.pdb1, chain A (#1.25) with AF3 E1 1-421.pdb, chain A (#122),
    6637 sequence alignment score = 1060.7 
    6638 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    6639 3.020) 
    6640  
    6641 
    6642 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    6643 
    6644 Chain information for AF3 E1 422-461.pdb #123 
    6645 --- 
    6646 Chain | Description 
    6647 A | No description available 
    6648  
    6649 
    6650 > matchmaker #123 to #1.25 & sel
    6651 
    6652 Parameters 
    6653 --- 
    6654 Chain pairing | bb 
    6655 Alignment algorithm | Needleman-Wunsch 
    6656 Similarity matrix | BLOSUM-62 
    6657 SS fraction | 0.3 
    6658 Gap open (HH/SS/other) | 18/18/6 
    6659 Gap extend | 1 
    6660 SS matrix |  |  | H | S | O 
    6661 ---|---|---|--- 
    6662 H | 6 | -9 | -6 
    6663 S |  | 6 | -6 
    6664 O |  |  | 4 
    6665 Iteration cutoff | 2 
    6666  
    6667 Matchmaker 3j0c.pdb1, chain A (#1.25) with AF3 E1 422-461.pdb, chain A (#123),
    6668 sequence alignment score = 626.9 
    6669 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    6670 2.776) 
    6671  
    6672 
    6673 > hide sel cartoons
    6674 
    6675 > select #1.25/B
    6676 
    6677 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    6678 
    6679 > show sel cartoons
    6680 
    6681 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    6682 
    6683 Chain information for AF3 E2 1-352.pdb #124 
    6684 --- 
    6685 Chain | Description 
    6686 B | No description available 
    6687  
    6688 
    6689 > matchmaker #124 to #1.25 & sel
    6690 
    6691 Parameters 
    6692 --- 
    6693 Chain pairing | bb 
    6694 Alignment algorithm | Needleman-Wunsch 
    6695 Similarity matrix | BLOSUM-62 
    6696 SS fraction | 0.3 
    6697 Gap open (HH/SS/other) | 18/18/6 
    6698 Gap extend | 1 
    6699 SS matrix |  |  | H | S | O 
    6700 ---|---|---|--- 
    6701 H | 6 | -9 | -6 
    6702 S |  | 6 | -6 
    6703 O |  |  | 4 
    6704 Iteration cutoff | 2 
    6705  
    6706 Matchmaker 3j0c.pdb1, chain B (#1.25) with AF3 E2 1-352.pdb, chain B (#124),
    6707 sequence alignment score = 583.7 
    6708 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    6709 5.933) 
    6710  
    6711 
    6712 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    6713 
    6714 Chain information for AF3 E2 353-438.pdb #125 
    6715 --- 
    6716 Chain | Description 
    6717 B | No description available 
    6718  
    6719 
    6720 > matchmaker #125 to #1.25 & sel
    6721 
    6722 Parameters 
    6723 --- 
    6724 Chain pairing | bb 
    6725 Alignment algorithm | Needleman-Wunsch 
    6726 Similarity matrix | BLOSUM-62 
    6727 SS fraction | 0.3 
    6728 Gap open (HH/SS/other) | 18/18/6 
    6729 Gap extend | 1 
    6730 SS matrix |  |  | H | S | O 
    6731 ---|---|---|--- 
    6732 H | 6 | -9 | -6 
    6733 S |  | 6 | -6 
    6734 O |  |  | 4 
    6735 Iteration cutoff | 2 
    6736  
    6737 Matchmaker 3j0c.pdb1, chain B (#1.25) with AF3 E2 353-438.pdb, chain B (#125),
    6738 sequence alignment score = 333.4 
    6739 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    6740 8.411) 
    6741  
    6742 
    6743 > hide sel cartoons
    6744 
    6745 > select #1.25/C
    6746 
    6747 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    6748 
    6749 > show sel cartoons
    6750 
    6751 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    6752 
    6753 Chain information for AF3 CA.pdb #126 
    6754 --- 
    6755 Chain | Description 
    6756 A | No description available 
    6757  
    6758 
    6759 > matchmaker #126 to #1.25 & sel
    6760 
    6761 Parameters 
    6762 --- 
    6763 Chain pairing | bb 
    6764 Alignment algorithm | Needleman-Wunsch 
    6765 Similarity matrix | BLOSUM-62 
    6766 SS fraction | 0.3 
    6767 Gap open (HH/SS/other) | 18/18/6 
    6768 Gap extend | 1 
    6769 SS matrix |  |  | H | S | O 
    6770 ---|---|---|--- 
    6771 H | 6 | -9 | -6 
    6772 S |  | 6 | -6 
    6773 O |  |  | 4 
    6774 Iteration cutoff | 2 
    6775  
    6776 Matchmaker 3j0c.pdb1, chain C (#1.25) with AF3 CA.pdb, chain A (#126),
    6777 sequence alignment score = 328.1 
    6778 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    6779 2.714) 
    6780  
    6781 
    6782 > hide sel cartoons
    6783 
    6784 > color #122 dodgerblue
    6785 
    6786 > color #123 dodgerblue
    6787 
    6788 > color #124 #00b305ff
    6789 
    6790 > color #125 #00b305ff
    6791 
    6792 > color #126 #f15839ff
    6793 
    6794 > select #1.26/A
    6795 
    6796 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    6797 
    6798 > show sel cartoons
    6799 
    6800 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    6801 
    6802 Chain information for AF3 E1 1-421.pdb #127 
    6803 --- 
    6804 Chain | Description 
    6805 A | No description available 
    6806  
    6807 
    6808 > matchmaker #127 to #1.26 & sel
    6809 
    6810 Parameters 
    6811 --- 
    6812 Chain pairing | bb 
    6813 Alignment algorithm | Needleman-Wunsch 
    6814 Similarity matrix | BLOSUM-62 
    6815 SS fraction | 0.3 
    6816 Gap open (HH/SS/other) | 18/18/6 
    6817 Gap extend | 1 
    6818 SS matrix |  |  | H | S | O 
    6819 ---|---|---|--- 
    6820 H | 6 | -9 | -6 
    6821 S |  | 6 | -6 
    6822 O |  |  | 4 
    6823 Iteration cutoff | 2 
    6824  
    6825 Matchmaker 3j0c.pdb1, chain A (#1.26) with AF3 E1 1-421.pdb, chain A (#127),
    6826 sequence alignment score = 1060.7 
    6827 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    6828 3.020) 
    6829  
    6830 
    6831 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    6832 
    6833 Chain information for AF3 E1 422-461.pdb #128 
    6834 --- 
    6835 Chain | Description 
    6836 A | No description available 
    6837  
    6838 
    6839 > matchmaker #128 to #1.26 & sel
    6840 
    6841 Parameters 
    6842 --- 
    6843 Chain pairing | bb 
    6844 Alignment algorithm | Needleman-Wunsch 
    6845 Similarity matrix | BLOSUM-62 
    6846 SS fraction | 0.3 
    6847 Gap open (HH/SS/other) | 18/18/6 
    6848 Gap extend | 1 
    6849 SS matrix |  |  | H | S | O 
    6850 ---|---|---|--- 
    6851 H | 6 | -9 | -6 
    6852 S |  | 6 | -6 
    6853 O |  |  | 4 
    6854 Iteration cutoff | 2 
    6855  
    6856 Matchmaker 3j0c.pdb1, chain A (#1.26) with AF3 E1 422-461.pdb, chain A (#128),
    6857 sequence alignment score = 626.9 
    6858 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    6859 2.775) 
    6860  
    6861 
    6862 > hide sel cartoons
    6863 
    6864 > select #1.26/B
    6865 
    6866 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    6867 
    6868 > show sel cartoons
    6869 
    6870 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    6871 
    6872 Chain information for AF3 E2 1-352.pdb #129 
    6873 --- 
    6874 Chain | Description 
    6875 B | No description available 
    6876  
    6877 
    6878 > matchmaker #129 to #1.26 & sel
    6879 
    6880 Parameters 
    6881 --- 
    6882 Chain pairing | bb 
    6883 Alignment algorithm | Needleman-Wunsch 
    6884 Similarity matrix | BLOSUM-62 
    6885 SS fraction | 0.3 
    6886 Gap open (HH/SS/other) | 18/18/6 
    6887 Gap extend | 1 
    6888 SS matrix |  |  | H | S | O 
    6889 ---|---|---|--- 
    6890 H | 6 | -9 | -6 
    6891 S |  | 6 | -6 
    6892 O |  |  | 4 
    6893 Iteration cutoff | 2 
    6894  
    6895 Matchmaker 3j0c.pdb1, chain B (#1.26) with AF3 E2 1-352.pdb, chain B (#129),
    6896 sequence alignment score = 583.7 
    6897 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    6898 5.933) 
    6899  
    6900 
    6901 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    6902 
    6903 Chain information for AF3 E2 353-438.pdb #130 
    6904 --- 
    6905 Chain | Description 
    6906 B | No description available 
    6907  
    6908 
    6909 > matchmaker #130 to #1.26 & sel
    6910 
    6911 Parameters 
    6912 --- 
    6913 Chain pairing | bb 
    6914 Alignment algorithm | Needleman-Wunsch 
    6915 Similarity matrix | BLOSUM-62 
    6916 SS fraction | 0.3 
    6917 Gap open (HH/SS/other) | 18/18/6 
    6918 Gap extend | 1 
    6919 SS matrix |  |  | H | S | O 
    6920 ---|---|---|--- 
    6921 H | 6 | -9 | -6 
    6922 S |  | 6 | -6 
    6923 O |  |  | 4 
    6924 Iteration cutoff | 2 
    6925  
    6926 Matchmaker 3j0c.pdb1, chain B (#1.26) with AF3 E2 353-438.pdb, chain B (#130),
    6927 sequence alignment score = 322.6 
    6928 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    6929 8.411) 
    6930  
    6931 
    6932 > hide sel cartoons
    6933 
    6934 > select #1.26/C
    6935 
    6936 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    6937 
    6938 > show sel cartoons
    6939 
    6940 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    6941 
    6942 Chain information for AF3 CA.pdb #131 
    6943 --- 
    6944 Chain | Description 
    6945 A | No description available 
    6946  
    6947 
    6948 > matchmaker #131 to #1.26 & sel
    6949 
    6950 Parameters 
    6951 --- 
    6952 Chain pairing | bb 
    6953 Alignment algorithm | Needleman-Wunsch 
    6954 Similarity matrix | BLOSUM-62 
    6955 SS fraction | 0.3 
    6956 Gap open (HH/SS/other) | 18/18/6 
    6957 Gap extend | 1 
    6958 SS matrix |  |  | H | S | O 
    6959 ---|---|---|--- 
    6960 H | 6 | -9 | -6 
    6961 S |  | 6 | -6 
    6962 O |  |  | 4 
    6963 Iteration cutoff | 2 
    6964  
    6965 Matchmaker 3j0c.pdb1, chain C (#1.26) with AF3 CA.pdb, chain A (#131),
    6966 sequence alignment score = 328.1 
    6967 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    6968 2.714) 
    6969  
    6970 
    6971 > hide sel cartoons
    6972 
    6973 > color #127 dodgerblue
    6974 
    6975 > color #128 dodgerblue
    6976 
    6977 > color #129 #00b305ff
    6978 
    6979 > color #130 #00b305ff
    6980 
    6981 > color #131 #f15839ff
    6982 
    6983 > select #1.27/A
    6984 
    6985 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    6986 
    6987 > show sel cartoons
    6988 
    6989 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    6990 
    6991 Chain information for AF3 E1 1-421.pdb #132 
    6992 --- 
    6993 Chain | Description 
    6994 A | No description available 
    6995  
    6996 
    6997 > matchmaker #132 to #1.27 & sel
    6998 
    6999 Parameters 
    7000 --- 
    7001 Chain pairing | bb 
    7002 Alignment algorithm | Needleman-Wunsch 
    7003 Similarity matrix | BLOSUM-62 
    7004 SS fraction | 0.3 
    7005 Gap open (HH/SS/other) | 18/18/6 
    7006 Gap extend | 1 
    7007 SS matrix |  |  | H | S | O 
    7008 ---|---|---|--- 
    7009 H | 6 | -9 | -6 
    7010 S |  | 6 | -6 
    7011 O |  |  | 4 
    7012 Iteration cutoff | 2 
    7013  
    7014 Matchmaker 3j0c.pdb1, chain A (#1.27) with AF3 E1 1-421.pdb, chain A (#132),
    7015 sequence alignment score = 1060.7 
    7016 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    7017 3.020) 
    7018  
    7019 
    7020 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    7021 
    7022 Chain information for AF3 E1 422-461.pdb #133 
    7023 --- 
    7024 Chain | Description 
    7025 A | No description available 
    7026  
    7027 
    7028 > matchmaker #133 to #1.27 & sel
    7029 
    7030 Parameters 
    7031 --- 
    7032 Chain pairing | bb 
    7033 Alignment algorithm | Needleman-Wunsch 
    7034 Similarity matrix | BLOSUM-62 
    7035 SS fraction | 0.3 
    7036 Gap open (HH/SS/other) | 18/18/6 
    7037 Gap extend | 1 
    7038 SS matrix |  |  | H | S | O 
    7039 ---|---|---|--- 
    7040 H | 6 | -9 | -6 
    7041 S |  | 6 | -6 
    7042 O |  |  | 4 
    7043 Iteration cutoff | 2 
    7044  
    7045 Matchmaker 3j0c.pdb1, chain A (#1.27) with AF3 E1 422-461.pdb, chain A (#133),
    7046 sequence alignment score = 626.9 
    7047 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    7048 2.775) 
    7049  
    7050 
    7051 > hide sel cartoons
    7052 
    7053 > select #1.27/B
    7054 
    7055 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    7056 
    7057 > show sel cartoons
    7058 
    7059 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    7060 
    7061 Chain information for AF3 E2 1-352.pdb #134 
    7062 --- 
    7063 Chain | Description 
    7064 B | No description available 
    7065  
    7066 
    7067 > matchmaker #134 to #1.27 & sel
    7068 
    7069 Parameters 
    7070 --- 
    7071 Chain pairing | bb 
    7072 Alignment algorithm | Needleman-Wunsch 
    7073 Similarity matrix | BLOSUM-62 
    7074 SS fraction | 0.3 
    7075 Gap open (HH/SS/other) | 18/18/6 
    7076 Gap extend | 1 
    7077 SS matrix |  |  | H | S | O 
    7078 ---|---|---|--- 
    7079 H | 6 | -9 | -6 
    7080 S |  | 6 | -6 
    7081 O |  |  | 4 
    7082 Iteration cutoff | 2 
    7083  
    7084 Matchmaker 3j0c.pdb1, chain B (#1.27) with AF3 E2 1-352.pdb, chain B (#134),
    7085 sequence alignment score = 583.7 
    7086 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    7087 5.933) 
    7088  
    7089 
    7090 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    7091 
    7092 Chain information for AF3 E2 353-438.pdb #135 
    7093 --- 
    7094 Chain | Description 
    7095 B | No description available 
    7096  
    7097 
    7098 > matchmaker #135 to #1.27 & sel
    7099 
    7100 Parameters 
    7101 --- 
    7102 Chain pairing | bb 
    7103 Alignment algorithm | Needleman-Wunsch 
    7104 Similarity matrix | BLOSUM-62 
    7105 SS fraction | 0.3 
    7106 Gap open (HH/SS/other) | 18/18/6 
    7107 Gap extend | 1 
    7108 SS matrix |  |  | H | S | O 
    7109 ---|---|---|--- 
    7110 H | 6 | -9 | -6 
    7111 S |  | 6 | -6 
    7112 O |  |  | 4 
    7113 Iteration cutoff | 2 
    7114  
    7115 Matchmaker 3j0c.pdb1, chain B (#1.27) with AF3 E2 353-438.pdb, chain B (#135),
    7116 sequence alignment score = 333.4 
    7117 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    7118 8.411) 
    7119  
    7120 
    7121 > hide sel cartoons
    7122 
    7123 > select #1.27/C
    7124 
    7125 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    7126 
    7127 > show sel cartoons
    7128 
    7129 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    7130 
    7131 Chain information for AF3 CA.pdb #136 
    7132 --- 
    7133 Chain | Description 
    7134 A | No description available 
    7135  
    7136 
    7137 > matchmaker #136 to #1.27 & sel
    7138 
    7139 Parameters 
    7140 --- 
    7141 Chain pairing | bb 
    7142 Alignment algorithm | Needleman-Wunsch 
    7143 Similarity matrix | BLOSUM-62 
    7144 SS fraction | 0.3 
    7145 Gap open (HH/SS/other) | 18/18/6 
    7146 Gap extend | 1 
    7147 SS matrix |  |  | H | S | O 
    7148 ---|---|---|--- 
    7149 H | 6 | -9 | -6 
    7150 S |  | 6 | -6 
    7151 O |  |  | 4 
    7152 Iteration cutoff | 2 
    7153  
    7154 Matchmaker 3j0c.pdb1, chain C (#1.27) with AF3 CA.pdb, chain A (#136),
    7155 sequence alignment score = 328.1 
    7156 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    7157 2.714) 
    7158  
    7159 
    7160 > hide sel cartoons
    7161 
    7162 > color #132 dodgerblue
    7163 
    7164 > color #133 dodgerblue
    7165 
    7166 > color #134 #00b305ff
    7167 
    7168 > color #135 #00b305ff
    7169 
    7170 > color #136 #f15839ff
    7171 
    7172 > select #1.28/A
    7173 
    7174 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    7175 
    7176 > show sel cartoons
    7177 
    7178 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    7179 
    7180 Chain information for AF3 E1 1-421.pdb #137 
    7181 --- 
    7182 Chain | Description 
    7183 A | No description available 
    7184  
    7185 
    7186 > matchmaker #137 to #1.28 & sel
    7187 
    7188 Parameters 
    7189 --- 
    7190 Chain pairing | bb 
    7191 Alignment algorithm | Needleman-Wunsch 
    7192 Similarity matrix | BLOSUM-62 
    7193 SS fraction | 0.3 
    7194 Gap open (HH/SS/other) | 18/18/6 
    7195 Gap extend | 1 
    7196 SS matrix |  |  | H | S | O 
    7197 ---|---|---|--- 
    7198 H | 6 | -9 | -6 
    7199 S |  | 6 | -6 
    7200 O |  |  | 4 
    7201 Iteration cutoff | 2 
    7202  
    7203 Matchmaker 3j0c.pdb1, chain A (#1.28) with AF3 E1 1-421.pdb, chain A (#137),
    7204 sequence alignment score = 1060.7 
    7205 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    7206 3.020) 
    7207  
    7208 
    7209 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    7210 
    7211 Chain information for AF3 E1 422-461.pdb #138 
    7212 --- 
    7213 Chain | Description 
    7214 A | No description available 
    7215  
    7216 
    7217 > matchmaker #138 to #1.28 & sel
    7218 
    7219 Parameters 
    7220 --- 
    7221 Chain pairing | bb 
    7222 Alignment algorithm | Needleman-Wunsch 
    7223 Similarity matrix | BLOSUM-62 
    7224 SS fraction | 0.3 
    7225 Gap open (HH/SS/other) | 18/18/6 
    7226 Gap extend | 1 
    7227 SS matrix |  |  | H | S | O 
    7228 ---|---|---|--- 
    7229 H | 6 | -9 | -6 
    7230 S |  | 6 | -6 
    7231 O |  |  | 4 
    7232 Iteration cutoff | 2 
    7233  
    7234 Matchmaker 3j0c.pdb1, chain A (#1.28) with AF3 E1 422-461.pdb, chain A (#138),
    7235 sequence alignment score = 626.9 
    7236 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    7237 2.776) 
    7238  
    7239 
    7240 > hide sel cartoons
    7241 
    7242 > select #1.28/B
    7243 
    7244 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    7245 
    7246 > show sel cartoons
    7247 
    7248 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    7249 
    7250 Chain information for AF3 E2 1-352.pdb #139 
    7251 --- 
    7252 Chain | Description 
    7253 B | No description available 
    7254  
    7255 
    7256 > matchmaker #139 to #1.28 & sel
    7257 
    7258 Parameters 
    7259 --- 
    7260 Chain pairing | bb 
    7261 Alignment algorithm | Needleman-Wunsch 
    7262 Similarity matrix | BLOSUM-62 
    7263 SS fraction | 0.3 
    7264 Gap open (HH/SS/other) | 18/18/6 
    7265 Gap extend | 1 
    7266 SS matrix |  |  | H | S | O 
    7267 ---|---|---|--- 
    7268 H | 6 | -9 | -6 
    7269 S |  | 6 | -6 
    7270 O |  |  | 4 
    7271 Iteration cutoff | 2 
    7272  
    7273 Matchmaker 3j0c.pdb1, chain B (#1.28) with AF3 E2 1-352.pdb, chain B (#139),
    7274 sequence alignment score = 583.7 
    7275 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    7276 5.933) 
    7277  
    7278 
    7279 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    7280 
    7281 Chain information for AF3 E2 353-438.pdb #140 
    7282 --- 
    7283 Chain | Description 
    7284 B | No description available 
    7285  
    7286 
    7287 > matchmaker #140 to #1.28 & sel
    7288 
    7289 Parameters 
    7290 --- 
    7291 Chain pairing | bb 
    7292 Alignment algorithm | Needleman-Wunsch 
    7293 Similarity matrix | BLOSUM-62 
    7294 SS fraction | 0.3 
    7295 Gap open (HH/SS/other) | 18/18/6 
    7296 Gap extend | 1 
    7297 SS matrix |  |  | H | S | O 
    7298 ---|---|---|--- 
    7299 H | 6 | -9 | -6 
    7300 S |  | 6 | -6 
    7301 O |  |  | 4 
    7302 Iteration cutoff | 2 
    7303  
    7304 Matchmaker 3j0c.pdb1, chain B (#1.28) with AF3 E2 353-438.pdb, chain B (#140),
    7305 sequence alignment score = 333.4 
    7306 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    7307 8.411) 
    7308  
    7309 
    7310 > hide sel cartoons
    7311 
    7312 > select #1.28/C
    7313 
    7314 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    7315 
    7316 > show sel cartoons
    7317 
    7318 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    7319 
    7320 Chain information for AF3 CA.pdb #141 
    7321 --- 
    7322 Chain | Description 
    7323 A | No description available 
    7324  
    7325 
    7326 > matchmaker #141 to #1.28 & sel
    7327 
    7328 Parameters 
    7329 --- 
    7330 Chain pairing | bb 
    7331 Alignment algorithm | Needleman-Wunsch 
    7332 Similarity matrix | BLOSUM-62 
    7333 SS fraction | 0.3 
    7334 Gap open (HH/SS/other) | 18/18/6 
    7335 Gap extend | 1 
    7336 SS matrix |  |  | H | S | O 
    7337 ---|---|---|--- 
    7338 H | 6 | -9 | -6 
    7339 S |  | 6 | -6 
    7340 O |  |  | 4 
    7341 Iteration cutoff | 2 
    7342  
    7343 Matchmaker 3j0c.pdb1, chain C (#1.28) with AF3 CA.pdb, chain A (#141),
    7344 sequence alignment score = 328.1 
    7345 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    7346 2.714) 
    7347  
    7348 
    7349 > hide sel cartoons
    7350 
    7351 > color #137 dodgerblue
    7352 
    7353 > color #138 dodgerblue
    7354 
    7355 > color #139 #00b305ff
    7356 
    7357 > color #140 #00b305ff
    7358 
    7359 > color #141 #f15839ff
    7360 
    7361 > select #1.29/A
    7362 
    7363 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    7364 
    7365 > show sel cartoons
    7366 
    7367 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    7368 
    7369 Chain information for AF3 E1 1-421.pdb #142 
    7370 --- 
    7371 Chain | Description 
    7372 A | No description available 
    7373  
    7374 
    7375 > matchmaker #142 to #1.29 & sel
    7376 
    7377 Parameters 
    7378 --- 
    7379 Chain pairing | bb 
    7380 Alignment algorithm | Needleman-Wunsch 
    7381 Similarity matrix | BLOSUM-62 
    7382 SS fraction | 0.3 
    7383 Gap open (HH/SS/other) | 18/18/6 
    7384 Gap extend | 1 
    7385 SS matrix |  |  | H | S | O 
    7386 ---|---|---|--- 
    7387 H | 6 | -9 | -6 
    7388 S |  | 6 | -6 
    7389 O |  |  | 4 
    7390 Iteration cutoff | 2 
    7391  
    7392 Matchmaker 3j0c.pdb1, chain A (#1.29) with AF3 E1 1-421.pdb, chain A (#142),
    7393 sequence alignment score = 1060.7 
    7394 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    7395 3.020) 
    7396  
    7397 
    7398 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    7399 
    7400 Chain information for AF3 E1 422-461.pdb #143 
    7401 --- 
    7402 Chain | Description 
    7403 A | No description available 
    7404  
    7405 
    7406 > matchmaker #143 to #1.29 & sel
    7407 
    7408 Parameters 
    7409 --- 
    7410 Chain pairing | bb 
    7411 Alignment algorithm | Needleman-Wunsch 
    7412 Similarity matrix | BLOSUM-62 
    7413 SS fraction | 0.3 
    7414 Gap open (HH/SS/other) | 18/18/6 
    7415 Gap extend | 1 
    7416 SS matrix |  |  | H | S | O 
    7417 ---|---|---|--- 
    7418 H | 6 | -9 | -6 
    7419 S |  | 6 | -6 
    7420 O |  |  | 4 
    7421 Iteration cutoff | 2 
    7422  
    7423 Matchmaker 3j0c.pdb1, chain A (#1.29) with AF3 E1 422-461.pdb, chain A (#143),
    7424 sequence alignment score = 626.9 
    7425 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    7426 2.775) 
    7427  
    7428 
    7429 > hide sel cartoons
    7430 
    7431 > select #1.29/B
    7432 
    7433 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    7434 
    7435 > show sel cartoons
    7436 
    7437 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    7438 
    7439 Chain information for AF3 E2 1-352.pdb #144 
    7440 --- 
    7441 Chain | Description 
    7442 B | No description available 
    7443  
    7444 
    7445 > matchmaker #144 to #1.29 & sel
    7446 
    7447 Parameters 
    7448 --- 
    7449 Chain pairing | bb 
    7450 Alignment algorithm | Needleman-Wunsch 
    7451 Similarity matrix | BLOSUM-62 
    7452 SS fraction | 0.3 
    7453 Gap open (HH/SS/other) | 18/18/6 
    7454 Gap extend | 1 
    7455 SS matrix |  |  | H | S | O 
    7456 ---|---|---|--- 
    7457 H | 6 | -9 | -6 
    7458 S |  | 6 | -6 
    7459 O |  |  | 4 
    7460 Iteration cutoff | 2 
    7461  
    7462 Matchmaker 3j0c.pdb1, chain B (#1.29) with AF3 E2 1-352.pdb, chain B (#144),
    7463 sequence alignment score = 583.7 
    7464 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    7465 5.933) 
    7466  
    7467 
    7468 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    7469 
    7470 Chain information for AF3 E2 353-438.pdb #145 
    7471 --- 
    7472 Chain | Description 
    7473 B | No description available 
    7474  
    7475 
    7476 > matchmaker #145 to #1.29 & sel
    7477 
    7478 Parameters 
    7479 --- 
    7480 Chain pairing | bb 
    7481 Alignment algorithm | Needleman-Wunsch 
    7482 Similarity matrix | BLOSUM-62 
    7483 SS fraction | 0.3 
    7484 Gap open (HH/SS/other) | 18/18/6 
    7485 Gap extend | 1 
    7486 SS matrix |  |  | H | S | O 
    7487 ---|---|---|--- 
    7488 H | 6 | -9 | -6 
    7489 S |  | 6 | -6 
    7490 O |  |  | 4 
    7491 Iteration cutoff | 2 
    7492  
    7493 Matchmaker 3j0c.pdb1, chain B (#1.29) with AF3 E2 353-438.pdb, chain B (#145),
    7494 sequence alignment score = 333.4 
    7495 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    7496 8.411) 
    7497  
    7498 
    7499 > hide sel cartoons
    7500 
    7501 > select #1.29/C
    7502 
    7503 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    7504 
    7505 > show sel cartoons
    7506 
    7507 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    7508 
    7509 Chain information for AF3 CA.pdb #146 
    7510 --- 
    7511 Chain | Description 
    7512 A | No description available 
    7513  
    7514 
    7515 > matchmaker #146 to #1.29 & sel
    7516 
    7517 Parameters 
    7518 --- 
    7519 Chain pairing | bb 
    7520 Alignment algorithm | Needleman-Wunsch 
    7521 Similarity matrix | BLOSUM-62 
    7522 SS fraction | 0.3 
    7523 Gap open (HH/SS/other) | 18/18/6 
    7524 Gap extend | 1 
    7525 SS matrix |  |  | H | S | O 
    7526 ---|---|---|--- 
    7527 H | 6 | -9 | -6 
    7528 S |  | 6 | -6 
    7529 O |  |  | 4 
    7530 Iteration cutoff | 2 
    7531  
    7532 Matchmaker 3j0c.pdb1, chain C (#1.29) with AF3 CA.pdb, chain A (#146),
    7533 sequence alignment score = 328.1 
    7534 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    7535 2.714) 
    7536  
    7537 
    7538 > hide sel cartoons
    7539 
    7540 > color #142 dodgerblue
    7541 
    7542 > color #143 dodgerblue
    7543 
    7544 > color #144 #00b305ff
    7545 
    7546 > color #145 #00b305ff
    7547 
    7548 > color #146 #f15839ff
    7549 
    7550 > select #1.30/A
    7551 
    7552 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    7553 
    7554 > show sel cartoons
    7555 
    7556 > select #1.30/B
    7557 
    7558 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    7559 
    7560 > select #1.30/A
    7561 
    7562 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    7563 
    7564 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    7565 
    7566 Chain information for AF3 E1 1-421.pdb #147 
    7567 --- 
    7568 Chain | Description 
    7569 A | No description available 
    7570  
    7571 
    7572 > matchmaker #147 to #1.30 & sel
    7573 
    7574 Parameters 
    7575 --- 
    7576 Chain pairing | bb 
    7577 Alignment algorithm | Needleman-Wunsch 
    7578 Similarity matrix | BLOSUM-62 
    7579 SS fraction | 0.3 
    7580 Gap open (HH/SS/other) | 18/18/6 
    7581 Gap extend | 1 
    7582 SS matrix |  |  | H | S | O 
    7583 ---|---|---|--- 
    7584 H | 6 | -9 | -6 
    7585 S |  | 6 | -6 
    7586 O |  |  | 4 
    7587 Iteration cutoff | 2 
    7588  
    7589 Matchmaker 3j0c.pdb1, chain A (#1.30) with AF3 E1 1-421.pdb, chain A (#147),
    7590 sequence alignment score = 1060.7 
    7591 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    7592 3.020) 
    7593  
    7594 
    7595 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    7596 
    7597 Chain information for AF3 E1 422-461.pdb #148 
    7598 --- 
    7599 Chain | Description 
    7600 A | No description available 
    7601  
    7602 
    7603 > matchmaker #148 to #1.30 & sel
    7604 
    7605 Parameters 
    7606 --- 
    7607 Chain pairing | bb 
    7608 Alignment algorithm | Needleman-Wunsch 
    7609 Similarity matrix | BLOSUM-62 
    7610 SS fraction | 0.3 
    7611 Gap open (HH/SS/other) | 18/18/6 
    7612 Gap extend | 1 
    7613 SS matrix |  |  | H | S | O 
    7614 ---|---|---|--- 
    7615 H | 6 | -9 | -6 
    7616 S |  | 6 | -6 
    7617 O |  |  | 4 
    7618 Iteration cutoff | 2 
    7619  
    7620 Matchmaker 3j0c.pdb1, chain A (#1.30) with AF3 E1 422-461.pdb, chain A (#148),
    7621 sequence alignment score = 626.9 
    7622 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    7623 2.775) 
    7624  
    7625 
    7626 > hide sel cartoons
    7627 
    7628 > select #1.30/B
    7629 
    7630 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    7631 
    7632 > show sel cartoons
    7633 
    7634 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    7635 
    7636 Chain information for AF3 E2 1-352.pdb #149 
    7637 --- 
    7638 Chain | Description 
    7639 B | No description available 
    7640  
    7641 
    7642 > matchmaker #149 to #1.30 & sel
    7643 
    7644 Parameters 
    7645 --- 
    7646 Chain pairing | bb 
    7647 Alignment algorithm | Needleman-Wunsch 
    7648 Similarity matrix | BLOSUM-62 
    7649 SS fraction | 0.3 
    7650 Gap open (HH/SS/other) | 18/18/6 
    7651 Gap extend | 1 
    7652 SS matrix |  |  | H | S | O 
    7653 ---|---|---|--- 
    7654 H | 6 | -9 | -6 
    7655 S |  | 6 | -6 
    7656 O |  |  | 4 
    7657 Iteration cutoff | 2 
    7658  
    7659 Matchmaker 3j0c.pdb1, chain B (#1.30) with AF3 E2 1-352.pdb, chain B (#149),
    7660 sequence alignment score = 583.7 
    7661 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    7662 5.933) 
    7663  
    7664 
    7665 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    7666 
    7667 Chain information for AF3 E2 353-438.pdb #150 
    7668 --- 
    7669 Chain | Description 
    7670 B | No description available 
    7671  
    7672 
    7673 > matchmaker #150 to #1.30 & sel
    7674 
    7675 Parameters 
    7676 --- 
    7677 Chain pairing | bb 
    7678 Alignment algorithm | Needleman-Wunsch 
    7679 Similarity matrix | BLOSUM-62 
    7680 SS fraction | 0.3 
    7681 Gap open (HH/SS/other) | 18/18/6 
    7682 Gap extend | 1 
    7683 SS matrix |  |  | H | S | O 
    7684 ---|---|---|--- 
    7685 H | 6 | -9 | -6 
    7686 S |  | 6 | -6 
    7687 O |  |  | 4 
    7688 Iteration cutoff | 2 
    7689  
    7690 Matchmaker 3j0c.pdb1, chain B (#1.30) with AF3 E2 353-438.pdb, chain B (#150),
    7691 sequence alignment score = 333.4 
    7692 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    7693 8.411) 
    7694  
    7695 
    7696 > hide sel cartoons
    7697 
    7698 > select #1.30/C
    7699 
    7700 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    7701 
    7702 > show sel cartoons
    7703 
    7704 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    7705 
    7706 Chain information for AF3 CA.pdb #151 
    7707 --- 
    7708 Chain | Description 
    7709 A | No description available 
    7710  
    7711 
    7712 > matchmaker #151 to #1.30 & sel
    7713 
    7714 Parameters 
    7715 --- 
    7716 Chain pairing | bb 
    7717 Alignment algorithm | Needleman-Wunsch 
    7718 Similarity matrix | BLOSUM-62 
    7719 SS fraction | 0.3 
    7720 Gap open (HH/SS/other) | 18/18/6 
    7721 Gap extend | 1 
    7722 SS matrix |  |  | H | S | O 
    7723 ---|---|---|--- 
    7724 H | 6 | -9 | -6 
    7725 S |  | 6 | -6 
    7726 O |  |  | 4 
    7727 Iteration cutoff | 2 
    7728  
    7729 Matchmaker 3j0c.pdb1, chain C (#1.30) with AF3 CA.pdb, chain A (#151),
    7730 sequence alignment score = 328.1 
    7731 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    7732 2.714) 
    7733  
    7734 
    7735 > hide sel cartoons
    7736 
    7737 > color #147 dodgerblue
    7738 
    7739 > color #148 dodgerblue
    7740 
    7741 > color #149 #00b305ff
    7742 
    7743 > color #150 #00b305ff
    7744 
    7745 > color #151 #f15839ff
    7746 
    7747 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    7748 
    7749 > select #1.31/A
    7750 
    7751 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    7752 
    7753 > show sel cartoons
    7754 
    7755 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    7756 
    7757 Chain information for AF3 E1 1-421.pdb #152 
    7758 --- 
    7759 Chain | Description 
    7760 A | No description available 
    7761  
    7762 
    7763 > matchmaker #152 to #1.31 & sel
    7764 
    7765 Parameters 
    7766 --- 
    7767 Chain pairing | bb 
    7768 Alignment algorithm | Needleman-Wunsch 
    7769 Similarity matrix | BLOSUM-62 
    7770 SS fraction | 0.3 
    7771 Gap open (HH/SS/other) | 18/18/6 
    7772 Gap extend | 1 
    7773 SS matrix |  |  | H | S | O 
    7774 ---|---|---|--- 
    7775 H | 6 | -9 | -6 
    7776 S |  | 6 | -6 
    7777 O |  |  | 4 
    7778 Iteration cutoff | 2 
    7779  
    7780 Matchmaker 3j0c.pdb1, chain A (#1.31) with AF3 E1 1-421.pdb, chain A (#152),
    7781 sequence alignment score = 1060.7 
    7782 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    7783 3.020) 
    7784  
    7785 
    7786 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    7787 
    7788 Chain information for AF3 E1 422-461.pdb #153 
    7789 --- 
    7790 Chain | Description 
    7791 A | No description available 
    7792  
    7793 
    7794 > matchmaker #153 to #1.31 & sel
    7795 
    7796 Parameters 
    7797 --- 
    7798 Chain pairing | bb 
    7799 Alignment algorithm | Needleman-Wunsch 
    7800 Similarity matrix | BLOSUM-62 
    7801 SS fraction | 0.3 
    7802 Gap open (HH/SS/other) | 18/18/6 
    7803 Gap extend | 1 
    7804 SS matrix |  |  | H | S | O 
    7805 ---|---|---|--- 
    7806 H | 6 | -9 | -6 
    7807 S |  | 6 | -6 
    7808 O |  |  | 4 
    7809 Iteration cutoff | 2 
    7810  
    7811 Matchmaker 3j0c.pdb1, chain A (#1.31) with AF3 E1 422-461.pdb, chain A (#153),
    7812 sequence alignment score = 626.9 
    7813 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    7814 2.775) 
    7815  
    7816 
    7817 > hide sel cartoons
    7818 
    7819 > select #1.31/B
    7820 
    7821 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    7822 
    7823 > show sel cartoons
    7824 
    7825 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    7826 
    7827 Chain information for AF3 E2 1-352.pdb #154 
    7828 --- 
    7829 Chain | Description 
    7830 B | No description available 
    7831  
    7832 
    7833 > matchmaker #154 to #1.31 & sel
    7834 
    7835 Parameters 
    7836 --- 
    7837 Chain pairing | bb 
    7838 Alignment algorithm | Needleman-Wunsch 
    7839 Similarity matrix | BLOSUM-62 
    7840 SS fraction | 0.3 
    7841 Gap open (HH/SS/other) | 18/18/6 
    7842 Gap extend | 1 
    7843 SS matrix |  |  | H | S | O 
    7844 ---|---|---|--- 
    7845 H | 6 | -9 | -6 
    7846 S |  | 6 | -6 
    7847 O |  |  | 4 
    7848 Iteration cutoff | 2 
    7849  
    7850 Matchmaker 3j0c.pdb1, chain B (#1.31) with AF3 E2 1-352.pdb, chain B (#154),
    7851 sequence alignment score = 583.7 
    7852 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    7853 5.933) 
    7854  
    7855 
    7856 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    7857 
    7858 Chain information for AF3 E2 353-438.pdb #155 
    7859 --- 
    7860 Chain | Description 
    7861 B | No description available 
    7862  
    7863 
    7864 > matchmaker #155 to #1.31 & sel
    7865 
    7866 Parameters 
    7867 --- 
    7868 Chain pairing | bb 
    7869 Alignment algorithm | Needleman-Wunsch 
    7870 Similarity matrix | BLOSUM-62 
    7871 SS fraction | 0.3 
    7872 Gap open (HH/SS/other) | 18/18/6 
    7873 Gap extend | 1 
    7874 SS matrix |  |  | H | S | O 
    7875 ---|---|---|--- 
    7876 H | 6 | -9 | -6 
    7877 S |  | 6 | -6 
    7878 O |  |  | 4 
    7879 Iteration cutoff | 2 
    7880  
    7881 Matchmaker 3j0c.pdb1, chain B (#1.31) with AF3 E2 353-438.pdb, chain B (#155),
    7882 sequence alignment score = 333.4 
    7883 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    7884 8.411) 
    7885  
    7886 
    7887 > select #1.31/C
    7888 
    7889 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    7890 
    7891 > show sel cartoons
    7892 
    7893 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    7894 
    7895 Chain information for AF3 CA.pdb #156 
    7896 --- 
    7897 Chain | Description 
    7898 A | No description available 
    7899  
    7900 
    7901 > matchmaker #156 to #1.31 & sel
    7902 
    7903 Parameters 
    7904 --- 
    7905 Chain pairing | bb 
    7906 Alignment algorithm | Needleman-Wunsch 
    7907 Similarity matrix | BLOSUM-62 
    7908 SS fraction | 0.3 
    7909 Gap open (HH/SS/other) | 18/18/6 
    7910 Gap extend | 1 
    7911 SS matrix |  |  | H | S | O 
    7912 ---|---|---|--- 
    7913 H | 6 | -9 | -6 
    7914 S |  | 6 | -6 
    7915 O |  |  | 4 
    7916 Iteration cutoff | 2 
    7917  
    7918 Matchmaker 3j0c.pdb1, chain C (#1.31) with AF3 CA.pdb, chain A (#156),
    7919 sequence alignment score = 328.1 
    7920 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    7921 2.714) 
    7922  
    7923 
    7924 > hide sel cartoons
    7925 
    7926 > select #1.31/B
    7927 
    7928 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    7929 
    7930 > hide sel cartoons
    7931 
    7932 > color #152 dodgerblue
    7933 
    7934 > color #153 dodgerblue
    7935 
    7936 > color #154 #00b305ff
    7937 
    7938 > color #155 #00b305ff
    7939 
    7940 > color #156 #f15839ff
    7941 
    7942 > select #1.32/A
    7943 
    7944 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    7945 
    7946 > show sel cartoons
    7947 
    7948 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    7949 
    7950 Chain information for AF3 E1 1-421.pdb #157 
    7951 --- 
    7952 Chain | Description 
    7953 A | No description available 
    7954  
    7955 
    7956 > matchmaker #157 to #1.32 & sel
    7957 
    7958 Parameters 
    7959 --- 
    7960 Chain pairing | bb 
    7961 Alignment algorithm | Needleman-Wunsch 
    7962 Similarity matrix | BLOSUM-62 
    7963 SS fraction | 0.3 
    7964 Gap open (HH/SS/other) | 18/18/6 
    7965 Gap extend | 1 
    7966 SS matrix |  |  | H | S | O 
    7967 ---|---|---|--- 
    7968 H | 6 | -9 | -6 
    7969 S |  | 6 | -6 
    7970 O |  |  | 4 
    7971 Iteration cutoff | 2 
    7972  
    7973 Matchmaker 3j0c.pdb1, chain A (#1.32) with AF3 E1 1-421.pdb, chain A (#157),
    7974 sequence alignment score = 1060.7 
    7975 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    7976 3.020) 
    7977  
    7978 
    7979 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    7980 
    7981 Chain information for AF3 E1 422-461.pdb #158 
    7982 --- 
    7983 Chain | Description 
    7984 A | No description available 
    7985  
    7986 
    7987 > matchmaker #158 to #1.32 & sel
    7988 
    7989 Parameters 
    7990 --- 
    7991 Chain pairing | bb 
    7992 Alignment algorithm | Needleman-Wunsch 
    7993 Similarity matrix | BLOSUM-62 
    7994 SS fraction | 0.3 
    7995 Gap open (HH/SS/other) | 18/18/6 
    7996 Gap extend | 1 
    7997 SS matrix |  |  | H | S | O 
    7998 ---|---|---|--- 
    7999 H | 6 | -9 | -6 
    8000 S |  | 6 | -6 
    8001 O |  |  | 4 
    8002 Iteration cutoff | 2 
    8003  
    8004 Matchmaker 3j0c.pdb1, chain A (#1.32) with AF3 E1 422-461.pdb, chain A (#158),
    8005 sequence alignment score = 626.9 
    8006 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    8007 2.775) 
    8008  
    8009 
    8010 > hide sel cartoons
    8011 
    8012 > select #1.32/B
    8013 
    8014 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    8015 
    8016 > show sel cartoons
    8017 
    8018 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    8019 
    8020 Chain information for AF3 E2 1-352.pdb #159 
    8021 --- 
    8022 Chain | Description 
    8023 B | No description available 
    8024  
    8025 
    8026 > matchmaker #159 to #1.32 & sel
    8027 
    8028 Parameters 
    8029 --- 
    8030 Chain pairing | bb 
    8031 Alignment algorithm | Needleman-Wunsch 
    8032 Similarity matrix | BLOSUM-62 
    8033 SS fraction | 0.3 
    8034 Gap open (HH/SS/other) | 18/18/6 
    8035 Gap extend | 1 
    8036 SS matrix |  |  | H | S | O 
    8037 ---|---|---|--- 
    8038 H | 6 | -9 | -6 
    8039 S |  | 6 | -6 
    8040 O |  |  | 4 
    8041 Iteration cutoff | 2 
    8042  
    8043 Matchmaker 3j0c.pdb1, chain B (#1.32) with AF3 E2 1-352.pdb, chain B (#159),
    8044 sequence alignment score = 583.7 
    8045 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    8046 5.933) 
    8047  
    8048 
    8049 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    8050 
    8051 Chain information for AF3 E2 353-438.pdb #160 
    8052 --- 
    8053 Chain | Description 
    8054 B | No description available 
    8055  
    8056 
    8057 > matchmaker #160 to #1.32 & sel
    8058 
    8059 Parameters 
    8060 --- 
    8061 Chain pairing | bb 
    8062 Alignment algorithm | Needleman-Wunsch 
    8063 Similarity matrix | BLOSUM-62 
    8064 SS fraction | 0.3 
    8065 Gap open (HH/SS/other) | 18/18/6 
    8066 Gap extend | 1 
    8067 SS matrix |  |  | H | S | O 
    8068 ---|---|---|--- 
    8069 H | 6 | -9 | -6 
    8070 S |  | 6 | -6 
    8071 O |  |  | 4 
    8072 Iteration cutoff | 2 
    8073  
    8074 Matchmaker 3j0c.pdb1, chain B (#1.32) with AF3 E2 353-438.pdb, chain B (#160),
    8075 sequence alignment score = 322.6 
    8076 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    8077 8.411) 
    8078  
    8079 
    8080 > hide sel cartoons
    8081 
    8082 > select #1.32/C
    8083 
    8084 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    8085 
    8086 > show sel cartoons
    8087 
    8088 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    8089 
    8090 Chain information for AF3 CA.pdb #161 
    8091 --- 
    8092 Chain | Description 
    8093 A | No description available 
    8094  
    8095 
    8096 > matchmaker #161 to #1.32 & sel
    8097 
    8098 Parameters 
    8099 --- 
    8100 Chain pairing | bb 
    8101 Alignment algorithm | Needleman-Wunsch 
    8102 Similarity matrix | BLOSUM-62 
    8103 SS fraction | 0.3 
    8104 Gap open (HH/SS/other) | 18/18/6 
    8105 Gap extend | 1 
    8106 SS matrix |  |  | H | S | O 
    8107 ---|---|---|--- 
    8108 H | 6 | -9 | -6 
    8109 S |  | 6 | -6 
    8110 O |  |  | 4 
    8111 Iteration cutoff | 2 
    8112  
    8113 Matchmaker 3j0c.pdb1, chain C (#1.32) with AF3 CA.pdb, chain A (#161),
    8114 sequence alignment score = 328.1 
    8115 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    8116 2.714) 
    8117  
    8118 
    8119 > hide sel cartoons
    8120 
    8121 > color #157 dodgerblue
    8122 
    8123 > color #158 dodgerblue
    8124 
    8125 > color #159 #00b305ff
    8126 
    8127 > color #160 #00b305ff
    8128 
    8129 > color #161 #f15839ff
    8130 
    8131 > select #1.33/A
    8132 
    8133 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    8134 
    8135 > show sel cartoons
    8136 
    8137 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    8138 
    8139 Chain information for AF3 E1 1-421.pdb #162 
    8140 --- 
    8141 Chain | Description 
    8142 A | No description available 
    8143  
    8144 
    8145 > matchmaker #162 to #1.33 & sel
    8146 
    8147 Parameters 
    8148 --- 
    8149 Chain pairing | bb 
    8150 Alignment algorithm | Needleman-Wunsch 
    8151 Similarity matrix | BLOSUM-62 
    8152 SS fraction | 0.3 
    8153 Gap open (HH/SS/other) | 18/18/6 
    8154 Gap extend | 1 
    8155 SS matrix |  |  | H | S | O 
    8156 ---|---|---|--- 
    8157 H | 6 | -9 | -6 
    8158 S |  | 6 | -6 
    8159 O |  |  | 4 
    8160 Iteration cutoff | 2 
    8161  
    8162 Matchmaker 3j0c.pdb1, chain A (#1.33) with AF3 E1 1-421.pdb, chain A (#162),
    8163 sequence alignment score = 1060.7 
    8164 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    8165 3.020) 
    8166  
    8167 
    8168 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    8169 
    8170 Chain information for AF3 E1 422-461.pdb #163 
    8171 --- 
    8172 Chain | Description 
    8173 A | No description available 
    8174  
    8175 
    8176 > matchmaker #163 to #1.33 & sel
    8177 
    8178 Parameters 
    8179 --- 
    8180 Chain pairing | bb 
    8181 Alignment algorithm | Needleman-Wunsch 
    8182 Similarity matrix | BLOSUM-62 
    8183 SS fraction | 0.3 
    8184 Gap open (HH/SS/other) | 18/18/6 
    8185 Gap extend | 1 
    8186 SS matrix |  |  | H | S | O 
    8187 ---|---|---|--- 
    8188 H | 6 | -9 | -6 
    8189 S |  | 6 | -6 
    8190 O |  |  | 4 
    8191 Iteration cutoff | 2 
    8192  
    8193 Matchmaker 3j0c.pdb1, chain A (#1.33) with AF3 E1 422-461.pdb, chain A (#163),
    8194 sequence alignment score = 626.9 
    8195 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    8196 2.775) 
    8197  
    8198 
    8199 > hide sel cartoons
    8200 
    8201 > select #1.33/B
    8202 
    8203 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    8204 
    8205 > show sel cartoons
    8206 
    8207 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    8208 
    8209 Chain information for AF3 E2 1-352.pdb #164 
    8210 --- 
    8211 Chain | Description 
    8212 B | No description available 
    8213  
    8214 
    8215 > matchmaker #164 to #1.33 & sel
    8216 
    8217 Parameters 
    8218 --- 
    8219 Chain pairing | bb 
    8220 Alignment algorithm | Needleman-Wunsch 
    8221 Similarity matrix | BLOSUM-62 
    8222 SS fraction | 0.3 
    8223 Gap open (HH/SS/other) | 18/18/6 
    8224 Gap extend | 1 
    8225 SS matrix |  |  | H | S | O 
    8226 ---|---|---|--- 
    8227 H | 6 | -9 | -6 
    8228 S |  | 6 | -6 
    8229 O |  |  | 4 
    8230 Iteration cutoff | 2 
    8231  
    8232 Matchmaker 3j0c.pdb1, chain B (#1.33) with AF3 E2 1-352.pdb, chain B (#164),
    8233 sequence alignment score = 583.7 
    8234 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    8235 5.933) 
    8236  
    8237 
    8238 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    8239 
    8240 Chain information for AF3 E2 353-438.pdb #165 
    8241 --- 
    8242 Chain | Description 
    8243 B | No description available 
    8244  
    8245 
    8246 > matchmaker #165 to #1.33 & sel
    8247 
    8248 Parameters 
    8249 --- 
    8250 Chain pairing | bb 
    8251 Alignment algorithm | Needleman-Wunsch 
    8252 Similarity matrix | BLOSUM-62 
    8253 SS fraction | 0.3 
    8254 Gap open (HH/SS/other) | 18/18/6 
    8255 Gap extend | 1 
    8256 SS matrix |  |  | H | S | O 
    8257 ---|---|---|--- 
    8258 H | 6 | -9 | -6 
    8259 S |  | 6 | -6 
    8260 O |  |  | 4 
    8261 Iteration cutoff | 2 
    8262  
    8263 Matchmaker 3j0c.pdb1, chain B (#1.33) with AF3 E2 353-438.pdb, chain B (#165),
    8264 sequence alignment score = 322.6 
    8265 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    8266 8.411) 
    8267  
    8268 
    8269 > hide sel cartoons
    8270 
    8271 > select #1.33/C
    8272 
    8273 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    8274 
    8275 > show sel cartoons
    8276 
    8277 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    8278 
    8279 Chain information for AF3 CA.pdb #166 
    8280 --- 
    8281 Chain | Description 
    8282 A | No description available 
    8283  
    8284 
    8285 > matchmaker #166 to #1.33 & sel
    8286 
    8287 Parameters 
    8288 --- 
    8289 Chain pairing | bb 
    8290 Alignment algorithm | Needleman-Wunsch 
    8291 Similarity matrix | BLOSUM-62 
    8292 SS fraction | 0.3 
    8293 Gap open (HH/SS/other) | 18/18/6 
    8294 Gap extend | 1 
    8295 SS matrix |  |  | H | S | O 
    8296 ---|---|---|--- 
    8297 H | 6 | -9 | -6 
    8298 S |  | 6 | -6 
    8299 O |  |  | 4 
    8300 Iteration cutoff | 2 
    8301  
    8302 Matchmaker 3j0c.pdb1, chain C (#1.33) with AF3 CA.pdb, chain A (#166),
    8303 sequence alignment score = 328.1 
    8304 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    8305 2.714) 
    8306  
    8307 
    8308 > hide sel cartoons
    8309 
    8310 > color #162 dodgerblue
    8311 
    8312 > color #163 dodgerblue
    8313 
    8314 > color #164 #00b305ff
    8315 
    8316 > color #165 #00b305ff
    8317 
    8318 > color #166 #f15839ff
    8319 
    8320 > select #1.34/A
    8321 
    8322 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    8323 
    8324 > show sel cartoons
    8325 
    8326 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    8327 
    8328 Chain information for AF3 E1 1-421.pdb #167 
    8329 --- 
    8330 Chain | Description 
    8331 A | No description available 
    8332  
    8333 
    8334 > matchmaker #167 to #1.34 & sel
    8335 
    8336 Parameters 
    8337 --- 
    8338 Chain pairing | bb 
    8339 Alignment algorithm | Needleman-Wunsch 
    8340 Similarity matrix | BLOSUM-62 
    8341 SS fraction | 0.3 
    8342 Gap open (HH/SS/other) | 18/18/6 
    8343 Gap extend | 1 
    8344 SS matrix |  |  | H | S | O 
    8345 ---|---|---|--- 
    8346 H | 6 | -9 | -6 
    8347 S |  | 6 | -6 
    8348 O |  |  | 4 
    8349 Iteration cutoff | 2 
    8350  
    8351 Matchmaker 3j0c.pdb1, chain A (#1.34) with AF3 E1 1-421.pdb, chain A (#167),
    8352 sequence alignment score = 1060.7 
    8353 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    8354 3.020) 
    8355  
    8356 
    8357 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    8358 
    8359 Chain information for AF3 E1 422-461.pdb #168 
    8360 --- 
    8361 Chain | Description 
    8362 A | No description available 
    8363  
    8364 
    8365 > matchmaker #168 to #1.34 & sel
    8366 
    8367 Parameters 
    8368 --- 
    8369 Chain pairing | bb 
    8370 Alignment algorithm | Needleman-Wunsch 
    8371 Similarity matrix | BLOSUM-62 
    8372 SS fraction | 0.3 
    8373 Gap open (HH/SS/other) | 18/18/6 
    8374 Gap extend | 1 
    8375 SS matrix |  |  | H | S | O 
    8376 ---|---|---|--- 
    8377 H | 6 | -9 | -6 
    8378 S |  | 6 | -6 
    8379 O |  |  | 4 
    8380 Iteration cutoff | 2 
    8381  
    8382 Matchmaker 3j0c.pdb1, chain A (#1.34) with AF3 E1 422-461.pdb, chain A (#168),
    8383 sequence alignment score = 626.9 
    8384 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    8385 2.776) 
    8386  
    8387 
    8388 > hide sel cartoons
    8389 
    8390 > select #1.34/B
    8391 
    8392 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    8393 
    8394 > show sel cartoons
    8395 
    8396 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    8397 
    8398 Chain information for AF3 E2 1-352.pdb #169 
    8399 --- 
    8400 Chain | Description 
    8401 B | No description available 
    8402  
    8403 
    8404 > matchmaker #169 to #1.34 & sel
    8405 
    8406 Parameters 
    8407 --- 
    8408 Chain pairing | bb 
    8409 Alignment algorithm | Needleman-Wunsch 
    8410 Similarity matrix | BLOSUM-62 
    8411 SS fraction | 0.3 
    8412 Gap open (HH/SS/other) | 18/18/6 
    8413 Gap extend | 1 
    8414 SS matrix |  |  | H | S | O 
    8415 ---|---|---|--- 
    8416 H | 6 | -9 | -6 
    8417 S |  | 6 | -6 
    8418 O |  |  | 4 
    8419 Iteration cutoff | 2 
    8420  
    8421 Matchmaker 3j0c.pdb1, chain B (#1.34) with AF3 E2 1-352.pdb, chain B (#169),
    8422 sequence alignment score = 583.7 
    8423 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    8424 5.933) 
    8425  
    8426 
    8427 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    8428 
    8429 Chain information for AF3 E2 353-438.pdb #170 
    8430 --- 
    8431 Chain | Description 
    8432 B | No description available 
    8433  
    8434 
    8435 > matchmaker #170 to #1.34 & sel
    8436 
    8437 Parameters 
    8438 --- 
    8439 Chain pairing | bb 
    8440 Alignment algorithm | Needleman-Wunsch 
    8441 Similarity matrix | BLOSUM-62 
    8442 SS fraction | 0.3 
    8443 Gap open (HH/SS/other) | 18/18/6 
    8444 Gap extend | 1 
    8445 SS matrix |  |  | H | S | O 
    8446 ---|---|---|--- 
    8447 H | 6 | -9 | -6 
    8448 S |  | 6 | -6 
    8449 O |  |  | 4 
    8450 Iteration cutoff | 2 
    8451  
    8452 Matchmaker 3j0c.pdb1, chain B (#1.34) with AF3 E2 353-438.pdb, chain B (#170),
    8453 sequence alignment score = 333.4 
    8454 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    8455 8.411) 
    8456  
    8457 
    8458 > hide sel cartoons
    8459 
    8460 > select #1.34/C
    8461 
    8462 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    8463 
    8464 > show sel cartoons
    8465 
    8466 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    8467 
    8468 Chain information for AF3 CA.pdb #171 
    8469 --- 
    8470 Chain | Description 
    8471 A | No description available 
    8472  
    8473 
    8474 > matchmaker #171 to #1.34 & sel
    8475 
    8476 Parameters 
    8477 --- 
    8478 Chain pairing | bb 
    8479 Alignment algorithm | Needleman-Wunsch 
    8480 Similarity matrix | BLOSUM-62 
    8481 SS fraction | 0.3 
    8482 Gap open (HH/SS/other) | 18/18/6 
    8483 Gap extend | 1 
    8484 SS matrix |  |  | H | S | O 
    8485 ---|---|---|--- 
    8486 H | 6 | -9 | -6 
    8487 S |  | 6 | -6 
    8488 O |  |  | 4 
    8489 Iteration cutoff | 2 
    8490  
    8491 Matchmaker 3j0c.pdb1, chain C (#1.34) with AF3 CA.pdb, chain A (#171),
    8492 sequence alignment score = 328.1 
    8493 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    8494 2.714) 
    8495  
    8496 
    8497 > hide sel cartoons
    8498 
    8499 > color #167 dodgerblue
    8500 
    8501 > color #168 dodgerblue
    8502 
    8503 > color #169 #00b305ff
    8504 
    8505 > color #170 #00b305ff
    8506 
    8507 > color #171 #f15839ff
    8508 
    8509 > select #1.35/A
    8510 
    8511 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    8512 
    8513 > show sel cartoons
    8514 
    8515 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    8516 
    8517 Chain information for AF3 E1 1-421.pdb #172 
    8518 --- 
    8519 Chain | Description 
    8520 A | No description available 
    8521  
    8522 
    8523 > matchmaker #172 to #1.35 & sel
    8524 
    8525 Parameters 
    8526 --- 
    8527 Chain pairing | bb 
    8528 Alignment algorithm | Needleman-Wunsch 
    8529 Similarity matrix | BLOSUM-62 
    8530 SS fraction | 0.3 
    8531 Gap open (HH/SS/other) | 18/18/6 
    8532 Gap extend | 1 
    8533 SS matrix |  |  | H | S | O 
    8534 ---|---|---|--- 
    8535 H | 6 | -9 | -6 
    8536 S |  | 6 | -6 
    8537 O |  |  | 4 
    8538 Iteration cutoff | 2 
    8539  
    8540 Matchmaker 3j0c.pdb1, chain A (#1.35) with AF3 E1 1-421.pdb, chain A (#172),
    8541 sequence alignment score = 1060.7 
    8542 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    8543 3.020) 
    8544  
    8545 
    8546 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    8547 
    8548 Chain information for AF3 E1 422-461.pdb #173 
    8549 --- 
    8550 Chain | Description 
    8551 A | No description available 
    8552  
    8553 
    8554 > matchmaker #173 to #1.35 & sel
    8555 
    8556 Parameters 
    8557 --- 
    8558 Chain pairing | bb 
    8559 Alignment algorithm | Needleman-Wunsch 
    8560 Similarity matrix | BLOSUM-62 
    8561 SS fraction | 0.3 
    8562 Gap open (HH/SS/other) | 18/18/6 
    8563 Gap extend | 1 
    8564 SS matrix |  |  | H | S | O 
    8565 ---|---|---|--- 
    8566 H | 6 | -9 | -6 
    8567 S |  | 6 | -6 
    8568 O |  |  | 4 
    8569 Iteration cutoff | 2 
    8570  
    8571 Matchmaker 3j0c.pdb1, chain A (#1.35) with AF3 E1 422-461.pdb, chain A (#173),
    8572 sequence alignment score = 626.9 
    8573 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    8574 2.775) 
    8575  
    8576 
    8577 > hide sel cartoons
    8578 
    8579 > select #1.35/B
    8580 
    8581 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    8582 
    8583 > show sel cartoons
    8584 
    8585 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    8586 
    8587 Chain information for AF3 E2 1-352.pdb #174 
    8588 --- 
    8589 Chain | Description 
    8590 B | No description available 
    8591  
    8592 
    8593 > matchmaker #174 to #1.35 & sel
    8594 
    8595 Parameters 
    8596 --- 
    8597 Chain pairing | bb 
    8598 Alignment algorithm | Needleman-Wunsch 
    8599 Similarity matrix | BLOSUM-62 
    8600 SS fraction | 0.3 
    8601 Gap open (HH/SS/other) | 18/18/6 
    8602 Gap extend | 1 
    8603 SS matrix |  |  | H | S | O 
    8604 ---|---|---|--- 
    8605 H | 6 | -9 | -6 
    8606 S |  | 6 | -6 
    8607 O |  |  | 4 
    8608 Iteration cutoff | 2 
    8609  
    8610 Matchmaker 3j0c.pdb1, chain B (#1.35) with AF3 E2 1-352.pdb, chain B (#174),
    8611 sequence alignment score = 583.7 
    8612 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    8613 5.933) 
    8614  
    8615 
    8616 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    8617 
    8618 Chain information for AF3 E2 353-438.pdb #175 
    8619 --- 
    8620 Chain | Description 
    8621 B | No description available 
    8622  
    8623 
    8624 > matchmaker #175 to #1.35 & sel
    8625 
    8626 Parameters 
    8627 --- 
    8628 Chain pairing | bb 
    8629 Alignment algorithm | Needleman-Wunsch 
    8630 Similarity matrix | BLOSUM-62 
    8631 SS fraction | 0.3 
    8632 Gap open (HH/SS/other) | 18/18/6 
    8633 Gap extend | 1 
    8634 SS matrix |  |  | H | S | O 
    8635 ---|---|---|--- 
    8636 H | 6 | -9 | -6 
    8637 S |  | 6 | -6 
    8638 O |  |  | 4 
    8639 Iteration cutoff | 2 
    8640  
    8641 Matchmaker 3j0c.pdb1, chain B (#1.35) with AF3 E2 353-438.pdb, chain B (#175),
    8642 sequence alignment score = 333.4 
    8643 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    8644 8.411) 
    8645  
    8646 
    8647 > hide sel cartoons
    8648 
    8649 > select #1.35/C
    8650 
    8651 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    8652 
    8653 > show sel cartoons
    8654 
    8655 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    8656 
    8657 Chain information for AF3 CA.pdb #176 
    8658 --- 
    8659 Chain | Description 
    8660 A | No description available 
    8661  
    8662 
    8663 > matchmaker #176 to #1.35 & sel
    8664 
    8665 Parameters 
    8666 --- 
    8667 Chain pairing | bb 
    8668 Alignment algorithm | Needleman-Wunsch 
    8669 Similarity matrix | BLOSUM-62 
    8670 SS fraction | 0.3 
    8671 Gap open (HH/SS/other) | 18/18/6 
    8672 Gap extend | 1 
    8673 SS matrix |  |  | H | S | O 
    8674 ---|---|---|--- 
    8675 H | 6 | -9 | -6 
    8676 S |  | 6 | -6 
    8677 O |  |  | 4 
    8678 Iteration cutoff | 2 
    8679  
    8680 Matchmaker 3j0c.pdb1, chain C (#1.35) with AF3 CA.pdb, chain A (#176),
    8681 sequence alignment score = 328.1 
    8682 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    8683 2.714) 
    8684  
    8685 
    8686 > hide sel cartoons
    8687 
    8688 > color #172 dodgerblue
    8689 
    8690 > color #173 dodgerblue
    8691 
    8692 > color #174 #00b305ff
    8693 
    8694 > color #175 #00b305ff
    8695 
    8696 > color #176 #f15839ff
    8697 
    8698 > select #1.36/A
    8699 
    8700 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    8701 
    8702 > show sel cartoons
    8703 
    8704 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    8705 
    8706 Chain information for AF3 E1 1-421.pdb #177 
    8707 --- 
    8708 Chain | Description 
    8709 A | No description available 
    8710  
    8711 
    8712 > matchmaker #177 to #1.36 & sel
    8713 
    8714 Parameters 
    8715 --- 
    8716 Chain pairing | bb 
    8717 Alignment algorithm | Needleman-Wunsch 
    8718 Similarity matrix | BLOSUM-62 
    8719 SS fraction | 0.3 
    8720 Gap open (HH/SS/other) | 18/18/6 
    8721 Gap extend | 1 
    8722 SS matrix |  |  | H | S | O 
    8723 ---|---|---|--- 
    8724 H | 6 | -9 | -6 
    8725 S |  | 6 | -6 
    8726 O |  |  | 4 
    8727 Iteration cutoff | 2 
    8728  
    8729 Matchmaker 3j0c.pdb1, chain A (#1.36) with AF3 E1 1-421.pdb, chain A (#177),
    8730 sequence alignment score = 1060.7 
    8731 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    8732 3.020) 
    8733  
    8734 
    8735 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    8736 
    8737 Chain information for AF3 E1 422-461.pdb #178 
    8738 --- 
    8739 Chain | Description 
    8740 A | No description available 
    8741  
    8742 
    8743 > matchmaker #178 to #1.36 & sel
    8744 
    8745 Parameters 
    8746 --- 
    8747 Chain pairing | bb 
    8748 Alignment algorithm | Needleman-Wunsch 
    8749 Similarity matrix | BLOSUM-62 
    8750 SS fraction | 0.3 
    8751 Gap open (HH/SS/other) | 18/18/6 
    8752 Gap extend | 1 
    8753 SS matrix |  |  | H | S | O 
    8754 ---|---|---|--- 
    8755 H | 6 | -9 | -6 
    8756 S |  | 6 | -6 
    8757 O |  |  | 4 
    8758 Iteration cutoff | 2 
    8759  
    8760 Matchmaker 3j0c.pdb1, chain A (#1.36) with AF3 E1 422-461.pdb, chain A (#178),
    8761 sequence alignment score = 626.9 
    8762 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    8763 2.776) 
    8764  
    8765 
    8766 > hide sel cartoons
    8767 
    8768 > select #1.36/B
    8769 
    8770 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    8771 
    8772 > show sel cartoons
    8773 
    8774 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    8775 
    8776 Chain information for AF3 E2 1-352.pdb #179 
    8777 --- 
    8778 Chain | Description 
    8779 B | No description available 
    8780  
    8781 
    8782 > matchmaker #179 to #1.36 & sel
    8783 
    8784 Parameters 
    8785 --- 
    8786 Chain pairing | bb 
    8787 Alignment algorithm | Needleman-Wunsch 
    8788 Similarity matrix | BLOSUM-62 
    8789 SS fraction | 0.3 
    8790 Gap open (HH/SS/other) | 18/18/6 
    8791 Gap extend | 1 
    8792 SS matrix |  |  | H | S | O 
    8793 ---|---|---|--- 
    8794 H | 6 | -9 | -6 
    8795 S |  | 6 | -6 
    8796 O |  |  | 4 
    8797 Iteration cutoff | 2 
    8798  
    8799 Matchmaker 3j0c.pdb1, chain B (#1.36) with AF3 E2 1-352.pdb, chain B (#179),
    8800 sequence alignment score = 583.7 
    8801 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    8802 5.933) 
    8803  
    8804 
    8805 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    8806 
    8807 Chain information for AF3 E2 353-438.pdb #180 
    8808 --- 
    8809 Chain | Description 
    8810 B | No description available 
    8811  
    8812 
    8813 > matchmaker #180 to #1.36 & sel
    8814 
    8815 Parameters 
    8816 --- 
    8817 Chain pairing | bb 
    8818 Alignment algorithm | Needleman-Wunsch 
    8819 Similarity matrix | BLOSUM-62 
    8820 SS fraction | 0.3 
    8821 Gap open (HH/SS/other) | 18/18/6 
    8822 Gap extend | 1 
    8823 SS matrix |  |  | H | S | O 
    8824 ---|---|---|--- 
    8825 H | 6 | -9 | -6 
    8826 S |  | 6 | -6 
    8827 O |  |  | 4 
    8828 Iteration cutoff | 2 
    8829  
    8830 Matchmaker 3j0c.pdb1, chain B (#1.36) with AF3 E2 353-438.pdb, chain B (#180),
    8831 sequence alignment score = 333.4 
    8832 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    8833 8.411) 
    8834  
    8835 
    8836 > hide sel cartoons
    8837 
    8838 > select #1.36/C
    8839 
    8840 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    8841 
    8842 > show sel cartoons
    8843 
    8844 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    8845 
    8846 Chain information for AF3 CA.pdb #181 
    8847 --- 
    8848 Chain | Description 
    8849 A | No description available 
    8850  
    8851 
    8852 > matchmaker #181 to #1.36 & sel
    8853 
    8854 Parameters 
    8855 --- 
    8856 Chain pairing | bb 
    8857 Alignment algorithm | Needleman-Wunsch 
    8858 Similarity matrix | BLOSUM-62 
    8859 SS fraction | 0.3 
    8860 Gap open (HH/SS/other) | 18/18/6 
    8861 Gap extend | 1 
    8862 SS matrix |  |  | H | S | O 
    8863 ---|---|---|--- 
    8864 H | 6 | -9 | -6 
    8865 S |  | 6 | -6 
    8866 O |  |  | 4 
    8867 Iteration cutoff | 2 
    8868  
    8869 Matchmaker 3j0c.pdb1, chain C (#1.36) with AF3 CA.pdb, chain A (#181),
    8870 sequence alignment score = 328.1 
    8871 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    8872 2.714) 
    8873  
    8874 
    8875 > hide sel cartoons
    8876 
    8877 > color #177 dodgerblue
    8878 
    8879 > color #178 dodgerblue
    8880 
    8881 > color #179 #00b305ff
    8882 
    8883 > color #180 #00b305ff
    8884 
    8885 > color #181 #f15839ff
    8886 
    8887 > select #1.37/A
    8888 
    8889 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    8890 
    8891 > show sel cartoons
    8892 
    8893 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    8894 
    8895 Chain information for AF3 E1 1-421.pdb #182 
    8896 --- 
    8897 Chain | Description 
    8898 A | No description available 
    8899  
    8900 
    8901 > matchmaker #182 to #1.37 & sel
    8902 
    8903 Parameters 
    8904 --- 
    8905 Chain pairing | bb 
    8906 Alignment algorithm | Needleman-Wunsch 
    8907 Similarity matrix | BLOSUM-62 
    8908 SS fraction | 0.3 
    8909 Gap open (HH/SS/other) | 18/18/6 
    8910 Gap extend | 1 
    8911 SS matrix |  |  | H | S | O 
    8912 ---|---|---|--- 
    8913 H | 6 | -9 | -6 
    8914 S |  | 6 | -6 
    8915 O |  |  | 4 
    8916 Iteration cutoff | 2 
    8917  
    8918 Matchmaker 3j0c.pdb1, chain A (#1.37) with AF3 E1 1-421.pdb, chain A (#182),
    8919 sequence alignment score = 1060.7 
    8920 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    8921 3.020) 
    8922  
    8923 
    8924 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    8925 
    8926 Chain information for AF3 E1 422-461.pdb #183 
    8927 --- 
    8928 Chain | Description 
    8929 A | No description available 
    8930  
    8931 
    8932 > matchmaker #183 to #1.37 & sel
    8933 
    8934 Parameters 
    8935 --- 
    8936 Chain pairing | bb 
    8937 Alignment algorithm | Needleman-Wunsch 
    8938 Similarity matrix | BLOSUM-62 
    8939 SS fraction | 0.3 
    8940 Gap open (HH/SS/other) | 18/18/6 
    8941 Gap extend | 1 
    8942 SS matrix |  |  | H | S | O 
    8943 ---|---|---|--- 
    8944 H | 6 | -9 | -6 
    8945 S |  | 6 | -6 
    8946 O |  |  | 4 
    8947 Iteration cutoff | 2 
    8948  
    8949 Matchmaker 3j0c.pdb1, chain A (#1.37) with AF3 E1 422-461.pdb, chain A (#183),
    8950 sequence alignment score = 626.9 
    8951 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    8952 2.775) 
    8953  
    8954 
    8955 > hide sel cartoons
    8956 
    8957 > select #1.37/B
    8958 
    8959 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    8960 
    8961 > show sel cartoons
    8962 
    8963 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    8964 
    8965 Chain information for AF3 E2 1-352.pdb #184 
    8966 --- 
    8967 Chain | Description 
    8968 B | No description available 
    8969  
    8970 
    8971 > matchmaker #184 to #1.37 & sel
    8972 
    8973 Parameters 
    8974 --- 
    8975 Chain pairing | bb 
    8976 Alignment algorithm | Needleman-Wunsch 
    8977 Similarity matrix | BLOSUM-62 
    8978 SS fraction | 0.3 
    8979 Gap open (HH/SS/other) | 18/18/6 
    8980 Gap extend | 1 
    8981 SS matrix |  |  | H | S | O 
    8982 ---|---|---|--- 
    8983 H | 6 | -9 | -6 
    8984 S |  | 6 | -6 
    8985 O |  |  | 4 
    8986 Iteration cutoff | 2 
    8987  
    8988 Matchmaker 3j0c.pdb1, chain B (#1.37) with AF3 E2 1-352.pdb, chain B (#184),
    8989 sequence alignment score = 583.7 
    8990 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    8991 5.933) 
    8992  
    8993 
    8994 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    8995 
    8996 Chain information for AF3 E2 353-438.pdb #185 
    8997 --- 
    8998 Chain | Description 
    8999 B | No description available 
    9000  
    9001 
    9002 > matchmaker #185 to #1.37 & sel
    9003 
    9004 Parameters 
    9005 --- 
    9006 Chain pairing | bb 
    9007 Alignment algorithm | Needleman-Wunsch 
    9008 Similarity matrix | BLOSUM-62 
    9009 SS fraction | 0.3 
    9010 Gap open (HH/SS/other) | 18/18/6 
    9011 Gap extend | 1 
    9012 SS matrix |  |  | H | S | O 
    9013 ---|---|---|--- 
    9014 H | 6 | -9 | -6 
    9015 S |  | 6 | -6 
    9016 O |  |  | 4 
    9017 Iteration cutoff | 2 
    9018  
    9019 Matchmaker 3j0c.pdb1, chain B (#1.37) with AF3 E2 353-438.pdb, chain B (#185),
    9020 sequence alignment score = 333.4 
    9021 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    9022 8.411) 
    9023  
    9024 
    9025 > hide sel cartoons
    9026 
    9027 > select #1.37/C
    9028 
    9029 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    9030 
    9031 > show sel cartoons
    9032 
    9033 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    9034 
    9035 Chain information for AF3 CA.pdb #186 
    9036 --- 
    9037 Chain | Description 
    9038 A | No description available 
    9039  
    9040 
    9041 > matchmaker #186 to #1.37 & sel
    9042 
    9043 Parameters 
    9044 --- 
    9045 Chain pairing | bb 
    9046 Alignment algorithm | Needleman-Wunsch 
    9047 Similarity matrix | BLOSUM-62 
    9048 SS fraction | 0.3 
    9049 Gap open (HH/SS/other) | 18/18/6 
    9050 Gap extend | 1 
    9051 SS matrix |  |  | H | S | O 
    9052 ---|---|---|--- 
    9053 H | 6 | -9 | -6 
    9054 S |  | 6 | -6 
    9055 O |  |  | 4 
    9056 Iteration cutoff | 2 
    9057  
    9058 Matchmaker 3j0c.pdb1, chain C (#1.37) with AF3 CA.pdb, chain A (#186),
    9059 sequence alignment score = 328.1 
    9060 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    9061 2.714) 
    9062  
    9063 
    9064 > hide sel cartoons
    9065 
    9066 > color #182 dodgerblue
    9067 
    9068 > color #183 dodgerblue
    9069 
    9070 > color #184 #00b305ff
    9071 
    9072 > color #185 #00b305ff
    9073 
    9074 > color #186 #f15839ff
    9075 
    9076 > select #1.38/A
    9077 
    9078 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    9079 
    9080 > show sel cartoons
    9081 
    9082 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    9083 
    9084 Chain information for AF3 E1 1-421.pdb #187 
    9085 --- 
    9086 Chain | Description 
    9087 A | No description available 
    9088  
    9089 
    9090 > matchmaker #187 to #1.38 & sel
    9091 
    9092 Parameters 
    9093 --- 
    9094 Chain pairing | bb 
    9095 Alignment algorithm | Needleman-Wunsch 
    9096 Similarity matrix | BLOSUM-62 
    9097 SS fraction | 0.3 
    9098 Gap open (HH/SS/other) | 18/18/6 
    9099 Gap extend | 1 
    9100 SS matrix |  |  | H | S | O 
    9101 ---|---|---|--- 
    9102 H | 6 | -9 | -6 
    9103 S |  | 6 | -6 
    9104 O |  |  | 4 
    9105 Iteration cutoff | 2 
    9106  
    9107 Matchmaker 3j0c.pdb1, chain A (#1.38) with AF3 E1 1-421.pdb, chain A (#187),
    9108 sequence alignment score = 1060.7 
    9109 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    9110 3.020) 
    9111  
    9112 
    9113 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    9114 
    9115 Chain information for AF3 E1 422-461.pdb #188 
    9116 --- 
    9117 Chain | Description 
    9118 A | No description available 
    9119  
    9120 
    9121 > matchmaker #188 to #1.38 & sel
    9122 
    9123 Parameters 
    9124 --- 
    9125 Chain pairing | bb 
    9126 Alignment algorithm | Needleman-Wunsch 
    9127 Similarity matrix | BLOSUM-62 
    9128 SS fraction | 0.3 
    9129 Gap open (HH/SS/other) | 18/18/6 
    9130 Gap extend | 1 
    9131 SS matrix |  |  | H | S | O 
    9132 ---|---|---|--- 
    9133 H | 6 | -9 | -6 
    9134 S |  | 6 | -6 
    9135 O |  |  | 4 
    9136 Iteration cutoff | 2 
    9137  
    9138 Matchmaker 3j0c.pdb1, chain A (#1.38) with AF3 E1 422-461.pdb, chain A (#188),
    9139 sequence alignment score = 626.9 
    9140 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    9141 2.776) 
    9142  
    9143 
    9144 > hide sel cartoons
    9145 
    9146 > select #1.38/B
    9147 
    9148 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    9149 
    9150 > show sel cartoons
    9151 
    9152 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    9153 
    9154 Chain information for AF3 E2 1-352.pdb #189 
    9155 --- 
    9156 Chain | Description 
    9157 B | No description available 
    9158  
    9159 
    9160 > matchmaker #189 to #1.38 & sel
    9161 
    9162 Parameters 
    9163 --- 
    9164 Chain pairing | bb 
    9165 Alignment algorithm | Needleman-Wunsch 
    9166 Similarity matrix | BLOSUM-62 
    9167 SS fraction | 0.3 
    9168 Gap open (HH/SS/other) | 18/18/6 
    9169 Gap extend | 1 
    9170 SS matrix |  |  | H | S | O 
    9171 ---|---|---|--- 
    9172 H | 6 | -9 | -6 
    9173 S |  | 6 | -6 
    9174 O |  |  | 4 
    9175 Iteration cutoff | 2 
    9176  
    9177 Matchmaker 3j0c.pdb1, chain B (#1.38) with AF3 E2 1-352.pdb, chain B (#189),
    9178 sequence alignment score = 583.7 
    9179 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    9180 5.933) 
    9181  
    9182 
    9183 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    9184 
    9185 Chain information for AF3 E2 353-438.pdb #190 
    9186 --- 
    9187 Chain | Description 
    9188 B | No description available 
    9189  
    9190 
    9191 > matchmaker #190 to #1.38 & sel
    9192 
    9193 Parameters 
    9194 --- 
    9195 Chain pairing | bb 
    9196 Alignment algorithm | Needleman-Wunsch 
    9197 Similarity matrix | BLOSUM-62 
    9198 SS fraction | 0.3 
    9199 Gap open (HH/SS/other) | 18/18/6 
    9200 Gap extend | 1 
    9201 SS matrix |  |  | H | S | O 
    9202 ---|---|---|--- 
    9203 H | 6 | -9 | -6 
    9204 S |  | 6 | -6 
    9205 O |  |  | 4 
    9206 Iteration cutoff | 2 
    9207  
    9208 Matchmaker 3j0c.pdb1, chain B (#1.38) with AF3 E2 353-438.pdb, chain B (#190),
    9209 sequence alignment score = 322.6 
    9210 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    9211 8.411) 
    9212  
    9213 
    9214 > hide sel cartoons
    9215 
    9216 > select #1.38/C
    9217 
    9218 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    9219 
    9220 > show sel cartoons
    9221 
    9222 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    9223 
    9224 Chain information for AF3 CA.pdb #191 
    9225 --- 
    9226 Chain | Description 
    9227 A | No description available 
    9228  
    9229 
    9230 > matchmaker #191 to #1.38 & sel
    9231 
    9232 Parameters 
    9233 --- 
    9234 Chain pairing | bb 
    9235 Alignment algorithm | Needleman-Wunsch 
    9236 Similarity matrix | BLOSUM-62 
    9237 SS fraction | 0.3 
    9238 Gap open (HH/SS/other) | 18/18/6 
    9239 Gap extend | 1 
    9240 SS matrix |  |  | H | S | O 
    9241 ---|---|---|--- 
    9242 H | 6 | -9 | -6 
    9243 S |  | 6 | -6 
    9244 O |  |  | 4 
    9245 Iteration cutoff | 2 
    9246  
    9247 Matchmaker 3j0c.pdb1, chain C (#1.38) with AF3 CA.pdb, chain A (#191),
    9248 sequence alignment score = 328.1 
    9249 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    9250 2.714) 
    9251  
    9252 
    9253 > hide sel cartoons
    9254 
    9255 > color #187 dodgerblue
    9256 
    9257 > color #188 dodgerblue
    9258 
    9259 > color #189 #00b305ff
    9260 
    9261 > color #190 #00b305ff
    9262 
    9263 > color #191 #f15839ff
    9264 
    9265 > select #1.39/A
    9266 
    9267 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    9268 
    9269 > show sel cartoons
    9270 
    9271 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    9272 
    9273 Chain information for AF3 E1 1-421.pdb #192 
    9274 --- 
    9275 Chain | Description 
    9276 A | No description available 
    9277  
    9278 
    9279 > matchmaker #192 to #1.39 & sel
    9280 
    9281 Parameters 
    9282 --- 
    9283 Chain pairing | bb 
    9284 Alignment algorithm | Needleman-Wunsch 
    9285 Similarity matrix | BLOSUM-62 
    9286 SS fraction | 0.3 
    9287 Gap open (HH/SS/other) | 18/18/6 
    9288 Gap extend | 1 
    9289 SS matrix |  |  | H | S | O 
    9290 ---|---|---|--- 
    9291 H | 6 | -9 | -6 
    9292 S |  | 6 | -6 
    9293 O |  |  | 4 
    9294 Iteration cutoff | 2 
    9295  
    9296 Matchmaker 3j0c.pdb1, chain A (#1.39) with AF3 E1 1-421.pdb, chain A (#192),
    9297 sequence alignment score = 1060.7 
    9298 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    9299 3.020) 
    9300  
    9301 
    9302 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    9303 
    9304 Chain information for AF3 E1 422-461.pdb #193 
    9305 --- 
    9306 Chain | Description 
    9307 A | No description available 
    9308  
    9309 
    9310 > matchmaker #193 to #1.39 & sel
    9311 
    9312 Parameters 
    9313 --- 
    9314 Chain pairing | bb 
    9315 Alignment algorithm | Needleman-Wunsch 
    9316 Similarity matrix | BLOSUM-62 
    9317 SS fraction | 0.3 
    9318 Gap open (HH/SS/other) | 18/18/6 
    9319 Gap extend | 1 
    9320 SS matrix |  |  | H | S | O 
    9321 ---|---|---|--- 
    9322 H | 6 | -9 | -6 
    9323 S |  | 6 | -6 
    9324 O |  |  | 4 
    9325 Iteration cutoff | 2 
    9326  
    9327 Matchmaker 3j0c.pdb1, chain A (#1.39) with AF3 E1 422-461.pdb, chain A (#193),
    9328 sequence alignment score = 626.9 
    9329 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    9330 2.776) 
    9331  
    9332 
    9333 > hide sel cartoons
    9334 
    9335 > select #1.39/B
    9336 
    9337 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    9338 
    9339 > show sel cartoons
    9340 
    9341 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    9342 
    9343 Chain information for AF3 E2 1-352.pdb #194 
    9344 --- 
    9345 Chain | Description 
    9346 B | No description available 
    9347  
    9348 
    9349 > matchmaker #194 to #1.39 & sel
    9350 
    9351 Parameters 
    9352 --- 
    9353 Chain pairing | bb 
    9354 Alignment algorithm | Needleman-Wunsch 
    9355 Similarity matrix | BLOSUM-62 
    9356 SS fraction | 0.3 
    9357 Gap open (HH/SS/other) | 18/18/6 
    9358 Gap extend | 1 
    9359 SS matrix |  |  | H | S | O 
    9360 ---|---|---|--- 
    9361 H | 6 | -9 | -6 
    9362 S |  | 6 | -6 
    9363 O |  |  | 4 
    9364 Iteration cutoff | 2 
    9365  
    9366 Matchmaker 3j0c.pdb1, chain B (#1.39) with AF3 E2 1-352.pdb, chain B (#194),
    9367 sequence alignment score = 583.7 
    9368 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    9369 5.933) 
    9370  
    9371 
    9372 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    9373 
    9374 Chain information for AF3 E2 353-438.pdb #195 
    9375 --- 
    9376 Chain | Description 
    9377 B | No description available 
    9378  
    9379 
    9380 > matchmaker #195 to #1.39 & sel
    9381 
    9382 Parameters 
    9383 --- 
    9384 Chain pairing | bb 
    9385 Alignment algorithm | Needleman-Wunsch 
    9386 Similarity matrix | BLOSUM-62 
    9387 SS fraction | 0.3 
    9388 Gap open (HH/SS/other) | 18/18/6 
    9389 Gap extend | 1 
    9390 SS matrix |  |  | H | S | O 
    9391 ---|---|---|--- 
    9392 H | 6 | -9 | -6 
    9393 S |  | 6 | -6 
    9394 O |  |  | 4 
    9395 Iteration cutoff | 2 
    9396  
    9397 Matchmaker 3j0c.pdb1, chain B (#1.39) with AF3 E2 353-438.pdb, chain B (#195),
    9398 sequence alignment score = 322.6 
    9399 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    9400 8.411) 
    9401  
    9402 
    9403 > hide sel cartoons
    9404 
    9405 > select #1.39/C
    9406 
    9407 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    9408 
    9409 > show sel atoms
    9410 
    9411 > hide sel atoms
    9412 
    9413 > show sel cartoons
    9414 
    9415 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    9416 
    9417 Chain information for AF3 CA.pdb #196 
    9418 --- 
    9419 Chain | Description 
    9420 A | No description available 
    9421  
    9422 
    9423 > matchmaker #196 to #1.39 & sel
    9424 
    9425 Parameters 
    9426 --- 
    9427 Chain pairing | bb 
    9428 Alignment algorithm | Needleman-Wunsch 
    9429 Similarity matrix | BLOSUM-62 
    9430 SS fraction | 0.3 
    9431 Gap open (HH/SS/other) | 18/18/6 
    9432 Gap extend | 1 
    9433 SS matrix |  |  | H | S | O 
    9434 ---|---|---|--- 
    9435 H | 6 | -9 | -6 
    9436 S |  | 6 | -6 
    9437 O |  |  | 4 
    9438 Iteration cutoff | 2 
    9439  
    9440 Matchmaker 3j0c.pdb1, chain C (#1.39) with AF3 CA.pdb, chain A (#196),
    9441 sequence alignment score = 328.1 
    9442 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    9443 2.714) 
    9444  
    9445 
    9446 > hide sel cartoons
    9447 
    9448 > color #192 dodgerblue
    9449 
    9450 > color #193 dodgerblue
    9451 
    9452 > color #194 #00b305ff
    9453 
    9454 > color #195 #00b305ff
    9455 
    9456 > color #196 #f15839ff
    9457 
    9458 > select #1.40/A
    9459 
    9460 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    9461 
    9462 > show sel cartoons
    9463 
    9464 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    9465 
    9466 Chain information for AF3 E1 1-421.pdb #197 
    9467 --- 
    9468 Chain | Description 
    9469 A | No description available 
    9470  
    9471 
    9472 > matchmaker #197 to #1.40 & sel
    9473 
    9474 Parameters 
    9475 --- 
    9476 Chain pairing | bb 
    9477 Alignment algorithm | Needleman-Wunsch 
    9478 Similarity matrix | BLOSUM-62 
    9479 SS fraction | 0.3 
    9480 Gap open (HH/SS/other) | 18/18/6 
    9481 Gap extend | 1 
    9482 SS matrix |  |  | H | S | O 
    9483 ---|---|---|--- 
    9484 H | 6 | -9 | -6 
    9485 S |  | 6 | -6 
    9486 O |  |  | 4 
    9487 Iteration cutoff | 2 
    9488  
    9489 Matchmaker 3j0c.pdb1, chain A (#1.40) with AF3 E1 1-421.pdb, chain A (#197),
    9490 sequence alignment score = 1060.7 
    9491 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    9492 3.020) 
    9493  
    9494 
    9495 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    9496 
    9497 Chain information for AF3 E1 422-461.pdb #198 
    9498 --- 
    9499 Chain | Description 
    9500 A | No description available 
    9501  
    9502 
    9503 > matchmaker #198 to #1.40 & sel
    9504 
    9505 Parameters 
    9506 --- 
    9507 Chain pairing | bb 
    9508 Alignment algorithm | Needleman-Wunsch 
    9509 Similarity matrix | BLOSUM-62 
    9510 SS fraction | 0.3 
    9511 Gap open (HH/SS/other) | 18/18/6 
    9512 Gap extend | 1 
    9513 SS matrix |  |  | H | S | O 
    9514 ---|---|---|--- 
    9515 H | 6 | -9 | -6 
    9516 S |  | 6 | -6 
    9517 O |  |  | 4 
    9518 Iteration cutoff | 2 
    9519  
    9520 Matchmaker 3j0c.pdb1, chain A (#1.40) with AF3 E1 422-461.pdb, chain A (#198),
    9521 sequence alignment score = 626.9 
    9522 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    9523 2.775) 
    9524  
    9525 
    9526 > hide sel cartoons
    9527 
    9528 [Repeated 1 time(s)]
    9529 
    9530 > select #1.40/B
    9531 
    9532 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    9533 
    9534 > show sel cartoons
    9535 
    9536 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    9537 
    9538 Chain information for AF3 E2 1-352.pdb #199 
    9539 --- 
    9540 Chain | Description 
    9541 B | No description available 
    9542  
    9543 
    9544 > matchmaker #199 to #1.40 & sel
    9545 
    9546 Parameters 
    9547 --- 
    9548 Chain pairing | bb 
    9549 Alignment algorithm | Needleman-Wunsch 
    9550 Similarity matrix | BLOSUM-62 
    9551 SS fraction | 0.3 
    9552 Gap open (HH/SS/other) | 18/18/6 
    9553 Gap extend | 1 
    9554 SS matrix |  |  | H | S | O 
    9555 ---|---|---|--- 
    9556 H | 6 | -9 | -6 
    9557 S |  | 6 | -6 
    9558 O |  |  | 4 
    9559 Iteration cutoff | 2 
    9560  
    9561 Matchmaker 3j0c.pdb1, chain B (#1.40) with AF3 E2 1-352.pdb, chain B (#199),
    9562 sequence alignment score = 583.7 
    9563 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    9564 5.933) 
    9565  
    9566 
    9567 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    9568 
    9569 Chain information for AF3 E2 353-438.pdb #200 
    9570 --- 
    9571 Chain | Description 
    9572 B | No description available 
    9573  
    9574 
    9575 > matchmaker #200 to #1.40 & sel
    9576 
    9577 Parameters 
    9578 --- 
    9579 Chain pairing | bb 
    9580 Alignment algorithm | Needleman-Wunsch 
    9581 Similarity matrix | BLOSUM-62 
    9582 SS fraction | 0.3 
    9583 Gap open (HH/SS/other) | 18/18/6 
    9584 Gap extend | 1 
    9585 SS matrix |  |  | H | S | O 
    9586 ---|---|---|--- 
    9587 H | 6 | -9 | -6 
    9588 S |  | 6 | -6 
    9589 O |  |  | 4 
    9590 Iteration cutoff | 2 
    9591  
    9592 Matchmaker 3j0c.pdb1, chain B (#1.40) with AF3 E2 353-438.pdb, chain B (#200),
    9593 sequence alignment score = 333.4 
    9594 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    9595 8.411) 
    9596  
    9597 
    9598 > hide sel cartoons
    9599 
    9600 > select #1.40/C
    9601 
    9602 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    9603 
    9604 > show sel cartoons
    9605 
    9606 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    9607 
    9608 Chain information for AF3 CA.pdb #201 
    9609 --- 
    9610 Chain | Description 
    9611 A | No description available 
    9612  
    9613 
    9614 > matchmaker #201 to #1.40 & sel
    9615 
    9616 Parameters 
    9617 --- 
    9618 Chain pairing | bb 
    9619 Alignment algorithm | Needleman-Wunsch 
    9620 Similarity matrix | BLOSUM-62 
    9621 SS fraction | 0.3 
    9622 Gap open (HH/SS/other) | 18/18/6 
    9623 Gap extend | 1 
    9624 SS matrix |  |  | H | S | O 
    9625 ---|---|---|--- 
    9626 H | 6 | -9 | -6 
    9627 S |  | 6 | -6 
    9628 O |  |  | 4 
    9629 Iteration cutoff | 2 
    9630  
    9631 Matchmaker 3j0c.pdb1, chain C (#1.40) with AF3 CA.pdb, chain A (#201),
    9632 sequence alignment score = 328.1 
    9633 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    9634 2.714) 
    9635  
    9636 
    9637 > hide sel cartoons
    9638 
    9639 > color #197 dodgerblue
    9640 
    9641 > color #198 dodgerblue
    9642 
    9643 > color #199 #00b305ff
    9644 
    9645 > color #200 #00b305ff
    9646 
    9647 > color #201 #f15839ff
    9648 
    9649 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    9650 
    9651 > select #1.41/A
    9652 
    9653 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    9654 
    9655 > show sel cartoons
    9656 
    9657 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    9658 
    9659 Chain information for AF3 E1 1-421.pdb #202 
    9660 --- 
    9661 Chain | Description 
    9662 A | No description available 
    9663  
    9664 
    9665 > matchmaker #202 to #1.41 & sel
    9666 
    9667 Parameters 
    9668 --- 
    9669 Chain pairing | bb 
    9670 Alignment algorithm | Needleman-Wunsch 
    9671 Similarity matrix | BLOSUM-62 
    9672 SS fraction | 0.3 
    9673 Gap open (HH/SS/other) | 18/18/6 
    9674 Gap extend | 1 
    9675 SS matrix |  |  | H | S | O 
    9676 ---|---|---|--- 
    9677 H | 6 | -9 | -6 
    9678 S |  | 6 | -6 
    9679 O |  |  | 4 
    9680 Iteration cutoff | 2 
    9681  
    9682 Matchmaker 3j0c.pdb1, chain A (#1.41) with AF3 E1 1-421.pdb, chain A (#202),
    9683 sequence alignment score = 1060.7 
    9684 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    9685 3.020) 
    9686  
    9687 
    9688 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    9689 
    9690 Chain information for AF3 E1 422-461.pdb #203 
    9691 --- 
    9692 Chain | Description 
    9693 A | No description available 
    9694  
    9695 
    9696 > matchmaker #203 to #1.41 & sel
    9697 
    9698 Parameters 
    9699 --- 
    9700 Chain pairing | bb 
    9701 Alignment algorithm | Needleman-Wunsch 
    9702 Similarity matrix | BLOSUM-62 
    9703 SS fraction | 0.3 
    9704 Gap open (HH/SS/other) | 18/18/6 
    9705 Gap extend | 1 
    9706 SS matrix |  |  | H | S | O 
    9707 ---|---|---|--- 
    9708 H | 6 | -9 | -6 
    9709 S |  | 6 | -6 
    9710 O |  |  | 4 
    9711 Iteration cutoff | 2 
    9712  
    9713 Matchmaker 3j0c.pdb1, chain A (#1.41) with AF3 E1 422-461.pdb, chain A (#203),
    9714 sequence alignment score = 626.9 
    9715 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    9716 2.776) 
    9717  
    9718 
    9719 > hide sel cartoons
    9720 
    9721 [Repeated 1 time(s)]
    9722 
    9723 > select #1.41/B
    9724 
    9725 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    9726 
    9727 > show sel cartoons
    9728 
    9729 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    9730 
    9731 Chain information for AF3 E2 1-352.pdb #204 
    9732 --- 
    9733 Chain | Description 
    9734 B | No description available 
    9735  
    9736 
    9737 > matchmaker #204 to #1.41 & sel
    9738 
    9739 Parameters 
    9740 --- 
    9741 Chain pairing | bb 
    9742 Alignment algorithm | Needleman-Wunsch 
    9743 Similarity matrix | BLOSUM-62 
    9744 SS fraction | 0.3 
    9745 Gap open (HH/SS/other) | 18/18/6 
    9746 Gap extend | 1 
    9747 SS matrix |  |  | H | S | O 
    9748 ---|---|---|--- 
    9749 H | 6 | -9 | -6 
    9750 S |  | 6 | -6 
    9751 O |  |  | 4 
    9752 Iteration cutoff | 2 
    9753  
    9754 Matchmaker 3j0c.pdb1, chain B (#1.41) with AF3 E2 1-352.pdb, chain B (#204),
    9755 sequence alignment score = 583.7 
    9756 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    9757 5.933) 
    9758  
    9759 
    9760 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    9761 
    9762 Chain information for AF3 E2 353-438.pdb #205 
    9763 --- 
    9764 Chain | Description 
    9765 B | No description available 
    9766  
    9767 
    9768 > matchmaker #205 to #1.41 & sel
    9769 
    9770 Parameters 
    9771 --- 
    9772 Chain pairing | bb 
    9773 Alignment algorithm | Needleman-Wunsch 
    9774 Similarity matrix | BLOSUM-62 
    9775 SS fraction | 0.3 
    9776 Gap open (HH/SS/other) | 18/18/6 
    9777 Gap extend | 1 
    9778 SS matrix |  |  | H | S | O 
    9779 ---|---|---|--- 
    9780 H | 6 | -9 | -6 
    9781 S |  | 6 | -6 
    9782 O |  |  | 4 
    9783 Iteration cutoff | 2 
    9784  
    9785 Matchmaker 3j0c.pdb1, chain B (#1.41) with AF3 E2 353-438.pdb, chain B (#205),
    9786 sequence alignment score = 322.6 
    9787 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    9788 8.411) 
    9789  
    9790 
    9791 > hide sel cartoons
    9792 
    9793 > select #1.41/C
    9794 
    9795 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    9796 
    9797 > show sel cartoons
    9798 
    9799 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    9800 
    9801 Chain information for AF3 CA.pdb #206 
    9802 --- 
    9803 Chain | Description 
    9804 A | No description available 
    9805  
    9806 
    9807 > matchmaker #206 to #1.41 & sel
    9808 
    9809 Parameters 
    9810 --- 
    9811 Chain pairing | bb 
    9812 Alignment algorithm | Needleman-Wunsch 
    9813 Similarity matrix | BLOSUM-62 
    9814 SS fraction | 0.3 
    9815 Gap open (HH/SS/other) | 18/18/6 
    9816 Gap extend | 1 
    9817 SS matrix |  |  | H | S | O 
    9818 ---|---|---|--- 
    9819 H | 6 | -9 | -6 
    9820 S |  | 6 | -6 
    9821 O |  |  | 4 
    9822 Iteration cutoff | 2 
    9823  
    9824 Matchmaker 3j0c.pdb1, chain C (#1.41) with AF3 CA.pdb, chain A (#206),
    9825 sequence alignment score = 328.1 
    9826 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    9827 2.714) 
    9828  
    9829 
    9830 > hide sel cartoons
    9831 
    9832 > color #202 dodgerblue
    9833 
    9834 > color #203 dodgerblue
    9835 
    9836 > color #204 #00b305ff
    9837 
    9838 > color #205 #00b305ff
    9839 
    9840 > color #206 #f15839ff
    9841 
    9842 > select #1.42/A
    9843 
    9844 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    9845 
    9846 > show sel cartoons
    9847 
    9848 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    9849 
    9850 Chain information for AF3 E1 1-421.pdb #207 
    9851 --- 
    9852 Chain | Description 
    9853 A | No description available 
    9854  
    9855 
    9856 > matchmaker #207 to #1.42 & sel
    9857 
    9858 Parameters 
    9859 --- 
    9860 Chain pairing | bb 
    9861 Alignment algorithm | Needleman-Wunsch 
    9862 Similarity matrix | BLOSUM-62 
    9863 SS fraction | 0.3 
    9864 Gap open (HH/SS/other) | 18/18/6 
    9865 Gap extend | 1 
    9866 SS matrix |  |  | H | S | O 
    9867 ---|---|---|--- 
    9868 H | 6 | -9 | -6 
    9869 S |  | 6 | -6 
    9870 O |  |  | 4 
    9871 Iteration cutoff | 2 
    9872  
    9873 Matchmaker 3j0c.pdb1, chain A (#1.42) with AF3 E1 1-421.pdb, chain A (#207),
    9874 sequence alignment score = 1060.7 
    9875 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    9876 3.020) 
    9877  
    9878 
    9879 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    9880 
    9881 Chain information for AF3 E1 422-461.pdb #208 
    9882 --- 
    9883 Chain | Description 
    9884 A | No description available 
    9885  
    9886 
    9887 > matchmaker #208 to #1.42 & sel
    9888 
    9889 Parameters 
    9890 --- 
    9891 Chain pairing | bb 
    9892 Alignment algorithm | Needleman-Wunsch 
    9893 Similarity matrix | BLOSUM-62 
    9894 SS fraction | 0.3 
    9895 Gap open (HH/SS/other) | 18/18/6 
    9896 Gap extend | 1 
    9897 SS matrix |  |  | H | S | O 
    9898 ---|---|---|--- 
    9899 H | 6 | -9 | -6 
    9900 S |  | 6 | -6 
    9901 O |  |  | 4 
    9902 Iteration cutoff | 2 
    9903  
    9904 Matchmaker 3j0c.pdb1, chain A (#1.42) with AF3 E1 422-461.pdb, chain A (#208),
    9905 sequence alignment score = 626.9 
    9906 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    9907 2.776) 
    9908  
    9909 
    9910 > hide sel cartoons
    9911 
    9912 > select #1.42/B
    9913 
    9914 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    9915 
    9916 > show sel cartoons
    9917 
    9918 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    9919 
    9920 Chain information for AF3 E2 1-352.pdb #209 
    9921 --- 
    9922 Chain | Description 
    9923 B | No description available 
    9924  
    9925 
    9926 > matchmaker #209 to #1.42 & sel
    9927 
    9928 Parameters 
    9929 --- 
    9930 Chain pairing | bb 
    9931 Alignment algorithm | Needleman-Wunsch 
    9932 Similarity matrix | BLOSUM-62 
    9933 SS fraction | 0.3 
    9934 Gap open (HH/SS/other) | 18/18/6 
    9935 Gap extend | 1 
    9936 SS matrix |  |  | H | S | O 
    9937 ---|---|---|--- 
    9938 H | 6 | -9 | -6 
    9939 S |  | 6 | -6 
    9940 O |  |  | 4 
    9941 Iteration cutoff | 2 
    9942  
    9943 Matchmaker 3j0c.pdb1, chain B (#1.42) with AF3 E2 1-352.pdb, chain B (#209),
    9944 sequence alignment score = 583.7 
    9945 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    9946 5.933) 
    9947  
    9948 
    9949 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    9950 
    9951 Chain information for AF3 E2 353-438.pdb #210 
    9952 --- 
    9953 Chain | Description 
    9954 B | No description available 
    9955  
    9956 
    9957 > matchmaker #210 to #1.42 & sel
    9958 
    9959 Parameters 
    9960 --- 
    9961 Chain pairing | bb 
    9962 Alignment algorithm | Needleman-Wunsch 
    9963 Similarity matrix | BLOSUM-62 
    9964 SS fraction | 0.3 
    9965 Gap open (HH/SS/other) | 18/18/6 
    9966 Gap extend | 1 
    9967 SS matrix |  |  | H | S | O 
    9968 ---|---|---|--- 
    9969 H | 6 | -9 | -6 
    9970 S |  | 6 | -6 
    9971 O |  |  | 4 
    9972 Iteration cutoff | 2 
    9973  
    9974 Matchmaker 3j0c.pdb1, chain B (#1.42) with AF3 E2 353-438.pdb, chain B (#210),
    9975 sequence alignment score = 322.6 
    9976 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    9977 8.411) 
    9978  
    9979 
    9980 > hide sel cartoons
    9981 
    9982 > select #1.42/C
    9983 
    9984 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    9985 
    9986 > show sel cartoons
    9987 
    9988 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    9989 
    9990 Chain information for AF3 CA.pdb #211 
    9991 --- 
    9992 Chain | Description 
    9993 A | No description available 
    9994  
    9995 
    9996 > matchmaker #211 to #1.42 & sel
    9997 
    9998 Parameters 
    9999 --- 
    10000 Chain pairing | bb 
    10001 Alignment algorithm | Needleman-Wunsch 
    10002 Similarity matrix | BLOSUM-62 
    10003 SS fraction | 0.3 
    10004 Gap open (HH/SS/other) | 18/18/6 
    10005 Gap extend | 1 
    10006 SS matrix |  |  | H | S | O 
    10007 ---|---|---|--- 
    10008 H | 6 | -9 | -6 
    10009 S |  | 6 | -6 
    10010 O |  |  | 4 
    10011 Iteration cutoff | 2 
    10012  
    10013 Matchmaker 3j0c.pdb1, chain C (#1.42) with AF3 CA.pdb, chain A (#211),
    10014 sequence alignment score = 328.1 
    10015 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    10016 2.714) 
    10017  
    10018 
    10019 > hide sel cartoons
    10020 
    10021 > color #207 dodgerblue
    10022 
    10023 > color #208 dodgerblue
    10024 
    10025 > color #209 #00b305ff
    10026 
    10027 > color #210 #00b305ff
    10028 
    10029 > color #211 #f15839ff
    10030 
    10031 > select #1.43/A
    10032 
    10033 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    10034 
    10035 > show sel cartoons
    10036 
    10037 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    10038 
    10039 Chain information for AF3 E1 1-421.pdb #212 
    10040 --- 
    10041 Chain | Description 
    10042 A | No description available 
    10043  
    10044 
    10045 > matchmaker #212 to #1.43 & sel
    10046 
    10047 Parameters 
    10048 --- 
    10049 Chain pairing | bb 
    10050 Alignment algorithm | Needleman-Wunsch 
    10051 Similarity matrix | BLOSUM-62 
    10052 SS fraction | 0.3 
    10053 Gap open (HH/SS/other) | 18/18/6 
    10054 Gap extend | 1 
    10055 SS matrix |  |  | H | S | O 
    10056 ---|---|---|--- 
    10057 H | 6 | -9 | -6 
    10058 S |  | 6 | -6 
    10059 O |  |  | 4 
    10060 Iteration cutoff | 2 
    10061  
    10062 Matchmaker 3j0c.pdb1, chain A (#1.43) with AF3 E1 1-421.pdb, chain A (#212),
    10063 sequence alignment score = 1060.7 
    10064 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    10065 3.020) 
    10066  
    10067 
    10068 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    10069 
    10070 Chain information for AF3 E1 422-461.pdb #213 
    10071 --- 
    10072 Chain | Description 
    10073 A | No description available 
    10074  
    10075 
    10076 > matchmaker #213 to #1.43 & sel
    10077 
    10078 Parameters 
    10079 --- 
    10080 Chain pairing | bb 
    10081 Alignment algorithm | Needleman-Wunsch 
    10082 Similarity matrix | BLOSUM-62 
    10083 SS fraction | 0.3 
    10084 Gap open (HH/SS/other) | 18/18/6 
    10085 Gap extend | 1 
    10086 SS matrix |  |  | H | S | O 
    10087 ---|---|---|--- 
    10088 H | 6 | -9 | -6 
    10089 S |  | 6 | -6 
    10090 O |  |  | 4 
    10091 Iteration cutoff | 2 
    10092  
    10093 Matchmaker 3j0c.pdb1, chain A (#1.43) with AF3 E1 422-461.pdb, chain A (#213),
    10094 sequence alignment score = 626.9 
    10095 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    10096 2.775) 
    10097  
    10098 
    10099 > hide sel cartoons
    10100 
    10101 > select #1.43/B
    10102 
    10103 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    10104 
    10105 > show sel cartoons
    10106 
    10107 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    10108 
    10109 Chain information for AF3 E2 1-352.pdb #214 
    10110 --- 
    10111 Chain | Description 
    10112 B | No description available 
    10113  
    10114 
    10115 > matchmaker #214 to #1.43 & sel
    10116 
    10117 Parameters 
    10118 --- 
    10119 Chain pairing | bb 
    10120 Alignment algorithm | Needleman-Wunsch 
    10121 Similarity matrix | BLOSUM-62 
    10122 SS fraction | 0.3 
    10123 Gap open (HH/SS/other) | 18/18/6 
    10124 Gap extend | 1 
    10125 SS matrix |  |  | H | S | O 
    10126 ---|---|---|--- 
    10127 H | 6 | -9 | -6 
    10128 S |  | 6 | -6 
    10129 O |  |  | 4 
    10130 Iteration cutoff | 2 
    10131  
    10132 Matchmaker 3j0c.pdb1, chain B (#1.43) with AF3 E2 1-352.pdb, chain B (#214),
    10133 sequence alignment score = 583.7 
    10134 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    10135 5.933) 
    10136  
    10137 
    10138 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    10139 
    10140 Chain information for AF3 E2 353-438.pdb #215 
    10141 --- 
    10142 Chain | Description 
    10143 B | No description available 
    10144  
    10145 
    10146 > matchmaker #215 to #1.43 & sel
    10147 
    10148 Parameters 
    10149 --- 
    10150 Chain pairing | bb 
    10151 Alignment algorithm | Needleman-Wunsch 
    10152 Similarity matrix | BLOSUM-62 
    10153 SS fraction | 0.3 
    10154 Gap open (HH/SS/other) | 18/18/6 
    10155 Gap extend | 1 
    10156 SS matrix |  |  | H | S | O 
    10157 ---|---|---|--- 
    10158 H | 6 | -9 | -6 
    10159 S |  | 6 | -6 
    10160 O |  |  | 4 
    10161 Iteration cutoff | 2 
    10162  
    10163 Matchmaker 3j0c.pdb1, chain B (#1.43) with AF3 E2 353-438.pdb, chain B (#215),
    10164 sequence alignment score = 333.4 
    10165 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    10166 8.411) 
    10167  
    10168 
    10169 > hide sel cartoons
    10170 
    10171 > select #1.43/C
    10172 
    10173 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    10174 
    10175 > show sel cartoons
    10176 
    10177 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    10178 
    10179 Chain information for AF3 CA.pdb #216 
    10180 --- 
    10181 Chain | Description 
    10182 A | No description available 
    10183  
    10184 
    10185 > matchmaker #216 to #1.43 & sel
    10186 
    10187 Parameters 
    10188 --- 
    10189 Chain pairing | bb 
    10190 Alignment algorithm | Needleman-Wunsch 
    10191 Similarity matrix | BLOSUM-62 
    10192 SS fraction | 0.3 
    10193 Gap open (HH/SS/other) | 18/18/6 
    10194 Gap extend | 1 
    10195 SS matrix |  |  | H | S | O 
    10196 ---|---|---|--- 
    10197 H | 6 | -9 | -6 
    10198 S |  | 6 | -6 
    10199 O |  |  | 4 
    10200 Iteration cutoff | 2 
    10201  
    10202 Matchmaker 3j0c.pdb1, chain C (#1.43) with AF3 CA.pdb, chain A (#216),
    10203 sequence alignment score = 328.1 
    10204 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    10205 2.714) 
    10206  
    10207 
    10208 > hide sel cartoons
    10209 
    10210 > color #212 dodgerblue
    10211 
    10212 > color #213 dodgerblue
    10213 
    10214 > color #214 #00b305ff
    10215 
    10216 > color #215 #00b305ff
    10217 
    10218 > color #216 #f15839ff
    10219 
    10220 > select #1.44/A
    10221 
    10222 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    10223 
    10224 > show sel cartoons
    10225 
    10226 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    10227 
    10228 Chain information for AF3 E1 1-421.pdb #217 
    10229 --- 
    10230 Chain | Description 
    10231 A | No description available 
    10232  
    10233 
    10234 > matchmaker #217 to #1.43 & sel
    10235 
    10236 No 'to' model specified 
    10237 
    10238 > matchmaker #217 to #1.44 & sel
    10239 
    10240 Parameters 
    10241 --- 
    10242 Chain pairing | bb 
    10243 Alignment algorithm | Needleman-Wunsch 
    10244 Similarity matrix | BLOSUM-62 
    10245 SS fraction | 0.3 
    10246 Gap open (HH/SS/other) | 18/18/6 
    10247 Gap extend | 1 
    10248 SS matrix |  |  | H | S | O 
    10249 ---|---|---|--- 
    10250 H | 6 | -9 | -6 
    10251 S |  | 6 | -6 
    10252 O |  |  | 4 
    10253 Iteration cutoff | 2 
    10254  
    10255 Matchmaker 3j0c.pdb1, chain A (#1.44) with AF3 E1 1-421.pdb, chain A (#217),
    10256 sequence alignment score = 1060.7 
    10257 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    10258 3.020) 
    10259  
    10260 
    10261 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    10262 
    10263 Chain information for AF3 E1 422-461.pdb #218 
    10264 --- 
    10265 Chain | Description 
    10266 A | No description available 
    10267  
    10268 
    10269 > matchmaker #218 to #1.44 & sel
    10270 
    10271 Parameters 
    10272 --- 
    10273 Chain pairing | bb 
    10274 Alignment algorithm | Needleman-Wunsch 
    10275 Similarity matrix | BLOSUM-62 
    10276 SS fraction | 0.3 
    10277 Gap open (HH/SS/other) | 18/18/6 
    10278 Gap extend | 1 
    10279 SS matrix |  |  | H | S | O 
    10280 ---|---|---|--- 
    10281 H | 6 | -9 | -6 
    10282 S |  | 6 | -6 
    10283 O |  |  | 4 
    10284 Iteration cutoff | 2 
    10285  
    10286 Matchmaker 3j0c.pdb1, chain A (#1.44) with AF3 E1 422-461.pdb, chain A (#218),
    10287 sequence alignment score = 626.9 
    10288 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    10289 2.775) 
    10290  
    10291 
    10292 > hide sel cartoons
    10293 
    10294 > select #1.44/B
    10295 
    10296 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    10297 
    10298 > show sel cartoons
    10299 
    10300 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    10301 
    10302 Chain information for AF3 E2 1-352.pdb #219 
    10303 --- 
    10304 Chain | Description 
    10305 B | No description available 
    10306  
    10307 
    10308 > matchmaker #219 to #1.44 & sel
    10309 
    10310 Parameters 
    10311 --- 
    10312 Chain pairing | bb 
    10313 Alignment algorithm | Needleman-Wunsch 
    10314 Similarity matrix | BLOSUM-62 
    10315 SS fraction | 0.3 
    10316 Gap open (HH/SS/other) | 18/18/6 
    10317 Gap extend | 1 
    10318 SS matrix |  |  | H | S | O 
    10319 ---|---|---|--- 
    10320 H | 6 | -9 | -6 
    10321 S |  | 6 | -6 
    10322 O |  |  | 4 
    10323 Iteration cutoff | 2 
    10324  
    10325 Matchmaker 3j0c.pdb1, chain B (#1.44) with AF3 E2 1-352.pdb, chain B (#219),
    10326 sequence alignment score = 583.7 
    10327 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    10328 5.933) 
    10329  
    10330 
    10331 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    10332 
    10333 Chain information for AF3 E2 353-438.pdb #220 
    10334 --- 
    10335 Chain | Description 
    10336 B | No description available 
    10337  
    10338 
    10339 > matchmaker #220 to #1.44 & sel
    10340 
    10341 Parameters 
    10342 --- 
    10343 Chain pairing | bb 
    10344 Alignment algorithm | Needleman-Wunsch 
    10345 Similarity matrix | BLOSUM-62 
    10346 SS fraction | 0.3 
    10347 Gap open (HH/SS/other) | 18/18/6 
    10348 Gap extend | 1 
    10349 SS matrix |  |  | H | S | O 
    10350 ---|---|---|--- 
    10351 H | 6 | -9 | -6 
    10352 S |  | 6 | -6 
    10353 O |  |  | 4 
    10354 Iteration cutoff | 2 
    10355  
    10356 Matchmaker 3j0c.pdb1, chain B (#1.44) with AF3 E2 353-438.pdb, chain B (#220),
    10357 sequence alignment score = 333.4 
    10358 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    10359 8.411) 
    10360  
    10361 
    10362 > hide sel cartoons
    10363 
    10364 > select #1.44/C
    10365 
    10366 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    10367 
    10368 > show sel cartoons
    10369 
    10370 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    10371 
    10372 Chain information for AF3 CA.pdb #221 
    10373 --- 
    10374 Chain | Description 
    10375 A | No description available 
    10376  
    10377 
    10378 > matchmaker #221 to #1.44 & sel
    10379 
    10380 Parameters 
    10381 --- 
    10382 Chain pairing | bb 
    10383 Alignment algorithm | Needleman-Wunsch 
    10384 Similarity matrix | BLOSUM-62 
    10385 SS fraction | 0.3 
    10386 Gap open (HH/SS/other) | 18/18/6 
    10387 Gap extend | 1 
    10388 SS matrix |  |  | H | S | O 
    10389 ---|---|---|--- 
    10390 H | 6 | -9 | -6 
    10391 S |  | 6 | -6 
    10392 O |  |  | 4 
    10393 Iteration cutoff | 2 
    10394  
    10395 Matchmaker 3j0c.pdb1, chain C (#1.44) with AF3 CA.pdb, chain A (#221),
    10396 sequence alignment score = 328.1 
    10397 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    10398 2.714) 
    10399  
    10400 
    10401 > hide sel cartoons
    10402 
    10403 > color #217 dodgerblue
    10404 
    10405 > color #218 dodgerblue
    10406 
    10407 > color #219 #00b305ff
    10408 
    10409 > color #220 #00b305ff
    10410 
    10411 > color #221 #f15839ff
    10412 
    10413 > select #1.45/A
    10414 
    10415 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    10416 
    10417 > show sel cartoons
    10418 
    10419 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    10420 
    10421 Chain information for AF3 E1 1-421.pdb #222 
    10422 --- 
    10423 Chain | Description 
    10424 A | No description available 
    10425  
    10426 
    10427 > matchmaker #222 to #1.45 & sel
    10428 
    10429 Parameters 
    10430 --- 
    10431 Chain pairing | bb 
    10432 Alignment algorithm | Needleman-Wunsch 
    10433 Similarity matrix | BLOSUM-62 
    10434 SS fraction | 0.3 
    10435 Gap open (HH/SS/other) | 18/18/6 
    10436 Gap extend | 1 
    10437 SS matrix |  |  | H | S | O 
    10438 ---|---|---|--- 
    10439 H | 6 | -9 | -6 
    10440 S |  | 6 | -6 
    10441 O |  |  | 4 
    10442 Iteration cutoff | 2 
    10443  
    10444 Matchmaker 3j0c.pdb1, chain A (#1.45) with AF3 E1 1-421.pdb, chain A (#222),
    10445 sequence alignment score = 1060.7 
    10446 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    10447 3.020) 
    10448  
    10449 
    10450 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    10451 
    10452 Chain information for AF3 E1 422-461.pdb #223 
    10453 --- 
    10454 Chain | Description 
    10455 A | No description available 
    10456  
    10457 
    10458 > matchmaker #223 to #1.45 & sel
    10459 
    10460 Parameters 
    10461 --- 
    10462 Chain pairing | bb 
    10463 Alignment algorithm | Needleman-Wunsch 
    10464 Similarity matrix | BLOSUM-62 
    10465 SS fraction | 0.3 
    10466 Gap open (HH/SS/other) | 18/18/6 
    10467 Gap extend | 1 
    10468 SS matrix |  |  | H | S | O 
    10469 ---|---|---|--- 
    10470 H | 6 | -9 | -6 
    10471 S |  | 6 | -6 
    10472 O |  |  | 4 
    10473 Iteration cutoff | 2 
    10474  
    10475 Matchmaker 3j0c.pdb1, chain A (#1.45) with AF3 E1 422-461.pdb, chain A (#223),
    10476 sequence alignment score = 626.9 
    10477 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    10478 2.775) 
    10479  
    10480 
    10481 > hide sel cartoons
    10482 
    10483 [Repeated 1 time(s)]
    10484 
    10485 > select #1.45/B
    10486 
    10487 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    10488 
    10489 > show sel cartoons
    10490 
    10491 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    10492 
    10493 Chain information for AF3 E2 1-352.pdb #224 
    10494 --- 
    10495 Chain | Description 
    10496 B | No description available 
    10497  
    10498 
    10499 > matchmaker #224 to #1.45 & sel
    10500 
    10501 Parameters 
    10502 --- 
    10503 Chain pairing | bb 
    10504 Alignment algorithm | Needleman-Wunsch 
    10505 Similarity matrix | BLOSUM-62 
    10506 SS fraction | 0.3 
    10507 Gap open (HH/SS/other) | 18/18/6 
    10508 Gap extend | 1 
    10509 SS matrix |  |  | H | S | O 
    10510 ---|---|---|--- 
    10511 H | 6 | -9 | -6 
    10512 S |  | 6 | -6 
    10513 O |  |  | 4 
    10514 Iteration cutoff | 2 
    10515  
    10516 Matchmaker 3j0c.pdb1, chain B (#1.45) with AF3 E2 1-352.pdb, chain B (#224),
    10517 sequence alignment score = 583.7 
    10518 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    10519 5.933) 
    10520  
    10521 
    10522 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    10523 
    10524 Chain information for AF3 E2 353-438.pdb #225 
    10525 --- 
    10526 Chain | Description 
    10527 B | No description available 
    10528  
    10529 
    10530 > matchmaker #225 to #1.45 & sel
    10531 
    10532 Parameters 
    10533 --- 
    10534 Chain pairing | bb 
    10535 Alignment algorithm | Needleman-Wunsch 
    10536 Similarity matrix | BLOSUM-62 
    10537 SS fraction | 0.3 
    10538 Gap open (HH/SS/other) | 18/18/6 
    10539 Gap extend | 1 
    10540 SS matrix |  |  | H | S | O 
    10541 ---|---|---|--- 
    10542 H | 6 | -9 | -6 
    10543 S |  | 6 | -6 
    10544 O |  |  | 4 
    10545 Iteration cutoff | 2 
    10546  
    10547 Matchmaker 3j0c.pdb1, chain B (#1.45) with AF3 E2 353-438.pdb, chain B (#225),
    10548 sequence alignment score = 333.4 
    10549 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    10550 8.411) 
    10551  
    10552 
    10553 > hide sel cartoons
    10554 
    10555 > select #1.45/C
    10556 
    10557 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    10558 
    10559 > show sel cartoons
    10560 
    10561 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    10562 
    10563 Chain information for AF3 CA.pdb #226 
    10564 --- 
    10565 Chain | Description 
    10566 A | No description available 
    10567  
    10568 
    10569 > matchmaker #226 to #1.45 & sel
    10570 
    10571 Parameters 
    10572 --- 
    10573 Chain pairing | bb 
    10574 Alignment algorithm | Needleman-Wunsch 
    10575 Similarity matrix | BLOSUM-62 
    10576 SS fraction | 0.3 
    10577 Gap open (HH/SS/other) | 18/18/6 
    10578 Gap extend | 1 
    10579 SS matrix |  |  | H | S | O 
    10580 ---|---|---|--- 
    10581 H | 6 | -9 | -6 
    10582 S |  | 6 | -6 
    10583 O |  |  | 4 
    10584 Iteration cutoff | 2 
    10585  
    10586 Matchmaker 3j0c.pdb1, chain C (#1.45) with AF3 CA.pdb, chain A (#226),
    10587 sequence alignment score = 328.1 
    10588 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    10589 2.714) 
    10590  
    10591 
    10592 > hide sel cartoons
    10593 
    10594 > color #222 dodgerblue
    10595 
    10596 > color #223 dodgerblue
    10597 
    10598 > color #224 #00b305ff
    10599 
    10600 > color #225 #00b305ff
    10601 
    10602 > color #226 #f15839ff
    10603 
    10604 > select #1.46/A
    10605 
    10606 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    10607 
    10608 > show sel cartoons
    10609 
    10610 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    10611 
    10612 Chain information for AF3 E1 1-421.pdb #227 
    10613 --- 
    10614 Chain | Description 
    10615 A | No description available 
    10616  
    10617 
    10618 > matchmaker #227 to #1.46 & sel
    10619 
    10620 Parameters 
    10621 --- 
    10622 Chain pairing | bb 
    10623 Alignment algorithm | Needleman-Wunsch 
    10624 Similarity matrix | BLOSUM-62 
    10625 SS fraction | 0.3 
    10626 Gap open (HH/SS/other) | 18/18/6 
    10627 Gap extend | 1 
    10628 SS matrix |  |  | H | S | O 
    10629 ---|---|---|--- 
    10630 H | 6 | -9 | -6 
    10631 S |  | 6 | -6 
    10632 O |  |  | 4 
    10633 Iteration cutoff | 2 
    10634  
    10635 Matchmaker 3j0c.pdb1, chain A (#1.46) with AF3 E1 1-421.pdb, chain A (#227),
    10636 sequence alignment score = 1060.7 
    10637 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    10638 3.020) 
    10639  
    10640 
    10641 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    10642 
    10643 Chain information for AF3 E1 422-461.pdb #228 
    10644 --- 
    10645 Chain | Description 
    10646 A | No description available 
    10647  
    10648 
    10649 > matchmaker #228 to #1.46 & sel
    10650 
    10651 Parameters 
    10652 --- 
    10653 Chain pairing | bb 
    10654 Alignment algorithm | Needleman-Wunsch 
    10655 Similarity matrix | BLOSUM-62 
    10656 SS fraction | 0.3 
    10657 Gap open (HH/SS/other) | 18/18/6 
    10658 Gap extend | 1 
    10659 SS matrix |  |  | H | S | O 
    10660 ---|---|---|--- 
    10661 H | 6 | -9 | -6 
    10662 S |  | 6 | -6 
    10663 O |  |  | 4 
    10664 Iteration cutoff | 2 
    10665  
    10666 Matchmaker 3j0c.pdb1, chain A (#1.46) with AF3 E1 422-461.pdb, chain A (#228),
    10667 sequence alignment score = 626.9 
    10668 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    10669 2.776) 
    10670  
    10671 
    10672 > hide sel cartoons
    10673 
    10674 > select #1.46/B
    10675 
    10676 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    10677 
    10678 > show sel cartoons
    10679 
    10680 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    10681 
    10682 Chain information for AF3 E2 1-352.pdb #229 
    10683 --- 
    10684 Chain | Description 
    10685 B | No description available 
    10686  
    10687 
    10688 > matchmaker #229 to #1.46 & sel
    10689 
    10690 Parameters 
    10691 --- 
    10692 Chain pairing | bb 
    10693 Alignment algorithm | Needleman-Wunsch 
    10694 Similarity matrix | BLOSUM-62 
    10695 SS fraction | 0.3 
    10696 Gap open (HH/SS/other) | 18/18/6 
    10697 Gap extend | 1 
    10698 SS matrix |  |  | H | S | O 
    10699 ---|---|---|--- 
    10700 H | 6 | -9 | -6 
    10701 S |  | 6 | -6 
    10702 O |  |  | 4 
    10703 Iteration cutoff | 2 
    10704  
    10705 Matchmaker 3j0c.pdb1, chain B (#1.46) with AF3 E2 1-352.pdb, chain B (#229),
    10706 sequence alignment score = 583.7 
    10707 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    10708 5.933) 
    10709  
    10710 
    10711 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    10712 
    10713 Chain information for AF3 E2 353-438.pdb #230 
    10714 --- 
    10715 Chain | Description 
    10716 B | No description available 
    10717  
    10718 
    10719 > matchmaker #230 to #1.46 & sel
    10720 
    10721 Parameters 
    10722 --- 
    10723 Chain pairing | bb 
    10724 Alignment algorithm | Needleman-Wunsch 
    10725 Similarity matrix | BLOSUM-62 
    10726 SS fraction | 0.3 
    10727 Gap open (HH/SS/other) | 18/18/6 
    10728 Gap extend | 1 
    10729 SS matrix |  |  | H | S | O 
    10730 ---|---|---|--- 
    10731 H | 6 | -9 | -6 
    10732 S |  | 6 | -6 
    10733 O |  |  | 4 
    10734 Iteration cutoff | 2 
    10735  
    10736 Matchmaker 3j0c.pdb1, chain B (#1.46) with AF3 E2 353-438.pdb, chain B (#230),
    10737 sequence alignment score = 333.4 
    10738 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    10739 8.411) 
    10740  
    10741 
    10742 > hide sel cartoons
    10743 
    10744 > select #1.46/C
    10745 
    10746 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    10747 
    10748 > show sel cartoons
    10749 
    10750 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    10751 
    10752 Chain information for AF3 CA.pdb #231 
    10753 --- 
    10754 Chain | Description 
    10755 A | No description available 
    10756  
    10757 
    10758 > matchmaker #231 to #1.46 & sel
    10759 
    10760 Parameters 
    10761 --- 
    10762 Chain pairing | bb 
    10763 Alignment algorithm | Needleman-Wunsch 
    10764 Similarity matrix | BLOSUM-62 
    10765 SS fraction | 0.3 
    10766 Gap open (HH/SS/other) | 18/18/6 
    10767 Gap extend | 1 
    10768 SS matrix |  |  | H | S | O 
    10769 ---|---|---|--- 
    10770 H | 6 | -9 | -6 
    10771 S |  | 6 | -6 
    10772 O |  |  | 4 
    10773 Iteration cutoff | 2 
    10774  
    10775 Matchmaker 3j0c.pdb1, chain C (#1.46) with AF3 CA.pdb, chain A (#231),
    10776 sequence alignment score = 328.1 
    10777 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    10778 2.714) 
    10779  
    10780 
    10781 > hide sel cartoons
    10782 
    10783 > color #227 #408ca2ff
    10784 
    10785 > color #227 dodgerblue
    10786 
    10787 > color #228 dodgerblue
    10788 
    10789 > color #229 #00b305ff
    10790 
    10791 > color #230 #00b305ff
    10792 
    10793 > color #231 #f15839ff
    10794 
    10795 > view sel
    10796 
    10797 No displayed objects specified. 
    10798 
    10799 > select
    10800 > #1.1/A#1.2/A#1.3/A#1.4/A#1.5/A#1.6/A#1.7/A#1.8/A#1.9/A#1.10/A#1.11/A#1.12/A#1.13/A#1.14/A#1.15/A#1.16/A#1.17/A#1.18/A#1.19/A#1.20/A#1.21/A#1.22/A#1.23/A#1.24/A#1.25/A#1.26/A#1.27/A#1.28/A#1.29/A#1.30/A#1.31/A#1.32/A#1.33/A#1.34/A#1.35/A#1.36/A#1.37/A#1.38/A#1.39/A#1.40/A#1.41/A#1.42/A#1.43/A#1.44/A#1.45/A#1.46/A#1.47/A#1.48/A#1.49/A#1.50/A#1.51/A#1.52/A#1.53/A#1.54/A#1.55/A#1.56/A#1.57/A#1.58/A#1.59/A#1.60/A#2/A#3/A#6/A#7/A#8/A#11/A#12/A#13/A#16/A#17/A#18/A#21/A#22/A#23/A#26/A#27/A#28/A#31/A#32/A#33/A#36/A#37/A#38/A#41/A#42/A#43/A#46/A#47/A#48/A#51/A#52/A#53/A#56/A#57/A#58/A#61/A#62/A#63/A#66/A#67/A#68/A#71/A#72/A#73/A#76/A#77/A#78/A#81/A#82/A#83/A#86/A#87/A#88/A#91/A#92/A#93/A#96/A#97/A#98/A#101/A#102/A#103/A#106/A#107/A#108/A#111/A#112/A#113/A#116/A#117/A#118/A#121/A#122/A#123/A#126/A#127/A#128/A#131/A#132/A#133/A#136/A#137/A#138/A#141/A#142/A#143/A#146/A#147/A#148/A#151/A#152/A#153/A#156/A#157/A#158/A#161/A#162/A#163/A#166/A#167/A#168/A#171/A#172/A#173/A#176/A#177/A#178/A#181/A#182/A#183/A#186/A#187/A#188/A#191/A#192/A#193/A#196/A#197/A#198/A#201/A#202/A#203/A#206/A#207/A#208/A#211/A#212/A#213/A#216/A#217/A#218/A#221/A#222/A#223/A#226/A#227/A#228/A#231/A
    10801 
    10802 418952 atoms, 429570 bonds, 55178 residues, 198 models selected 
    10803 
    10804 > view sel
    10805 
    10806 > select clear
    10807 
    10808 > select #1.47/A
    10809 
    10810 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    10811 
    10812 > show sel cartoons
    10813 
    10814 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    10815 
    10816 Chain information for AF3 E1 1-421.pdb #232 
    10817 --- 
    10818 Chain | Description 
    10819 A | No description available 
    10820  
    10821 
    10822 > matchmaker #232 to #1.47 & sel
    10823 
    10824 Parameters 
    10825 --- 
    10826 Chain pairing | bb 
    10827 Alignment algorithm | Needleman-Wunsch 
    10828 Similarity matrix | BLOSUM-62 
    10829 SS fraction | 0.3 
    10830 Gap open (HH/SS/other) | 18/18/6 
    10831 Gap extend | 1 
    10832 SS matrix |  |  | H | S | O 
    10833 ---|---|---|--- 
    10834 H | 6 | -9 | -6 
    10835 S |  | 6 | -6 
    10836 O |  |  | 4 
    10837 Iteration cutoff | 2 
    10838  
    10839 Matchmaker 3j0c.pdb1, chain A (#1.47) with AF3 E1 1-421.pdb, chain A (#232),
    10840 sequence alignment score = 1060.7 
    10841 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    10842 3.020) 
    10843  
    10844 
    10845 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    10846 
    10847 Chain information for AF3 E1 422-461.pdb #233 
    10848 --- 
    10849 Chain | Description 
    10850 A | No description available 
    10851  
    10852 
    10853 > matchmaker #233 to #1.47 & sel
    10854 
    10855 Parameters 
    10856 --- 
    10857 Chain pairing | bb 
    10858 Alignment algorithm | Needleman-Wunsch 
    10859 Similarity matrix | BLOSUM-62 
    10860 SS fraction | 0.3 
    10861 Gap open (HH/SS/other) | 18/18/6 
    10862 Gap extend | 1 
    10863 SS matrix |  |  | H | S | O 
    10864 ---|---|---|--- 
    10865 H | 6 | -9 | -6 
    10866 S |  | 6 | -6 
    10867 O |  |  | 4 
    10868 Iteration cutoff | 2 
    10869  
    10870 Matchmaker 3j0c.pdb1, chain A (#1.47) with AF3 E1 422-461.pdb, chain A (#233),
    10871 sequence alignment score = 626.9 
    10872 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    10873 2.775) 
    10874  
    10875 
    10876 > hide sel cartoons
    10877 
    10878 > select #1.47/B
    10879 
    10880 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    10881 
    10882 > show sel cartoons
    10883 
    10884 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    10885 
    10886 Chain information for AF3 E2 1-352.pdb #234 
    10887 --- 
    10888 Chain | Description 
    10889 B | No description available 
    10890  
    10891 
    10892 > matchmaker #234 to #1.47 & sel
    10893 
    10894 Parameters 
    10895 --- 
    10896 Chain pairing | bb 
    10897 Alignment algorithm | Needleman-Wunsch 
    10898 Similarity matrix | BLOSUM-62 
    10899 SS fraction | 0.3 
    10900 Gap open (HH/SS/other) | 18/18/6 
    10901 Gap extend | 1 
    10902 SS matrix |  |  | H | S | O 
    10903 ---|---|---|--- 
    10904 H | 6 | -9 | -6 
    10905 S |  | 6 | -6 
    10906 O |  |  | 4 
    10907 Iteration cutoff | 2 
    10908  
    10909 Matchmaker 3j0c.pdb1, chain B (#1.47) with AF3 E2 1-352.pdb, chain B (#234),
    10910 sequence alignment score = 583.7 
    10911 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    10912 5.933) 
    10913  
    10914 
    10915 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    10916 
    10917 Chain information for AF3 E2 353-438.pdb #235 
    10918 --- 
    10919 Chain | Description 
    10920 B | No description available 
    10921  
    10922 
    10923 > matchmaker #235 to #1.47 & sel
    10924 
    10925 Parameters 
    10926 --- 
    10927 Chain pairing | bb 
    10928 Alignment algorithm | Needleman-Wunsch 
    10929 Similarity matrix | BLOSUM-62 
    10930 SS fraction | 0.3 
    10931 Gap open (HH/SS/other) | 18/18/6 
    10932 Gap extend | 1 
    10933 SS matrix |  |  | H | S | O 
    10934 ---|---|---|--- 
    10935 H | 6 | -9 | -6 
    10936 S |  | 6 | -6 
    10937 O |  |  | 4 
    10938 Iteration cutoff | 2 
    10939  
    10940 Matchmaker 3j0c.pdb1, chain B (#1.47) with AF3 E2 353-438.pdb, chain B (#235),
    10941 sequence alignment score = 322.6 
    10942 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    10943 8.411) 
    10944  
    10945 
    10946 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    10947 
    10948 Chain information for AF3 CA.pdb #236 
    10949 --- 
    10950 Chain | Description 
    10951 A | No description available 
    10952  
    10953 
    10954 > hide sel cartoons
    10955 
    10956 > select #1.47/C
    10957 
    10958 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    10959 
    10960 > show sel cartoons
    10961 
    10962 > matchmaker #236 to #1.47 & sel
    10963 
    10964 Parameters 
    10965 --- 
    10966 Chain pairing | bb 
    10967 Alignment algorithm | Needleman-Wunsch 
    10968 Similarity matrix | BLOSUM-62 
    10969 SS fraction | 0.3 
    10970 Gap open (HH/SS/other) | 18/18/6 
    10971 Gap extend | 1 
    10972 SS matrix |  |  | H | S | O 
    10973 ---|---|---|--- 
    10974 H | 6 | -9 | -6 
    10975 S |  | 6 | -6 
    10976 O |  |  | 4 
    10977 Iteration cutoff | 2 
    10978  
    10979 Matchmaker 3j0c.pdb1, chain C (#1.47) with AF3 CA.pdb, chain A (#236),
    10980 sequence alignment score = 328.1 
    10981 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    10982 2.714) 
    10983  
    10984 
    10985 > hide sel cartoons
    10986 
    10987 > color #232 dodgerblue
    10988 
    10989 > color #233 dodgerblue
    10990 
    10991 > color #234 #00b305ff
    10992 
    10993 > color #235 #00b305ff
    10994 
    10995 > color #236 #f15839ff
    10996 
    10997 > select #1.48/A
    10998 
    10999 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    11000 
    11001 > show sel cartoons
    11002 
    11003 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    11004 
    11005 Chain information for AF3 E1 1-421.pdb #237 
    11006 --- 
    11007 Chain | Description 
    11008 A | No description available 
    11009  
    11010 
    11011 > matchmaker #237 to #1.48 & sel
    11012 
    11013 Parameters 
    11014 --- 
    11015 Chain pairing | bb 
    11016 Alignment algorithm | Needleman-Wunsch 
    11017 Similarity matrix | BLOSUM-62 
    11018 SS fraction | 0.3 
    11019 Gap open (HH/SS/other) | 18/18/6 
    11020 Gap extend | 1 
    11021 SS matrix |  |  | H | S | O 
    11022 ---|---|---|--- 
    11023 H | 6 | -9 | -6 
    11024 S |  | 6 | -6 
    11025 O |  |  | 4 
    11026 Iteration cutoff | 2 
    11027  
    11028 Matchmaker 3j0c.pdb1, chain A (#1.48) with AF3 E1 1-421.pdb, chain A (#237),
    11029 sequence alignment score = 1060.7 
    11030 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    11031 3.020) 
    11032  
    11033 
    11034 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    11035 
    11036 Chain information for AF3 E1 422-461.pdb #238 
    11037 --- 
    11038 Chain | Description 
    11039 A | No description available 
    11040  
    11041 
    11042 > matchmaker #238 to #1.48 & sel
    11043 
    11044 Parameters 
    11045 --- 
    11046 Chain pairing | bb 
    11047 Alignment algorithm | Needleman-Wunsch 
    11048 Similarity matrix | BLOSUM-62 
    11049 SS fraction | 0.3 
    11050 Gap open (HH/SS/other) | 18/18/6 
    11051 Gap extend | 1 
    11052 SS matrix |  |  | H | S | O 
    11053 ---|---|---|--- 
    11054 H | 6 | -9 | -6 
    11055 S |  | 6 | -6 
    11056 O |  |  | 4 
    11057 Iteration cutoff | 2 
    11058  
    11059 Matchmaker 3j0c.pdb1, chain A (#1.48) with AF3 E1 422-461.pdb, chain A (#238),
    11060 sequence alignment score = 626.9 
    11061 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    11062 2.775) 
    11063  
    11064 
    11065 > hide sel cartoons
    11066 
    11067 > select #1.48/B
    11068 
    11069 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    11070 
    11071 > show sel cartoons
    11072 
    11073 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    11074 
    11075 Chain information for AF3 E2 1-352.pdb #239 
    11076 --- 
    11077 Chain | Description 
    11078 B | No description available 
    11079  
    11080 
    11081 > matchmaker #239 to #1.48 & sel
    11082 
    11083 Parameters 
    11084 --- 
    11085 Chain pairing | bb 
    11086 Alignment algorithm | Needleman-Wunsch 
    11087 Similarity matrix | BLOSUM-62 
    11088 SS fraction | 0.3 
    11089 Gap open (HH/SS/other) | 18/18/6 
    11090 Gap extend | 1 
    11091 SS matrix |  |  | H | S | O 
    11092 ---|---|---|--- 
    11093 H | 6 | -9 | -6 
    11094 S |  | 6 | -6 
    11095 O |  |  | 4 
    11096 Iteration cutoff | 2 
    11097  
    11098 Matchmaker 3j0c.pdb1, chain B (#1.48) with AF3 E2 1-352.pdb, chain B (#239),
    11099 sequence alignment score = 583.7 
    11100 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    11101 5.933) 
    11102  
    11103 
    11104 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    11105 
    11106 Chain information for AF3 E2 353-438.pdb #240 
    11107 --- 
    11108 Chain | Description 
    11109 B | No description available 
    11110  
    11111 
    11112 > matchmaker #240 to #1.48 & sel
    11113 
    11114 Parameters 
    11115 --- 
    11116 Chain pairing | bb 
    11117 Alignment algorithm | Needleman-Wunsch 
    11118 Similarity matrix | BLOSUM-62 
    11119 SS fraction | 0.3 
    11120 Gap open (HH/SS/other) | 18/18/6 
    11121 Gap extend | 1 
    11122 SS matrix |  |  | H | S | O 
    11123 ---|---|---|--- 
    11124 H | 6 | -9 | -6 
    11125 S |  | 6 | -6 
    11126 O |  |  | 4 
    11127 Iteration cutoff | 2 
    11128  
    11129 Matchmaker 3j0c.pdb1, chain B (#1.48) with AF3 E2 353-438.pdb, chain B (#240),
    11130 sequence alignment score = 322.6 
    11131 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    11132 8.411) 
    11133  
    11134 
    11135 > hide sel cartoons
    11136 
    11137 > select #1.48/B
    11138 
    11139 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    11140 
    11141 > show sel cartoons
    11142 
    11143 > hide sel cartoons
    11144 
    11145 > select #1.48/C
    11146 
    11147 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    11148 
    11149 > show sel cartoons
    11150 
    11151 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    11152 
    11153 Chain information for AF3 CA.pdb #241 
    11154 --- 
    11155 Chain | Description 
    11156 A | No description available 
    11157  
    11158 
    11159 > matchmaker #241 to #1.48 & sel
    11160 
    11161 Parameters 
    11162 --- 
    11163 Chain pairing | bb 
    11164 Alignment algorithm | Needleman-Wunsch 
    11165 Similarity matrix | BLOSUM-62 
    11166 SS fraction | 0.3 
    11167 Gap open (HH/SS/other) | 18/18/6 
    11168 Gap extend | 1 
    11169 SS matrix |  |  | H | S | O 
    11170 ---|---|---|--- 
    11171 H | 6 | -9 | -6 
    11172 S |  | 6 | -6 
    11173 O |  |  | 4 
    11174 Iteration cutoff | 2 
    11175  
    11176 Matchmaker 3j0c.pdb1, chain C (#1.48) with AF3 CA.pdb, chain A (#241),
    11177 sequence alignment score = 328.1 
    11178 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    11179 2.714) 
    11180  
    11181 
    11182 > hide sel cartoons
    11183 
    11184 > color #237 dodgerblue
    11185 
    11186 > color #238 dodgerblue
    11187 
    11188 > color #239 #00b305ff
    11189 
    11190 > color #241 #f15839ff
    11191 
    11192 > color #240 #00b305ff
    11193 
    11194 > select #1.49/A
    11195 
    11196 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    11197 
    11198 > show sel cartoons
    11199 
    11200 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    11201 
    11202 Chain information for AF3 E1 1-421.pdb #242 
    11203 --- 
    11204 Chain | Description 
    11205 A | No description available 
    11206  
    11207 
    11208 > matchmaker #242 to #1.49 & sel
    11209 
    11210 Parameters 
    11211 --- 
    11212 Chain pairing | bb 
    11213 Alignment algorithm | Needleman-Wunsch 
    11214 Similarity matrix | BLOSUM-62 
    11215 SS fraction | 0.3 
    11216 Gap open (HH/SS/other) | 18/18/6 
    11217 Gap extend | 1 
    11218 SS matrix |  |  | H | S | O 
    11219 ---|---|---|--- 
    11220 H | 6 | -9 | -6 
    11221 S |  | 6 | -6 
    11222 O |  |  | 4 
    11223 Iteration cutoff | 2 
    11224  
    11225 Matchmaker 3j0c.pdb1, chain A (#1.49) with AF3 E1 1-421.pdb, chain A (#242),
    11226 sequence alignment score = 1060.7 
    11227 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    11228 3.020) 
    11229  
    11230 
    11231 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    11232 
    11233 Chain information for AF3 E1 422-461.pdb #243 
    11234 --- 
    11235 Chain | Description 
    11236 A | No description available 
    11237  
    11238 
    11239 > matchmaker #243 to #1.49 & sel
    11240 
    11241 Parameters 
    11242 --- 
    11243 Chain pairing | bb 
    11244 Alignment algorithm | Needleman-Wunsch 
    11245 Similarity matrix | BLOSUM-62 
    11246 SS fraction | 0.3 
    11247 Gap open (HH/SS/other) | 18/18/6 
    11248 Gap extend | 1 
    11249 SS matrix |  |  | H | S | O 
    11250 ---|---|---|--- 
    11251 H | 6 | -9 | -6 
    11252 S |  | 6 | -6 
    11253 O |  |  | 4 
    11254 Iteration cutoff | 2 
    11255  
    11256 Matchmaker 3j0c.pdb1, chain A (#1.49) with AF3 E1 422-461.pdb, chain A (#243),
    11257 sequence alignment score = 626.9 
    11258 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    11259 2.776) 
    11260  
    11261 
    11262 > hide sel cartoons
    11263 
    11264 > select #1.49/B
    11265 
    11266 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    11267 
    11268 > show sel cartoons
    11269 
    11270 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    11271 
    11272 Chain information for AF3 E2 1-352.pdb #244 
    11273 --- 
    11274 Chain | Description 
    11275 B | No description available 
    11276  
    11277 
    11278 > matchmaker #244 to #1.49 & sel
    11279 
    11280 Parameters 
    11281 --- 
    11282 Chain pairing | bb 
    11283 Alignment algorithm | Needleman-Wunsch 
    11284 Similarity matrix | BLOSUM-62 
    11285 SS fraction | 0.3 
    11286 Gap open (HH/SS/other) | 18/18/6 
    11287 Gap extend | 1 
    11288 SS matrix |  |  | H | S | O 
    11289 ---|---|---|--- 
    11290 H | 6 | -9 | -6 
    11291 S |  | 6 | -6 
    11292 O |  |  | 4 
    11293 Iteration cutoff | 2 
    11294  
    11295 Matchmaker 3j0c.pdb1, chain B (#1.49) with AF3 E2 1-352.pdb, chain B (#244),
    11296 sequence alignment score = 583.7 
    11297 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    11298 5.933) 
    11299  
    11300 
    11301 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    11302 
    11303 Chain information for AF3 E2 353-438.pdb #245 
    11304 --- 
    11305 Chain | Description 
    11306 B | No description available 
    11307  
    11308 
    11309 > matchmaker #245 to #1.49 & sel
    11310 
    11311 Parameters 
    11312 --- 
    11313 Chain pairing | bb 
    11314 Alignment algorithm | Needleman-Wunsch 
    11315 Similarity matrix | BLOSUM-62 
    11316 SS fraction | 0.3 
    11317 Gap open (HH/SS/other) | 18/18/6 
    11318 Gap extend | 1 
    11319 SS matrix |  |  | H | S | O 
    11320 ---|---|---|--- 
    11321 H | 6 | -9 | -6 
    11322 S |  | 6 | -6 
    11323 O |  |  | 4 
    11324 Iteration cutoff | 2 
    11325  
    11326 Matchmaker 3j0c.pdb1, chain B (#1.49) with AF3 E2 353-438.pdb, chain B (#245),
    11327 sequence alignment score = 333.4 
    11328 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    11329 8.411) 
    11330  
    11331 
    11332 > hide sel cartoons
    11333 
    11334 > select #1.49/C
    11335 
    11336 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    11337 
    11338 > show sel cartoons
    11339 
    11340 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    11341 
    11342 Chain information for AF3 CA.pdb #246 
    11343 --- 
    11344 Chain | Description 
    11345 A | No description available 
    11346  
    11347 
    11348 > matchmaker #246 to #1.49 & sel
    11349 
    11350 Parameters 
    11351 --- 
    11352 Chain pairing | bb 
    11353 Alignment algorithm | Needleman-Wunsch 
    11354 Similarity matrix | BLOSUM-62 
    11355 SS fraction | 0.3 
    11356 Gap open (HH/SS/other) | 18/18/6 
    11357 Gap extend | 1 
    11358 SS matrix |  |  | H | S | O 
    11359 ---|---|---|--- 
    11360 H | 6 | -9 | -6 
    11361 S |  | 6 | -6 
    11362 O |  |  | 4 
    11363 Iteration cutoff | 2 
    11364  
    11365 Matchmaker 3j0c.pdb1, chain C (#1.49) with AF3 CA.pdb, chain A (#246),
    11366 sequence alignment score = 328.1 
    11367 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    11368 2.714) 
    11369  
    11370 
    11371 > hide sel cartoons
    11372 
    11373 > color #242 dodgerblue
    11374 
    11375 > color #243 dodgerblue
    11376 
    11377 > color #244 #00b305ff
    11378 
    11379 > color #245 #00b305ff
    11380 
    11381 > color #245 #f15839ff
    11382 
    11383 > color #245 #00b305ff
    11384 
    11385 > color #246 #f15839ff
    11386 
    11387 > select #1.50/A
    11388 
    11389 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    11390 
    11391 > show sel cartoons
    11392 
    11393 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    11394 
    11395 Chain information for AF3 E1 1-421.pdb #247 
    11396 --- 
    11397 Chain | Description 
    11398 A | No description available 
    11399  
    11400 
    11401 > matchmaker #247 to #1.49 & sel
    11402 
    11403 No 'to' model specified 
    11404 
    11405 > matchmaker #247 to #1.50 & sel
    11406 
    11407 Parameters 
    11408 --- 
    11409 Chain pairing | bb 
    11410 Alignment algorithm | Needleman-Wunsch 
    11411 Similarity matrix | BLOSUM-62 
    11412 SS fraction | 0.3 
    11413 Gap open (HH/SS/other) | 18/18/6 
    11414 Gap extend | 1 
    11415 SS matrix |  |  | H | S | O 
    11416 ---|---|---|--- 
    11417 H | 6 | -9 | -6 
    11418 S |  | 6 | -6 
    11419 O |  |  | 4 
    11420 Iteration cutoff | 2 
    11421  
    11422 Matchmaker 3j0c.pdb1, chain A (#1.50) with AF3 E1 1-421.pdb, chain A (#247),
    11423 sequence alignment score = 1060.7 
    11424 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    11425 3.020) 
    11426  
    11427 
    11428 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    11429 
    11430 Chain information for AF3 E1 422-461.pdb #248 
    11431 --- 
    11432 Chain | Description 
    11433 A | No description available 
    11434  
    11435 
    11436 > matchmaker #248 to #1.50 & sel
    11437 
    11438 Parameters 
    11439 --- 
    11440 Chain pairing | bb 
    11441 Alignment algorithm | Needleman-Wunsch 
    11442 Similarity matrix | BLOSUM-62 
    11443 SS fraction | 0.3 
    11444 Gap open (HH/SS/other) | 18/18/6 
    11445 Gap extend | 1 
    11446 SS matrix |  |  | H | S | O 
    11447 ---|---|---|--- 
    11448 H | 6 | -9 | -6 
    11449 S |  | 6 | -6 
    11450 O |  |  | 4 
    11451 Iteration cutoff | 2 
    11452  
    11453 Matchmaker 3j0c.pdb1, chain A (#1.50) with AF3 E1 422-461.pdb, chain A (#248),
    11454 sequence alignment score = 626.9 
    11455 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    11456 2.776) 
    11457  
    11458 
    11459 > hide sel cartoons
    11460 
    11461 > select #1.50/B
    11462 
    11463 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    11464 
    11465 > show sel cartoons
    11466 
    11467 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    11468 
    11469 Chain information for AF3 E2 1-352.pdb #249 
    11470 --- 
    11471 Chain | Description 
    11472 B | No description available 
    11473  
    11474 
    11475 > matchmaker #249 to #1.50 & sel
    11476 
    11477 Parameters 
    11478 --- 
    11479 Chain pairing | bb 
    11480 Alignment algorithm | Needleman-Wunsch 
    11481 Similarity matrix | BLOSUM-62 
    11482 SS fraction | 0.3 
    11483 Gap open (HH/SS/other) | 18/18/6 
    11484 Gap extend | 1 
    11485 SS matrix |  |  | H | S | O 
    11486 ---|---|---|--- 
    11487 H | 6 | -9 | -6 
    11488 S |  | 6 | -6 
    11489 O |  |  | 4 
    11490 Iteration cutoff | 2 
    11491  
    11492 Matchmaker 3j0c.pdb1, chain B (#1.50) with AF3 E2 1-352.pdb, chain B (#249),
    11493 sequence alignment score = 583.7 
    11494 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    11495 5.933) 
    11496  
    11497 
    11498 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    11499 
    11500 Chain information for AF3 E2 353-438.pdb #250 
    11501 --- 
    11502 Chain | Description 
    11503 B | No description available 
    11504  
    11505 
    11506 > matchmaker #250 to #1.50 & sel
    11507 
    11508 Parameters 
    11509 --- 
    11510 Chain pairing | bb 
    11511 Alignment algorithm | Needleman-Wunsch 
    11512 Similarity matrix | BLOSUM-62 
    11513 SS fraction | 0.3 
    11514 Gap open (HH/SS/other) | 18/18/6 
    11515 Gap extend | 1 
    11516 SS matrix |  |  | H | S | O 
    11517 ---|---|---|--- 
    11518 H | 6 | -9 | -6 
    11519 S |  | 6 | -6 
    11520 O |  |  | 4 
    11521 Iteration cutoff | 2 
    11522  
    11523 Matchmaker 3j0c.pdb1, chain B (#1.50) with AF3 E2 353-438.pdb, chain B (#250),
    11524 sequence alignment score = 333.4 
    11525 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    11526 8.411) 
    11527  
    11528 
    11529 > hide sel cartoons
    11530 
    11531 > select #1.50/C
    11532 
    11533 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    11534 
    11535 > show sel cartoons
    11536 
    11537 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    11538 
    11539 Chain information for AF3 CA.pdb #251 
    11540 --- 
    11541 Chain | Description 
    11542 A | No description available 
    11543  
    11544 
    11545 > matchmaker #251 to #1.50 & sel
    11546 
    11547 Parameters 
    11548 --- 
    11549 Chain pairing | bb 
    11550 Alignment algorithm | Needleman-Wunsch 
    11551 Similarity matrix | BLOSUM-62 
    11552 SS fraction | 0.3 
    11553 Gap open (HH/SS/other) | 18/18/6 
    11554 Gap extend | 1 
    11555 SS matrix |  |  | H | S | O 
    11556 ---|---|---|--- 
    11557 H | 6 | -9 | -6 
    11558 S |  | 6 | -6 
    11559 O |  |  | 4 
    11560 Iteration cutoff | 2 
    11561  
    11562 Matchmaker 3j0c.pdb1, chain C (#1.50) with AF3 CA.pdb, chain A (#251),
    11563 sequence alignment score = 328.1 
    11564 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    11565 2.714) 
    11566  
    11567 
    11568 > hide sel cartoons
    11569 
    11570 > color #247 dodgerblue
    11571 
    11572 > color #248 dodgerblue
    11573 
    11574 > color #249 #00b305ff
    11575 
    11576 > color #250 #00b305ff
    11577 
    11578 > color #251 #f15839ff
    11579 
    11580 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    11581 
    11582 > select #1.51/A
    11583 
    11584 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    11585 
    11586 > show sel cartoons
    11587 
    11588 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    11589 
    11590 Chain information for AF3 E1 1-421.pdb #252 
    11591 --- 
    11592 Chain | Description 
    11593 A | No description available 
    11594  
    11595 
    11596 > matchmaker #252 to #1.51 & sel
    11597 
    11598 Parameters 
    11599 --- 
    11600 Chain pairing | bb 
    11601 Alignment algorithm | Needleman-Wunsch 
    11602 Similarity matrix | BLOSUM-62 
    11603 SS fraction | 0.3 
    11604 Gap open (HH/SS/other) | 18/18/6 
    11605 Gap extend | 1 
    11606 SS matrix |  |  | H | S | O 
    11607 ---|---|---|--- 
    11608 H | 6 | -9 | -6 
    11609 S |  | 6 | -6 
    11610 O |  |  | 4 
    11611 Iteration cutoff | 2 
    11612  
    11613 Matchmaker 3j0c.pdb1, chain A (#1.51) with AF3 E1 1-421.pdb, chain A (#252),
    11614 sequence alignment score = 1060.7 
    11615 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    11616 3.020) 
    11617  
    11618 
    11619 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    11620 
    11621 Chain information for AF3 E1 422-461.pdb #253 
    11622 --- 
    11623 Chain | Description 
    11624 A | No description available 
    11625  
    11626 
    11627 > matchmaker #253 to #1.51 & sel
    11628 
    11629 Parameters 
    11630 --- 
    11631 Chain pairing | bb 
    11632 Alignment algorithm | Needleman-Wunsch 
    11633 Similarity matrix | BLOSUM-62 
    11634 SS fraction | 0.3 
    11635 Gap open (HH/SS/other) | 18/18/6 
    11636 Gap extend | 1 
    11637 SS matrix |  |  | H | S | O 
    11638 ---|---|---|--- 
    11639 H | 6 | -9 | -6 
    11640 S |  | 6 | -6 
    11641 O |  |  | 4 
    11642 Iteration cutoff | 2 
    11643  
    11644 Matchmaker 3j0c.pdb1, chain A (#1.51) with AF3 E1 422-461.pdb, chain A (#253),
    11645 sequence alignment score = 626.9 
    11646 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    11647 2.776) 
    11648  
    11649 
    11650 > hide sel cartoons
    11651 
    11652 > select #1.51/B
    11653 
    11654 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    11655 
    11656 > show sel cartoons
    11657 
    11658 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    11659 
    11660 Chain information for AF3 E2 1-352.pdb #254 
    11661 --- 
    11662 Chain | Description 
    11663 B | No description available 
    11664  
    11665 
    11666 > matchmaker #254 to #1.51 & sel
    11667 
    11668 Parameters 
    11669 --- 
    11670 Chain pairing | bb 
    11671 Alignment algorithm | Needleman-Wunsch 
    11672 Similarity matrix | BLOSUM-62 
    11673 SS fraction | 0.3 
    11674 Gap open (HH/SS/other) | 18/18/6 
    11675 Gap extend | 1 
    11676 SS matrix |  |  | H | S | O 
    11677 ---|---|---|--- 
    11678 H | 6 | -9 | -6 
    11679 S |  | 6 | -6 
    11680 O |  |  | 4 
    11681 Iteration cutoff | 2 
    11682  
    11683 Matchmaker 3j0c.pdb1, chain B (#1.51) with AF3 E2 1-352.pdb, chain B (#254),
    11684 sequence alignment score = 583.7 
    11685 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    11686 5.933) 
    11687  
    11688 
    11689 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    11690 
    11691 Chain information for AF3 E2 353-438.pdb #255 
    11692 --- 
    11693 Chain | Description 
    11694 B | No description available 
    11695  
    11696 
    11697 > matchmaker #255 to #1.51 & sel
    11698 
    11699 Parameters 
    11700 --- 
    11701 Chain pairing | bb 
    11702 Alignment algorithm | Needleman-Wunsch 
    11703 Similarity matrix | BLOSUM-62 
    11704 SS fraction | 0.3 
    11705 Gap open (HH/SS/other) | 18/18/6 
    11706 Gap extend | 1 
    11707 SS matrix |  |  | H | S | O 
    11708 ---|---|---|--- 
    11709 H | 6 | -9 | -6 
    11710 S |  | 6 | -6 
    11711 O |  |  | 4 
    11712 Iteration cutoff | 2 
    11713  
    11714 Matchmaker 3j0c.pdb1, chain B (#1.51) with AF3 E2 353-438.pdb, chain B (#255),
    11715 sequence alignment score = 322.6 
    11716 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    11717 8.411) 
    11718  
    11719 
    11720 > hide sel cartoons
    11721 
    11722 > select #1.51/C
    11723 
    11724 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    11725 
    11726 > show sel cartoons
    11727 
    11728 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    11729 
    11730 Chain information for AF3 CA.pdb #256 
    11731 --- 
    11732 Chain | Description 
    11733 A | No description available 
    11734  
    11735 
    11736 > matchmaker #256 to #1.51 & sel
    11737 
    11738 Parameters 
    11739 --- 
    11740 Chain pairing | bb 
    11741 Alignment algorithm | Needleman-Wunsch 
    11742 Similarity matrix | BLOSUM-62 
    11743 SS fraction | 0.3 
    11744 Gap open (HH/SS/other) | 18/18/6 
    11745 Gap extend | 1 
    11746 SS matrix |  |  | H | S | O 
    11747 ---|---|---|--- 
    11748 H | 6 | -9 | -6 
    11749 S |  | 6 | -6 
    11750 O |  |  | 4 
    11751 Iteration cutoff | 2 
    11752  
    11753 Matchmaker 3j0c.pdb1, chain C (#1.51) with AF3 CA.pdb, chain A (#256),
    11754 sequence alignment score = 328.1 
    11755 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    11756 2.714) 
    11757  
    11758 
    11759 > matchmaker #256 to #1.51 & sel
    11760 
    11761 Parameters 
    11762 --- 
    11763 Chain pairing | bb 
    11764 Alignment algorithm | Needleman-Wunsch 
    11765 Similarity matrix | BLOSUM-62 
    11766 SS fraction | 0.3 
    11767 Gap open (HH/SS/other) | 18/18/6 
    11768 Gap extend | 1 
    11769 SS matrix |  |  | H | S | O 
    11770 ---|---|---|--- 
    11771 H | 6 | -9 | -6 
    11772 S |  | 6 | -6 
    11773 O |  |  | 4 
    11774 Iteration cutoff | 2 
    11775  
    11776 Matchmaker 3j0c.pdb1, chain C (#1.51) with AF3 CA.pdb, chain A (#256),
    11777 sequence alignment score = 328.1 
    11778 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    11779 2.714) 
    11780  
    11781 
    11782 > hide sel cartoons
    11783 
    11784 > color #252 dodgerblue
    11785 
    11786 > color #253 dodgerblue
    11787 
    11788 > color #254 #00b305ff
    11789 
    11790 > color #255 #00b305ff
    11791 
    11792 > color #256 #f15839ff
    11793 
    11794 > select #1.52/A
    11795 
    11796 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    11797 
    11798 > show sel cartoons
    11799 
    11800 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    11801 
    11802 Chain information for AF3 E1 1-421.pdb #257 
    11803 --- 
    11804 Chain | Description 
    11805 A | No description available 
    11806  
    11807 
    11808 > matchmaker #257 to #1.52 & sel
    11809 
    11810 Parameters 
    11811 --- 
    11812 Chain pairing | bb 
    11813 Alignment algorithm | Needleman-Wunsch 
    11814 Similarity matrix | BLOSUM-62 
    11815 SS fraction | 0.3 
    11816 Gap open (HH/SS/other) | 18/18/6 
    11817 Gap extend | 1 
    11818 SS matrix |  |  | H | S | O 
    11819 ---|---|---|--- 
    11820 H | 6 | -9 | -6 
    11821 S |  | 6 | -6 
    11822 O |  |  | 4 
    11823 Iteration cutoff | 2 
    11824  
    11825 Matchmaker 3j0c.pdb1, chain A (#1.52) with AF3 E1 1-421.pdb, chain A (#257),
    11826 sequence alignment score = 1060.7 
    11827 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    11828 3.020) 
    11829  
    11830 
    11831 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    11832 
    11833 Chain information for AF3 E1 422-461.pdb #258 
    11834 --- 
    11835 Chain | Description 
    11836 A | No description available 
    11837  
    11838 
    11839 > matchmaker #258 to #1.52 & sel
    11840 
    11841 Parameters 
    11842 --- 
    11843 Chain pairing | bb 
    11844 Alignment algorithm | Needleman-Wunsch 
    11845 Similarity matrix | BLOSUM-62 
    11846 SS fraction | 0.3 
    11847 Gap open (HH/SS/other) | 18/18/6 
    11848 Gap extend | 1 
    11849 SS matrix |  |  | H | S | O 
    11850 ---|---|---|--- 
    11851 H | 6 | -9 | -6 
    11852 S |  | 6 | -6 
    11853 O |  |  | 4 
    11854 Iteration cutoff | 2 
    11855  
    11856 Matchmaker 3j0c.pdb1, chain A (#1.52) with AF3 E1 422-461.pdb, chain A (#258),
    11857 sequence alignment score = 626.9 
    11858 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    11859 2.775) 
    11860  
    11861 
    11862 > hide sel cartoons
    11863 
    11864 > select #1.52/B
    11865 
    11866 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    11867 
    11868 > show sel cartoons
    11869 
    11870 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    11871 
    11872 Chain information for AF3 E2 1-352.pdb #259 
    11873 --- 
    11874 Chain | Description 
    11875 B | No description available 
    11876  
    11877 
    11878 > matchmaker #259 to #1.52 & sel
    11879 
    11880 Parameters 
    11881 --- 
    11882 Chain pairing | bb 
    11883 Alignment algorithm | Needleman-Wunsch 
    11884 Similarity matrix | BLOSUM-62 
    11885 SS fraction | 0.3 
    11886 Gap open (HH/SS/other) | 18/18/6 
    11887 Gap extend | 1 
    11888 SS matrix |  |  | H | S | O 
    11889 ---|---|---|--- 
    11890 H | 6 | -9 | -6 
    11891 S |  | 6 | -6 
    11892 O |  |  | 4 
    11893 Iteration cutoff | 2 
    11894  
    11895 Matchmaker 3j0c.pdb1, chain B (#1.52) with AF3 E2 1-352.pdb, chain B (#259),
    11896 sequence alignment score = 583.7 
    11897 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    11898 5.933) 
    11899  
    11900 
    11901 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    11902 
    11903 Chain information for AF3 E2 353-438.pdb #260 
    11904 --- 
    11905 Chain | Description 
    11906 B | No description available 
    11907  
    11908 
    11909 > matchmaker #260 to #1.52 & sel
    11910 
    11911 Parameters 
    11912 --- 
    11913 Chain pairing | bb 
    11914 Alignment algorithm | Needleman-Wunsch 
    11915 Similarity matrix | BLOSUM-62 
    11916 SS fraction | 0.3 
    11917 Gap open (HH/SS/other) | 18/18/6 
    11918 Gap extend | 1 
    11919 SS matrix |  |  | H | S | O 
    11920 ---|---|---|--- 
    11921 H | 6 | -9 | -6 
    11922 S |  | 6 | -6 
    11923 O |  |  | 4 
    11924 Iteration cutoff | 2 
    11925  
    11926 Matchmaker 3j0c.pdb1, chain B (#1.52) with AF3 E2 353-438.pdb, chain B (#260),
    11927 sequence alignment score = 333.4 
    11928 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    11929 8.411) 
    11930  
    11931 
    11932 > hide sel cartoons
    11933 
    11934 > select #1.52/C
    11935 
    11936 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    11937 
    11938 > show sel cartoons
    11939 
    11940 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    11941 
    11942 Chain information for AF3 CA.pdb #261 
    11943 --- 
    11944 Chain | Description 
    11945 A | No description available 
    11946  
    11947 
    11948 > matchmaker #261 to #1.52 & sel
    11949 
    11950 Parameters 
    11951 --- 
    11952 Chain pairing | bb 
    11953 Alignment algorithm | Needleman-Wunsch 
    11954 Similarity matrix | BLOSUM-62 
    11955 SS fraction | 0.3 
    11956 Gap open (HH/SS/other) | 18/18/6 
    11957 Gap extend | 1 
    11958 SS matrix |  |  | H | S | O 
    11959 ---|---|---|--- 
    11960 H | 6 | -9 | -6 
    11961 S |  | 6 | -6 
    11962 O |  |  | 4 
    11963 Iteration cutoff | 2 
    11964  
    11965 Matchmaker 3j0c.pdb1, chain C (#1.52) with AF3 CA.pdb, chain A (#261),
    11966 sequence alignment score = 328.1 
    11967 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    11968 2.714) 
    11969  
    11970 
    11971 > hide sel cartoons
    11972 
    11973 [Repeated 1 time(s)]
    11974 
    11975 > color #257 dodgerblue
    11976 
    11977 > color #258 dodgerblue
    11978 
    11979 > color #259 #00b305ff
    11980 
    11981 > color #260 #00b305ff
    11982 
    11983 > color #261 #f15839ff
    11984 
    11985 The cached device pixel ratio value was stale on window expose. Please file a
    11986 QTBUG which explains how to reproduce. 
    11987 
    11988 > select
    11989 
    11990 2325488 atoms, 2385760 bonds, 301652 residues, 321 models selected 
    11991 
    11992 > hide sel cartoons
    11993 
    11994 > select up
    11995 
    11996 2325488 atoms, 2385760 bonds, 301652 residues, 321 models selected 
    11997 
    11998 > show #176 target m
    11999 
    12000 > show sel cartoons
    12001 
    12002 > hide #!1 models
    12003 
    12004 > select subtract #1
    12005 
    12006 417248 atoms, 427076 bonds, 55172 residues, 260 models selected 
    12007 
    12008 > select clear
    12009 
    12010 > hide #2 models
    12011 
    12012 > hide #3 models
    12013 
    12014 > hide #4 models
    12015 
    12016 > hide #5 models
    12017 
    12018 > hide #6 models
    12019 
    12020 > hide #7 models
    12021 
    12022 > hide #8 models
    12023 
    12024 > hide #9 models
    12025 
    12026 > hide #10 models
    12027 
    12028 > hide #11 models
    12029 
    12030 > hide #12 models
    12031 
    12032 > hide #13 models
    12033 
    12034 > hide #14 models
    12035 
    12036 > hide #15 models
    12037 
    12038 > hide #16 models
    12039 
    12040 > hide #17 models
    12041 
    12042 > show #16 models
    12043 
    12044 > show #17 models
    12045 
    12046 > hide #18 models
    12047 
    12048 > hide #19 models
    12049 
    12050 > hide #20 models
    12051 
    12052 > hide #21 models
    12053 
    12054 > hide #22 models
    12055 
    12056 > hide #23 models
    12057 
    12058 > hide #24 models
    12059 
    12060 > hide #25 models
    12061 
    12062 > hide #16 models
    12063 
    12064 > hide #17 models
    12065 
    12066 > hide #26 models
    12067 
    12068 > hide #27 models
    12069 
    12070 > hide #28 models
    12071 
    12072 > hide #29 models
    12073 
    12074 > hide #30 models
    12075 
    12076 > hide #31 models
    12077 
    12078 > hide #32 models
    12079 
    12080 > hide #33 models
    12081 
    12082 > hide #34 models
    12083 
    12084 > show #34 models
    12085 
    12086 > hide #35 models
    12087 
    12088 The cached device pixel ratio value was stale on window expose. Please file a
    12089 QTBUG which explains how to reproduce. 
    12090 
    12091 > hide #37 target m
    12092 
    12093 > hide #34 models
    12094 
    12095 > hide #36 models
    12096 
    12097 > hide #38 models
    12098 
    12099 > hide #39 models
    12100 
    12101 > hide #40 models
    12102 
    12103 > hide #41 models
    12104 
    12105 > hide #42 models
    12106 
    12107 > hide #43 models
    12108 
    12109 > hide #44 models
    12110 
    12111 > hide #45 models
    12112 
    12113 > hide #46 models
    12114 
    12115 > hide #47 models
    12116 
    12117 > hide #48 models
    12118 
    12119 > hide #49 models
    12120 
    12121 > hide #50 models
    12122 
    12123 > hide #51 models
    12124 
    12125 > hide #52 models
    12126 
    12127 > hide #53 models
    12128 
    12129 > hide #54 models
    12130 
    12131 > hide #55 models
    12132 
    12133 > hide #56 models
    12134 
    12135 > hide #57 models
    12136 
    12137 > hide #58 models
    12138 
    12139 > hide #59 models
    12140 
    12141 > hide #60 models
    12142 
    12143 > hide #61 models
    12144 
    12145 > hide #62 models
    12146 
    12147 > hide #63 models
    12148 
    12149 > hide #64 models
    12150 
    12151 > hide #65 models
    12152 
    12153 > hide #66 models
    12154 
    12155 > hide #67 models
    12156 
    12157 > hide #68 models
    12158 
    12159 > hide #69 models
    12160 
    12161 > hide #70 models
    12162 
    12163 > hide #71 models
    12164 
    12165 > hide #72 models
    12166 
    12167 > hide #73 models
    12168 
    12169 > hide #74 models
    12170 
    12171 > hide #75 models
    12172 
    12173 > hide #76 models
    12174 
    12175 > hide #77 models
    12176 
    12177 > hide #78 models
    12178 
    12179 > hide #79 models
    12180 
    12181 > hide #80 models
    12182 
    12183 > hide #81 models
    12184 
    12185 > hide #82 models
    12186 
    12187 > hide #83 models
    12188 
    12189 > hide #84 models
    12190 
    12191 > hide #85 models
    12192 
    12193 > hide #86 models
    12194 
    12195 > hide #87 models
    12196 
    12197 > hide #88 models
    12198 
    12199 > hide #89 models
    12200 
    12201 > hide #90 models
    12202 
    12203 > hide #91 models
    12204 
    12205 > hide #92 models
    12206 
    12207 > hide #93 models
    12208 
    12209 > hide #94 models
    12210 
    12211 > hide #95 models
    12212 
    12213 > hide #96 models
    12214 
    12215 > hide #97 models
    12216 
    12217 > hide #98 models
    12218 
    12219 > hide #99 models
    12220 
    12221 > hide #100 models
    12222 
    12223 > hide #101 models
    12224 
    12225 > hide #102 models
    12226 
    12227 > hide #103 models
    12228 
    12229 > hide #104 models
    12230 
    12231 > hide #105 models
    12232 
    12233 > hide #106 models
    12234 
    12235 > hide #107 models
    12236 
    12237 > hide #108 models
    12238 
    12239 > hide #109 models
    12240 
    12241 > hide #110 models
    12242 
    12243 > hide #111 models
    12244 
    12245 > hide #112 models
    12246 
    12247 > hide #113 models
    12248 
    12249 > hide #114 models
    12250 
    12251 > hide #115 models
    12252 
    12253 > hide #116 models
    12254 
    12255 > hide #117 models
    12256 
    12257 > hide #118 models
    12258 
    12259 > hide #119 models
    12260 
    12261 > hide #120 models
    12262 
    12263 > hide #121 models
    12264 
    12265 > hide #122 models
    12266 
    12267 > hide #123 models
    12268 
    12269 > hide #124 models
    12270 
    12271 > hide #125 models
    12272 
    12273 > hide #126 models
    12274 
    12275 > hide #127 models
    12276 
    12277 > hide #128 models
    12278 
    12279 > hide #129 models
    12280 
    12281 > hide #130 models
    12282 
    12283 > hide #131 models
    12284 
    12285 > hide #132 models
    12286 
    12287 > hide #133 models
    12288 
    12289 > hide #134 models
    12290 
    12291 > hide #135 models
    12292 
    12293 > hide #136 models
    12294 
    12295 > hide #137 models
    12296 
    12297 > hide #138 models
    12298 
    12299 > hide #139 models
    12300 
    12301 > hide #140 models
    12302 
    12303 > hide #141 models
    12304 
    12305 > hide #142 models
    12306 
    12307 > hide #143 models
    12308 
    12309 > hide #144 models
    12310 
    12311 > hide #145 models
    12312 
    12313 > hide #146 models
    12314 
    12315 > hide #147 models
    12316 
    12317 > hide #148 models
    12318 
    12319 > hide #149 models
    12320 
    12321 > hide #150 models
    12322 
    12323 > hide #151 models
    12324 
    12325 > hide #152 models
    12326 
    12327 > hide #153 models
    12328 
    12329 > hide #154 models
    12330 
    12331 > hide #155 models
    12332 
    12333 > hide #156 models
    12334 
    12335 > hide #157 models
    12336 
    12337 > hide #158 models
    12338 
    12339 > hide #159 models
    12340 
    12341 > hide #160 models
    12342 
    12343 > hide #161 models
    12344 
    12345 > hide #162 models
    12346 
    12347 > hide #163 models
    12348 
    12349 > hide #164 models
    12350 
    12351 > hide #165 models
    12352 
    12353 > hide #166 models
    12354 
    12355 > hide #167 models
    12356 
    12357 > hide #168 models
    12358 
    12359 > hide #169 models
    12360 
    12361 > hide #170 models
    12362 
    12363 > hide #171 models
    12364 
    12365 > hide #172 models
    12366 
    12367 > hide #173 models
    12368 
    12369 > hide #174 models
    12370 
    12371 > hide #175 models
    12372 
    12373 > hide #176 models
    12374 
    12375 > hide #177 models
    12376 
    12377 > hide #178 models
    12378 
    12379 > hide #179 models
    12380 
    12381 > hide #180 models
    12382 
    12383 > hide #181 models
    12384 
    12385 > hide #182 models
    12386 
    12387 > hide #183 models
    12388 
    12389 > hide #184 models
    12390 
    12391 > hide #185 models
    12392 
    12393 > hide #186 models
    12394 
    12395 > hide #187 models
    12396 
    12397 > hide #188 models
    12398 
    12399 > hide #189 models
    12400 
    12401 > hide #190 models
    12402 
    12403 > hide #191 models
    12404 
    12405 > hide #192 models
    12406 
    12407 > hide #193 models
    12408 
    12409 > hide #194 models
    12410 
    12411 > hide #195 models
    12412 
    12413 > hide #196 models
    12414 
    12415 > hide #197 models
    12416 
    12417 > hide #198 models
    12418 
    12419 > hide #199 models
    12420 
    12421 > hide #200 models
    12422 
    12423 > hide #201 models
    12424 
    12425 > hide #202 models
    12426 
    12427 > hide #203 models
    12428 
    12429 > hide #204 models
    12430 
    12431 > hide #205 models
    12432 
    12433 > hide #206 models
    12434 
    12435 > hide #207 models
    12436 
    12437 > hide #208 models
    12438 
    12439 > hide #209 models
    12440 
    12441 > hide #210 models
    12442 
    12443 > hide #211 models
    12444 
    12445 > hide #212 models
    12446 
    12447 > hide #213 models
    12448 
    12449 > hide #214 models
    12450 
    12451 > hide #215 models
    12452 
    12453 > hide #216 models
    12454 
    12455 > hide #217 models
    12456 
    12457 > hide #218 models
    12458 
    12459 > hide #219 models
    12460 
    12461 > hide #220 models
    12462 
    12463 > hide #221 models
    12464 
    12465 > hide #222 models
    12466 
    12467 > hide #223 models
    12468 
    12469 > hide #224 models
    12470 
    12471 > hide #225 models
    12472 
    12473 > hide #226 models
    12474 
    12475 > hide #227 models
    12476 
    12477 > hide #228 models
    12478 
    12479 > hide #229 models
    12480 
    12481 > hide #230 models
    12482 
    12483 > hide #231 models
    12484 
    12485 > hide #232 models
    12486 
    12487 > hide #233 models
    12488 
    12489 > hide #234 models
    12490 
    12491 > hide #235 models
    12492 
    12493 > hide #236 models
    12494 
    12495 > hide #237 models
    12496 
    12497 > hide #238 models
    12498 
    12499 > hide #239 models
    12500 
    12501 > hide #240 models
    12502 
    12503 > hide #241 models
    12504 
    12505 > hide #242 models
    12506 
    12507 > hide #243 models
    12508 
    12509 > hide #244 models
    12510 
    12511 > hide #245 models
    12512 
    12513 > hide #246 models
    12514 
    12515 > hide #247 models
    12516 
    12517 > hide #248 models
    12518 
    12519 > hide #249 models
    12520 
    12521 > hide #250 models
    12522 
    12523 > hide #251 models
    12524 
    12525 > hide #252 models
    12526 
    12527 > hide #253 models
    12528 
    12529 > hide #254 models
    12530 
    12531 > hide #255 models
    12532 
    12533 > hide #256 models
    12534 
    12535 > hide #257 models
    12536 
    12537 > hide #258 models
    12538 
    12539 > hide #259 models
    12540 
    12541 > hide #260 models
    12542 
    12543 > hide #261 models
    12544 
    12545 > select #1.53/A
    12546 
    12547 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    12548 
    12549 > select #1.52/A
    12550 
    12551 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    12552 
    12553 > view sel
    12554 
    12555 No displayed objects specified. 
    12556 
    12557 > show #!1 models
    12558 
    12559 > select ~sel & ##selected
    12560 
    12561 28434 atoms, 29183 bonds, 3666 residues, 1 model selected 
    12562 
    12563 > hide sel cartoons
    12564 
    12565 > select
    12566 > #1.1/A#1.2/A#1.3/A#1.4/A#1.5/A#1.6/A#1.7/A#1.8/A#1.9/A#1.10/A#1.11/A#1.12/A#1.13/A#1.14/A#1.15/A#1.16/A#1.17/A#1.18/A#1.19/A#1.20/A#1.21/A#1.22/A#1.23/A#1.24/A#1.25/A#1.26/A#1.27/A#1.28/A#1.29/A#1.30/A#1.31/A#1.32/A#1.33/A#1.34/A#1.35/A#1.36/A#1.37/A#1.38/A#1.39/A#1.40/A#1.41/A#1.42/A#1.43/A#1.44/A#1.45/A#1.46/A#1.47/A#1.48/A#1.49/A#1.50/A#1.51/A#1.52/A#1.53/A#1.54/A#1.55/A#1.56/A#1.57/A#1.58/A#1.59/A#1.60/A#2/A#3/A#6/A#7/A#8/A#11/A#12/A#13/A#16/A#17/A#18/A#21/A#22/A#23/A#26/A#27/A#28/A#31/A#32/A#33/A#36/A#37/A#38/A#41/A#42/A#43/A#46/A#47/A#48/A#51/A#52/A#53/A#56/A#57/A#58/A#61/A#62/A#63/A#66/A#67/A#68/A#71/A#72/A#73/A#76/A#77/A#78/A#81/A#82/A#83/A#86/A#87/A#88/A#91/A#92/A#93/A#96/A#97/A#98/A#101/A#102/A#103/A#106/A#107/A#108/A#111/A#112/A#113/A#116/A#117/A#118/A#121/A#122/A#123/A#126/A#127/A#128/A#131/A#132/A#133/A#136/A#137/A#138/A#141/A#142/A#143/A#146/A#147/A#148/A#151/A#152/A#153/A#156/A#157/A#158/A#161/A#162/A#163/A#166/A#167/A#168/A#171/A#172/A#173/A#176/A#177/A#178/A#181/A#182/A#183/A#186/A#187/A#188/A#191/A#192/A#193/A#196/A#197/A#198/A#201/A#202/A#203/A#206/A#207/A#208/A#211/A#212/A#213/A#216/A#217/A#218/A#221/A#222/A#223/A#226/A#227/A#228/A#231/A#232/A#233/A#236/A#237/A#238/A#241/A#242/A#243/A#246/A#247/A#248/A#251/A#252/A#253/A#256/A#257/A#258/A#261/A
    12567 
    12568 447224 atoms, 458514 bonds, 58916 residues, 216 models selected 
    12569 
    12570 > select
    12571 
    12572 2325488 atoms, 2385760 bonds, 301652 residues, 321 models selected 
    12573 
    12574 > hide sel & #1.1-60 cartoons
    12575 
    12576 > select #1.53/A
    12577 
    12578 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    12579 
    12580 > show sel cartoons
    12581 
    12582 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    12583 
    12584 Chain information for AF3 E1 1-421.pdb #262 
    12585 --- 
    12586 Chain | Description 
    12587 A | No description available 
    12588  
    12589 
    12590 > matchmaker #262 to #1.53 & sel
    12591 
    12592 Parameters 
    12593 --- 
    12594 Chain pairing | bb 
    12595 Alignment algorithm | Needleman-Wunsch 
    12596 Similarity matrix | BLOSUM-62 
    12597 SS fraction | 0.3 
    12598 Gap open (HH/SS/other) | 18/18/6 
    12599 Gap extend | 1 
    12600 SS matrix |  |  | H | S | O 
    12601 ---|---|---|--- 
    12602 H | 6 | -9 | -6 
    12603 S |  | 6 | -6 
    12604 O |  |  | 4 
    12605 Iteration cutoff | 2 
    12606  
    12607 Matchmaker 3j0c.pdb1, chain A (#1.53) with AF3 E1 1-421.pdb, chain A (#262),
    12608 sequence alignment score = 1060.7 
    12609 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    12610 3.020) 
    12611  
    12612 
    12613 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    12614 
    12615 Chain information for AF3 E1 422-461.pdb #263 
    12616 --- 
    12617 Chain | Description 
    12618 A | No description available 
    12619  
    12620 
    12621 > matchmaker #263 to #1.53 & sel
    12622 
    12623 Parameters 
    12624 --- 
    12625 Chain pairing | bb 
    12626 Alignment algorithm | Needleman-Wunsch 
    12627 Similarity matrix | BLOSUM-62 
    12628 SS fraction | 0.3 
    12629 Gap open (HH/SS/other) | 18/18/6 
    12630 Gap extend | 1 
    12631 SS matrix |  |  | H | S | O 
    12632 ---|---|---|--- 
    12633 H | 6 | -9 | -6 
    12634 S |  | 6 | -6 
    12635 O |  |  | 4 
    12636 Iteration cutoff | 2 
    12637  
    12638 Matchmaker 3j0c.pdb1, chain A (#1.53) with AF3 E1 422-461.pdb, chain A (#263),
    12639 sequence alignment score = 626.9 
    12640 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    12641 2.775) 
    12642  
    12643 
    12644 > hide sel cartoons
    12645 
    12646 > select #1.53/B
    12647 
    12648 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    12649 
    12650 > show sel cartoons
    12651 
    12652 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    12653 
    12654 Chain information for AF3 E2 1-352.pdb #264 
    12655 --- 
    12656 Chain | Description 
    12657 B | No description available 
    12658  
    12659 
    12660 > matchmaker #264 to #1.53 & sel
    12661 
    12662 Parameters 
    12663 --- 
    12664 Chain pairing | bb 
    12665 Alignment algorithm | Needleman-Wunsch 
    12666 Similarity matrix | BLOSUM-62 
    12667 SS fraction | 0.3 
    12668 Gap open (HH/SS/other) | 18/18/6 
    12669 Gap extend | 1 
    12670 SS matrix |  |  | H | S | O 
    12671 ---|---|---|--- 
    12672 H | 6 | -9 | -6 
    12673 S |  | 6 | -6 
    12674 O |  |  | 4 
    12675 Iteration cutoff | 2 
    12676  
    12677 Matchmaker 3j0c.pdb1, chain B (#1.53) with AF3 E2 1-352.pdb, chain B (#264),
    12678 sequence alignment score = 583.7 
    12679 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    12680 5.933) 
    12681  
    12682 
    12683 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    12684 
    12685 Chain information for AF3 E2 353-438.pdb #265 
    12686 --- 
    12687 Chain | Description 
    12688 B | No description available 
    12689  
    12690 
    12691 > matchmaker #265 to #1.53 & sel
    12692 
    12693 Parameters 
    12694 --- 
    12695 Chain pairing | bb 
    12696 Alignment algorithm | Needleman-Wunsch 
    12697 Similarity matrix | BLOSUM-62 
    12698 SS fraction | 0.3 
    12699 Gap open (HH/SS/other) | 18/18/6 
    12700 Gap extend | 1 
    12701 SS matrix |  |  | H | S | O 
    12702 ---|---|---|--- 
    12703 H | 6 | -9 | -6 
    12704 S |  | 6 | -6 
    12705 O |  |  | 4 
    12706 Iteration cutoff | 2 
    12707  
    12708 Matchmaker 3j0c.pdb1, chain B (#1.53) with AF3 E2 353-438.pdb, chain B (#265),
    12709 sequence alignment score = 333.4 
    12710 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    12711 8.411) 
    12712  
    12713 
    12714 > hide sel cartoons
    12715 
    12716 > select #1.53/C
    12717 
    12718 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    12719 
    12720 > show sel cartoons
    12721 
    12722 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    12723 
    12724 Chain information for AF3 CA.pdb #266 
    12725 --- 
    12726 Chain | Description 
    12727 A | No description available 
    12728  
    12729 
    12730 > matchmaker #266 to #1.53 & sel
    12731 
    12732 Parameters 
    12733 --- 
    12734 Chain pairing | bb 
    12735 Alignment algorithm | Needleman-Wunsch 
    12736 Similarity matrix | BLOSUM-62 
    12737 SS fraction | 0.3 
    12738 Gap open (HH/SS/other) | 18/18/6 
    12739 Gap extend | 1 
    12740 SS matrix |  |  | H | S | O 
    12741 ---|---|---|--- 
    12742 H | 6 | -9 | -6 
    12743 S |  | 6 | -6 
    12744 O |  |  | 4 
    12745 Iteration cutoff | 2 
    12746  
    12747 Matchmaker 3j0c.pdb1, chain C (#1.53) with AF3 CA.pdb, chain A (#266),
    12748 sequence alignment score = 328.1 
    12749 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    12750 2.714) 
    12751  
    12752 
    12753 > hide sel cartoons
    12754 
    12755 > select #1.54/A
    12756 
    12757 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    12758 
    12759 > show sel cartoons
    12760 
    12761 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    12762 
    12763 Chain information for AF3 E1 1-421.pdb #267 
    12764 --- 
    12765 Chain | Description 
    12766 A | No description available 
    12767  
    12768 
    12769 > matchmaker #267 to #1.54 & sel
    12770 
    12771 Parameters 
    12772 --- 
    12773 Chain pairing | bb 
    12774 Alignment algorithm | Needleman-Wunsch 
    12775 Similarity matrix | BLOSUM-62 
    12776 SS fraction | 0.3 
    12777 Gap open (HH/SS/other) | 18/18/6 
    12778 Gap extend | 1 
    12779 SS matrix |  |  | H | S | O 
    12780 ---|---|---|--- 
    12781 H | 6 | -9 | -6 
    12782 S |  | 6 | -6 
    12783 O |  |  | 4 
    12784 Iteration cutoff | 2 
    12785  
    12786 Matchmaker 3j0c.pdb1, chain A (#1.54) with AF3 E1 1-421.pdb, chain A (#267),
    12787 sequence alignment score = 1060.7 
    12788 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    12789 3.020) 
    12790  
    12791 
    12792 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    12793 
    12794 Chain information for AF3 E1 422-461.pdb #268 
    12795 --- 
    12796 Chain | Description 
    12797 A | No description available 
    12798  
    12799 
    12800 > matchmaker #268 to #1.54 & sel
    12801 
    12802 Parameters 
    12803 --- 
    12804 Chain pairing | bb 
    12805 Alignment algorithm | Needleman-Wunsch 
    12806 Similarity matrix | BLOSUM-62 
    12807 SS fraction | 0.3 
    12808 Gap open (HH/SS/other) | 18/18/6 
    12809 Gap extend | 1 
    12810 SS matrix |  |  | H | S | O 
    12811 ---|---|---|--- 
    12812 H | 6 | -9 | -6 
    12813 S |  | 6 | -6 
    12814 O |  |  | 4 
    12815 Iteration cutoff | 2 
    12816  
    12817 Matchmaker 3j0c.pdb1, chain A (#1.54) with AF3 E1 422-461.pdb, chain A (#268),
    12818 sequence alignment score = 626.9 
    12819 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    12820 2.776) 
    12821  
    12822 
    12823 > matchmaker #268 to #1.54 & sel
    12824 
    12825 Parameters 
    12826 --- 
    12827 Chain pairing | bb 
    12828 Alignment algorithm | Needleman-Wunsch 
    12829 Similarity matrix | BLOSUM-62 
    12830 SS fraction | 0.3 
    12831 Gap open (HH/SS/other) | 18/18/6 
    12832 Gap extend | 1 
    12833 SS matrix |  |  | H | S | O 
    12834 ---|---|---|--- 
    12835 H | 6 | -9 | -6 
    12836 S |  | 6 | -6 
    12837 O |  |  | 4 
    12838 Iteration cutoff | 2 
    12839  
    12840 Matchmaker 3j0c.pdb1, chain A (#1.54) with AF3 E1 422-461.pdb, chain A (#268),
    12841 sequence alignment score = 626.9 
    12842 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    12843 2.776) 
    12844  
    12845 
    12846 > hide sel cartoons
    12847 
    12848 > select #1.54/B
    12849 
    12850 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    12851 
    12852 > show sel cartoons
    12853 
    12854 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    12855 
    12856 Chain information for AF3 E2 1-352.pdb #269 
    12857 --- 
    12858 Chain | Description 
    12859 B | No description available 
    12860  
    12861 
    12862 > matchmaker #269 to #1.54 & sel
    12863 
    12864 Parameters 
    12865 --- 
    12866 Chain pairing | bb 
    12867 Alignment algorithm | Needleman-Wunsch 
    12868 Similarity matrix | BLOSUM-62 
    12869 SS fraction | 0.3 
    12870 Gap open (HH/SS/other) | 18/18/6 
    12871 Gap extend | 1 
    12872 SS matrix |  |  | H | S | O 
    12873 ---|---|---|--- 
    12874 H | 6 | -9 | -6 
    12875 S |  | 6 | -6 
    12876 O |  |  | 4 
    12877 Iteration cutoff | 2 
    12878  
    12879 Matchmaker 3j0c.pdb1, chain B (#1.54) with AF3 E2 1-352.pdb, chain B (#269),
    12880 sequence alignment score = 583.7 
    12881 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    12882 5.933) 
    12883  
    12884 
    12885 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    12886 
    12887 Chain information for AF3 E2 353-438.pdb #270 
    12888 --- 
    12889 Chain | Description 
    12890 B | No description available 
    12891  
    12892 
    12893 > matchmaker #270 to #1.54 & sel
    12894 
    12895 Parameters 
    12896 --- 
    12897 Chain pairing | bb 
    12898 Alignment algorithm | Needleman-Wunsch 
    12899 Similarity matrix | BLOSUM-62 
    12900 SS fraction | 0.3 
    12901 Gap open (HH/SS/other) | 18/18/6 
    12902 Gap extend | 1 
    12903 SS matrix |  |  | H | S | O 
    12904 ---|---|---|--- 
    12905 H | 6 | -9 | -6 
    12906 S |  | 6 | -6 
    12907 O |  |  | 4 
    12908 Iteration cutoff | 2 
    12909  
    12910 Matchmaker 3j0c.pdb1, chain B (#1.54) with AF3 E2 353-438.pdb, chain B (#270),
    12911 sequence alignment score = 333.4 
    12912 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    12913 8.411) 
    12914  
    12915 
    12916 > hide sel cartoons
    12917 
    12918 > select #1.54/C
    12919 
    12920 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    12921 
    12922 > show sel cartoons
    12923 
    12924 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    12925 
    12926 Chain information for AF3 CA.pdb #271 
    12927 --- 
    12928 Chain | Description 
    12929 A | No description available 
    12930  
    12931 
    12932 > matchmaker #271 to #1.54 & sel
    12933 
    12934 Parameters 
    12935 --- 
    12936 Chain pairing | bb 
    12937 Alignment algorithm | Needleman-Wunsch 
    12938 Similarity matrix | BLOSUM-62 
    12939 SS fraction | 0.3 
    12940 Gap open (HH/SS/other) | 18/18/6 
    12941 Gap extend | 1 
    12942 SS matrix |  |  | H | S | O 
    12943 ---|---|---|--- 
    12944 H | 6 | -9 | -6 
    12945 S |  | 6 | -6 
    12946 O |  |  | 4 
    12947 Iteration cutoff | 2 
    12948  
    12949 Matchmaker 3j0c.pdb1, chain C (#1.54) with AF3 CA.pdb, chain A (#271),
    12950 sequence alignment score = 328.1 
    12951 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    12952 2.714) 
    12953  
    12954 
    12955 > hide sel cartoons
    12956 
    12957 > color #262 dodgerblue
    12958 
    12959 > color #263 dodgerblue
    12960 
    12961 > color #264 #00b305ff
    12962 
    12963 > color #265 #00b305ff
    12964 
    12965 > color #266 #f15839ff
    12966 
    12967 > color #267 dodgerblue
    12968 
    12969 > color #268 dodgerblue
    12970 
    12971 > color #269 #00b305ff
    12972 
    12973 > color #270 #00b305ff
    12974 
    12975 > color #271 #f15839ff
    12976 
    12977 > select #1.55/A
    12978 
    12979 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    12980 
    12981 > show sel cartoons
    12982 
    12983 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    12984 
    12985 Chain information for AF3 E1 1-421.pdb #272 
    12986 --- 
    12987 Chain | Description 
    12988 A | No description available 
    12989  
    12990 
    12991 > matchmaker #272 to #1.54 & sel
    12992 
    12993 No 'to' model specified 
    12994 
    12995 > matchmaker #272 to #1.55 & sel
    12996 
    12997 Parameters 
    12998 --- 
    12999 Chain pairing | bb 
    13000 Alignment algorithm | Needleman-Wunsch 
    13001 Similarity matrix | BLOSUM-62 
    13002 SS fraction | 0.3 
    13003 Gap open (HH/SS/other) | 18/18/6 
    13004 Gap extend | 1 
    13005 SS matrix |  |  | H | S | O 
    13006 ---|---|---|--- 
    13007 H | 6 | -9 | -6 
    13008 S |  | 6 | -6 
    13009 O |  |  | 4 
    13010 Iteration cutoff | 2 
    13011  
    13012 Matchmaker 3j0c.pdb1, chain A (#1.55) with AF3 E1 1-421.pdb, chain A (#272),
    13013 sequence alignment score = 1060.7 
    13014 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    13015 3.020) 
    13016  
    13017 
    13018 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    13019 
    13020 Chain information for AF3 E1 422-461.pdb #273 
    13021 --- 
    13022 Chain | Description 
    13023 A | No description available 
    13024  
    13025 
    13026 > matchmaker #273 to #1.55 & sel
    13027 
    13028 Parameters 
    13029 --- 
    13030 Chain pairing | bb 
    13031 Alignment algorithm | Needleman-Wunsch 
    13032 Similarity matrix | BLOSUM-62 
    13033 SS fraction | 0.3 
    13034 Gap open (HH/SS/other) | 18/18/6 
    13035 Gap extend | 1 
    13036 SS matrix |  |  | H | S | O 
    13037 ---|---|---|--- 
    13038 H | 6 | -9 | -6 
    13039 S |  | 6 | -6 
    13040 O |  |  | 4 
    13041 Iteration cutoff | 2 
    13042  
    13043 Matchmaker 3j0c.pdb1, chain A (#1.55) with AF3 E1 422-461.pdb, chain A (#273),
    13044 sequence alignment score = 626.9 
    13045 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    13046 2.775) 
    13047  
    13048 
    13049 > hide sel cartoons
    13050 
    13051 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    13052 
    13053 Chain information for AF3 E2 1-352.pdb #274 
    13054 --- 
    13055 Chain | Description 
    13056 B | No description available 
    13057  
    13058 
    13059 > select #1.55/B
    13060 
    13061 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    13062 
    13063 > show sel cartoons
    13064 
    13065 > matchmaker #274 to #1.55 & sel
    13066 
    13067 Parameters 
    13068 --- 
    13069 Chain pairing | bb 
    13070 Alignment algorithm | Needleman-Wunsch 
    13071 Similarity matrix | BLOSUM-62 
    13072 SS fraction | 0.3 
    13073 Gap open (HH/SS/other) | 18/18/6 
    13074 Gap extend | 1 
    13075 SS matrix |  |  | H | S | O 
    13076 ---|---|---|--- 
    13077 H | 6 | -9 | -6 
    13078 S |  | 6 | -6 
    13079 O |  |  | 4 
    13080 Iteration cutoff | 2 
    13081  
    13082 Matchmaker 3j0c.pdb1, chain B (#1.55) with AF3 E2 1-352.pdb, chain B (#274),
    13083 sequence alignment score = 583.7 
    13084 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    13085 5.933) 
    13086  
    13087 
    13088 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    13089 
    13090 Chain information for AF3 E2 353-438.pdb #275 
    13091 --- 
    13092 Chain | Description 
    13093 B | No description available 
    13094  
    13095 
    13096 > matchmaker #275 to #1.55 & sel
    13097 
    13098 Parameters 
    13099 --- 
    13100 Chain pairing | bb 
    13101 Alignment algorithm | Needleman-Wunsch 
    13102 Similarity matrix | BLOSUM-62 
    13103 SS fraction | 0.3 
    13104 Gap open (HH/SS/other) | 18/18/6 
    13105 Gap extend | 1 
    13106 SS matrix |  |  | H | S | O 
    13107 ---|---|---|--- 
    13108 H | 6 | -9 | -6 
    13109 S |  | 6 | -6 
    13110 O |  |  | 4 
    13111 Iteration cutoff | 2 
    13112  
    13113 Matchmaker 3j0c.pdb1, chain B (#1.55) with AF3 E2 353-438.pdb, chain B (#275),
    13114 sequence alignment score = 322.6 
    13115 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    13116 8.411) 
    13117  
    13118 
    13119 > hide sel cartoons
    13120 
    13121 > select #1.55/C
    13122 
    13123 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    13124 
    13125 > show sel cartoons
    13126 
    13127 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    13128 
    13129 Chain information for AF3 CA.pdb #276 
    13130 --- 
    13131 Chain | Description 
    13132 A | No description available 
    13133  
    13134 
    13135 > matchmaker #276 to #1.55 & sel
    13136 
    13137 Parameters 
    13138 --- 
    13139 Chain pairing | bb 
    13140 Alignment algorithm | Needleman-Wunsch 
    13141 Similarity matrix | BLOSUM-62 
    13142 SS fraction | 0.3 
    13143 Gap open (HH/SS/other) | 18/18/6 
    13144 Gap extend | 1 
    13145 SS matrix |  |  | H | S | O 
    13146 ---|---|---|--- 
    13147 H | 6 | -9 | -6 
    13148 S |  | 6 | -6 
    13149 O |  |  | 4 
    13150 Iteration cutoff | 2 
    13151  
    13152 Matchmaker 3j0c.pdb1, chain C (#1.55) with AF3 CA.pdb, chain A (#276),
    13153 sequence alignment score = 328.1 
    13154 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    13155 2.714) 
    13156  
    13157 
    13158 > hide sel cartoons
    13159 
    13160 > color #272 dodgerblue
    13161 
    13162 > color #273 dodgerblue
    13163 
    13164 > color #274 #00b305ff
    13165 
    13166 > color #275 #00b305ff
    13167 
    13168 > color #276 #f15839ff
    13169 
    13170 > select #1.56/A
    13171 
    13172 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    13173 
    13174 > show sel cartoons
    13175 
    13176 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    13177 
    13178 Chain information for AF3 E1 1-421.pdb #277 
    13179 --- 
    13180 Chain | Description 
    13181 A | No description available 
    13182  
    13183 
    13184 > matchmaker #277 to #1.55 & sel
    13185 
    13186 No 'to' model specified 
    13187 
    13188 > matchmaker #277 to #1.56 & sel
    13189 
    13190 Parameters 
    13191 --- 
    13192 Chain pairing | bb 
    13193 Alignment algorithm | Needleman-Wunsch 
    13194 Similarity matrix | BLOSUM-62 
    13195 SS fraction | 0.3 
    13196 Gap open (HH/SS/other) | 18/18/6 
    13197 Gap extend | 1 
    13198 SS matrix |  |  | H | S | O 
    13199 ---|---|---|--- 
    13200 H | 6 | -9 | -6 
    13201 S |  | 6 | -6 
    13202 O |  |  | 4 
    13203 Iteration cutoff | 2 
    13204  
    13205 Matchmaker 3j0c.pdb1, chain A (#1.56) with AF3 E1 1-421.pdb, chain A (#277),
    13206 sequence alignment score = 1060.7 
    13207 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    13208 3.020) 
    13209  
    13210 
    13211 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    13212 
    13213 Chain information for AF3 E1 422-461.pdb #278 
    13214 --- 
    13215 Chain | Description 
    13216 A | No description available 
    13217  
    13218 
    13219 > matchmaker #278 to #1.56 & sel
    13220 
    13221 Parameters 
    13222 --- 
    13223 Chain pairing | bb 
    13224 Alignment algorithm | Needleman-Wunsch 
    13225 Similarity matrix | BLOSUM-62 
    13226 SS fraction | 0.3 
    13227 Gap open (HH/SS/other) | 18/18/6 
    13228 Gap extend | 1 
    13229 SS matrix |  |  | H | S | O 
    13230 ---|---|---|--- 
    13231 H | 6 | -9 | -6 
    13232 S |  | 6 | -6 
    13233 O |  |  | 4 
    13234 Iteration cutoff | 2 
    13235  
    13236 Matchmaker 3j0c.pdb1, chain A (#1.56) with AF3 E1 422-461.pdb, chain A (#278),
    13237 sequence alignment score = 626.9 
    13238 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    13239 2.775) 
    13240  
    13241 
    13242 > hide sel cartoons
    13243 
    13244 > select #1.56/B
    13245 
    13246 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    13247 
    13248 > show sel cartoons
    13249 
    13250 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    13251 
    13252 Chain information for AF3 E2 1-352.pdb #279 
    13253 --- 
    13254 Chain | Description 
    13255 B | No description available 
    13256  
    13257 
    13258 > matchmaker #279 to #1.56 & sel
    13259 
    13260 Parameters 
    13261 --- 
    13262 Chain pairing | bb 
    13263 Alignment algorithm | Needleman-Wunsch 
    13264 Similarity matrix | BLOSUM-62 
    13265 SS fraction | 0.3 
    13266 Gap open (HH/SS/other) | 18/18/6 
    13267 Gap extend | 1 
    13268 SS matrix |  |  | H | S | O 
    13269 ---|---|---|--- 
    13270 H | 6 | -9 | -6 
    13271 S |  | 6 | -6 
    13272 O |  |  | 4 
    13273 Iteration cutoff | 2 
    13274  
    13275 Matchmaker 3j0c.pdb1, chain B (#1.56) with AF3 E2 1-352.pdb, chain B (#279),
    13276 sequence alignment score = 583.7 
    13277 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    13278 5.933) 
    13279  
    13280 
    13281 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    13282 
    13283 Chain information for AF3 E2 353-438.pdb #280 
    13284 --- 
    13285 Chain | Description 
    13286 B | No description available 
    13287  
    13288 
    13289 > matchmaker #280 to #1.56 & sel
    13290 
    13291 Parameters 
    13292 --- 
    13293 Chain pairing | bb 
    13294 Alignment algorithm | Needleman-Wunsch 
    13295 Similarity matrix | BLOSUM-62 
    13296 SS fraction | 0.3 
    13297 Gap open (HH/SS/other) | 18/18/6 
    13298 Gap extend | 1 
    13299 SS matrix |  |  | H | S | O 
    13300 ---|---|---|--- 
    13301 H | 6 | -9 | -6 
    13302 S |  | 6 | -6 
    13303 O |  |  | 4 
    13304 Iteration cutoff | 2 
    13305  
    13306 Matchmaker 3j0c.pdb1, chain B (#1.56) with AF3 E2 353-438.pdb, chain B (#280),
    13307 sequence alignment score = 333.4 
    13308 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    13309 8.411) 
    13310  
    13311 
    13312 > hide sel cartoons
    13313 
    13314 > select #1.56/C
    13315 
    13316 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    13317 
    13318 > show sel cartoons
    13319 
    13320 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    13321 
    13322 Chain information for AF3 CA.pdb #281 
    13323 --- 
    13324 Chain | Description 
    13325 A | No description available 
    13326  
    13327 
    13328 > matchmaker #281 to #1.56 & sel
    13329 
    13330 Parameters 
    13331 --- 
    13332 Chain pairing | bb 
    13333 Alignment algorithm | Needleman-Wunsch 
    13334 Similarity matrix | BLOSUM-62 
    13335 SS fraction | 0.3 
    13336 Gap open (HH/SS/other) | 18/18/6 
    13337 Gap extend | 1 
    13338 SS matrix |  |  | H | S | O 
    13339 ---|---|---|--- 
    13340 H | 6 | -9 | -6 
    13341 S |  | 6 | -6 
    13342 O |  |  | 4 
    13343 Iteration cutoff | 2 
    13344  
    13345 Matchmaker 3j0c.pdb1, chain C (#1.56) with AF3 CA.pdb, chain A (#281),
    13346 sequence alignment score = 328.1 
    13347 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    13348 2.714) 
    13349  
    13350 
    13351 > hide sel cartoons
    13352 
    13353 > color #277 dodgerblue
    13354 
    13355 > color #278 dodgerblue
    13356 
    13357 > color #279 #00b305ff
    13358 
    13359 > color #280 #00b305ff
    13360 
    13361 > color #281 #f15839ff
    13362 
    13363 > select #1.57/A
    13364 
    13365 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    13366 
    13367 > show sel cartoons
    13368 
    13369 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    13370 
    13371 Chain information for AF3 E1 1-421.pdb #282 
    13372 --- 
    13373 Chain | Description 
    13374 A | No description available 
    13375  
    13376 
    13377 > matchmaker #282 to #1.56 & sel
    13378 
    13379 No 'to' model specified 
    13380 
    13381 > matchmaker #282 to #1.57 & sel
    13382 
    13383 Parameters 
    13384 --- 
    13385 Chain pairing | bb 
    13386 Alignment algorithm | Needleman-Wunsch 
    13387 Similarity matrix | BLOSUM-62 
    13388 SS fraction | 0.3 
    13389 Gap open (HH/SS/other) | 18/18/6 
    13390 Gap extend | 1 
    13391 SS matrix |  |  | H | S | O 
    13392 ---|---|---|--- 
    13393 H | 6 | -9 | -6 
    13394 S |  | 6 | -6 
    13395 O |  |  | 4 
    13396 Iteration cutoff | 2 
    13397  
    13398 Matchmaker 3j0c.pdb1, chain A (#1.57) with AF3 E1 1-421.pdb, chain A (#282),
    13399 sequence alignment score = 1060.7 
    13400 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    13401 3.020) 
    13402  
    13403 
    13404 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    13405 
    13406 Chain information for AF3 E1 422-461.pdb #283 
    13407 --- 
    13408 Chain | Description 
    13409 A | No description available 
    13410  
    13411 
    13412 > matchmaker #283 to #1.57 & sel
    13413 
    13414 Parameters 
    13415 --- 
    13416 Chain pairing | bb 
    13417 Alignment algorithm | Needleman-Wunsch 
    13418 Similarity matrix | BLOSUM-62 
    13419 SS fraction | 0.3 
    13420 Gap open (HH/SS/other) | 18/18/6 
    13421 Gap extend | 1 
    13422 SS matrix |  |  | H | S | O 
    13423 ---|---|---|--- 
    13424 H | 6 | -9 | -6 
    13425 S |  | 6 | -6 
    13426 O |  |  | 4 
    13427 Iteration cutoff | 2 
    13428  
    13429 Matchmaker 3j0c.pdb1, chain A (#1.57) with AF3 E1 422-461.pdb, chain A (#283),
    13430 sequence alignment score = 626.9 
    13431 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    13432 2.776) 
    13433  
    13434 
    13435 > hide sel cartoons
    13436 
    13437 > select #1.57/B
    13438 
    13439 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    13440 
    13441 > show sel cartoons
    13442 
    13443 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    13444 
    13445 Chain information for AF3 E2 1-352.pdb #284 
    13446 --- 
    13447 Chain | Description 
    13448 B | No description available 
    13449  
    13450 
    13451 > matchmaker #284 to #1.57 & sel
    13452 
    13453 Parameters 
    13454 --- 
    13455 Chain pairing | bb 
    13456 Alignment algorithm | Needleman-Wunsch 
    13457 Similarity matrix | BLOSUM-62 
    13458 SS fraction | 0.3 
    13459 Gap open (HH/SS/other) | 18/18/6 
    13460 Gap extend | 1 
    13461 SS matrix |  |  | H | S | O 
    13462 ---|---|---|--- 
    13463 H | 6 | -9 | -6 
    13464 S |  | 6 | -6 
    13465 O |  |  | 4 
    13466 Iteration cutoff | 2 
    13467  
    13468 Matchmaker 3j0c.pdb1, chain B (#1.57) with AF3 E2 1-352.pdb, chain B (#284),
    13469 sequence alignment score = 583.7 
    13470 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    13471 5.933) 
    13472  
    13473 
    13474 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    13475 
    13476 Chain information for AF3 E2 353-438.pdb #285 
    13477 --- 
    13478 Chain | Description 
    13479 B | No description available 
    13480  
    13481 
    13482 > matchmaker #285 to #1.57 & sel
    13483 
    13484 Parameters 
    13485 --- 
    13486 Chain pairing | bb 
    13487 Alignment algorithm | Needleman-Wunsch 
    13488 Similarity matrix | BLOSUM-62 
    13489 SS fraction | 0.3 
    13490 Gap open (HH/SS/other) | 18/18/6 
    13491 Gap extend | 1 
    13492 SS matrix |  |  | H | S | O 
    13493 ---|---|---|--- 
    13494 H | 6 | -9 | -6 
    13495 S |  | 6 | -6 
    13496 O |  |  | 4 
    13497 Iteration cutoff | 2 
    13498  
    13499 Matchmaker 3j0c.pdb1, chain B (#1.57) with AF3 E2 353-438.pdb, chain B (#285),
    13500 sequence alignment score = 333.4 
    13501 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    13502 8.411) 
    13503  
    13504 
    13505 > hide sel cartoons
    13506 
    13507 [Repeated 1 time(s)]
    13508 
    13509 > select #1.57/C
    13510 
    13511 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    13512 
    13513 > show sel cartoons
    13514 
    13515 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    13516 
    13517 Chain information for AF3 CA.pdb #286 
    13518 --- 
    13519 Chain | Description 
    13520 A | No description available 
    13521  
    13522 
    13523 > matchmaker #286 to #1.57 & sel
    13524 
    13525 Parameters 
    13526 --- 
    13527 Chain pairing | bb 
    13528 Alignment algorithm | Needleman-Wunsch 
    13529 Similarity matrix | BLOSUM-62 
    13530 SS fraction | 0.3 
    13531 Gap open (HH/SS/other) | 18/18/6 
    13532 Gap extend | 1 
    13533 SS matrix |  |  | H | S | O 
    13534 ---|---|---|--- 
    13535 H | 6 | -9 | -6 
    13536 S |  | 6 | -6 
    13537 O |  |  | 4 
    13538 Iteration cutoff | 2 
    13539  
    13540 Matchmaker 3j0c.pdb1, chain C (#1.57) with AF3 CA.pdb, chain A (#286),
    13541 sequence alignment score = 328.1 
    13542 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    13543 2.714) 
    13544  
    13545 
    13546 > hide sel cartoons
    13547 
    13548 > color #282 dodgerblue
    13549 
    13550 > color #283 dodgerblue
    13551 
    13552 > color #284 #00b305ff
    13553 
    13554 > color #285 #00b305ff
    13555 
    13556 > color #286 #f15839ff
    13557 
    13558 > select #1.58/A
    13559 
    13560 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    13561 
    13562 > show sel cartoons
    13563 
    13564 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    13565 
    13566 Chain information for AF3 E1 1-421.pdb #287 
    13567 --- 
    13568 Chain | Description 
    13569 A | No description available 
    13570  
    13571 
    13572 > matchmaker #287 to #1.58 & sel
    13573 
    13574 Parameters 
    13575 --- 
    13576 Chain pairing | bb 
    13577 Alignment algorithm | Needleman-Wunsch 
    13578 Similarity matrix | BLOSUM-62 
    13579 SS fraction | 0.3 
    13580 Gap open (HH/SS/other) | 18/18/6 
    13581 Gap extend | 1 
    13582 SS matrix |  |  | H | S | O 
    13583 ---|---|---|--- 
    13584 H | 6 | -9 | -6 
    13585 S |  | 6 | -6 
    13586 O |  |  | 4 
    13587 Iteration cutoff | 2 
    13588  
    13589 Matchmaker 3j0c.pdb1, chain A (#1.58) with AF3 E1 1-421.pdb, chain A (#287),
    13590 sequence alignment score = 1060.7 
    13591 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    13592 3.020) 
    13593  
    13594 
    13595 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    13596 
    13597 Chain information for AF3 E1 422-461.pdb #288 
    13598 --- 
    13599 Chain | Description 
    13600 A | No description available 
    13601  
    13602 
    13603 > matchmaker #288 to #1.58 & sel
    13604 
    13605 Parameters 
    13606 --- 
    13607 Chain pairing | bb 
    13608 Alignment algorithm | Needleman-Wunsch 
    13609 Similarity matrix | BLOSUM-62 
    13610 SS fraction | 0.3 
    13611 Gap open (HH/SS/other) | 18/18/6 
    13612 Gap extend | 1 
    13613 SS matrix |  |  | H | S | O 
    13614 ---|---|---|--- 
    13615 H | 6 | -9 | -6 
    13616 S |  | 6 | -6 
    13617 O |  |  | 4 
    13618 Iteration cutoff | 2 
    13619  
    13620 Matchmaker 3j0c.pdb1, chain A (#1.58) with AF3 E1 422-461.pdb, chain A (#288),
    13621 sequence alignment score = 626.9 
    13622 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    13623 2.775) 
    13624  
    13625 
    13626 > hide sel cartoons
    13627 
    13628 > select #1.58/B
    13629 
    13630 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    13631 
    13632 > show sel cartoons
    13633 
    13634 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    13635 
    13636 Chain information for AF3 E2 1-352.pdb #289 
    13637 --- 
    13638 Chain | Description 
    13639 B | No description available 
    13640  
    13641 
    13642 > matchmaker #289 to #1.58 & sel
    13643 
    13644 Parameters 
    13645 --- 
    13646 Chain pairing | bb 
    13647 Alignment algorithm | Needleman-Wunsch 
    13648 Similarity matrix | BLOSUM-62 
    13649 SS fraction | 0.3 
    13650 Gap open (HH/SS/other) | 18/18/6 
    13651 Gap extend | 1 
    13652 SS matrix |  |  | H | S | O 
    13653 ---|---|---|--- 
    13654 H | 6 | -9 | -6 
    13655 S |  | 6 | -6 
    13656 O |  |  | 4 
    13657 Iteration cutoff | 2 
    13658  
    13659 Matchmaker 3j0c.pdb1, chain B (#1.58) with AF3 E2 1-352.pdb, chain B (#289),
    13660 sequence alignment score = 583.7 
    13661 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    13662 5.933) 
    13663  
    13664 
    13665 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    13666 
    13667 Chain information for AF3 E2 353-438.pdb #290 
    13668 --- 
    13669 Chain | Description 
    13670 B | No description available 
    13671  
    13672 
    13673 > matchmaker #290 to #1.58 & sel
    13674 
    13675 Parameters 
    13676 --- 
    13677 Chain pairing | bb 
    13678 Alignment algorithm | Needleman-Wunsch 
    13679 Similarity matrix | BLOSUM-62 
    13680 SS fraction | 0.3 
    13681 Gap open (HH/SS/other) | 18/18/6 
    13682 Gap extend | 1 
    13683 SS matrix |  |  | H | S | O 
    13684 ---|---|---|--- 
    13685 H | 6 | -9 | -6 
    13686 S |  | 6 | -6 
    13687 O |  |  | 4 
    13688 Iteration cutoff | 2 
    13689  
    13690 Matchmaker 3j0c.pdb1, chain B (#1.58) with AF3 E2 353-438.pdb, chain B (#290),
    13691 sequence alignment score = 322.6 
    13692 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    13693 8.411) 
    13694  
    13695 
    13696 > hide sel cartoons
    13697 
    13698 > select #1.58/C
    13699 
    13700 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    13701 
    13702 > show sel cartoons
    13703 
    13704 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    13705 
    13706 Chain information for AF3 CA.pdb #291 
    13707 --- 
    13708 Chain | Description 
    13709 A | No description available 
    13710  
    13711 
    13712 > matchmaker #291 to #1.58 & sel
    13713 
    13714 Parameters 
    13715 --- 
    13716 Chain pairing | bb 
    13717 Alignment algorithm | Needleman-Wunsch 
    13718 Similarity matrix | BLOSUM-62 
    13719 SS fraction | 0.3 
    13720 Gap open (HH/SS/other) | 18/18/6 
    13721 Gap extend | 1 
    13722 SS matrix |  |  | H | S | O 
    13723 ---|---|---|--- 
    13724 H | 6 | -9 | -6 
    13725 S |  | 6 | -6 
    13726 O |  |  | 4 
    13727 Iteration cutoff | 2 
    13728  
    13729 Matchmaker 3j0c.pdb1, chain C (#1.58) with AF3 CA.pdb, chain A (#291),
    13730 sequence alignment score = 328.1 
    13731 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    13732 2.714) 
    13733  
    13734 
    13735 > hide sel cartoons
    13736 
    13737 > color #287 dodgerblue
    13738 
    13739 > color #288 dodgerblue
    13740 
    13741 > color #289 #00b305ff
    13742 
    13743 > color #290 #00b305ff
    13744 
    13745 > color #291 #f15839ff
    13746 
    13747 > select #1.59/A
    13748 
    13749 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    13750 
    13751 > show sel cartoons
    13752 
    13753 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    13754 
    13755 Chain information for AF3 E1 1-421.pdb #292 
    13756 --- 
    13757 Chain | Description 
    13758 A | No description available 
    13759  
    13760 
    13761 > matchmaker #291 to #1.59 & sel
    13762 
    13763 Parameters 
    13764 --- 
    13765 Chain pairing | bb 
    13766 Alignment algorithm | Needleman-Wunsch 
    13767 Similarity matrix | BLOSUM-62 
    13768 SS fraction | 0.3 
    13769 Gap open (HH/SS/other) | 18/18/6 
    13770 Gap extend | 1 
    13771 SS matrix |  |  | H | S | O 
    13772 ---|---|---|--- 
    13773 H | 6 | -9 | -6 
    13774 S |  | 6 | -6 
    13775 O |  |  | 4 
    13776 Iteration cutoff | 2 
    13777  
    13778 Matchmaker 3j0c.pdb1, chain A (#1.59) with AF3 CA.pdb, chain A (#291),
    13779 sequence alignment score = 32.6 
    13780 RMSD between 11 pruned atom pairs is 1.204 angstroms; (across all 110 pairs:
    13781 22.675) 
    13782  
    13783 
    13784 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    13785 
    13786 Chain information for AF3 E1 422-461.pdb #293 
    13787 --- 
    13788 Chain | Description 
    13789 A | No description available 
    13790  
    13791 
    13792 > matchmaker #291 to #1.58 & sel
    13793 
    13794 No 'to' model specified 
    13795 
    13796 > select #1.58/C
    13797 
    13798 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    13799 
    13800 > show sel cartoons
    13801 
    13802 > matchmaker #291 to #1.58 & sel
    13803 
    13804 Parameters 
    13805 --- 
    13806 Chain pairing | bb 
    13807 Alignment algorithm | Needleman-Wunsch 
    13808 Similarity matrix | BLOSUM-62 
    13809 SS fraction | 0.3 
    13810 Gap open (HH/SS/other) | 18/18/6 
    13811 Gap extend | 1 
    13812 SS matrix |  |  | H | S | O 
    13813 ---|---|---|--- 
    13814 H | 6 | -9 | -6 
    13815 S |  | 6 | -6 
    13816 O |  |  | 4 
    13817 Iteration cutoff | 2 
    13818  
    13819 Matchmaker 3j0c.pdb1, chain C (#1.58) with AF3 CA.pdb, chain A (#291),
    13820 sequence alignment score = 328.1 
    13821 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    13822 2.714) 
    13823  
    13824 
    13825 > hide sel cartoons
    13826 
    13827 > select #1.59/A
    13828 
    13829 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    13830 
    13831 > matchmaker #292 to #1.59 & sel
    13832 
    13833 Parameters 
    13834 --- 
    13835 Chain pairing | bb 
    13836 Alignment algorithm | Needleman-Wunsch 
    13837 Similarity matrix | BLOSUM-62 
    13838 SS fraction | 0.3 
    13839 Gap open (HH/SS/other) | 18/18/6 
    13840 Gap extend | 1 
    13841 SS matrix |  |  | H | S | O 
    13842 ---|---|---|--- 
    13843 H | 6 | -9 | -6 
    13844 S |  | 6 | -6 
    13845 O |  |  | 4 
    13846 Iteration cutoff | 2 
    13847  
    13848 Matchmaker 3j0c.pdb1, chain A (#1.59) with AF3 E1 1-421.pdb, chain A (#292),
    13849 sequence alignment score = 1060.7 
    13850 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    13851 3.020) 
    13852  
    13853 
    13854 > matchmaker #293 to #1.59 & sel
    13855 
    13856 Parameters 
    13857 --- 
    13858 Chain pairing | bb 
    13859 Alignment algorithm | Needleman-Wunsch 
    13860 Similarity matrix | BLOSUM-62 
    13861 SS fraction | 0.3 
    13862 Gap open (HH/SS/other) | 18/18/6 
    13863 Gap extend | 1 
    13864 SS matrix |  |  | H | S | O 
    13865 ---|---|---|--- 
    13866 H | 6 | -9 | -6 
    13867 S |  | 6 | -6 
    13868 O |  |  | 4 
    13869 Iteration cutoff | 2 
    13870  
    13871 Matchmaker 3j0c.pdb1, chain A (#1.59) with AF3 E1 422-461.pdb, chain A (#293),
    13872 sequence alignment score = 626.9 
    13873 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    13874 2.776) 
    13875  
    13876 
    13877 > select #1.39/B
    13878 
    13879 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    13880 
    13881 > select #1.59/A
    13882 
    13883 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    13884 
    13885 > hide sel cartoons
    13886 
    13887 > select #1.59/B
    13888 
    13889 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    13890 
    13891 > show sel cartoons
    13892 
    13893 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    13894 
    13895 Chain information for AF3 E2 1-352.pdb #294 
    13896 --- 
    13897 Chain | Description 
    13898 B | No description available 
    13899  
    13900 
    13901 > matchmaker #294 to #1.59 & sel
    13902 
    13903 Parameters 
    13904 --- 
    13905 Chain pairing | bb 
    13906 Alignment algorithm | Needleman-Wunsch 
    13907 Similarity matrix | BLOSUM-62 
    13908 SS fraction | 0.3 
    13909 Gap open (HH/SS/other) | 18/18/6 
    13910 Gap extend | 1 
    13911 SS matrix |  |  | H | S | O 
    13912 ---|---|---|--- 
    13913 H | 6 | -9 | -6 
    13914 S |  | 6 | -6 
    13915 O |  |  | 4 
    13916 Iteration cutoff | 2 
    13917  
    13918 Matchmaker 3j0c.pdb1, chain B (#1.59) with AF3 E2 1-352.pdb, chain B (#294),
    13919 sequence alignment score = 583.7 
    13920 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    13921 5.933) 
    13922  
    13923 
    13924 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    13925 
    13926 Chain information for AF3 E2 353-438.pdb #295 
    13927 --- 
    13928 Chain | Description 
    13929 B | No description available 
    13930  
    13931 
    13932 > matchmaker #295 to #1.59 & sel
    13933 
    13934 Parameters 
    13935 --- 
    13936 Chain pairing | bb 
    13937 Alignment algorithm | Needleman-Wunsch 
    13938 Similarity matrix | BLOSUM-62 
    13939 SS fraction | 0.3 
    13940 Gap open (HH/SS/other) | 18/18/6 
    13941 Gap extend | 1 
    13942 SS matrix |  |  | H | S | O 
    13943 ---|---|---|--- 
    13944 H | 6 | -9 | -6 
    13945 S |  | 6 | -6 
    13946 O |  |  | 4 
    13947 Iteration cutoff | 2 
    13948  
    13949 Matchmaker 3j0c.pdb1, chain B (#1.59) with AF3 E2 353-438.pdb, chain B (#295),
    13950 sequence alignment score = 322.6 
    13951 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    13952 8.411) 
    13953  
    13954 
    13955 > hide sel cartoons
    13956 
    13957 > select #1.59/C
    13958 
    13959 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    13960 
    13961 > show sel cartoons
    13962 
    13963 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    13964 
    13965 Chain information for AF3 CA.pdb #296 
    13966 --- 
    13967 Chain | Description 
    13968 A | No description available 
    13969  
    13970 
    13971 > matchmaker #296 to #1.59 & sel
    13972 
    13973 Parameters 
    13974 --- 
    13975 Chain pairing | bb 
    13976 Alignment algorithm | Needleman-Wunsch 
    13977 Similarity matrix | BLOSUM-62 
    13978 SS fraction | 0.3 
    13979 Gap open (HH/SS/other) | 18/18/6 
    13980 Gap extend | 1 
    13981 SS matrix |  |  | H | S | O 
    13982 ---|---|---|--- 
    13983 H | 6 | -9 | -6 
    13984 S |  | 6 | -6 
    13985 O |  |  | 4 
    13986 Iteration cutoff | 2 
    13987  
    13988 Matchmaker 3j0c.pdb1, chain C (#1.59) with AF3 CA.pdb, chain A (#296),
    13989 sequence alignment score = 328.1 
    13990 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    13991 2.714) 
    13992  
    13993 
    13994 > hide sel cartoons
    13995 
    13996 > color #292 dodgerblue
    13997 
    13998 > color #293 dodgerblue
    13999 
    14000 > color #294 #00b305ff
    14001 
    14002 > color #295 #00b305ff
    14003 
    14004 > color #296 #f15839ff
    14005 
    14006 > select #1.60/A
    14007 
    14008 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    14009 
    14010 > show sel cartoons
    14011 
    14012 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    14013 
    14014 Chain information for AF3 E1 1-421.pdb #297 
    14015 --- 
    14016 Chain | Description 
    14017 A | No description available 
    14018  
    14019 
    14020 > matchmaker #297 to #1.60 & sel
    14021 
    14022 Parameters 
    14023 --- 
    14024 Chain pairing | bb 
    14025 Alignment algorithm | Needleman-Wunsch 
    14026 Similarity matrix | BLOSUM-62 
    14027 SS fraction | 0.3 
    14028 Gap open (HH/SS/other) | 18/18/6 
    14029 Gap extend | 1 
    14030 SS matrix |  |  | H | S | O 
    14031 ---|---|---|--- 
    14032 H | 6 | -9 | -6 
    14033 S |  | 6 | -6 
    14034 O |  |  | 4 
    14035 Iteration cutoff | 2 
    14036  
    14037 Matchmaker 3j0c.pdb1, chain A (#1.60) with AF3 E1 1-421.pdb, chain A (#297),
    14038 sequence alignment score = 1060.7 
    14039 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    14040 3.020) 
    14041  
    14042 
    14043 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    14044 
    14045 Chain information for AF3 E1 422-461.pdb #298 
    14046 --- 
    14047 Chain | Description 
    14048 A | No description available 
    14049  
    14050 
    14051 > matchmaker #298 to #1.60 & sel
    14052 
    14053 Parameters 
    14054 --- 
    14055 Chain pairing | bb 
    14056 Alignment algorithm | Needleman-Wunsch 
    14057 Similarity matrix | BLOSUM-62 
    14058 SS fraction | 0.3 
    14059 Gap open (HH/SS/other) | 18/18/6 
    14060 Gap extend | 1 
    14061 SS matrix |  |  | H | S | O 
    14062 ---|---|---|--- 
    14063 H | 6 | -9 | -6 
    14064 S |  | 6 | -6 
    14065 O |  |  | 4 
    14066 Iteration cutoff | 2 
    14067  
    14068 Matchmaker 3j0c.pdb1, chain A (#1.60) with AF3 E1 422-461.pdb, chain A (#298),
    14069 sequence alignment score = 626.9 
    14070 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    14071 2.776) 
    14072  
    14073 
    14074 > hide sel cartoons
    14075 
    14076 > select #1.60/B
    14077 
    14078 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    14079 
    14080 > show sel cartoons
    14081 
    14082 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    14083 
    14084 Chain information for AF3 E2 1-352.pdb #299 
    14085 --- 
    14086 Chain | Description 
    14087 B | No description available 
    14088  
    14089 
    14090 > matchmaker #299 to #1.60 & sel
    14091 
    14092 Parameters 
    14093 --- 
    14094 Chain pairing | bb 
    14095 Alignment algorithm | Needleman-Wunsch 
    14096 Similarity matrix | BLOSUM-62 
    14097 SS fraction | 0.3 
    14098 Gap open (HH/SS/other) | 18/18/6 
    14099 Gap extend | 1 
    14100 SS matrix |  |  | H | S | O 
    14101 ---|---|---|--- 
    14102 H | 6 | -9 | -6 
    14103 S |  | 6 | -6 
    14104 O |  |  | 4 
    14105 Iteration cutoff | 2 
    14106  
    14107 Matchmaker 3j0c.pdb1, chain B (#1.60) with AF3 E2 1-352.pdb, chain B (#299),
    14108 sequence alignment score = 583.7 
    14109 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    14110 5.933) 
    14111  
    14112 
    14113 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    14114 
    14115 Chain information for AF3 E2 353-438.pdb #300 
    14116 --- 
    14117 Chain | Description 
    14118 B | No description available 
    14119  
    14120 
    14121 > matchmaker #300 to #1.60 & sel
    14122 
    14123 Parameters 
    14124 --- 
    14125 Chain pairing | bb 
    14126 Alignment algorithm | Needleman-Wunsch 
    14127 Similarity matrix | BLOSUM-62 
    14128 SS fraction | 0.3 
    14129 Gap open (HH/SS/other) | 18/18/6 
    14130 Gap extend | 1 
    14131 SS matrix |  |  | H | S | O 
    14132 ---|---|---|--- 
    14133 H | 6 | -9 | -6 
    14134 S |  | 6 | -6 
    14135 O |  |  | 4 
    14136 Iteration cutoff | 2 
    14137  
    14138 Matchmaker 3j0c.pdb1, chain B (#1.60) with AF3 E2 353-438.pdb, chain B (#300),
    14139 sequence alignment score = 333.4 
    14140 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    14141 8.411) 
    14142  
    14143 
    14144 > hide sel cartoons
    14145 
    14146 > select #1.60/C
    14147 
    14148 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    14149 
    14150 > show sel cartoons
    14151 
    14152 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    14153 
    14154 Chain information for AF3 CA.pdb #301 
    14155 --- 
    14156 Chain | Description 
    14157 A | No description available 
    14158  
    14159 
    14160 > matchmaker #301 to #1.60 & sel
    14161 
    14162 Parameters 
    14163 --- 
    14164 Chain pairing | bb 
    14165 Alignment algorithm | Needleman-Wunsch 
    14166 Similarity matrix | BLOSUM-62 
    14167 SS fraction | 0.3 
    14168 Gap open (HH/SS/other) | 18/18/6 
    14169 Gap extend | 1 
    14170 SS matrix |  |  | H | S | O 
    14171 ---|---|---|--- 
    14172 H | 6 | -9 | -6 
    14173 S |  | 6 | -6 
    14174 O |  |  | 4 
    14175 Iteration cutoff | 2 
    14176  
    14177 Matchmaker 3j0c.pdb1, chain C (#1.60) with AF3 CA.pdb, chain A (#301),
    14178 sequence alignment score = 328.1 
    14179 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    14180 2.714) 
    14181  
    14182 
    14183 > hide sel cartoons
    14184 
    14185 > color #297 dodgerblue
    14186 
    14187 > color #298 dodgerblue
    14188 
    14189 > color #299 #00b305ff
    14190 
    14191 > color #300 #00b305ff
    14192 
    14193 > color #301 #f15839ff
    14194 
    14195 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    14196 
    14197 ——— End of log from Mon Jul 15 16:48:15 2024 ———
    14198 
    14199 opened ChimeraX session 
    14200 
    14201 > show #2 models
    14202 
    14203 > show #3 models
    14204 
    14205 > show #4 models
    14206 
    14207 > show #5 models
    14208 
    14209 > show #6 models
    14210 
    14211 The cached device pixel ratio value was stale on window expose. Please file a
    14212 QTBUG which explains how to reproduce. 
    14213 
    14214 [Repeated 1 time(s)]
    14215 
    14216 > hide #2-6,262-301#1.2-60 target m
    14217 
    14218 > show #1.2 target m
    14219 
    14220 > hide #1.1 target m
    14221 
    14222 > hide #!1 models
    14223 
    14224 > show #2 models
    14225 
    14226 > show #3 models
    14227 
    14228 > show #4 models
    14229 
    14230 The cached device pixel ratio value was stale on window expose. Please file a
    14231 QTBUG which explains how to reproduce. 
    14232 
    14233 > show #5 models
    14234 
    14235 > show #6 models
    14236 
    14237 > show #7 models
    14238 
    14239 > show #8 models
    14240 
    14241 > show #9 models
    14242 
    14243 > show #10 models
    14244 
    14245 > show #11 models
    14246 
    14247 > show #12 models
    14248 
    14249 > show #13 models
    14250 
    14251 > show #14 models
    14252 
    14253 > show #15 models
    14254 
    14255 > show #16 models
    14256 
    14257 > show #17 models
    14258 
    14259 > show #18 models
    14260 
    14261 > show #19 models
    14262 
    14263 > show #20 models
    14264 
    14265 > show #21 models
    14266 
    14267 > show #22 models
    14268 
    14269 > show #23 models
    14270 
    14271 > show #24 models
    14272 
    14273 > show #25 models
    14274 
    14275 > show #26 models
    14276 
    14277 > show #27 models
    14278 
    14279 > show #28 models
    14280 
    14281 > show #29 models
    14282 
    14283 > show #30 models
    14284 
    14285 > show #31 models
    14286 
    14287 > show #32 models
    14288 
    14289 > show #33 models
    14290 
    14291 > show #34 models
    14292 
    14293 > show #35 models
    14294 
    14295 > show #36 models
    14296 
    14297 > show #37 models
    14298 
    14299 > show #38 models
    14300 
    14301 > show #39 models
    14302 
    14303 > show #40 models
    14304 
    14305 > show #41 models
    14306 
    14307 > show #42 models
    14308 
    14309 > show #43 models
    14310 
    14311 > show #44 models
    14312 
    14313 > show #45 models
    14314 
    14315 > show #46 models
    14316 
    14317 > show #47 models
    14318 
    14319 > show #48 models
    14320 
    14321 > show #49 models
    14322 
    14323 > show #50 models
    14324 
    14325 > show #51 models
    14326 
    14327 > show #52 models
    14328 
    14329 > show #53 models
    14330 
    14331 > show #54 models
    14332 
    14333 > show #55 models
    14334 
    14335 > show #56 models
    14336 
    14337 > show #57 models
    14338 
    14339 > show #58 models
    14340 
    14341 > show #59 models
    14342 
    14343 > show #60 models
    14344 
    14345 > show #61 models
    14346 
    14347 > show #62 models
    14348 
    14349 > show #63 models
    14350 
    14351 > show #64 models
    14352 
    14353 > show #65 models
    14354 
    14355 > show #66 models
    14356 
    14357 > show #67 models
    14358 
    14359 > show #68 models
    14360 
    14361 > show #69 models
    14362 
    14363 > show #70 models
    14364 
    14365 > show #71 models
    14366 
    14367 > show #72 models
    14368 
    14369 > show #73 models
    14370 
    14371 > show #74 models
    14372 
    14373 > show #75 models
    14374 
    14375 > show #76 models
    14376 
    14377 > show #77 models
    14378 
    14379 > show #78 models
    14380 
    14381 > show #79 models
    14382 
    14383 > show #80 models
    14384 
    14385 > show #81 models
    14386 
    14387 > show #82 models
    14388 
    14389 The cached device pixel ratio value was stale on window expose. Please file a
    14390 QTBUG which explains how to reproduce. 
    14391 
    14392 > show #82-301 models
    14393 
    14394 > hide #2-301 models
    14395 
    14396 > show #2-301 models
    14397 
    14398 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    14399 
    14400 ——— End of log from Mon Jul 15 16:59:09 2024 ———
    14401 
    14402 opened ChimeraX session 
    14403 
    14404 The cached device pixel ratio value was stale on window expose. Please file a
    14405 QTBUG which explains how to reproduce. 
    14406 
    14407 > select #1.1/D
    14408 
    14409 3370 atoms, 3467 bonds, 442 residues, 1 model selected 
    14410 
    14411 > show #2-301 cartoons
    14412 
    14413 > view sel
    14414 
    14415 No displayed objects specified. 
    14416 
    14417 > select add #1
    14418 
    14419 1908240 atoms, 1958684 bonds, 246480 residues, 61 models selected 
    14420 
    14421 > hide #1.2 models
    14422 
    14423 > show #1.1 models
    14424 
    14425 > hide #1.1 models
    14426 
    14427 > show #1.1 models
    14428 
    14429 > show sel & #1.1 cartoons
    14430 
    14431 > hide #1.1 models
    14432 
    14433 > hide #!1 models
    14434 
    14435 > show #1.1 models
    14436 
    14437 The cached device pixel ratio value was stale on window expose. Please file a
    14438 QTBUG which explains how to reproduce. 
    14439 
    14440 > select subtract #1
    14441 
    14442 Nothing selected 
    14443 
    14444 > hide #!1 models
    14445 
    14446 > hide #1.1 models
    14447 
    14448 > show #1.1 models
    14449 
    14450 > show #1.2 models
    14451 
    14452 > show #1.3 models
    14453 
    14454 > show #1.4 models
    14455 
    14456 > select
    14457 
    14458 2389680 atoms, 2451464 bonds, 310140 residues, 361 models selected 
    14459 
    14460 > show sel & #2-301#1.1-4 cartoons
    14461 
    14462 > hide #!1 models
    14463 
    14464 > show #!1 models
    14465 
    14466 > show #1.5 models
    14467 
    14468 > show #1.6 models
    14469 
    14470 > show #1.7 models
    14471 
    14472 > hide #1.7 models
    14473 
    14474 > show #1.7 models
    14475 
    14476 > show #1.8 models
    14477 
    14478 > ui tool show "Selection Inspector"
    14479 
    14480 The cached device pixel ratio value was stale on window expose. Please file a
    14481 QTBUG which explains how to reproduce. 
    14482 
    14483 [Repeated 1 time(s)]
    14484 
    14485 > setattr sel struct display true
    14486 
    14487 Assigning display attribute to 360 items 
    14488 
    14489 > select #1.1/A
    14490 
    14491 3370 atoms, 3467 bonds, 442 residues, 1 model selected 
    14492 
    14493 > select ~sel & ##selected
    14494 
    14495 28434 atoms, 29221 bonds, 3666 residues, 1 model selected 
    14496 
    14497 > hide sel cartoons
    14498 
    14499 > select
    14500 
    14501 2389680 atoms, 2451464 bonds, 310140 residues, 361 models selected 
    14502 
    14503 > hide sel cartoons
    14504 
    14505 > select #1.1/A
    14506 
    14507 3370 atoms, 3467 bonds, 442 residues, 1 model selected 
    14508 
    14509 > show sel cartoons
    14510 
    14511 > hide sel cartoons
    14512 
    14513 > select #1.1/D
    14514 
    14515 3370 atoms, 3467 bonds, 442 residues, 1 model selected 
    14516 
    14517 > show sel cartoons
    14518 
    14519 > ui tool show Matchmaker
    14520 
    14521 The cached device pixel ratio value was stale on window expose. Please file a
    14522 QTBUG which explains how to reproduce. 
    14523 
    14524 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    14525 
    14526 Chain information for AF3 E1 1-421.pdb #302 
    14527 --- 
    14528 Chain | Description 
    14529 A | No description available 
    14530  
    14531 
    14532 > matchmaker #301 to #1.1 & sel
    14533 
    14534 Parameters 
    14535 --- 
    14536 Chain pairing | bb 
    14537 Alignment algorithm | Needleman-Wunsch 
    14538 Similarity matrix | BLOSUM-62 
    14539 SS fraction | 0.3 
    14540 Gap open (HH/SS/other) | 18/18/6 
    14541 Gap extend | 1 
    14542 SS matrix |  |  | H | S | O 
    14543 ---|---|---|--- 
    14544 H | 6 | -9 | -6 
    14545 S |  | 6 | -6 
    14546 O |  |  | 4 
    14547 Iteration cutoff | 2 
    14548  
    14549 Matchmaker 3j0c.pdb1, chain D (#1.1) with AF3 CA.pdb, chain A (#301), sequence
    14550 alignment score = 32.6 
    14551 RMSD between 11 pruned atom pairs is 1.228 angstroms; (across all 110 pairs:
    14552 22.710) 
    14553  
    14554 
    14555 > select #1.60/C
    14556 
    14557 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    14558 
    14559 > show sel cartoons
    14560 
    14561 > hide #301 models
    14562 
    14563 > show #301 models
    14564 
    14565 > select add #301
    14566 
    14567 2536 atoms, 2591 bonds, 324 residues, 2 models selected 
    14568 
    14569 > hide #301 models
    14570 
    14571 > show #301 models
    14572 
    14573 > color #301 #f15839ff
    14574 
    14575 > show sel cartoons
    14576 
    14577 > select subtract #301
    14578 
    14579 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    14580 
    14581 > matchmaker #301 to #1.60 & sel
    14582 
    14583 Parameters 
    14584 --- 
    14585 Chain pairing | bb 
    14586 Alignment algorithm | Needleman-Wunsch 
    14587 Similarity matrix | BLOSUM-62 
    14588 SS fraction | 0.3 
    14589 Gap open (HH/SS/other) | 18/18/6 
    14590 Gap extend | 1 
    14591 SS matrix |  |  | H | S | O 
    14592 ---|---|---|--- 
    14593 H | 6 | -9 | -6 
    14594 S |  | 6 | -6 
    14595 O |  |  | 4 
    14596 Iteration cutoff | 2 
    14597  
    14598 Matchmaker 3j0c.pdb1, chain C (#1.60) with AF3 CA.pdb, chain A (#301),
    14599 sequence alignment score = 328.1 
    14600 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    14601 2.714) 
    14602  
    14603 
    14604 > hide sel cartoons
    14605 
    14606 > hide #301 models
    14607 
    14608 > select #1.1/D
    14609 
    14610 3370 atoms, 3467 bonds, 442 residues, 1 model selected 
    14611 
    14612 > matchmaker #302 to #1.1 & sel
    14613 
    14614 Parameters 
    14615 --- 
    14616 Chain pairing | bb 
    14617 Alignment algorithm | Needleman-Wunsch 
    14618 Similarity matrix | BLOSUM-62 
    14619 SS fraction | 0.3 
    14620 Gap open (HH/SS/other) | 18/18/6 
    14621 Gap extend | 1 
    14622 SS matrix |  |  | H | S | O 
    14623 ---|---|---|--- 
    14624 H | 6 | -9 | -6 
    14625 S |  | 6 | -6 
    14626 O |  |  | 4 
    14627 Iteration cutoff | 2 
    14628  
    14629 Matchmaker 3j0c.pdb1, chain D (#1.1) with AF3 E1 1-421.pdb, chain A (#302),
    14630 sequence alignment score = 1060.7 
    14631 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    14632 3.032) 
    14633  
    14634 
    14635 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    14636 
    14637 Chain information for AF3 E1 422-461.pdb #303 
    14638 --- 
    14639 Chain | Description 
    14640 A | No description available 
    14641  
    14642 
    14643 > matchmaker #303 to #1.1 & sel
    14644 
    14645 Parameters 
    14646 --- 
    14647 Chain pairing | bb 
    14648 Alignment algorithm | Needleman-Wunsch 
    14649 Similarity matrix | BLOSUM-62 
    14650 SS fraction | 0.3 
    14651 Gap open (HH/SS/other) | 18/18/6 
    14652 Gap extend | 1 
    14653 SS matrix |  |  | H | S | O 
    14654 ---|---|---|--- 
    14655 H | 6 | -9 | -6 
    14656 S |  | 6 | -6 
    14657 O |  |  | 4 
    14658 Iteration cutoff | 2 
    14659  
    14660 Matchmaker 3j0c.pdb1, chain D (#1.1) with AF3 E1 422-461.pdb, chain A (#303),
    14661 sequence alignment score = 626.9 
    14662 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    14663 2.916) 
    14664  
    14665 
    14666 > select #1.1/E
    14667 
    14668 3304 atoms, 3400 bonds, 423 residues, 1 model selected 
    14669 
    14670 > show sel cartoons
    14671 
    14672 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    14673 
    14674 Chain information for AF3 E2 1-352.pdb #304 
    14675 --- 
    14676 Chain | Description 
    14677 B | No description available 
    14678  
    14679 
    14680 > matchmaker #304 to #1.1 & sel
    14681 
    14682 Parameters 
    14683 --- 
    14684 Chain pairing | bb 
    14685 Alignment algorithm | Needleman-Wunsch 
    14686 Similarity matrix | BLOSUM-62 
    14687 SS fraction | 0.3 
    14688 Gap open (HH/SS/other) | 18/18/6 
    14689 Gap extend | 1 
    14690 SS matrix |  |  | H | S | O 
    14691 ---|---|---|--- 
    14692 H | 6 | -9 | -6 
    14693 S |  | 6 | -6 
    14694 O |  |  | 4 
    14695 Iteration cutoff | 2 
    14696  
    14697 Matchmaker 3j0c.pdb1, chain E (#1.1) with AF3 E2 1-352.pdb, chain B (#304),
    14698 sequence alignment score = 594.5 
    14699 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    14700 6.147) 
    14701  
    14702 
    14703 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    14704 
    14705 Chain information for AF3 E2 353-438.pdb #305 
    14706 --- 
    14707 Chain | Description 
    14708 B | No description available 
    14709  
    14710 
    14711 > matchmaker #305 to #1.1 & sel
    14712 
    14713 Parameters 
    14714 --- 
    14715 Chain pairing | bb 
    14716 Alignment algorithm | Needleman-Wunsch 
    14717 Similarity matrix | BLOSUM-62 
    14718 SS fraction | 0.3 
    14719 Gap open (HH/SS/other) | 18/18/6 
    14720 Gap extend | 1 
    14721 SS matrix |  |  | H | S | O 
    14722 ---|---|---|--- 
    14723 H | 6 | -9 | -6 
    14724 S |  | 6 | -6 
    14725 O |  |  | 4 
    14726 Iteration cutoff | 2 
    14727  
    14728 Matchmaker 3j0c.pdb1, chain E (#1.1) with AF3 E2 353-438.pdb, chain B (#305),
    14729 sequence alignment score = 340.2 
    14730 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    14731 8.673) 
    14732  
    14733 
    14734 > select #1.1/F
    14735 
    14736 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    14737 
    14738 > show sel cartoons
    14739 
    14740 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    14741 
    14742 Chain information for AF3 CA.pdb #306 
    14743 --- 
    14744 Chain | Description 
    14745 A | No description available 
    14746  
    14747 
    14748 > matchmaker #306 to #1.1 & sel
    14749 
    14750 Parameters 
    14751 --- 
    14752 Chain pairing | bb 
    14753 Alignment algorithm | Needleman-Wunsch 
    14754 Similarity matrix | BLOSUM-62 
    14755 SS fraction | 0.3 
    14756 Gap open (HH/SS/other) | 18/18/6 
    14757 Gap extend | 1 
    14758 SS matrix |  |  | H | S | O 
    14759 ---|---|---|--- 
    14760 H | 6 | -9 | -6 
    14761 S |  | 6 | -6 
    14762 O |  |  | 4 
    14763 Iteration cutoff | 2 
    14764  
    14765 Matchmaker 3j0c.pdb1, chain F (#1.1) with AF3 CA.pdb, chain A (#306), sequence
    14766 alignment score = 335.3 
    14767 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    14768 2.550) 
    14769  
    14770 
    14771 > hide sel cartoons
    14772 
    14773 > select #1.1/F
    14774 
    14775 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    14776 
    14777 > show sel cartoons
    14778 
    14779 > hide sel cartoons
    14780 
    14781 > select #1.1/E
    14782 
    14783 3304 atoms, 3400 bonds, 423 residues, 1 model selected 
    14784 
    14785 > hide sel cartoons
    14786 
    14787 > select #1.1/D
    14788 
    14789 3370 atoms, 3467 bonds, 442 residues, 1 model selected 
    14790 
    14791 > hide sel cartoons
    14792 
    14793 > color #302 dodgerblue
    14794 
    14795 > color #303 dodgerblue
    14796 
    14797 > color #304 #00b305ff
    14798 
    14799 > color #305 #00b305ff
    14800 
    14801 > color #306 #f15839ff
    14802 
    14803 > select #1.2/D
    14804 
    14805 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    14806 
    14807 > show sel cartoons
    14808 
    14809 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    14810 
    14811 Chain information for AF3 E1 1-421.pdb #307 
    14812 --- 
    14813 Chain | Description 
    14814 A | No description available 
    14815  
    14816 
    14817 > matchmaker #307 to #1.2 & sel
    14818 
    14819 Parameters 
    14820 --- 
    14821 Chain pairing | bb 
    14822 Alignment algorithm | Needleman-Wunsch 
    14823 Similarity matrix | BLOSUM-62 
    14824 SS fraction | 0.3 
    14825 Gap open (HH/SS/other) | 18/18/6 
    14826 Gap extend | 1 
    14827 SS matrix |  |  | H | S | O 
    14828 ---|---|---|--- 
    14829 H | 6 | -9 | -6 
    14830 S |  | 6 | -6 
    14831 O |  |  | 4 
    14832 Iteration cutoff | 2 
    14833  
    14834 Matchmaker 3j0c.pdb1, chain D (#1.2) with AF3 E1 1-421.pdb, chain A (#307),
    14835 sequence alignment score = 1060.7 
    14836 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    14837 3.032) 
    14838  
    14839 
    14840 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    14841 
    14842 Chain information for AF3 E1 422-461.pdb #308 
    14843 --- 
    14844 Chain | Description 
    14845 A | No description available 
    14846  
    14847 
    14848 > matchmaker #308 to #1.2 & sel
    14849 
    14850 Parameters 
    14851 --- 
    14852 Chain pairing | bb 
    14853 Alignment algorithm | Needleman-Wunsch 
    14854 Similarity matrix | BLOSUM-62 
    14855 SS fraction | 0.3 
    14856 Gap open (HH/SS/other) | 18/18/6 
    14857 Gap extend | 1 
    14858 SS matrix |  |  | H | S | O 
    14859 ---|---|---|--- 
    14860 H | 6 | -9 | -6 
    14861 S |  | 6 | -6 
    14862 O |  |  | 4 
    14863 Iteration cutoff | 2 
    14864  
    14865 Matchmaker 3j0c.pdb1, chain D (#1.2) with AF3 E1 422-461.pdb, chain A (#308),
    14866 sequence alignment score = 626.9 
    14867 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    14868 2.916) 
    14869  
    14870 
    14871 > hide sel cartoons
    14872 
    14873 [Repeated 1 time(s)]
    14874 
    14875 > select #1.2/E
    14876 
    14877 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    14878 
    14879 > show sel cartoons
    14880 
    14881 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    14882 
    14883 Chain information for AF3 E2 1-352.pdb #309 
    14884 --- 
    14885 Chain | Description 
    14886 B | No description available 
    14887  
    14888 
    14889 > matchmaker #309 to #1.2 & sel
    14890 
    14891 Parameters 
    14892 --- 
    14893 Chain pairing | bb 
    14894 Alignment algorithm | Needleman-Wunsch 
    14895 Similarity matrix | BLOSUM-62 
    14896 SS fraction | 0.3 
    14897 Gap open (HH/SS/other) | 18/18/6 
    14898 Gap extend | 1 
    14899 SS matrix |  |  | H | S | O 
    14900 ---|---|---|--- 
    14901 H | 6 | -9 | -6 
    14902 S |  | 6 | -6 
    14903 O |  |  | 4 
    14904 Iteration cutoff | 2 
    14905  
    14906 Matchmaker 3j0c.pdb1, chain E (#1.2) with AF3 E2 1-352.pdb, chain B (#309),
    14907 sequence alignment score = 594.5 
    14908 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    14909 6.147) 
    14910  
    14911 
    14912 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    14913 
    14914 Chain information for AF3 E2 353-438.pdb #310 
    14915 --- 
    14916 Chain | Description 
    14917 B | No description available 
    14918  
    14919 
    14920 > matchmaker #310 to #1.2 & sel
    14921 
    14922 Parameters 
    14923 --- 
    14924 Chain pairing | bb 
    14925 Alignment algorithm | Needleman-Wunsch 
    14926 Similarity matrix | BLOSUM-62 
    14927 SS fraction | 0.3 
    14928 Gap open (HH/SS/other) | 18/18/6 
    14929 Gap extend | 1 
    14930 SS matrix |  |  | H | S | O 
    14931 ---|---|---|--- 
    14932 H | 6 | -9 | -6 
    14933 S |  | 6 | -6 
    14934 O |  |  | 4 
    14935 Iteration cutoff | 2 
    14936  
    14937 Matchmaker 3j0c.pdb1, chain E (#1.2) with AF3 E2 353-438.pdb, chain B (#310),
    14938 sequence alignment score = 340.2 
    14939 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    14940 8.673) 
    14941  
    14942 
    14943 > hide sel cartoons
    14944 
    14945 > select #1.2/F
    14946 
    14947 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    14948 
    14949 > show sel cartoons
    14950 
    14951 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    14952 
    14953 Chain information for AF3 CA.pdb #311 
    14954 --- 
    14955 Chain | Description 
    14956 A | No description available 
    14957  
    14958 
    14959 > matchmaker #311 to #1.2 & sel
    14960 
    14961 Parameters 
    14962 --- 
    14963 Chain pairing | bb 
    14964 Alignment algorithm | Needleman-Wunsch 
    14965 Similarity matrix | BLOSUM-62 
    14966 SS fraction | 0.3 
    14967 Gap open (HH/SS/other) | 18/18/6 
    14968 Gap extend | 1 
    14969 SS matrix |  |  | H | S | O 
    14970 ---|---|---|--- 
    14971 H | 6 | -9 | -6 
    14972 S |  | 6 | -6 
    14973 O |  |  | 4 
    14974 Iteration cutoff | 2 
    14975  
    14976 Matchmaker 3j0c.pdb1, chain F (#1.2) with AF3 CA.pdb, chain A (#311), sequence
    14977 alignment score = 335.3 
    14978 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    14979 2.550) 
    14980  
    14981 
    14982 > hide sel cartoons
    14983 
    14984 > color #307 dodgerblue
    14985 
    14986 > color #308 dodgerblue
    14987 
    14988 > color #309 #00b305ff
    14989 
    14990 > color #310 #00b305ff
    14991 
    14992 > color #311 #f15839ff
    14993 
    14994 > select #1.3/D
    14995 
    14996 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    14997 
    14998 > show sel cartoons
    14999 
    15000 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    15001 
    15002 Chain information for AF3 E1 1-421.pdb #312 
    15003 --- 
    15004 Chain | Description 
    15005 A | No description available 
    15006  
    15007 
    15008 > matchmaker #312 to #1.2 & sel
    15009 
    15010 No 'to' model specified 
    15011 
    15012 > matchmaker #312 to #1.3 & sel
    15013 
    15014 Parameters 
    15015 --- 
    15016 Chain pairing | bb 
    15017 Alignment algorithm | Needleman-Wunsch 
    15018 Similarity matrix | BLOSUM-62 
    15019 SS fraction | 0.3 
    15020 Gap open (HH/SS/other) | 18/18/6 
    15021 Gap extend | 1 
    15022 SS matrix |  |  | H | S | O 
    15023 ---|---|---|--- 
    15024 H | 6 | -9 | -6 
    15025 S |  | 6 | -6 
    15026 O |  |  | 4 
    15027 Iteration cutoff | 2 
    15028  
    15029 Matchmaker 3j0c.pdb1, chain D (#1.3) with AF3 E1 1-421.pdb, chain A (#312),
    15030 sequence alignment score = 1060.7 
    15031 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    15032 3.032) 
    15033  
    15034 
    15035 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    15036 
    15037 Chain information for AF3 E1 422-461.pdb #313 
    15038 --- 
    15039 Chain | Description 
    15040 A | No description available 
    15041  
    15042 
    15043 > matchmaker #313 to #1.3 & sel
    15044 
    15045 Parameters 
    15046 --- 
    15047 Chain pairing | bb 
    15048 Alignment algorithm | Needleman-Wunsch 
    15049 Similarity matrix | BLOSUM-62 
    15050 SS fraction | 0.3 
    15051 Gap open (HH/SS/other) | 18/18/6 
    15052 Gap extend | 1 
    15053 SS matrix |  |  | H | S | O 
    15054 ---|---|---|--- 
    15055 H | 6 | -9 | -6 
    15056 S |  | 6 | -6 
    15057 O |  |  | 4 
    15058 Iteration cutoff | 2 
    15059  
    15060 Matchmaker 3j0c.pdb1, chain D (#1.3) with AF3 E1 422-461.pdb, chain A (#313),
    15061 sequence alignment score = 626.9 
    15062 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    15063 2.916) 
    15064  
    15065 
    15066 > hide sel cartoons
    15067 
    15068 > select #1.3/B
    15069 
    15070 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    15071 
    15072 > select #1.3/E
    15073 
    15074 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    15075 
    15076 > show sel cartoons
    15077 
    15078 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    15079 
    15080 Chain information for AF3 E2 1-352.pdb #314 
    15081 --- 
    15082 Chain | Description 
    15083 B | No description available 
    15084  
    15085 
    15086 > matchmaker #314 to #1.3 & sel
    15087 
    15088 Parameters 
    15089 --- 
    15090 Chain pairing | bb 
    15091 Alignment algorithm | Needleman-Wunsch 
    15092 Similarity matrix | BLOSUM-62 
    15093 SS fraction | 0.3 
    15094 Gap open (HH/SS/other) | 18/18/6 
    15095 Gap extend | 1 
    15096 SS matrix |  |  | H | S | O 
    15097 ---|---|---|--- 
    15098 H | 6 | -9 | -6 
    15099 S |  | 6 | -6 
    15100 O |  |  | 4 
    15101 Iteration cutoff | 2 
    15102  
    15103 Matchmaker 3j0c.pdb1, chain E (#1.3) with AF3 E2 1-352.pdb, chain B (#314),
    15104 sequence alignment score = 594.5 
    15105 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    15106 6.147) 
    15107  
    15108 
    15109 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    15110 
    15111 Chain information for AF3 E2 353-438.pdb #315 
    15112 --- 
    15113 Chain | Description 
    15114 B | No description available 
    15115  
    15116 
    15117 > matchmaker #315 to #1.3 & sel
    15118 
    15119 Parameters 
    15120 --- 
    15121 Chain pairing | bb 
    15122 Alignment algorithm | Needleman-Wunsch 
    15123 Similarity matrix | BLOSUM-62 
    15124 SS fraction | 0.3 
    15125 Gap open (HH/SS/other) | 18/18/6 
    15126 Gap extend | 1 
    15127 SS matrix |  |  | H | S | O 
    15128 ---|---|---|--- 
    15129 H | 6 | -9 | -6 
    15130 S |  | 6 | -6 
    15131 O |  |  | 4 
    15132 Iteration cutoff | 2 
    15133  
    15134 Matchmaker 3j0c.pdb1, chain E (#1.3) with AF3 E2 353-438.pdb, chain B (#315),
    15135 sequence alignment score = 340.2 
    15136 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    15137 8.673) 
    15138  
    15139 
    15140 > hide sel cartoons
    15141 
    15142 > select #1.3/F
    15143 
    15144 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    15145 
    15146 > show sel cartoons
    15147 
    15148 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    15149 
    15150 Chain information for AF3 CA.pdb #316 
    15151 --- 
    15152 Chain | Description 
    15153 A | No description available 
    15154  
    15155 
    15156 > matchmaker #316 to #1.3 & sel
    15157 
    15158 Parameters 
    15159 --- 
    15160 Chain pairing | bb 
    15161 Alignment algorithm | Needleman-Wunsch 
    15162 Similarity matrix | BLOSUM-62 
    15163 SS fraction | 0.3 
    15164 Gap open (HH/SS/other) | 18/18/6 
    15165 Gap extend | 1 
    15166 SS matrix |  |  | H | S | O 
    15167 ---|---|---|--- 
    15168 H | 6 | -9 | -6 
    15169 S |  | 6 | -6 
    15170 O |  |  | 4 
    15171 Iteration cutoff | 2 
    15172  
    15173 Matchmaker 3j0c.pdb1, chain F (#1.3) with AF3 CA.pdb, chain A (#316), sequence
    15174 alignment score = 335.3 
    15175 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    15176 2.550) 
    15177  
    15178 
    15179 > hide sel cartoons
    15180 
    15181 > color #312 dodgerblue
    15182 
    15183 > color #313 dodgerblue
    15184 
    15185 > color #314 #00b305ff
    15186 
    15187 > color #315 #00b305ff
    15188 
    15189 > color #316 #f15839ff
    15190 
    15191 > select #1.4/D
    15192 
    15193 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    15194 
    15195 > show sel cartoons
    15196 
    15197 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    15198 
    15199 Chain information for AF3 E1 1-421.pdb #317 
    15200 --- 
    15201 Chain | Description 
    15202 A | No description available 
    15203  
    15204 
    15205 > matchmaker #317 to #1.4 & sel
    15206 
    15207 Parameters 
    15208 --- 
    15209 Chain pairing | bb 
    15210 Alignment algorithm | Needleman-Wunsch 
    15211 Similarity matrix | BLOSUM-62 
    15212 SS fraction | 0.3 
    15213 Gap open (HH/SS/other) | 18/18/6 
    15214 Gap extend | 1 
    15215 SS matrix |  |  | H | S | O 
    15216 ---|---|---|--- 
    15217 H | 6 | -9 | -6 
    15218 S |  | 6 | -6 
    15219 O |  |  | 4 
    15220 Iteration cutoff | 2 
    15221  
    15222 Matchmaker 3j0c.pdb1, chain D (#1.4) with AF3 E1 1-421.pdb, chain A (#317),
    15223 sequence alignment score = 1060.7 
    15224 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    15225 3.032) 
    15226  
    15227 
    15228 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    15229 
    15230 Chain information for AF3 E1 422-461.pdb #318 
    15231 --- 
    15232 Chain | Description 
    15233 A | No description available 
    15234  
    15235 
    15236 > matchmaker #318 to #1.4 & sel
    15237 
    15238 Parameters 
    15239 --- 
    15240 Chain pairing | bb 
    15241 Alignment algorithm | Needleman-Wunsch 
    15242 Similarity matrix | BLOSUM-62 
    15243 SS fraction | 0.3 
    15244 Gap open (HH/SS/other) | 18/18/6 
    15245 Gap extend | 1 
    15246 SS matrix |  |  | H | S | O 
    15247 ---|---|---|--- 
    15248 H | 6 | -9 | -6 
    15249 S |  | 6 | -6 
    15250 O |  |  | 4 
    15251 Iteration cutoff | 2 
    15252  
    15253 Matchmaker 3j0c.pdb1, chain D (#1.4) with AF3 E1 422-461.pdb, chain A (#318),
    15254 sequence alignment score = 626.9 
    15255 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    15256 2.916) 
    15257  
    15258 
    15259 > hide sel cartoons
    15260 
    15261 > select #1.4/E
    15262 
    15263 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    15264 
    15265 > show sel cartoons
    15266 
    15267 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    15268 
    15269 Chain information for AF3 E2 1-352.pdb #319 
    15270 --- 
    15271 Chain | Description 
    15272 B | No description available 
    15273  
    15274 
    15275 > matchmaker #319 to #1.4 & sel
    15276 
    15277 Parameters 
    15278 --- 
    15279 Chain pairing | bb 
    15280 Alignment algorithm | Needleman-Wunsch 
    15281 Similarity matrix | BLOSUM-62 
    15282 SS fraction | 0.3 
    15283 Gap open (HH/SS/other) | 18/18/6 
    15284 Gap extend | 1 
    15285 SS matrix |  |  | H | S | O 
    15286 ---|---|---|--- 
    15287 H | 6 | -9 | -6 
    15288 S |  | 6 | -6 
    15289 O |  |  | 4 
    15290 Iteration cutoff | 2 
    15291  
    15292 Matchmaker 3j0c.pdb1, chain E (#1.4) with AF3 E2 1-352.pdb, chain B (#319),
    15293 sequence alignment score = 594.5 
    15294 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    15295 6.147) 
    15296  
    15297 
    15298 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    15299 
    15300 Chain information for AF3 E2 353-438.pdb #320 
    15301 --- 
    15302 Chain | Description 
    15303 B | No description available 
    15304  
    15305 
    15306 > matchmaker #320 to #1.4 & sel
    15307 
    15308 Parameters 
    15309 --- 
    15310 Chain pairing | bb 
    15311 Alignment algorithm | Needleman-Wunsch 
    15312 Similarity matrix | BLOSUM-62 
    15313 SS fraction | 0.3 
    15314 Gap open (HH/SS/other) | 18/18/6 
    15315 Gap extend | 1 
    15316 SS matrix |  |  | H | S | O 
    15317 ---|---|---|--- 
    15318 H | 6 | -9 | -6 
    15319 S |  | 6 | -6 
    15320 O |  |  | 4 
    15321 Iteration cutoff | 2 
    15322  
    15323 Matchmaker 3j0c.pdb1, chain E (#1.4) with AF3 E2 353-438.pdb, chain B (#320),
    15324 sequence alignment score = 340.2 
    15325 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    15326 8.673) 
    15327  
    15328 
    15329 > hide sel cartoons
    15330 
    15331 > select #1.4/F
    15332 
    15333 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    15334 
    15335 > show sel cartoons
    15336 
    15337 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    15338 
    15339 Chain information for AF3 CA.pdb #321 
    15340 --- 
    15341 Chain | Description 
    15342 A | No description available 
    15343  
    15344 
    15345 > matchmaker #321 to #1.4 & sel
    15346 
    15347 Parameters 
    15348 --- 
    15349 Chain pairing | bb 
    15350 Alignment algorithm | Needleman-Wunsch 
    15351 Similarity matrix | BLOSUM-62 
    15352 SS fraction | 0.3 
    15353 Gap open (HH/SS/other) | 18/18/6 
    15354 Gap extend | 1 
    15355 SS matrix |  |  | H | S | O 
    15356 ---|---|---|--- 
    15357 H | 6 | -9 | -6 
    15358 S |  | 6 | -6 
    15359 O |  |  | 4 
    15360 Iteration cutoff | 2 
    15361  
    15362 Matchmaker 3j0c.pdb1, chain F (#1.4) with AF3 CA.pdb, chain A (#321), sequence
    15363 alignment score = 335.3 
    15364 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    15365 2.550) 
    15366  
    15367 
    15368 > hide sel cartoons
    15369 
    15370 > color #317 dodgerblue
    15371 
    15372 > color #318 dodgerblue
    15373 
    15374 > color #319 #00b305ff
    15375 
    15376 > color #320 #00b305ff
    15377 
    15378 > color #321 #f15839ff
    15379 
    15380 > select #1.5/D
    15381 
    15382 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    15383 
    15384 > show sel cartoons
    15385 
    15386 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    15387 
    15388 Chain information for AF3 E1 1-421.pdb #322 
    15389 --- 
    15390 Chain | Description 
    15391 A | No description available 
    15392  
    15393 
    15394 > matchmaker #322 to #1.5 & sel
    15395 
    15396 Parameters 
    15397 --- 
    15398 Chain pairing | bb 
    15399 Alignment algorithm | Needleman-Wunsch 
    15400 Similarity matrix | BLOSUM-62 
    15401 SS fraction | 0.3 
    15402 Gap open (HH/SS/other) | 18/18/6 
    15403 Gap extend | 1 
    15404 SS matrix |  |  | H | S | O 
    15405 ---|---|---|--- 
    15406 H | 6 | -9 | -6 
    15407 S |  | 6 | -6 
    15408 O |  |  | 4 
    15409 Iteration cutoff | 2 
    15410  
    15411 Matchmaker 3j0c.pdb1, chain D (#1.5) with AF3 E1 1-421.pdb, chain A (#322),
    15412 sequence alignment score = 1060.7 
    15413 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    15414 3.032) 
    15415  
    15416 
    15417 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    15418 
    15419 Chain information for AF3 E1 422-461.pdb #323 
    15420 --- 
    15421 Chain | Description 
    15422 A | No description available 
    15423  
    15424 
    15425 > matchmaker #323 to #1.5 & sel
    15426 
    15427 Parameters 
    15428 --- 
    15429 Chain pairing | bb 
    15430 Alignment algorithm | Needleman-Wunsch 
    15431 Similarity matrix | BLOSUM-62 
    15432 SS fraction | 0.3 
    15433 Gap open (HH/SS/other) | 18/18/6 
    15434 Gap extend | 1 
    15435 SS matrix |  |  | H | S | O 
    15436 ---|---|---|--- 
    15437 H | 6 | -9 | -6 
    15438 S |  | 6 | -6 
    15439 O |  |  | 4 
    15440 Iteration cutoff | 2 
    15441  
    15442 Matchmaker 3j0c.pdb1, chain D (#1.5) with AF3 E1 422-461.pdb, chain A (#323),
    15443 sequence alignment score = 626.9 
    15444 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    15445 2.915) 
    15446  
    15447 
    15448 > hide sel cartoons
    15449 
    15450 > select #1.5/E
    15451 
    15452 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    15453 
    15454 > show sel cartoons
    15455 
    15456 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    15457 
    15458 Chain information for AF3 E2 1-352.pdb #324 
    15459 --- 
    15460 Chain | Description 
    15461 B | No description available 
    15462  
    15463 
    15464 > matchmaker #324 to #1.5 & sel
    15465 
    15466 Parameters 
    15467 --- 
    15468 Chain pairing | bb 
    15469 Alignment algorithm | Needleman-Wunsch 
    15470 Similarity matrix | BLOSUM-62 
    15471 SS fraction | 0.3 
    15472 Gap open (HH/SS/other) | 18/18/6 
    15473 Gap extend | 1 
    15474 SS matrix |  |  | H | S | O 
    15475 ---|---|---|--- 
    15476 H | 6 | -9 | -6 
    15477 S |  | 6 | -6 
    15478 O |  |  | 4 
    15479 Iteration cutoff | 2 
    15480  
    15481 Matchmaker 3j0c.pdb1, chain E (#1.5) with AF3 E2 1-352.pdb, chain B (#324),
    15482 sequence alignment score = 594.5 
    15483 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    15484 6.147) 
    15485  
    15486 
    15487 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    15488 
    15489 Chain information for AF3 E2 353-438.pdb #325 
    15490 --- 
    15491 Chain | Description 
    15492 B | No description available 
    15493  
    15494 
    15495 > matchmaker #325 to #1.5 & sel
    15496 
    15497 Parameters 
    15498 --- 
    15499 Chain pairing | bb 
    15500 Alignment algorithm | Needleman-Wunsch 
    15501 Similarity matrix | BLOSUM-62 
    15502 SS fraction | 0.3 
    15503 Gap open (HH/SS/other) | 18/18/6 
    15504 Gap extend | 1 
    15505 SS matrix |  |  | H | S | O 
    15506 ---|---|---|--- 
    15507 H | 6 | -9 | -6 
    15508 S |  | 6 | -6 
    15509 O |  |  | 4 
    15510 Iteration cutoff | 2 
    15511  
    15512 Matchmaker 3j0c.pdb1, chain E (#1.5) with AF3 E2 353-438.pdb, chain B (#325),
    15513 sequence alignment score = 340.2 
    15514 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    15515 8.673) 
    15516  
    15517 
    15518 > hide sel cartoons
    15519 
    15520 > select #1.5/F
    15521 
    15522 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    15523 
    15524 > show sel cartoons
    15525 
    15526 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    15527 
    15528 Chain information for AF3 CA.pdb #326 
    15529 --- 
    15530 Chain | Description 
    15531 A | No description available 
    15532  
    15533 
    15534 > matchmaker #326 to #1.5 & sel
    15535 
    15536 Parameters 
    15537 --- 
    15538 Chain pairing | bb 
    15539 Alignment algorithm | Needleman-Wunsch 
    15540 Similarity matrix | BLOSUM-62 
    15541 SS fraction | 0.3 
    15542 Gap open (HH/SS/other) | 18/18/6 
    15543 Gap extend | 1 
    15544 SS matrix |  |  | H | S | O 
    15545 ---|---|---|--- 
    15546 H | 6 | -9 | -6 
    15547 S |  | 6 | -6 
    15548 O |  |  | 4 
    15549 Iteration cutoff | 2 
    15550  
    15551 Matchmaker 3j0c.pdb1, chain F (#1.5) with AF3 CA.pdb, chain A (#326), sequence
    15552 alignment score = 335.3 
    15553 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    15554 2.550) 
    15555  
    15556 
    15557 > hide sel cartoons
    15558 
    15559 > color #322 dodgerblue
    15560 
    15561 > color #323 dodgerblue
    15562 
    15563 > color #324 #00b305ff
    15564 
    15565 > color #325 #00b305ff
    15566 
    15567 > color #326 #f15839ff
    15568 
    15569 > select #1.6/D
    15570 
    15571 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    15572 
    15573 > show sel cartoons
    15574 
    15575 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    15576 
    15577 Chain information for AF3 E1 1-421.pdb #327 
    15578 --- 
    15579 Chain | Description 
    15580 A | No description available 
    15581  
    15582 
    15583 > matchmaker #327 to #1.6 & sel
    15584 
    15585 Parameters 
    15586 --- 
    15587 Chain pairing | bb 
    15588 Alignment algorithm | Needleman-Wunsch 
    15589 Similarity matrix | BLOSUM-62 
    15590 SS fraction | 0.3 
    15591 Gap open (HH/SS/other) | 18/18/6 
    15592 Gap extend | 1 
    15593 SS matrix |  |  | H | S | O 
    15594 ---|---|---|--- 
    15595 H | 6 | -9 | -6 
    15596 S |  | 6 | -6 
    15597 O |  |  | 4 
    15598 Iteration cutoff | 2 
    15599  
    15600 Matchmaker 3j0c.pdb1, chain D (#1.6) with AF3 E1 1-421.pdb, chain A (#327),
    15601 sequence alignment score = 1060.7 
    15602 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    15603 3.032) 
    15604  
    15605 
    15606 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    15607 
    15608 Chain information for AF3 E1 422-461.pdb #328 
    15609 --- 
    15610 Chain | Description 
    15611 A | No description available 
    15612  
    15613 
    15614 > matchmaker #328 to #1.6 & sel
    15615 
    15616 Parameters 
    15617 --- 
    15618 Chain pairing | bb 
    15619 Alignment algorithm | Needleman-Wunsch 
    15620 Similarity matrix | BLOSUM-62 
    15621 SS fraction | 0.3 
    15622 Gap open (HH/SS/other) | 18/18/6 
    15623 Gap extend | 1 
    15624 SS matrix |  |  | H | S | O 
    15625 ---|---|---|--- 
    15626 H | 6 | -9 | -6 
    15627 S |  | 6 | -6 
    15628 O |  |  | 4 
    15629 Iteration cutoff | 2 
    15630  
    15631 Matchmaker 3j0c.pdb1, chain D (#1.6) with AF3 E1 422-461.pdb, chain A (#328),
    15632 sequence alignment score = 626.9 
    15633 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    15634 2.916) 
    15635  
    15636 
    15637 > hide sel cartoons
    15638 
    15639 > select #1.6/E
    15640 
    15641 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    15642 
    15643 > show sel cartoons
    15644 
    15645 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    15646 
    15647 Chain information for AF3 E2 1-352.pdb #329 
    15648 --- 
    15649 Chain | Description 
    15650 B | No description available 
    15651  
    15652 
    15653 > matchmaker #329 to #1.6 & sel
    15654 
    15655 Parameters 
    15656 --- 
    15657 Chain pairing | bb 
    15658 Alignment algorithm | Needleman-Wunsch 
    15659 Similarity matrix | BLOSUM-62 
    15660 SS fraction | 0.3 
    15661 Gap open (HH/SS/other) | 18/18/6 
    15662 Gap extend | 1 
    15663 SS matrix |  |  | H | S | O 
    15664 ---|---|---|--- 
    15665 H | 6 | -9 | -6 
    15666 S |  | 6 | -6 
    15667 O |  |  | 4 
    15668 Iteration cutoff | 2 
    15669  
    15670 Matchmaker 3j0c.pdb1, chain E (#1.6) with AF3 E2 1-352.pdb, chain B (#329),
    15671 sequence alignment score = 594.5 
    15672 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    15673 6.147) 
    15674  
    15675 
    15676 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    15677 
    15678 Chain information for AF3 E2 353-438.pdb #330 
    15679 --- 
    15680 Chain | Description 
    15681 B | No description available 
    15682  
    15683 
    15684 > matchmaker #330 to #1.6 & sel
    15685 
    15686 Parameters 
    15687 --- 
    15688 Chain pairing | bb 
    15689 Alignment algorithm | Needleman-Wunsch 
    15690 Similarity matrix | BLOSUM-62 
    15691 SS fraction | 0.3 
    15692 Gap open (HH/SS/other) | 18/18/6 
    15693 Gap extend | 1 
    15694 SS matrix |  |  | H | S | O 
    15695 ---|---|---|--- 
    15696 H | 6 | -9 | -6 
    15697 S |  | 6 | -6 
    15698 O |  |  | 4 
    15699 Iteration cutoff | 2 
    15700  
    15701 Matchmaker 3j0c.pdb1, chain E (#1.6) with AF3 E2 353-438.pdb, chain B (#330),
    15702 sequence alignment score = 340.2 
    15703 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    15704 8.673) 
    15705  
    15706 
    15707 > hide sel cartoons
    15708 
    15709 > select #1.6/F
    15710 
    15711 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    15712 
    15713 > show sel cartoons
    15714 
    15715 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    15716 
    15717 Chain information for AF3 CA.pdb #331 
    15718 --- 
    15719 Chain | Description 
    15720 A | No description available 
    15721  
    15722 
    15723 > matchmaker #331 to #1.6 & sel
    15724 
    15725 Parameters 
    15726 --- 
    15727 Chain pairing | bb 
    15728 Alignment algorithm | Needleman-Wunsch 
    15729 Similarity matrix | BLOSUM-62 
    15730 SS fraction | 0.3 
    15731 Gap open (HH/SS/other) | 18/18/6 
    15732 Gap extend | 1 
    15733 SS matrix |  |  | H | S | O 
    15734 ---|---|---|--- 
    15735 H | 6 | -9 | -6 
    15736 S |  | 6 | -6 
    15737 O |  |  | 4 
    15738 Iteration cutoff | 2 
    15739  
    15740 Matchmaker 3j0c.pdb1, chain F (#1.6) with AF3 CA.pdb, chain A (#331), sequence
    15741 alignment score = 335.3 
    15742 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    15743 2.550) 
    15744  
    15745 
    15746 > hide sel cartoons
    15747 
    15748 > color #327 dodgerblue
    15749 
    15750 > color #328 dodgerblue
    15751 
    15752 > color #329 #00b305ff
    15753 
    15754 > color #330 #00b305ff
    15755 
    15756 > color #331 #f15839ff
    15757 
    15758 > select #1.7/D
    15759 
    15760 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    15761 
    15762 > show sel cartoons
    15763 
    15764 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    15765 
    15766 Chain information for AF3 E1 1-421.pdb #332 
    15767 --- 
    15768 Chain | Description 
    15769 A | No description available 
    15770  
    15771 
    15772 > matchmaker #332 to #1.7 & sel
    15773 
    15774 Parameters 
    15775 --- 
    15776 Chain pairing | bb 
    15777 Alignment algorithm | Needleman-Wunsch 
    15778 Similarity matrix | BLOSUM-62 
    15779 SS fraction | 0.3 
    15780 Gap open (HH/SS/other) | 18/18/6 
    15781 Gap extend | 1 
    15782 SS matrix |  |  | H | S | O 
    15783 ---|---|---|--- 
    15784 H | 6 | -9 | -6 
    15785 S |  | 6 | -6 
    15786 O |  |  | 4 
    15787 Iteration cutoff | 2 
    15788  
    15789 Matchmaker 3j0c.pdb1, chain D (#1.7) with AF3 E1 1-421.pdb, chain A (#332),
    15790 sequence alignment score = 1060.7 
    15791 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    15792 3.032) 
    15793  
    15794 
    15795 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    15796 
    15797 Chain information for AF3 E1 422-461.pdb #333 
    15798 --- 
    15799 Chain | Description 
    15800 A | No description available 
    15801  
    15802 
    15803 > matchmaker #333 to #1.7 & sel
    15804 
    15805 Parameters 
    15806 --- 
    15807 Chain pairing | bb 
    15808 Alignment algorithm | Needleman-Wunsch 
    15809 Similarity matrix | BLOSUM-62 
    15810 SS fraction | 0.3 
    15811 Gap open (HH/SS/other) | 18/18/6 
    15812 Gap extend | 1 
    15813 SS matrix |  |  | H | S | O 
    15814 ---|---|---|--- 
    15815 H | 6 | -9 | -6 
    15816 S |  | 6 | -6 
    15817 O |  |  | 4 
    15818 Iteration cutoff | 2 
    15819  
    15820 Matchmaker 3j0c.pdb1, chain D (#1.7) with AF3 E1 422-461.pdb, chain A (#333),
    15821 sequence alignment score = 626.9 
    15822 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    15823 2.916) 
    15824  
    15825 
    15826 > hide sel cartoons
    15827 
    15828 > select #1.7/E
    15829 
    15830 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    15831 
    15832 > show sel cartoons
    15833 
    15834 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    15835 
    15836 Chain information for AF3 E2 1-352.pdb #334 
    15837 --- 
    15838 Chain | Description 
    15839 B | No description available 
    15840  
    15841 
    15842 > matchmaker #334 to #1.7 & sel
    15843 
    15844 Parameters 
    15845 --- 
    15846 Chain pairing | bb 
    15847 Alignment algorithm | Needleman-Wunsch 
    15848 Similarity matrix | BLOSUM-62 
    15849 SS fraction | 0.3 
    15850 Gap open (HH/SS/other) | 18/18/6 
    15851 Gap extend | 1 
    15852 SS matrix |  |  | H | S | O 
    15853 ---|---|---|--- 
    15854 H | 6 | -9 | -6 
    15855 S |  | 6 | -6 
    15856 O |  |  | 4 
    15857 Iteration cutoff | 2 
    15858  
    15859 Matchmaker 3j0c.pdb1, chain E (#1.7) with AF3 E2 1-352.pdb, chain B (#334),
    15860 sequence alignment score = 594.5 
    15861 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    15862 6.147) 
    15863  
    15864 
    15865 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    15866 
    15867 Chain information for AF3 E2 353-438.pdb #335 
    15868 --- 
    15869 Chain | Description 
    15870 B | No description available 
    15871  
    15872 
    15873 > matchmaker #335 to #1.7 & sel
    15874 
    15875 Parameters 
    15876 --- 
    15877 Chain pairing | bb 
    15878 Alignment algorithm | Needleman-Wunsch 
    15879 Similarity matrix | BLOSUM-62 
    15880 SS fraction | 0.3 
    15881 Gap open (HH/SS/other) | 18/18/6 
    15882 Gap extend | 1 
    15883 SS matrix |  |  | H | S | O 
    15884 ---|---|---|--- 
    15885 H | 6 | -9 | -6 
    15886 S |  | 6 | -6 
    15887 O |  |  | 4 
    15888 Iteration cutoff | 2 
    15889  
    15890 Matchmaker 3j0c.pdb1, chain E (#1.7) with AF3 E2 353-438.pdb, chain B (#335),
    15891 sequence alignment score = 340.2 
    15892 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    15893 8.673) 
    15894  
    15895 
    15896 > hide sel cartoons
    15897 
    15898 > select #1.7/F
    15899 
    15900 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    15901 
    15902 > show sel cartoons
    15903 
    15904 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    15905 
    15906 Chain information for AF3 CA.pdb #336 
    15907 --- 
    15908 Chain | Description 
    15909 A | No description available 
    15910  
    15911 
    15912 > matchmaker #336 to #1.7 & sel
    15913 
    15914 Parameters 
    15915 --- 
    15916 Chain pairing | bb 
    15917 Alignment algorithm | Needleman-Wunsch 
    15918 Similarity matrix | BLOSUM-62 
    15919 SS fraction | 0.3 
    15920 Gap open (HH/SS/other) | 18/18/6 
    15921 Gap extend | 1 
    15922 SS matrix |  |  | H | S | O 
    15923 ---|---|---|--- 
    15924 H | 6 | -9 | -6 
    15925 S |  | 6 | -6 
    15926 O |  |  | 4 
    15927 Iteration cutoff | 2 
    15928  
    15929 Matchmaker 3j0c.pdb1, chain F (#1.7) with AF3 CA.pdb, chain A (#336), sequence
    15930 alignment score = 335.3 
    15931 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    15932 2.550) 
    15933  
    15934 
    15935 > hide sel cartoons
    15936 
    15937 > color #332 dodgerblue
    15938 
    15939 > color #333 dodgerblue
    15940 
    15941 > color #334 #00b305ff
    15942 
    15943 > color #335 #00b305ff
    15944 
    15945 > color #336 #f15839ff
    15946 
    15947 > select #1.8/D
    15948 
    15949 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    15950 
    15951 > show sel cartoons
    15952 
    15953 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    15954 
    15955 Chain information for AF3 E1 1-421.pdb #337 
    15956 --- 
    15957 Chain | Description 
    15958 A | No description available 
    15959  
    15960 
    15961 > matchmaker #337 to #1.8 & sel
    15962 
    15963 Parameters 
    15964 --- 
    15965 Chain pairing | bb 
    15966 Alignment algorithm | Needleman-Wunsch 
    15967 Similarity matrix | BLOSUM-62 
    15968 SS fraction | 0.3 
    15969 Gap open (HH/SS/other) | 18/18/6 
    15970 Gap extend | 1 
    15971 SS matrix |  |  | H | S | O 
    15972 ---|---|---|--- 
    15973 H | 6 | -9 | -6 
    15974 S |  | 6 | -6 
    15975 O |  |  | 4 
    15976 Iteration cutoff | 2 
    15977  
    15978 Matchmaker 3j0c.pdb1, chain D (#1.8) with AF3 E1 1-421.pdb, chain A (#337),
    15979 sequence alignment score = 1060.7 
    15980 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    15981 3.032) 
    15982  
    15983 
    15984 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    15985 
    15986 Chain information for AF3 E1 422-461.pdb #338 
    15987 --- 
    15988 Chain | Description 
    15989 A | No description available 
    15990  
    15991 
    15992 > matchmaker #338 to #1.8 & sel
    15993 
    15994 Parameters 
    15995 --- 
    15996 Chain pairing | bb 
    15997 Alignment algorithm | Needleman-Wunsch 
    15998 Similarity matrix | BLOSUM-62 
    15999 SS fraction | 0.3 
    16000 Gap open (HH/SS/other) | 18/18/6 
    16001 Gap extend | 1 
    16002 SS matrix |  |  | H | S | O 
    16003 ---|---|---|--- 
    16004 H | 6 | -9 | -6 
    16005 S |  | 6 | -6 
    16006 O |  |  | 4 
    16007 Iteration cutoff | 2 
    16008  
    16009 Matchmaker 3j0c.pdb1, chain D (#1.8) with AF3 E1 422-461.pdb, chain A (#338),
    16010 sequence alignment score = 626.9 
    16011 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    16012 2.916) 
    16013  
    16014 
    16015 > hide sel cartoons
    16016 
    16017 > select #1.8/E
    16018 
    16019 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    16020 
    16021 > show sel cartoons
    16022 
    16023 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    16024 
    16025 Chain information for AF3 E2 1-352.pdb #339 
    16026 --- 
    16027 Chain | Description 
    16028 B | No description available 
    16029  
    16030 
    16031 > matchmaker #339 to #1.8 & sel
    16032 
    16033 Parameters 
    16034 --- 
    16035 Chain pairing | bb 
    16036 Alignment algorithm | Needleman-Wunsch 
    16037 Similarity matrix | BLOSUM-62 
    16038 SS fraction | 0.3 
    16039 Gap open (HH/SS/other) | 18/18/6 
    16040 Gap extend | 1 
    16041 SS matrix |  |  | H | S | O 
    16042 ---|---|---|--- 
    16043 H | 6 | -9 | -6 
    16044 S |  | 6 | -6 
    16045 O |  |  | 4 
    16046 Iteration cutoff | 2 
    16047  
    16048 Matchmaker 3j0c.pdb1, chain E (#1.8) with AF3 E2 1-352.pdb, chain B (#339),
    16049 sequence alignment score = 594.5 
    16050 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    16051 6.147) 
    16052  
    16053 
    16054 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    16055 
    16056 Chain information for AF3 E2 353-438.pdb #340 
    16057 --- 
    16058 Chain | Description 
    16059 B | No description available 
    16060  
    16061 
    16062 > matchmaker #340 to #1.8 & sel
    16063 
    16064 Parameters 
    16065 --- 
    16066 Chain pairing | bb 
    16067 Alignment algorithm | Needleman-Wunsch 
    16068 Similarity matrix | BLOSUM-62 
    16069 SS fraction | 0.3 
    16070 Gap open (HH/SS/other) | 18/18/6 
    16071 Gap extend | 1 
    16072 SS matrix |  |  | H | S | O 
    16073 ---|---|---|--- 
    16074 H | 6 | -9 | -6 
    16075 S |  | 6 | -6 
    16076 O |  |  | 4 
    16077 Iteration cutoff | 2 
    16078  
    16079 Matchmaker 3j0c.pdb1, chain E (#1.8) with AF3 E2 353-438.pdb, chain B (#340),
    16080 sequence alignment score = 340.2 
    16081 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    16082 8.673) 
    16083  
    16084 
    16085 > hide sel cartoons
    16086 
    16087 > select #1.8/F
    16088 
    16089 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    16090 
    16091 > show sel cartoons
    16092 
    16093 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    16094 
    16095 Chain information for AF3 CA.pdb #341 
    16096 --- 
    16097 Chain | Description 
    16098 A | No description available 
    16099  
    16100 
    16101 > matchmaker #341 to #1.8 & sel
    16102 
    16103 Parameters 
    16104 --- 
    16105 Chain pairing | bb 
    16106 Alignment algorithm | Needleman-Wunsch 
    16107 Similarity matrix | BLOSUM-62 
    16108 SS fraction | 0.3 
    16109 Gap open (HH/SS/other) | 18/18/6 
    16110 Gap extend | 1 
    16111 SS matrix |  |  | H | S | O 
    16112 ---|---|---|--- 
    16113 H | 6 | -9 | -6 
    16114 S |  | 6 | -6 
    16115 O |  |  | 4 
    16116 Iteration cutoff | 2 
    16117  
    16118 Matchmaker 3j0c.pdb1, chain F (#1.8) with AF3 CA.pdb, chain A (#341), sequence
    16119 alignment score = 335.3 
    16120 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    16121 2.550) 
    16122  
    16123 
    16124 > hide sel cartoons
    16125 
    16126 > color #337 dodgerblue
    16127 
    16128 > color #338 dodgerblue
    16129 
    16130 > color #339 #00b305ff
    16131 
    16132 > color #340 #00b305ff
    16133 
    16134 > color #341 #f15839ff
    16135 
    16136 > select #1.9/D
    16137 
    16138 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    16139 
    16140 > show sel cartoons
    16141 
    16142 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    16143 
    16144 Chain information for AF3 E1 1-421.pdb #342 
    16145 --- 
    16146 Chain | Description 
    16147 A | No description available 
    16148  
    16149 
    16150 > matchmaker #342 to #1.9 & sel
    16151 
    16152 Parameters 
    16153 --- 
    16154 Chain pairing | bb 
    16155 Alignment algorithm | Needleman-Wunsch 
    16156 Similarity matrix | BLOSUM-62 
    16157 SS fraction | 0.3 
    16158 Gap open (HH/SS/other) | 18/18/6 
    16159 Gap extend | 1 
    16160 SS matrix |  |  | H | S | O 
    16161 ---|---|---|--- 
    16162 H | 6 | -9 | -6 
    16163 S |  | 6 | -6 
    16164 O |  |  | 4 
    16165 Iteration cutoff | 2 
    16166  
    16167 Matchmaker 3j0c.pdb1, chain D (#1.9) with AF3 E1 1-421.pdb, chain A (#342),
    16168 sequence alignment score = 1060.7 
    16169 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    16170 3.032) 
    16171  
    16172 
    16173 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    16174 
    16175 Chain information for AF3 E1 422-461.pdb #343 
    16176 --- 
    16177 Chain | Description 
    16178 A | No description available 
    16179  
    16180 
    16181 > matchmaker #343 to #1.9 & sel
    16182 
    16183 Parameters 
    16184 --- 
    16185 Chain pairing | bb 
    16186 Alignment algorithm | Needleman-Wunsch 
    16187 Similarity matrix | BLOSUM-62 
    16188 SS fraction | 0.3 
    16189 Gap open (HH/SS/other) | 18/18/6 
    16190 Gap extend | 1 
    16191 SS matrix |  |  | H | S | O 
    16192 ---|---|---|--- 
    16193 H | 6 | -9 | -6 
    16194 S |  | 6 | -6 
    16195 O |  |  | 4 
    16196 Iteration cutoff | 2 
    16197  
    16198 Matchmaker 3j0c.pdb1, chain D (#1.9) with AF3 E1 422-461.pdb, chain A (#343),
    16199 sequence alignment score = 626.9 
    16200 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    16201 2.916) 
    16202  
    16203 
    16204 > hide sel cartoons
    16205 
    16206 > select #1.9/E
    16207 
    16208 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    16209 
    16210 > show sel cartoons
    16211 
    16212 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    16213 
    16214 Chain information for AF3 E2 1-352.pdb #344 
    16215 --- 
    16216 Chain | Description 
    16217 B | No description available 
    16218  
    16219 
    16220 > matchmaker #344 to #1.9 & sel
    16221 
    16222 Parameters 
    16223 --- 
    16224 Chain pairing | bb 
    16225 Alignment algorithm | Needleman-Wunsch 
    16226 Similarity matrix | BLOSUM-62 
    16227 SS fraction | 0.3 
    16228 Gap open (HH/SS/other) | 18/18/6 
    16229 Gap extend | 1 
    16230 SS matrix |  |  | H | S | O 
    16231 ---|---|---|--- 
    16232 H | 6 | -9 | -6 
    16233 S |  | 6 | -6 
    16234 O |  |  | 4 
    16235 Iteration cutoff | 2 
    16236  
    16237 Matchmaker 3j0c.pdb1, chain E (#1.9) with AF3 E2 1-352.pdb, chain B (#344),
    16238 sequence alignment score = 594.5 
    16239 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    16240 6.147) 
    16241  
    16242 
    16243 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    16244 
    16245 Chain information for AF3 E2 353-438.pdb #345 
    16246 --- 
    16247 Chain | Description 
    16248 B | No description available 
    16249  
    16250 
    16251 > matchmaker #345 to #1.9 & sel
    16252 
    16253 Parameters 
    16254 --- 
    16255 Chain pairing | bb 
    16256 Alignment algorithm | Needleman-Wunsch 
    16257 Similarity matrix | BLOSUM-62 
    16258 SS fraction | 0.3 
    16259 Gap open (HH/SS/other) | 18/18/6 
    16260 Gap extend | 1 
    16261 SS matrix |  |  | H | S | O 
    16262 ---|---|---|--- 
    16263 H | 6 | -9 | -6 
    16264 S |  | 6 | -6 
    16265 O |  |  | 4 
    16266 Iteration cutoff | 2 
    16267  
    16268 Matchmaker 3j0c.pdb1, chain E (#1.9) with AF3 E2 353-438.pdb, chain B (#345),
    16269 sequence alignment score = 340.2 
    16270 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    16271 8.673) 
    16272  
    16273 
    16274 > hide sel cartoons
    16275 
    16276 > select #1.9/F
    16277 
    16278 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    16279 
    16280 > show sel cartoons
    16281 
    16282 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    16283 
    16284 Chain information for AF3 CA.pdb #346 
    16285 --- 
    16286 Chain | Description 
    16287 A | No description available 
    16288  
    16289 
    16290 > matchmaker #346 to #1.9 & sel
    16291 
    16292 Parameters 
    16293 --- 
    16294 Chain pairing | bb 
    16295 Alignment algorithm | Needleman-Wunsch 
    16296 Similarity matrix | BLOSUM-62 
    16297 SS fraction | 0.3 
    16298 Gap open (HH/SS/other) | 18/18/6 
    16299 Gap extend | 1 
    16300 SS matrix |  |  | H | S | O 
    16301 ---|---|---|--- 
    16302 H | 6 | -9 | -6 
    16303 S |  | 6 | -6 
    16304 O |  |  | 4 
    16305 Iteration cutoff | 2 
    16306  
    16307 Matchmaker 3j0c.pdb1, chain F (#1.9) with AF3 CA.pdb, chain A (#346), sequence
    16308 alignment score = 335.3 
    16309 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    16310 2.550) 
    16311  
    16312 
    16313 > hide sel cartoons
    16314 
    16315 > color #342 dodgerblue
    16316 
    16317 > color #343 dodgerblue
    16318 
    16319 > color #344 #00b305ff
    16320 
    16321 > color #345 #00b305ff
    16322 
    16323 > color #346 #f15839ff
    16324 
    16325 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    16326 
    16327 > hide #302-346 models
    16328 
    16329 > select #1.10/D
    16330 
    16331 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    16332 
    16333 > show sel cartoons
    16334 
    16335 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    16336 
    16337 Chain information for AF3 E1 1-421.pdb #347 
    16338 --- 
    16339 Chain | Description 
    16340 A | No description available 
    16341  
    16342 
    16343 > matchmaker #347 to #1.10 & sel
    16344 
    16345 Parameters 
    16346 --- 
    16347 Chain pairing | bb 
    16348 Alignment algorithm | Needleman-Wunsch 
    16349 Similarity matrix | BLOSUM-62 
    16350 SS fraction | 0.3 
    16351 Gap open (HH/SS/other) | 18/18/6 
    16352 Gap extend | 1 
    16353 SS matrix |  |  | H | S | O 
    16354 ---|---|---|--- 
    16355 H | 6 | -9 | -6 
    16356 S |  | 6 | -6 
    16357 O |  |  | 4 
    16358 Iteration cutoff | 2 
    16359  
    16360 Matchmaker 3j0c.pdb1, chain D (#1.10) with AF3 E1 1-421.pdb, chain A (#347),
    16361 sequence alignment score = 1060.7 
    16362 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    16363 3.032) 
    16364  
    16365 
    16366 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    16367 
    16368 Chain information for AF3 E1 422-461.pdb #348 
    16369 --- 
    16370 Chain | Description 
    16371 A | No description available 
    16372  
    16373 
    16374 > matchmaker #348 to #1.10 & sel
    16375 
    16376 Parameters 
    16377 --- 
    16378 Chain pairing | bb 
    16379 Alignment algorithm | Needleman-Wunsch 
    16380 Similarity matrix | BLOSUM-62 
    16381 SS fraction | 0.3 
    16382 Gap open (HH/SS/other) | 18/18/6 
    16383 Gap extend | 1 
    16384 SS matrix |  |  | H | S | O 
    16385 ---|---|---|--- 
    16386 H | 6 | -9 | -6 
    16387 S |  | 6 | -6 
    16388 O |  |  | 4 
    16389 Iteration cutoff | 2 
    16390  
    16391 Matchmaker 3j0c.pdb1, chain D (#1.10) with AF3 E1 422-461.pdb, chain A (#348),
    16392 sequence alignment score = 626.9 
    16393 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    16394 2.916) 
    16395  
    16396 
    16397 > hide sel cartoons
    16398 
    16399 > select #1.10/E
    16400 
    16401 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    16402 
    16403 > show sel cartoons
    16404 
    16405 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    16406 
    16407 Chain information for AF3 E2 1-352.pdb #349 
    16408 --- 
    16409 Chain | Description 
    16410 B | No description available 
    16411  
    16412 
    16413 > matchmaker #349 to #1.10 & sel
    16414 
    16415 Parameters 
    16416 --- 
    16417 Chain pairing | bb 
    16418 Alignment algorithm | Needleman-Wunsch 
    16419 Similarity matrix | BLOSUM-62 
    16420 SS fraction | 0.3 
    16421 Gap open (HH/SS/other) | 18/18/6 
    16422 Gap extend | 1 
    16423 SS matrix |  |  | H | S | O 
    16424 ---|---|---|--- 
    16425 H | 6 | -9 | -6 
    16426 S |  | 6 | -6 
    16427 O |  |  | 4 
    16428 Iteration cutoff | 2 
    16429  
    16430 Matchmaker 3j0c.pdb1, chain E (#1.10) with AF3 E2 1-352.pdb, chain B (#349),
    16431 sequence alignment score = 594.5 
    16432 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    16433 6.147) 
    16434  
    16435 
    16436 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    16437 
    16438 Chain information for AF3 E2 353-438.pdb #350 
    16439 --- 
    16440 Chain | Description 
    16441 B | No description available 
    16442  
    16443 
    16444 > matchmaker #350 to #1.10 & sel
    16445 
    16446 Parameters 
    16447 --- 
    16448 Chain pairing | bb 
    16449 Alignment algorithm | Needleman-Wunsch 
    16450 Similarity matrix | BLOSUM-62 
    16451 SS fraction | 0.3 
    16452 Gap open (HH/SS/other) | 18/18/6 
    16453 Gap extend | 1 
    16454 SS matrix |  |  | H | S | O 
    16455 ---|---|---|--- 
    16456 H | 6 | -9 | -6 
    16457 S |  | 6 | -6 
    16458 O |  |  | 4 
    16459 Iteration cutoff | 2 
    16460  
    16461 Matchmaker 3j0c.pdb1, chain E (#1.10) with AF3 E2 353-438.pdb, chain B (#350),
    16462 sequence alignment score = 340.2 
    16463 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    16464 8.673) 
    16465  
    16466 
    16467 > hide sel cartoons
    16468 
    16469 > select #1.10/F
    16470 
    16471 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    16472 
    16473 > show sel cartoons
    16474 
    16475 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    16476 
    16477 Chain information for AF3 CA.pdb #351 
    16478 --- 
    16479 Chain | Description 
    16480 A | No description available 
    16481  
    16482 
    16483 > matchmaker #351 to #1.10 & sel
    16484 
    16485 Parameters 
    16486 --- 
    16487 Chain pairing | bb 
    16488 Alignment algorithm | Needleman-Wunsch 
    16489 Similarity matrix | BLOSUM-62 
    16490 SS fraction | 0.3 
    16491 Gap open (HH/SS/other) | 18/18/6 
    16492 Gap extend | 1 
    16493 SS matrix |  |  | H | S | O 
    16494 ---|---|---|--- 
    16495 H | 6 | -9 | -6 
    16496 S |  | 6 | -6 
    16497 O |  |  | 4 
    16498 Iteration cutoff | 2 
    16499  
    16500 Matchmaker 3j0c.pdb1, chain F (#1.10) with AF3 CA.pdb, chain A (#351),
    16501 sequence alignment score = 335.3 
    16502 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    16503 2.550) 
    16504  
    16505 
    16506 > hide sel cartoons
    16507 
    16508 > color #347 dodgerblue
    16509 
    16510 > color #348 dodgerblue
    16511 
    16512 > color #349 #00b305ff
    16513 
    16514 > color #350 #00b305ff
    16515 
    16516 > color #351 #f15839ff
    16517 
    16518 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    16519 
    16520 > select #1.11/D
    16521 
    16522 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    16523 
    16524 > show sel cartoons
    16525 
    16526 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    16527 
    16528 Chain information for AF3 E1 1-421.pdb #352 
    16529 --- 
    16530 Chain | Description 
    16531 A | No description available 
    16532  
    16533 
    16534 > matchmaker #352 to #1.11 & sel
    16535 
    16536 Parameters 
    16537 --- 
    16538 Chain pairing | bb 
    16539 Alignment algorithm | Needleman-Wunsch 
    16540 Similarity matrix | BLOSUM-62 
    16541 SS fraction | 0.3 
    16542 Gap open (HH/SS/other) | 18/18/6 
    16543 Gap extend | 1 
    16544 SS matrix |  |  | H | S | O 
    16545 ---|---|---|--- 
    16546 H | 6 | -9 | -6 
    16547 S |  | 6 | -6 
    16548 O |  |  | 4 
    16549 Iteration cutoff | 2 
    16550  
    16551 Matchmaker 3j0c.pdb1, chain D (#1.11) with AF3 E1 1-421.pdb, chain A (#352),
    16552 sequence alignment score = 1060.7 
    16553 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    16554 3.032) 
    16555  
    16556 
    16557 > view sel
    16558 
    16559 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    16560 
    16561 Chain information for AF3 E1 422-461.pdb #353 
    16562 --- 
    16563 Chain | Description 
    16564 A | No description available 
    16565  
    16566 
    16567 > matchmaker #353 to #1.11 & sel
    16568 
    16569 Parameters 
    16570 --- 
    16571 Chain pairing | bb 
    16572 Alignment algorithm | Needleman-Wunsch 
    16573 Similarity matrix | BLOSUM-62 
    16574 SS fraction | 0.3 
    16575 Gap open (HH/SS/other) | 18/18/6 
    16576 Gap extend | 1 
    16577 SS matrix |  |  | H | S | O 
    16578 ---|---|---|--- 
    16579 H | 6 | -9 | -6 
    16580 S |  | 6 | -6 
    16581 O |  |  | 4 
    16582 Iteration cutoff | 2 
    16583  
    16584 Matchmaker 3j0c.pdb1, chain D (#1.11) with AF3 E1 422-461.pdb, chain A (#353),
    16585 sequence alignment score = 626.9 
    16586 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    16587 2.916) 
    16588  
    16589 
    16590 > hide sel cartoons
    16591 
    16592 > select #1.11/E
    16593 
    16594 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    16595 
    16596 > show sel cartoons
    16597 
    16598 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    16599 
    16600 Chain information for AF3 E2 1-352.pdb #354 
    16601 --- 
    16602 Chain | Description 
    16603 B | No description available 
    16604  
    16605 
    16606 > matchmaker #354 to #1.11 & sel
    16607 
    16608 Parameters 
    16609 --- 
    16610 Chain pairing | bb 
    16611 Alignment algorithm | Needleman-Wunsch 
    16612 Similarity matrix | BLOSUM-62 
    16613 SS fraction | 0.3 
    16614 Gap open (HH/SS/other) | 18/18/6 
    16615 Gap extend | 1 
    16616 SS matrix |  |  | H | S | O 
    16617 ---|---|---|--- 
    16618 H | 6 | -9 | -6 
    16619 S |  | 6 | -6 
    16620 O |  |  | 4 
    16621 Iteration cutoff | 2 
    16622  
    16623 Matchmaker 3j0c.pdb1, chain E (#1.11) with AF3 E2 1-352.pdb, chain B (#354),
    16624 sequence alignment score = 594.5 
    16625 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    16626 6.147) 
    16627  
    16628 
    16629 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    16630 
    16631 Chain information for AF3 E2 353-438.pdb #355 
    16632 --- 
    16633 Chain | Description 
    16634 B | No description available 
    16635  
    16636 
    16637 > matchmaker #355 to #1.11 & sel
    16638 
    16639 Parameters 
    16640 --- 
    16641 Chain pairing | bb 
    16642 Alignment algorithm | Needleman-Wunsch 
    16643 Similarity matrix | BLOSUM-62 
    16644 SS fraction | 0.3 
    16645 Gap open (HH/SS/other) | 18/18/6 
    16646 Gap extend | 1 
    16647 SS matrix |  |  | H | S | O 
    16648 ---|---|---|--- 
    16649 H | 6 | -9 | -6 
    16650 S |  | 6 | -6 
    16651 O |  |  | 4 
    16652 Iteration cutoff | 2 
    16653  
    16654 Matchmaker 3j0c.pdb1, chain E (#1.11) with AF3 E2 353-438.pdb, chain B (#355),
    16655 sequence alignment score = 340.2 
    16656 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    16657 8.673) 
    16658  
    16659 
    16660 > hide sel cartoons
    16661 
    16662 > select #1.11/F
    16663 
    16664 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    16665 
    16666 > show sel cartoons
    16667 
    16668 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    16669 
    16670 Chain information for AF3 CA.pdb #356 
    16671 --- 
    16672 Chain | Description 
    16673 A | No description available 
    16674  
    16675 
    16676 > matchmaker #356 to #1.11 & sel
    16677 
    16678 Parameters 
    16679 --- 
    16680 Chain pairing | bb 
    16681 Alignment algorithm | Needleman-Wunsch 
    16682 Similarity matrix | BLOSUM-62 
    16683 SS fraction | 0.3 
    16684 Gap open (HH/SS/other) | 18/18/6 
    16685 Gap extend | 1 
    16686 SS matrix |  |  | H | S | O 
    16687 ---|---|---|--- 
    16688 H | 6 | -9 | -6 
    16689 S |  | 6 | -6 
    16690 O |  |  | 4 
    16691 Iteration cutoff | 2 
    16692  
    16693 Matchmaker 3j0c.pdb1, chain F (#1.11) with AF3 CA.pdb, chain A (#356),
    16694 sequence alignment score = 335.3 
    16695 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    16696 2.550) 
    16697  
    16698 
    16699 > hide sel cartoons
    16700 
    16701 > color #352 dodgerblue
    16702 
    16703 > color #353 dodgerblue
    16704 
    16705 > color #354 #00b305ff
    16706 
    16707 > color #355 #00b305ff
    16708 
    16709 > color #356 #f15839ff
    16710 
    16711 > select #1.12/D
    16712 
    16713 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    16714 
    16715 > show sel cartoons
    16716 
    16717 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    16718 
    16719 Chain information for AF3 E1 1-421.pdb #357 
    16720 --- 
    16721 Chain | Description 
    16722 A | No description available 
    16723  
    16724 
    16725 > matchmaker #357 to #1.11 & sel
    16726 
    16727 No 'to' model specified 
    16728 
    16729 > matchmaker #357 to #1.12 & sel
    16730 
    16731 Parameters 
    16732 --- 
    16733 Chain pairing | bb 
    16734 Alignment algorithm | Needleman-Wunsch 
    16735 Similarity matrix | BLOSUM-62 
    16736 SS fraction | 0.3 
    16737 Gap open (HH/SS/other) | 18/18/6 
    16738 Gap extend | 1 
    16739 SS matrix |  |  | H | S | O 
    16740 ---|---|---|--- 
    16741 H | 6 | -9 | -6 
    16742 S |  | 6 | -6 
    16743 O |  |  | 4 
    16744 Iteration cutoff | 2 
    16745  
    16746 Matchmaker 3j0c.pdb1, chain D (#1.12) with AF3 E1 1-421.pdb, chain A (#357),
    16747 sequence alignment score = 1060.7 
    16748 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    16749 3.032) 
    16750  
    16751 
    16752 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    16753 
    16754 Chain information for AF3 E1 422-461.pdb #358 
    16755 --- 
    16756 Chain | Description 
    16757 A | No description available 
    16758  
    16759 
    16760 > matchmaker #358 to #1.12 & sel
    16761 
    16762 Parameters 
    16763 --- 
    16764 Chain pairing | bb 
    16765 Alignment algorithm | Needleman-Wunsch 
    16766 Similarity matrix | BLOSUM-62 
    16767 SS fraction | 0.3 
    16768 Gap open (HH/SS/other) | 18/18/6 
    16769 Gap extend | 1 
    16770 SS matrix |  |  | H | S | O 
    16771 ---|---|---|--- 
    16772 H | 6 | -9 | -6 
    16773 S |  | 6 | -6 
    16774 O |  |  | 4 
    16775 Iteration cutoff | 2 
    16776  
    16777 Matchmaker 3j0c.pdb1, chain D (#1.12) with AF3 E1 422-461.pdb, chain A (#358),
    16778 sequence alignment score = 626.9 
    16779 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    16780 2.916) 
    16781  
    16782 
    16783 > hide sel cartoons
    16784 
    16785 > select #1.12/E
    16786 
    16787 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    16788 
    16789 > show sel cartoons
    16790 
    16791 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    16792 
    16793 Chain information for AF3 E2 1-352.pdb #359 
    16794 --- 
    16795 Chain | Description 
    16796 B | No description available 
    16797  
    16798 
    16799 > matchmaker #359 to #1.12 & sel
    16800 
    16801 Parameters 
    16802 --- 
    16803 Chain pairing | bb 
    16804 Alignment algorithm | Needleman-Wunsch 
    16805 Similarity matrix | BLOSUM-62 
    16806 SS fraction | 0.3 
    16807 Gap open (HH/SS/other) | 18/18/6 
    16808 Gap extend | 1 
    16809 SS matrix |  |  | H | S | O 
    16810 ---|---|---|--- 
    16811 H | 6 | -9 | -6 
    16812 S |  | 6 | -6 
    16813 O |  |  | 4 
    16814 Iteration cutoff | 2 
    16815  
    16816 Matchmaker 3j0c.pdb1, chain E (#1.12) with AF3 E2 1-352.pdb, chain B (#359),
    16817 sequence alignment score = 594.5 
    16818 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    16819 6.147) 
    16820  
    16821 
    16822 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    16823 
    16824 Chain information for AF3 E2 353-438.pdb #360 
    16825 --- 
    16826 Chain | Description 
    16827 B | No description available 
    16828  
    16829 
    16830 > matchmaker #360 to #1.12 & sel
    16831 
    16832 Parameters 
    16833 --- 
    16834 Chain pairing | bb 
    16835 Alignment algorithm | Needleman-Wunsch 
    16836 Similarity matrix | BLOSUM-62 
    16837 SS fraction | 0.3 
    16838 Gap open (HH/SS/other) | 18/18/6 
    16839 Gap extend | 1 
    16840 SS matrix |  |  | H | S | O 
    16841 ---|---|---|--- 
    16842 H | 6 | -9 | -6 
    16843 S |  | 6 | -6 
    16844 O |  |  | 4 
    16845 Iteration cutoff | 2 
    16846  
    16847 Matchmaker 3j0c.pdb1, chain E (#1.12) with AF3 E2 353-438.pdb, chain B (#360),
    16848 sequence alignment score = 340.2 
    16849 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    16850 8.673) 
    16851  
    16852 
    16853 > hide sel cartoons
    16854 
    16855 > select #1.12/F
    16856 
    16857 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    16858 
    16859 > show sel cartoons
    16860 
    16861 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    16862 
    16863 Chain information for AF3 CA.pdb #361 
    16864 --- 
    16865 Chain | Description 
    16866 A | No description available 
    16867  
    16868 
    16869 > matchmaker #361 to #1.12 & sel
    16870 
    16871 Parameters 
    16872 --- 
    16873 Chain pairing | bb 
    16874 Alignment algorithm | Needleman-Wunsch 
    16875 Similarity matrix | BLOSUM-62 
    16876 SS fraction | 0.3 
    16877 Gap open (HH/SS/other) | 18/18/6 
    16878 Gap extend | 1 
    16879 SS matrix |  |  | H | S | O 
    16880 ---|---|---|--- 
    16881 H | 6 | -9 | -6 
    16882 S |  | 6 | -6 
    16883 O |  |  | 4 
    16884 Iteration cutoff | 2 
    16885  
    16886 Matchmaker 3j0c.pdb1, chain F (#1.12) with AF3 CA.pdb, chain A (#361),
    16887 sequence alignment score = 335.3 
    16888 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    16889 2.550) 
    16890  
    16891 
    16892 > hide sel cartoons
    16893 
    16894 > color #357 dodgerblue
    16895 
    16896 > color #358 dodgerblue
    16897 
    16898 > color #359 #00b305ff
    16899 
    16900 > color #360 #00b305ff
    16901 
    16902 > color #361 #f15839ff
    16903 
    16904 > select #1.13/D
    16905 
    16906 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    16907 
    16908 > show sel cartoons
    16909 
    16910 > lighting soft
    16911 
    16912 > lighting full
    16913 
    16914 > lighting simple
    16915 
    16916 > lighting soft
    16917 
    16918 [Repeated 1 time(s)]
    16919 
    16920 > view
    16921 
    16922 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    16923 
    16924 Chain information for AF3 E1 1-421.pdb #362 
    16925 --- 
    16926 Chain | Description 
    16927 A | No description available 
    16928  
    16929 
    16930 > matchmaker #362 to #1.13 & sel
    16931 
    16932 Parameters 
    16933 --- 
    16934 Chain pairing | bb 
    16935 Alignment algorithm | Needleman-Wunsch 
    16936 Similarity matrix | BLOSUM-62 
    16937 SS fraction | 0.3 
    16938 Gap open (HH/SS/other) | 18/18/6 
    16939 Gap extend | 1 
    16940 SS matrix |  |  | H | S | O 
    16941 ---|---|---|--- 
    16942 H | 6 | -9 | -6 
    16943 S |  | 6 | -6 
    16944 O |  |  | 4 
    16945 Iteration cutoff | 2 
    16946  
    16947 Matchmaker 3j0c.pdb1, chain D (#1.13) with AF3 E1 1-421.pdb, chain A (#362),
    16948 sequence alignment score = 1060.7 
    16949 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    16950 3.032) 
    16951  
    16952 
    16953 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    16954 
    16955 Chain information for AF3 E1 422-461.pdb #363 
    16956 --- 
    16957 Chain | Description 
    16958 A | No description available 
    16959  
    16960 
    16961 > matchmaker #363 to #1.13 & sel
    16962 
    16963 Parameters 
    16964 --- 
    16965 Chain pairing | bb 
    16966 Alignment algorithm | Needleman-Wunsch 
    16967 Similarity matrix | BLOSUM-62 
    16968 SS fraction | 0.3 
    16969 Gap open (HH/SS/other) | 18/18/6 
    16970 Gap extend | 1 
    16971 SS matrix |  |  | H | S | O 
    16972 ---|---|---|--- 
    16973 H | 6 | -9 | -6 
    16974 S |  | 6 | -6 
    16975 O |  |  | 4 
    16976 Iteration cutoff | 2 
    16977  
    16978 Matchmaker 3j0c.pdb1, chain D (#1.13) with AF3 E1 422-461.pdb, chain A (#363),
    16979 sequence alignment score = 626.9 
    16980 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    16981 2.916) 
    16982  
    16983 
    16984 > hide sel cartoons
    16985 
    16986 > lighting simple
    16987 
    16988 > select #1.13/E
    16989 
    16990 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    16991 
    16992 > show sel cartoons
    16993 
    16994 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    16995 
    16996 Chain information for AF3 E2 1-352.pdb #364 
    16997 --- 
    16998 Chain | Description 
    16999 B | No description available 
    17000  
    17001 
    17002 > matchmaker #364 to #1.13 & sel
    17003 
    17004 Parameters 
    17005 --- 
    17006 Chain pairing | bb 
    17007 Alignment algorithm | Needleman-Wunsch 
    17008 Similarity matrix | BLOSUM-62 
    17009 SS fraction | 0.3 
    17010 Gap open (HH/SS/other) | 18/18/6 
    17011 Gap extend | 1 
    17012 SS matrix |  |  | H | S | O 
    17013 ---|---|---|--- 
    17014 H | 6 | -9 | -6 
    17015 S |  | 6 | -6 
    17016 O |  |  | 4 
    17017 Iteration cutoff | 2 
    17018  
    17019 Matchmaker 3j0c.pdb1, chain E (#1.13) with AF3 E2 1-352.pdb, chain B (#364),
    17020 sequence alignment score = 594.5 
    17021 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    17022 6.147) 
    17023  
    17024 
    17025 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    17026 
    17027 Chain information for AF3 E2 353-438.pdb #365 
    17028 --- 
    17029 Chain | Description 
    17030 B | No description available 
    17031  
    17032 
    17033 > matchmaker #365 to #1.13 & sel
    17034 
    17035 Parameters 
    17036 --- 
    17037 Chain pairing | bb 
    17038 Alignment algorithm | Needleman-Wunsch 
    17039 Similarity matrix | BLOSUM-62 
    17040 SS fraction | 0.3 
    17041 Gap open (HH/SS/other) | 18/18/6 
    17042 Gap extend | 1 
    17043 SS matrix |  |  | H | S | O 
    17044 ---|---|---|--- 
    17045 H | 6 | -9 | -6 
    17046 S |  | 6 | -6 
    17047 O |  |  | 4 
    17048 Iteration cutoff | 2 
    17049  
    17050 Matchmaker 3j0c.pdb1, chain E (#1.13) with AF3 E2 353-438.pdb, chain B (#365),
    17051 sequence alignment score = 340.2 
    17052 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    17053 8.673) 
    17054  
    17055 
    17056 > hide sel cartoons
    17057 
    17058 > select #1.13/F
    17059 
    17060 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    17061 
    17062 > show sel cartoons
    17063 
    17064 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    17065 
    17066 Chain information for AF3 CA.pdb #366 
    17067 --- 
    17068 Chain | Description 
    17069 A | No description available 
    17070  
    17071 
    17072 > matchmaker #366 to #1.13 & sel
    17073 
    17074 Parameters 
    17075 --- 
    17076 Chain pairing | bb 
    17077 Alignment algorithm | Needleman-Wunsch 
    17078 Similarity matrix | BLOSUM-62 
    17079 SS fraction | 0.3 
    17080 Gap open (HH/SS/other) | 18/18/6 
    17081 Gap extend | 1 
    17082 SS matrix |  |  | H | S | O 
    17083 ---|---|---|--- 
    17084 H | 6 | -9 | -6 
    17085 S |  | 6 | -6 
    17086 O |  |  | 4 
    17087 Iteration cutoff | 2 
    17088  
    17089 Matchmaker 3j0c.pdb1, chain F (#1.13) with AF3 CA.pdb, chain A (#366),
    17090 sequence alignment score = 335.3 
    17091 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    17092 2.550) 
    17093  
    17094 
    17095 > hide sel cartoons
    17096 
    17097 > color #362 dodgerblue
    17098 
    17099 > color #363 dodgerblue
    17100 
    17101 > color #364 #00b305ff
    17102 
    17103 > color #365 #00b305ff
    17104 
    17105 > color #366 #f15839ff
    17106 
    17107 > select #1.14/D
    17108 
    17109 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    17110 
    17111 > show sel cartoons
    17112 
    17113 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    17114 
    17115 Chain information for AF3 E1 1-421.pdb #367 
    17116 --- 
    17117 Chain | Description 
    17118 A | No description available 
    17119  
    17120 
    17121 > matchmaker #367 to #1.14 & sel
    17122 
    17123 Parameters 
    17124 --- 
    17125 Chain pairing | bb 
    17126 Alignment algorithm | Needleman-Wunsch 
    17127 Similarity matrix | BLOSUM-62 
    17128 SS fraction | 0.3 
    17129 Gap open (HH/SS/other) | 18/18/6 
    17130 Gap extend | 1 
    17131 SS matrix |  |  | H | S | O 
    17132 ---|---|---|--- 
    17133 H | 6 | -9 | -6 
    17134 S |  | 6 | -6 
    17135 O |  |  | 4 
    17136 Iteration cutoff | 2 
    17137  
    17138 Matchmaker 3j0c.pdb1, chain D (#1.14) with AF3 E1 1-421.pdb, chain A (#367),
    17139 sequence alignment score = 1060.7 
    17140 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    17141 3.032) 
    17142  
    17143 
    17144 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    17145 
    17146 Chain information for AF3 E1 422-461.pdb #368 
    17147 --- 
    17148 Chain | Description 
    17149 A | No description available 
    17150  
    17151 
    17152 > matchmaker #368 to #1.14 & sel
    17153 
    17154 Parameters 
    17155 --- 
    17156 Chain pairing | bb 
    17157 Alignment algorithm | Needleman-Wunsch 
    17158 Similarity matrix | BLOSUM-62 
    17159 SS fraction | 0.3 
    17160 Gap open (HH/SS/other) | 18/18/6 
    17161 Gap extend | 1 
    17162 SS matrix |  |  | H | S | O 
    17163 ---|---|---|--- 
    17164 H | 6 | -9 | -6 
    17165 S |  | 6 | -6 
    17166 O |  |  | 4 
    17167 Iteration cutoff | 2 
    17168  
    17169 Matchmaker 3j0c.pdb1, chain D (#1.14) with AF3 E1 422-461.pdb, chain A (#368),
    17170 sequence alignment score = 626.9 
    17171 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    17172 2.916) 
    17173  
    17174 
    17175 > hide sel cartoons
    17176 
    17177 > select #1.14/E
    17178 
    17179 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    17180 
    17181 > show sel cartoons
    17182 
    17183 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    17184 
    17185 Chain information for AF3 E2 1-352.pdb #369 
    17186 --- 
    17187 Chain | Description 
    17188 B | No description available 
    17189  
    17190 
    17191 > matchmaker #369 to #1.14 & sel
    17192 
    17193 Parameters 
    17194 --- 
    17195 Chain pairing | bb 
    17196 Alignment algorithm | Needleman-Wunsch 
    17197 Similarity matrix | BLOSUM-62 
    17198 SS fraction | 0.3 
    17199 Gap open (HH/SS/other) | 18/18/6 
    17200 Gap extend | 1 
    17201 SS matrix |  |  | H | S | O 
    17202 ---|---|---|--- 
    17203 H | 6 | -9 | -6 
    17204 S |  | 6 | -6 
    17205 O |  |  | 4 
    17206 Iteration cutoff | 2 
    17207  
    17208 Matchmaker 3j0c.pdb1, chain E (#1.14) with AF3 E2 1-352.pdb, chain B (#369),
    17209 sequence alignment score = 594.5 
    17210 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    17211 6.147) 
    17212  
    17213 
    17214 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    17215 
    17216 Chain information for AF3 E2 353-438.pdb #370 
    17217 --- 
    17218 Chain | Description 
    17219 B | No description available 
    17220  
    17221 
    17222 > matchmaker #370 to #1.14 & sel
    17223 
    17224 Parameters 
    17225 --- 
    17226 Chain pairing | bb 
    17227 Alignment algorithm | Needleman-Wunsch 
    17228 Similarity matrix | BLOSUM-62 
    17229 SS fraction | 0.3 
    17230 Gap open (HH/SS/other) | 18/18/6 
    17231 Gap extend | 1 
    17232 SS matrix |  |  | H | S | O 
    17233 ---|---|---|--- 
    17234 H | 6 | -9 | -6 
    17235 S |  | 6 | -6 
    17236 O |  |  | 4 
    17237 Iteration cutoff | 2 
    17238  
    17239 Matchmaker 3j0c.pdb1, chain E (#1.14) with AF3 E2 353-438.pdb, chain B (#370),
    17240 sequence alignment score = 340.2 
    17241 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    17242 8.673) 
    17243  
    17244 
    17245 > hide sel cartoons
    17246 
    17247 > select #1.14/F
    17248 
    17249 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    17250 
    17251 > show sel cartoons
    17252 
    17253 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    17254 
    17255 Chain information for AF3 CA.pdb #371 
    17256 --- 
    17257 Chain | Description 
    17258 A | No description available 
    17259  
    17260 
    17261 > matchmaker #371 to #1.14 & sel
    17262 
    17263 Parameters 
    17264 --- 
    17265 Chain pairing | bb 
    17266 Alignment algorithm | Needleman-Wunsch 
    17267 Similarity matrix | BLOSUM-62 
    17268 SS fraction | 0.3 
    17269 Gap open (HH/SS/other) | 18/18/6 
    17270 Gap extend | 1 
    17271 SS matrix |  |  | H | S | O 
    17272 ---|---|---|--- 
    17273 H | 6 | -9 | -6 
    17274 S |  | 6 | -6 
    17275 O |  |  | 4 
    17276 Iteration cutoff | 2 
    17277  
    17278 Matchmaker 3j0c.pdb1, chain F (#1.14) with AF3 CA.pdb, chain A (#371),
    17279 sequence alignment score = 335.3 
    17280 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    17281 2.550) 
    17282  
    17283 
    17284 > hide sel cartoons
    17285 
    17286 > color #367 dodgerblue
    17287 
    17288 > color #368 dodgerblue
    17289 
    17290 > color #369 #00b305ff
    17291 
    17292 > color #370 #00b305ff
    17293 
    17294 > color #371 #f15839ff
    17295 
    17296 > select #1.16/D
    17297 
    17298 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    17299 
    17300 > show sel cartoons
    17301 
    17302 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    17303 
    17304 Chain information for AF3 E1 1-421.pdb #372 
    17305 --- 
    17306 Chain | Description 
    17307 A | No description available 
    17308  
    17309 
    17310 > hide sel cartoons
    17311 
    17312 > select #1.15/D
    17313 
    17314 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    17315 
    17316 > show sel cartoons
    17317 
    17318 > matchmaker #372 to #1.15 & sel
    17319 
    17320 Parameters 
    17321 --- 
    17322 Chain pairing | bb 
    17323 Alignment algorithm | Needleman-Wunsch 
    17324 Similarity matrix | BLOSUM-62 
    17325 SS fraction | 0.3 
    17326 Gap open (HH/SS/other) | 18/18/6 
    17327 Gap extend | 1 
    17328 SS matrix |  |  | H | S | O 
    17329 ---|---|---|--- 
    17330 H | 6 | -9 | -6 
    17331 S |  | 6 | -6 
    17332 O |  |  | 4 
    17333 Iteration cutoff | 2 
    17334  
    17335 Matchmaker 3j0c.pdb1, chain D (#1.15) with AF3 E1 1-421.pdb, chain A (#372),
    17336 sequence alignment score = 1060.7 
    17337 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    17338 3.032) 
    17339  
    17340 
    17341 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    17342 
    17343 Chain information for AF3 E1 422-461.pdb #373 
    17344 --- 
    17345 Chain | Description 
    17346 A | No description available 
    17347  
    17348 
    17349 > matchmaker #373 to #1.15 & sel
    17350 
    17351 Parameters 
    17352 --- 
    17353 Chain pairing | bb 
    17354 Alignment algorithm | Needleman-Wunsch 
    17355 Similarity matrix | BLOSUM-62 
    17356 SS fraction | 0.3 
    17357 Gap open (HH/SS/other) | 18/18/6 
    17358 Gap extend | 1 
    17359 SS matrix |  |  | H | S | O 
    17360 ---|---|---|--- 
    17361 H | 6 | -9 | -6 
    17362 S |  | 6 | -6 
    17363 O |  |  | 4 
    17364 Iteration cutoff | 2 
    17365  
    17366 Matchmaker 3j0c.pdb1, chain D (#1.15) with AF3 E1 422-461.pdb, chain A (#373),
    17367 sequence alignment score = 626.9 
    17368 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    17369 2.916) 
    17370  
    17371 
    17372 > hide sel cartoons
    17373 
    17374 > select #1.15/E
    17375 
    17376 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    17377 
    17378 > show sel cartoons
    17379 
    17380 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    17381 
    17382 Chain information for AF3 E2 1-352.pdb #374 
    17383 --- 
    17384 Chain | Description 
    17385 B | No description available 
    17386  
    17387 
    17388 > matchmaker #374 to #1.15 & sel
    17389 
    17390 Parameters 
    17391 --- 
    17392 Chain pairing | bb 
    17393 Alignment algorithm | Needleman-Wunsch 
    17394 Similarity matrix | BLOSUM-62 
    17395 SS fraction | 0.3 
    17396 Gap open (HH/SS/other) | 18/18/6 
    17397 Gap extend | 1 
    17398 SS matrix |  |  | H | S | O 
    17399 ---|---|---|--- 
    17400 H | 6 | -9 | -6 
    17401 S |  | 6 | -6 
    17402 O |  |  | 4 
    17403 Iteration cutoff | 2 
    17404  
    17405 Matchmaker 3j0c.pdb1, chain E (#1.15) with AF3 E2 1-352.pdb, chain B (#374),
    17406 sequence alignment score = 594.5 
    17407 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    17408 6.147) 
    17409  
    17410 
    17411 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    17412 
    17413 Chain information for AF3 E2 353-438.pdb #375 
    17414 --- 
    17415 Chain | Description 
    17416 B | No description available 
    17417  
    17418 
    17419 > matchmaker #375 to #1.15 & sel
    17420 
    17421 Parameters 
    17422 --- 
    17423 Chain pairing | bb 
    17424 Alignment algorithm | Needleman-Wunsch 
    17425 Similarity matrix | BLOSUM-62 
    17426 SS fraction | 0.3 
    17427 Gap open (HH/SS/other) | 18/18/6 
    17428 Gap extend | 1 
    17429 SS matrix |  |  | H | S | O 
    17430 ---|---|---|--- 
    17431 H | 6 | -9 | -6 
    17432 S |  | 6 | -6 
    17433 O |  |  | 4 
    17434 Iteration cutoff | 2 
    17435  
    17436 Matchmaker 3j0c.pdb1, chain E (#1.15) with AF3 E2 353-438.pdb, chain B (#375),
    17437 sequence alignment score = 340.2 
    17438 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    17439 8.673) 
    17440  
    17441 
    17442 > hide sel cartoons
    17443 
    17444 > select #1.15/F
    17445 
    17446 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    17447 
    17448 > show sel cartoons
    17449 
    17450 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    17451 
    17452 Chain information for AF3 CA.pdb #376 
    17453 --- 
    17454 Chain | Description 
    17455 A | No description available 
    17456  
    17457 
    17458 > matchmaker #376 to #1.15 & sel
    17459 
    17460 Parameters 
    17461 --- 
    17462 Chain pairing | bb 
    17463 Alignment algorithm | Needleman-Wunsch 
    17464 Similarity matrix | BLOSUM-62 
    17465 SS fraction | 0.3 
    17466 Gap open (HH/SS/other) | 18/18/6 
    17467 Gap extend | 1 
    17468 SS matrix |  |  | H | S | O 
    17469 ---|---|---|--- 
    17470 H | 6 | -9 | -6 
    17471 S |  | 6 | -6 
    17472 O |  |  | 4 
    17473 Iteration cutoff | 2 
    17474  
    17475 Matchmaker 3j0c.pdb1, chain F (#1.15) with AF3 CA.pdb, chain A (#376),
    17476 sequence alignment score = 335.3 
    17477 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    17478 2.550) 
    17479  
    17480 
    17481 > hide sel cartoons
    17482 
    17483 > color #372 dodgerblue
    17484 
    17485 > color #373 dodgerblue
    17486 
    17487 > color #374 #00b305ff
    17488 
    17489 > color #375 #00b305ff
    17490 
    17491 > color #376 #f15839ff
    17492 
    17493 > select #1.16/D
    17494 
    17495 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    17496 
    17497 > show sel cartoons
    17498 
    17499 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    17500 
    17501 Chain information for AF3 E1 1-421.pdb #377 
    17502 --- 
    17503 Chain | Description 
    17504 A | No description available 
    17505  
    17506 
    17507 > matchmaker #377 to #1.15 & sel
    17508 
    17509 No 'to' model specified 
    17510 
    17511 > matchmaker #377 to #1.16 & sel
    17512 
    17513 Parameters 
    17514 --- 
    17515 Chain pairing | bb 
    17516 Alignment algorithm | Needleman-Wunsch 
    17517 Similarity matrix | BLOSUM-62 
    17518 SS fraction | 0.3 
    17519 Gap open (HH/SS/other) | 18/18/6 
    17520 Gap extend | 1 
    17521 SS matrix |  |  | H | S | O 
    17522 ---|---|---|--- 
    17523 H | 6 | -9 | -6 
    17524 S |  | 6 | -6 
    17525 O |  |  | 4 
    17526 Iteration cutoff | 2 
    17527  
    17528 Matchmaker 3j0c.pdb1, chain D (#1.16) with AF3 E1 1-421.pdb, chain A (#377),
    17529 sequence alignment score = 1060.7 
    17530 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    17531 3.032) 
    17532  
    17533 
    17534 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    17535 
    17536 Chain information for AF3 E1 422-461.pdb #378 
    17537 --- 
    17538 Chain | Description 
    17539 A | No description available 
    17540  
    17541 
    17542 > matchmaker #378 to #1.16 & sel
    17543 
    17544 Parameters 
    17545 --- 
    17546 Chain pairing | bb 
    17547 Alignment algorithm | Needleman-Wunsch 
    17548 Similarity matrix | BLOSUM-62 
    17549 SS fraction | 0.3 
    17550 Gap open (HH/SS/other) | 18/18/6 
    17551 Gap extend | 1 
    17552 SS matrix |  |  | H | S | O 
    17553 ---|---|---|--- 
    17554 H | 6 | -9 | -6 
    17555 S |  | 6 | -6 
    17556 O |  |  | 4 
    17557 Iteration cutoff | 2 
    17558  
    17559 Matchmaker 3j0c.pdb1, chain D (#1.16) with AF3 E1 422-461.pdb, chain A (#378),
    17560 sequence alignment score = 626.9 
    17561 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    17562 2.916) 
    17563  
    17564 
    17565 > hide sel cartoons
    17566 
    17567 > select #1.16/E
    17568 
    17569 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    17570 
    17571 > show sel cartoons
    17572 
    17573 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    17574 
    17575 Chain information for AF3 E2 1-352.pdb #379 
    17576 --- 
    17577 Chain | Description 
    17578 B | No description available 
    17579  
    17580 
    17581 > matchmaker #379 to #1.16 & sel
    17582 
    17583 Parameters 
    17584 --- 
    17585 Chain pairing | bb 
    17586 Alignment algorithm | Needleman-Wunsch 
    17587 Similarity matrix | BLOSUM-62 
    17588 SS fraction | 0.3 
    17589 Gap open (HH/SS/other) | 18/18/6 
    17590 Gap extend | 1 
    17591 SS matrix |  |  | H | S | O 
    17592 ---|---|---|--- 
    17593 H | 6 | -9 | -6 
    17594 S |  | 6 | -6 
    17595 O |  |  | 4 
    17596 Iteration cutoff | 2 
    17597  
    17598 Matchmaker 3j0c.pdb1, chain E (#1.16) with AF3 E2 1-352.pdb, chain B (#379),
    17599 sequence alignment score = 594.5 
    17600 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    17601 6.147) 
    17602  
    17603 
    17604 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    17605 
    17606 Chain information for AF3 E2 353-438.pdb #380 
    17607 --- 
    17608 Chain | Description 
    17609 B | No description available 
    17610  
    17611 
    17612 > matchmaker #380 to #1.16 & sel
    17613 
    17614 Parameters 
    17615 --- 
    17616 Chain pairing | bb 
    17617 Alignment algorithm | Needleman-Wunsch 
    17618 Similarity matrix | BLOSUM-62 
    17619 SS fraction | 0.3 
    17620 Gap open (HH/SS/other) | 18/18/6 
    17621 Gap extend | 1 
    17622 SS matrix |  |  | H | S | O 
    17623 ---|---|---|--- 
    17624 H | 6 | -9 | -6 
    17625 S |  | 6 | -6 
    17626 O |  |  | 4 
    17627 Iteration cutoff | 2 
    17628  
    17629 Matchmaker 3j0c.pdb1, chain E (#1.16) with AF3 E2 353-438.pdb, chain B (#380),
    17630 sequence alignment score = 340.2 
    17631 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    17632 8.673) 
    17633  
    17634 
    17635 > hide sel cartoons
    17636 
    17637 > select #1.16/F
    17638 
    17639 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    17640 
    17641 > show sel cartoons
    17642 
    17643 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    17644 
    17645 Chain information for AF3 CA.pdb #381 
    17646 --- 
    17647 Chain | Description 
    17648 A | No description available 
    17649  
    17650 
    17651 > matchmaker #381 to #1.16 & sel
    17652 
    17653 Parameters 
    17654 --- 
    17655 Chain pairing | bb 
    17656 Alignment algorithm | Needleman-Wunsch 
    17657 Similarity matrix | BLOSUM-62 
    17658 SS fraction | 0.3 
    17659 Gap open (HH/SS/other) | 18/18/6 
    17660 Gap extend | 1 
    17661 SS matrix |  |  | H | S | O 
    17662 ---|---|---|--- 
    17663 H | 6 | -9 | -6 
    17664 S |  | 6 | -6 
    17665 O |  |  | 4 
    17666 Iteration cutoff | 2 
    17667  
    17668 Matchmaker 3j0c.pdb1, chain F (#1.16) with AF3 CA.pdb, chain A (#381),
    17669 sequence alignment score = 335.3 
    17670 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    17671 2.550) 
    17672  
    17673 
    17674 > hide sel cartoons
    17675 
    17676 > color #377 dodgerblue
    17677 
    17678 > color #378 dodgerblue
    17679 
    17680 > color #379 #00b305ff
    17681 
    17682 > color #380 #00b305ff
    17683 
    17684 > color #381 #f15839ff
    17685 
    17686 > select #1.17/D
    17687 
    17688 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    17689 
    17690 > show sel cartoons
    17691 
    17692 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    17693 
    17694 Chain information for AF3 E1 1-421.pdb #382 
    17695 --- 
    17696 Chain | Description 
    17697 A | No description available 
    17698  
    17699 
    17700 > matchmaker #382 to #1.17 & sel
    17701 
    17702 Parameters 
    17703 --- 
    17704 Chain pairing | bb 
    17705 Alignment algorithm | Needleman-Wunsch 
    17706 Similarity matrix | BLOSUM-62 
    17707 SS fraction | 0.3 
    17708 Gap open (HH/SS/other) | 18/18/6 
    17709 Gap extend | 1 
    17710 SS matrix |  |  | H | S | O 
    17711 ---|---|---|--- 
    17712 H | 6 | -9 | -6 
    17713 S |  | 6 | -6 
    17714 O |  |  | 4 
    17715 Iteration cutoff | 2 
    17716  
    17717 Matchmaker 3j0c.pdb1, chain D (#1.17) with AF3 E1 1-421.pdb, chain A (#382),
    17718 sequence alignment score = 1060.7 
    17719 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    17720 3.032) 
    17721  
    17722 
    17723 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    17724 
    17725 Chain information for AF3 E1 422-461.pdb #383 
    17726 --- 
    17727 Chain | Description 
    17728 A | No description available 
    17729  
    17730 
    17731 > matchmaker #383 to #1.17 & sel
    17732 
    17733 Parameters 
    17734 --- 
    17735 Chain pairing | bb 
    17736 Alignment algorithm | Needleman-Wunsch 
    17737 Similarity matrix | BLOSUM-62 
    17738 SS fraction | 0.3 
    17739 Gap open (HH/SS/other) | 18/18/6 
    17740 Gap extend | 1 
    17741 SS matrix |  |  | H | S | O 
    17742 ---|---|---|--- 
    17743 H | 6 | -9 | -6 
    17744 S |  | 6 | -6 
    17745 O |  |  | 4 
    17746 Iteration cutoff | 2 
    17747  
    17748 Matchmaker 3j0c.pdb1, chain D (#1.17) with AF3 E1 422-461.pdb, chain A (#383),
    17749 sequence alignment score = 626.9 
    17750 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    17751 2.915) 
    17752  
    17753 
    17754 > hide sel cartoons
    17755 
    17756 > select #1.17/E
    17757 
    17758 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    17759 
    17760 > show sel cartoons
    17761 
    17762 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    17763 
    17764 Chain information for AF3 E2 1-352.pdb #384 
    17765 --- 
    17766 Chain | Description 
    17767 B | No description available 
    17768  
    17769 
    17770 > matchmaker #384 to #1.17 & sel
    17771 
    17772 Parameters 
    17773 --- 
    17774 Chain pairing | bb 
    17775 Alignment algorithm | Needleman-Wunsch 
    17776 Similarity matrix | BLOSUM-62 
    17777 SS fraction | 0.3 
    17778 Gap open (HH/SS/other) | 18/18/6 
    17779 Gap extend | 1 
    17780 SS matrix |  |  | H | S | O 
    17781 ---|---|---|--- 
    17782 H | 6 | -9 | -6 
    17783 S |  | 6 | -6 
    17784 O |  |  | 4 
    17785 Iteration cutoff | 2 
    17786  
    17787 Matchmaker 3j0c.pdb1, chain E (#1.17) with AF3 E2 1-352.pdb, chain B (#384),
    17788 sequence alignment score = 594.5 
    17789 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    17790 6.147) 
    17791  
    17792 
    17793 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    17794 
    17795 Chain information for AF3 E2 353-438.pdb #385 
    17796 --- 
    17797 Chain | Description 
    17798 B | No description available 
    17799  
    17800 
    17801 > matchmaker #385 to #1.17 & sel
    17802 
    17803 Parameters 
    17804 --- 
    17805 Chain pairing | bb 
    17806 Alignment algorithm | Needleman-Wunsch 
    17807 Similarity matrix | BLOSUM-62 
    17808 SS fraction | 0.3 
    17809 Gap open (HH/SS/other) | 18/18/6 
    17810 Gap extend | 1 
    17811 SS matrix |  |  | H | S | O 
    17812 ---|---|---|--- 
    17813 H | 6 | -9 | -6 
    17814 S |  | 6 | -6 
    17815 O |  |  | 4 
    17816 Iteration cutoff | 2 
    17817  
    17818 Matchmaker 3j0c.pdb1, chain E (#1.17) with AF3 E2 353-438.pdb, chain B (#385),
    17819 sequence alignment score = 340.2 
    17820 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    17821 8.673) 
    17822  
    17823 
    17824 > hide sel cartoons
    17825 
    17826 > select #1.17/F
    17827 
    17828 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    17829 
    17830 > show sel cartoons
    17831 
    17832 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    17833 
    17834 Chain information for AF3 CA.pdb #386 
    17835 --- 
    17836 Chain | Description 
    17837 A | No description available 
    17838  
    17839 
    17840 > matchmaker #386 to #1.17 & sel
    17841 
    17842 Parameters 
    17843 --- 
    17844 Chain pairing | bb 
    17845 Alignment algorithm | Needleman-Wunsch 
    17846 Similarity matrix | BLOSUM-62 
    17847 SS fraction | 0.3 
    17848 Gap open (HH/SS/other) | 18/18/6 
    17849 Gap extend | 1 
    17850 SS matrix |  |  | H | S | O 
    17851 ---|---|---|--- 
    17852 H | 6 | -9 | -6 
    17853 S |  | 6 | -6 
    17854 O |  |  | 4 
    17855 Iteration cutoff | 2 
    17856  
    17857 Matchmaker 3j0c.pdb1, chain F (#1.17) with AF3 CA.pdb, chain A (#386),
    17858 sequence alignment score = 335.3 
    17859 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    17860 2.550) 
    17861  
    17862 
    17863 > hide sel cartoons
    17864 
    17865 > color #382 dodgerblue
    17866 
    17867 > color #383 dodgerblue
    17868 
    17869 > color #384 #00b305ff
    17870 
    17871 > color #385 #00b305ff
    17872 
    17873 > color #386 #f15839ff
    17874 
    17875 > select #1.18/D
    17876 
    17877 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    17878 
    17879 > show sel cartoons
    17880 
    17881 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    17882 
    17883 Chain information for AF3 E1 1-421.pdb #387 
    17884 --- 
    17885 Chain | Description 
    17886 A | No description available 
    17887  
    17888 
    17889 > matchmaker #387 to #1.17 & sel
    17890 
    17891 No 'to' model specified 
    17892 
    17893 > matchmaker #387 to #1.18 & sel
    17894 
    17895 Parameters 
    17896 --- 
    17897 Chain pairing | bb 
    17898 Alignment algorithm | Needleman-Wunsch 
    17899 Similarity matrix | BLOSUM-62 
    17900 SS fraction | 0.3 
    17901 Gap open (HH/SS/other) | 18/18/6 
    17902 Gap extend | 1 
    17903 SS matrix |  |  | H | S | O 
    17904 ---|---|---|--- 
    17905 H | 6 | -9 | -6 
    17906 S |  | 6 | -6 
    17907 O |  |  | 4 
    17908 Iteration cutoff | 2 
    17909  
    17910 Matchmaker 3j0c.pdb1, chain D (#1.18) with AF3 E1 1-421.pdb, chain A (#387),
    17911 sequence alignment score = 1060.7 
    17912 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    17913 3.032) 
    17914  
    17915 
    17916 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    17917 
    17918 Chain information for AF3 E1 422-461.pdb #388 
    17919 --- 
    17920 Chain | Description 
    17921 A | No description available 
    17922  
    17923 
    17924 > matchmaker #388 to #1.18 & sel
    17925 
    17926 Parameters 
    17927 --- 
    17928 Chain pairing | bb 
    17929 Alignment algorithm | Needleman-Wunsch 
    17930 Similarity matrix | BLOSUM-62 
    17931 SS fraction | 0.3 
    17932 Gap open (HH/SS/other) | 18/18/6 
    17933 Gap extend | 1 
    17934 SS matrix |  |  | H | S | O 
    17935 ---|---|---|--- 
    17936 H | 6 | -9 | -6 
    17937 S |  | 6 | -6 
    17938 O |  |  | 4 
    17939 Iteration cutoff | 2 
    17940  
    17941 Matchmaker 3j0c.pdb1, chain D (#1.18) with AF3 E1 422-461.pdb, chain A (#388),
    17942 sequence alignment score = 626.9 
    17943 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    17944 2.916) 
    17945  
    17946 
    17947 > hide sel cartoons
    17948 
    17949 > select #1.18/E
    17950 
    17951 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    17952 
    17953 > show sel cartoons
    17954 
    17955 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    17956 
    17957 Chain information for AF3 E2 1-352.pdb #389 
    17958 --- 
    17959 Chain | Description 
    17960 B | No description available 
    17961  
    17962 
    17963 > matchmaker #389 to #1.18 & sel
    17964 
    17965 Parameters 
    17966 --- 
    17967 Chain pairing | bb 
    17968 Alignment algorithm | Needleman-Wunsch 
    17969 Similarity matrix | BLOSUM-62 
    17970 SS fraction | 0.3 
    17971 Gap open (HH/SS/other) | 18/18/6 
    17972 Gap extend | 1 
    17973 SS matrix |  |  | H | S | O 
    17974 ---|---|---|--- 
    17975 H | 6 | -9 | -6 
    17976 S |  | 6 | -6 
    17977 O |  |  | 4 
    17978 Iteration cutoff | 2 
    17979  
    17980 Matchmaker 3j0c.pdb1, chain E (#1.18) with AF3 E2 1-352.pdb, chain B (#389),
    17981 sequence alignment score = 594.5 
    17982 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    17983 6.147) 
    17984  
    17985 
    17986 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    17987 
    17988 Chain information for AF3 E2 353-438.pdb #390 
    17989 --- 
    17990 Chain | Description 
    17991 B | No description available 
    17992  
    17993 
    17994 > matchmaker #390 to #1.18 & sel
    17995 
    17996 Parameters 
    17997 --- 
    17998 Chain pairing | bb 
    17999 Alignment algorithm | Needleman-Wunsch 
    18000 Similarity matrix | BLOSUM-62 
    18001 SS fraction | 0.3 
    18002 Gap open (HH/SS/other) | 18/18/6 
    18003 Gap extend | 1 
    18004 SS matrix |  |  | H | S | O 
    18005 ---|---|---|--- 
    18006 H | 6 | -9 | -6 
    18007 S |  | 6 | -6 
    18008 O |  |  | 4 
    18009 Iteration cutoff | 2 
    18010  
    18011 Matchmaker 3j0c.pdb1, chain E (#1.18) with AF3 E2 353-438.pdb, chain B (#390),
    18012 sequence alignment score = 340.2 
    18013 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    18014 8.673) 
    18015  
    18016 
    18017 > hide sel cartoons
    18018 
    18019 > select #1.18/F
    18020 
    18021 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    18022 
    18023 > show sel cartoons
    18024 
    18025 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    18026 
    18027 Chain information for AF3 CA.pdb #391 
    18028 --- 
    18029 Chain | Description 
    18030 A | No description available 
    18031  
    18032 
    18033 > matchmaker #391 to #1.18 & sel
    18034 
    18035 Parameters 
    18036 --- 
    18037 Chain pairing | bb 
    18038 Alignment algorithm | Needleman-Wunsch 
    18039 Similarity matrix | BLOSUM-62 
    18040 SS fraction | 0.3 
    18041 Gap open (HH/SS/other) | 18/18/6 
    18042 Gap extend | 1 
    18043 SS matrix |  |  | H | S | O 
    18044 ---|---|---|--- 
    18045 H | 6 | -9 | -6 
    18046 S |  | 6 | -6 
    18047 O |  |  | 4 
    18048 Iteration cutoff | 2 
    18049  
    18050 Matchmaker 3j0c.pdb1, chain F (#1.18) with AF3 CA.pdb, chain A (#391),
    18051 sequence alignment score = 335.3 
    18052 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    18053 2.550) 
    18054  
    18055 
    18056 > hide sel cartoons
    18057 
    18058 > color #387 dodgerblue
    18059 
    18060 > color #388 dodgerblue
    18061 
    18062 > color #389 #00b305ff
    18063 
    18064 > color #390 #00b305ff
    18065 
    18066 > color #391 #f15839ff
    18067 
    18068 > select #1.19/D
    18069 
    18070 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    18071 
    18072 > show sel cartoons
    18073 
    18074 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    18075 
    18076 Chain information for AF3 E1 1-421.pdb #392 
    18077 --- 
    18078 Chain | Description 
    18079 A | No description available 
    18080  
    18081 
    18082 > matchmaker #391 to #1.19 & sel
    18083 
    18084 Parameters 
    18085 --- 
    18086 Chain pairing | bb 
    18087 Alignment algorithm | Needleman-Wunsch 
    18088 Similarity matrix | BLOSUM-62 
    18089 SS fraction | 0.3 
    18090 Gap open (HH/SS/other) | 18/18/6 
    18091 Gap extend | 1 
    18092 SS matrix |  |  | H | S | O 
    18093 ---|---|---|--- 
    18094 H | 6 | -9 | -6 
    18095 S |  | 6 | -6 
    18096 O |  |  | 4 
    18097 Iteration cutoff | 2 
    18098  
    18099 Matchmaker 3j0c.pdb1, chain D (#1.19) with AF3 CA.pdb, chain A (#391),
    18100 sequence alignment score = 32.6 
    18101 RMSD between 11 pruned atom pairs is 1.228 angstroms; (across all 110 pairs:
    18102 22.710) 
    18103  
    18104 
    18105 > select #1.18/F
    18106 
    18107 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    18108 
    18109 > show sel cartoons
    18110 
    18111 > matchmaker #391 to #1.18 & sel
    18112 
    18113 Parameters 
    18114 --- 
    18115 Chain pairing | bb 
    18116 Alignment algorithm | Needleman-Wunsch 
    18117 Similarity matrix | BLOSUM-62 
    18118 SS fraction | 0.3 
    18119 Gap open (HH/SS/other) | 18/18/6 
    18120 Gap extend | 1 
    18121 SS matrix |  |  | H | S | O 
    18122 ---|---|---|--- 
    18123 H | 6 | -9 | -6 
    18124 S |  | 6 | -6 
    18125 O |  |  | 4 
    18126 Iteration cutoff | 2 
    18127  
    18128 Matchmaker 3j0c.pdb1, chain F (#1.18) with AF3 CA.pdb, chain A (#391),
    18129 sequence alignment score = 335.3 
    18130 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    18131 2.550) 
    18132  
    18133 
    18134 > hide sel cartoons
    18135 
    18136 > select #1.19/D
    18137 
    18138 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    18139 
    18140 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    18141 
    18142 Chain information for AF3 E1 1-421.pdb #393 
    18143 --- 
    18144 Chain | Description 
    18145 A | No description available 
    18146  
    18147 
    18148 The cached device pixel ratio value was stale on window expose. Please file a
    18149 QTBUG which explains how to reproduce. 
    18150 
    18151 > close #393
    18152 
    18153 > matchmaker #392 to #1.19 & sel
    18154 
    18155 Parameters 
    18156 --- 
    18157 Chain pairing | bb 
    18158 Alignment algorithm | Needleman-Wunsch 
    18159 Similarity matrix | BLOSUM-62 
    18160 SS fraction | 0.3 
    18161 Gap open (HH/SS/other) | 18/18/6 
    18162 Gap extend | 1 
    18163 SS matrix |  |  | H | S | O 
    18164 ---|---|---|--- 
    18165 H | 6 | -9 | -6 
    18166 S |  | 6 | -6 
    18167 O |  |  | 4 
    18168 Iteration cutoff | 2 
    18169  
    18170 Matchmaker 3j0c.pdb1, chain D (#1.19) with AF3 E1 1-421.pdb, chain A (#392),
    18171 sequence alignment score = 1060.7 
    18172 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    18173 3.032) 
    18174  
    18175 
    18176 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    18177 
    18178 Chain information for AF3 E1 422-461.pdb #393 
    18179 --- 
    18180 Chain | Description 
    18181 A | No description available 
    18182  
    18183 
    18184 > matchmaker #393 to #1.19 & sel
    18185 
    18186 Parameters 
    18187 --- 
    18188 Chain pairing | bb 
    18189 Alignment algorithm | Needleman-Wunsch 
    18190 Similarity matrix | BLOSUM-62 
    18191 SS fraction | 0.3 
    18192 Gap open (HH/SS/other) | 18/18/6 
    18193 Gap extend | 1 
    18194 SS matrix |  |  | H | S | O 
    18195 ---|---|---|--- 
    18196 H | 6 | -9 | -6 
    18197 S |  | 6 | -6 
    18198 O |  |  | 4 
    18199 Iteration cutoff | 2 
    18200  
    18201 Matchmaker 3j0c.pdb1, chain D (#1.19) with AF3 E1 422-461.pdb, chain A (#393),
    18202 sequence alignment score = 626.9 
    18203 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    18204 2.916) 
    18205  
    18206 
    18207 > hide sel cartoons
    18208 
    18209 > select #1.19/E
    18210 
    18211 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    18212 
    18213 > show sel cartoons
    18214 
    18215 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    18216 
    18217 Chain information for AF3 E2 1-352.pdb #394 
    18218 --- 
    18219 Chain | Description 
    18220 B | No description available 
    18221  
    18222 
    18223 > matchmaker #394 to #1.19 & sel
    18224 
    18225 Parameters 
    18226 --- 
    18227 Chain pairing | bb 
    18228 Alignment algorithm | Needleman-Wunsch 
    18229 Similarity matrix | BLOSUM-62 
    18230 SS fraction | 0.3 
    18231 Gap open (HH/SS/other) | 18/18/6 
    18232 Gap extend | 1 
    18233 SS matrix |  |  | H | S | O 
    18234 ---|---|---|--- 
    18235 H | 6 | -9 | -6 
    18236 S |  | 6 | -6 
    18237 O |  |  | 4 
    18238 Iteration cutoff | 2 
    18239  
    18240 Matchmaker 3j0c.pdb1, chain E (#1.19) with AF3 E2 1-352.pdb, chain B (#394),
    18241 sequence alignment score = 594.5 
    18242 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    18243 6.147) 
    18244  
    18245 
    18246 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    18247 
    18248 Chain information for AF3 E2 353-438.pdb #395 
    18249 --- 
    18250 Chain | Description 
    18251 B | No description available 
    18252  
    18253 
    18254 > matchmaker #395 to #1.19 & sel
    18255 
    18256 Parameters 
    18257 --- 
    18258 Chain pairing | bb 
    18259 Alignment algorithm | Needleman-Wunsch 
    18260 Similarity matrix | BLOSUM-62 
    18261 SS fraction | 0.3 
    18262 Gap open (HH/SS/other) | 18/18/6 
    18263 Gap extend | 1 
    18264 SS matrix |  |  | H | S | O 
    18265 ---|---|---|--- 
    18266 H | 6 | -9 | -6 
    18267 S |  | 6 | -6 
    18268 O |  |  | 4 
    18269 Iteration cutoff | 2 
    18270  
    18271 Matchmaker 3j0c.pdb1, chain E (#1.19) with AF3 E2 353-438.pdb, chain B (#395),
    18272 sequence alignment score = 340.2 
    18273 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    18274 8.673) 
    18275  
    18276 
    18277 > hide sel cartoons
    18278 
    18279 > select #1.19/F
    18280 
    18281 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    18282 
    18283 > show sel cartoons
    18284 
    18285 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    18286 
    18287 Chain information for AF3 CA.pdb #396 
    18288 --- 
    18289 Chain | Description 
    18290 A | No description available 
    18291  
    18292 
    18293 > matchmaker #396 to #1.19 & sel
    18294 
    18295 Parameters 
    18296 --- 
    18297 Chain pairing | bb 
    18298 Alignment algorithm | Needleman-Wunsch 
    18299 Similarity matrix | BLOSUM-62 
    18300 SS fraction | 0.3 
    18301 Gap open (HH/SS/other) | 18/18/6 
    18302 Gap extend | 1 
    18303 SS matrix |  |  | H | S | O 
    18304 ---|---|---|--- 
    18305 H | 6 | -9 | -6 
    18306 S |  | 6 | -6 
    18307 O |  |  | 4 
    18308 Iteration cutoff | 2 
    18309  
    18310 Matchmaker 3j0c.pdb1, chain F (#1.19) with AF3 CA.pdb, chain A (#396),
    18311 sequence alignment score = 335.3 
    18312 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    18313 2.550) 
    18314  
    18315 
    18316 > hide sel cartoons
    18317 
    18318 > color #392 dodgerblue
    18319 
    18320 > color #393 dodgerblue
    18321 
    18322 > color #394 #00b305ff
    18323 
    18324 > color #395 #00b305ff
    18325 
    18326 > color #396 #f15839ff
    18327 
    18328 > select #1.20/D
    18329 
    18330 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    18331 
    18332 > show sel cartoons
    18333 
    18334 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    18335 
    18336 Chain information for AF3 E1 1-421.pdb #397 
    18337 --- 
    18338 Chain | Description 
    18339 A | No description available 
    18340  
    18341 
    18342 > matchmaker #397 to #1.20 & sel
    18343 
    18344 Parameters 
    18345 --- 
    18346 Chain pairing | bb 
    18347 Alignment algorithm | Needleman-Wunsch 
    18348 Similarity matrix | BLOSUM-62 
    18349 SS fraction | 0.3 
    18350 Gap open (HH/SS/other) | 18/18/6 
    18351 Gap extend | 1 
    18352 SS matrix |  |  | H | S | O 
    18353 ---|---|---|--- 
    18354 H | 6 | -9 | -6 
    18355 S |  | 6 | -6 
    18356 O |  |  | 4 
    18357 Iteration cutoff | 2 
    18358  
    18359 Matchmaker 3j0c.pdb1, chain D (#1.20) with AF3 E1 1-421.pdb, chain A (#397),
    18360 sequence alignment score = 1060.7 
    18361 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    18362 3.032) 
    18363  
    18364 
    18365 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    18366 
    18367 Chain information for AF3 E1 422-461.pdb #398 
    18368 --- 
    18369 Chain | Description 
    18370 A | No description available 
    18371  
    18372 
    18373 > matchmaker #398 to #1.20 & sel
    18374 
    18375 Parameters 
    18376 --- 
    18377 Chain pairing | bb 
    18378 Alignment algorithm | Needleman-Wunsch 
    18379 Similarity matrix | BLOSUM-62 
    18380 SS fraction | 0.3 
    18381 Gap open (HH/SS/other) | 18/18/6 
    18382 Gap extend | 1 
    18383 SS matrix |  |  | H | S | O 
    18384 ---|---|---|--- 
    18385 H | 6 | -9 | -6 
    18386 S |  | 6 | -6 
    18387 O |  |  | 4 
    18388 Iteration cutoff | 2 
    18389  
    18390 Matchmaker 3j0c.pdb1, chain D (#1.20) with AF3 E1 422-461.pdb, chain A (#398),
    18391 sequence alignment score = 626.9 
    18392 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    18393 2.916) 
    18394  
    18395 
    18396 > hide sel cartoons
    18397 
    18398 > select #1.20/E
    18399 
    18400 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    18401 
    18402 > show sel cartoons
    18403 
    18404 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    18405 
    18406 Chain information for AF3 E2 1-352.pdb #399 
    18407 --- 
    18408 Chain | Description 
    18409 B | No description available 
    18410  
    18411 
    18412 > matchmaker #399 to #1.20 & sel
    18413 
    18414 Parameters 
    18415 --- 
    18416 Chain pairing | bb 
    18417 Alignment algorithm | Needleman-Wunsch 
    18418 Similarity matrix | BLOSUM-62 
    18419 SS fraction | 0.3 
    18420 Gap open (HH/SS/other) | 18/18/6 
    18421 Gap extend | 1 
    18422 SS matrix |  |  | H | S | O 
    18423 ---|---|---|--- 
    18424 H | 6 | -9 | -6 
    18425 S |  | 6 | -6 
    18426 O |  |  | 4 
    18427 Iteration cutoff | 2 
    18428  
    18429 Matchmaker 3j0c.pdb1, chain E (#1.20) with AF3 E2 1-352.pdb, chain B (#399),
    18430 sequence alignment score = 594.5 
    18431 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    18432 6.147) 
    18433  
    18434 
    18435 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    18436 
    18437 Chain information for AF3 E2 353-438.pdb #400 
    18438 --- 
    18439 Chain | Description 
    18440 B | No description available 
    18441  
    18442 
    18443 > matchmaker #400 to #1.20 & sel
    18444 
    18445 Parameters 
    18446 --- 
    18447 Chain pairing | bb 
    18448 Alignment algorithm | Needleman-Wunsch 
    18449 Similarity matrix | BLOSUM-62 
    18450 SS fraction | 0.3 
    18451 Gap open (HH/SS/other) | 18/18/6 
    18452 Gap extend | 1 
    18453 SS matrix |  |  | H | S | O 
    18454 ---|---|---|--- 
    18455 H | 6 | -9 | -6 
    18456 S |  | 6 | -6 
    18457 O |  |  | 4 
    18458 Iteration cutoff | 2 
    18459  
    18460 Matchmaker 3j0c.pdb1, chain E (#1.20) with AF3 E2 353-438.pdb, chain B (#400),
    18461 sequence alignment score = 340.2 
    18462 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    18463 8.673) 
    18464  
    18465 
    18466 > hide sel cartoons
    18467 
    18468 > select #1.20/F
    18469 
    18470 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    18471 
    18472 > show sel cartoons
    18473 
    18474 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    18475 
    18476 Chain information for AF3 CA.pdb #401 
    18477 --- 
    18478 Chain | Description 
    18479 A | No description available 
    18480  
    18481 
    18482 > matchmaker #401 to #1.20 & sel
    18483 
    18484 Parameters 
    18485 --- 
    18486 Chain pairing | bb 
    18487 Alignment algorithm | Needleman-Wunsch 
    18488 Similarity matrix | BLOSUM-62 
    18489 SS fraction | 0.3 
    18490 Gap open (HH/SS/other) | 18/18/6 
    18491 Gap extend | 1 
    18492 SS matrix |  |  | H | S | O 
    18493 ---|---|---|--- 
    18494 H | 6 | -9 | -6 
    18495 S |  | 6 | -6 
    18496 O |  |  | 4 
    18497 Iteration cutoff | 2 
    18498  
    18499 Matchmaker 3j0c.pdb1, chain F (#1.20) with AF3 CA.pdb, chain A (#401),
    18500 sequence alignment score = 335.3 
    18501 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    18502 2.550) 
    18503  
    18504 
    18505 > hide sel cartoons
    18506 
    18507 > color #397 dodgerblue
    18508 
    18509 > color #398 dodgerblue
    18510 
    18511 > color #399 #00b305ff
    18512 
    18513 > color #400 #00b305ff
    18514 
    18515 > color #401 #f15839ff
    18516 
    18517 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    18518 
    18519 > select add #347
    18520 
    18521 4419 atoms, 4528 bonds, 583 residues, 2 models selected 
    18522 
    18523 > select subtract #347
    18524 
    18525 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    18526 
    18527 > select add #347
    18528 
    18529 4419 atoms, 4528 bonds, 583 residues, 2 models selected 
    18530 
    18531 > select subtract #347
    18532 
    18533 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    18534 
    18535 > hide #347-396 models
    18536 
    18537 > select #1.21/D
    18538 
    18539 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    18540 
    18541 > show sel cartoons
    18542 
    18543 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    18544 
    18545 Chain information for AF3 E1 1-421.pdb #402 
    18546 --- 
    18547 Chain | Description 
    18548 A | No description available 
    18549  
    18550 
    18551 > matchmaker #402 to #1.21 & sel
    18552 
    18553 Parameters 
    18554 --- 
    18555 Chain pairing | bb 
    18556 Alignment algorithm | Needleman-Wunsch 
    18557 Similarity matrix | BLOSUM-62 
    18558 SS fraction | 0.3 
    18559 Gap open (HH/SS/other) | 18/18/6 
    18560 Gap extend | 1 
    18561 SS matrix |  |  | H | S | O 
    18562 ---|---|---|--- 
    18563 H | 6 | -9 | -6 
    18564 S |  | 6 | -6 
    18565 O |  |  | 4 
    18566 Iteration cutoff | 2 
    18567  
    18568 Matchmaker 3j0c.pdb1, chain D (#1.21) with AF3 E1 1-421.pdb, chain A (#402),
    18569 sequence alignment score = 1060.7 
    18570 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    18571 3.032) 
    18572  
    18573 
    18574 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    18575 
    18576 Chain information for AF3 E1 422-461.pdb #403 
    18577 --- 
    18578 Chain | Description 
    18579 A | No description available 
    18580  
    18581 
    18582 > matchmaker #403 to #1.21 & sel
    18583 
    18584 Parameters 
    18585 --- 
    18586 Chain pairing | bb 
    18587 Alignment algorithm | Needleman-Wunsch 
    18588 Similarity matrix | BLOSUM-62 
    18589 SS fraction | 0.3 
    18590 Gap open (HH/SS/other) | 18/18/6 
    18591 Gap extend | 1 
    18592 SS matrix |  |  | H | S | O 
    18593 ---|---|---|--- 
    18594 H | 6 | -9 | -6 
    18595 S |  | 6 | -6 
    18596 O |  |  | 4 
    18597 Iteration cutoff | 2 
    18598  
    18599 Matchmaker 3j0c.pdb1, chain D (#1.21) with AF3 E1 422-461.pdb, chain A (#403),
    18600 sequence alignment score = 626.9 
    18601 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    18602 2.916) 
    18603  
    18604 
    18605 > hide sel cartoons
    18606 
    18607 > select #1.21/E
    18608 
    18609 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    18610 
    18611 > show sel cartoons
    18612 
    18613 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    18614 
    18615 Chain information for AF3 E2 1-352.pdb #404 
    18616 --- 
    18617 Chain | Description 
    18618 B | No description available 
    18619  
    18620 
    18621 > matchmaker #404 to #1.21 & sel
    18622 
    18623 Parameters 
    18624 --- 
    18625 Chain pairing | bb 
    18626 Alignment algorithm | Needleman-Wunsch 
    18627 Similarity matrix | BLOSUM-62 
    18628 SS fraction | 0.3 
    18629 Gap open (HH/SS/other) | 18/18/6 
    18630 Gap extend | 1 
    18631 SS matrix |  |  | H | S | O 
    18632 ---|---|---|--- 
    18633 H | 6 | -9 | -6 
    18634 S |  | 6 | -6 
    18635 O |  |  | 4 
    18636 Iteration cutoff | 2 
    18637  
    18638 Matchmaker 3j0c.pdb1, chain E (#1.21) with AF3 E2 1-352.pdb, chain B (#404),
    18639 sequence alignment score = 594.5 
    18640 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    18641 6.147) 
    18642  
    18643 
    18644 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    18645 
    18646 Chain information for AF3 E2 353-438.pdb #405 
    18647 --- 
    18648 Chain | Description 
    18649 B | No description available 
    18650  
    18651 
    18652 > matchmaker #405 to #1.21 & sel
    18653 
    18654 Parameters 
    18655 --- 
    18656 Chain pairing | bb 
    18657 Alignment algorithm | Needleman-Wunsch 
    18658 Similarity matrix | BLOSUM-62 
    18659 SS fraction | 0.3 
    18660 Gap open (HH/SS/other) | 18/18/6 
    18661 Gap extend | 1 
    18662 SS matrix |  |  | H | S | O 
    18663 ---|---|---|--- 
    18664 H | 6 | -9 | -6 
    18665 S |  | 6 | -6 
    18666 O |  |  | 4 
    18667 Iteration cutoff | 2 
    18668  
    18669 Matchmaker 3j0c.pdb1, chain E (#1.21) with AF3 E2 353-438.pdb, chain B (#405),
    18670 sequence alignment score = 340.2 
    18671 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    18672 8.673) 
    18673  
    18674 
    18675 > hide sel cartoons
    18676 
    18677 > select #1.21/F
    18678 
    18679 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    18680 
    18681 > show sel cartoons
    18682 
    18683 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    18684 
    18685 Chain information for AF3 CA.pdb #406 
    18686 --- 
    18687 Chain | Description 
    18688 A | No description available 
    18689  
    18690 
    18691 > matchmaker #406 to #1.21 & sel
    18692 
    18693 Parameters 
    18694 --- 
    18695 Chain pairing | bb 
    18696 Alignment algorithm | Needleman-Wunsch 
    18697 Similarity matrix | BLOSUM-62 
    18698 SS fraction | 0.3 
    18699 Gap open (HH/SS/other) | 18/18/6 
    18700 Gap extend | 1 
    18701 SS matrix |  |  | H | S | O 
    18702 ---|---|---|--- 
    18703 H | 6 | -9 | -6 
    18704 S |  | 6 | -6 
    18705 O |  |  | 4 
    18706 Iteration cutoff | 2 
    18707  
    18708 Matchmaker 3j0c.pdb1, chain F (#1.21) with AF3 CA.pdb, chain A (#406),
    18709 sequence alignment score = 335.3 
    18710 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    18711 2.550) 
    18712  
    18713 
    18714 > hide sel cartoons
    18715 
    18716 > color #402 dodgerblue
    18717 
    18718 > color #403 dodgerblue
    18719 
    18720 > color #404 #00b305ff
    18721 
    18722 > color #405 #00b305ff
    18723 
    18724 > color #406 #f15839ff
    18725 
    18726 > select #1.22/D
    18727 
    18728 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    18729 
    18730 > show sel cartoons
    18731 
    18732 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    18733 
    18734 Chain information for AF3 E1 1-421.pdb #407 
    18735 --- 
    18736 Chain | Description 
    18737 A | No description available 
    18738  
    18739 
    18740 > matchmaker #407 to #1.22 & sel
    18741 
    18742 Parameters 
    18743 --- 
    18744 Chain pairing | bb 
    18745 Alignment algorithm | Needleman-Wunsch 
    18746 Similarity matrix | BLOSUM-62 
    18747 SS fraction | 0.3 
    18748 Gap open (HH/SS/other) | 18/18/6 
    18749 Gap extend | 1 
    18750 SS matrix |  |  | H | S | O 
    18751 ---|---|---|--- 
    18752 H | 6 | -9 | -6 
    18753 S |  | 6 | -6 
    18754 O |  |  | 4 
    18755 Iteration cutoff | 2 
    18756  
    18757 Matchmaker 3j0c.pdb1, chain D (#1.22) with AF3 E1 1-421.pdb, chain A (#407),
    18758 sequence alignment score = 1060.7 
    18759 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    18760 3.032) 
    18761  
    18762 
    18763 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    18764 
    18765 Chain information for AF3 E1 422-461.pdb #408 
    18766 --- 
    18767 Chain | Description 
    18768 A | No description available 
    18769  
    18770 
    18771 > matchmaker #408 to #1.22 & sel
    18772 
    18773 Parameters 
    18774 --- 
    18775 Chain pairing | bb 
    18776 Alignment algorithm | Needleman-Wunsch 
    18777 Similarity matrix | BLOSUM-62 
    18778 SS fraction | 0.3 
    18779 Gap open (HH/SS/other) | 18/18/6 
    18780 Gap extend | 1 
    18781 SS matrix |  |  | H | S | O 
    18782 ---|---|---|--- 
    18783 H | 6 | -9 | -6 
    18784 S |  | 6 | -6 
    18785 O |  |  | 4 
    18786 Iteration cutoff | 2 
    18787  
    18788 Matchmaker 3j0c.pdb1, chain D (#1.22) with AF3 E1 422-461.pdb, chain A (#408),
    18789 sequence alignment score = 626.9 
    18790 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    18791 2.916) 
    18792  
    18793 
    18794 > hide sel cartoons
    18795 
    18796 > select #1.22/E
    18797 
    18798 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    18799 
    18800 > show sel cartoons
    18801 
    18802 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    18803 
    18804 Chain information for AF3 E2 1-352.pdb #409 
    18805 --- 
    18806 Chain | Description 
    18807 B | No description available 
    18808  
    18809 
    18810 > matchmaker #409 to #1.22 & sel
    18811 
    18812 Parameters 
    18813 --- 
    18814 Chain pairing | bb 
    18815 Alignment algorithm | Needleman-Wunsch 
    18816 Similarity matrix | BLOSUM-62 
    18817 SS fraction | 0.3 
    18818 Gap open (HH/SS/other) | 18/18/6 
    18819 Gap extend | 1 
    18820 SS matrix |  |  | H | S | O 
    18821 ---|---|---|--- 
    18822 H | 6 | -9 | -6 
    18823 S |  | 6 | -6 
    18824 O |  |  | 4 
    18825 Iteration cutoff | 2 
    18826  
    18827 Matchmaker 3j0c.pdb1, chain E (#1.22) with AF3 E2 1-352.pdb, chain B (#409),
    18828 sequence alignment score = 594.5 
    18829 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    18830 6.147) 
    18831  
    18832 
    18833 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    18834 
    18835 Chain information for AF3 E2 353-438.pdb #410 
    18836 --- 
    18837 Chain | Description 
    18838 B | No description available 
    18839  
    18840 
    18841 > matchmaker #410 to #1.22 & sel
    18842 
    18843 Parameters 
    18844 --- 
    18845 Chain pairing | bb 
    18846 Alignment algorithm | Needleman-Wunsch 
    18847 Similarity matrix | BLOSUM-62 
    18848 SS fraction | 0.3 
    18849 Gap open (HH/SS/other) | 18/18/6 
    18850 Gap extend | 1 
    18851 SS matrix |  |  | H | S | O 
    18852 ---|---|---|--- 
    18853 H | 6 | -9 | -6 
    18854 S |  | 6 | -6 
    18855 O |  |  | 4 
    18856 Iteration cutoff | 2 
    18857  
    18858 Matchmaker 3j0c.pdb1, chain E (#1.22) with AF3 E2 353-438.pdb, chain B (#410),
    18859 sequence alignment score = 340.2 
    18860 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    18861 8.673) 
    18862  
    18863 
    18864 > select #1.22/F
    18865 
    18866 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    18867 
    18868 > show sel cartoons
    18869 
    18870 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    18871 
    18872 Chain information for AF3 CA.pdb #411 
    18873 --- 
    18874 Chain | Description 
    18875 A | No description available 
    18876  
    18877 
    18878 > matchmaker #411 to #1.22 & sel
    18879 
    18880 Parameters 
    18881 --- 
    18882 Chain pairing | bb 
    18883 Alignment algorithm | Needleman-Wunsch 
    18884 Similarity matrix | BLOSUM-62 
    18885 SS fraction | 0.3 
    18886 Gap open (HH/SS/other) | 18/18/6 
    18887 Gap extend | 1 
    18888 SS matrix |  |  | H | S | O 
    18889 ---|---|---|--- 
    18890 H | 6 | -9 | -6 
    18891 S |  | 6 | -6 
    18892 O |  |  | 4 
    18893 Iteration cutoff | 2 
    18894  
    18895 Matchmaker 3j0c.pdb1, chain F (#1.22) with AF3 CA.pdb, chain A (#411),
    18896 sequence alignment score = 335.3 
    18897 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    18898 2.550) 
    18899  
    18900 
    18901 > hide sel cartoons
    18902 
    18903 > color #407 dodgerblue
    18904 
    18905 > color #408 dodgerblue
    18906 
    18907 > color #409 #00b305ff
    18908 
    18909 > color #410 #00b305ff
    18910 
    18911 > color #411 #f15839ff
    18912 
    18913 > select #1.22/E
    18914 
    18915 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    18916 
    18917 > hide sel cartoons
    18918 
    18919 > select #1.23/D
    18920 
    18921 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    18922 
    18923 > show sel cartoons
    18924 
    18925 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    18926 
    18927 Chain information for AF3 E1 1-421.pdb #412 
    18928 --- 
    18929 Chain | Description 
    18930 A | No description available 
    18931  
    18932 
    18933 > matchmaker #412 to #1.23 & sel
    18934 
    18935 Parameters 
    18936 --- 
    18937 Chain pairing | bb 
    18938 Alignment algorithm | Needleman-Wunsch 
    18939 Similarity matrix | BLOSUM-62 
    18940 SS fraction | 0.3 
    18941 Gap open (HH/SS/other) | 18/18/6 
    18942 Gap extend | 1 
    18943 SS matrix |  |  | H | S | O 
    18944 ---|---|---|--- 
    18945 H | 6 | -9 | -6 
    18946 S |  | 6 | -6 
    18947 O |  |  | 4 
    18948 Iteration cutoff | 2 
    18949  
    18950 Matchmaker 3j0c.pdb1, chain D (#1.23) with AF3 E1 1-421.pdb, chain A (#412),
    18951 sequence alignment score = 1060.7 
    18952 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    18953 3.032) 
    18954  
    18955 
    18956 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    18957 
    18958 Chain information for AF3 E1 422-461.pdb #413 
    18959 --- 
    18960 Chain | Description 
    18961 A | No description available 
    18962  
    18963 
    18964 > matchmaker #413 to #1.23 & sel
    18965 
    18966 Parameters 
    18967 --- 
    18968 Chain pairing | bb 
    18969 Alignment algorithm | Needleman-Wunsch 
    18970 Similarity matrix | BLOSUM-62 
    18971 SS fraction | 0.3 
    18972 Gap open (HH/SS/other) | 18/18/6 
    18973 Gap extend | 1 
    18974 SS matrix |  |  | H | S | O 
    18975 ---|---|---|--- 
    18976 H | 6 | -9 | -6 
    18977 S |  | 6 | -6 
    18978 O |  |  | 4 
    18979 Iteration cutoff | 2 
    18980  
    18981 Matchmaker 3j0c.pdb1, chain D (#1.23) with AF3 E1 422-461.pdb, chain A (#413),
    18982 sequence alignment score = 626.9 
    18983 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    18984 2.916) 
    18985  
    18986 
    18987 > hide sel cartoons
    18988 
    18989 > select #1.23/F
    18990 
    18991 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    18992 
    18993 > show sel cartoons
    18994 
    18995 > hide sel cartoons
    18996 
    18997 > select #1.23/E
    18998 
    18999 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    19000 
    19001 > show sel cartoons
    19002 
    19003 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    19004 
    19005 Chain information for AF3 E2 1-352.pdb #414 
    19006 --- 
    19007 Chain | Description 
    19008 B | No description available 
    19009  
    19010 
    19011 > matchmaker #414 to #1.23 & sel
    19012 
    19013 Parameters 
    19014 --- 
    19015 Chain pairing | bb 
    19016 Alignment algorithm | Needleman-Wunsch 
    19017 Similarity matrix | BLOSUM-62 
    19018 SS fraction | 0.3 
    19019 Gap open (HH/SS/other) | 18/18/6 
    19020 Gap extend | 1 
    19021 SS matrix |  |  | H | S | O 
    19022 ---|---|---|--- 
    19023 H | 6 | -9 | -6 
    19024 S |  | 6 | -6 
    19025 O |  |  | 4 
    19026 Iteration cutoff | 2 
    19027  
    19028 Matchmaker 3j0c.pdb1, chain E (#1.23) with AF3 E2 1-352.pdb, chain B (#414),
    19029 sequence alignment score = 594.5 
    19030 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    19031 6.147) 
    19032  
    19033 
    19034 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    19035 
    19036 Chain information for AF3 E2 353-438.pdb #415 
    19037 --- 
    19038 Chain | Description 
    19039 B | No description available 
    19040  
    19041 
    19042 > matchmaker #415 to #1.23 & sel
    19043 
    19044 Parameters 
    19045 --- 
    19046 Chain pairing | bb 
    19047 Alignment algorithm | Needleman-Wunsch 
    19048 Similarity matrix | BLOSUM-62 
    19049 SS fraction | 0.3 
    19050 Gap open (HH/SS/other) | 18/18/6 
    19051 Gap extend | 1 
    19052 SS matrix |  |  | H | S | O 
    19053 ---|---|---|--- 
    19054 H | 6 | -9 | -6 
    19055 S |  | 6 | -6 
    19056 O |  |  | 4 
    19057 Iteration cutoff | 2 
    19058  
    19059 Matchmaker 3j0c.pdb1, chain E (#1.23) with AF3 E2 353-438.pdb, chain B (#415),
    19060 sequence alignment score = 340.2 
    19061 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    19062 8.673) 
    19063  
    19064 
    19065 > hide sel cartoons
    19066 
    19067 > select #1.23/F
    19068 
    19069 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    19070 
    19071 > show sel cartoons
    19072 
    19073 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    19074 
    19075 Chain information for AF3 CA.pdb #416 
    19076 --- 
    19077 Chain | Description 
    19078 A | No description available 
    19079  
    19080 
    19081 > matchmaker #416 to #1.23 & sel
    19082 
    19083 Parameters 
    19084 --- 
    19085 Chain pairing | bb 
    19086 Alignment algorithm | Needleman-Wunsch 
    19087 Similarity matrix | BLOSUM-62 
    19088 SS fraction | 0.3 
    19089 Gap open (HH/SS/other) | 18/18/6 
    19090 Gap extend | 1 
    19091 SS matrix |  |  | H | S | O 
    19092 ---|---|---|--- 
    19093 H | 6 | -9 | -6 
    19094 S |  | 6 | -6 
    19095 O |  |  | 4 
    19096 Iteration cutoff | 2 
    19097  
    19098 Matchmaker 3j0c.pdb1, chain F (#1.23) with AF3 CA.pdb, chain A (#416),
    19099 sequence alignment score = 335.3 
    19100 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    19101 2.550) 
    19102  
    19103 
    19104 > hide sel cartoons
    19105 
    19106 > color #412 dodgerblue
    19107 
    19108 > color #413 dodgerblue
    19109 
    19110 > color #414 #00b305ff
    19111 
    19112 > color #415 #00b305ff
    19113 
    19114 > color #416 #f15839ff
    19115 
    19116 > select #1.24/D
    19117 
    19118 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    19119 
    19120 > show sel cartoons
    19121 
    19122 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    19123 
    19124 Chain information for AF3 E1 1-421.pdb #417 
    19125 --- 
    19126 Chain | Description 
    19127 A | No description available 
    19128  
    19129 
    19130 > matchmaker #417 to #1.24 & sel
    19131 
    19132 Parameters 
    19133 --- 
    19134 Chain pairing | bb 
    19135 Alignment algorithm | Needleman-Wunsch 
    19136 Similarity matrix | BLOSUM-62 
    19137 SS fraction | 0.3 
    19138 Gap open (HH/SS/other) | 18/18/6 
    19139 Gap extend | 1 
    19140 SS matrix |  |  | H | S | O 
    19141 ---|---|---|--- 
    19142 H | 6 | -9 | -6 
    19143 S |  | 6 | -6 
    19144 O |  |  | 4 
    19145 Iteration cutoff | 2 
    19146  
    19147 Matchmaker 3j0c.pdb1, chain D (#1.24) with AF3 E1 1-421.pdb, chain A (#417),
    19148 sequence alignment score = 1060.7 
    19149 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    19150 3.032) 
    19151  
    19152 
    19153 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    19154 
    19155 Chain information for AF3 E1 422-461.pdb #418 
    19156 --- 
    19157 Chain | Description 
    19158 A | No description available 
    19159  
    19160 
    19161 > matchmaker #418 to #1.24 & sel
    19162 
    19163 Parameters 
    19164 --- 
    19165 Chain pairing | bb 
    19166 Alignment algorithm | Needleman-Wunsch 
    19167 Similarity matrix | BLOSUM-62 
    19168 SS fraction | 0.3 
    19169 Gap open (HH/SS/other) | 18/18/6 
    19170 Gap extend | 1 
    19171 SS matrix |  |  | H | S | O 
    19172 ---|---|---|--- 
    19173 H | 6 | -9 | -6 
    19174 S |  | 6 | -6 
    19175 O |  |  | 4 
    19176 Iteration cutoff | 2 
    19177  
    19178 Matchmaker 3j0c.pdb1, chain D (#1.24) with AF3 E1 422-461.pdb, chain A (#418),
    19179 sequence alignment score = 626.9 
    19180 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    19181 2.916) 
    19182  
    19183 
    19184 > hide sel cartoons
    19185 
    19186 > select #1.24/E
    19187 
    19188 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    19189 
    19190 > show sel cartoons
    19191 
    19192 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    19193 
    19194 Chain information for AF3 E2 1-352.pdb #419 
    19195 --- 
    19196 Chain | Description 
    19197 B | No description available 
    19198  
    19199 
    19200 > matchmaker #419 to #1.24 & sel
    19201 
    19202 Parameters 
    19203 --- 
    19204 Chain pairing | bb 
    19205 Alignment algorithm | Needleman-Wunsch 
    19206 Similarity matrix | BLOSUM-62 
    19207 SS fraction | 0.3 
    19208 Gap open (HH/SS/other) | 18/18/6 
    19209 Gap extend | 1 
    19210 SS matrix |  |  | H | S | O 
    19211 ---|---|---|--- 
    19212 H | 6 | -9 | -6 
    19213 S |  | 6 | -6 
    19214 O |  |  | 4 
    19215 Iteration cutoff | 2 
    19216  
    19217 Matchmaker 3j0c.pdb1, chain E (#1.24) with AF3 E2 1-352.pdb, chain B (#419),
    19218 sequence alignment score = 594.5 
    19219 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    19220 6.147) 
    19221  
    19222 
    19223 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    19224 
    19225 Chain information for AF3 E2 353-438.pdb #420 
    19226 --- 
    19227 Chain | Description 
    19228 B | No description available 
    19229  
    19230 
    19231 > matchmaker #420 to #1.24 & sel
    19232 
    19233 Parameters 
    19234 --- 
    19235 Chain pairing | bb 
    19236 Alignment algorithm | Needleman-Wunsch 
    19237 Similarity matrix | BLOSUM-62 
    19238 SS fraction | 0.3 
    19239 Gap open (HH/SS/other) | 18/18/6 
    19240 Gap extend | 1 
    19241 SS matrix |  |  | H | S | O 
    19242 ---|---|---|--- 
    19243 H | 6 | -9 | -6 
    19244 S |  | 6 | -6 
    19245 O |  |  | 4 
    19246 Iteration cutoff | 2 
    19247  
    19248 Matchmaker 3j0c.pdb1, chain E (#1.24) with AF3 E2 353-438.pdb, chain B (#420),
    19249 sequence alignment score = 340.2 
    19250 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    19251 8.673) 
    19252  
    19253 
    19254 > hide sel cartoons
    19255 
    19256 > select #1.24/F
    19257 
    19258 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    19259 
    19260 > show sel cartoons
    19261 
    19262 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    19263 
    19264 Chain information for AF3 CA.pdb #421 
    19265 --- 
    19266 Chain | Description 
    19267 A | No description available 
    19268  
    19269 
    19270 > matchmaker #421 to #1.24 & sel
    19271 
    19272 Parameters 
    19273 --- 
    19274 Chain pairing | bb 
    19275 Alignment algorithm | Needleman-Wunsch 
    19276 Similarity matrix | BLOSUM-62 
    19277 SS fraction | 0.3 
    19278 Gap open (HH/SS/other) | 18/18/6 
    19279 Gap extend | 1 
    19280 SS matrix |  |  | H | S | O 
    19281 ---|---|---|--- 
    19282 H | 6 | -9 | -6 
    19283 S |  | 6 | -6 
    19284 O |  |  | 4 
    19285 Iteration cutoff | 2 
    19286  
    19287 Matchmaker 3j0c.pdb1, chain F (#1.24) with AF3 CA.pdb, chain A (#421),
    19288 sequence alignment score = 335.3 
    19289 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    19290 2.550) 
    19291  
    19292 
    19293 > hide sel cartoons
    19294 
    19295 > color #417 dodgerblue
    19296 
    19297 > color #418 dodgerblue
    19298 
    19299 > color #419 #00b305ff
    19300 
    19301 > color #420 #00b305ff
    19302 
    19303 > color #421 #f15839ff
    19304 
    19305 > select #1.25/D
    19306 
    19307 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    19308 
    19309 > show sel cartoons
    19310 
    19311 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    19312 
    19313 Chain information for AF3 E1 1-421.pdb #422 
    19314 --- 
    19315 Chain | Description 
    19316 A | No description available 
    19317  
    19318 
    19319 > matchmaker #422 to #1.25 & sel
    19320 
    19321 Parameters 
    19322 --- 
    19323 Chain pairing | bb 
    19324 Alignment algorithm | Needleman-Wunsch 
    19325 Similarity matrix | BLOSUM-62 
    19326 SS fraction | 0.3 
    19327 Gap open (HH/SS/other) | 18/18/6 
    19328 Gap extend | 1 
    19329 SS matrix |  |  | H | S | O 
    19330 ---|---|---|--- 
    19331 H | 6 | -9 | -6 
    19332 S |  | 6 | -6 
    19333 O |  |  | 4 
    19334 Iteration cutoff | 2 
    19335  
    19336 Matchmaker 3j0c.pdb1, chain D (#1.25) with AF3 E1 1-421.pdb, chain A (#422),
    19337 sequence alignment score = 1060.7 
    19338 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    19339 3.032) 
    19340  
    19341 
    19342 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    19343 
    19344 Chain information for AF3 E1 422-461.pdb #423 
    19345 --- 
    19346 Chain | Description 
    19347 A | No description available 
    19348  
    19349 
    19350 > matchmaker #423 to #1.25 & sel
    19351 
    19352 Parameters 
    19353 --- 
    19354 Chain pairing | bb 
    19355 Alignment algorithm | Needleman-Wunsch 
    19356 Similarity matrix | BLOSUM-62 
    19357 SS fraction | 0.3 
    19358 Gap open (HH/SS/other) | 18/18/6 
    19359 Gap extend | 1 
    19360 SS matrix |  |  | H | S | O 
    19361 ---|---|---|--- 
    19362 H | 6 | -9 | -6 
    19363 S |  | 6 | -6 
    19364 O |  |  | 4 
    19365 Iteration cutoff | 2 
    19366  
    19367 Matchmaker 3j0c.pdb1, chain D (#1.25) with AF3 E1 422-461.pdb, chain A (#423),
    19368 sequence alignment score = 626.9 
    19369 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    19370 2.916) 
    19371  
    19372 
    19373 > hide sel cartoons
    19374 
    19375 > select #1.25/E
    19376 
    19377 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    19378 
    19379 > show sel cartoons
    19380 
    19381 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    19382 
    19383 Chain information for AF3 E2 1-352.pdb #424 
    19384 --- 
    19385 Chain | Description 
    19386 B | No description available 
    19387  
    19388 
    19389 > matchmaker #424 to #1.25 & sel
    19390 
    19391 Parameters 
    19392 --- 
    19393 Chain pairing | bb 
    19394 Alignment algorithm | Needleman-Wunsch 
    19395 Similarity matrix | BLOSUM-62 
    19396 SS fraction | 0.3 
    19397 Gap open (HH/SS/other) | 18/18/6 
    19398 Gap extend | 1 
    19399 SS matrix |  |  | H | S | O 
    19400 ---|---|---|--- 
    19401 H | 6 | -9 | -6 
    19402 S |  | 6 | -6 
    19403 O |  |  | 4 
    19404 Iteration cutoff | 2 
    19405  
    19406 Matchmaker 3j0c.pdb1, chain E (#1.25) with AF3 E2 1-352.pdb, chain B (#424),
    19407 sequence alignment score = 594.5 
    19408 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    19409 6.147) 
    19410  
    19411 
    19412 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    19413 
    19414 Chain information for AF3 E2 353-438.pdb #425 
    19415 --- 
    19416 Chain | Description 
    19417 B | No description available 
    19418  
    19419 
    19420 > matchmaker #425 to #1.25 & sel
    19421 
    19422 Parameters 
    19423 --- 
    19424 Chain pairing | bb 
    19425 Alignment algorithm | Needleman-Wunsch 
    19426 Similarity matrix | BLOSUM-62 
    19427 SS fraction | 0.3 
    19428 Gap open (HH/SS/other) | 18/18/6 
    19429 Gap extend | 1 
    19430 SS matrix |  |  | H | S | O 
    19431 ---|---|---|--- 
    19432 H | 6 | -9 | -6 
    19433 S |  | 6 | -6 
    19434 O |  |  | 4 
    19435 Iteration cutoff | 2 
    19436  
    19437 Matchmaker 3j0c.pdb1, chain E (#1.25) with AF3 E2 353-438.pdb, chain B (#425),
    19438 sequence alignment score = 340.2 
    19439 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    19440 8.673) 
    19441  
    19442 
    19443 > hide sel cartoons
    19444 
    19445 > select #1.25/F
    19446 
    19447 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    19448 
    19449 > show sel cartoons
    19450 
    19451 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    19452 
    19453 Chain information for AF3 CA.pdb #426 
    19454 --- 
    19455 Chain | Description 
    19456 A | No description available 
    19457  
    19458 
    19459 > matchmaker #426 to #1.25 & sel
    19460 
    19461 Parameters 
    19462 --- 
    19463 Chain pairing | bb 
    19464 Alignment algorithm | Needleman-Wunsch 
    19465 Similarity matrix | BLOSUM-62 
    19466 SS fraction | 0.3 
    19467 Gap open (HH/SS/other) | 18/18/6 
    19468 Gap extend | 1 
    19469 SS matrix |  |  | H | S | O 
    19470 ---|---|---|--- 
    19471 H | 6 | -9 | -6 
    19472 S |  | 6 | -6 
    19473 O |  |  | 4 
    19474 Iteration cutoff | 2 
    19475  
    19476 Matchmaker 3j0c.pdb1, chain F (#1.25) with AF3 CA.pdb, chain A (#426),
    19477 sequence alignment score = 335.3 
    19478 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    19479 2.550) 
    19480  
    19481 
    19482 > hide sel cartoons
    19483 
    19484 > color #422 dodgerblue
    19485 
    19486 > color #423 dodgerblue
    19487 
    19488 > color #424 #00b305ff
    19489 
    19490 > color #425 #00b305ff
    19491 
    19492 > color #426 #f15839ff
    19493 
    19494 > select #1.26/D
    19495 
    19496 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    19497 
    19498 > show sel cartoons
    19499 
    19500 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    19501 
    19502 Chain information for AF3 E1 1-421.pdb #427 
    19503 --- 
    19504 Chain | Description 
    19505 A | No description available 
    19506  
    19507 
    19508 > matchmaker #427 to #1.26 & sel
    19509 
    19510 Parameters 
    19511 --- 
    19512 Chain pairing | bb 
    19513 Alignment algorithm | Needleman-Wunsch 
    19514 Similarity matrix | BLOSUM-62 
    19515 SS fraction | 0.3 
    19516 Gap open (HH/SS/other) | 18/18/6 
    19517 Gap extend | 1 
    19518 SS matrix |  |  | H | S | O 
    19519 ---|---|---|--- 
    19520 H | 6 | -9 | -6 
    19521 S |  | 6 | -6 
    19522 O |  |  | 4 
    19523 Iteration cutoff | 2 
    19524  
    19525 Matchmaker 3j0c.pdb1, chain D (#1.26) with AF3 E1 1-421.pdb, chain A (#427),
    19526 sequence alignment score = 1060.7 
    19527 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    19528 3.032) 
    19529  
    19530 
    19531 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    19532 
    19533 Chain information for AF3 E1 422-461.pdb #428 
    19534 --- 
    19535 Chain | Description 
    19536 A | No description available 
    19537  
    19538 
    19539 > matchmaker #428 to #1.26 & sel
    19540 
    19541 Parameters 
    19542 --- 
    19543 Chain pairing | bb 
    19544 Alignment algorithm | Needleman-Wunsch 
    19545 Similarity matrix | BLOSUM-62 
    19546 SS fraction | 0.3 
    19547 Gap open (HH/SS/other) | 18/18/6 
    19548 Gap extend | 1 
    19549 SS matrix |  |  | H | S | O 
    19550 ---|---|---|--- 
    19551 H | 6 | -9 | -6 
    19552 S |  | 6 | -6 
    19553 O |  |  | 4 
    19554 Iteration cutoff | 2 
    19555  
    19556 Matchmaker 3j0c.pdb1, chain D (#1.26) with AF3 E1 422-461.pdb, chain A (#428),
    19557 sequence alignment score = 626.9 
    19558 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    19559 2.916) 
    19560  
    19561 
    19562 > hide sel cartoons
    19563 
    19564 > select #1.26/E
    19565 
    19566 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    19567 
    19568 > show sel cartoons
    19569 
    19570 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    19571 
    19572 Chain information for AF3 E2 1-352.pdb #429 
    19573 --- 
    19574 Chain | Description 
    19575 B | No description available 
    19576  
    19577 
    19578 > matchmaker #429 to #1.26 & sel
    19579 
    19580 Parameters 
    19581 --- 
    19582 Chain pairing | bb 
    19583 Alignment algorithm | Needleman-Wunsch 
    19584 Similarity matrix | BLOSUM-62 
    19585 SS fraction | 0.3 
    19586 Gap open (HH/SS/other) | 18/18/6 
    19587 Gap extend | 1 
    19588 SS matrix |  |  | H | S | O 
    19589 ---|---|---|--- 
    19590 H | 6 | -9 | -6 
    19591 S |  | 6 | -6 
    19592 O |  |  | 4 
    19593 Iteration cutoff | 2 
    19594  
    19595 Matchmaker 3j0c.pdb1, chain E (#1.26) with AF3 E2 1-352.pdb, chain B (#429),
    19596 sequence alignment score = 594.5 
    19597 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    19598 6.147) 
    19599  
    19600 
    19601 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    19602 
    19603 Chain information for AF3 E2 353-438.pdb #430 
    19604 --- 
    19605 Chain | Description 
    19606 B | No description available 
    19607  
    19608 
    19609 > matchmaker #430 to #1.26 & sel
    19610 
    19611 Parameters 
    19612 --- 
    19613 Chain pairing | bb 
    19614 Alignment algorithm | Needleman-Wunsch 
    19615 Similarity matrix | BLOSUM-62 
    19616 SS fraction | 0.3 
    19617 Gap open (HH/SS/other) | 18/18/6 
    19618 Gap extend | 1 
    19619 SS matrix |  |  | H | S | O 
    19620 ---|---|---|--- 
    19621 H | 6 | -9 | -6 
    19622 S |  | 6 | -6 
    19623 O |  |  | 4 
    19624 Iteration cutoff | 2 
    19625  
    19626 Matchmaker 3j0c.pdb1, chain E (#1.26) with AF3 E2 353-438.pdb, chain B (#430),
    19627 sequence alignment score = 340.2 
    19628 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    19629 8.673) 
    19630  
    19631 
    19632 > hide sel cartoons
    19633 
    19634 > select #1.26/F
    19635 
    19636 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    19637 
    19638 > show sel cartoons
    19639 
    19640 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    19641 
    19642 Chain information for AF3 CA.pdb #431 
    19643 --- 
    19644 Chain | Description 
    19645 A | No description available 
    19646  
    19647 
    19648 > matchmaker #431 to #1.26 & sel
    19649 
    19650 Parameters 
    19651 --- 
    19652 Chain pairing | bb 
    19653 Alignment algorithm | Needleman-Wunsch 
    19654 Similarity matrix | BLOSUM-62 
    19655 SS fraction | 0.3 
    19656 Gap open (HH/SS/other) | 18/18/6 
    19657 Gap extend | 1 
    19658 SS matrix |  |  | H | S | O 
    19659 ---|---|---|--- 
    19660 H | 6 | -9 | -6 
    19661 S |  | 6 | -6 
    19662 O |  |  | 4 
    19663 Iteration cutoff | 2 
    19664  
    19665 Matchmaker 3j0c.pdb1, chain F (#1.26) with AF3 CA.pdb, chain A (#431),
    19666 sequence alignment score = 335.3 
    19667 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    19668 2.550) 
    19669  
    19670 
    19671 > hide sel cartoons
    19672 
    19673 > color #427 dodgerblue
    19674 
    19675 > color #428 dodgerblue
    19676 
    19677 > color #429 #00b305ff
    19678 
    19679 > color #430 #00b305ff
    19680 
    19681 > color #431 #f15839ff
    19682 
    19683 > select #1.27/D
    19684 
    19685 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    19686 
    19687 > show sel cartoons
    19688 
    19689 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    19690 
    19691 Chain information for AF3 E1 1-421.pdb #432 
    19692 --- 
    19693 Chain | Description 
    19694 A | No description available 
    19695  
    19696 
    19697 > matchmaker #432 to #1.27 & sel
    19698 
    19699 Parameters 
    19700 --- 
    19701 Chain pairing | bb 
    19702 Alignment algorithm | Needleman-Wunsch 
    19703 Similarity matrix | BLOSUM-62 
    19704 SS fraction | 0.3 
    19705 Gap open (HH/SS/other) | 18/18/6 
    19706 Gap extend | 1 
    19707 SS matrix |  |  | H | S | O 
    19708 ---|---|---|--- 
    19709 H | 6 | -9 | -6 
    19710 S |  | 6 | -6 
    19711 O |  |  | 4 
    19712 Iteration cutoff | 2 
    19713  
    19714 Matchmaker 3j0c.pdb1, chain D (#1.27) with AF3 E1 1-421.pdb, chain A (#432),
    19715 sequence alignment score = 1060.7 
    19716 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    19717 3.032) 
    19718  
    19719 
    19720 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    19721 
    19722 Chain information for AF3 E1 422-461.pdb #433 
    19723 --- 
    19724 Chain | Description 
    19725 A | No description available 
    19726  
    19727 
    19728 > matchmaker #433 to #1.27 & sel
    19729 
    19730 Parameters 
    19731 --- 
    19732 Chain pairing | bb 
    19733 Alignment algorithm | Needleman-Wunsch 
    19734 Similarity matrix | BLOSUM-62 
    19735 SS fraction | 0.3 
    19736 Gap open (HH/SS/other) | 18/18/6 
    19737 Gap extend | 1 
    19738 SS matrix |  |  | H | S | O 
    19739 ---|---|---|--- 
    19740 H | 6 | -9 | -6 
    19741 S |  | 6 | -6 
    19742 O |  |  | 4 
    19743 Iteration cutoff | 2 
    19744  
    19745 Matchmaker 3j0c.pdb1, chain D (#1.27) with AF3 E1 422-461.pdb, chain A (#433),
    19746 sequence alignment score = 626.9 
    19747 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    19748 2.916) 
    19749  
    19750 
    19751 > hide sel cartoons
    19752 
    19753 > select #1.27/E
    19754 
    19755 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    19756 
    19757 > show sel cartoons
    19758 
    19759 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    19760 
    19761 Chain information for AF3 E2 1-352.pdb #434 
    19762 --- 
    19763 Chain | Description 
    19764 B | No description available 
    19765  
    19766 
    19767 > matchmaker #434 to #1.27 & sel
    19768 
    19769 Parameters 
    19770 --- 
    19771 Chain pairing | bb 
    19772 Alignment algorithm | Needleman-Wunsch 
    19773 Similarity matrix | BLOSUM-62 
    19774 SS fraction | 0.3 
    19775 Gap open (HH/SS/other) | 18/18/6 
    19776 Gap extend | 1 
    19777 SS matrix |  |  | H | S | O 
    19778 ---|---|---|--- 
    19779 H | 6 | -9 | -6 
    19780 S |  | 6 | -6 
    19781 O |  |  | 4 
    19782 Iteration cutoff | 2 
    19783  
    19784 Matchmaker 3j0c.pdb1, chain E (#1.27) with AF3 E2 1-352.pdb, chain B (#434),
    19785 sequence alignment score = 594.5 
    19786 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    19787 6.147) 
    19788  
    19789 
    19790 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    19791 
    19792 Chain information for AF3 E2 353-438.pdb #435 
    19793 --- 
    19794 Chain | Description 
    19795 B | No description available 
    19796  
    19797 
    19798 > matchmaker #435 to #1.27 & sel
    19799 
    19800 Parameters 
    19801 --- 
    19802 Chain pairing | bb 
    19803 Alignment algorithm | Needleman-Wunsch 
    19804 Similarity matrix | BLOSUM-62 
    19805 SS fraction | 0.3 
    19806 Gap open (HH/SS/other) | 18/18/6 
    19807 Gap extend | 1 
    19808 SS matrix |  |  | H | S | O 
    19809 ---|---|---|--- 
    19810 H | 6 | -9 | -6 
    19811 S |  | 6 | -6 
    19812 O |  |  | 4 
    19813 Iteration cutoff | 2 
    19814  
    19815 Matchmaker 3j0c.pdb1, chain E (#1.27) with AF3 E2 353-438.pdb, chain B (#435),
    19816 sequence alignment score = 340.2 
    19817 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    19818 8.673) 
    19819  
    19820 
    19821 > hide sel cartoons
    19822 
    19823 > select #1.27/F
    19824 
    19825 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    19826 
    19827 > show sel cartoons
    19828 
    19829 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    19830 
    19831 Chain information for AF3 CA.pdb #436 
    19832 --- 
    19833 Chain | Description 
    19834 A | No description available 
    19835  
    19836 
    19837 > matchmaker #436 to #1.27 & sel
    19838 
    19839 Parameters 
    19840 --- 
    19841 Chain pairing | bb 
    19842 Alignment algorithm | Needleman-Wunsch 
    19843 Similarity matrix | BLOSUM-62 
    19844 SS fraction | 0.3 
    19845 Gap open (HH/SS/other) | 18/18/6 
    19846 Gap extend | 1 
    19847 SS matrix |  |  | H | S | O 
    19848 ---|---|---|--- 
    19849 H | 6 | -9 | -6 
    19850 S |  | 6 | -6 
    19851 O |  |  | 4 
    19852 Iteration cutoff | 2 
    19853  
    19854 Matchmaker 3j0c.pdb1, chain F (#1.27) with AF3 CA.pdb, chain A (#436),
    19855 sequence alignment score = 335.3 
    19856 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    19857 2.550) 
    19858  
    19859 
    19860 > hide sel cartoons
    19861 
    19862 > color #432 dodgerblue
    19863 
    19864 > color #433 dodgerblue
    19865 
    19866 > color #434 #00b305ff
    19867 
    19868 > color #435 #00b305ff
    19869 
    19870 > color #436 #f15839ff
    19871 
    19872 > select #1.28/D
    19873 
    19874 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    19875 
    19876 > show sel cartoons
    19877 
    19878 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    19879 
    19880 Chain information for AF3 E1 1-421.pdb #437 
    19881 --- 
    19882 Chain | Description 
    19883 A | No description available 
    19884  
    19885 
    19886 > matchmaker #437 to #1.28 & sel
    19887 
    19888 Parameters 
    19889 --- 
    19890 Chain pairing | bb 
    19891 Alignment algorithm | Needleman-Wunsch 
    19892 Similarity matrix | BLOSUM-62 
    19893 SS fraction | 0.3 
    19894 Gap open (HH/SS/other) | 18/18/6 
    19895 Gap extend | 1 
    19896 SS matrix |  |  | H | S | O 
    19897 ---|---|---|--- 
    19898 H | 6 | -9 | -6 
    19899 S |  | 6 | -6 
    19900 O |  |  | 4 
    19901 Iteration cutoff | 2 
    19902  
    19903 Matchmaker 3j0c.pdb1, chain D (#1.28) with AF3 E1 1-421.pdb, chain A (#437),
    19904 sequence alignment score = 1060.7 
    19905 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    19906 3.032) 
    19907  
    19908 
    19909 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    19910 
    19911 Chain information for AF3 E1 422-461.pdb #438 
    19912 --- 
    19913 Chain | Description 
    19914 A | No description available 
    19915  
    19916 
    19917 > matchmaker #438 to #1.28 & sel
    19918 
    19919 Parameters 
    19920 --- 
    19921 Chain pairing | bb 
    19922 Alignment algorithm | Needleman-Wunsch 
    19923 Similarity matrix | BLOSUM-62 
    19924 SS fraction | 0.3 
    19925 Gap open (HH/SS/other) | 18/18/6 
    19926 Gap extend | 1 
    19927 SS matrix |  |  | H | S | O 
    19928 ---|---|---|--- 
    19929 H | 6 | -9 | -6 
    19930 S |  | 6 | -6 
    19931 O |  |  | 4 
    19932 Iteration cutoff | 2 
    19933  
    19934 Matchmaker 3j0c.pdb1, chain D (#1.28) with AF3 E1 422-461.pdb, chain A (#438),
    19935 sequence alignment score = 626.9 
    19936 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    19937 2.916) 
    19938  
    19939 
    19940 > hide sel cartoons
    19941 
    19942 > select #1.28/E
    19943 
    19944 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    19945 
    19946 > show sel cartoons
    19947 
    19948 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    19949 
    19950 Chain information for AF3 E2 1-352.pdb #439 
    19951 --- 
    19952 Chain | Description 
    19953 B | No description available 
    19954  
    19955 
    19956 > matchmaker #439 to #1.28 & sel
    19957 
    19958 Parameters 
    19959 --- 
    19960 Chain pairing | bb 
    19961 Alignment algorithm | Needleman-Wunsch 
    19962 Similarity matrix | BLOSUM-62 
    19963 SS fraction | 0.3 
    19964 Gap open (HH/SS/other) | 18/18/6 
    19965 Gap extend | 1 
    19966 SS matrix |  |  | H | S | O 
    19967 ---|---|---|--- 
    19968 H | 6 | -9 | -6 
    19969 S |  | 6 | -6 
    19970 O |  |  | 4 
    19971 Iteration cutoff | 2 
    19972  
    19973 Matchmaker 3j0c.pdb1, chain E (#1.28) with AF3 E2 1-352.pdb, chain B (#439),
    19974 sequence alignment score = 594.5 
    19975 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    19976 6.147) 
    19977  
    19978 
    19979 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    19980 
    19981 Chain information for AF3 E2 353-438.pdb #440 
    19982 --- 
    19983 Chain | Description 
    19984 B | No description available 
    19985  
    19986 
    19987 > matchmaker #440 to #1.28 & sel
    19988 
    19989 Parameters 
    19990 --- 
    19991 Chain pairing | bb 
    19992 Alignment algorithm | Needleman-Wunsch 
    19993 Similarity matrix | BLOSUM-62 
    19994 SS fraction | 0.3 
    19995 Gap open (HH/SS/other) | 18/18/6 
    19996 Gap extend | 1 
    19997 SS matrix |  |  | H | S | O 
    19998 ---|---|---|--- 
    19999 H | 6 | -9 | -6 
    20000 S |  | 6 | -6 
    20001 O |  |  | 4 
    20002 Iteration cutoff | 2 
    20003  
    20004 Matchmaker 3j0c.pdb1, chain E (#1.28) with AF3 E2 353-438.pdb, chain B (#440),
    20005 sequence alignment score = 340.2 
    20006 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    20007 8.673) 
    20008  
    20009 
    20010 > hide sel cartoons
    20011 
    20012 > select #1.28/F
    20013 
    20014 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    20015 
    20016 > show sel cartoons
    20017 
    20018 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    20019 
    20020 Chain information for AF3 CA.pdb #441 
    20021 --- 
    20022 Chain | Description 
    20023 A | No description available 
    20024  
    20025 
    20026 > matchmaker #441 to #1.28 & sel
    20027 
    20028 Parameters 
    20029 --- 
    20030 Chain pairing | bb 
    20031 Alignment algorithm | Needleman-Wunsch 
    20032 Similarity matrix | BLOSUM-62 
    20033 SS fraction | 0.3 
    20034 Gap open (HH/SS/other) | 18/18/6 
    20035 Gap extend | 1 
    20036 SS matrix |  |  | H | S | O 
    20037 ---|---|---|--- 
    20038 H | 6 | -9 | -6 
    20039 S |  | 6 | -6 
    20040 O |  |  | 4 
    20041 Iteration cutoff | 2 
    20042  
    20043 Matchmaker 3j0c.pdb1, chain F (#1.28) with AF3 CA.pdb, chain A (#441),
    20044 sequence alignment score = 335.3 
    20045 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    20046 2.550) 
    20047  
    20048 
    20049 > hide sel cartoons
    20050 
    20051 > color #437 dodgerblue
    20052 
    20053 > color #438 dodgerblue
    20054 
    20055 > color #439 #00b305ff
    20056 
    20057 > color #440 #00b305ff
    20058 
    20059 > color #441 #f15839ff
    20060 
    20061 > select #1.29/D
    20062 
    20063 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    20064 
    20065 > show sel cartoons
    20066 
    20067 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    20068 
    20069 Chain information for AF3 E1 1-421.pdb #442 
    20070 --- 
    20071 Chain | Description 
    20072 A | No description available 
    20073  
    20074 
    20075 > matchmaker #442 to #1.29 & sel
    20076 
    20077 Parameters 
    20078 --- 
    20079 Chain pairing | bb 
    20080 Alignment algorithm | Needleman-Wunsch 
    20081 Similarity matrix | BLOSUM-62 
    20082 SS fraction | 0.3 
    20083 Gap open (HH/SS/other) | 18/18/6 
    20084 Gap extend | 1 
    20085 SS matrix |  |  | H | S | O 
    20086 ---|---|---|--- 
    20087 H | 6 | -9 | -6 
    20088 S |  | 6 | -6 
    20089 O |  |  | 4 
    20090 Iteration cutoff | 2 
    20091  
    20092 Matchmaker 3j0c.pdb1, chain D (#1.29) with AF3 E1 1-421.pdb, chain A (#442),
    20093 sequence alignment score = 1060.7 
    20094 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    20095 3.032) 
    20096  
    20097 
    20098 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    20099 
    20100 Chain information for AF3 E1 422-461.pdb #443 
    20101 --- 
    20102 Chain | Description 
    20103 A | No description available 
    20104  
    20105 
    20106 > matchmaker #443 to #1.29 & sel
    20107 
    20108 Parameters 
    20109 --- 
    20110 Chain pairing | bb 
    20111 Alignment algorithm | Needleman-Wunsch 
    20112 Similarity matrix | BLOSUM-62 
    20113 SS fraction | 0.3 
    20114 Gap open (HH/SS/other) | 18/18/6 
    20115 Gap extend | 1 
    20116 SS matrix |  |  | H | S | O 
    20117 ---|---|---|--- 
    20118 H | 6 | -9 | -6 
    20119 S |  | 6 | -6 
    20120 O |  |  | 4 
    20121 Iteration cutoff | 2 
    20122  
    20123 Matchmaker 3j0c.pdb1, chain D (#1.29) with AF3 E1 422-461.pdb, chain A (#443),
    20124 sequence alignment score = 626.9 
    20125 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    20126 2.916) 
    20127  
    20128 
    20129 > hide sel cartoons
    20130 
    20131 > select #1.29/E
    20132 
    20133 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    20134 
    20135 > show sel cartoons
    20136 
    20137 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    20138 
    20139 Chain information for AF3 E2 1-352.pdb #444 
    20140 --- 
    20141 Chain | Description 
    20142 B | No description available 
    20143  
    20144 
    20145 > matchmaker #444 to #1.29 & sel
    20146 
    20147 Parameters 
    20148 --- 
    20149 Chain pairing | bb 
    20150 Alignment algorithm | Needleman-Wunsch 
    20151 Similarity matrix | BLOSUM-62 
    20152 SS fraction | 0.3 
    20153 Gap open (HH/SS/other) | 18/18/6 
    20154 Gap extend | 1 
    20155 SS matrix |  |  | H | S | O 
    20156 ---|---|---|--- 
    20157 H | 6 | -9 | -6 
    20158 S |  | 6 | -6 
    20159 O |  |  | 4 
    20160 Iteration cutoff | 2 
    20161  
    20162 Matchmaker 3j0c.pdb1, chain E (#1.29) with AF3 E2 1-352.pdb, chain B (#444),
    20163 sequence alignment score = 594.5 
    20164 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    20165 6.147) 
    20166  
    20167 
    20168 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    20169 
    20170 Chain information for AF3 E2 353-438.pdb #445 
    20171 --- 
    20172 Chain | Description 
    20173 B | No description available 
    20174  
    20175 
    20176 > matchmaker #445 to #1.29 & sel
    20177 
    20178 Parameters 
    20179 --- 
    20180 Chain pairing | bb 
    20181 Alignment algorithm | Needleman-Wunsch 
    20182 Similarity matrix | BLOSUM-62 
    20183 SS fraction | 0.3 
    20184 Gap open (HH/SS/other) | 18/18/6 
    20185 Gap extend | 1 
    20186 SS matrix |  |  | H | S | O 
    20187 ---|---|---|--- 
    20188 H | 6 | -9 | -6 
    20189 S |  | 6 | -6 
    20190 O |  |  | 4 
    20191 Iteration cutoff | 2 
    20192  
    20193 Matchmaker 3j0c.pdb1, chain E (#1.29) with AF3 E2 353-438.pdb, chain B (#445),
    20194 sequence alignment score = 340.2 
    20195 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    20196 8.673) 
    20197  
    20198 
    20199 > hide sel cartoons
    20200 
    20201 > select #1.29/F
    20202 
    20203 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    20204 
    20205 > show sel cartoons
    20206 
    20207 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    20208 
    20209 Chain information for AF3 CA.pdb #446 
    20210 --- 
    20211 Chain | Description 
    20212 A | No description available 
    20213  
    20214 
    20215 > matchmaker #446 to #1.29 & sel
    20216 
    20217 Parameters 
    20218 --- 
    20219 Chain pairing | bb 
    20220 Alignment algorithm | Needleman-Wunsch 
    20221 Similarity matrix | BLOSUM-62 
    20222 SS fraction | 0.3 
    20223 Gap open (HH/SS/other) | 18/18/6 
    20224 Gap extend | 1 
    20225 SS matrix |  |  | H | S | O 
    20226 ---|---|---|--- 
    20227 H | 6 | -9 | -6 
    20228 S |  | 6 | -6 
    20229 O |  |  | 4 
    20230 Iteration cutoff | 2 
    20231  
    20232 Matchmaker 3j0c.pdb1, chain F (#1.29) with AF3 CA.pdb, chain A (#446),
    20233 sequence alignment score = 335.3 
    20234 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    20235 2.550) 
    20236  
    20237 
    20238 > hide sel cartoons
    20239 
    20240 > color #442 dodgerblue
    20241 
    20242 > color #443 dodgerblue
    20243 
    20244 > color #444 #00b305ff
    20245 
    20246 > color #445 #00b305ff
    20247 
    20248 > color #446 #f15839ff
    20249 
    20250 > select #1.30/D
    20251 
    20252 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    20253 
    20254 > show sel cartoons
    20255 
    20256 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    20257 
    20258 Chain information for AF3 E1 1-421.pdb #447 
    20259 --- 
    20260 Chain | Description 
    20261 A | No description available 
    20262  
    20263 
    20264 > matchmaker #447 to #1.30 & sel
    20265 
    20266 Parameters 
    20267 --- 
    20268 Chain pairing | bb 
    20269 Alignment algorithm | Needleman-Wunsch 
    20270 Similarity matrix | BLOSUM-62 
    20271 SS fraction | 0.3 
    20272 Gap open (HH/SS/other) | 18/18/6 
    20273 Gap extend | 1 
    20274 SS matrix |  |  | H | S | O 
    20275 ---|---|---|--- 
    20276 H | 6 | -9 | -6 
    20277 S |  | 6 | -6 
    20278 O |  |  | 4 
    20279 Iteration cutoff | 2 
    20280  
    20281 Matchmaker 3j0c.pdb1, chain D (#1.30) with AF3 E1 1-421.pdb, chain A (#447),
    20282 sequence alignment score = 1060.7 
    20283 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    20284 3.032) 
    20285  
    20286 
    20287 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    20288 
    20289 Chain information for AF3 E1 422-461.pdb #448 
    20290 --- 
    20291 Chain | Description 
    20292 A | No description available 
    20293  
    20294 
    20295 > matchmaker #448 to #1.30 & sel
    20296 
    20297 Parameters 
    20298 --- 
    20299 Chain pairing | bb 
    20300 Alignment algorithm | Needleman-Wunsch 
    20301 Similarity matrix | BLOSUM-62 
    20302 SS fraction | 0.3 
    20303 Gap open (HH/SS/other) | 18/18/6 
    20304 Gap extend | 1 
    20305 SS matrix |  |  | H | S | O 
    20306 ---|---|---|--- 
    20307 H | 6 | -9 | -6 
    20308 S |  | 6 | -6 
    20309 O |  |  | 4 
    20310 Iteration cutoff | 2 
    20311  
    20312 Matchmaker 3j0c.pdb1, chain D (#1.30) with AF3 E1 422-461.pdb, chain A (#448),
    20313 sequence alignment score = 626.9 
    20314 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    20315 2.916) 
    20316  
    20317 
    20318 > hide sel cartoons
    20319 
    20320 > select #1.30/E
    20321 
    20322 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    20323 
    20324 > show sel cartoons
    20325 
    20326 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    20327 
    20328 Chain information for AF3 E2 1-352.pdb #449 
    20329 --- 
    20330 Chain | Description 
    20331 B | No description available 
    20332  
    20333 
    20334 > matchmaker #449 to #1.30 & sel
    20335 
    20336 Parameters 
    20337 --- 
    20338 Chain pairing | bb 
    20339 Alignment algorithm | Needleman-Wunsch 
    20340 Similarity matrix | BLOSUM-62 
    20341 SS fraction | 0.3 
    20342 Gap open (HH/SS/other) | 18/18/6 
    20343 Gap extend | 1 
    20344 SS matrix |  |  | H | S | O 
    20345 ---|---|---|--- 
    20346 H | 6 | -9 | -6 
    20347 S |  | 6 | -6 
    20348 O |  |  | 4 
    20349 Iteration cutoff | 2 
    20350  
    20351 Matchmaker 3j0c.pdb1, chain E (#1.30) with AF3 E2 1-352.pdb, chain B (#449),
    20352 sequence alignment score = 594.5 
    20353 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    20354 6.147) 
    20355  
    20356 
    20357 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    20358 
    20359 Chain information for AF3 E2 353-438.pdb #450 
    20360 --- 
    20361 Chain | Description 
    20362 B | No description available 
    20363  
    20364 
    20365 > matchmaker #450 to #1.30 & sel
    20366 
    20367 Parameters 
    20368 --- 
    20369 Chain pairing | bb 
    20370 Alignment algorithm | Needleman-Wunsch 
    20371 Similarity matrix | BLOSUM-62 
    20372 SS fraction | 0.3 
    20373 Gap open (HH/SS/other) | 18/18/6 
    20374 Gap extend | 1 
    20375 SS matrix |  |  | H | S | O 
    20376 ---|---|---|--- 
    20377 H | 6 | -9 | -6 
    20378 S |  | 6 | -6 
    20379 O |  |  | 4 
    20380 Iteration cutoff | 2 
    20381  
    20382 Matchmaker 3j0c.pdb1, chain E (#1.30) with AF3 E2 353-438.pdb, chain B (#450),
    20383 sequence alignment score = 340.2 
    20384 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    20385 8.673) 
    20386  
    20387 
    20388 > hide sel cartoons
    20389 
    20390 > select #1.30/F
    20391 
    20392 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    20393 
    20394 > show sel cartoons
    20395 
    20396 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    20397 
    20398 Chain information for AF3 CA.pdb #451 
    20399 --- 
    20400 Chain | Description 
    20401 A | No description available 
    20402  
    20403 
    20404 > matchmaker #451 to #1.30 & sel
    20405 
    20406 Parameters 
    20407 --- 
    20408 Chain pairing | bb 
    20409 Alignment algorithm | Needleman-Wunsch 
    20410 Similarity matrix | BLOSUM-62 
    20411 SS fraction | 0.3 
    20412 Gap open (HH/SS/other) | 18/18/6 
    20413 Gap extend | 1 
    20414 SS matrix |  |  | H | S | O 
    20415 ---|---|---|--- 
    20416 H | 6 | -9 | -6 
    20417 S |  | 6 | -6 
    20418 O |  |  | 4 
    20419 Iteration cutoff | 2 
    20420  
    20421 Matchmaker 3j0c.pdb1, chain F (#1.30) with AF3 CA.pdb, chain A (#451),
    20422 sequence alignment score = 335.3 
    20423 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    20424 2.550) 
    20425  
    20426 
    20427 > hide sel cartoons
    20428 
    20429 > color #447 dodgerblue
    20430 
    20431 > color #448 dodgerblue
    20432 
    20433 > color #449 #00b305ff
    20434 
    20435 > color #450 #00b305ff
    20436 
    20437 > color #451 #f15839ff
    20438 
    20439 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    20440 
    20441 > hide #397-451 models
    20442 
    20443 > select #1.31/D
    20444 
    20445 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    20446 
    20447 > show sel cartoons
    20448 
    20449 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    20450 
    20451 Chain information for AF3 E1 1-421.pdb #452 
    20452 --- 
    20453 Chain | Description 
    20454 A | No description available 
    20455  
    20456 
    20457 > matchmaker #452 to #1.31 & sel
    20458 
    20459 Parameters 
    20460 --- 
    20461 Chain pairing | bb 
    20462 Alignment algorithm | Needleman-Wunsch 
    20463 Similarity matrix | BLOSUM-62 
    20464 SS fraction | 0.3 
    20465 Gap open (HH/SS/other) | 18/18/6 
    20466 Gap extend | 1 
    20467 SS matrix |  |  | H | S | O 
    20468 ---|---|---|--- 
    20469 H | 6 | -9 | -6 
    20470 S |  | 6 | -6 
    20471 O |  |  | 4 
    20472 Iteration cutoff | 2 
    20473  
    20474 Matchmaker 3j0c.pdb1, chain D (#1.31) with AF3 E1 1-421.pdb, chain A (#452),
    20475 sequence alignment score = 1060.7 
    20476 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    20477 3.032) 
    20478  
    20479 
    20480 > view sel
    20481 
    20482 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    20483 
    20484 Chain information for AF3 E1 422-461.pdb #453 
    20485 --- 
    20486 Chain | Description 
    20487 A | No description available 
    20488  
    20489 
    20490 > matchmaker #453 to #1.31 & sel
    20491 
    20492 Parameters 
    20493 --- 
    20494 Chain pairing | bb 
    20495 Alignment algorithm | Needleman-Wunsch 
    20496 Similarity matrix | BLOSUM-62 
    20497 SS fraction | 0.3 
    20498 Gap open (HH/SS/other) | 18/18/6 
    20499 Gap extend | 1 
    20500 SS matrix |  |  | H | S | O 
    20501 ---|---|---|--- 
    20502 H | 6 | -9 | -6 
    20503 S |  | 6 | -6 
    20504 O |  |  | 4 
    20505 Iteration cutoff | 2 
    20506  
    20507 Matchmaker 3j0c.pdb1, chain D (#1.31) with AF3 E1 422-461.pdb, chain A (#453),
    20508 sequence alignment score = 626.9 
    20509 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    20510 2.916) 
    20511  
    20512 
    20513 > view
    20514 
    20515 > hide sel cartoons
    20516 
    20517 > select #1.31/E
    20518 
    20519 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    20520 
    20521 > show sel cartoons
    20522 
    20523 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    20524 
    20525 Chain information for AF3 E2 1-352.pdb #454 
    20526 --- 
    20527 Chain | Description 
    20528 B | No description available 
    20529  
    20530 
    20531 > matchmaker #454 to #1.31 & sel
    20532 
    20533 Parameters 
    20534 --- 
    20535 Chain pairing | bb 
    20536 Alignment algorithm | Needleman-Wunsch 
    20537 Similarity matrix | BLOSUM-62 
    20538 SS fraction | 0.3 
    20539 Gap open (HH/SS/other) | 18/18/6 
    20540 Gap extend | 1 
    20541 SS matrix |  |  | H | S | O 
    20542 ---|---|---|--- 
    20543 H | 6 | -9 | -6 
    20544 S |  | 6 | -6 
    20545 O |  |  | 4 
    20546 Iteration cutoff | 2 
    20547  
    20548 Matchmaker 3j0c.pdb1, chain E (#1.31) with AF3 E2 1-352.pdb, chain B (#454),
    20549 sequence alignment score = 594.5 
    20550 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    20551 6.147) 
    20552  
    20553 
    20554 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    20555 
    20556 Chain information for AF3 E2 353-438.pdb #455 
    20557 --- 
    20558 Chain | Description 
    20559 B | No description available 
    20560  
    20561 
    20562 > matchmaker #455 to #1.31 & sel
    20563 
    20564 Parameters 
    20565 --- 
    20566 Chain pairing | bb 
    20567 Alignment algorithm | Needleman-Wunsch 
    20568 Similarity matrix | BLOSUM-62 
    20569 SS fraction | 0.3 
    20570 Gap open (HH/SS/other) | 18/18/6 
    20571 Gap extend | 1 
    20572 SS matrix |  |  | H | S | O 
    20573 ---|---|---|--- 
    20574 H | 6 | -9 | -6 
    20575 S |  | 6 | -6 
    20576 O |  |  | 4 
    20577 Iteration cutoff | 2 
    20578  
    20579 Matchmaker 3j0c.pdb1, chain E (#1.31) with AF3 E2 353-438.pdb, chain B (#455),
    20580 sequence alignment score = 340.2 
    20581 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    20582 8.673) 
    20583  
    20584 
    20585 > hide sel cartoons
    20586 
    20587 > select #1.31/F
    20588 
    20589 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    20590 
    20591 > show sel cartoons
    20592 
    20593 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    20594 
    20595 Chain information for AF3 CA.pdb #456 
    20596 --- 
    20597 Chain | Description 
    20598 A | No description available 
    20599  
    20600 
    20601 > matchmaker #456 to #1.31 & sel
    20602 
    20603 Parameters 
    20604 --- 
    20605 Chain pairing | bb 
    20606 Alignment algorithm | Needleman-Wunsch 
    20607 Similarity matrix | BLOSUM-62 
    20608 SS fraction | 0.3 
    20609 Gap open (HH/SS/other) | 18/18/6 
    20610 Gap extend | 1 
    20611 SS matrix |  |  | H | S | O 
    20612 ---|---|---|--- 
    20613 H | 6 | -9 | -6 
    20614 S |  | 6 | -6 
    20615 O |  |  | 4 
    20616 Iteration cutoff | 2 
    20617  
    20618 Matchmaker 3j0c.pdb1, chain F (#1.31) with AF3 CA.pdb, chain A (#456),
    20619 sequence alignment score = 335.3 
    20620 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    20621 2.550) 
    20622  
    20623 
    20624 > hide sel cartoons
    20625 
    20626 > color #452 dodgerblue
    20627 
    20628 > color #453 dodgerblue
    20629 
    20630 > color #454 #00b305ff
    20631 
    20632 > color #455 #00b305ff
    20633 
    20634 > color #456 #f15839ff
    20635 
    20636 > select #1.32/D
    20637 
    20638 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    20639 
    20640 > show sel cartoons
    20641 
    20642 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    20643 
    20644 Chain information for AF3 E1 1-421.pdb #457 
    20645 --- 
    20646 Chain | Description 
    20647 A | No description available 
    20648  
    20649 
    20650 > matchmaker #457 to #1.32 & sel
    20651 
    20652 Parameters 
    20653 --- 
    20654 Chain pairing | bb 
    20655 Alignment algorithm | Needleman-Wunsch 
    20656 Similarity matrix | BLOSUM-62 
    20657 SS fraction | 0.3 
    20658 Gap open (HH/SS/other) | 18/18/6 
    20659 Gap extend | 1 
    20660 SS matrix |  |  | H | S | O 
    20661 ---|---|---|--- 
    20662 H | 6 | -9 | -6 
    20663 S |  | 6 | -6 
    20664 O |  |  | 4 
    20665 Iteration cutoff | 2 
    20666  
    20667 Matchmaker 3j0c.pdb1, chain D (#1.32) with AF3 E1 1-421.pdb, chain A (#457),
    20668 sequence alignment score = 1060.7 
    20669 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    20670 3.032) 
    20671  
    20672 
    20673 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    20674 
    20675 Chain information for AF3 E1 422-461.pdb #458 
    20676 --- 
    20677 Chain | Description 
    20678 A | No description available 
    20679  
    20680 
    20681 > matchmaker #458 to #1.32 & sel
    20682 
    20683 Parameters 
    20684 --- 
    20685 Chain pairing | bb 
    20686 Alignment algorithm | Needleman-Wunsch 
    20687 Similarity matrix | BLOSUM-62 
    20688 SS fraction | 0.3 
    20689 Gap open (HH/SS/other) | 18/18/6 
    20690 Gap extend | 1 
    20691 SS matrix |  |  | H | S | O 
    20692 ---|---|---|--- 
    20693 H | 6 | -9 | -6 
    20694 S |  | 6 | -6 
    20695 O |  |  | 4 
    20696 Iteration cutoff | 2 
    20697  
    20698 Matchmaker 3j0c.pdb1, chain D (#1.32) with AF3 E1 422-461.pdb, chain A (#458),
    20699 sequence alignment score = 626.9 
    20700 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    20701 2.916) 
    20702  
    20703 
    20704 > hide sel cartoons
    20705 
    20706 > select #1.31/E
    20707 
    20708 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    20709 
    20710 > show sel cartoons
    20711 
    20712 > hide sel cartoons
    20713 
    20714 > select #1.32/E
    20715 
    20716 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    20717 
    20718 > show sel cartoons
    20719 
    20720 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    20721 
    20722 Chain information for AF3 E2 1-352.pdb #459 
    20723 --- 
    20724 Chain | Description 
    20725 B | No description available 
    20726  
    20727 
    20728 > matchmaker #459 to #1.32 & sel
    20729 
    20730 Parameters 
    20731 --- 
    20732 Chain pairing | bb 
    20733 Alignment algorithm | Needleman-Wunsch 
    20734 Similarity matrix | BLOSUM-62 
    20735 SS fraction | 0.3 
    20736 Gap open (HH/SS/other) | 18/18/6 
    20737 Gap extend | 1 
    20738 SS matrix |  |  | H | S | O 
    20739 ---|---|---|--- 
    20740 H | 6 | -9 | -6 
    20741 S |  | 6 | -6 
    20742 O |  |  | 4 
    20743 Iteration cutoff | 2 
    20744  
    20745 Matchmaker 3j0c.pdb1, chain E (#1.32) with AF3 E2 1-352.pdb, chain B (#459),
    20746 sequence alignment score = 594.5 
    20747 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    20748 6.147) 
    20749  
    20750 
    20751 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    20752 
    20753 Chain information for AF3 E2 353-438.pdb #460 
    20754 --- 
    20755 Chain | Description 
    20756 B | No description available 
    20757  
    20758 
    20759 > matchmaker #460 to #1.32 & sel
    20760 
    20761 Parameters 
    20762 --- 
    20763 Chain pairing | bb 
    20764 Alignment algorithm | Needleman-Wunsch 
    20765 Similarity matrix | BLOSUM-62 
    20766 SS fraction | 0.3 
    20767 Gap open (HH/SS/other) | 18/18/6 
    20768 Gap extend | 1 
    20769 SS matrix |  |  | H | S | O 
    20770 ---|---|---|--- 
    20771 H | 6 | -9 | -6 
    20772 S |  | 6 | -6 
    20773 O |  |  | 4 
    20774 Iteration cutoff | 2 
    20775  
    20776 Matchmaker 3j0c.pdb1, chain E (#1.32) with AF3 E2 353-438.pdb, chain B (#460),
    20777 sequence alignment score = 340.2 
    20778 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    20779 8.673) 
    20780  
    20781 
    20782 > hide sel cartoons
    20783 
    20784 > select #1.32/F
    20785 
    20786 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    20787 
    20788 > show sel cartoons
    20789 
    20790 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    20791 
    20792 Chain information for AF3 CA.pdb #461 
    20793 --- 
    20794 Chain | Description 
    20795 A | No description available 
    20796  
    20797 
    20798 > matchmaker #461 to #1.32 & sel
    20799 
    20800 Parameters 
    20801 --- 
    20802 Chain pairing | bb 
    20803 Alignment algorithm | Needleman-Wunsch 
    20804 Similarity matrix | BLOSUM-62 
    20805 SS fraction | 0.3 
    20806 Gap open (HH/SS/other) | 18/18/6 
    20807 Gap extend | 1 
    20808 SS matrix |  |  | H | S | O 
    20809 ---|---|---|--- 
    20810 H | 6 | -9 | -6 
    20811 S |  | 6 | -6 
    20812 O |  |  | 4 
    20813 Iteration cutoff | 2 
    20814  
    20815 Matchmaker 3j0c.pdb1, chain F (#1.32) with AF3 CA.pdb, chain A (#461),
    20816 sequence alignment score = 335.3 
    20817 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    20818 2.550) 
    20819  
    20820 
    20821 > hide sel cartoons
    20822 
    20823 > color #457 dodgerblue
    20824 
    20825 > color #458 dodgerblue
    20826 
    20827 > color #459 #00b305ff
    20828 
    20829 > color #460 #00b305ff
    20830 
    20831 > color #461 #f15839ff
    20832 
    20833 > select #1.33/D
    20834 
    20835 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    20836 
    20837 > show sel cartoons
    20838 
    20839 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    20840 
    20841 Chain information for AF3 E1 1-421.pdb #462 
    20842 --- 
    20843 Chain | Description 
    20844 A | No description available 
    20845  
    20846 
    20847 > matchmaker #462 to #1.33 & sel
    20848 
    20849 Parameters 
    20850 --- 
    20851 Chain pairing | bb 
    20852 Alignment algorithm | Needleman-Wunsch 
    20853 Similarity matrix | BLOSUM-62 
    20854 SS fraction | 0.3 
    20855 Gap open (HH/SS/other) | 18/18/6 
    20856 Gap extend | 1 
    20857 SS matrix |  |  | H | S | O 
    20858 ---|---|---|--- 
    20859 H | 6 | -9 | -6 
    20860 S |  | 6 | -6 
    20861 O |  |  | 4 
    20862 Iteration cutoff | 2 
    20863  
    20864 Matchmaker 3j0c.pdb1, chain D (#1.33) with AF3 E1 1-421.pdb, chain A (#462),
    20865 sequence alignment score = 1060.7 
    20866 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    20867 3.032) 
    20868  
    20869 
    20870 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    20871 
    20872 Chain information for AF3 E1 422-461.pdb #463 
    20873 --- 
    20874 Chain | Description 
    20875 A | No description available 
    20876  
    20877 
    20878 > matchmaker #463 to #1.33 & sel
    20879 
    20880 Parameters 
    20881 --- 
    20882 Chain pairing | bb 
    20883 Alignment algorithm | Needleman-Wunsch 
    20884 Similarity matrix | BLOSUM-62 
    20885 SS fraction | 0.3 
    20886 Gap open (HH/SS/other) | 18/18/6 
    20887 Gap extend | 1 
    20888 SS matrix |  |  | H | S | O 
    20889 ---|---|---|--- 
    20890 H | 6 | -9 | -6 
    20891 S |  | 6 | -6 
    20892 O |  |  | 4 
    20893 Iteration cutoff | 2 
    20894  
    20895 Matchmaker 3j0c.pdb1, chain D (#1.33) with AF3 E1 422-461.pdb, chain A (#463),
    20896 sequence alignment score = 626.9 
    20897 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    20898 2.916) 
    20899  
    20900 
    20901 > hide sel cartoons
    20902 
    20903 > select #1.33/E
    20904 
    20905 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    20906 
    20907 > show sel cartoons
    20908 
    20909 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    20910 
    20911 Chain information for AF3 E2 1-352.pdb #464 
    20912 --- 
    20913 Chain | Description 
    20914 B | No description available 
    20915  
    20916 
    20917 > matchmaker #464 to #1.33 & sel
    20918 
    20919 Parameters 
    20920 --- 
    20921 Chain pairing | bb 
    20922 Alignment algorithm | Needleman-Wunsch 
    20923 Similarity matrix | BLOSUM-62 
    20924 SS fraction | 0.3 
    20925 Gap open (HH/SS/other) | 18/18/6 
    20926 Gap extend | 1 
    20927 SS matrix |  |  | H | S | O 
    20928 ---|---|---|--- 
    20929 H | 6 | -9 | -6 
    20930 S |  | 6 | -6 
    20931 O |  |  | 4 
    20932 Iteration cutoff | 2 
    20933  
    20934 Matchmaker 3j0c.pdb1, chain E (#1.33) with AF3 E2 1-352.pdb, chain B (#464),
    20935 sequence alignment score = 594.5 
    20936 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    20937 6.147) 
    20938  
    20939 
    20940 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    20941 
    20942 Chain information for AF3 E2 353-438.pdb #465 
    20943 --- 
    20944 Chain | Description 
    20945 B | No description available 
    20946  
    20947 
    20948 > matchmaker #465 to #1.33 & sel
    20949 
    20950 Parameters 
    20951 --- 
    20952 Chain pairing | bb 
    20953 Alignment algorithm | Needleman-Wunsch 
    20954 Similarity matrix | BLOSUM-62 
    20955 SS fraction | 0.3 
    20956 Gap open (HH/SS/other) | 18/18/6 
    20957 Gap extend | 1 
    20958 SS matrix |  |  | H | S | O 
    20959 ---|---|---|--- 
    20960 H | 6 | -9 | -6 
    20961 S |  | 6 | -6 
    20962 O |  |  | 4 
    20963 Iteration cutoff | 2 
    20964  
    20965 Matchmaker 3j0c.pdb1, chain E (#1.33) with AF3 E2 353-438.pdb, chain B (#465),
    20966 sequence alignment score = 340.2 
    20967 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    20968 8.673) 
    20969  
    20970 
    20971 > hide sel cartoons
    20972 
    20973 > select #1.33/F
    20974 
    20975 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    20976 
    20977 > show sel cartoons
    20978 
    20979 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    20980 
    20981 Chain information for AF3 CA.pdb #466 
    20982 --- 
    20983 Chain | Description 
    20984 A | No description available 
    20985  
    20986 
    20987 > matchmaker #466 to #1.33 & sel
    20988 
    20989 Parameters 
    20990 --- 
    20991 Chain pairing | bb 
    20992 Alignment algorithm | Needleman-Wunsch 
    20993 Similarity matrix | BLOSUM-62 
    20994 SS fraction | 0.3 
    20995 Gap open (HH/SS/other) | 18/18/6 
    20996 Gap extend | 1 
    20997 SS matrix |  |  | H | S | O 
    20998 ---|---|---|--- 
    20999 H | 6 | -9 | -6 
    21000 S |  | 6 | -6 
    21001 O |  |  | 4 
    21002 Iteration cutoff | 2 
    21003  
    21004 Matchmaker 3j0c.pdb1, chain F (#1.33) with AF3 CA.pdb, chain A (#466),
    21005 sequence alignment score = 335.3 
    21006 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    21007 2.550) 
    21008  
    21009 
    21010 > hide sel cartoons
    21011 
    21012 > color #462 dodgerblue
    21013 
    21014 > color #463 dodgerblue
    21015 
    21016 > color #464 #00b305ff
    21017 
    21018 > color #465 #00b305ff
    21019 
    21020 > color #466 #f15839ff
    21021 
    21022 > select #1.34/D
    21023 
    21024 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    21025 
    21026 > show sel cartoons
    21027 
    21028 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    21029 
    21030 Chain information for AF3 E1 1-421.pdb #467 
    21031 --- 
    21032 Chain | Description 
    21033 A | No description available 
    21034  
    21035 
    21036 > view
    21037 
    21038 > matchmaker #467 to #1.34 & sel
    21039 
    21040 Parameters 
    21041 --- 
    21042 Chain pairing | bb 
    21043 Alignment algorithm | Needleman-Wunsch 
    21044 Similarity matrix | BLOSUM-62 
    21045 SS fraction | 0.3 
    21046 Gap open (HH/SS/other) | 18/18/6 
    21047 Gap extend | 1 
    21048 SS matrix |  |  | H | S | O 
    21049 ---|---|---|--- 
    21050 H | 6 | -9 | -6 
    21051 S |  | 6 | -6 
    21052 O |  |  | 4 
    21053 Iteration cutoff | 2 
    21054  
    21055 Matchmaker 3j0c.pdb1, chain D (#1.34) with AF3 E1 1-421.pdb, chain A (#467),
    21056 sequence alignment score = 1060.7 
    21057 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    21058 3.032) 
    21059  
    21060 
    21061 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    21062 
    21063 Chain information for AF3 E1 422-461.pdb #468 
    21064 --- 
    21065 Chain | Description 
    21066 A | No description available 
    21067  
    21068 
    21069 > matchmaker #468 to #1.34 & sel
    21070 
    21071 Parameters 
    21072 --- 
    21073 Chain pairing | bb 
    21074 Alignment algorithm | Needleman-Wunsch 
    21075 Similarity matrix | BLOSUM-62 
    21076 SS fraction | 0.3 
    21077 Gap open (HH/SS/other) | 18/18/6 
    21078 Gap extend | 1 
    21079 SS matrix |  |  | H | S | O 
    21080 ---|---|---|--- 
    21081 H | 6 | -9 | -6 
    21082 S |  | 6 | -6 
    21083 O |  |  | 4 
    21084 Iteration cutoff | 2 
    21085  
    21086 Matchmaker 3j0c.pdb1, chain D (#1.34) with AF3 E1 422-461.pdb, chain A (#468),
    21087 sequence alignment score = 626.9 
    21088 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    21089 2.916) 
    21090  
    21091 
    21092 > hide sel cartoons
    21093 
    21094 > select #1.34/E
    21095 
    21096 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    21097 
    21098 > show sel cartoons
    21099 
    21100 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    21101 
    21102 Chain information for AF3 E2 1-352.pdb #469 
    21103 --- 
    21104 Chain | Description 
    21105 B | No description available 
    21106  
    21107 
    21108 > matchmaker #469 to #1.34 & sel
    21109 
    21110 Parameters 
    21111 --- 
    21112 Chain pairing | bb 
    21113 Alignment algorithm | Needleman-Wunsch 
    21114 Similarity matrix | BLOSUM-62 
    21115 SS fraction | 0.3 
    21116 Gap open (HH/SS/other) | 18/18/6 
    21117 Gap extend | 1 
    21118 SS matrix |  |  | H | S | O 
    21119 ---|---|---|--- 
    21120 H | 6 | -9 | -6 
    21121 S |  | 6 | -6 
    21122 O |  |  | 4 
    21123 Iteration cutoff | 2 
    21124  
    21125 Matchmaker 3j0c.pdb1, chain E (#1.34) with AF3 E2 1-352.pdb, chain B (#469),
    21126 sequence alignment score = 594.5 
    21127 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    21128 6.147) 
    21129  
    21130 
    21131 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    21132 
    21133 Chain information for AF3 E2 353-438.pdb #470 
    21134 --- 
    21135 Chain | Description 
    21136 B | No description available 
    21137  
    21138 
    21139 > matchmaker #470 to #1.34 & sel
    21140 
    21141 Parameters 
    21142 --- 
    21143 Chain pairing | bb 
    21144 Alignment algorithm | Needleman-Wunsch 
    21145 Similarity matrix | BLOSUM-62 
    21146 SS fraction | 0.3 
    21147 Gap open (HH/SS/other) | 18/18/6 
    21148 Gap extend | 1 
    21149 SS matrix |  |  | H | S | O 
    21150 ---|---|---|--- 
    21151 H | 6 | -9 | -6 
    21152 S |  | 6 | -6 
    21153 O |  |  | 4 
    21154 Iteration cutoff | 2 
    21155  
    21156 Matchmaker 3j0c.pdb1, chain E (#1.34) with AF3 E2 353-438.pdb, chain B (#470),
    21157 sequence alignment score = 340.2 
    21158 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    21159 8.673) 
    21160  
    21161 
    21162 > hide sel cartoons
    21163 
    21164 > select #1.34/F
    21165 
    21166 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    21167 
    21168 > show sel cartoons
    21169 
    21170 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    21171 
    21172 Chain information for AF3 CA.pdb #471 
    21173 --- 
    21174 Chain | Description 
    21175 A | No description available 
    21176  
    21177 
    21178 > matchmaker #471 to #1.34 & sel
    21179 
    21180 Parameters 
    21181 --- 
    21182 Chain pairing | bb 
    21183 Alignment algorithm | Needleman-Wunsch 
    21184 Similarity matrix | BLOSUM-62 
    21185 SS fraction | 0.3 
    21186 Gap open (HH/SS/other) | 18/18/6 
    21187 Gap extend | 1 
    21188 SS matrix |  |  | H | S | O 
    21189 ---|---|---|--- 
    21190 H | 6 | -9 | -6 
    21191 S |  | 6 | -6 
    21192 O |  |  | 4 
    21193 Iteration cutoff | 2 
    21194  
    21195 Matchmaker 3j0c.pdb1, chain F (#1.34) with AF3 CA.pdb, chain A (#471),
    21196 sequence alignment score = 335.3 
    21197 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    21198 2.550) 
    21199  
    21200 
    21201 > hide sel cartoons
    21202 
    21203 > color #467 dodgerblue
    21204 
    21205 > color #468 dodgerblue
    21206 
    21207 > color #469 #00b305ff
    21208 
    21209 > color #470 #00b305ff
    21210 
    21211 > color #471 #f15839ff
    21212 
    21213 > select #1.35/D
    21214 
    21215 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    21216 
    21217 > show sel cartoons
    21218 
    21219 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    21220 
    21221 Chain information for AF3 E1 1-421.pdb #472 
    21222 --- 
    21223 Chain | Description 
    21224 A | No description available 
    21225  
    21226 
    21227 > matchmaker #472 to #1.35 & sel
    21228 
    21229 Parameters 
    21230 --- 
    21231 Chain pairing | bb 
    21232 Alignment algorithm | Needleman-Wunsch 
    21233 Similarity matrix | BLOSUM-62 
    21234 SS fraction | 0.3 
    21235 Gap open (HH/SS/other) | 18/18/6 
    21236 Gap extend | 1 
    21237 SS matrix |  |  | H | S | O 
    21238 ---|---|---|--- 
    21239 H | 6 | -9 | -6 
    21240 S |  | 6 | -6 
    21241 O |  |  | 4 
    21242 Iteration cutoff | 2 
    21243  
    21244 Matchmaker 3j0c.pdb1, chain D (#1.35) with AF3 E1 1-421.pdb, chain A (#472),
    21245 sequence alignment score = 1060.7 
    21246 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    21247 3.032) 
    21248  
    21249 
    21250 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    21251 
    21252 Chain information for AF3 E1 422-461.pdb #473 
    21253 --- 
    21254 Chain | Description 
    21255 A | No description available 
    21256  
    21257 
    21258 > matchmaker #473 to #1.35 & sel
    21259 
    21260 Parameters 
    21261 --- 
    21262 Chain pairing | bb 
    21263 Alignment algorithm | Needleman-Wunsch 
    21264 Similarity matrix | BLOSUM-62 
    21265 SS fraction | 0.3 
    21266 Gap open (HH/SS/other) | 18/18/6 
    21267 Gap extend | 1 
    21268 SS matrix |  |  | H | S | O 
    21269 ---|---|---|--- 
    21270 H | 6 | -9 | -6 
    21271 S |  | 6 | -6 
    21272 O |  |  | 4 
    21273 Iteration cutoff | 2 
    21274  
    21275 Matchmaker 3j0c.pdb1, chain D (#1.35) with AF3 E1 422-461.pdb, chain A (#473),
    21276 sequence alignment score = 626.9 
    21277 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    21278 2.916) 
    21279  
    21280 
    21281 > hide sel cartoons
    21282 
    21283 > select #1.35/E
    21284 
    21285 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    21286 
    21287 > show sel cartoons
    21288 
    21289 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    21290 
    21291 Chain information for AF3 E2 1-352.pdb #474 
    21292 --- 
    21293 Chain | Description 
    21294 B | No description available 
    21295  
    21296 
    21297 > matchmaker #474 to #1.35 & sel
    21298 
    21299 Parameters 
    21300 --- 
    21301 Chain pairing | bb 
    21302 Alignment algorithm | Needleman-Wunsch 
    21303 Similarity matrix | BLOSUM-62 
    21304 SS fraction | 0.3 
    21305 Gap open (HH/SS/other) | 18/18/6 
    21306 Gap extend | 1 
    21307 SS matrix |  |  | H | S | O 
    21308 ---|---|---|--- 
    21309 H | 6 | -9 | -6 
    21310 S |  | 6 | -6 
    21311 O |  |  | 4 
    21312 Iteration cutoff | 2 
    21313  
    21314 Matchmaker 3j0c.pdb1, chain E (#1.35) with AF3 E2 1-352.pdb, chain B (#474),
    21315 sequence alignment score = 594.5 
    21316 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    21317 6.147) 
    21318  
    21319 
    21320 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    21321 
    21322 Chain information for AF3 E2 353-438.pdb #475 
    21323 --- 
    21324 Chain | Description 
    21325 B | No description available 
    21326  
    21327 
    21328 > matchmaker #475 to #1.35 & sel
    21329 
    21330 Parameters 
    21331 --- 
    21332 Chain pairing | bb 
    21333 Alignment algorithm | Needleman-Wunsch 
    21334 Similarity matrix | BLOSUM-62 
    21335 SS fraction | 0.3 
    21336 Gap open (HH/SS/other) | 18/18/6 
    21337 Gap extend | 1 
    21338 SS matrix |  |  | H | S | O 
    21339 ---|---|---|--- 
    21340 H | 6 | -9 | -6 
    21341 S |  | 6 | -6 
    21342 O |  |  | 4 
    21343 Iteration cutoff | 2 
    21344  
    21345 Matchmaker 3j0c.pdb1, chain E (#1.35) with AF3 E2 353-438.pdb, chain B (#475),
    21346 sequence alignment score = 340.2 
    21347 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    21348 8.673) 
    21349  
    21350 
    21351 > hide sel cartoons
    21352 
    21353 > select #1.35/F
    21354 
    21355 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    21356 
    21357 > show sel cartoons
    21358 
    21359 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    21360 
    21361 Chain information for AF3 CA.pdb #476 
    21362 --- 
    21363 Chain | Description 
    21364 A | No description available 
    21365  
    21366 
    21367 > matchmaker #476 to #1.35 & sel
    21368 
    21369 Parameters 
    21370 --- 
    21371 Chain pairing | bb 
    21372 Alignment algorithm | Needleman-Wunsch 
    21373 Similarity matrix | BLOSUM-62 
    21374 SS fraction | 0.3 
    21375 Gap open (HH/SS/other) | 18/18/6 
    21376 Gap extend | 1 
    21377 SS matrix |  |  | H | S | O 
    21378 ---|---|---|--- 
    21379 H | 6 | -9 | -6 
    21380 S |  | 6 | -6 
    21381 O |  |  | 4 
    21382 Iteration cutoff | 2 
    21383  
    21384 Matchmaker 3j0c.pdb1, chain F (#1.35) with AF3 CA.pdb, chain A (#476),
    21385 sequence alignment score = 335.3 
    21386 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    21387 2.550) 
    21388  
    21389 
    21390 > hide sel cartoons
    21391 
    21392 > color #472 dodgerblue
    21393 
    21394 > color #473 dodgerblue
    21395 
    21396 > color #474 #00b305ff
    21397 
    21398 > color #475 #00b305ff
    21399 
    21400 > color #476 #f15839ff
    21401 
    21402 > select #1.36/D
    21403 
    21404 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    21405 
    21406 > show sel cartoons
    21407 
    21408 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    21409 
    21410 Chain information for AF3 E1 1-421.pdb #477 
    21411 --- 
    21412 Chain | Description 
    21413 A | No description available 
    21414  
    21415 
    21416 > matchmaker #477 to #1.36 & sel
    21417 
    21418 Parameters 
    21419 --- 
    21420 Chain pairing | bb 
    21421 Alignment algorithm | Needleman-Wunsch 
    21422 Similarity matrix | BLOSUM-62 
    21423 SS fraction | 0.3 
    21424 Gap open (HH/SS/other) | 18/18/6 
    21425 Gap extend | 1 
    21426 SS matrix |  |  | H | S | O 
    21427 ---|---|---|--- 
    21428 H | 6 | -9 | -6 
    21429 S |  | 6 | -6 
    21430 O |  |  | 4 
    21431 Iteration cutoff | 2 
    21432  
    21433 Matchmaker 3j0c.pdb1, chain D (#1.36) with AF3 E1 1-421.pdb, chain A (#477),
    21434 sequence alignment score = 1060.7 
    21435 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    21436 3.032) 
    21437  
    21438 
    21439 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    21440 
    21441 Chain information for AF3 E1 422-461.pdb #478 
    21442 --- 
    21443 Chain | Description 
    21444 A | No description available 
    21445  
    21446 
    21447 > matchmaker #478 to #1.36 & sel
    21448 
    21449 Parameters 
    21450 --- 
    21451 Chain pairing | bb 
    21452 Alignment algorithm | Needleman-Wunsch 
    21453 Similarity matrix | BLOSUM-62 
    21454 SS fraction | 0.3 
    21455 Gap open (HH/SS/other) | 18/18/6 
    21456 Gap extend | 1 
    21457 SS matrix |  |  | H | S | O 
    21458 ---|---|---|--- 
    21459 H | 6 | -9 | -6 
    21460 S |  | 6 | -6 
    21461 O |  |  | 4 
    21462 Iteration cutoff | 2 
    21463  
    21464 Matchmaker 3j0c.pdb1, chain D (#1.36) with AF3 E1 422-461.pdb, chain A (#478),
    21465 sequence alignment score = 626.9 
    21466 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    21467 2.916) 
    21468  
    21469 
    21470 > hide sel cartoons
    21471 
    21472 > select #1.36/E
    21473 
    21474 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    21475 
    21476 > show sel cartoons
    21477 
    21478 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    21479 
    21480 Chain information for AF3 E2 1-352.pdb #479 
    21481 --- 
    21482 Chain | Description 
    21483 B | No description available 
    21484  
    21485 
    21486 > matchmaker #479 to #1.36 & sel
    21487 
    21488 Parameters 
    21489 --- 
    21490 Chain pairing | bb 
    21491 Alignment algorithm | Needleman-Wunsch 
    21492 Similarity matrix | BLOSUM-62 
    21493 SS fraction | 0.3 
    21494 Gap open (HH/SS/other) | 18/18/6 
    21495 Gap extend | 1 
    21496 SS matrix |  |  | H | S | O 
    21497 ---|---|---|--- 
    21498 H | 6 | -9 | -6 
    21499 S |  | 6 | -6 
    21500 O |  |  | 4 
    21501 Iteration cutoff | 2 
    21502  
    21503 Matchmaker 3j0c.pdb1, chain E (#1.36) with AF3 E2 1-352.pdb, chain B (#479),
    21504 sequence alignment score = 594.5 
    21505 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    21506 6.147) 
    21507  
    21508 
    21509 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    21510 
    21511 Chain information for AF3 E2 353-438.pdb #480 
    21512 --- 
    21513 Chain | Description 
    21514 B | No description available 
    21515  
    21516 
    21517 > matchmaker #480 to #1.36 & sel
    21518 
    21519 Parameters 
    21520 --- 
    21521 Chain pairing | bb 
    21522 Alignment algorithm | Needleman-Wunsch 
    21523 Similarity matrix | BLOSUM-62 
    21524 SS fraction | 0.3 
    21525 Gap open (HH/SS/other) | 18/18/6 
    21526 Gap extend | 1 
    21527 SS matrix |  |  | H | S | O 
    21528 ---|---|---|--- 
    21529 H | 6 | -9 | -6 
    21530 S |  | 6 | -6 
    21531 O |  |  | 4 
    21532 Iteration cutoff | 2 
    21533  
    21534 Matchmaker 3j0c.pdb1, chain E (#1.36) with AF3 E2 353-438.pdb, chain B (#480),
    21535 sequence alignment score = 340.2 
    21536 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    21537 8.673) 
    21538  
    21539 
    21540 > hide sel cartoons
    21541 
    21542 > select #1.36/F
    21543 
    21544 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    21545 
    21546 > show sel cartoons
    21547 
    21548 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    21549 
    21550 Chain information for AF3 CA.pdb #481 
    21551 --- 
    21552 Chain | Description 
    21553 A | No description available 
    21554  
    21555 
    21556 > matchmaker #481 to #1.36 & sel
    21557 
    21558 Parameters 
    21559 --- 
    21560 Chain pairing | bb 
    21561 Alignment algorithm | Needleman-Wunsch 
    21562 Similarity matrix | BLOSUM-62 
    21563 SS fraction | 0.3 
    21564 Gap open (HH/SS/other) | 18/18/6 
    21565 Gap extend | 1 
    21566 SS matrix |  |  | H | S | O 
    21567 ---|---|---|--- 
    21568 H | 6 | -9 | -6 
    21569 S |  | 6 | -6 
    21570 O |  |  | 4 
    21571 Iteration cutoff | 2 
    21572  
    21573 Matchmaker 3j0c.pdb1, chain F (#1.36) with AF3 CA.pdb, chain A (#481),
    21574 sequence alignment score = 335.3 
    21575 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    21576 2.550) 
    21577  
    21578 
    21579 > hide sel cartoons
    21580 
    21581 > color #477 dodgerblue
    21582 
    21583 > color #478 dodgerblue
    21584 
    21585 > color #479 #00b305ff
    21586 
    21587 > color #480 #00b305ff
    21588 
    21589 > color #481 #f15839ff
    21590 
    21591 > select #1.37/D
    21592 
    21593 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    21594 
    21595 > show sel cartoons
    21596 
    21597 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    21598 
    21599 Chain information for AF3 E1 1-421.pdb #482 
    21600 --- 
    21601 Chain | Description 
    21602 A | No description available 
    21603  
    21604 
    21605 > matchmaker #482 to #1.37 & sel
    21606 
    21607 Parameters 
    21608 --- 
    21609 Chain pairing | bb 
    21610 Alignment algorithm | Needleman-Wunsch 
    21611 Similarity matrix | BLOSUM-62 
    21612 SS fraction | 0.3 
    21613 Gap open (HH/SS/other) | 18/18/6 
    21614 Gap extend | 1 
    21615 SS matrix |  |  | H | S | O 
    21616 ---|---|---|--- 
    21617 H | 6 | -9 | -6 
    21618 S |  | 6 | -6 
    21619 O |  |  | 4 
    21620 Iteration cutoff | 2 
    21621  
    21622 Matchmaker 3j0c.pdb1, chain D (#1.37) with AF3 E1 1-421.pdb, chain A (#482),
    21623 sequence alignment score = 1060.7 
    21624 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    21625 3.032) 
    21626  
    21627 
    21628 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    21629 
    21630 Chain information for AF3 E1 422-461.pdb #483 
    21631 --- 
    21632 Chain | Description 
    21633 A | No description available 
    21634  
    21635 
    21636 > matchmaker #483 to #1.37 & sel
    21637 
    21638 Parameters 
    21639 --- 
    21640 Chain pairing | bb 
    21641 Alignment algorithm | Needleman-Wunsch 
    21642 Similarity matrix | BLOSUM-62 
    21643 SS fraction | 0.3 
    21644 Gap open (HH/SS/other) | 18/18/6 
    21645 Gap extend | 1 
    21646 SS matrix |  |  | H | S | O 
    21647 ---|---|---|--- 
    21648 H | 6 | -9 | -6 
    21649 S |  | 6 | -6 
    21650 O |  |  | 4 
    21651 Iteration cutoff | 2 
    21652  
    21653 Matchmaker 3j0c.pdb1, chain D (#1.37) with AF3 E1 422-461.pdb, chain A (#483),
    21654 sequence alignment score = 626.9 
    21655 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    21656 2.916) 
    21657  
    21658 
    21659 > hide sel cartoons
    21660 
    21661 > select #1.37/E
    21662 
    21663 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    21664 
    21665 > show sel cartoons
    21666 
    21667 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    21668 
    21669 Chain information for AF3 E2 1-352.pdb #484 
    21670 --- 
    21671 Chain | Description 
    21672 B | No description available 
    21673  
    21674 
    21675 > matchmaker #484 to #1.37 & sel
    21676 
    21677 Parameters 
    21678 --- 
    21679 Chain pairing | bb 
    21680 Alignment algorithm | Needleman-Wunsch 
    21681 Similarity matrix | BLOSUM-62 
    21682 SS fraction | 0.3 
    21683 Gap open (HH/SS/other) | 18/18/6 
    21684 Gap extend | 1 
    21685 SS matrix |  |  | H | S | O 
    21686 ---|---|---|--- 
    21687 H | 6 | -9 | -6 
    21688 S |  | 6 | -6 
    21689 O |  |  | 4 
    21690 Iteration cutoff | 2 
    21691  
    21692 Matchmaker 3j0c.pdb1, chain E (#1.37) with AF3 E2 1-352.pdb, chain B (#484),
    21693 sequence alignment score = 594.5 
    21694 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    21695 6.147) 
    21696  
    21697 
    21698 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    21699 
    21700 Chain information for AF3 E2 353-438.pdb #485 
    21701 --- 
    21702 Chain | Description 
    21703 B | No description available 
    21704  
    21705 
    21706 > matchmaker #485 to #1.37 & sel
    21707 
    21708 Parameters 
    21709 --- 
    21710 Chain pairing | bb 
    21711 Alignment algorithm | Needleman-Wunsch 
    21712 Similarity matrix | BLOSUM-62 
    21713 SS fraction | 0.3 
    21714 Gap open (HH/SS/other) | 18/18/6 
    21715 Gap extend | 1 
    21716 SS matrix |  |  | H | S | O 
    21717 ---|---|---|--- 
    21718 H | 6 | -9 | -6 
    21719 S |  | 6 | -6 
    21720 O |  |  | 4 
    21721 Iteration cutoff | 2 
    21722  
    21723 Matchmaker 3j0c.pdb1, chain E (#1.37) with AF3 E2 353-438.pdb, chain B (#485),
    21724 sequence alignment score = 340.2 
    21725 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    21726 8.673) 
    21727  
    21728 
    21729 > hide sel cartoons
    21730 
    21731 [Repeated 1 time(s)]
    21732 
    21733 > select #1.37/F
    21734 
    21735 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    21736 
    21737 > show sel cartoons
    21738 
    21739 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    21740 
    21741 Chain information for AF3 CA.pdb #486 
    21742 --- 
    21743 Chain | Description 
    21744 A | No description available 
    21745  
    21746 
    21747 > matchmaker #486 to #1.37 & sel
    21748 
    21749 Parameters 
    21750 --- 
    21751 Chain pairing | bb 
    21752 Alignment algorithm | Needleman-Wunsch 
    21753 Similarity matrix | BLOSUM-62 
    21754 SS fraction | 0.3 
    21755 Gap open (HH/SS/other) | 18/18/6 
    21756 Gap extend | 1 
    21757 SS matrix |  |  | H | S | O 
    21758 ---|---|---|--- 
    21759 H | 6 | -9 | -6 
    21760 S |  | 6 | -6 
    21761 O |  |  | 4 
    21762 Iteration cutoff | 2 
    21763  
    21764 Matchmaker 3j0c.pdb1, chain F (#1.37) with AF3 CA.pdb, chain A (#486),
    21765 sequence alignment score = 335.3 
    21766 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    21767 2.550) 
    21768  
    21769 
    21770 > hide sel cartoons
    21771 
    21772 [Repeated 1 time(s)]
    21773 
    21774 > color #482 dodgerblue
    21775 
    21776 > color #483 dodgerblue
    21777 
    21778 > color #484 #00b305ff
    21779 
    21780 > color #485 #00b305ff
    21781 
    21782 > color #486 #f15839ff
    21783 
    21784 > select #1.38/D
    21785 
    21786 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    21787 
    21788 > show sel cartoons
    21789 
    21790 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    21791 
    21792 Chain information for AF3 E1 1-421.pdb #487 
    21793 --- 
    21794 Chain | Description 
    21795 A | No description available 
    21796  
    21797 
    21798 > matchmaker #487 to #1.38 & sel
    21799 
    21800 Parameters 
    21801 --- 
    21802 Chain pairing | bb 
    21803 Alignment algorithm | Needleman-Wunsch 
    21804 Similarity matrix | BLOSUM-62 
    21805 SS fraction | 0.3 
    21806 Gap open (HH/SS/other) | 18/18/6 
    21807 Gap extend | 1 
    21808 SS matrix |  |  | H | S | O 
    21809 ---|---|---|--- 
    21810 H | 6 | -9 | -6 
    21811 S |  | 6 | -6 
    21812 O |  |  | 4 
    21813 Iteration cutoff | 2 
    21814  
    21815 Matchmaker 3j0c.pdb1, chain D (#1.38) with AF3 E1 1-421.pdb, chain A (#487),
    21816 sequence alignment score = 1060.7 
    21817 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    21818 3.032) 
    21819  
    21820 
    21821 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    21822 
    21823 Chain information for AF3 E1 422-461.pdb #488 
    21824 --- 
    21825 Chain | Description 
    21826 A | No description available 
    21827  
    21828 
    21829 > matchmaker #488 to #1.38 & sel
    21830 
    21831 Parameters 
    21832 --- 
    21833 Chain pairing | bb 
    21834 Alignment algorithm | Needleman-Wunsch 
    21835 Similarity matrix | BLOSUM-62 
    21836 SS fraction | 0.3 
    21837 Gap open (HH/SS/other) | 18/18/6 
    21838 Gap extend | 1 
    21839 SS matrix |  |  | H | S | O 
    21840 ---|---|---|--- 
    21841 H | 6 | -9 | -6 
    21842 S |  | 6 | -6 
    21843 O |  |  | 4 
    21844 Iteration cutoff | 2 
    21845  
    21846 Matchmaker 3j0c.pdb1, chain D (#1.38) with AF3 E1 422-461.pdb, chain A (#488),
    21847 sequence alignment score = 626.9 
    21848 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    21849 2.916) 
    21850  
    21851 
    21852 > hide sel cartoons
    21853 
    21854 > select #1.38/E
    21855 
    21856 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    21857 
    21858 > show sel cartoons
    21859 
    21860 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    21861 
    21862 Chain information for AF3 E2 1-352.pdb #489 
    21863 --- 
    21864 Chain | Description 
    21865 B | No description available 
    21866  
    21867 
    21868 > matchmaker #489 to #1.38 & sel
    21869 
    21870 Parameters 
    21871 --- 
    21872 Chain pairing | bb 
    21873 Alignment algorithm | Needleman-Wunsch 
    21874 Similarity matrix | BLOSUM-62 
    21875 SS fraction | 0.3 
    21876 Gap open (HH/SS/other) | 18/18/6 
    21877 Gap extend | 1 
    21878 SS matrix |  |  | H | S | O 
    21879 ---|---|---|--- 
    21880 H | 6 | -9 | -6 
    21881 S |  | 6 | -6 
    21882 O |  |  | 4 
    21883 Iteration cutoff | 2 
    21884  
    21885 Matchmaker 3j0c.pdb1, chain E (#1.38) with AF3 E2 1-352.pdb, chain B (#489),
    21886 sequence alignment score = 594.5 
    21887 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    21888 6.147) 
    21889  
    21890 
    21891 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    21892 
    21893 Chain information for AF3 E2 353-438.pdb #490 
    21894 --- 
    21895 Chain | Description 
    21896 B | No description available 
    21897  
    21898 
    21899 > matchmaker #490 to #1.38 & sel
    21900 
    21901 Parameters 
    21902 --- 
    21903 Chain pairing | bb 
    21904 Alignment algorithm | Needleman-Wunsch 
    21905 Similarity matrix | BLOSUM-62 
    21906 SS fraction | 0.3 
    21907 Gap open (HH/SS/other) | 18/18/6 
    21908 Gap extend | 1 
    21909 SS matrix |  |  | H | S | O 
    21910 ---|---|---|--- 
    21911 H | 6 | -9 | -6 
    21912 S |  | 6 | -6 
    21913 O |  |  | 4 
    21914 Iteration cutoff | 2 
    21915  
    21916 Matchmaker 3j0c.pdb1, chain E (#1.38) with AF3 E2 353-438.pdb, chain B (#490),
    21917 sequence alignment score = 340.2 
    21918 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    21919 8.673) 
    21920  
    21921 
    21922 > hide sel cartoons
    21923 
    21924 > select #1.38/F
    21925 
    21926 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    21927 
    21928 > show sel cartoons
    21929 
    21930 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    21931 
    21932 Chain information for AF3 CA.pdb #491 
    21933 --- 
    21934 Chain | Description 
    21935 A | No description available 
    21936  
    21937 
    21938 > matchmaker #491 to #1.38 & sel
    21939 
    21940 Parameters 
    21941 --- 
    21942 Chain pairing | bb 
    21943 Alignment algorithm | Needleman-Wunsch 
    21944 Similarity matrix | BLOSUM-62 
    21945 SS fraction | 0.3 
    21946 Gap open (HH/SS/other) | 18/18/6 
    21947 Gap extend | 1 
    21948 SS matrix |  |  | H | S | O 
    21949 ---|---|---|--- 
    21950 H | 6 | -9 | -6 
    21951 S |  | 6 | -6 
    21952 O |  |  | 4 
    21953 Iteration cutoff | 2 
    21954  
    21955 Matchmaker 3j0c.pdb1, chain F (#1.38) with AF3 CA.pdb, chain A (#491),
    21956 sequence alignment score = 335.3 
    21957 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    21958 2.550) 
    21959  
    21960 
    21961 > hide sel cartoons
    21962 
    21963 [Repeated 1 time(s)]
    21964 
    21965 > color #487 dodgerblue
    21966 
    21967 > color #488 dodgerblue
    21968 
    21969 > color #489 #00b305ff
    21970 
    21971 > color #490 #00b305ff
    21972 
    21973 > color #491 #f15839ff
    21974 
    21975 > select #1.39/D
    21976 
    21977 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    21978 
    21979 > show sel cartoons
    21980 
    21981 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    21982 
    21983 Chain information for AF3 E1 1-421.pdb #492 
    21984 --- 
    21985 Chain | Description 
    21986 A | No description available 
    21987  
    21988 
    21989 > matchmaker #492 to #1.39 & sel
    21990 
    21991 Parameters 
    21992 --- 
    21993 Chain pairing | bb 
    21994 Alignment algorithm | Needleman-Wunsch 
    21995 Similarity matrix | BLOSUM-62 
    21996 SS fraction | 0.3 
    21997 Gap open (HH/SS/other) | 18/18/6 
    21998 Gap extend | 1 
    21999 SS matrix |  |  | H | S | O 
    22000 ---|---|---|--- 
    22001 H | 6 | -9 | -6 
    22002 S |  | 6 | -6 
    22003 O |  |  | 4 
    22004 Iteration cutoff | 2 
    22005  
    22006 Matchmaker 3j0c.pdb1, chain D (#1.39) with AF3 E1 1-421.pdb, chain A (#492),
    22007 sequence alignment score = 1060.7 
    22008 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    22009 3.032) 
    22010  
    22011 
    22012 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    22013 
    22014 Chain information for AF3 E1 422-461.pdb #493 
    22015 --- 
    22016 Chain | Description 
    22017 A | No description available 
    22018  
    22019 
    22020 > matchmaker #493 to #1.39 & sel
    22021 
    22022 Parameters 
    22023 --- 
    22024 Chain pairing | bb 
    22025 Alignment algorithm | Needleman-Wunsch 
    22026 Similarity matrix | BLOSUM-62 
    22027 SS fraction | 0.3 
    22028 Gap open (HH/SS/other) | 18/18/6 
    22029 Gap extend | 1 
    22030 SS matrix |  |  | H | S | O 
    22031 ---|---|---|--- 
    22032 H | 6 | -9 | -6 
    22033 S |  | 6 | -6 
    22034 O |  |  | 4 
    22035 Iteration cutoff | 2 
    22036  
    22037 Matchmaker 3j0c.pdb1, chain D (#1.39) with AF3 E1 422-461.pdb, chain A (#493),
    22038 sequence alignment score = 626.9 
    22039 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    22040 2.916) 
    22041  
    22042 
    22043 > hide sel cartoons
    22044 
    22045 > select #1.39/E
    22046 
    22047 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    22048 
    22049 > show sel cartoons
    22050 
    22051 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    22052 
    22053 Chain information for AF3 E2 1-352.pdb #494 
    22054 --- 
    22055 Chain | Description 
    22056 B | No description available 
    22057  
    22058 
    22059 > matchmaker #494 to #1.39 & sel
    22060 
    22061 Parameters 
    22062 --- 
    22063 Chain pairing | bb 
    22064 Alignment algorithm | Needleman-Wunsch 
    22065 Similarity matrix | BLOSUM-62 
    22066 SS fraction | 0.3 
    22067 Gap open (HH/SS/other) | 18/18/6 
    22068 Gap extend | 1 
    22069 SS matrix |  |  | H | S | O 
    22070 ---|---|---|--- 
    22071 H | 6 | -9 | -6 
    22072 S |  | 6 | -6 
    22073 O |  |  | 4 
    22074 Iteration cutoff | 2 
    22075  
    22076 Matchmaker 3j0c.pdb1, chain E (#1.39) with AF3 E2 1-352.pdb, chain B (#494),
    22077 sequence alignment score = 594.5 
    22078 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    22079 6.147) 
    22080  
    22081 
    22082 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    22083 
    22084 Chain information for AF3 E2 353-438.pdb #495 
    22085 --- 
    22086 Chain | Description 
    22087 B | No description available 
    22088  
    22089 
    22090 > matchmaker #495 to #1.39 & sel
    22091 
    22092 Parameters 
    22093 --- 
    22094 Chain pairing | bb 
    22095 Alignment algorithm | Needleman-Wunsch 
    22096 Similarity matrix | BLOSUM-62 
    22097 SS fraction | 0.3 
    22098 Gap open (HH/SS/other) | 18/18/6 
    22099 Gap extend | 1 
    22100 SS matrix |  |  | H | S | O 
    22101 ---|---|---|--- 
    22102 H | 6 | -9 | -6 
    22103 S |  | 6 | -6 
    22104 O |  |  | 4 
    22105 Iteration cutoff | 2 
    22106  
    22107 Matchmaker 3j0c.pdb1, chain E (#1.39) with AF3 E2 353-438.pdb, chain B (#495),
    22108 sequence alignment score = 340.2 
    22109 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    22110 8.673) 
    22111  
    22112 
    22113 > hide sel cartoons
    22114 
    22115 > select #1.39/F
    22116 
    22117 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    22118 
    22119 > show sel cartoons
    22120 
    22121 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    22122 
    22123 Chain information for AF3 CA.pdb #496 
    22124 --- 
    22125 Chain | Description 
    22126 A | No description available 
    22127  
    22128 
    22129 > matchmaker #496 to #1.39 & sel
    22130 
    22131 Parameters 
    22132 --- 
    22133 Chain pairing | bb 
    22134 Alignment algorithm | Needleman-Wunsch 
    22135 Similarity matrix | BLOSUM-62 
    22136 SS fraction | 0.3 
    22137 Gap open (HH/SS/other) | 18/18/6 
    22138 Gap extend | 1 
    22139 SS matrix |  |  | H | S | O 
    22140 ---|---|---|--- 
    22141 H | 6 | -9 | -6 
    22142 S |  | 6 | -6 
    22143 O |  |  | 4 
    22144 Iteration cutoff | 2 
    22145  
    22146 Matchmaker 3j0c.pdb1, chain F (#1.39) with AF3 CA.pdb, chain A (#496),
    22147 sequence alignment score = 335.3 
    22148 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    22149 2.550) 
    22150  
    22151 
    22152 > hide sel cartoons
    22153 
    22154 > color #492 dodgerblue
    22155 
    22156 > color #493 dodgerblue
    22157 
    22158 > color #494 #00b305ff
    22159 
    22160 > color #495 #00b305ff
    22161 
    22162 > color #496 #f15839ff
    22163 
    22164 > select #1.40/D
    22165 
    22166 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    22167 
    22168 > show sel cartoons
    22169 
    22170 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    22171 
    22172 Chain information for AF3 E1 1-421.pdb #497 
    22173 --- 
    22174 Chain | Description 
    22175 A | No description available 
    22176  
    22177 
    22178 > matchmaker #497 to #1.40 & sel
    22179 
    22180 Parameters 
    22181 --- 
    22182 Chain pairing | bb 
    22183 Alignment algorithm | Needleman-Wunsch 
    22184 Similarity matrix | BLOSUM-62 
    22185 SS fraction | 0.3 
    22186 Gap open (HH/SS/other) | 18/18/6 
    22187 Gap extend | 1 
    22188 SS matrix |  |  | H | S | O 
    22189 ---|---|---|--- 
    22190 H | 6 | -9 | -6 
    22191 S |  | 6 | -6 
    22192 O |  |  | 4 
    22193 Iteration cutoff | 2 
    22194  
    22195 Matchmaker 3j0c.pdb1, chain D (#1.40) with AF3 E1 1-421.pdb, chain A (#497),
    22196 sequence alignment score = 1060.7 
    22197 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    22198 3.032) 
    22199  
    22200 
    22201 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    22202 
    22203 Chain information for AF3 E1 422-461.pdb #498 
    22204 --- 
    22205 Chain | Description 
    22206 A | No description available 
    22207  
    22208 
    22209 > matchmaker #498 to #1.40 & sel
    22210 
    22211 Parameters 
    22212 --- 
    22213 Chain pairing | bb 
    22214 Alignment algorithm | Needleman-Wunsch 
    22215 Similarity matrix | BLOSUM-62 
    22216 SS fraction | 0.3 
    22217 Gap open (HH/SS/other) | 18/18/6 
    22218 Gap extend | 1 
    22219 SS matrix |  |  | H | S | O 
    22220 ---|---|---|--- 
    22221 H | 6 | -9 | -6 
    22222 S |  | 6 | -6 
    22223 O |  |  | 4 
    22224 Iteration cutoff | 2 
    22225  
    22226 Matchmaker 3j0c.pdb1, chain D (#1.40) with AF3 E1 422-461.pdb, chain A (#498),
    22227 sequence alignment score = 626.9 
    22228 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    22229 2.916) 
    22230  
    22231 
    22232 > hide sel cartoons
    22233 
    22234 > select #1.40/E
    22235 
    22236 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    22237 
    22238 > show sel cartoons
    22239 
    22240 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    22241 
    22242 Chain information for AF3 E2 1-352.pdb #499 
    22243 --- 
    22244 Chain | Description 
    22245 B | No description available 
    22246  
    22247 
    22248 > matchmaker #499 to #1.40 & sel
    22249 
    22250 Parameters 
    22251 --- 
    22252 Chain pairing | bb 
    22253 Alignment algorithm | Needleman-Wunsch 
    22254 Similarity matrix | BLOSUM-62 
    22255 SS fraction | 0.3 
    22256 Gap open (HH/SS/other) | 18/18/6 
    22257 Gap extend | 1 
    22258 SS matrix |  |  | H | S | O 
    22259 ---|---|---|--- 
    22260 H | 6 | -9 | -6 
    22261 S |  | 6 | -6 
    22262 O |  |  | 4 
    22263 Iteration cutoff | 2 
    22264  
    22265 Matchmaker 3j0c.pdb1, chain E (#1.40) with AF3 E2 1-352.pdb, chain B (#499),
    22266 sequence alignment score = 594.5 
    22267 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    22268 6.147) 
    22269  
    22270 
    22271 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    22272 
    22273 Chain information for AF3 E2 353-438.pdb #500 
    22274 --- 
    22275 Chain | Description 
    22276 B | No description available 
    22277  
    22278 
    22279 > matchmaker #500 to #1.40 & sel
    22280 
    22281 Parameters 
    22282 --- 
    22283 Chain pairing | bb 
    22284 Alignment algorithm | Needleman-Wunsch 
    22285 Similarity matrix | BLOSUM-62 
    22286 SS fraction | 0.3 
    22287 Gap open (HH/SS/other) | 18/18/6 
    22288 Gap extend | 1 
    22289 SS matrix |  |  | H | S | O 
    22290 ---|---|---|--- 
    22291 H | 6 | -9 | -6 
    22292 S |  | 6 | -6 
    22293 O |  |  | 4 
    22294 Iteration cutoff | 2 
    22295  
    22296 Matchmaker 3j0c.pdb1, chain E (#1.40) with AF3 E2 353-438.pdb, chain B (#500),
    22297 sequence alignment score = 340.2 
    22298 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    22299 8.673) 
    22300  
    22301 
    22302 > select #1.40/F
    22303 
    22304 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    22305 
    22306 > show sel cartoons
    22307 
    22308 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    22309 
    22310 Chain information for AF3 CA.pdb #501 
    22311 --- 
    22312 Chain | Description 
    22313 A | No description available 
    22314  
    22315 
    22316 > matchmaker #501 to #1.40 & sel
    22317 
    22318 Parameters 
    22319 --- 
    22320 Chain pairing | bb 
    22321 Alignment algorithm | Needleman-Wunsch 
    22322 Similarity matrix | BLOSUM-62 
    22323 SS fraction | 0.3 
    22324 Gap open (HH/SS/other) | 18/18/6 
    22325 Gap extend | 1 
    22326 SS matrix |  |  | H | S | O 
    22327 ---|---|---|--- 
    22328 H | 6 | -9 | -6 
    22329 S |  | 6 | -6 
    22330 O |  |  | 4 
    22331 Iteration cutoff | 2 
    22332  
    22333 Matchmaker 3j0c.pdb1, chain F (#1.40) with AF3 CA.pdb, chain A (#501),
    22334 sequence alignment score = 335.3 
    22335 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    22336 2.550) 
    22337  
    22338 
    22339 > hide sel cartoons
    22340 
    22341 > select #1.40/E
    22342 
    22343 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    22344 
    22345 > hide sel cartoons
    22346 
    22347 > color #497 dodgerblue
    22348 
    22349 > color #498 dodgerblue
    22350 
    22351 > color #499 #00b305ff
    22352 
    22353 > color #500 #00b305ff
    22354 
    22355 > color #501 #f15839ff
    22356 
    22357 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    22358 
    22359 > hide #452-501 models
    22360 
    22361 > select #1.41/D
    22362 
    22363 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    22364 
    22365 > show sel cartoons
    22366 
    22367 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    22368 
    22369 Chain information for AF3 E1 1-421.pdb #502 
    22370 --- 
    22371 Chain | Description 
    22372 A | No description available 
    22373  
    22374 
    22375 > matchmaker #502 to #1.41 & sel
    22376 
    22377 Parameters 
    22378 --- 
    22379 Chain pairing | bb 
    22380 Alignment algorithm | Needleman-Wunsch 
    22381 Similarity matrix | BLOSUM-62 
    22382 SS fraction | 0.3 
    22383 Gap open (HH/SS/other) | 18/18/6 
    22384 Gap extend | 1 
    22385 SS matrix |  |  | H | S | O 
    22386 ---|---|---|--- 
    22387 H | 6 | -9 | -6 
    22388 S |  | 6 | -6 
    22389 O |  |  | 4 
    22390 Iteration cutoff | 2 
    22391  
    22392 Matchmaker 3j0c.pdb1, chain D (#1.41) with AF3 E1 1-421.pdb, chain A (#502),
    22393 sequence alignment score = 1060.7 
    22394 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    22395 3.032) 
    22396  
    22397 
    22398 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    22399 
    22400 Chain information for AF3 E1 422-461.pdb #503 
    22401 --- 
    22402 Chain | Description 
    22403 A | No description available 
    22404  
    22405 
    22406 > matchmaker #503 to #1.41 & sel
    22407 
    22408 Parameters 
    22409 --- 
    22410 Chain pairing | bb 
    22411 Alignment algorithm | Needleman-Wunsch 
    22412 Similarity matrix | BLOSUM-62 
    22413 SS fraction | 0.3 
    22414 Gap open (HH/SS/other) | 18/18/6 
    22415 Gap extend | 1 
    22416 SS matrix |  |  | H | S | O 
    22417 ---|---|---|--- 
    22418 H | 6 | -9 | -6 
    22419 S |  | 6 | -6 
    22420 O |  |  | 4 
    22421 Iteration cutoff | 2 
    22422  
    22423 Matchmaker 3j0c.pdb1, chain D (#1.41) with AF3 E1 422-461.pdb, chain A (#503),
    22424 sequence alignment score = 626.9 
    22425 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    22426 2.916) 
    22427  
    22428 
    22429 > hide sel cartoons
    22430 
    22431 > select #1.41/E
    22432 
    22433 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    22434 
    22435 > show sel cartoons
    22436 
    22437 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    22438 
    22439 Chain information for AF3 E2 1-352.pdb #504 
    22440 --- 
    22441 Chain | Description 
    22442 B | No description available 
    22443  
    22444 
    22445 > matchmaker #504 to #1.41 & sel
    22446 
    22447 Parameters 
    22448 --- 
    22449 Chain pairing | bb 
    22450 Alignment algorithm | Needleman-Wunsch 
    22451 Similarity matrix | BLOSUM-62 
    22452 SS fraction | 0.3 
    22453 Gap open (HH/SS/other) | 18/18/6 
    22454 Gap extend | 1 
    22455 SS matrix |  |  | H | S | O 
    22456 ---|---|---|--- 
    22457 H | 6 | -9 | -6 
    22458 S |  | 6 | -6 
    22459 O |  |  | 4 
    22460 Iteration cutoff | 2 
    22461  
    22462 Matchmaker 3j0c.pdb1, chain E (#1.41) with AF3 E2 1-352.pdb, chain B (#504),
    22463 sequence alignment score = 594.5 
    22464 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    22465 6.147) 
    22466  
    22467 
    22468 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    22469 
    22470 Chain information for AF3 E2 353-438.pdb #505 
    22471 --- 
    22472 Chain | Description 
    22473 B | No description available 
    22474  
    22475 
    22476 > matchmaker #505 to #1.41 & sel
    22477 
    22478 Parameters 
    22479 --- 
    22480 Chain pairing | bb 
    22481 Alignment algorithm | Needleman-Wunsch 
    22482 Similarity matrix | BLOSUM-62 
    22483 SS fraction | 0.3 
    22484 Gap open (HH/SS/other) | 18/18/6 
    22485 Gap extend | 1 
    22486 SS matrix |  |  | H | S | O 
    22487 ---|---|---|--- 
    22488 H | 6 | -9 | -6 
    22489 S |  | 6 | -6 
    22490 O |  |  | 4 
    22491 Iteration cutoff | 2 
    22492  
    22493 Matchmaker 3j0c.pdb1, chain E (#1.41) with AF3 E2 353-438.pdb, chain B (#505),
    22494 sequence alignment score = 340.2 
    22495 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    22496 8.673) 
    22497  
    22498 
    22499 > hide sel cartoons
    22500 
    22501 > select #1.41/F
    22502 
    22503 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    22504 
    22505 > show sel cartoons
    22506 
    22507 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    22508 
    22509 Chain information for AF3 CA.pdb #506 
    22510 --- 
    22511 Chain | Description 
    22512 A | No description available 
    22513  
    22514 
    22515 > matchmaker #506 to #1.41 & sel
    22516 
    22517 Parameters 
    22518 --- 
    22519 Chain pairing | bb 
    22520 Alignment algorithm | Needleman-Wunsch 
    22521 Similarity matrix | BLOSUM-62 
    22522 SS fraction | 0.3 
    22523 Gap open (HH/SS/other) | 18/18/6 
    22524 Gap extend | 1 
    22525 SS matrix |  |  | H | S | O 
    22526 ---|---|---|--- 
    22527 H | 6 | -9 | -6 
    22528 S |  | 6 | -6 
    22529 O |  |  | 4 
    22530 Iteration cutoff | 2 
    22531  
    22532 Matchmaker 3j0c.pdb1, chain F (#1.41) with AF3 CA.pdb, chain A (#506),
    22533 sequence alignment score = 335.3 
    22534 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    22535 2.550) 
    22536  
    22537 
    22538 > hide sel cartoons
    22539 
    22540 [Repeated 1 time(s)]
    22541 
    22542 > color #502 dodgerblue
    22543 
    22544 > color #503 dodgerblue
    22545 
    22546 > color #504 #00b305ff
    22547 
    22548 > color #505 #00b305ff
    22549 
    22550 > color #506 #f15839ff
    22551 
    22552 > select #1.42/D
    22553 
    22554 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    22555 
    22556 > show sel cartoons
    22557 
    22558 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    22559 
    22560 Chain information for AF3 E1 1-421.pdb #507 
    22561 --- 
    22562 Chain | Description 
    22563 A | No description available 
    22564  
    22565 
    22566 > matchmaker #507 to #1.42 & sel
    22567 
    22568 Parameters 
    22569 --- 
    22570 Chain pairing | bb 
    22571 Alignment algorithm | Needleman-Wunsch 
    22572 Similarity matrix | BLOSUM-62 
    22573 SS fraction | 0.3 
    22574 Gap open (HH/SS/other) | 18/18/6 
    22575 Gap extend | 1 
    22576 SS matrix |  |  | H | S | O 
    22577 ---|---|---|--- 
    22578 H | 6 | -9 | -6 
    22579 S |  | 6 | -6 
    22580 O |  |  | 4 
    22581 Iteration cutoff | 2 
    22582  
    22583 Matchmaker 3j0c.pdb1, chain D (#1.42) with AF3 E1 1-421.pdb, chain A (#507),
    22584 sequence alignment score = 1060.7 
    22585 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    22586 3.032) 
    22587  
    22588 
    22589 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    22590 
    22591 Chain information for AF3 E1 422-461.pdb #508 
    22592 --- 
    22593 Chain | Description 
    22594 A | No description available 
    22595  
    22596 
    22597 > matchmaker #508 to #1.42 & sel
    22598 
    22599 Parameters 
    22600 --- 
    22601 Chain pairing | bb 
    22602 Alignment algorithm | Needleman-Wunsch 
    22603 Similarity matrix | BLOSUM-62 
    22604 SS fraction | 0.3 
    22605 Gap open (HH/SS/other) | 18/18/6 
    22606 Gap extend | 1 
    22607 SS matrix |  |  | H | S | O 
    22608 ---|---|---|--- 
    22609 H | 6 | -9 | -6 
    22610 S |  | 6 | -6 
    22611 O |  |  | 4 
    22612 Iteration cutoff | 2 
    22613  
    22614 Matchmaker 3j0c.pdb1, chain D (#1.42) with AF3 E1 422-461.pdb, chain A (#508),
    22615 sequence alignment score = 626.9 
    22616 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    22617 2.916) 
    22618  
    22619 
    22620 > hide sel cartoons
    22621 
    22622 > select #1.42/E
    22623 
    22624 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    22625 
    22626 > show sel cartoons
    22627 
    22628 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    22629 
    22630 Chain information for AF3 E2 1-352.pdb #509 
    22631 --- 
    22632 Chain | Description 
    22633 B | No description available 
    22634  
    22635 
    22636 > matchmaker #509 to #1.42 & sel
    22637 
    22638 Parameters 
    22639 --- 
    22640 Chain pairing | bb 
    22641 Alignment algorithm | Needleman-Wunsch 
    22642 Similarity matrix | BLOSUM-62 
    22643 SS fraction | 0.3 
    22644 Gap open (HH/SS/other) | 18/18/6 
    22645 Gap extend | 1 
    22646 SS matrix |  |  | H | S | O 
    22647 ---|---|---|--- 
    22648 H | 6 | -9 | -6 
    22649 S |  | 6 | -6 
    22650 O |  |  | 4 
    22651 Iteration cutoff | 2 
    22652  
    22653 Matchmaker 3j0c.pdb1, chain E (#1.42) with AF3 E2 1-352.pdb, chain B (#509),
    22654 sequence alignment score = 594.5 
    22655 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    22656 6.147) 
    22657  
    22658 
    22659 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    22660 
    22661 Chain information for AF3 E2 353-438.pdb #510 
    22662 --- 
    22663 Chain | Description 
    22664 B | No description available 
    22665  
    22666 
    22667 > matchmaker #510 to #1.42 & sel
    22668 
    22669 Parameters 
    22670 --- 
    22671 Chain pairing | bb 
    22672 Alignment algorithm | Needleman-Wunsch 
    22673 Similarity matrix | BLOSUM-62 
    22674 SS fraction | 0.3 
    22675 Gap open (HH/SS/other) | 18/18/6 
    22676 Gap extend | 1 
    22677 SS matrix |  |  | H | S | O 
    22678 ---|---|---|--- 
    22679 H | 6 | -9 | -6 
    22680 S |  | 6 | -6 
    22681 O |  |  | 4 
    22682 Iteration cutoff | 2 
    22683  
    22684 Matchmaker 3j0c.pdb1, chain E (#1.42) with AF3 E2 353-438.pdb, chain B (#510),
    22685 sequence alignment score = 340.2 
    22686 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    22687 8.673) 
    22688  
    22689 
    22690 > hide sel cartoons
    22691 
    22692 > select #1.42/F
    22693 
    22694 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    22695 
    22696 > show sel cartoons
    22697 
    22698 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    22699 
    22700 Chain information for AF3 CA.pdb #511 
    22701 --- 
    22702 Chain | Description 
    22703 A | No description available 
    22704  
    22705 
    22706 > matchmaker #511 to #1.42 & sel
    22707 
    22708 Parameters 
    22709 --- 
    22710 Chain pairing | bb 
    22711 Alignment algorithm | Needleman-Wunsch 
    22712 Similarity matrix | BLOSUM-62 
    22713 SS fraction | 0.3 
    22714 Gap open (HH/SS/other) | 18/18/6 
    22715 Gap extend | 1 
    22716 SS matrix |  |  | H | S | O 
    22717 ---|---|---|--- 
    22718 H | 6 | -9 | -6 
    22719 S |  | 6 | -6 
    22720 O |  |  | 4 
    22721 Iteration cutoff | 2 
    22722  
    22723 Matchmaker 3j0c.pdb1, chain F (#1.42) with AF3 CA.pdb, chain A (#511),
    22724 sequence alignment score = 335.3 
    22725 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    22726 2.550) 
    22727  
    22728 
    22729 > hide sel cartoons
    22730 
    22731 > color #507 dodgerblue
    22732 
    22733 > color #508 dodgerblue
    22734 
    22735 > color #509 #00b305ff
    22736 
    22737 > color #510 #00b305ff
    22738 
    22739 > color #511 #f15839ff
    22740 
    22741 > select #1.43/D
    22742 
    22743 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    22744 
    22745 > show sel cartoons
    22746 
    22747 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    22748 
    22749 Chain information for AF3 E1 1-421.pdb #512 
    22750 --- 
    22751 Chain | Description 
    22752 A | No description available 
    22753  
    22754 
    22755 > matchmaker #512 to #1.43 & sel
    22756 
    22757 Parameters 
    22758 --- 
    22759 Chain pairing | bb 
    22760 Alignment algorithm | Needleman-Wunsch 
    22761 Similarity matrix | BLOSUM-62 
    22762 SS fraction | 0.3 
    22763 Gap open (HH/SS/other) | 18/18/6 
    22764 Gap extend | 1 
    22765 SS matrix |  |  | H | S | O 
    22766 ---|---|---|--- 
    22767 H | 6 | -9 | -6 
    22768 S |  | 6 | -6 
    22769 O |  |  | 4 
    22770 Iteration cutoff | 2 
    22771  
    22772 Matchmaker 3j0c.pdb1, chain D (#1.43) with AF3 E1 1-421.pdb, chain A (#512),
    22773 sequence alignment score = 1060.7 
    22774 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    22775 3.032) 
    22776  
    22777 
    22778 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    22779 
    22780 Chain information for AF3 E1 422-461.pdb #513 
    22781 --- 
    22782 Chain | Description 
    22783 A | No description available 
    22784  
    22785 
    22786 > matchmaker #513 to #1.43 & sel
    22787 
    22788 Parameters 
    22789 --- 
    22790 Chain pairing | bb 
    22791 Alignment algorithm | Needleman-Wunsch 
    22792 Similarity matrix | BLOSUM-62 
    22793 SS fraction | 0.3 
    22794 Gap open (HH/SS/other) | 18/18/6 
    22795 Gap extend | 1 
    22796 SS matrix |  |  | H | S | O 
    22797 ---|---|---|--- 
    22798 H | 6 | -9 | -6 
    22799 S |  | 6 | -6 
    22800 O |  |  | 4 
    22801 Iteration cutoff | 2 
    22802  
    22803 Matchmaker 3j0c.pdb1, chain D (#1.43) with AF3 E1 422-461.pdb, chain A (#513),
    22804 sequence alignment score = 626.9 
    22805 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    22806 2.916) 
    22807  
    22808 
    22809 > hide sel cartoons
    22810 
    22811 > select #1.43/E
    22812 
    22813 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    22814 
    22815 > show sel cartoons
    22816 
    22817 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    22818 
    22819 Chain information for AF3 E2 1-352.pdb #514 
    22820 --- 
    22821 Chain | Description 
    22822 B | No description available 
    22823  
    22824 
    22825 > matchmaker #514 to #1.43 & sel
    22826 
    22827 Parameters 
    22828 --- 
    22829 Chain pairing | bb 
    22830 Alignment algorithm | Needleman-Wunsch 
    22831 Similarity matrix | BLOSUM-62 
    22832 SS fraction | 0.3 
    22833 Gap open (HH/SS/other) | 18/18/6 
    22834 Gap extend | 1 
    22835 SS matrix |  |  | H | S | O 
    22836 ---|---|---|--- 
    22837 H | 6 | -9 | -6 
    22838 S |  | 6 | -6 
    22839 O |  |  | 4 
    22840 Iteration cutoff | 2 
    22841  
    22842 Matchmaker 3j0c.pdb1, chain E (#1.43) with AF3 E2 1-352.pdb, chain B (#514),
    22843 sequence alignment score = 594.5 
    22844 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    22845 6.147) 
    22846  
    22847 
    22848 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    22849 
    22850 Chain information for AF3 E2 353-438.pdb #515 
    22851 --- 
    22852 Chain | Description 
    22853 B | No description available 
    22854  
    22855 
    22856 > matchmaker #515 to #1.43 & sel
    22857 
    22858 Parameters 
    22859 --- 
    22860 Chain pairing | bb 
    22861 Alignment algorithm | Needleman-Wunsch 
    22862 Similarity matrix | BLOSUM-62 
    22863 SS fraction | 0.3 
    22864 Gap open (HH/SS/other) | 18/18/6 
    22865 Gap extend | 1 
    22866 SS matrix |  |  | H | S | O 
    22867 ---|---|---|--- 
    22868 H | 6 | -9 | -6 
    22869 S |  | 6 | -6 
    22870 O |  |  | 4 
    22871 Iteration cutoff | 2 
    22872  
    22873 Matchmaker 3j0c.pdb1, chain E (#1.43) with AF3 E2 353-438.pdb, chain B (#515),
    22874 sequence alignment score = 340.2 
    22875 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    22876 8.673) 
    22877  
    22878 
    22879 > hide sel cartoons
    22880 
    22881 > select #1.43/F
    22882 
    22883 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    22884 
    22885 > show sel cartoons
    22886 
    22887 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    22888 
    22889 Chain information for AF3 CA.pdb #516 
    22890 --- 
    22891 Chain | Description 
    22892 A | No description available 
    22893  
    22894 
    22895 > matchmaker #516 to #1.43 & sel
    22896 
    22897 Parameters 
    22898 --- 
    22899 Chain pairing | bb 
    22900 Alignment algorithm | Needleman-Wunsch 
    22901 Similarity matrix | BLOSUM-62 
    22902 SS fraction | 0.3 
    22903 Gap open (HH/SS/other) | 18/18/6 
    22904 Gap extend | 1 
    22905 SS matrix |  |  | H | S | O 
    22906 ---|---|---|--- 
    22907 H | 6 | -9 | -6 
    22908 S |  | 6 | -6 
    22909 O |  |  | 4 
    22910 Iteration cutoff | 2 
    22911  
    22912 Matchmaker 3j0c.pdb1, chain F (#1.43) with AF3 CA.pdb, chain A (#516),
    22913 sequence alignment score = 335.3 
    22914 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    22915 2.550) 
    22916  
    22917 
    22918 > hide sel cartoons
    22919 
    22920 > color #512 dodgerblue
    22921 
    22922 > color #513 dodgerblue
    22923 
    22924 > color #515 #00b305ff
    22925 
    22926 > color #516 #f15839ff
    22927 
    22928 > select #1.44/D
    22929 
    22930 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    22931 
    22932 > show sel cartoons
    22933 
    22934 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    22935 
    22936 Chain information for AF3 E1 1-421.pdb #517 
    22937 --- 
    22938 Chain | Description 
    22939 A | No description available 
    22940  
    22941 
    22942 > matchmaker #517 to #1.44 & sel
    22943 
    22944 Parameters 
    22945 --- 
    22946 Chain pairing | bb 
    22947 Alignment algorithm | Needleman-Wunsch 
    22948 Similarity matrix | BLOSUM-62 
    22949 SS fraction | 0.3 
    22950 Gap open (HH/SS/other) | 18/18/6 
    22951 Gap extend | 1 
    22952 SS matrix |  |  | H | S | O 
    22953 ---|---|---|--- 
    22954 H | 6 | -9 | -6 
    22955 S |  | 6 | -6 
    22956 O |  |  | 4 
    22957 Iteration cutoff | 2 
    22958  
    22959 Matchmaker 3j0c.pdb1, chain D (#1.44) with AF3 E1 1-421.pdb, chain A (#517),
    22960 sequence alignment score = 1060.7 
    22961 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    22962 3.032) 
    22963  
    22964 
    22965 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    22966 
    22967 Chain information for AF3 E1 422-461.pdb #518 
    22968 --- 
    22969 Chain | Description 
    22970 A | No description available 
    22971  
    22972 
    22973 > matchmaker #518 to #1.44 & sel
    22974 
    22975 Parameters 
    22976 --- 
    22977 Chain pairing | bb 
    22978 Alignment algorithm | Needleman-Wunsch 
    22979 Similarity matrix | BLOSUM-62 
    22980 SS fraction | 0.3 
    22981 Gap open (HH/SS/other) | 18/18/6 
    22982 Gap extend | 1 
    22983 SS matrix |  |  | H | S | O 
    22984 ---|---|---|--- 
    22985 H | 6 | -9 | -6 
    22986 S |  | 6 | -6 
    22987 O |  |  | 4 
    22988 Iteration cutoff | 2 
    22989  
    22990 Matchmaker 3j0c.pdb1, chain D (#1.44) with AF3 E1 422-461.pdb, chain A (#518),
    22991 sequence alignment score = 626.9 
    22992 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    22993 2.916) 
    22994  
    22995 
    22996 > hide sel cartoons
    22997 
    22998 > select #1.44/E
    22999 
    23000 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    23001 
    23002 > show sel cartoons
    23003 
    23004 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    23005 
    23006 Chain information for AF3 E2 1-352.pdb #519 
    23007 --- 
    23008 Chain | Description 
    23009 B | No description available 
    23010  
    23011 
    23012 > matchmaker #519 to #1.44 & sel
    23013 
    23014 Parameters 
    23015 --- 
    23016 Chain pairing | bb 
    23017 Alignment algorithm | Needleman-Wunsch 
    23018 Similarity matrix | BLOSUM-62 
    23019 SS fraction | 0.3 
    23020 Gap open (HH/SS/other) | 18/18/6 
    23021 Gap extend | 1 
    23022 SS matrix |  |  | H | S | O 
    23023 ---|---|---|--- 
    23024 H | 6 | -9 | -6 
    23025 S |  | 6 | -6 
    23026 O |  |  | 4 
    23027 Iteration cutoff | 2 
    23028  
    23029 Matchmaker 3j0c.pdb1, chain E (#1.44) with AF3 E2 1-352.pdb, chain B (#519),
    23030 sequence alignment score = 594.5 
    23031 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    23032 6.147) 
    23033  
    23034 
    23035 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    23036 
    23037 Chain information for AF3 E2 353-438.pdb #520 
    23038 --- 
    23039 Chain | Description 
    23040 B | No description available 
    23041  
    23042 
    23043 > matchmaker #520 to #1.44 & sel
    23044 
    23045 Parameters 
    23046 --- 
    23047 Chain pairing | bb 
    23048 Alignment algorithm | Needleman-Wunsch 
    23049 Similarity matrix | BLOSUM-62 
    23050 SS fraction | 0.3 
    23051 Gap open (HH/SS/other) | 18/18/6 
    23052 Gap extend | 1 
    23053 SS matrix |  |  | H | S | O 
    23054 ---|---|---|--- 
    23055 H | 6 | -9 | -6 
    23056 S |  | 6 | -6 
    23057 O |  |  | 4 
    23058 Iteration cutoff | 2 
    23059  
    23060 Matchmaker 3j0c.pdb1, chain E (#1.44) with AF3 E2 353-438.pdb, chain B (#520),
    23061 sequence alignment score = 340.2 
    23062 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    23063 8.673) 
    23064  
    23065 
    23066 > hide sel cartoons
    23067 
    23068 > select #1.44/F
    23069 
    23070 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    23071 
    23072 > show sel cartoons
    23073 
    23074 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    23075 
    23076 Chain information for AF3 CA.pdb #521 
    23077 --- 
    23078 Chain | Description 
    23079 A | No description available 
    23080  
    23081 
    23082 > matchmaker #521 to #1.44 & sel
    23083 
    23084 Parameters 
    23085 --- 
    23086 Chain pairing | bb 
    23087 Alignment algorithm | Needleman-Wunsch 
    23088 Similarity matrix | BLOSUM-62 
    23089 SS fraction | 0.3 
    23090 Gap open (HH/SS/other) | 18/18/6 
    23091 Gap extend | 1 
    23092 SS matrix |  |  | H | S | O 
    23093 ---|---|---|--- 
    23094 H | 6 | -9 | -6 
    23095 S |  | 6 | -6 
    23096 O |  |  | 4 
    23097 Iteration cutoff | 2 
    23098  
    23099 Matchmaker 3j0c.pdb1, chain F (#1.44) with AF3 CA.pdb, chain A (#521),
    23100 sequence alignment score = 335.3 
    23101 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    23102 2.550) 
    23103  
    23104 
    23105 > hide sel cartoons
    23106 
    23107 > color #517 dodgerblue
    23108 
    23109 > color #518 dodgerblue
    23110 
    23111 > color #519 #00b305ff
    23112 
    23113 > color #520 #00b305ff
    23114 
    23115 > color #521 #f15839ff
    23116 
    23117 > select #1.45/D
    23118 
    23119 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    23120 
    23121 > show sel cartoons
    23122 
    23123 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    23124 
    23125 Chain information for AF3 E1 1-421.pdb #522 
    23126 --- 
    23127 Chain | Description 
    23128 A | No description available 
    23129  
    23130 
    23131 > matchmaker #522 to #1.45 & sel
    23132 
    23133 Parameters 
    23134 --- 
    23135 Chain pairing | bb 
    23136 Alignment algorithm | Needleman-Wunsch 
    23137 Similarity matrix | BLOSUM-62 
    23138 SS fraction | 0.3 
    23139 Gap open (HH/SS/other) | 18/18/6 
    23140 Gap extend | 1 
    23141 SS matrix |  |  | H | S | O 
    23142 ---|---|---|--- 
    23143 H | 6 | -9 | -6 
    23144 S |  | 6 | -6 
    23145 O |  |  | 4 
    23146 Iteration cutoff | 2 
    23147  
    23148 Matchmaker 3j0c.pdb1, chain D (#1.45) with AF3 E1 1-421.pdb, chain A (#522),
    23149 sequence alignment score = 1060.7 
    23150 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    23151 3.032) 
    23152  
    23153 
    23154 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    23155 
    23156 Chain information for AF3 E1 422-461.pdb #523 
    23157 --- 
    23158 Chain | Description 
    23159 A | No description available 
    23160  
    23161 
    23162 > matchmaker #523 to #1.45 & sel
    23163 
    23164 Parameters 
    23165 --- 
    23166 Chain pairing | bb 
    23167 Alignment algorithm | Needleman-Wunsch 
    23168 Similarity matrix | BLOSUM-62 
    23169 SS fraction | 0.3 
    23170 Gap open (HH/SS/other) | 18/18/6 
    23171 Gap extend | 1 
    23172 SS matrix |  |  | H | S | O 
    23173 ---|---|---|--- 
    23174 H | 6 | -9 | -6 
    23175 S |  | 6 | -6 
    23176 O |  |  | 4 
    23177 Iteration cutoff | 2 
    23178  
    23179 Matchmaker 3j0c.pdb1, chain D (#1.45) with AF3 E1 422-461.pdb, chain A (#523),
    23180 sequence alignment score = 626.9 
    23181 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    23182 2.916) 
    23183  
    23184 
    23185 > hide sel cartoons
    23186 
    23187 > select #1.45/E
    23188 
    23189 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    23190 
    23191 > show sel cartoons
    23192 
    23193 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    23194 
    23195 Chain information for AF3 E2 1-352.pdb #524 
    23196 --- 
    23197 Chain | Description 
    23198 B | No description available 
    23199  
    23200 
    23201 > matchmaker #524 to #1.45 & sel
    23202 
    23203 Parameters 
    23204 --- 
    23205 Chain pairing | bb 
    23206 Alignment algorithm | Needleman-Wunsch 
    23207 Similarity matrix | BLOSUM-62 
    23208 SS fraction | 0.3 
    23209 Gap open (HH/SS/other) | 18/18/6 
    23210 Gap extend | 1 
    23211 SS matrix |  |  | H | S | O 
    23212 ---|---|---|--- 
    23213 H | 6 | -9 | -6 
    23214 S |  | 6 | -6 
    23215 O |  |  | 4 
    23216 Iteration cutoff | 2 
    23217  
    23218 Matchmaker 3j0c.pdb1, chain E (#1.45) with AF3 E2 1-352.pdb, chain B (#524),
    23219 sequence alignment score = 594.5 
    23220 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    23221 6.147) 
    23222  
    23223 
    23224 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    23225 
    23226 Chain information for AF3 E2 353-438.pdb #525 
    23227 --- 
    23228 Chain | Description 
    23229 B | No description available 
    23230  
    23231 
    23232 > matchmaker #525 to #1.45 & sel
    23233 
    23234 Parameters 
    23235 --- 
    23236 Chain pairing | bb 
    23237 Alignment algorithm | Needleman-Wunsch 
    23238 Similarity matrix | BLOSUM-62 
    23239 SS fraction | 0.3 
    23240 Gap open (HH/SS/other) | 18/18/6 
    23241 Gap extend | 1 
    23242 SS matrix |  |  | H | S | O 
    23243 ---|---|---|--- 
    23244 H | 6 | -9 | -6 
    23245 S |  | 6 | -6 
    23246 O |  |  | 4 
    23247 Iteration cutoff | 2 
    23248  
    23249 Matchmaker 3j0c.pdb1, chain E (#1.45) with AF3 E2 353-438.pdb, chain B (#525),
    23250 sequence alignment score = 340.2 
    23251 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    23252 8.673) 
    23253  
    23254 
    23255 > hide sel cartoons
    23256 
    23257 > select #1.45/F
    23258 
    23259 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    23260 
    23261 > show sel cartoons
    23262 
    23263 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    23264 
    23265 Chain information for AF3 CA.pdb #526 
    23266 --- 
    23267 Chain | Description 
    23268 A | No description available 
    23269  
    23270 
    23271 > matchmaker #526 to #1.45 & sel
    23272 
    23273 Parameters 
    23274 --- 
    23275 Chain pairing | bb 
    23276 Alignment algorithm | Needleman-Wunsch 
    23277 Similarity matrix | BLOSUM-62 
    23278 SS fraction | 0.3 
    23279 Gap open (HH/SS/other) | 18/18/6 
    23280 Gap extend | 1 
    23281 SS matrix |  |  | H | S | O 
    23282 ---|---|---|--- 
    23283 H | 6 | -9 | -6 
    23284 S |  | 6 | -6 
    23285 O |  |  | 4 
    23286 Iteration cutoff | 2 
    23287  
    23288 Matchmaker 3j0c.pdb1, chain F (#1.45) with AF3 CA.pdb, chain A (#526),
    23289 sequence alignment score = 335.3 
    23290 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    23291 2.550) 
    23292  
    23293 
    23294 > hide sel cartoons
    23295 
    23296 > color #522 dodgerblue
    23297 
    23298 > color #523 dodgerblue
    23299 
    23300 > color #524 #00b305ff
    23301 
    23302 > color #525 #00b305ff
    23303 
    23304 > color #526 #f15839ff
    23305 
    23306 > select #1.46/D
    23307 
    23308 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    23309 
    23310 > show sel cartoons
    23311 
    23312 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    23313 
    23314 Chain information for AF3 E1 1-421.pdb #527 
    23315 --- 
    23316 Chain | Description 
    23317 A | No description available 
    23318  
    23319 
    23320 > matchmaker #527 to #1.46 & sel
    23321 
    23322 Parameters 
    23323 --- 
    23324 Chain pairing | bb 
    23325 Alignment algorithm | Needleman-Wunsch 
    23326 Similarity matrix | BLOSUM-62 
    23327 SS fraction | 0.3 
    23328 Gap open (HH/SS/other) | 18/18/6 
    23329 Gap extend | 1 
    23330 SS matrix |  |  | H | S | O 
    23331 ---|---|---|--- 
    23332 H | 6 | -9 | -6 
    23333 S |  | 6 | -6 
    23334 O |  |  | 4 
    23335 Iteration cutoff | 2 
    23336  
    23337 Matchmaker 3j0c.pdb1, chain D (#1.46) with AF3 E1 1-421.pdb, chain A (#527),
    23338 sequence alignment score = 1060.7 
    23339 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    23340 3.032) 
    23341  
    23342 
    23343 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    23344 
    23345 Chain information for AF3 E1 422-461.pdb #528 
    23346 --- 
    23347 Chain | Description 
    23348 A | No description available 
    23349  
    23350 
    23351 > matchmaker #528 to #1.46 & sel
    23352 
    23353 Parameters 
    23354 --- 
    23355 Chain pairing | bb 
    23356 Alignment algorithm | Needleman-Wunsch 
    23357 Similarity matrix | BLOSUM-62 
    23358 SS fraction | 0.3 
    23359 Gap open (HH/SS/other) | 18/18/6 
    23360 Gap extend | 1 
    23361 SS matrix |  |  | H | S | O 
    23362 ---|---|---|--- 
    23363 H | 6 | -9 | -6 
    23364 S |  | 6 | -6 
    23365 O |  |  | 4 
    23366 Iteration cutoff | 2 
    23367  
    23368 Matchmaker 3j0c.pdb1, chain D (#1.46) with AF3 E1 422-461.pdb, chain A (#528),
    23369 sequence alignment score = 626.9 
    23370 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    23371 2.916) 
    23372  
    23373 
    23374 > hide sel cartoons
    23375 
    23376 > select #1.46/E
    23377 
    23378 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    23379 
    23380 > show sel cartoons
    23381 
    23382 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    23383 
    23384 Chain information for AF3 E2 1-352.pdb #529 
    23385 --- 
    23386 Chain | Description 
    23387 B | No description available 
    23388  
    23389 
    23390 > matchmaker #529 to #1.46 & sel
    23391 
    23392 Parameters 
    23393 --- 
    23394 Chain pairing | bb 
    23395 Alignment algorithm | Needleman-Wunsch 
    23396 Similarity matrix | BLOSUM-62 
    23397 SS fraction | 0.3 
    23398 Gap open (HH/SS/other) | 18/18/6 
    23399 Gap extend | 1 
    23400 SS matrix |  |  | H | S | O 
    23401 ---|---|---|--- 
    23402 H | 6 | -9 | -6 
    23403 S |  | 6 | -6 
    23404 O |  |  | 4 
    23405 Iteration cutoff | 2 
    23406  
    23407 Matchmaker 3j0c.pdb1, chain E (#1.46) with AF3 E2 1-352.pdb, chain B (#529),
    23408 sequence alignment score = 594.5 
    23409 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    23410 6.147) 
    23411  
    23412 
    23413 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    23414 
    23415 Chain information for AF3 E2 353-438.pdb #530 
    23416 --- 
    23417 Chain | Description 
    23418 B | No description available 
    23419  
    23420 
    23421 > matchmaker #530 to #1.46 & sel
    23422 
    23423 Parameters 
    23424 --- 
    23425 Chain pairing | bb 
    23426 Alignment algorithm | Needleman-Wunsch 
    23427 Similarity matrix | BLOSUM-62 
    23428 SS fraction | 0.3 
    23429 Gap open (HH/SS/other) | 18/18/6 
    23430 Gap extend | 1 
    23431 SS matrix |  |  | H | S | O 
    23432 ---|---|---|--- 
    23433 H | 6 | -9 | -6 
    23434 S |  | 6 | -6 
    23435 O |  |  | 4 
    23436 Iteration cutoff | 2 
    23437  
    23438 Matchmaker 3j0c.pdb1, chain E (#1.46) with AF3 E2 353-438.pdb, chain B (#530),
    23439 sequence alignment score = 340.2 
    23440 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    23441 8.673) 
    23442  
    23443 
    23444 > hide sel cartoons
    23445 
    23446 > select #1.46/F
    23447 
    23448 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    23449 
    23450 > show sel cartoons
    23451 
    23452 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    23453 
    23454 Chain information for AF3 CA.pdb #531 
    23455 --- 
    23456 Chain | Description 
    23457 A | No description available 
    23458  
    23459 
    23460 > matchmaker #531 to #1.46 & sel
    23461 
    23462 Parameters 
    23463 --- 
    23464 Chain pairing | bb 
    23465 Alignment algorithm | Needleman-Wunsch 
    23466 Similarity matrix | BLOSUM-62 
    23467 SS fraction | 0.3 
    23468 Gap open (HH/SS/other) | 18/18/6 
    23469 Gap extend | 1 
    23470 SS matrix |  |  | H | S | O 
    23471 ---|---|---|--- 
    23472 H | 6 | -9 | -6 
    23473 S |  | 6 | -6 
    23474 O |  |  | 4 
    23475 Iteration cutoff | 2 
    23476  
    23477 Matchmaker 3j0c.pdb1, chain F (#1.46) with AF3 CA.pdb, chain A (#531),
    23478 sequence alignment score = 335.3 
    23479 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    23480 2.550) 
    23481  
    23482 
    23483 > hide sel cartoons
    23484 
    23485 > color #527 dodgerblue
    23486 
    23487 > color #528 dodgerblue
    23488 
    23489 > color #529 #00b305ff
    23490 
    23491 > color #530 #00b305ff
    23492 
    23493 > color #531 #f15839ff
    23494 
    23495 > select #1.47/D
    23496 
    23497 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    23498 
    23499 > show sel cartoons
    23500 
    23501 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    23502 
    23503 Chain information for AF3 E1 1-421.pdb #532 
    23504 --- 
    23505 Chain | Description 
    23506 A | No description available 
    23507  
    23508 
    23509 > matchmaker #532 to #1.47 & sel
    23510 
    23511 Parameters 
    23512 --- 
    23513 Chain pairing | bb 
    23514 Alignment algorithm | Needleman-Wunsch 
    23515 Similarity matrix | BLOSUM-62 
    23516 SS fraction | 0.3 
    23517 Gap open (HH/SS/other) | 18/18/6 
    23518 Gap extend | 1 
    23519 SS matrix |  |  | H | S | O 
    23520 ---|---|---|--- 
    23521 H | 6 | -9 | -6 
    23522 S |  | 6 | -6 
    23523 O |  |  | 4 
    23524 Iteration cutoff | 2 
    23525  
    23526 Matchmaker 3j0c.pdb1, chain D (#1.47) with AF3 E1 1-421.pdb, chain A (#532),
    23527 sequence alignment score = 1060.7 
    23528 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    23529 3.032) 
    23530  
    23531 
    23532 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    23533 
    23534 Chain information for AF3 E1 422-461.pdb #533 
    23535 --- 
    23536 Chain | Description 
    23537 A | No description available 
    23538  
    23539 
    23540 > matchmaker #533 to #1.47 & sel
    23541 
    23542 Parameters 
    23543 --- 
    23544 Chain pairing | bb 
    23545 Alignment algorithm | Needleman-Wunsch 
    23546 Similarity matrix | BLOSUM-62 
    23547 SS fraction | 0.3 
    23548 Gap open (HH/SS/other) | 18/18/6 
    23549 Gap extend | 1 
    23550 SS matrix |  |  | H | S | O 
    23551 ---|---|---|--- 
    23552 H | 6 | -9 | -6 
    23553 S |  | 6 | -6 
    23554 O |  |  | 4 
    23555 Iteration cutoff | 2 
    23556  
    23557 Matchmaker 3j0c.pdb1, chain D (#1.47) with AF3 E1 422-461.pdb, chain A (#533),
    23558 sequence alignment score = 626.9 
    23559 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    23560 2.916) 
    23561  
    23562 
    23563 > hide sel cartoons
    23564 
    23565 > select #1.47/E
    23566 
    23567 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    23568 
    23569 > show sel cartoons
    23570 
    23571 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    23572 
    23573 Chain information for AF3 E2 1-352.pdb #534 
    23574 --- 
    23575 Chain | Description 
    23576 B | No description available 
    23577  
    23578 
    23579 > matchmaker #534 to #1.47 & sel
    23580 
    23581 Parameters 
    23582 --- 
    23583 Chain pairing | bb 
    23584 Alignment algorithm | Needleman-Wunsch 
    23585 Similarity matrix | BLOSUM-62 
    23586 SS fraction | 0.3 
    23587 Gap open (HH/SS/other) | 18/18/6 
    23588 Gap extend | 1 
    23589 SS matrix |  |  | H | S | O 
    23590 ---|---|---|--- 
    23591 H | 6 | -9 | -6 
    23592 S |  | 6 | -6 
    23593 O |  |  | 4 
    23594 Iteration cutoff | 2 
    23595  
    23596 Matchmaker 3j0c.pdb1, chain E (#1.47) with AF3 E2 1-352.pdb, chain B (#534),
    23597 sequence alignment score = 594.5 
    23598 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    23599 6.147) 
    23600  
    23601 
    23602 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    23603 
    23604 Chain information for AF3 E2 353-438.pdb #535 
    23605 --- 
    23606 Chain | Description 
    23607 B | No description available 
    23608  
    23609 
    23610 > matchmaker #535 to #1.47 & sel
    23611 
    23612 Parameters 
    23613 --- 
    23614 Chain pairing | bb 
    23615 Alignment algorithm | Needleman-Wunsch 
    23616 Similarity matrix | BLOSUM-62 
    23617 SS fraction | 0.3 
    23618 Gap open (HH/SS/other) | 18/18/6 
    23619 Gap extend | 1 
    23620 SS matrix |  |  | H | S | O 
    23621 ---|---|---|--- 
    23622 H | 6 | -9 | -6 
    23623 S |  | 6 | -6 
    23624 O |  |  | 4 
    23625 Iteration cutoff | 2 
    23626  
    23627 Matchmaker 3j0c.pdb1, chain E (#1.47) with AF3 E2 353-438.pdb, chain B (#535),
    23628 sequence alignment score = 340.2 
    23629 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    23630 8.673) 
    23631  
    23632 
    23633 > hide sel cartoons
    23634 
    23635 > select #1.47/F
    23636 
    23637 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    23638 
    23639 > show sel cartoons
    23640 
    23641 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    23642 
    23643 Chain information for AF3 CA.pdb #536 
    23644 --- 
    23645 Chain | Description 
    23646 A | No description available 
    23647  
    23648 
    23649 > matchmaker #536 to #1.47 & sel
    23650 
    23651 Parameters 
    23652 --- 
    23653 Chain pairing | bb 
    23654 Alignment algorithm | Needleman-Wunsch 
    23655 Similarity matrix | BLOSUM-62 
    23656 SS fraction | 0.3 
    23657 Gap open (HH/SS/other) | 18/18/6 
    23658 Gap extend | 1 
    23659 SS matrix |  |  | H | S | O 
    23660 ---|---|---|--- 
    23661 H | 6 | -9 | -6 
    23662 S |  | 6 | -6 
    23663 O |  |  | 4 
    23664 Iteration cutoff | 2 
    23665  
    23666 Matchmaker 3j0c.pdb1, chain F (#1.47) with AF3 CA.pdb, chain A (#536),
    23667 sequence alignment score = 335.3 
    23668 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    23669 2.550) 
    23670  
    23671 
    23672 > hide sel cartoons
    23673 
    23674 > color #532 dodgerblue
    23675 
    23676 > color #533 dodgerblue
    23677 
    23678 > color #534 #00b305ff
    23679 
    23680 > color #535 #00b305ff
    23681 
    23682 > color #536 #f15839ff
    23683 
    23684 > select #1.48/D
    23685 
    23686 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    23687 
    23688 > show sel cartoons
    23689 
    23690 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    23691 
    23692 Chain information for AF3 E1 1-421.pdb #537 
    23693 --- 
    23694 Chain | Description 
    23695 A | No description available 
    23696  
    23697 
    23698 > matchmaker #537 to #1.48 & sel
    23699 
    23700 Parameters 
    23701 --- 
    23702 Chain pairing | bb 
    23703 Alignment algorithm | Needleman-Wunsch 
    23704 Similarity matrix | BLOSUM-62 
    23705 SS fraction | 0.3 
    23706 Gap open (HH/SS/other) | 18/18/6 
    23707 Gap extend | 1 
    23708 SS matrix |  |  | H | S | O 
    23709 ---|---|---|--- 
    23710 H | 6 | -9 | -6 
    23711 S |  | 6 | -6 
    23712 O |  |  | 4 
    23713 Iteration cutoff | 2 
    23714  
    23715 Matchmaker 3j0c.pdb1, chain D (#1.48) with AF3 E1 1-421.pdb, chain A (#537),
    23716 sequence alignment score = 1060.7 
    23717 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    23718 3.032) 
    23719  
    23720 
    23721 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    23722 
    23723 Chain information for AF3 E1 422-461.pdb #538 
    23724 --- 
    23725 Chain | Description 
    23726 A | No description available 
    23727  
    23728 
    23729 > matchmaker #538 to #1.48 & sel
    23730 
    23731 Parameters 
    23732 --- 
    23733 Chain pairing | bb 
    23734 Alignment algorithm | Needleman-Wunsch 
    23735 Similarity matrix | BLOSUM-62 
    23736 SS fraction | 0.3 
    23737 Gap open (HH/SS/other) | 18/18/6 
    23738 Gap extend | 1 
    23739 SS matrix |  |  | H | S | O 
    23740 ---|---|---|--- 
    23741 H | 6 | -9 | -6 
    23742 S |  | 6 | -6 
    23743 O |  |  | 4 
    23744 Iteration cutoff | 2 
    23745  
    23746 Matchmaker 3j0c.pdb1, chain D (#1.48) with AF3 E1 422-461.pdb, chain A (#538),
    23747 sequence alignment score = 626.9 
    23748 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    23749 2.916) 
    23750  
    23751 
    23752 > hide sel cartoons
    23753 
    23754 > select #1.48/E
    23755 
    23756 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    23757 
    23758 > show sel cartoons
    23759 
    23760 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    23761 
    23762 Chain information for AF3 E2 1-352.pdb #539 
    23763 --- 
    23764 Chain | Description 
    23765 B | No description available 
    23766  
    23767 
    23768 > matchmaker #539 to #1.48 & sel
    23769 
    23770 Parameters 
    23771 --- 
    23772 Chain pairing | bb 
    23773 Alignment algorithm | Needleman-Wunsch 
    23774 Similarity matrix | BLOSUM-62 
    23775 SS fraction | 0.3 
    23776 Gap open (HH/SS/other) | 18/18/6 
    23777 Gap extend | 1 
    23778 SS matrix |  |  | H | S | O 
    23779 ---|---|---|--- 
    23780 H | 6 | -9 | -6 
    23781 S |  | 6 | -6 
    23782 O |  |  | 4 
    23783 Iteration cutoff | 2 
    23784  
    23785 Matchmaker 3j0c.pdb1, chain E (#1.48) with AF3 E2 1-352.pdb, chain B (#539),
    23786 sequence alignment score = 594.5 
    23787 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    23788 6.147) 
    23789  
    23790 
    23791 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    23792 
    23793 Chain information for AF3 E2 353-438.pdb #540 
    23794 --- 
    23795 Chain | Description 
    23796 B | No description available 
    23797  
    23798 
    23799 > matchmaker #540 to #1.48 & sel
    23800 
    23801 Parameters 
    23802 --- 
    23803 Chain pairing | bb 
    23804 Alignment algorithm | Needleman-Wunsch 
    23805 Similarity matrix | BLOSUM-62 
    23806 SS fraction | 0.3 
    23807 Gap open (HH/SS/other) | 18/18/6 
    23808 Gap extend | 1 
    23809 SS matrix |  |  | H | S | O 
    23810 ---|---|---|--- 
    23811 H | 6 | -9 | -6 
    23812 S |  | 6 | -6 
    23813 O |  |  | 4 
    23814 Iteration cutoff | 2 
    23815  
    23816 Matchmaker 3j0c.pdb1, chain E (#1.48) with AF3 E2 353-438.pdb, chain B (#540),
    23817 sequence alignment score = 340.2 
    23818 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    23819 8.673) 
    23820  
    23821 
    23822 > hide sel cartoons
    23823 
    23824 > select #1.48/F
    23825 
    23826 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    23827 
    23828 > show sel cartoons
    23829 
    23830 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    23831 
    23832 Chain information for AF3 CA.pdb #541 
    23833 --- 
    23834 Chain | Description 
    23835 A | No description available 
    23836  
    23837 
    23838 > matchmaker #541 to #1.48 & sel
    23839 
    23840 Parameters 
    23841 --- 
    23842 Chain pairing | bb 
    23843 Alignment algorithm | Needleman-Wunsch 
    23844 Similarity matrix | BLOSUM-62 
    23845 SS fraction | 0.3 
    23846 Gap open (HH/SS/other) | 18/18/6 
    23847 Gap extend | 1 
    23848 SS matrix |  |  | H | S | O 
    23849 ---|---|---|--- 
    23850 H | 6 | -9 | -6 
    23851 S |  | 6 | -6 
    23852 O |  |  | 4 
    23853 Iteration cutoff | 2 
    23854  
    23855 Matchmaker 3j0c.pdb1, chain F (#1.48) with AF3 CA.pdb, chain A (#541),
    23856 sequence alignment score = 335.3 
    23857 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    23858 2.550) 
    23859  
    23860 
    23861 > hide sel cartoons
    23862 
    23863 > color #537 dodgerblue
    23864 
    23865 > color #538 dodgerblue
    23866 
    23867 > color #539 #00b305ff
    23868 
    23869 > color #540 #00b305ff
    23870 
    23871 > color #541 #f15839ff
    23872 
    23873 > select #1.49/D
    23874 
    23875 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    23876 
    23877 > show sel cartoons
    23878 
    23879 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    23880 
    23881 Chain information for AF3 E1 1-421.pdb #542 
    23882 --- 
    23883 Chain | Description 
    23884 A | No description available 
    23885  
    23886 
    23887 > matchmaker #542 to #1.49 & sel
    23888 
    23889 Parameters 
    23890 --- 
    23891 Chain pairing | bb 
    23892 Alignment algorithm | Needleman-Wunsch 
    23893 Similarity matrix | BLOSUM-62 
    23894 SS fraction | 0.3 
    23895 Gap open (HH/SS/other) | 18/18/6 
    23896 Gap extend | 1 
    23897 SS matrix |  |  | H | S | O 
    23898 ---|---|---|--- 
    23899 H | 6 | -9 | -6 
    23900 S |  | 6 | -6 
    23901 O |  |  | 4 
    23902 Iteration cutoff | 2 
    23903  
    23904 Matchmaker 3j0c.pdb1, chain D (#1.49) with AF3 E1 1-421.pdb, chain A (#542),
    23905 sequence alignment score = 1060.7 
    23906 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    23907 3.032) 
    23908  
    23909 
    23910 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    23911 
    23912 Chain information for AF3 E1 422-461.pdb #543 
    23913 --- 
    23914 Chain | Description 
    23915 A | No description available 
    23916  
    23917 
    23918 > matchmaker #543 to #1.49 & sel
    23919 
    23920 Parameters 
    23921 --- 
    23922 Chain pairing | bb 
    23923 Alignment algorithm | Needleman-Wunsch 
    23924 Similarity matrix | BLOSUM-62 
    23925 SS fraction | 0.3 
    23926 Gap open (HH/SS/other) | 18/18/6 
    23927 Gap extend | 1 
    23928 SS matrix |  |  | H | S | O 
    23929 ---|---|---|--- 
    23930 H | 6 | -9 | -6 
    23931 S |  | 6 | -6 
    23932 O |  |  | 4 
    23933 Iteration cutoff | 2 
    23934  
    23935 Matchmaker 3j0c.pdb1, chain D (#1.49) with AF3 E1 422-461.pdb, chain A (#543),
    23936 sequence alignment score = 626.9 
    23937 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    23938 2.916) 
    23939  
    23940 
    23941 > hide sel cartoons
    23942 
    23943 > select #1.49/E
    23944 
    23945 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    23946 
    23947 > show sel cartoons
    23948 
    23949 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    23950 
    23951 Chain information for AF3 E2 1-352.pdb #544 
    23952 --- 
    23953 Chain | Description 
    23954 B | No description available 
    23955  
    23956 
    23957 > matchmaker #544 to #1.49 & sel
    23958 
    23959 Parameters 
    23960 --- 
    23961 Chain pairing | bb 
    23962 Alignment algorithm | Needleman-Wunsch 
    23963 Similarity matrix | BLOSUM-62 
    23964 SS fraction | 0.3 
    23965 Gap open (HH/SS/other) | 18/18/6 
    23966 Gap extend | 1 
    23967 SS matrix |  |  | H | S | O 
    23968 ---|---|---|--- 
    23969 H | 6 | -9 | -6 
    23970 S |  | 6 | -6 
    23971 O |  |  | 4 
    23972 Iteration cutoff | 2 
    23973  
    23974 Matchmaker 3j0c.pdb1, chain E (#1.49) with AF3 E2 1-352.pdb, chain B (#544),
    23975 sequence alignment score = 594.5 
    23976 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    23977 6.147) 
    23978  
    23979 
    23980 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    23981 
    23982 Chain information for AF3 E2 353-438.pdb #545 
    23983 --- 
    23984 Chain | Description 
    23985 B | No description available 
    23986  
    23987 
    23988 > matchmaker #545 to #1.49 & sel
    23989 
    23990 Parameters 
    23991 --- 
    23992 Chain pairing | bb 
    23993 Alignment algorithm | Needleman-Wunsch 
    23994 Similarity matrix | BLOSUM-62 
    23995 SS fraction | 0.3 
    23996 Gap open (HH/SS/other) | 18/18/6 
    23997 Gap extend | 1 
    23998 SS matrix |  |  | H | S | O 
    23999 ---|---|---|--- 
    24000 H | 6 | -9 | -6 
    24001 S |  | 6 | -6 
    24002 O |  |  | 4 
    24003 Iteration cutoff | 2 
    24004  
    24005 Matchmaker 3j0c.pdb1, chain E (#1.49) with AF3 E2 353-438.pdb, chain B (#545),
    24006 sequence alignment score = 340.2 
    24007 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    24008 8.673) 
    24009  
    24010 
    24011 > hide sel cartoons
    24012 
    24013 > select #1.49/F
    24014 
    24015 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    24016 
    24017 > show sel cartoons
    24018 
    24019 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    24020 
    24021 Chain information for AF3 CA.pdb #546 
    24022 --- 
    24023 Chain | Description 
    24024 A | No description available 
    24025  
    24026 
    24027 > matchmaker #546 to #1.49 & sel
    24028 
    24029 Parameters 
    24030 --- 
    24031 Chain pairing | bb 
    24032 Alignment algorithm | Needleman-Wunsch 
    24033 Similarity matrix | BLOSUM-62 
    24034 SS fraction | 0.3 
    24035 Gap open (HH/SS/other) | 18/18/6 
    24036 Gap extend | 1 
    24037 SS matrix |  |  | H | S | O 
    24038 ---|---|---|--- 
    24039 H | 6 | -9 | -6 
    24040 S |  | 6 | -6 
    24041 O |  |  | 4 
    24042 Iteration cutoff | 2 
    24043  
    24044 Matchmaker 3j0c.pdb1, chain F (#1.49) with AF3 CA.pdb, chain A (#546),
    24045 sequence alignment score = 335.3 
    24046 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    24047 2.550) 
    24048  
    24049 
    24050 > hide sel cartoons
    24051 
    24052 > color #542 dodgerblue
    24053 
    24054 > color #543 dodgerblue
    24055 
    24056 > color #544 #00b305ff
    24057 
    24058 > color #545 #00b305ff
    24059 
    24060 > color #546 #f15839ff
    24061 
    24062 > select #1.50/D
    24063 
    24064 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    24065 
    24066 > show sel cartoons
    24067 
    24068 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    24069 
    24070 Chain information for AF3 E1 1-421.pdb #547 
    24071 --- 
    24072 Chain | Description 
    24073 A | No description available 
    24074  
    24075 
    24076 > matchmaker #547 to #1.50 & sel
    24077 
    24078 Parameters 
    24079 --- 
    24080 Chain pairing | bb 
    24081 Alignment algorithm | Needleman-Wunsch 
    24082 Similarity matrix | BLOSUM-62 
    24083 SS fraction | 0.3 
    24084 Gap open (HH/SS/other) | 18/18/6 
    24085 Gap extend | 1 
    24086 SS matrix |  |  | H | S | O 
    24087 ---|---|---|--- 
    24088 H | 6 | -9 | -6 
    24089 S |  | 6 | -6 
    24090 O |  |  | 4 
    24091 Iteration cutoff | 2 
    24092  
    24093 Matchmaker 3j0c.pdb1, chain D (#1.50) with AF3 E1 1-421.pdb, chain A (#547),
    24094 sequence alignment score = 1060.7 
    24095 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    24096 3.032) 
    24097  
    24098 
    24099 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    24100 
    24101 Chain information for AF3 E1 422-461.pdb #548 
    24102 --- 
    24103 Chain | Description 
    24104 A | No description available 
    24105  
    24106 
    24107 > matchmaker #548 to #1.50 & sel
    24108 
    24109 Parameters 
    24110 --- 
    24111 Chain pairing | bb 
    24112 Alignment algorithm | Needleman-Wunsch 
    24113 Similarity matrix | BLOSUM-62 
    24114 SS fraction | 0.3 
    24115 Gap open (HH/SS/other) | 18/18/6 
    24116 Gap extend | 1 
    24117 SS matrix |  |  | H | S | O 
    24118 ---|---|---|--- 
    24119 H | 6 | -9 | -6 
    24120 S |  | 6 | -6 
    24121 O |  |  | 4 
    24122 Iteration cutoff | 2 
    24123  
    24124 Matchmaker 3j0c.pdb1, chain D (#1.50) with AF3 E1 422-461.pdb, chain A (#548),
    24125 sequence alignment score = 626.9 
    24126 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    24127 2.916) 
    24128  
    24129 
    24130 > hide sel cartoons
    24131 
    24132 > select #1.50/E
    24133 
    24134 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    24135 
    24136 > show sel cartoons
    24137 
    24138 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    24139 
    24140 Chain information for AF3 E2 1-352.pdb #549 
    24141 --- 
    24142 Chain | Description 
    24143 B | No description available 
    24144  
    24145 
    24146 > matchmaker #549 to #1.50 & sel
    24147 
    24148 Parameters 
    24149 --- 
    24150 Chain pairing | bb 
    24151 Alignment algorithm | Needleman-Wunsch 
    24152 Similarity matrix | BLOSUM-62 
    24153 SS fraction | 0.3 
    24154 Gap open (HH/SS/other) | 18/18/6 
    24155 Gap extend | 1 
    24156 SS matrix |  |  | H | S | O 
    24157 ---|---|---|--- 
    24158 H | 6 | -9 | -6 
    24159 S |  | 6 | -6 
    24160 O |  |  | 4 
    24161 Iteration cutoff | 2 
    24162  
    24163 Matchmaker 3j0c.pdb1, chain E (#1.50) with AF3 E2 1-352.pdb, chain B (#549),
    24164 sequence alignment score = 594.5 
    24165 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    24166 6.147) 
    24167  
    24168 
    24169 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    24170 
    24171 Chain information for AF3 E2 353-438.pdb #550 
    24172 --- 
    24173 Chain | Description 
    24174 B | No description available 
    24175  
    24176 
    24177 > matchmaker #550 to #1.50 & sel
    24178 
    24179 Parameters 
    24180 --- 
    24181 Chain pairing | bb 
    24182 Alignment algorithm | Needleman-Wunsch 
    24183 Similarity matrix | BLOSUM-62 
    24184 SS fraction | 0.3 
    24185 Gap open (HH/SS/other) | 18/18/6 
    24186 Gap extend | 1 
    24187 SS matrix |  |  | H | S | O 
    24188 ---|---|---|--- 
    24189 H | 6 | -9 | -6 
    24190 S |  | 6 | -6 
    24191 O |  |  | 4 
    24192 Iteration cutoff | 2 
    24193  
    24194 Matchmaker 3j0c.pdb1, chain E (#1.50) with AF3 E2 353-438.pdb, chain B (#550),
    24195 sequence alignment score = 340.2 
    24196 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    24197 8.673) 
    24198  
    24199 
    24200 > hide sel cartoons
    24201 
    24202 > select #1.50/F
    24203 
    24204 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    24205 
    24206 > show sel cartoons
    24207 
    24208 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    24209 
    24210 Chain information for AF3 CA.pdb #551 
    24211 --- 
    24212 Chain | Description 
    24213 A | No description available 
    24214  
    24215 
    24216 > matchmaker #551 to #1.50 & sel
    24217 
    24218 Parameters 
    24219 --- 
    24220 Chain pairing | bb 
    24221 Alignment algorithm | Needleman-Wunsch 
    24222 Similarity matrix | BLOSUM-62 
    24223 SS fraction | 0.3 
    24224 Gap open (HH/SS/other) | 18/18/6 
    24225 Gap extend | 1 
    24226 SS matrix |  |  | H | S | O 
    24227 ---|---|---|--- 
    24228 H | 6 | -9 | -6 
    24229 S |  | 6 | -6 
    24230 O |  |  | 4 
    24231 Iteration cutoff | 2 
    24232  
    24233 Matchmaker 3j0c.pdb1, chain F (#1.50) with AF3 CA.pdb, chain A (#551),
    24234 sequence alignment score = 335.3 
    24235 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    24236 2.550) 
    24237  
    24238 
    24239 > hide sel cartoons
    24240 
    24241 > color #547 dodgerblue
    24242 
    24243 > color #548 dodgerblue
    24244 
    24245 > color #549 #00b305ff
    24246 
    24247 > color #550 #00b305ff
    24248 
    24249 > color #551 #f15839ff
    24250 
    24251 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    24252 
    24253 > hide #502-551 models
    24254 
    24255 > show #547 models
    24256 
    24257 > show #548 models
    24258 
    24259 > select #1.50/D
    24260 
    24261 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    24262 
    24263 > show sel cartoons
    24264 
    24265 > hide sel cartoons
    24266 
    24267 [Repeated 1 time(s)]
    24268 
    24269 > hide #547 models
    24270 
    24271 > hide #548 models
    24272 
    24273 > select #1.51/D
    24274 
    24275 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    24276 
    24277 > show sel cartoons
    24278 
    24279 > view
    24280 
    24281 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    24282 
    24283 Chain information for AF3 E1 1-421.pdb #552 
    24284 --- 
    24285 Chain | Description 
    24286 A | No description available 
    24287  
    24288 
    24289 > matchmaker #552 to #1.51 & sel
    24290 
    24291 Parameters 
    24292 --- 
    24293 Chain pairing | bb 
    24294 Alignment algorithm | Needleman-Wunsch 
    24295 Similarity matrix | BLOSUM-62 
    24296 SS fraction | 0.3 
    24297 Gap open (HH/SS/other) | 18/18/6 
    24298 Gap extend | 1 
    24299 SS matrix |  |  | H | S | O 
    24300 ---|---|---|--- 
    24301 H | 6 | -9 | -6 
    24302 S |  | 6 | -6 
    24303 O |  |  | 4 
    24304 Iteration cutoff | 2 
    24305  
    24306 Matchmaker 3j0c.pdb1, chain D (#1.51) with AF3 E1 1-421.pdb, chain A (#552),
    24307 sequence alignment score = 1060.7 
    24308 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    24309 3.032) 
    24310  
    24311 
    24312 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    24313 
    24314 Chain information for AF3 E1 422-461.pdb #553 
    24315 --- 
    24316 Chain | Description 
    24317 A | No description available 
    24318  
    24319 
    24320 > matchmaker #553 to #1.51 & sel
    24321 
    24322 Parameters 
    24323 --- 
    24324 Chain pairing | bb 
    24325 Alignment algorithm | Needleman-Wunsch 
    24326 Similarity matrix | BLOSUM-62 
    24327 SS fraction | 0.3 
    24328 Gap open (HH/SS/other) | 18/18/6 
    24329 Gap extend | 1 
    24330 SS matrix |  |  | H | S | O 
    24331 ---|---|---|--- 
    24332 H | 6 | -9 | -6 
    24333 S |  | 6 | -6 
    24334 O |  |  | 4 
    24335 Iteration cutoff | 2 
    24336  
    24337 Matchmaker 3j0c.pdb1, chain D (#1.51) with AF3 E1 422-461.pdb, chain A (#553),
    24338 sequence alignment score = 626.9 
    24339 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    24340 2.916) 
    24341  
    24342 
    24343 > hide sel cartoons
    24344 
    24345 > select #1.51/E
    24346 
    24347 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    24348 
    24349 > show sel cartoons
    24350 
    24351 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    24352 
    24353 Chain information for AF3 E2 1-352.pdb #554 
    24354 --- 
    24355 Chain | Description 
    24356 B | No description available 
    24357  
    24358 
    24359 > matchmaker #554 to #1.51 & sel
    24360 
    24361 Parameters 
    24362 --- 
    24363 Chain pairing | bb 
    24364 Alignment algorithm | Needleman-Wunsch 
    24365 Similarity matrix | BLOSUM-62 
    24366 SS fraction | 0.3 
    24367 Gap open (HH/SS/other) | 18/18/6 
    24368 Gap extend | 1 
    24369 SS matrix |  |  | H | S | O 
    24370 ---|---|---|--- 
    24371 H | 6 | -9 | -6 
    24372 S |  | 6 | -6 
    24373 O |  |  | 4 
    24374 Iteration cutoff | 2 
    24375  
    24376 Matchmaker 3j0c.pdb1, chain E (#1.51) with AF3 E2 1-352.pdb, chain B (#554),
    24377 sequence alignment score = 594.5 
    24378 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    24379 6.147) 
    24380  
    24381 
    24382 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    24383 
    24384 Chain information for AF3 E2 353-438.pdb #555 
    24385 --- 
    24386 Chain | Description 
    24387 B | No description available 
    24388  
    24389 
    24390 > matchmaker #555 to #1.51 & sel
    24391 
    24392 Parameters 
    24393 --- 
    24394 Chain pairing | bb 
    24395 Alignment algorithm | Needleman-Wunsch 
    24396 Similarity matrix | BLOSUM-62 
    24397 SS fraction | 0.3 
    24398 Gap open (HH/SS/other) | 18/18/6 
    24399 Gap extend | 1 
    24400 SS matrix |  |  | H | S | O 
    24401 ---|---|---|--- 
    24402 H | 6 | -9 | -6 
    24403 S |  | 6 | -6 
    24404 O |  |  | 4 
    24405 Iteration cutoff | 2 
    24406  
    24407 Matchmaker 3j0c.pdb1, chain E (#1.51) with AF3 E2 353-438.pdb, chain B (#555),
    24408 sequence alignment score = 340.2 
    24409 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    24410 8.673) 
    24411  
    24412 
    24413 > hide sel cartoons
    24414 
    24415 > select #1.51/F
    24416 
    24417 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    24418 
    24419 > show sel cartoons
    24420 
    24421 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    24422 
    24423 Chain information for AF3 CA.pdb #556 
    24424 --- 
    24425 Chain | Description 
    24426 A | No description available 
    24427  
    24428 
    24429 > matchmaker #556 to #1.51 & sel
    24430 
    24431 Parameters 
    24432 --- 
    24433 Chain pairing | bb 
    24434 Alignment algorithm | Needleman-Wunsch 
    24435 Similarity matrix | BLOSUM-62 
    24436 SS fraction | 0.3 
    24437 Gap open (HH/SS/other) | 18/18/6 
    24438 Gap extend | 1 
    24439 SS matrix |  |  | H | S | O 
    24440 ---|---|---|--- 
    24441 H | 6 | -9 | -6 
    24442 S |  | 6 | -6 
    24443 O |  |  | 4 
    24444 Iteration cutoff | 2 
    24445  
    24446 Matchmaker 3j0c.pdb1, chain F (#1.51) with AF3 CA.pdb, chain A (#556),
    24447 sequence alignment score = 335.3 
    24448 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    24449 2.550) 
    24450  
    24451 
    24452 > hide sel cartoons
    24453 
    24454 > color #552 dodgerblue
    24455 
    24456 > color #553 dodgerblue
    24457 
    24458 > color #554 #00b305ff
    24459 
    24460 > color #555 #00b305ff
    24461 
    24462 > color #556 #f15839ff
    24463 
    24464 > select #1.52/D
    24465 
    24466 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    24467 
    24468 > show sel cartoons
    24469 
    24470 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    24471 
    24472 Chain information for AF3 E1 1-421.pdb #557 
    24473 --- 
    24474 Chain | Description 
    24475 A | No description available 
    24476  
    24477 
    24478 > matchmaker #557 to #1.52 & sel
    24479 
    24480 Parameters 
    24481 --- 
    24482 Chain pairing | bb 
    24483 Alignment algorithm | Needleman-Wunsch 
    24484 Similarity matrix | BLOSUM-62 
    24485 SS fraction | 0.3 
    24486 Gap open (HH/SS/other) | 18/18/6 
    24487 Gap extend | 1 
    24488 SS matrix |  |  | H | S | O 
    24489 ---|---|---|--- 
    24490 H | 6 | -9 | -6 
    24491 S |  | 6 | -6 
    24492 O |  |  | 4 
    24493 Iteration cutoff | 2 
    24494  
    24495 Matchmaker 3j0c.pdb1, chain D (#1.52) with AF3 E1 1-421.pdb, chain A (#557),
    24496 sequence alignment score = 1060.7 
    24497 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    24498 3.032) 
    24499  
    24500 
    24501 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    24502 
    24503 Chain information for AF3 E1 422-461.pdb #558 
    24504 --- 
    24505 Chain | Description 
    24506 A | No description available 
    24507  
    24508 
    24509 > matchmaker #558 to #1.52 & sel
    24510 
    24511 Parameters 
    24512 --- 
    24513 Chain pairing | bb 
    24514 Alignment algorithm | Needleman-Wunsch 
    24515 Similarity matrix | BLOSUM-62 
    24516 SS fraction | 0.3 
    24517 Gap open (HH/SS/other) | 18/18/6 
    24518 Gap extend | 1 
    24519 SS matrix |  |  | H | S | O 
    24520 ---|---|---|--- 
    24521 H | 6 | -9 | -6 
    24522 S |  | 6 | -6 
    24523 O |  |  | 4 
    24524 Iteration cutoff | 2 
    24525  
    24526 Matchmaker 3j0c.pdb1, chain D (#1.52) with AF3 E1 422-461.pdb, chain A (#558),
    24527 sequence alignment score = 626.9 
    24528 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    24529 2.916) 
    24530  
    24531 
    24532 > hide sel cartoons
    24533 
    24534 > select #1.52/E
    24535 
    24536 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    24537 
    24538 > show sel cartoons
    24539 
    24540 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    24541 
    24542 Chain information for AF3 E2 1-352.pdb #559 
    24543 --- 
    24544 Chain | Description 
    24545 B | No description available 
    24546  
    24547 
    24548 > matchmaker #559 to #1.52 & sel
    24549 
    24550 Parameters 
    24551 --- 
    24552 Chain pairing | bb 
    24553 Alignment algorithm | Needleman-Wunsch 
    24554 Similarity matrix | BLOSUM-62 
    24555 SS fraction | 0.3 
    24556 Gap open (HH/SS/other) | 18/18/6 
    24557 Gap extend | 1 
    24558 SS matrix |  |  | H | S | O 
    24559 ---|---|---|--- 
    24560 H | 6 | -9 | -6 
    24561 S |  | 6 | -6 
    24562 O |  |  | 4 
    24563 Iteration cutoff | 2 
    24564  
    24565 Matchmaker 3j0c.pdb1, chain E (#1.52) with AF3 E2 1-352.pdb, chain B (#559),
    24566 sequence alignment score = 594.5 
    24567 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    24568 6.147) 
    24569  
    24570 
    24571 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    24572 
    24573 Chain information for AF3 E2 353-438.pdb #560 
    24574 --- 
    24575 Chain | Description 
    24576 B | No description available 
    24577  
    24578 
    24579 > matchmaker #560 to #1.52 & sel
    24580 
    24581 Parameters 
    24582 --- 
    24583 Chain pairing | bb 
    24584 Alignment algorithm | Needleman-Wunsch 
    24585 Similarity matrix | BLOSUM-62 
    24586 SS fraction | 0.3 
    24587 Gap open (HH/SS/other) | 18/18/6 
    24588 Gap extend | 1 
    24589 SS matrix |  |  | H | S | O 
    24590 ---|---|---|--- 
    24591 H | 6 | -9 | -6 
    24592 S |  | 6 | -6 
    24593 O |  |  | 4 
    24594 Iteration cutoff | 2 
    24595  
    24596 Matchmaker 3j0c.pdb1, chain E (#1.52) with AF3 E2 353-438.pdb, chain B (#560),
    24597 sequence alignment score = 340.2 
    24598 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    24599 8.673) 
    24600  
    24601 
    24602 > hide sel cartoons
    24603 
    24604 > select #1.52/F
    24605 
    24606 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    24607 
    24608 > show sel cartoons
    24609 
    24610 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    24611 
    24612 Chain information for AF3 CA.pdb #561 
    24613 --- 
    24614 Chain | Description 
    24615 A | No description available 
    24616  
    24617 
    24618 > matchmaker #561 to #1.52 & sel
    24619 
    24620 Parameters 
    24621 --- 
    24622 Chain pairing | bb 
    24623 Alignment algorithm | Needleman-Wunsch 
    24624 Similarity matrix | BLOSUM-62 
    24625 SS fraction | 0.3 
    24626 Gap open (HH/SS/other) | 18/18/6 
    24627 Gap extend | 1 
    24628 SS matrix |  |  | H | S | O 
    24629 ---|---|---|--- 
    24630 H | 6 | -9 | -6 
    24631 S |  | 6 | -6 
    24632 O |  |  | 4 
    24633 Iteration cutoff | 2 
    24634  
    24635 Matchmaker 3j0c.pdb1, chain F (#1.52) with AF3 CA.pdb, chain A (#561),
    24636 sequence alignment score = 335.3 
    24637 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    24638 2.550) 
    24639  
    24640 
    24641 > hide sel cartoons
    24642 
    24643 > color #557 dodgerblue
    24644 
    24645 > color #558 dodgerblue
    24646 
    24647 > color #559 #00b305ff
    24648 
    24649 > color #560 #00b305ff
    24650 
    24651 > color #561 #f15839ff
    24652 
    24653 > select #1.53/D
    24654 
    24655 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    24656 
    24657 > select #1.53/D
    24658 
    24659 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    24660 
    24661 > show sel cartoons
    24662 
    24663 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    24664 
    24665 Chain information for AF3 E1 1-421.pdb #562 
    24666 --- 
    24667 Chain | Description 
    24668 A | No description available 
    24669  
    24670 
    24671 > matchmaker #562 to #1.53 & sel
    24672 
    24673 Parameters 
    24674 --- 
    24675 Chain pairing | bb 
    24676 Alignment algorithm | Needleman-Wunsch 
    24677 Similarity matrix | BLOSUM-62 
    24678 SS fraction | 0.3 
    24679 Gap open (HH/SS/other) | 18/18/6 
    24680 Gap extend | 1 
    24681 SS matrix |  |  | H | S | O 
    24682 ---|---|---|--- 
    24683 H | 6 | -9 | -6 
    24684 S |  | 6 | -6 
    24685 O |  |  | 4 
    24686 Iteration cutoff | 2 
    24687  
    24688 Matchmaker 3j0c.pdb1, chain D (#1.53) with AF3 E1 1-421.pdb, chain A (#562),
    24689 sequence alignment score = 1060.7 
    24690 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    24691 3.032) 
    24692  
    24693 
    24694 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    24695 
    24696 Chain information for AF3 E1 422-461.pdb #563 
    24697 --- 
    24698 Chain | Description 
    24699 A | No description available 
    24700  
    24701 
    24702 > matchmaker #563 to #1.53 & sel
    24703 
    24704 Parameters 
    24705 --- 
    24706 Chain pairing | bb 
    24707 Alignment algorithm | Needleman-Wunsch 
    24708 Similarity matrix | BLOSUM-62 
    24709 SS fraction | 0.3 
    24710 Gap open (HH/SS/other) | 18/18/6 
    24711 Gap extend | 1 
    24712 SS matrix |  |  | H | S | O 
    24713 ---|---|---|--- 
    24714 H | 6 | -9 | -6 
    24715 S |  | 6 | -6 
    24716 O |  |  | 4 
    24717 Iteration cutoff | 2 
    24718  
    24719 Matchmaker 3j0c.pdb1, chain D (#1.53) with AF3 E1 422-461.pdb, chain A (#563),
    24720 sequence alignment score = 626.9 
    24721 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    24722 2.916) 
    24723  
    24724 
    24725 > hide sel cartoons
    24726 
    24727 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    24728 
    24729 Chain information for AF3 E2 1-352.pdb #564 
    24730 --- 
    24731 Chain | Description 
    24732 B | No description available 
    24733  
    24734 
    24735 > select #1.53/E
    24736 
    24737 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    24738 
    24739 > show sel cartoons
    24740 
    24741 > matchmaker #564 to #1.53 & sel
    24742 
    24743 Parameters 
    24744 --- 
    24745 Chain pairing | bb 
    24746 Alignment algorithm | Needleman-Wunsch 
    24747 Similarity matrix | BLOSUM-62 
    24748 SS fraction | 0.3 
    24749 Gap open (HH/SS/other) | 18/18/6 
    24750 Gap extend | 1 
    24751 SS matrix |  |  | H | S | O 
    24752 ---|---|---|--- 
    24753 H | 6 | -9 | -6 
    24754 S |  | 6 | -6 
    24755 O |  |  | 4 
    24756 Iteration cutoff | 2 
    24757  
    24758 Matchmaker 3j0c.pdb1, chain E (#1.53) with AF3 E2 1-352.pdb, chain B (#564),
    24759 sequence alignment score = 594.5 
    24760 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    24761 6.147) 
    24762  
    24763 
    24764 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    24765 
    24766 Chain information for AF3 E2 353-438.pdb #565 
    24767 --- 
    24768 Chain | Description 
    24769 B | No description available 
    24770  
    24771 
    24772 > matchmaker #565 to #1.53 & sel
    24773 
    24774 Parameters 
    24775 --- 
    24776 Chain pairing | bb 
    24777 Alignment algorithm | Needleman-Wunsch 
    24778 Similarity matrix | BLOSUM-62 
    24779 SS fraction | 0.3 
    24780 Gap open (HH/SS/other) | 18/18/6 
    24781 Gap extend | 1 
    24782 SS matrix |  |  | H | S | O 
    24783 ---|---|---|--- 
    24784 H | 6 | -9 | -6 
    24785 S |  | 6 | -6 
    24786 O |  |  | 4 
    24787 Iteration cutoff | 2 
    24788  
    24789 Matchmaker 3j0c.pdb1, chain E (#1.53) with AF3 E2 353-438.pdb, chain B (#565),
    24790 sequence alignment score = 340.2 
    24791 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    24792 8.673) 
    24793  
    24794 
    24795 > hide sel cartoons
    24796 
    24797 > select #1.53/F
    24798 
    24799 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    24800 
    24801 > show sel cartoons
    24802 
    24803 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    24804 
    24805 Chain information for AF3 CA.pdb #566 
    24806 --- 
    24807 Chain | Description 
    24808 A | No description available 
    24809  
    24810 
    24811 > matchmaker #566 to #1.53 & sel
    24812 
    24813 Parameters 
    24814 --- 
    24815 Chain pairing | bb 
    24816 Alignment algorithm | Needleman-Wunsch 
    24817 Similarity matrix | BLOSUM-62 
    24818 SS fraction | 0.3 
    24819 Gap open (HH/SS/other) | 18/18/6 
    24820 Gap extend | 1 
    24821 SS matrix |  |  | H | S | O 
    24822 ---|---|---|--- 
    24823 H | 6 | -9 | -6 
    24824 S |  | 6 | -6 
    24825 O |  |  | 4 
    24826 Iteration cutoff | 2 
    24827  
    24828 Matchmaker 3j0c.pdb1, chain F (#1.53) with AF3 CA.pdb, chain A (#566),
    24829 sequence alignment score = 335.3 
    24830 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    24831 2.550) 
    24832  
    24833 
    24834 > hide sel cartoons
    24835 
    24836 > color #562 dodgerblue
    24837 
    24838 > color #563 dodgerblue
    24839 
    24840 > color #564 #00b305ff
    24841 
    24842 > color #565 #00b305ff
    24843 
    24844 > color #566 #f15839ff
    24845 
    24846 > select #1.54/D
    24847 
    24848 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    24849 
    24850 > show sel cartoons
    24851 
    24852 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    24853 
    24854 Chain information for AF3 E1 1-421.pdb #567 
    24855 --- 
    24856 Chain | Description 
    24857 A | No description available 
    24858  
    24859 
    24860 > matchmaker #567 to #1.53 & sel
    24861 
    24862 No 'to' model specified 
    24863 
    24864 > matchmaker #567 to #1.54 & sel
    24865 
    24866 Parameters 
    24867 --- 
    24868 Chain pairing | bb 
    24869 Alignment algorithm | Needleman-Wunsch 
    24870 Similarity matrix | BLOSUM-62 
    24871 SS fraction | 0.3 
    24872 Gap open (HH/SS/other) | 18/18/6 
    24873 Gap extend | 1 
    24874 SS matrix |  |  | H | S | O 
    24875 ---|---|---|--- 
    24876 H | 6 | -9 | -6 
    24877 S |  | 6 | -6 
    24878 O |  |  | 4 
    24879 Iteration cutoff | 2 
    24880  
    24881 Matchmaker 3j0c.pdb1, chain D (#1.54) with AF3 E1 1-421.pdb, chain A (#567),
    24882 sequence alignment score = 1060.7 
    24883 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    24884 3.032) 
    24885  
    24886 
    24887 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    24888 
    24889 Chain information for AF3 E1 422-461.pdb #568 
    24890 --- 
    24891 Chain | Description 
    24892 A | No description available 
    24893  
    24894 
    24895 > matchmaker #568 to #1.54 & sel
    24896 
    24897 Parameters 
    24898 --- 
    24899 Chain pairing | bb 
    24900 Alignment algorithm | Needleman-Wunsch 
    24901 Similarity matrix | BLOSUM-62 
    24902 SS fraction | 0.3 
    24903 Gap open (HH/SS/other) | 18/18/6 
    24904 Gap extend | 1 
    24905 SS matrix |  |  | H | S | O 
    24906 ---|---|---|--- 
    24907 H | 6 | -9 | -6 
    24908 S |  | 6 | -6 
    24909 O |  |  | 4 
    24910 Iteration cutoff | 2 
    24911  
    24912 Matchmaker 3j0c.pdb1, chain D (#1.54) with AF3 E1 422-461.pdb, chain A (#568),
    24913 sequence alignment score = 626.9 
    24914 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    24915 2.916) 
    24916  
    24917 
    24918 > hide sel cartoons
    24919 
    24920 > select #1.54/E
    24921 
    24922 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    24923 
    24924 > show sel cartoons
    24925 
    24926 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    24927 
    24928 Chain information for AF3 E2 1-352.pdb #569 
    24929 --- 
    24930 Chain | Description 
    24931 B | No description available 
    24932  
    24933 
    24934 > matchmaker #569 to #1.54 & sel
    24935 
    24936 Parameters 
    24937 --- 
    24938 Chain pairing | bb 
    24939 Alignment algorithm | Needleman-Wunsch 
    24940 Similarity matrix | BLOSUM-62 
    24941 SS fraction | 0.3 
    24942 Gap open (HH/SS/other) | 18/18/6 
    24943 Gap extend | 1 
    24944 SS matrix |  |  | H | S | O 
    24945 ---|---|---|--- 
    24946 H | 6 | -9 | -6 
    24947 S |  | 6 | -6 
    24948 O |  |  | 4 
    24949 Iteration cutoff | 2 
    24950  
    24951 Matchmaker 3j0c.pdb1, chain E (#1.54) with AF3 E2 1-352.pdb, chain B (#569),
    24952 sequence alignment score = 594.5 
    24953 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    24954 6.147) 
    24955  
    24956 
    24957 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    24958 
    24959 Chain information for AF3 E2 353-438.pdb #570 
    24960 --- 
    24961 Chain | Description 
    24962 B | No description available 
    24963  
    24964 
    24965 > matchmaker #570 to #1.54 & sel
    24966 
    24967 Parameters 
    24968 --- 
    24969 Chain pairing | bb 
    24970 Alignment algorithm | Needleman-Wunsch 
    24971 Similarity matrix | BLOSUM-62 
    24972 SS fraction | 0.3 
    24973 Gap open (HH/SS/other) | 18/18/6 
    24974 Gap extend | 1 
    24975 SS matrix |  |  | H | S | O 
    24976 ---|---|---|--- 
    24977 H | 6 | -9 | -6 
    24978 S |  | 6 | -6 
    24979 O |  |  | 4 
    24980 Iteration cutoff | 2 
    24981  
    24982 Matchmaker 3j0c.pdb1, chain E (#1.54) with AF3 E2 353-438.pdb, chain B (#570),
    24983 sequence alignment score = 340.2 
    24984 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    24985 8.673) 
    24986  
    24987 
    24988 > hide sel cartoons
    24989 
    24990 > select #1.54/F
    24991 
    24992 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    24993 
    24994 > show sel cartoons
    24995 
    24996 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    24997 
    24998 Chain information for AF3 CA.pdb #571 
    24999 --- 
    25000 Chain | Description 
    25001 A | No description available 
    25002  
    25003 
    25004 > matchmaker #571 to #1.54 & sel
    25005 
    25006 Parameters 
    25007 --- 
    25008 Chain pairing | bb 
    25009 Alignment algorithm | Needleman-Wunsch 
    25010 Similarity matrix | BLOSUM-62 
    25011 SS fraction | 0.3 
    25012 Gap open (HH/SS/other) | 18/18/6 
    25013 Gap extend | 1 
    25014 SS matrix |  |  | H | S | O 
    25015 ---|---|---|--- 
    25016 H | 6 | -9 | -6 
    25017 S |  | 6 | -6 
    25018 O |  |  | 4 
    25019 Iteration cutoff | 2 
    25020  
    25021 Matchmaker 3j0c.pdb1, chain F (#1.54) with AF3 CA.pdb, chain A (#571),
    25022 sequence alignment score = 335.3 
    25023 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    25024 2.550) 
    25025  
    25026 
    25027 > hide sel cartoons
    25028 
    25029 > color #567 dodgerblue
    25030 
    25031 > color #568 dodgerblue
    25032 
    25033 > color #569 #00b305ff
    25034 
    25035 > color #570 #00b305ff
    25036 
    25037 > color #571 #f15839ff
    25038 
    25039 > select #1.55/D
    25040 
    25041 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    25042 
    25043 > show sel cartoons
    25044 
    25045 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    25046 
    25047 Chain information for AF3 E1 1-421.pdb #572 
    25048 --- 
    25049 Chain | Description 
    25050 A | No description available 
    25051  
    25052 
    25053 > matchmaker #572 to #1.55 & sel
    25054 
    25055 Parameters 
    25056 --- 
    25057 Chain pairing | bb 
    25058 Alignment algorithm | Needleman-Wunsch 
    25059 Similarity matrix | BLOSUM-62 
    25060 SS fraction | 0.3 
    25061 Gap open (HH/SS/other) | 18/18/6 
    25062 Gap extend | 1 
    25063 SS matrix |  |  | H | S | O 
    25064 ---|---|---|--- 
    25065 H | 6 | -9 | -6 
    25066 S |  | 6 | -6 
    25067 O |  |  | 4 
    25068 Iteration cutoff | 2 
    25069  
    25070 Matchmaker 3j0c.pdb1, chain D (#1.55) with AF3 E1 1-421.pdb, chain A (#572),
    25071 sequence alignment score = 1060.7 
    25072 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    25073 3.032) 
    25074  
    25075 
    25076 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    25077 
    25078 Chain information for AF3 E1 422-461.pdb #573 
    25079 --- 
    25080 Chain | Description 
    25081 A | No description available 
    25082  
    25083 
    25084 > matchmaker #573 to #1.55 & sel
    25085 
    25086 Parameters 
    25087 --- 
    25088 Chain pairing | bb 
    25089 Alignment algorithm | Needleman-Wunsch 
    25090 Similarity matrix | BLOSUM-62 
    25091 SS fraction | 0.3 
    25092 Gap open (HH/SS/other) | 18/18/6 
    25093 Gap extend | 1 
    25094 SS matrix |  |  | H | S | O 
    25095 ---|---|---|--- 
    25096 H | 6 | -9 | -6 
    25097 S |  | 6 | -6 
    25098 O |  |  | 4 
    25099 Iteration cutoff | 2 
    25100  
    25101 Matchmaker 3j0c.pdb1, chain D (#1.55) with AF3 E1 422-461.pdb, chain A (#573),
    25102 sequence alignment score = 626.9 
    25103 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    25104 2.916) 
    25105  
    25106 
    25107 > hide sel cartoons
    25108 
    25109 > select #1.55/E
    25110 
    25111 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    25112 
    25113 > show sel cartoons
    25114 
    25115 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    25116 
    25117 Chain information for AF3 E2 1-352.pdb #574 
    25118 --- 
    25119 Chain | Description 
    25120 B | No description available 
    25121  
    25122 
    25123 > matchmaker #574 to #1.55 & sel
    25124 
    25125 Parameters 
    25126 --- 
    25127 Chain pairing | bb 
    25128 Alignment algorithm | Needleman-Wunsch 
    25129 Similarity matrix | BLOSUM-62 
    25130 SS fraction | 0.3 
    25131 Gap open (HH/SS/other) | 18/18/6 
    25132 Gap extend | 1 
    25133 SS matrix |  |  | H | S | O 
    25134 ---|---|---|--- 
    25135 H | 6 | -9 | -6 
    25136 S |  | 6 | -6 
    25137 O |  |  | 4 
    25138 Iteration cutoff | 2 
    25139  
    25140 Matchmaker 3j0c.pdb1, chain E (#1.55) with AF3 E2 1-352.pdb, chain B (#574),
    25141 sequence alignment score = 594.5 
    25142 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    25143 6.147) 
    25144  
    25145 
    25146 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    25147 
    25148 Chain information for AF3 E2 353-438.pdb #575 
    25149 --- 
    25150 Chain | Description 
    25151 B | No description available 
    25152  
    25153 
    25154 > matchmaker #575 to #1.55 & sel
    25155 
    25156 Parameters 
    25157 --- 
    25158 Chain pairing | bb 
    25159 Alignment algorithm | Needleman-Wunsch 
    25160 Similarity matrix | BLOSUM-62 
    25161 SS fraction | 0.3 
    25162 Gap open (HH/SS/other) | 18/18/6 
    25163 Gap extend | 1 
    25164 SS matrix |  |  | H | S | O 
    25165 ---|---|---|--- 
    25166 H | 6 | -9 | -6 
    25167 S |  | 6 | -6 
    25168 O |  |  | 4 
    25169 Iteration cutoff | 2 
    25170  
    25171 Matchmaker 3j0c.pdb1, chain E (#1.55) with AF3 E2 353-438.pdb, chain B (#575),
    25172 sequence alignment score = 340.2 
    25173 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    25174 8.673) 
    25175  
    25176 
    25177 > hide sel cartoons
    25178 
    25179 The cached device pixel ratio value was stale on window expose. Please file a
    25180 QTBUG which explains how to reproduce. 
    25181 
    25182 > select #1.55/F
    25183 
    25184 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    25185 
    25186 > show sel cartoons
    25187 
    25188 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    25189 
    25190 Chain information for AF3 CA.pdb #576 
    25191 --- 
    25192 Chain | Description 
    25193 A | No description available 
    25194  
    25195 
    25196 > matchmaker #576 to #1.55 & sel
    25197 
    25198 Parameters 
    25199 --- 
    25200 Chain pairing | bb 
    25201 Alignment algorithm | Needleman-Wunsch 
    25202 Similarity matrix | BLOSUM-62 
    25203 SS fraction | 0.3 
    25204 Gap open (HH/SS/other) | 18/18/6 
    25205 Gap extend | 1 
    25206 SS matrix |  |  | H | S | O 
    25207 ---|---|---|--- 
    25208 H | 6 | -9 | -6 
    25209 S |  | 6 | -6 
    25210 O |  |  | 4 
    25211 Iteration cutoff | 2 
    25212  
    25213 Matchmaker 3j0c.pdb1, chain F (#1.55) with AF3 CA.pdb, chain A (#576),
    25214 sequence alignment score = 335.3 
    25215 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    25216 2.550) 
    25217  
    25218 
    25219 > hide sel cartoons
    25220 
    25221 > color #572 dodgerblue
    25222 
    25223 > color #573 dodgerblue
    25224 
    25225 > color #574 #00b305ff
    25226 
    25227 > color #575 #00b305ff
    25228 
    25229 > color #576 #f15839ff
    25230 
    25231 > select #1.56/D
    25232 
    25233 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    25234 
    25235 > show sel cartoons
    25236 
    25237 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    25238 
    25239 Chain information for AF3 E1 1-421.pdb #577 
    25240 --- 
    25241 Chain | Description 
    25242 A | No description available 
    25243  
    25244 
    25245 > matchmaker #577 to #1.56 & sel
    25246 
    25247 Parameters 
    25248 --- 
    25249 Chain pairing | bb 
    25250 Alignment algorithm | Needleman-Wunsch 
    25251 Similarity matrix | BLOSUM-62 
    25252 SS fraction | 0.3 
    25253 Gap open (HH/SS/other) | 18/18/6 
    25254 Gap extend | 1 
    25255 SS matrix |  |  | H | S | O 
    25256 ---|---|---|--- 
    25257 H | 6 | -9 | -6 
    25258 S |  | 6 | -6 
    25259 O |  |  | 4 
    25260 Iteration cutoff | 2 
    25261  
    25262 Matchmaker 3j0c.pdb1, chain D (#1.56) with AF3 E1 1-421.pdb, chain A (#577),
    25263 sequence alignment score = 1060.7 
    25264 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    25265 3.032) 
    25266  
    25267 
    25268 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    25269 
    25270 Chain information for AF3 E1 422-461.pdb #578 
    25271 --- 
    25272 Chain | Description 
    25273 A | No description available 
    25274  
    25275 
    25276 > matchmaker #578 to #1.56 & sel
    25277 
    25278 Parameters 
    25279 --- 
    25280 Chain pairing | bb 
    25281 Alignment algorithm | Needleman-Wunsch 
    25282 Similarity matrix | BLOSUM-62 
    25283 SS fraction | 0.3 
    25284 Gap open (HH/SS/other) | 18/18/6 
    25285 Gap extend | 1 
    25286 SS matrix |  |  | H | S | O 
    25287 ---|---|---|--- 
    25288 H | 6 | -9 | -6 
    25289 S |  | 6 | -6 
    25290 O |  |  | 4 
    25291 Iteration cutoff | 2 
    25292  
    25293 Matchmaker 3j0c.pdb1, chain D (#1.56) with AF3 E1 422-461.pdb, chain A (#578),
    25294 sequence alignment score = 626.9 
    25295 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    25296 2.916) 
    25297  
    25298 
    25299 > hide sel cartoons
    25300 
    25301 > select #1.56/E
    25302 
    25303 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    25304 
    25305 > show sel cartoons
    25306 
    25307 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    25308 
    25309 Chain information for AF3 E2 1-352.pdb #579 
    25310 --- 
    25311 Chain | Description 
    25312 B | No description available 
    25313  
    25314 
    25315 > matchmaker #579 to #1.56 & sel
    25316 
    25317 Parameters 
    25318 --- 
    25319 Chain pairing | bb 
    25320 Alignment algorithm | Needleman-Wunsch 
    25321 Similarity matrix | BLOSUM-62 
    25322 SS fraction | 0.3 
    25323 Gap open (HH/SS/other) | 18/18/6 
    25324 Gap extend | 1 
    25325 SS matrix |  |  | H | S | O 
    25326 ---|---|---|--- 
    25327 H | 6 | -9 | -6 
    25328 S |  | 6 | -6 
    25329 O |  |  | 4 
    25330 Iteration cutoff | 2 
    25331  
    25332 Matchmaker 3j0c.pdb1, chain E (#1.56) with AF3 E2 1-352.pdb, chain B (#579),
    25333 sequence alignment score = 594.5 
    25334 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    25335 6.147) 
    25336  
    25337 
    25338 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    25339 
    25340 Chain information for AF3 E2 353-438.pdb #580 
    25341 --- 
    25342 Chain | Description 
    25343 B | No description available 
    25344  
    25345 
    25346 > matchmaker #580 to #1.56 & sel
    25347 
    25348 Parameters 
    25349 --- 
    25350 Chain pairing | bb 
    25351 Alignment algorithm | Needleman-Wunsch 
    25352 Similarity matrix | BLOSUM-62 
    25353 SS fraction | 0.3 
    25354 Gap open (HH/SS/other) | 18/18/6 
    25355 Gap extend | 1 
    25356 SS matrix |  |  | H | S | O 
    25357 ---|---|---|--- 
    25358 H | 6 | -9 | -6 
    25359 S |  | 6 | -6 
    25360 O |  |  | 4 
    25361 Iteration cutoff | 2 
    25362  
    25363 Matchmaker 3j0c.pdb1, chain E (#1.56) with AF3 E2 353-438.pdb, chain B (#580),
    25364 sequence alignment score = 340.2 
    25365 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    25366 8.673) 
    25367  
    25368 
    25369 > hide sel cartoons
    25370 
    25371 > select #1.56/F
    25372 
    25373 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    25374 
    25375 > show sel cartoons
    25376 
    25377 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    25378 
    25379 Chain information for AF3 CA.pdb #581 
    25380 --- 
    25381 Chain | Description 
    25382 A | No description available 
    25383  
    25384 
    25385 > matchmaker #581 to #1.56 & sel
    25386 
    25387 Parameters 
    25388 --- 
    25389 Chain pairing | bb 
    25390 Alignment algorithm | Needleman-Wunsch 
    25391 Similarity matrix | BLOSUM-62 
    25392 SS fraction | 0.3 
    25393 Gap open (HH/SS/other) | 18/18/6 
    25394 Gap extend | 1 
    25395 SS matrix |  |  | H | S | O 
    25396 ---|---|---|--- 
    25397 H | 6 | -9 | -6 
    25398 S |  | 6 | -6 
    25399 O |  |  | 4 
    25400 Iteration cutoff | 2 
    25401  
    25402 Matchmaker 3j0c.pdb1, chain F (#1.56) with AF3 CA.pdb, chain A (#581),
    25403 sequence alignment score = 335.3 
    25404 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    25405 2.550) 
    25406  
    25407 
    25408 > hide sel cartoons
    25409 
    25410 > color #577 dodgerblue
    25411 
    25412 > color #578 dodgerblue
    25413 
    25414 > color #579 #00b305ff
    25415 
    25416 > color #580 #00b305ff
    25417 
    25418 > color #581 #f15839ff
    25419 
    25420 > select #1.57/D
    25421 
    25422 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    25423 
    25424 > show sel cartoons
    25425 
    25426 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    25427 
    25428 Chain information for AF3 E1 1-421.pdb #582 
    25429 --- 
    25430 Chain | Description 
    25431 A | No description available 
    25432  
    25433 
    25434 > matchmaker #582 to #1.57 & sel
    25435 
    25436 Parameters 
    25437 --- 
    25438 Chain pairing | bb 
    25439 Alignment algorithm | Needleman-Wunsch 
    25440 Similarity matrix | BLOSUM-62 
    25441 SS fraction | 0.3 
    25442 Gap open (HH/SS/other) | 18/18/6 
    25443 Gap extend | 1 
    25444 SS matrix |  |  | H | S | O 
    25445 ---|---|---|--- 
    25446 H | 6 | -9 | -6 
    25447 S |  | 6 | -6 
    25448 O |  |  | 4 
    25449 Iteration cutoff | 2 
    25450  
    25451 Matchmaker 3j0c.pdb1, chain D (#1.57) with AF3 E1 1-421.pdb, chain A (#582),
    25452 sequence alignment score = 1060.7 
    25453 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    25454 3.032) 
    25455  
    25456 
    25457 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    25458 
    25459 Chain information for AF3 E1 422-461.pdb #583 
    25460 --- 
    25461 Chain | Description 
    25462 A | No description available 
    25463  
    25464 
    25465 > matchmaker #583 to #1.57 & sel
    25466 
    25467 Parameters 
    25468 --- 
    25469 Chain pairing | bb 
    25470 Alignment algorithm | Needleman-Wunsch 
    25471 Similarity matrix | BLOSUM-62 
    25472 SS fraction | 0.3 
    25473 Gap open (HH/SS/other) | 18/18/6 
    25474 Gap extend | 1 
    25475 SS matrix |  |  | H | S | O 
    25476 ---|---|---|--- 
    25477 H | 6 | -9 | -6 
    25478 S |  | 6 | -6 
    25479 O |  |  | 4 
    25480 Iteration cutoff | 2 
    25481  
    25482 Matchmaker 3j0c.pdb1, chain D (#1.57) with AF3 E1 422-461.pdb, chain A (#583),
    25483 sequence alignment score = 626.9 
    25484 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    25485 2.916) 
    25486  
    25487 
    25488 > hide sel cartoons
    25489 
    25490 > select #1.57/E
    25491 
    25492 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    25493 
    25494 > show sel cartoons
    25495 
    25496 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    25497 
    25498 Chain information for AF3 E2 1-352.pdb #584 
    25499 --- 
    25500 Chain | Description 
    25501 B | No description available 
    25502  
    25503 
    25504 > matchmaker #584 to #1.57 & sel
    25505 
    25506 Parameters 
    25507 --- 
    25508 Chain pairing | bb 
    25509 Alignment algorithm | Needleman-Wunsch 
    25510 Similarity matrix | BLOSUM-62 
    25511 SS fraction | 0.3 
    25512 Gap open (HH/SS/other) | 18/18/6 
    25513 Gap extend | 1 
    25514 SS matrix |  |  | H | S | O 
    25515 ---|---|---|--- 
    25516 H | 6 | -9 | -6 
    25517 S |  | 6 | -6 
    25518 O |  |  | 4 
    25519 Iteration cutoff | 2 
    25520  
    25521 Matchmaker 3j0c.pdb1, chain E (#1.57) with AF3 E2 1-352.pdb, chain B (#584),
    25522 sequence alignment score = 594.5 
    25523 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    25524 6.147) 
    25525  
    25526 
    25527 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    25528 
    25529 Chain information for AF3 E2 353-438.pdb #585 
    25530 --- 
    25531 Chain | Description 
    25532 B | No description available 
    25533  
    25534 
    25535 > matchmaker #585 to #1.57 & sel
    25536 
    25537 Parameters 
    25538 --- 
    25539 Chain pairing | bb 
    25540 Alignment algorithm | Needleman-Wunsch 
    25541 Similarity matrix | BLOSUM-62 
    25542 SS fraction | 0.3 
    25543 Gap open (HH/SS/other) | 18/18/6 
    25544 Gap extend | 1 
    25545 SS matrix |  |  | H | S | O 
    25546 ---|---|---|--- 
    25547 H | 6 | -9 | -6 
    25548 S |  | 6 | -6 
    25549 O |  |  | 4 
    25550 Iteration cutoff | 2 
    25551  
    25552 Matchmaker 3j0c.pdb1, chain E (#1.57) with AF3 E2 353-438.pdb, chain B (#585),
    25553 sequence alignment score = 340.2 
    25554 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    25555 8.673) 
    25556  
    25557 
    25558 > hide sel cartoons
    25559 
    25560 > select #1.57/F
    25561 
    25562 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    25563 
    25564 > show sel cartoons
    25565 
    25566 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    25567 
    25568 Chain information for AF3 CA.pdb #586 
    25569 --- 
    25570 Chain | Description 
    25571 A | No description available 
    25572  
    25573 
    25574 > matchmaker #586 to #1.57 & sel
    25575 
    25576 Parameters 
    25577 --- 
    25578 Chain pairing | bb 
    25579 Alignment algorithm | Needleman-Wunsch 
    25580 Similarity matrix | BLOSUM-62 
    25581 SS fraction | 0.3 
    25582 Gap open (HH/SS/other) | 18/18/6 
    25583 Gap extend | 1 
    25584 SS matrix |  |  | H | S | O 
    25585 ---|---|---|--- 
    25586 H | 6 | -9 | -6 
    25587 S |  | 6 | -6 
    25588 O |  |  | 4 
    25589 Iteration cutoff | 2 
    25590  
    25591 Matchmaker 3j0c.pdb1, chain F (#1.57) with AF3 CA.pdb, chain A (#586),
    25592 sequence alignment score = 335.3 
    25593 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    25594 2.550) 
    25595  
    25596 
    25597 > hide sel cartoons
    25598 
    25599 > color #582 dodgerblue
    25600 
    25601 > color #583 dodgerblue
    25602 
    25603 > color #584 #00b305ff
    25604 
    25605 > color #585 #00b305ff
    25606 
    25607 > color #586 #f15839ff
    25608 
    25609 > select #1.58/D
    25610 
    25611 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    25612 
    25613 > show sel cartoons
    25614 
    25615 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    25616 
    25617 Chain information for AF3 E1 1-421.pdb #587 
    25618 --- 
    25619 Chain | Description 
    25620 A | No description available 
    25621  
    25622 
    25623 > matchmaker #587 to #1.58 & sel
    25624 
    25625 Parameters 
    25626 --- 
    25627 Chain pairing | bb 
    25628 Alignment algorithm | Needleman-Wunsch 
    25629 Similarity matrix | BLOSUM-62 
    25630 SS fraction | 0.3 
    25631 Gap open (HH/SS/other) | 18/18/6 
    25632 Gap extend | 1 
    25633 SS matrix |  |  | H | S | O 
    25634 ---|---|---|--- 
    25635 H | 6 | -9 | -6 
    25636 S |  | 6 | -6 
    25637 O |  |  | 4 
    25638 Iteration cutoff | 2 
    25639  
    25640 Matchmaker 3j0c.pdb1, chain D (#1.58) with AF3 E1 1-421.pdb, chain A (#587),
    25641 sequence alignment score = 1060.7 
    25642 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    25643 3.032) 
    25644  
    25645 
    25646 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    25647 
    25648 Chain information for AF3 E1 422-461.pdb #588 
    25649 --- 
    25650 Chain | Description 
    25651 A | No description available 
    25652  
    25653 
    25654 > matchmaker #588 to #1.58 & sel
    25655 
    25656 Parameters 
    25657 --- 
    25658 Chain pairing | bb 
    25659 Alignment algorithm | Needleman-Wunsch 
    25660 Similarity matrix | BLOSUM-62 
    25661 SS fraction | 0.3 
    25662 Gap open (HH/SS/other) | 18/18/6 
    25663 Gap extend | 1 
    25664 SS matrix |  |  | H | S | O 
    25665 ---|---|---|--- 
    25666 H | 6 | -9 | -6 
    25667 S |  | 6 | -6 
    25668 O |  |  | 4 
    25669 Iteration cutoff | 2 
    25670  
    25671 Matchmaker 3j0c.pdb1, chain D (#1.58) with AF3 E1 422-461.pdb, chain A (#588),
    25672 sequence alignment score = 626.9 
    25673 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    25674 2.916) 
    25675  
    25676 
    25677 > hide sel atoms
    25678 
    25679 > hide sel cartoons
    25680 
    25681 > select #1.58/E
    25682 
    25683 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    25684 
    25685 > show sel cartoons
    25686 
    25687 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    25688 
    25689 Chain information for AF3 E2 1-352.pdb #589 
    25690 --- 
    25691 Chain | Description 
    25692 B | No description available 
    25693  
    25694 
    25695 > matchmaker #589 to #1.58 & sel
    25696 
    25697 Parameters 
    25698 --- 
    25699 Chain pairing | bb 
    25700 Alignment algorithm | Needleman-Wunsch 
    25701 Similarity matrix | BLOSUM-62 
    25702 SS fraction | 0.3 
    25703 Gap open (HH/SS/other) | 18/18/6 
    25704 Gap extend | 1 
    25705 SS matrix |  |  | H | S | O 
    25706 ---|---|---|--- 
    25707 H | 6 | -9 | -6 
    25708 S |  | 6 | -6 
    25709 O |  |  | 4 
    25710 Iteration cutoff | 2 
    25711  
    25712 Matchmaker 3j0c.pdb1, chain E (#1.58) with AF3 E2 1-352.pdb, chain B (#589),
    25713 sequence alignment score = 594.5 
    25714 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    25715 6.147) 
    25716  
    25717 
    25718 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    25719 
    25720 Chain information for AF3 E2 353-438.pdb #590 
    25721 --- 
    25722 Chain | Description 
    25723 B | No description available 
    25724  
    25725 
    25726 > matchmaker #590 to #1.58 & sel
    25727 
    25728 Parameters 
    25729 --- 
    25730 Chain pairing | bb 
    25731 Alignment algorithm | Needleman-Wunsch 
    25732 Similarity matrix | BLOSUM-62 
    25733 SS fraction | 0.3 
    25734 Gap open (HH/SS/other) | 18/18/6 
    25735 Gap extend | 1 
    25736 SS matrix |  |  | H | S | O 
    25737 ---|---|---|--- 
    25738 H | 6 | -9 | -6 
    25739 S |  | 6 | -6 
    25740 O |  |  | 4 
    25741 Iteration cutoff | 2 
    25742  
    25743 Matchmaker 3j0c.pdb1, chain E (#1.58) with AF3 E2 353-438.pdb, chain B (#590),
    25744 sequence alignment score = 340.2 
    25745 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    25746 8.673) 
    25747  
    25748 
    25749 > hide sel cartoons
    25750 
    25751 > select #1.58/F
    25752 
    25753 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    25754 
    25755 > show sel cartoons
    25756 
    25757 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    25758 
    25759 Chain information for AF3 CA.pdb #591 
    25760 --- 
    25761 Chain | Description 
    25762 A | No description available 
    25763  
    25764 
    25765 > matchmaker #591 to #1.58 & sel
    25766 
    25767 Parameters 
    25768 --- 
    25769 Chain pairing | bb 
    25770 Alignment algorithm | Needleman-Wunsch 
    25771 Similarity matrix | BLOSUM-62 
    25772 SS fraction | 0.3 
    25773 Gap open (HH/SS/other) | 18/18/6 
    25774 Gap extend | 1 
    25775 SS matrix |  |  | H | S | O 
    25776 ---|---|---|--- 
    25777 H | 6 | -9 | -6 
    25778 S |  | 6 | -6 
    25779 O |  |  | 4 
    25780 Iteration cutoff | 2 
    25781  
    25782 Matchmaker 3j0c.pdb1, chain F (#1.58) with AF3 CA.pdb, chain A (#591),
    25783 sequence alignment score = 335.3 
    25784 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    25785 2.550) 
    25786  
    25787 
    25788 > hide sel cartoons
    25789 
    25790 > color #587 dodgerblue
    25791 
    25792 > color #588 dodgerblue
    25793 
    25794 > color #589 #00b305ff
    25795 
    25796 > color #590 #00b305ff
    25797 
    25798 > color #591 #f15839ff
    25799 
    25800 > select #1.59/D
    25801 
    25802 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    25803 
    25804 > show sel cartoons
    25805 
    25806 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    25807 
    25808 Chain information for AF3 E1 1-421.pdb #592 
    25809 --- 
    25810 Chain | Description 
    25811 A | No description available 
    25812  
    25813 
    25814 > matchmaker #592 to #1.59 & sel
    25815 
    25816 Parameters 
    25817 --- 
    25818 Chain pairing | bb 
    25819 Alignment algorithm | Needleman-Wunsch 
    25820 Similarity matrix | BLOSUM-62 
    25821 SS fraction | 0.3 
    25822 Gap open (HH/SS/other) | 18/18/6 
    25823 Gap extend | 1 
    25824 SS matrix |  |  | H | S | O 
    25825 ---|---|---|--- 
    25826 H | 6 | -9 | -6 
    25827 S |  | 6 | -6 
    25828 O |  |  | 4 
    25829 Iteration cutoff | 2 
    25830  
    25831 Matchmaker 3j0c.pdb1, chain D (#1.59) with AF3 E1 1-421.pdb, chain A (#592),
    25832 sequence alignment score = 1060.7 
    25833 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    25834 3.032) 
    25835  
    25836 
    25837 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    25838 
    25839 Chain information for AF3 E1 422-461.pdb #593 
    25840 --- 
    25841 Chain | Description 
    25842 A | No description available 
    25843  
    25844 
    25845 > matchmaker #593 to #1.59 & sel
    25846 
    25847 Parameters 
    25848 --- 
    25849 Chain pairing | bb 
    25850 Alignment algorithm | Needleman-Wunsch 
    25851 Similarity matrix | BLOSUM-62 
    25852 SS fraction | 0.3 
    25853 Gap open (HH/SS/other) | 18/18/6 
    25854 Gap extend | 1 
    25855 SS matrix |  |  | H | S | O 
    25856 ---|---|---|--- 
    25857 H | 6 | -9 | -6 
    25858 S |  | 6 | -6 
    25859 O |  |  | 4 
    25860 Iteration cutoff | 2 
    25861  
    25862 Matchmaker 3j0c.pdb1, chain D (#1.59) with AF3 E1 422-461.pdb, chain A (#593),
    25863 sequence alignment score = 626.9 
    25864 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    25865 2.916) 
    25866  
    25867 
    25868 > hide sel cartoons
    25869 
    25870 > select #1.59/E
    25871 
    25872 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    25873 
    25874 > show sel cartoons
    25875 
    25876 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    25877 
    25878 Chain information for AF3 E2 1-352.pdb #594 
    25879 --- 
    25880 Chain | Description 
    25881 B | No description available 
    25882  
    25883 
    25884 > matchmaker #594 to #1.59 & sel
    25885 
    25886 Parameters 
    25887 --- 
    25888 Chain pairing | bb 
    25889 Alignment algorithm | Needleman-Wunsch 
    25890 Similarity matrix | BLOSUM-62 
    25891 SS fraction | 0.3 
    25892 Gap open (HH/SS/other) | 18/18/6 
    25893 Gap extend | 1 
    25894 SS matrix |  |  | H | S | O 
    25895 ---|---|---|--- 
    25896 H | 6 | -9 | -6 
    25897 S |  | 6 | -6 
    25898 O |  |  | 4 
    25899 Iteration cutoff | 2 
    25900  
    25901 Matchmaker 3j0c.pdb1, chain E (#1.59) with AF3 E2 1-352.pdb, chain B (#594),
    25902 sequence alignment score = 594.5 
    25903 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    25904 6.147) 
    25905  
    25906 
    25907 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    25908 
    25909 Chain information for AF3 E2 353-438.pdb #595 
    25910 --- 
    25911 Chain | Description 
    25912 B | No description available 
    25913  
    25914 
    25915 > matchmaker #595 to #1.59 & sel
    25916 
    25917 Parameters 
    25918 --- 
    25919 Chain pairing | bb 
    25920 Alignment algorithm | Needleman-Wunsch 
    25921 Similarity matrix | BLOSUM-62 
    25922 SS fraction | 0.3 
    25923 Gap open (HH/SS/other) | 18/18/6 
    25924 Gap extend | 1 
    25925 SS matrix |  |  | H | S | O 
    25926 ---|---|---|--- 
    25927 H | 6 | -9 | -6 
    25928 S |  | 6 | -6 
    25929 O |  |  | 4 
    25930 Iteration cutoff | 2 
    25931  
    25932 Matchmaker 3j0c.pdb1, chain E (#1.59) with AF3 E2 353-438.pdb, chain B (#595),
    25933 sequence alignment score = 340.2 
    25934 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    25935 8.673) 
    25936  
    25937 
    25938 > hide sel cartoons
    25939 
    25940 > select #1.59/F
    25941 
    25942 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    25943 
    25944 > show sel cartoons
    25945 
    25946 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    25947 
    25948 Chain information for AF3 CA.pdb #596 
    25949 --- 
    25950 Chain | Description 
    25951 A | No description available 
    25952  
    25953 
    25954 > matchmaker #596 to #1.59 & sel
    25955 
    25956 Parameters 
    25957 --- 
    25958 Chain pairing | bb 
    25959 Alignment algorithm | Needleman-Wunsch 
    25960 Similarity matrix | BLOSUM-62 
    25961 SS fraction | 0.3 
    25962 Gap open (HH/SS/other) | 18/18/6 
    25963 Gap extend | 1 
    25964 SS matrix |  |  | H | S | O 
    25965 ---|---|---|--- 
    25966 H | 6 | -9 | -6 
    25967 S |  | 6 | -6 
    25968 O |  |  | 4 
    25969 Iteration cutoff | 2 
    25970  
    25971 Matchmaker 3j0c.pdb1, chain F (#1.59) with AF3 CA.pdb, chain A (#596),
    25972 sequence alignment score = 335.3 
    25973 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    25974 2.550) 
    25975  
    25976 
    25977 > hide sel atoms
    25978 
    25979 > hide sel cartoons
    25980 
    25981 > color #592 dodgerblue
    25982 
    25983 > color #593 dodgerblue
    25984 
    25985 > color #594 #00b305ff
    25986 
    25987 > color #595 #00b305ff
    25988 
    25989 > color #596 #f15839ff
    25990 
    25991 > select #1.60/D
    25992 
    25993 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    25994 
    25995 > show sel cartoons
    25996 
    25997 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    25998 
    25999 Chain information for AF3 E1 1-421.pdb #597 
    26000 --- 
    26001 Chain | Description 
    26002 A | No description available 
    26003  
    26004 
    26005 > matchmaker #597 to #1.60 & sel
    26006 
    26007 Parameters 
    26008 --- 
    26009 Chain pairing | bb 
    26010 Alignment algorithm | Needleman-Wunsch 
    26011 Similarity matrix | BLOSUM-62 
    26012 SS fraction | 0.3 
    26013 Gap open (HH/SS/other) | 18/18/6 
    26014 Gap extend | 1 
    26015 SS matrix |  |  | H | S | O 
    26016 ---|---|---|--- 
    26017 H | 6 | -9 | -6 
    26018 S |  | 6 | -6 
    26019 O |  |  | 4 
    26020 Iteration cutoff | 2 
    26021  
    26022 Matchmaker 3j0c.pdb1, chain D (#1.60) with AF3 E1 1-421.pdb, chain A (#597),
    26023 sequence alignment score = 1060.7 
    26024 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    26025 3.032) 
    26026  
    26027 
    26028 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    26029 
    26030 Chain information for AF3 E1 422-461.pdb #598 
    26031 --- 
    26032 Chain | Description 
    26033 A | No description available 
    26034  
    26035 
    26036 > matchmaker #598 to #1.60 & sel
    26037 
    26038 Parameters 
    26039 --- 
    26040 Chain pairing | bb 
    26041 Alignment algorithm | Needleman-Wunsch 
    26042 Similarity matrix | BLOSUM-62 
    26043 SS fraction | 0.3 
    26044 Gap open (HH/SS/other) | 18/18/6 
    26045 Gap extend | 1 
    26046 SS matrix |  |  | H | S | O 
    26047 ---|---|---|--- 
    26048 H | 6 | -9 | -6 
    26049 S |  | 6 | -6 
    26050 O |  |  | 4 
    26051 Iteration cutoff | 2 
    26052  
    26053 Matchmaker 3j0c.pdb1, chain D (#1.60) with AF3 E1 422-461.pdb, chain A (#598),
    26054 sequence alignment score = 626.9 
    26055 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    26056 2.916) 
    26057  
    26058 
    26059 > hide sel cartoons
    26060 
    26061 > select #1.60/E
    26062 
    26063 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    26064 
    26065 > show sel cartoons
    26066 
    26067 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    26068 
    26069 Chain information for AF3 E2 1-352.pdb #599 
    26070 --- 
    26071 Chain | Description 
    26072 B | No description available 
    26073  
    26074 
    26075 > matchmaker #599 to #1.60 & sel
    26076 
    26077 Parameters 
    26078 --- 
    26079 Chain pairing | bb 
    26080 Alignment algorithm | Needleman-Wunsch 
    26081 Similarity matrix | BLOSUM-62 
    26082 SS fraction | 0.3 
    26083 Gap open (HH/SS/other) | 18/18/6 
    26084 Gap extend | 1 
    26085 SS matrix |  |  | H | S | O 
    26086 ---|---|---|--- 
    26087 H | 6 | -9 | -6 
    26088 S |  | 6 | -6 
    26089 O |  |  | 4 
    26090 Iteration cutoff | 2 
    26091  
    26092 Matchmaker 3j0c.pdb1, chain E (#1.60) with AF3 E2 1-352.pdb, chain B (#599),
    26093 sequence alignment score = 594.5 
    26094 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    26095 6.147) 
    26096  
    26097 
    26098 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    26099 
    26100 Chain information for AF3 E2 353-438.pdb #600 
    26101 --- 
    26102 Chain | Description 
    26103 B | No description available 
    26104  
    26105 
    26106 > matchmaker #600 to #1.60 & sel
    26107 
    26108 Parameters 
    26109 --- 
    26110 Chain pairing | bb 
    26111 Alignment algorithm | Needleman-Wunsch 
    26112 Similarity matrix | BLOSUM-62 
    26113 SS fraction | 0.3 
    26114 Gap open (HH/SS/other) | 18/18/6 
    26115 Gap extend | 1 
    26116 SS matrix |  |  | H | S | O 
    26117 ---|---|---|--- 
    26118 H | 6 | -9 | -6 
    26119 S |  | 6 | -6 
    26120 O |  |  | 4 
    26121 Iteration cutoff | 2 
    26122  
    26123 Matchmaker 3j0c.pdb1, chain E (#1.60) with AF3 E2 353-438.pdb, chain B (#600),
    26124 sequence alignment score = 340.2 
    26125 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    26126 8.673) 
    26127  
    26128 
    26129 > hide sel cartoons
    26130 
    26131 > select #1.60/F
    26132 
    26133 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    26134 
    26135 > show sel cartoons
    26136 
    26137 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    26138 
    26139 Chain information for AF3 CA.pdb #601 
    26140 --- 
    26141 Chain | Description 
    26142 A | No description available 
    26143  
    26144 
    26145 > matchmaker #601 to #1.60 & sel
    26146 
    26147 Parameters 
    26148 --- 
    26149 Chain pairing | bb 
    26150 Alignment algorithm | Needleman-Wunsch 
    26151 Similarity matrix | BLOSUM-62 
    26152 SS fraction | 0.3 
    26153 Gap open (HH/SS/other) | 18/18/6 
    26154 Gap extend | 1 
    26155 SS matrix |  |  | H | S | O 
    26156 ---|---|---|--- 
    26157 H | 6 | -9 | -6 
    26158 S |  | 6 | -6 
    26159 O |  |  | 4 
    26160 Iteration cutoff | 2 
    26161  
    26162 Matchmaker 3j0c.pdb1, chain F (#1.60) with AF3 CA.pdb, chain A (#601),
    26163 sequence alignment score = 335.3 
    26164 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    26165 2.550) 
    26166  
    26167 
    26168 > hide sel cartoons
    26169 
    26170 > color #597 dodgerblue
    26171 
    26172 > color #598 dodgerblue
    26173 
    26174 > color #599 #00b305ff
    26175 
    26176 > color #600 #00b305ff
    26177 
    26178 > color #601 #f15839ff
    26179 
    26180 > view sel
    26181 
    26182 No displayed objects specified. 
    26183 
    26184 > view
    26185 
    26186 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    26187 
    26188 > show #2-601 models
    26189 
    26190 > view
    26191 
    26192 > hide sel cartoons
    26193 
    26194 > save /Users/Jean/Desktop/image1.png supersample 3
    26195 
    26196 > hide #300 models
    26197 
    26198 > show #300 models
    26199 
    26200 > hide #299 models
    26201 
    26202 > show #299 models
    26203 
    26204 > hide #299 models
    26205 
    26206 > show #299 models
    26207 
    26208 > select
    26209 
    26210 2871120 atoms, 2944244 bonds, 373800 residues, 661 models selected 
    26211 
    26212 > show sel cartoons
    26213 
    26214 > hide #!1 models
    26215 
    26216 > select subtract #1
    26217 
    26218 962880 atoms, 985560 bonds, 127320 residues, 600 models selected 
    26219 
    26220 > select clear
    26221 
    26222 > view
    26223 
    26224 > hide #2-601 cartoons
    26225 
    26226 > show #2-601 atoms
    26227 
    26228 > style #2-601 sphere
    26229 
    26230 Changed 962880 atom styles 
    26231 
    26232 > save /Users/Jean/Desktop/image1.png supersample 3
    26233 
    26234 > view
    26235 
    26236 > color #514 #00b305ff
    26237 
    26238 > view
    26239 
    26240 > hide #2-601 atoms
    26241 
    26242 > show #2-601 cartoons
    26243 
    26244 > save /Users/Jean/Desktop/image2.png supersample 3
    26245 
    26246 > hide #2-601 cartoons
    26247 
    26248 > select #1.1/G
    26249 
    26250 3370 atoms, 3467 bonds, 442 residues, 1 model selected 
    26251 
    26252 > show #2-601 cartoons
    26253 
    26254 > select clear
    26255 
    26256 > hide #2-601 cartoons
    26257 
    26258 > select clear
    26259 
    26260 > select #1.1/G
    26261 
    26262 3370 atoms, 3467 bonds, 442 residues, 1 model selected 
    26263 
    26264 > show #2-601 cartoons
    26265 
    26266 > hide #2-601 models
    26267 
    26268 > select #1.1/G
    26269 
    26270 3370 atoms, 3467 bonds, 442 residues, 1 model selected 
    26271 
    26272 > view sel
    26273 
    26274 No displayed objects specified. 
    26275 
    26276 > show #!1 models
    26277 
    26278 > select ~sel & ##selected
    26279 
    26280 28434 atoms, 29221 bonds, 3666 residues, 1 model selected 
    26281 
    26282 > select ~sel
    26283 
    26284 2842686 atoms, 2915023 bonds, 370134 residues, 661 models selected 
    26285 
    26286 > hide sel & #1.1-60 cartoons
    26287 
    26288 > select #1.1/G
    26289 
    26290 3370 atoms, 3467 bonds, 442 residues, 1 model selected 
    26291 
    26292 > show sel cartoons
    26293 
    26294 > ui mousemode right select
    26295 
    26296 > select clear
    26297 
    26298 > select #1.1/B:287
    26299 
    26300 8 atoms, 7 bonds, 1 residue, 1 model selected 
    26301 
    26302 > select #1.1/G
    26303 
    26304 3370 atoms, 3467 bonds, 442 residues, 1 model selected 
    26305 
    26306 > hide #1.1 models
    26307 
    26308 > show #1.1 models
    26309 
    26310 > hide #1.1 models
    26311 
    26312 > show #1.1 models
    26313 
    26314 > select add #1.1
    26315 
    26316 31804 atoms, 32688 bonds, 4108 residues, 1 model selected 
    26317 
    26318 > select subtract #1.1
    26319 
    26320 Nothing selected 
    26321 
    26322 > select #1.1/G
    26323 
    26324 3370 atoms, 3467 bonds, 442 residues, 1 model selected 
    26325 
    26326 > select ~sel & ##selected
    26327 
    26328 28434 atoms, 29221 bonds, 3666 residues, 1 model selected 
    26329 
    26330 > hide sel cartoons
    26331 
    26332 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    26333 
    26334 Chain information for AF3 E1 1-421.pdb #602 
    26335 --- 
    26336 Chain | Description 
    26337 A | No description available 
    26338  
    26339 
    26340 > view sel
    26341 
    26342 No displayed objects specified. 
    26343 
    26344 > view
    26345 
    26346 > matchmaker #602 to #1.1 & sel
    26347 
    26348 Parameters 
    26349 --- 
    26350 Chain pairing | bb 
    26351 Alignment algorithm | Needleman-Wunsch 
    26352 Similarity matrix | BLOSUM-62 
    26353 SS fraction | 0.3 
    26354 Gap open (HH/SS/other) | 18/18/6 
    26355 Gap extend | 1 
    26356 SS matrix |  |  | H | S | O 
    26357 ---|---|---|--- 
    26358 H | 6 | -9 | -6 
    26359 S |  | 6 | -6 
    26360 O |  |  | 4 
    26361 Iteration cutoff | 2 
    26362  
    26363 Matchmaker 3j0c.pdb1, chain A (#1.1) with AF3 E1 1-421.pdb, chain A (#602),
    26364 sequence alignment score = 1060.7 
    26365 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    26366 3.020) 
    26367  
    26368 
    26369 > select #1.1/G
    26370 
    26371 3370 atoms, 3467 bonds, 442 residues, 1 model selected 
    26372 
    26373 > matchmaker #602 to #1.1 & sel
    26374 
    26375 Parameters 
    26376 --- 
    26377 Chain pairing | bb 
    26378 Alignment algorithm | Needleman-Wunsch 
    26379 Similarity matrix | BLOSUM-62 
    26380 SS fraction | 0.3 
    26381 Gap open (HH/SS/other) | 18/18/6 
    26382 Gap extend | 1 
    26383 SS matrix |  |  | H | S | O 
    26384 ---|---|---|--- 
    26385 H | 6 | -9 | -6 
    26386 S |  | 6 | -6 
    26387 O |  |  | 4 
    26388 Iteration cutoff | 2 
    26389  
    26390 Matchmaker 3j0c.pdb1, chain G (#1.1) with AF3 E1 1-421.pdb, chain A (#602),
    26391 sequence alignment score = 1060.7 
    26392 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    26393 2.985) 
    26394  
    26395 
    26396 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    26397 
    26398 Chain information for AF3 E1 422-461.pdb #603 
    26399 --- 
    26400 Chain | Description 
    26401 A | No description available 
    26402  
    26403 
    26404 > matchmaker #603 to #1.1 & sel
    26405 
    26406 Parameters 
    26407 --- 
    26408 Chain pairing | bb 
    26409 Alignment algorithm | Needleman-Wunsch 
    26410 Similarity matrix | BLOSUM-62 
    26411 SS fraction | 0.3 
    26412 Gap open (HH/SS/other) | 18/18/6 
    26413 Gap extend | 1 
    26414 SS matrix |  |  | H | S | O 
    26415 ---|---|---|--- 
    26416 H | 6 | -9 | -6 
    26417 S |  | 6 | -6 
    26418 O |  |  | 4 
    26419 Iteration cutoff | 2 
    26420  
    26421 Matchmaker 3j0c.pdb1, chain G (#1.1) with AF3 E1 422-461.pdb, chain A (#603),
    26422 sequence alignment score = 626.9 
    26423 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    26424 2.997) 
    26425  
    26426 
    26427 > hide sel cartoons
    26428 
    26429 > select #1.1/H
    26430 
    26431 3304 atoms, 3400 bonds, 423 residues, 1 model selected 
    26432 
    26433 > show sel cartoons
    26434 
    26435 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    26436 
    26437 Chain information for AF3 E2 1-352.pdb #604 
    26438 --- 
    26439 Chain | Description 
    26440 B | No description available 
    26441  
    26442 
    26443 > matchmaker #603 to #1.1 & sel
    26444 
    26445 Parameters 
    26446 --- 
    26447 Chain pairing | bb 
    26448 Alignment algorithm | Needleman-Wunsch 
    26449 Similarity matrix | BLOSUM-62 
    26450 SS fraction | 0.3 
    26451 Gap open (HH/SS/other) | 18/18/6 
    26452 Gap extend | 1 
    26453 SS matrix |  |  | H | S | O 
    26454 ---|---|---|--- 
    26455 H | 6 | -9 | -6 
    26456 S |  | 6 | -6 
    26457 O |  |  | 4 
    26458 Iteration cutoff | 2 
    26459  
    26460 Matchmaker 3j0c.pdb1, chain H (#1.1) with AF3 E1 422-461.pdb, chain A (#603),
    26461 sequence alignment score = 9.2 
    26462 RMSD between 6 pruned atom pairs is 0.871 angstroms; (across all 11 pairs:
    26463 3.614) 
    26464  
    26465 
    26466 > select #1.1/G
    26467 
    26468 3370 atoms, 3467 bonds, 442 residues, 1 model selected 
    26469 
    26470 > show sel cartoons
    26471 
    26472 > matchmaker #603 to #1.1 & sel
    26473 
    26474 Parameters 
    26475 --- 
    26476 Chain pairing | bb 
    26477 Alignment algorithm | Needleman-Wunsch 
    26478 Similarity matrix | BLOSUM-62 
    26479 SS fraction | 0.3 
    26480 Gap open (HH/SS/other) | 18/18/6 
    26481 Gap extend | 1 
    26482 SS matrix |  |  | H | S | O 
    26483 ---|---|---|--- 
    26484 H | 6 | -9 | -6 
    26485 S |  | 6 | -6 
    26486 O |  |  | 4 
    26487 Iteration cutoff | 2 
    26488  
    26489 Matchmaker 3j0c.pdb1, chain G (#1.1) with AF3 E1 422-461.pdb, chain A (#603),
    26490 sequence alignment score = 626.9 
    26491 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    26492 2.997) 
    26493  
    26494 
    26495 > matchmaker #604 to #1.2 & sel
    26496 
    26497 No 'to' model specified 
    26498 
    26499 > matchmaker #604 to #1.1 & sel
    26500 
    26501 Parameters 
    26502 --- 
    26503 Chain pairing | bb 
    26504 Alignment algorithm | Needleman-Wunsch 
    26505 Similarity matrix | BLOSUM-62 
    26506 SS fraction | 0.3 
    26507 Gap open (HH/SS/other) | 18/18/6 
    26508 Gap extend | 1 
    26509 SS matrix |  |  | H | S | O 
    26510 ---|---|---|--- 
    26511 H | 6 | -9 | -6 
    26512 S |  | 6 | -6 
    26513 O |  |  | 4 
    26514 Iteration cutoff | 2 
    26515  
    26516 Matchmaker 3j0c.pdb1, chain G (#1.1) with AF3 E2 1-352.pdb, chain B (#604),
    26517 sequence alignment score = 71.8 
    26518 RMSD between 4 pruned atom pairs is 1.398 angstroms; (across all 265 pairs:
    26519 48.114) 
    26520  
    26521 
    26522 > select #1.1/H
    26523 
    26524 3304 atoms, 3400 bonds, 423 residues, 1 model selected 
    26525 
    26526 > matchmaker #604 to #1.1 & sel
    26527 
    26528 Parameters 
    26529 --- 
    26530 Chain pairing | bb 
    26531 Alignment algorithm | Needleman-Wunsch 
    26532 Similarity matrix | BLOSUM-62 
    26533 SS fraction | 0.3 
    26534 Gap open (HH/SS/other) | 18/18/6 
    26535 Gap extend | 1 
    26536 SS matrix |  |  | H | S | O 
    26537 ---|---|---|--- 
    26538 H | 6 | -9 | -6 
    26539 S |  | 6 | -6 
    26540 O |  |  | 4 
    26541 Iteration cutoff | 2 
    26542  
    26543 Matchmaker 3j0c.pdb1, chain H (#1.1) with AF3 E2 1-352.pdb, chain B (#604),
    26544 sequence alignment score = 590.9 
    26545 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    26546 6.107) 
    26547  
    26548 
    26549 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    26550 
    26551 Chain information for AF3 E2 353-438.pdb #605 
    26552 --- 
    26553 Chain | Description 
    26554 B | No description available 
    26555  
    26556 
    26557 > matchmaker #605 to #1.1 & sel
    26558 
    26559 Parameters 
    26560 --- 
    26561 Chain pairing | bb 
    26562 Alignment algorithm | Needleman-Wunsch 
    26563 Similarity matrix | BLOSUM-62 
    26564 SS fraction | 0.3 
    26565 Gap open (HH/SS/other) | 18/18/6 
    26566 Gap extend | 1 
    26567 SS matrix |  |  | H | S | O 
    26568 ---|---|---|--- 
    26569 H | 6 | -9 | -6 
    26570 S |  | 6 | -6 
    26571 O |  |  | 4 
    26572 Iteration cutoff | 2 
    26573  
    26574 Matchmaker 3j0c.pdb1, chain H (#1.1) with AF3 E2 353-438.pdb, chain B (#605),
    26575 sequence alignment score = 329.4 
    26576 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    26577 8.150) 
    26578  
    26579 
    26580 > select #1.1/H
    26581 
    26582 3304 atoms, 3400 bonds, 423 residues, 1 model selected 
    26583 
    26584 > show sel cartoons
    26585 
    26586 [Repeated 1 time(s)]
    26587 
    26588 > select #1.1/H
    26589 
    26590 3304 atoms, 3400 bonds, 423 residues, 1 model selected 
    26591 
    26592 > select #1.1/H
    26593 
    26594 3304 atoms, 3400 bonds, 423 residues, 1 model selected 
    26595 
    26596 > show sel cartoons
    26597 
    26598 > show sel atoms
    26599 
    26600 > hide sel cartoons
    26601 
    26602 > hide sel atoms
    26603 
    26604 > select #1.1/G
    26605 
    26606 3370 atoms, 3467 bonds, 442 residues, 1 model selected 
    26607 
    26608 > hide sel cartoons
    26609 
    26610 > select #1.1/I
    26611 
    26612 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    26613 
    26614 > show sel cartoons
    26615 
    26616 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    26617 
    26618 Chain information for AF3 CA.pdb #606 
    26619 --- 
    26620 Chain | Description 
    26621 A | No description available 
    26622  
    26623 
    26624 > matchmaker #606 to #1.1 & sel
    26625 
    26626 Parameters 
    26627 --- 
    26628 Chain pairing | bb 
    26629 Alignment algorithm | Needleman-Wunsch 
    26630 Similarity matrix | BLOSUM-62 
    26631 SS fraction | 0.3 
    26632 Gap open (HH/SS/other) | 18/18/6 
    26633 Gap extend | 1 
    26634 SS matrix |  |  | H | S | O 
    26635 ---|---|---|--- 
    26636 H | 6 | -9 | -6 
    26637 S |  | 6 | -6 
    26638 O |  |  | 4 
    26639 Iteration cutoff | 2 
    26640  
    26641 Matchmaker 3j0c.pdb1, chain I (#1.1) with AF3 CA.pdb, chain A (#606), sequence
    26642 alignment score = 306.5 
    26643 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    26644 2.689) 
    26645  
    26646 
    26647 > hide sel cartoons
    26648 
    26649 > color #602 dodgerblue
    26650 
    26651 > color #603 dodgerblue
    26652 
    26653 > color #604 #00b305ff
    26654 
    26655 > color #605 #00b305ff
    26656 
    26657 > color #606 #f15839ff
    26658 
    26659 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    26660 
    26661 ——— End of log from Tue Jul 16 18:02:55 2024 ———
    26662 
    26663 opened ChimeraX session 
    26664 
    26665 > ui tool show Matchmaker
    26666 
    26667 The cached device pixel ratio value was stale on window expose. Please file a
    26668 QTBUG which explains how to reproduce. 
    26669 
    26670 > select #1.2/G
    26671 
    26672 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    26673 
    26674 > show sel cartoons
    26675 
    26676 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    26677 
    26678 Chain information for AF3 E1 1-421.pdb #607 
    26679 --- 
    26680 Chain | Description 
    26681 A | No description available 
    26682  
    26683 
    26684 > matchmaker #607 to #1.2 & sel
    26685 
    26686 Parameters 
    26687 --- 
    26688 Chain pairing | bb 
    26689 Alignment algorithm | Needleman-Wunsch 
    26690 Similarity matrix | BLOSUM-62 
    26691 SS fraction | 0.3 
    26692 Gap open (HH/SS/other) | 18/18/6 
    26693 Gap extend | 1 
    26694 SS matrix |  |  | H | S | O 
    26695 ---|---|---|--- 
    26696 H | 6 | -9 | -6 
    26697 S |  | 6 | -6 
    26698 O |  |  | 4 
    26699 Iteration cutoff | 2 
    26700  
    26701 Matchmaker 3j0c.pdb1, chain G (#1.2) with AF3 E1 1-421.pdb, chain A (#607),
    26702 sequence alignment score = 1060.7 
    26703 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    26704 2.985) 
    26705  
    26706 
    26707 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    26708 
    26709 Chain information for AF3 E1 422-461.pdb #608 
    26710 --- 
    26711 Chain | Description 
    26712 A | No description available 
    26713  
    26714 
    26715 > matchmaker #608 to #1.2 & sel
    26716 
    26717 Parameters 
    26718 --- 
    26719 Chain pairing | bb 
    26720 Alignment algorithm | Needleman-Wunsch 
    26721 Similarity matrix | BLOSUM-62 
    26722 SS fraction | 0.3 
    26723 Gap open (HH/SS/other) | 18/18/6 
    26724 Gap extend | 1 
    26725 SS matrix |  |  | H | S | O 
    26726 ---|---|---|--- 
    26727 H | 6 | -9 | -6 
    26728 S |  | 6 | -6 
    26729 O |  |  | 4 
    26730 Iteration cutoff | 2 
    26731  
    26732 Matchmaker 3j0c.pdb1, chain G (#1.2) with AF3 E1 422-461.pdb, chain A (#608),
    26733 sequence alignment score = 626.9 
    26734 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    26735 2.997) 
    26736  
    26737 
    26738 > select #1.2/H
    26739 
    26740 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    26741 
    26742 > show sel cartoons
    26743 
    26744 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    26745 
    26746 Chain information for AF3 E2 1-352.pdb #609 
    26747 --- 
    26748 Chain | Description 
    26749 B | No description available 
    26750  
    26751 
    26752 > matchmaker #609 to #1.2 & sel
    26753 
    26754 Parameters 
    26755 --- 
    26756 Chain pairing | bb 
    26757 Alignment algorithm | Needleman-Wunsch 
    26758 Similarity matrix | BLOSUM-62 
    26759 SS fraction | 0.3 
    26760 Gap open (HH/SS/other) | 18/18/6 
    26761 Gap extend | 1 
    26762 SS matrix |  |  | H | S | O 
    26763 ---|---|---|--- 
    26764 H | 6 | -9 | -6 
    26765 S |  | 6 | -6 
    26766 O |  |  | 4 
    26767 Iteration cutoff | 2 
    26768  
    26769 Matchmaker 3j0c.pdb1, chain H (#1.2) with AF3 E2 1-352.pdb, chain B (#609),
    26770 sequence alignment score = 590.9 
    26771 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    26772 6.107) 
    26773  
    26774 
    26775 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    26776 
    26777 Chain information for AF3 E2 353-438.pdb #610 
    26778 --- 
    26779 Chain | Description 
    26780 B | No description available 
    26781  
    26782 
    26783 > matchmaker #610 to #1.2 & sel
    26784 
    26785 Parameters 
    26786 --- 
    26787 Chain pairing | bb 
    26788 Alignment algorithm | Needleman-Wunsch 
    26789 Similarity matrix | BLOSUM-62 
    26790 SS fraction | 0.3 
    26791 Gap open (HH/SS/other) | 18/18/6 
    26792 Gap extend | 1 
    26793 SS matrix |  |  | H | S | O 
    26794 ---|---|---|--- 
    26795 H | 6 | -9 | -6 
    26796 S |  | 6 | -6 
    26797 O |  |  | 4 
    26798 Iteration cutoff | 2 
    26799  
    26800 Matchmaker 3j0c.pdb1, chain H (#1.2) with AF3 E2 353-438.pdb, chain B (#610),
    26801 sequence alignment score = 329.4 
    26802 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    26803 8.150) 
    26804  
    26805 
    26806 > hide sel cartoons
    26807 
    26808 > select #1.2/I
    26809 
    26810 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    26811 
    26812 > show sel cartoons
    26813 
    26814 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    26815 
    26816 Chain information for AF3 CA.pdb #611 
    26817 --- 
    26818 Chain | Description 
    26819 A | No description available 
    26820  
    26821 
    26822 > matchmaker #611 to #1.2 & sel
    26823 
    26824 Parameters 
    26825 --- 
    26826 Chain pairing | bb 
    26827 Alignment algorithm | Needleman-Wunsch 
    26828 Similarity matrix | BLOSUM-62 
    26829 SS fraction | 0.3 
    26830 Gap open (HH/SS/other) | 18/18/6 
    26831 Gap extend | 1 
    26832 SS matrix |  |  | H | S | O 
    26833 ---|---|---|--- 
    26834 H | 6 | -9 | -6 
    26835 S |  | 6 | -6 
    26836 O |  |  | 4 
    26837 Iteration cutoff | 2 
    26838  
    26839 Matchmaker 3j0c.pdb1, chain I (#1.2) with AF3 CA.pdb, chain A (#611), sequence
    26840 alignment score = 306.5 
    26841 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    26842 2.689) 
    26843  
    26844 
    26845 > hide sel cartoons
    26846 
    26847 > color #607 dodgerblue
    26848 
    26849 > color #608 dodgerblue
    26850 
    26851 > color #609 #00b305ff
    26852 
    26853 > color #610 #00b305ff
    26854 
    26855 > color #611 #f15839ff
    26856 
    26857 > select #1.2/G
    26858 
    26859 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    26860 
    26861 > hide sel cartoons
    26862 
    26863 > select #1.3/G
    26864 
    26865 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    26866 
    26867 > show sel cartoons
    26868 
    26869 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    26870 
    26871 Chain information for AF3 E1 1-421.pdb #612 
    26872 --- 
    26873 Chain | Description 
    26874 A | No description available 
    26875  
    26876 
    26877 > matchmaker #612 to #1.2 & sel
    26878 
    26879 No 'to' model specified 
    26880 
    26881 > matchmaker #612 to #1.3 & sel
    26882 
    26883 Parameters 
    26884 --- 
    26885 Chain pairing | bb 
    26886 Alignment algorithm | Needleman-Wunsch 
    26887 Similarity matrix | BLOSUM-62 
    26888 SS fraction | 0.3 
    26889 Gap open (HH/SS/other) | 18/18/6 
    26890 Gap extend | 1 
    26891 SS matrix |  |  | H | S | O 
    26892 ---|---|---|--- 
    26893 H | 6 | -9 | -6 
    26894 S |  | 6 | -6 
    26895 O |  |  | 4 
    26896 Iteration cutoff | 2 
    26897  
    26898 Matchmaker 3j0c.pdb1, chain G (#1.3) with AF3 E1 1-421.pdb, chain A (#612),
    26899 sequence alignment score = 1060.7 
    26900 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    26901 2.985) 
    26902  
    26903 
    26904 > matchmaker #612 to #1.3 & sel
    26905 
    26906 Parameters 
    26907 --- 
    26908 Chain pairing | bb 
    26909 Alignment algorithm | Needleman-Wunsch 
    26910 Similarity matrix | BLOSUM-62 
    26911 SS fraction | 0.3 
    26912 Gap open (HH/SS/other) | 18/18/6 
    26913 Gap extend | 1 
    26914 SS matrix |  |  | H | S | O 
    26915 ---|---|---|--- 
    26916 H | 6 | -9 | -6 
    26917 S |  | 6 | -6 
    26918 O |  |  | 4 
    26919 Iteration cutoff | 2 
    26920  
    26921 Matchmaker 3j0c.pdb1, chain G (#1.3) with AF3 E1 1-421.pdb, chain A (#612),
    26922 sequence alignment score = 1060.7 
    26923 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    26924 2.985) 
    26925  
    26926 
    26927 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    26928 
    26929 Chain information for AF3 E1 422-461.pdb #613 
    26930 --- 
    26931 Chain | Description 
    26932 A | No description available 
    26933  
    26934 
    26935 > matchmaker #613 to #1.3 & sel
    26936 
    26937 Parameters 
    26938 --- 
    26939 Chain pairing | bb 
    26940 Alignment algorithm | Needleman-Wunsch 
    26941 Similarity matrix | BLOSUM-62 
    26942 SS fraction | 0.3 
    26943 Gap open (HH/SS/other) | 18/18/6 
    26944 Gap extend | 1 
    26945 SS matrix |  |  | H | S | O 
    26946 ---|---|---|--- 
    26947 H | 6 | -9 | -6 
    26948 S |  | 6 | -6 
    26949 O |  |  | 4 
    26950 Iteration cutoff | 2 
    26951  
    26952 Matchmaker 3j0c.pdb1, chain G (#1.3) with AF3 E1 422-461.pdb, chain A (#613),
    26953 sequence alignment score = 626.9 
    26954 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    26955 2.997) 
    26956  
    26957 
    26958 > hide sel cartoons
    26959 
    26960 > select #1.3/H
    26961 
    26962 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    26963 
    26964 > show sel cartoons
    26965 
    26966 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    26967 
    26968 Chain information for AF3 E2 1-352.pdb #614 
    26969 --- 
    26970 Chain | Description 
    26971 B | No description available 
    26972  
    26973 
    26974 > matchmaker #614 to #1.3 & sel
    26975 
    26976 Parameters 
    26977 --- 
    26978 Chain pairing | bb 
    26979 Alignment algorithm | Needleman-Wunsch 
    26980 Similarity matrix | BLOSUM-62 
    26981 SS fraction | 0.3 
    26982 Gap open (HH/SS/other) | 18/18/6 
    26983 Gap extend | 1 
    26984 SS matrix |  |  | H | S | O 
    26985 ---|---|---|--- 
    26986 H | 6 | -9 | -6 
    26987 S |  | 6 | -6 
    26988 O |  |  | 4 
    26989 Iteration cutoff | 2 
    26990  
    26991 Matchmaker 3j0c.pdb1, chain H (#1.3) with AF3 E2 1-352.pdb, chain B (#614),
    26992 sequence alignment score = 590.9 
    26993 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    26994 6.107) 
    26995  
    26996 
    26997 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    26998 
    26999 Chain information for AF3 E2 353-438.pdb #615 
    27000 --- 
    27001 Chain | Description 
    27002 B | No description available 
    27003  
    27004 
    27005 > matchmaker #615 to #1.3 & sel
    27006 
    27007 Parameters 
    27008 --- 
    27009 Chain pairing | bb 
    27010 Alignment algorithm | Needleman-Wunsch 
    27011 Similarity matrix | BLOSUM-62 
    27012 SS fraction | 0.3 
    27013 Gap open (HH/SS/other) | 18/18/6 
    27014 Gap extend | 1 
    27015 SS matrix |  |  | H | S | O 
    27016 ---|---|---|--- 
    27017 H | 6 | -9 | -6 
    27018 S |  | 6 | -6 
    27019 O |  |  | 4 
    27020 Iteration cutoff | 2 
    27021  
    27022 Matchmaker 3j0c.pdb1, chain H (#1.3) with AF3 E2 353-438.pdb, chain B (#615),
    27023 sequence alignment score = 329.4 
    27024 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    27025 8.150) 
    27026  
    27027 
    27028 > hide sel cartoons
    27029 
    27030 > select #1.3/I
    27031 
    27032 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    27033 
    27034 > show sel cartoons
    27035 
    27036 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    27037 
    27038 Chain information for AF3 CA.pdb #616 
    27039 --- 
    27040 Chain | Description 
    27041 A | No description available 
    27042  
    27043 
    27044 > matchmaker #616 to #1.3 & sel
    27045 
    27046 Parameters 
    27047 --- 
    27048 Chain pairing | bb 
    27049 Alignment algorithm | Needleman-Wunsch 
    27050 Similarity matrix | BLOSUM-62 
    27051 SS fraction | 0.3 
    27052 Gap open (HH/SS/other) | 18/18/6 
    27053 Gap extend | 1 
    27054 SS matrix |  |  | H | S | O 
    27055 ---|---|---|--- 
    27056 H | 6 | -9 | -6 
    27057 S |  | 6 | -6 
    27058 O |  |  | 4 
    27059 Iteration cutoff | 2 
    27060  
    27061 Matchmaker 3j0c.pdb1, chain I (#1.3) with AF3 CA.pdb, chain A (#616), sequence
    27062 alignment score = 306.5 
    27063 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    27064 2.689) 
    27065  
    27066 
    27067 > hide sel cartoons
    27068 
    27069 > color #612 dodgerblue
    27070 
    27071 > color #613 dodgerblue
    27072 
    27073 > color #614 #00b305ff
    27074 
    27075 > color #615 #00b305ff
    27076 
    27077 > color #616 #f15839ff
    27078 
    27079 > select #1.4/G
    27080 
    27081 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    27082 
    27083 > show sel cartoons
    27084 
    27085 > hide sel cartoons
    27086 
    27087 > select #1.3/H
    27088 
    27089 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    27090 
    27091 > show sel cartoons
    27092 
    27093 > hide sel cartoons
    27094 
    27095 > select #1.4/G
    27096 
    27097 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    27098 
    27099 > show sel cartoons
    27100 
    27101 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    27102 
    27103 Chain information for AF3 E1 1-421.pdb #617 
    27104 --- 
    27105 Chain | Description 
    27106 A | No description available 
    27107  
    27108 
    27109 > matchmaker #617 to #1.4 & sel
    27110 
    27111 Parameters 
    27112 --- 
    27113 Chain pairing | bb 
    27114 Alignment algorithm | Needleman-Wunsch 
    27115 Similarity matrix | BLOSUM-62 
    27116 SS fraction | 0.3 
    27117 Gap open (HH/SS/other) | 18/18/6 
    27118 Gap extend | 1 
    27119 SS matrix |  |  | H | S | O 
    27120 ---|---|---|--- 
    27121 H | 6 | -9 | -6 
    27122 S |  | 6 | -6 
    27123 O |  |  | 4 
    27124 Iteration cutoff | 2 
    27125  
    27126 Matchmaker 3j0c.pdb1, chain G (#1.4) with AF3 E1 1-421.pdb, chain A (#617),
    27127 sequence alignment score = 1060.7 
    27128 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    27129 2.985) 
    27130  
    27131 
    27132 > hide sel cartoons
    27133 
    27134 > show sel cartoons
    27135 
    27136 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    27137 
    27138 Chain information for AF3 E1 422-461.pdb #618 
    27139 --- 
    27140 Chain | Description 
    27141 A | No description available 
    27142  
    27143 
    27144 > matchmaker #618 to #1.4 & sel
    27145 
    27146 Parameters 
    27147 --- 
    27148 Chain pairing | bb 
    27149 Alignment algorithm | Needleman-Wunsch 
    27150 Similarity matrix | BLOSUM-62 
    27151 SS fraction | 0.3 
    27152 Gap open (HH/SS/other) | 18/18/6 
    27153 Gap extend | 1 
    27154 SS matrix |  |  | H | S | O 
    27155 ---|---|---|--- 
    27156 H | 6 | -9 | -6 
    27157 S |  | 6 | -6 
    27158 O |  |  | 4 
    27159 Iteration cutoff | 2 
    27160  
    27161 Matchmaker 3j0c.pdb1, chain G (#1.4) with AF3 E1 422-461.pdb, chain A (#618),
    27162 sequence alignment score = 626.9 
    27163 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    27164 2.997) 
    27165  
    27166 
    27167 > hide sel cartoons
    27168 
    27169 > select #1.4/H
    27170 
    27171 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    27172 
    27173 > show sel cartoons
    27174 
    27175 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    27176 
    27177 Chain information for AF3 E2 1-352.pdb #619 
    27178 --- 
    27179 Chain | Description 
    27180 B | No description available 
    27181  
    27182 
    27183 > matchmaker #619 to #1.4 & sel
    27184 
    27185 Parameters 
    27186 --- 
    27187 Chain pairing | bb 
    27188 Alignment algorithm | Needleman-Wunsch 
    27189 Similarity matrix | BLOSUM-62 
    27190 SS fraction | 0.3 
    27191 Gap open (HH/SS/other) | 18/18/6 
    27192 Gap extend | 1 
    27193 SS matrix |  |  | H | S | O 
    27194 ---|---|---|--- 
    27195 H | 6 | -9 | -6 
    27196 S |  | 6 | -6 
    27197 O |  |  | 4 
    27198 Iteration cutoff | 2 
    27199  
    27200 Matchmaker 3j0c.pdb1, chain H (#1.4) with AF3 E2 1-352.pdb, chain B (#619),
    27201 sequence alignment score = 590.9 
    27202 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    27203 6.107) 
    27204  
    27205 
    27206 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    27207 
    27208 Chain information for AF3 E2 353-438.pdb #620 
    27209 --- 
    27210 Chain | Description 
    27211 B | No description available 
    27212  
    27213 
    27214 > matchmaker #620 to #1.4 & sel
    27215 
    27216 Parameters 
    27217 --- 
    27218 Chain pairing | bb 
    27219 Alignment algorithm | Needleman-Wunsch 
    27220 Similarity matrix | BLOSUM-62 
    27221 SS fraction | 0.3 
    27222 Gap open (HH/SS/other) | 18/18/6 
    27223 Gap extend | 1 
    27224 SS matrix |  |  | H | S | O 
    27225 ---|---|---|--- 
    27226 H | 6 | -9 | -6 
    27227 S |  | 6 | -6 
    27228 O |  |  | 4 
    27229 Iteration cutoff | 2 
    27230  
    27231 Matchmaker 3j0c.pdb1, chain H (#1.4) with AF3 E2 353-438.pdb, chain B (#620),
    27232 sequence alignment score = 329.4 
    27233 RMSD between 40 pruned atom pairs is 0.937 angstroms; (across all 84 pairs:
    27234 8.150) 
    27235  
    27236 
    27237 > hide sel cartoons
    27238 
    27239 > select #1.4/I
    27240 
    27241 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    27242 
    27243 > show sel cartoons
    27244 
    27245 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    27246 
    27247 Chain information for AF3 CA.pdb #621 
    27248 --- 
    27249 Chain | Description 
    27250 A | No description available 
    27251  
    27252 
    27253 > matchmaker #621 to #1.4 & sel
    27254 
    27255 Parameters 
    27256 --- 
    27257 Chain pairing | bb 
    27258 Alignment algorithm | Needleman-Wunsch 
    27259 Similarity matrix | BLOSUM-62 
    27260 SS fraction | 0.3 
    27261 Gap open (HH/SS/other) | 18/18/6 
    27262 Gap extend | 1 
    27263 SS matrix |  |  | H | S | O 
    27264 ---|---|---|--- 
    27265 H | 6 | -9 | -6 
    27266 S |  | 6 | -6 
    27267 O |  |  | 4 
    27268 Iteration cutoff | 2 
    27269  
    27270 Matchmaker 3j0c.pdb1, chain I (#1.4) with AF3 CA.pdb, chain A (#621), sequence
    27271 alignment score = 306.5 
    27272 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    27273 2.689) 
    27274  
    27275 
    27276 > hide sel cartoons
    27277 
    27278 > color #617 dodgerblue
    27279 
    27280 > color #618 dodgerblue
    27281 
    27282 > color #619 #00b305ff
    27283 
    27284 > color #620 #00b305ff
    27285 
    27286 > color #621 #f15839ff
    27287 
    27288 > select #1.5/G
    27289 
    27290 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    27291 
    27292 > show sel cartoons
    27293 
    27294 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    27295 
    27296 Chain information for AF3 E1 1-421.pdb #622 
    27297 --- 
    27298 Chain | Description 
    27299 A | No description available 
    27300  
    27301 
    27302 > matchmaker #622 to #1.4 & sel
    27303 
    27304 No 'to' model specified 
    27305 
    27306 > matchmaker #622 to #1.5 & sel
    27307 
    27308 Parameters 
    27309 --- 
    27310 Chain pairing | bb 
    27311 Alignment algorithm | Needleman-Wunsch 
    27312 Similarity matrix | BLOSUM-62 
    27313 SS fraction | 0.3 
    27314 Gap open (HH/SS/other) | 18/18/6 
    27315 Gap extend | 1 
    27316 SS matrix |  |  | H | S | O 
    27317 ---|---|---|--- 
    27318 H | 6 | -9 | -6 
    27319 S |  | 6 | -6 
    27320 O |  |  | 4 
    27321 Iteration cutoff | 2 
    27322  
    27323 Matchmaker 3j0c.pdb1, chain G (#1.5) with AF3 E1 1-421.pdb, chain A (#622),
    27324 sequence alignment score = 1060.7 
    27325 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    27326 2.985) 
    27327  
    27328 
    27329 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    27330 
    27331 Chain information for AF3 E1 422-461.pdb #623 
    27332 --- 
    27333 Chain | Description 
    27334 A | No description available 
    27335  
    27336 
    27337 > matchmaker #623 to #1.5 & sel
    27338 
    27339 Parameters 
    27340 --- 
    27341 Chain pairing | bb 
    27342 Alignment algorithm | Needleman-Wunsch 
    27343 Similarity matrix | BLOSUM-62 
    27344 SS fraction | 0.3 
    27345 Gap open (HH/SS/other) | 18/18/6 
    27346 Gap extend | 1 
    27347 SS matrix |  |  | H | S | O 
    27348 ---|---|---|--- 
    27349 H | 6 | -9 | -6 
    27350 S |  | 6 | -6 
    27351 O |  |  | 4 
    27352 Iteration cutoff | 2 
    27353  
    27354 Matchmaker 3j0c.pdb1, chain G (#1.5) with AF3 E1 422-461.pdb, chain A (#623),
    27355 sequence alignment score = 626.9 
    27356 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    27357 2.997) 
    27358  
    27359 
    27360 > hide sel cartoons
    27361 
    27362 > select #1.5/H
    27363 
    27364 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    27365 
    27366 > show sel cartoons
    27367 
    27368 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    27369 
    27370 Chain information for AF3 E2 1-352.pdb #624 
    27371 --- 
    27372 Chain | Description 
    27373 B | No description available 
    27374  
    27375 
    27376 > matchmaker #624 to #1.5 & sel
    27377 
    27378 Parameters 
    27379 --- 
    27380 Chain pairing | bb 
    27381 Alignment algorithm | Needleman-Wunsch 
    27382 Similarity matrix | BLOSUM-62 
    27383 SS fraction | 0.3 
    27384 Gap open (HH/SS/other) | 18/18/6 
    27385 Gap extend | 1 
    27386 SS matrix |  |  | H | S | O 
    27387 ---|---|---|--- 
    27388 H | 6 | -9 | -6 
    27389 S |  | 6 | -6 
    27390 O |  |  | 4 
    27391 Iteration cutoff | 2 
    27392  
    27393 Matchmaker 3j0c.pdb1, chain H (#1.5) with AF3 E2 1-352.pdb, chain B (#624),
    27394 sequence alignment score = 590.9 
    27395 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    27396 6.107) 
    27397  
    27398 
    27399 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    27400 
    27401 Chain information for AF3 E2 353-438.pdb #625 
    27402 --- 
    27403 Chain | Description 
    27404 B | No description available 
    27405  
    27406 
    27407 > hide sel cartoons
    27408 
    27409 > show sel cartoons
    27410 
    27411 > matchmaker #625 to #1.5 & sel
    27412 
    27413 Parameters 
    27414 --- 
    27415 Chain pairing | bb 
    27416 Alignment algorithm | Needleman-Wunsch 
    27417 Similarity matrix | BLOSUM-62 
    27418 SS fraction | 0.3 
    27419 Gap open (HH/SS/other) | 18/18/6 
    27420 Gap extend | 1 
    27421 SS matrix |  |  | H | S | O 
    27422 ---|---|---|--- 
    27423 H | 6 | -9 | -6 
    27424 S |  | 6 | -6 
    27425 O |  |  | 4 
    27426 Iteration cutoff | 2 
    27427  
    27428 Matchmaker 3j0c.pdb1, chain H (#1.5) with AF3 E2 353-438.pdb, chain B (#625),
    27429 sequence alignment score = 329.4 
    27430 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    27431 8.150) 
    27432  
    27433 
    27434 > select #1.5/I
    27435 
    27436 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    27437 
    27438 > show sel cartoons
    27439 
    27440 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    27441 
    27442 Chain information for AF3 CA.pdb #626 
    27443 --- 
    27444 Chain | Description 
    27445 A | No description available 
    27446  
    27447 
    27448 > matchmaker #626 to #1.5 & sel
    27449 
    27450 Parameters 
    27451 --- 
    27452 Chain pairing | bb 
    27453 Alignment algorithm | Needleman-Wunsch 
    27454 Similarity matrix | BLOSUM-62 
    27455 SS fraction | 0.3 
    27456 Gap open (HH/SS/other) | 18/18/6 
    27457 Gap extend | 1 
    27458 SS matrix |  |  | H | S | O 
    27459 ---|---|---|--- 
    27460 H | 6 | -9 | -6 
    27461 S |  | 6 | -6 
    27462 O |  |  | 4 
    27463 Iteration cutoff | 2 
    27464  
    27465 Matchmaker 3j0c.pdb1, chain I (#1.5) with AF3 CA.pdb, chain A (#626), sequence
    27466 alignment score = 306.5 
    27467 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    27468 2.689) 
    27469  
    27470 
    27471 > hide sel cartoons
    27472 
    27473 > color #622 dodgerblue
    27474 
    27475 > color #623 dodgerblue
    27476 
    27477 > color #624 #00b305ff
    27478 
    27479 > color #625 #00b305ff
    27480 
    27481 > color #626 #f15839ff
    27482 
    27483 > select #1.5/H
    27484 
    27485 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    27486 
    27487 > hide sel cartoons
    27488 
    27489 > select #1.6/G
    27490 
    27491 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    27492 
    27493 > show sel cartoons
    27494 
    27495 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    27496 
    27497 Chain information for AF3 E1 1-421.pdb #627 
    27498 --- 
    27499 Chain | Description 
    27500 A | No description available 
    27501  
    27502 
    27503 > matchmaker #627 to #1.6 & sel
    27504 
    27505 Parameters 
    27506 --- 
    27507 Chain pairing | bb 
    27508 Alignment algorithm | Needleman-Wunsch 
    27509 Similarity matrix | BLOSUM-62 
    27510 SS fraction | 0.3 
    27511 Gap open (HH/SS/other) | 18/18/6 
    27512 Gap extend | 1 
    27513 SS matrix |  |  | H | S | O 
    27514 ---|---|---|--- 
    27515 H | 6 | -9 | -6 
    27516 S |  | 6 | -6 
    27517 O |  |  | 4 
    27518 Iteration cutoff | 2 
    27519  
    27520 Matchmaker 3j0c.pdb1, chain G (#1.6) with AF3 E1 1-421.pdb, chain A (#627),
    27521 sequence alignment score = 1060.7 
    27522 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    27523 2.985) 
    27524  
    27525 
    27526 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    27527 
    27528 Chain information for AF3 E1 422-461.pdb #628 
    27529 --- 
    27530 Chain | Description 
    27531 A | No description available 
    27532  
    27533 
    27534 > matchmaker #628 to #1.6 & sel
    27535 
    27536 Parameters 
    27537 --- 
    27538 Chain pairing | bb 
    27539 Alignment algorithm | Needleman-Wunsch 
    27540 Similarity matrix | BLOSUM-62 
    27541 SS fraction | 0.3 
    27542 Gap open (HH/SS/other) | 18/18/6 
    27543 Gap extend | 1 
    27544 SS matrix |  |  | H | S | O 
    27545 ---|---|---|--- 
    27546 H | 6 | -9 | -6 
    27547 S |  | 6 | -6 
    27548 O |  |  | 4 
    27549 Iteration cutoff | 2 
    27550  
    27551 Matchmaker 3j0c.pdb1, chain G (#1.6) with AF3 E1 422-461.pdb, chain A (#628),
    27552 sequence alignment score = 626.9 
    27553 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    27554 2.997) 
    27555  
    27556 
    27557 > hide sel cartoons
    27558 
    27559 > select #1.6/H
    27560 
    27561 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    27562 
    27563 > show sel cartoons
    27564 
    27565 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    27566 
    27567 Chain information for AF3 E2 1-352.pdb #629 
    27568 --- 
    27569 Chain | Description 
    27570 B | No description available 
    27571  
    27572 
    27573 > matchmaker #629 to #1.6 & sel
    27574 
    27575 Parameters 
    27576 --- 
    27577 Chain pairing | bb 
    27578 Alignment algorithm | Needleman-Wunsch 
    27579 Similarity matrix | BLOSUM-62 
    27580 SS fraction | 0.3 
    27581 Gap open (HH/SS/other) | 18/18/6 
    27582 Gap extend | 1 
    27583 SS matrix |  |  | H | S | O 
    27584 ---|---|---|--- 
    27585 H | 6 | -9 | -6 
    27586 S |  | 6 | -6 
    27587 O |  |  | 4 
    27588 Iteration cutoff | 2 
    27589  
    27590 Matchmaker 3j0c.pdb1, chain H (#1.6) with AF3 E2 1-352.pdb, chain B (#629),
    27591 sequence alignment score = 590.9 
    27592 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    27593 6.107) 
    27594  
    27595 
    27596 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    27597 
    27598 Chain information for AF3 E2 353-438.pdb #630 
    27599 --- 
    27600 Chain | Description 
    27601 B | No description available 
    27602  
    27603 
    27604 > matchmaker #630 to #1.6 & sel
    27605 
    27606 Parameters 
    27607 --- 
    27608 Chain pairing | bb 
    27609 Alignment algorithm | Needleman-Wunsch 
    27610 Similarity matrix | BLOSUM-62 
    27611 SS fraction | 0.3 
    27612 Gap open (HH/SS/other) | 18/18/6 
    27613 Gap extend | 1 
    27614 SS matrix |  |  | H | S | O 
    27615 ---|---|---|--- 
    27616 H | 6 | -9 | -6 
    27617 S |  | 6 | -6 
    27618 O |  |  | 4 
    27619 Iteration cutoff | 2 
    27620  
    27621 Matchmaker 3j0c.pdb1, chain H (#1.6) with AF3 E2 353-438.pdb, chain B (#630),
    27622 sequence alignment score = 329.4 
    27623 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    27624 8.150) 
    27625  
    27626 
    27627 > hide sel cartoons
    27628 
    27629 > select #1.6/I
    27630 
    27631 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    27632 
    27633 > show sel cartoons
    27634 
    27635 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    27636 
    27637 Chain information for AF3 CA.pdb #631 
    27638 --- 
    27639 Chain | Description 
    27640 A | No description available 
    27641  
    27642 
    27643 > matchmaker #631 to #1.6 & sel
    27644 
    27645 Parameters 
    27646 --- 
    27647 Chain pairing | bb 
    27648 Alignment algorithm | Needleman-Wunsch 
    27649 Similarity matrix | BLOSUM-62 
    27650 SS fraction | 0.3 
    27651 Gap open (HH/SS/other) | 18/18/6 
    27652 Gap extend | 1 
    27653 SS matrix |  |  | H | S | O 
    27654 ---|---|---|--- 
    27655 H | 6 | -9 | -6 
    27656 S |  | 6 | -6 
    27657 O |  |  | 4 
    27658 Iteration cutoff | 2 
    27659  
    27660 Matchmaker 3j0c.pdb1, chain I (#1.6) with AF3 CA.pdb, chain A (#631), sequence
    27661 alignment score = 306.5 
    27662 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    27663 2.689) 
    27664  
    27665 
    27666 > hide sel cartoons
    27667 
    27668 > color #627 dodgerblue
    27669 
    27670 > color #628 dodgerblue
    27671 
    27672 > color #629 #00b305ff
    27673 
    27674 > color #630 #00b305ff
    27675 
    27676 > color #631 #f15839ff
    27677 
    27678 > select #1.7/G
    27679 
    27680 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    27681 
    27682 > show sel cartoons
    27683 
    27684 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    27685 
    27686 Chain information for AF3 E1 1-421.pdb #632 
    27687 --- 
    27688 Chain | Description 
    27689 A | No description available 
    27690  
    27691 
    27692 > matchmaker #632 to #1.7 & sel
    27693 
    27694 Parameters 
    27695 --- 
    27696 Chain pairing | bb 
    27697 Alignment algorithm | Needleman-Wunsch 
    27698 Similarity matrix | BLOSUM-62 
    27699 SS fraction | 0.3 
    27700 Gap open (HH/SS/other) | 18/18/6 
    27701 Gap extend | 1 
    27702 SS matrix |  |  | H | S | O 
    27703 ---|---|---|--- 
    27704 H | 6 | -9 | -6 
    27705 S |  | 6 | -6 
    27706 O |  |  | 4 
    27707 Iteration cutoff | 2 
    27708  
    27709 Matchmaker 3j0c.pdb1, chain G (#1.7) with AF3 E1 1-421.pdb, chain A (#632),
    27710 sequence alignment score = 1060.7 
    27711 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    27712 2.985) 
    27713  
    27714 
    27715 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    27716 
    27717 Chain information for AF3 E1 422-461.pdb #633 
    27718 --- 
    27719 Chain | Description 
    27720 A | No description available 
    27721  
    27722 
    27723 > matchmaker #633 to #1.7 & sel
    27724 
    27725 Parameters 
    27726 --- 
    27727 Chain pairing | bb 
    27728 Alignment algorithm | Needleman-Wunsch 
    27729 Similarity matrix | BLOSUM-62 
    27730 SS fraction | 0.3 
    27731 Gap open (HH/SS/other) | 18/18/6 
    27732 Gap extend | 1 
    27733 SS matrix |  |  | H | S | O 
    27734 ---|---|---|--- 
    27735 H | 6 | -9 | -6 
    27736 S |  | 6 | -6 
    27737 O |  |  | 4 
    27738 Iteration cutoff | 2 
    27739  
    27740 Matchmaker 3j0c.pdb1, chain G (#1.7) with AF3 E1 422-461.pdb, chain A (#633),
    27741 sequence alignment score = 626.9 
    27742 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    27743 2.997) 
    27744  
    27745 
    27746 > hide sel cartoons
    27747 
    27748 > select #1.7/H
    27749 
    27750 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    27751 
    27752 > show sel cartoons
    27753 
    27754 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    27755 
    27756 Chain information for AF3 E2 1-352.pdb #634 
    27757 --- 
    27758 Chain | Description 
    27759 B | No description available 
    27760  
    27761 
    27762 > matchmaker #634 to #1.7 & sel
    27763 
    27764 Parameters 
    27765 --- 
    27766 Chain pairing | bb 
    27767 Alignment algorithm | Needleman-Wunsch 
    27768 Similarity matrix | BLOSUM-62 
    27769 SS fraction | 0.3 
    27770 Gap open (HH/SS/other) | 18/18/6 
    27771 Gap extend | 1 
    27772 SS matrix |  |  | H | S | O 
    27773 ---|---|---|--- 
    27774 H | 6 | -9 | -6 
    27775 S |  | 6 | -6 
    27776 O |  |  | 4 
    27777 Iteration cutoff | 2 
    27778  
    27779 Matchmaker 3j0c.pdb1, chain H (#1.7) with AF3 E2 1-352.pdb, chain B (#634),
    27780 sequence alignment score = 590.9 
    27781 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    27782 6.107) 
    27783  
    27784 
    27785 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    27786 
    27787 Chain information for AF3 E2 353-438.pdb #635 
    27788 --- 
    27789 Chain | Description 
    27790 B | No description available 
    27791  
    27792 
    27793 > matchmaker #635 to #1.7 & sel
    27794 
    27795 Parameters 
    27796 --- 
    27797 Chain pairing | bb 
    27798 Alignment algorithm | Needleman-Wunsch 
    27799 Similarity matrix | BLOSUM-62 
    27800 SS fraction | 0.3 
    27801 Gap open (HH/SS/other) | 18/18/6 
    27802 Gap extend | 1 
    27803 SS matrix |  |  | H | S | O 
    27804 ---|---|---|--- 
    27805 H | 6 | -9 | -6 
    27806 S |  | 6 | -6 
    27807 O |  |  | 4 
    27808 Iteration cutoff | 2 
    27809  
    27810 Matchmaker 3j0c.pdb1, chain H (#1.7) with AF3 E2 353-438.pdb, chain B (#635),
    27811 sequence alignment score = 329.4 
    27812 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    27813 8.150) 
    27814  
    27815 
    27816 > hide sel cartoons
    27817 
    27818 > select #1.7/I
    27819 
    27820 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    27821 
    27822 > show sel cartoons
    27823 
    27824 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    27825 
    27826 Chain information for AF3 CA.pdb #636 
    27827 --- 
    27828 Chain | Description 
    27829 A | No description available 
    27830  
    27831 
    27832 > matchmaker #636 to #1.7 & sel
    27833 
    27834 Parameters 
    27835 --- 
    27836 Chain pairing | bb 
    27837 Alignment algorithm | Needleman-Wunsch 
    27838 Similarity matrix | BLOSUM-62 
    27839 SS fraction | 0.3 
    27840 Gap open (HH/SS/other) | 18/18/6 
    27841 Gap extend | 1 
    27842 SS matrix |  |  | H | S | O 
    27843 ---|---|---|--- 
    27844 H | 6 | -9 | -6 
    27845 S |  | 6 | -6 
    27846 O |  |  | 4 
    27847 Iteration cutoff | 2 
    27848  
    27849 Matchmaker 3j0c.pdb1, chain I (#1.7) with AF3 CA.pdb, chain A (#636), sequence
    27850 alignment score = 306.5 
    27851 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    27852 2.689) 
    27853  
    27854 
    27855 > hide sel cartoons
    27856 
    27857 > color #632 dodgerblue
    27858 
    27859 > color #633 dodgerblue
    27860 
    27861 > color #634 #00b305ff
    27862 
    27863 > color #635 #00b305ff
    27864 
    27865 > color #636 #f15839ff
    27866 
    27867 > select #1.8/G
    27868 
    27869 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    27870 
    27871 > show sel cartoons
    27872 
    27873 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    27874 
    27875 Chain information for AF3 E1 1-421.pdb #637 
    27876 --- 
    27877 Chain | Description 
    27878 A | No description available 
    27879  
    27880 
    27881 > matchmaker #637 to #1.7 & sel
    27882 
    27883 No 'to' model specified 
    27884 
    27885 > matchmaker #637 to #1.8 & sel
    27886 
    27887 Parameters 
    27888 --- 
    27889 Chain pairing | bb 
    27890 Alignment algorithm | Needleman-Wunsch 
    27891 Similarity matrix | BLOSUM-62 
    27892 SS fraction | 0.3 
    27893 Gap open (HH/SS/other) | 18/18/6 
    27894 Gap extend | 1 
    27895 SS matrix |  |  | H | S | O 
    27896 ---|---|---|--- 
    27897 H | 6 | -9 | -6 
    27898 S |  | 6 | -6 
    27899 O |  |  | 4 
    27900 Iteration cutoff | 2 
    27901  
    27902 Matchmaker 3j0c.pdb1, chain G (#1.8) with AF3 E1 1-421.pdb, chain A (#637),
    27903 sequence alignment score = 1060.7 
    27904 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    27905 2.985) 
    27906  
    27907 
    27908 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    27909 
    27910 Chain information for AF3 E1 422-461.pdb #638 
    27911 --- 
    27912 Chain | Description 
    27913 A | No description available 
    27914  
    27915 
    27916 > matchmaker #638 to #1.8 & sel
    27917 
    27918 Parameters 
    27919 --- 
    27920 Chain pairing | bb 
    27921 Alignment algorithm | Needleman-Wunsch 
    27922 Similarity matrix | BLOSUM-62 
    27923 SS fraction | 0.3 
    27924 Gap open (HH/SS/other) | 18/18/6 
    27925 Gap extend | 1 
    27926 SS matrix |  |  | H | S | O 
    27927 ---|---|---|--- 
    27928 H | 6 | -9 | -6 
    27929 S |  | 6 | -6 
    27930 O |  |  | 4 
    27931 Iteration cutoff | 2 
    27932  
    27933 Matchmaker 3j0c.pdb1, chain G (#1.8) with AF3 E1 422-461.pdb, chain A (#638),
    27934 sequence alignment score = 626.9 
    27935 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    27936 2.997) 
    27937  
    27938 
    27939 > hide sel cartoons
    27940 
    27941 > select #1.8/H
    27942 
    27943 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    27944 
    27945 > show sel cartoons
    27946 
    27947 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    27948 
    27949 Chain information for AF3 E2 1-352.pdb #639 
    27950 --- 
    27951 Chain | Description 
    27952 B | No description available 
    27953  
    27954 
    27955 > matchmaker #639 to #1.8 & sel
    27956 
    27957 Parameters 
    27958 --- 
    27959 Chain pairing | bb 
    27960 Alignment algorithm | Needleman-Wunsch 
    27961 Similarity matrix | BLOSUM-62 
    27962 SS fraction | 0.3 
    27963 Gap open (HH/SS/other) | 18/18/6 
    27964 Gap extend | 1 
    27965 SS matrix |  |  | H | S | O 
    27966 ---|---|---|--- 
    27967 H | 6 | -9 | -6 
    27968 S |  | 6 | -6 
    27969 O |  |  | 4 
    27970 Iteration cutoff | 2 
    27971  
    27972 Matchmaker 3j0c.pdb1, chain H (#1.8) with AF3 E2 1-352.pdb, chain B (#639),
    27973 sequence alignment score = 590.9 
    27974 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    27975 6.107) 
    27976  
    27977 
    27978 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    27979 
    27980 Chain information for AF3 E2 353-438.pdb #640 
    27981 --- 
    27982 Chain | Description 
    27983 B | No description available 
    27984  
    27985 
    27986 > matchmaker #640 to #1.8 & sel
    27987 
    27988 Parameters 
    27989 --- 
    27990 Chain pairing | bb 
    27991 Alignment algorithm | Needleman-Wunsch 
    27992 Similarity matrix | BLOSUM-62 
    27993 SS fraction | 0.3 
    27994 Gap open (HH/SS/other) | 18/18/6 
    27995 Gap extend | 1 
    27996 SS matrix |  |  | H | S | O 
    27997 ---|---|---|--- 
    27998 H | 6 | -9 | -6 
    27999 S |  | 6 | -6 
    28000 O |  |  | 4 
    28001 Iteration cutoff | 2 
    28002  
    28003 Matchmaker 3j0c.pdb1, chain H (#1.8) with AF3 E2 353-438.pdb, chain B (#640),
    28004 sequence alignment score = 329.4 
    28005 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    28006 8.150) 
    28007  
    28008 
    28009 > hide sel cartoons
    28010 
    28011 > select #1.8/I
    28012 
    28013 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    28014 
    28015 > show sel cartoons
    28016 
    28017 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    28018 
    28019 Chain information for AF3 CA.pdb #641 
    28020 --- 
    28021 Chain | Description 
    28022 A | No description available 
    28023  
    28024 
    28025 > matchmaker #641 to #1.8 & sel
    28026 
    28027 Parameters 
    28028 --- 
    28029 Chain pairing | bb 
    28030 Alignment algorithm | Needleman-Wunsch 
    28031 Similarity matrix | BLOSUM-62 
    28032 SS fraction | 0.3 
    28033 Gap open (HH/SS/other) | 18/18/6 
    28034 Gap extend | 1 
    28035 SS matrix |  |  | H | S | O 
    28036 ---|---|---|--- 
    28037 H | 6 | -9 | -6 
    28038 S |  | 6 | -6 
    28039 O |  |  | 4 
    28040 Iteration cutoff | 2 
    28041  
    28042 Matchmaker 3j0c.pdb1, chain I (#1.8) with AF3 CA.pdb, chain A (#641), sequence
    28043 alignment score = 306.5 
    28044 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    28045 2.689) 
    28046  
    28047 
    28048 > hide sel cartoons
    28049 
    28050 > color #637 dodgerblue
    28051 
    28052 > color #638 dodgerblue
    28053 
    28054 > color #639 #00b305ff
    28055 
    28056 > color #640 #00b305ff
    28057 
    28058 > color #641 #f15839ff
    28059 
    28060 > select #1.9/G
    28061 
    28062 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    28063 
    28064 > show sel cartoons
    28065 
    28066 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    28067 
    28068 Chain information for AF3 E1 1-421.pdb #642 
    28069 --- 
    28070 Chain | Description 
    28071 A | No description available 
    28072  
    28073 
    28074 > matchmaker #642 to #1.8 & sel
    28075 
    28076 No 'to' model specified 
    28077 
    28078 > matchmaker #642 to #1.9 & sel
    28079 
    28080 Parameters 
    28081 --- 
    28082 Chain pairing | bb 
    28083 Alignment algorithm | Needleman-Wunsch 
    28084 Similarity matrix | BLOSUM-62 
    28085 SS fraction | 0.3 
    28086 Gap open (HH/SS/other) | 18/18/6 
    28087 Gap extend | 1 
    28088 SS matrix |  |  | H | S | O 
    28089 ---|---|---|--- 
    28090 H | 6 | -9 | -6 
    28091 S |  | 6 | -6 
    28092 O |  |  | 4 
    28093 Iteration cutoff | 2 
    28094  
    28095 Matchmaker 3j0c.pdb1, chain G (#1.9) with AF3 E1 1-421.pdb, chain A (#642),
    28096 sequence alignment score = 1060.7 
    28097 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    28098 2.985) 
    28099  
    28100 
    28101 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    28102 
    28103 Chain information for AF3 E1 422-461.pdb #643 
    28104 --- 
    28105 Chain | Description 
    28106 A | No description available 
    28107  
    28108 
    28109 > matchmaker #643 to #1.9 & sel
    28110 
    28111 Parameters 
    28112 --- 
    28113 Chain pairing | bb 
    28114 Alignment algorithm | Needleman-Wunsch 
    28115 Similarity matrix | BLOSUM-62 
    28116 SS fraction | 0.3 
    28117 Gap open (HH/SS/other) | 18/18/6 
    28118 Gap extend | 1 
    28119 SS matrix |  |  | H | S | O 
    28120 ---|---|---|--- 
    28121 H | 6 | -9 | -6 
    28122 S |  | 6 | -6 
    28123 O |  |  | 4 
    28124 Iteration cutoff | 2 
    28125  
    28126 Matchmaker 3j0c.pdb1, chain G (#1.9) with AF3 E1 422-461.pdb, chain A (#643),
    28127 sequence alignment score = 626.9 
    28128 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    28129 2.997) 
    28130  
    28131 
    28132 > hide sel cartoons
    28133 
    28134 > select #1.9/H
    28135 
    28136 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    28137 
    28138 > show sel cartoons
    28139 
    28140 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    28141 
    28142 Chain information for AF3 E2 1-352.pdb #644 
    28143 --- 
    28144 Chain | Description 
    28145 B | No description available 
    28146  
    28147 
    28148 > matchmaker #644 to #1.9 & sel
    28149 
    28150 Parameters 
    28151 --- 
    28152 Chain pairing | bb 
    28153 Alignment algorithm | Needleman-Wunsch 
    28154 Similarity matrix | BLOSUM-62 
    28155 SS fraction | 0.3 
    28156 Gap open (HH/SS/other) | 18/18/6 
    28157 Gap extend | 1 
    28158 SS matrix |  |  | H | S | O 
    28159 ---|---|---|--- 
    28160 H | 6 | -9 | -6 
    28161 S |  | 6 | -6 
    28162 O |  |  | 4 
    28163 Iteration cutoff | 2 
    28164  
    28165 Matchmaker 3j0c.pdb1, chain H (#1.9) with AF3 E2 1-352.pdb, chain B (#644),
    28166 sequence alignment score = 590.9 
    28167 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    28168 6.107) 
    28169  
    28170 
    28171 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    28172 
    28173 Chain information for AF3 E2 353-438.pdb #645 
    28174 --- 
    28175 Chain | Description 
    28176 B | No description available 
    28177  
    28178 
    28179 > matchmaker #645 to #1.9 & sel
    28180 
    28181 Parameters 
    28182 --- 
    28183 Chain pairing | bb 
    28184 Alignment algorithm | Needleman-Wunsch 
    28185 Similarity matrix | BLOSUM-62 
    28186 SS fraction | 0.3 
    28187 Gap open (HH/SS/other) | 18/18/6 
    28188 Gap extend | 1 
    28189 SS matrix |  |  | H | S | O 
    28190 ---|---|---|--- 
    28191 H | 6 | -9 | -6 
    28192 S |  | 6 | -6 
    28193 O |  |  | 4 
    28194 Iteration cutoff | 2 
    28195  
    28196 Matchmaker 3j0c.pdb1, chain H (#1.9) with AF3 E2 353-438.pdb, chain B (#645),
    28197 sequence alignment score = 329.4 
    28198 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    28199 8.150) 
    28200  
    28201 
    28202 > hide sel cartoons
    28203 
    28204 > select #1.9/I
    28205 
    28206 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    28207 
    28208 > show sel cartoons
    28209 
    28210 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    28211 
    28212 Chain information for AF3 CA.pdb #646 
    28213 --- 
    28214 Chain | Description 
    28215 A | No description available 
    28216  
    28217 
    28218 > matchmaker #646 to #1.9 & sel
    28219 
    28220 Parameters 
    28221 --- 
    28222 Chain pairing | bb 
    28223 Alignment algorithm | Needleman-Wunsch 
    28224 Similarity matrix | BLOSUM-62 
    28225 SS fraction | 0.3 
    28226 Gap open (HH/SS/other) | 18/18/6 
    28227 Gap extend | 1 
    28228 SS matrix |  |  | H | S | O 
    28229 ---|---|---|--- 
    28230 H | 6 | -9 | -6 
    28231 S |  | 6 | -6 
    28232 O |  |  | 4 
    28233 Iteration cutoff | 2 
    28234  
    28235 Matchmaker 3j0c.pdb1, chain I (#1.9) with AF3 CA.pdb, chain A (#646), sequence
    28236 alignment score = 306.5 
    28237 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    28238 2.689) 
    28239  
    28240 
    28241 > hide sel cartoons
    28242 
    28243 > color #642 dodgerblue
    28244 
    28245 > color #643 dodgerblue
    28246 
    28247 > color #644 #00b305ff
    28248 
    28249 > color #645 #00b305ff
    28250 
    28251 > color #646 #f15839ff
    28252 
    28253 > select #1.10/G
    28254 
    28255 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    28256 
    28257 > show sel cartoons
    28258 
    28259 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    28260 
    28261 Chain information for AF3 E1 1-421.pdb #647 
    28262 --- 
    28263 Chain | Description 
    28264 A | No description available 
    28265  
    28266 
    28267 > matchmaker #647 to #1.10 & sel
    28268 
    28269 Parameters 
    28270 --- 
    28271 Chain pairing | bb 
    28272 Alignment algorithm | Needleman-Wunsch 
    28273 Similarity matrix | BLOSUM-62 
    28274 SS fraction | 0.3 
    28275 Gap open (HH/SS/other) | 18/18/6 
    28276 Gap extend | 1 
    28277 SS matrix |  |  | H | S | O 
    28278 ---|---|---|--- 
    28279 H | 6 | -9 | -6 
    28280 S |  | 6 | -6 
    28281 O |  |  | 4 
    28282 Iteration cutoff | 2 
    28283  
    28284 Matchmaker 3j0c.pdb1, chain G (#1.10) with AF3 E1 1-421.pdb, chain A (#647),
    28285 sequence alignment score = 1060.7 
    28286 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    28287 2.985) 
    28288  
    28289 
    28290 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    28291 
    28292 Chain information for AF3 E1 422-461.pdb #648 
    28293 --- 
    28294 Chain | Description 
    28295 A | No description available 
    28296  
    28297 
    28298 > matchmaker #648 to #1.10 & sel
    28299 
    28300 Parameters 
    28301 --- 
    28302 Chain pairing | bb 
    28303 Alignment algorithm | Needleman-Wunsch 
    28304 Similarity matrix | BLOSUM-62 
    28305 SS fraction | 0.3 
    28306 Gap open (HH/SS/other) | 18/18/6 
    28307 Gap extend | 1 
    28308 SS matrix |  |  | H | S | O 
    28309 ---|---|---|--- 
    28310 H | 6 | -9 | -6 
    28311 S |  | 6 | -6 
    28312 O |  |  | 4 
    28313 Iteration cutoff | 2 
    28314  
    28315 Matchmaker 3j0c.pdb1, chain G (#1.10) with AF3 E1 422-461.pdb, chain A (#648),
    28316 sequence alignment score = 626.9 
    28317 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    28318 2.996) 
    28319  
    28320 
    28321 > hide sel cartoons
    28322 
    28323 > select #1.10/H
    28324 
    28325 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    28326 
    28327 > show sel cartoons
    28328 
    28329 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    28330 
    28331 Chain information for AF3 E2 1-352.pdb #649 
    28332 --- 
    28333 Chain | Description 
    28334 B | No description available 
    28335  
    28336 
    28337 > matchmaker #649 to #1.10 & sel
    28338 
    28339 Parameters 
    28340 --- 
    28341 Chain pairing | bb 
    28342 Alignment algorithm | Needleman-Wunsch 
    28343 Similarity matrix | BLOSUM-62 
    28344 SS fraction | 0.3 
    28345 Gap open (HH/SS/other) | 18/18/6 
    28346 Gap extend | 1 
    28347 SS matrix |  |  | H | S | O 
    28348 ---|---|---|--- 
    28349 H | 6 | -9 | -6 
    28350 S |  | 6 | -6 
    28351 O |  |  | 4 
    28352 Iteration cutoff | 2 
    28353  
    28354 Matchmaker 3j0c.pdb1, chain H (#1.10) with AF3 E2 1-352.pdb, chain B (#649),
    28355 sequence alignment score = 590.9 
    28356 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    28357 6.107) 
    28358  
    28359 
    28360 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    28361 
    28362 Chain information for AF3 E2 353-438.pdb #650 
    28363 --- 
    28364 Chain | Description 
    28365 B | No description available 
    28366  
    28367 
    28368 > matchmaker #650 to #1.10 & sel
    28369 
    28370 Parameters 
    28371 --- 
    28372 Chain pairing | bb 
    28373 Alignment algorithm | Needleman-Wunsch 
    28374 Similarity matrix | BLOSUM-62 
    28375 SS fraction | 0.3 
    28376 Gap open (HH/SS/other) | 18/18/6 
    28377 Gap extend | 1 
    28378 SS matrix |  |  | H | S | O 
    28379 ---|---|---|--- 
    28380 H | 6 | -9 | -6 
    28381 S |  | 6 | -6 
    28382 O |  |  | 4 
    28383 Iteration cutoff | 2 
    28384  
    28385 Matchmaker 3j0c.pdb1, chain H (#1.10) with AF3 E2 353-438.pdb, chain B (#650),
    28386 sequence alignment score = 329.4 
    28387 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    28388 8.151) 
    28389  
    28390 
    28391 > hide sel cartoons
    28392 
    28393 > select #1.10/I
    28394 
    28395 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    28396 
    28397 > show sel cartoons
    28398 
    28399 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    28400 
    28401 Chain information for AF3 CA.pdb #651 
    28402 --- 
    28403 Chain | Description 
    28404 A | No description available 
    28405  
    28406 
    28407 > matchmaker #651 to #1.10 & sel
    28408 
    28409 Parameters 
    28410 --- 
    28411 Chain pairing | bb 
    28412 Alignment algorithm | Needleman-Wunsch 
    28413 Similarity matrix | BLOSUM-62 
    28414 SS fraction | 0.3 
    28415 Gap open (HH/SS/other) | 18/18/6 
    28416 Gap extend | 1 
    28417 SS matrix |  |  | H | S | O 
    28418 ---|---|---|--- 
    28419 H | 6 | -9 | -6 
    28420 S |  | 6 | -6 
    28421 O |  |  | 4 
    28422 Iteration cutoff | 2 
    28423  
    28424 Matchmaker 3j0c.pdb1, chain I (#1.10) with AF3 CA.pdb, chain A (#651),
    28425 sequence alignment score = 306.5 
    28426 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    28427 2.689) 
    28428  
    28429 
    28430 > hide sel cartoons
    28431 
    28432 > color #647 dodgerblue
    28433 
    28434 > color #648 dodgerblue
    28435 
    28436 > color #649 #00b305ff
    28437 
    28438 > color #650 #00b305ff
    28439 
    28440 > color #651 #f15839ff
    28441 
    28442 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    28443 
    28444 > hide #602 models
    28445 
    28446 > hide #603 models
    28447 
    28448 > hide #604 models
    28449 
    28450 > hide #605 models
    28451 
    28452 > hide #606 models
    28453 
    28454 > hide #607 models
    28455 
    28456 > hide #608 models
    28457 
    28458 > hide #609 models
    28459 
    28460 > hide #610 models
    28461 
    28462 > hide #611 models
    28463 
    28464 > hide #612 models
    28465 
    28466 > hide #613 models
    28467 
    28468 > hide #614 models
    28469 
    28470 > hide #615 models
    28471 
    28472 > hide #616 models
    28473 
    28474 > hide #617 models
    28475 
    28476 > hide #618 models
    28477 
    28478 > hide #619 models
    28479 
    28480 > hide #620 models
    28481 
    28482 > hide #621 models
    28483 
    28484 > hide #622 models
    28485 
    28486 > hide #623 models
    28487 
    28488 > hide #624 models
    28489 
    28490 > hide #625 models
    28491 
    28492 > hide #626 models
    28493 
    28494 > hide #627 models
    28495 
    28496 > hide #628 models
    28497 
    28498 > hide #629 models
    28499 
    28500 > hide #630 models
    28501 
    28502 > hide #631 models
    28503 
    28504 > hide #632 models
    28505 
    28506 > hide #633 models
    28507 
    28508 > hide #634 models
    28509 
    28510 > hide #635 models
    28511 
    28512 > hide #636 models
    28513 
    28514 > hide #637 models
    28515 
    28516 > hide #638 models
    28517 
    28518 > hide #639 models
    28519 
    28520 > hide #640 models
    28521 
    28522 > hide #641 models
    28523 
    28524 > hide #642 models
    28525 
    28526 > hide #643 models
    28527 
    28528 > hide #644 models
    28529 
    28530 > hide #645 models
    28531 
    28532 > hide #646 models
    28533 
    28534 > hide #647 models
    28535 
    28536 > hide #648 models
    28537 
    28538 > hide #649 models
    28539 
    28540 > hide #650 models
    28541 
    28542 > hide #651 models
    28543 
    28544 > select #1.11/G
    28545 
    28546 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    28547 
    28548 > show sel cartoons
    28549 
    28550 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    28551 
    28552 Chain information for AF3 E1 1-421.pdb #652 
    28553 --- 
    28554 Chain | Description 
    28555 A | No description available 
    28556  
    28557 
    28558 > matchmaker #652 to #1.11 & sel
    28559 
    28560 Parameters 
    28561 --- 
    28562 Chain pairing | bb 
    28563 Alignment algorithm | Needleman-Wunsch 
    28564 Similarity matrix | BLOSUM-62 
    28565 SS fraction | 0.3 
    28566 Gap open (HH/SS/other) | 18/18/6 
    28567 Gap extend | 1 
    28568 SS matrix |  |  | H | S | O 
    28569 ---|---|---|--- 
    28570 H | 6 | -9 | -6 
    28571 S |  | 6 | -6 
    28572 O |  |  | 4 
    28573 Iteration cutoff | 2 
    28574  
    28575 Matchmaker 3j0c.pdb1, chain G (#1.11) with AF3 E1 1-421.pdb, chain A (#652),
    28576 sequence alignment score = 1060.7 
    28577 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    28578 2.985) 
    28579  
    28580 
    28581 > view
    28582 
    28583 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    28584 
    28585 Chain information for AF3 E1 422-461.pdb #653 
    28586 --- 
    28587 Chain | Description 
    28588 A | No description available 
    28589  
    28590 
    28591 > matchmaker #653 to #1.11 & sel
    28592 
    28593 Parameters 
    28594 --- 
    28595 Chain pairing | bb 
    28596 Alignment algorithm | Needleman-Wunsch 
    28597 Similarity matrix | BLOSUM-62 
    28598 SS fraction | 0.3 
    28599 Gap open (HH/SS/other) | 18/18/6 
    28600 Gap extend | 1 
    28601 SS matrix |  |  | H | S | O 
    28602 ---|---|---|--- 
    28603 H | 6 | -9 | -6 
    28604 S |  | 6 | -6 
    28605 O |  |  | 4 
    28606 Iteration cutoff | 2 
    28607  
    28608 Matchmaker 3j0c.pdb1, chain G (#1.11) with AF3 E1 422-461.pdb, chain A (#653),
    28609 sequence alignment score = 626.9 
    28610 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    28611 2.997) 
    28612  
    28613 
    28614 > hide sel cartoons
    28615 
    28616 > select #1.11/H
    28617 
    28618 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    28619 
    28620 > show sel cartoons
    28621 
    28622 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    28623 
    28624 Chain information for AF3 E2 1-352.pdb #654 
    28625 --- 
    28626 Chain | Description 
    28627 B | No description available 
    28628  
    28629 
    28630 > matchmaker #654 to #1.11 & sel
    28631 
    28632 Parameters 
    28633 --- 
    28634 Chain pairing | bb 
    28635 Alignment algorithm | Needleman-Wunsch 
    28636 Similarity matrix | BLOSUM-62 
    28637 SS fraction | 0.3 
    28638 Gap open (HH/SS/other) | 18/18/6 
    28639 Gap extend | 1 
    28640 SS matrix |  |  | H | S | O 
    28641 ---|---|---|--- 
    28642 H | 6 | -9 | -6 
    28643 S |  | 6 | -6 
    28644 O |  |  | 4 
    28645 Iteration cutoff | 2 
    28646  
    28647 Matchmaker 3j0c.pdb1, chain H (#1.11) with AF3 E2 1-352.pdb, chain B (#654),
    28648 sequence alignment score = 590.9 
    28649 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    28650 6.107) 
    28651  
    28652 
    28653 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    28654 
    28655 Chain information for AF3 E2 353-438.pdb #655 
    28656 --- 
    28657 Chain | Description 
    28658 B | No description available 
    28659  
    28660 
    28661 > matchmaker #655 to #1.11 & sel
    28662 
    28663 Parameters 
    28664 --- 
    28665 Chain pairing | bb 
    28666 Alignment algorithm | Needleman-Wunsch 
    28667 Similarity matrix | BLOSUM-62 
    28668 SS fraction | 0.3 
    28669 Gap open (HH/SS/other) | 18/18/6 
    28670 Gap extend | 1 
    28671 SS matrix |  |  | H | S | O 
    28672 ---|---|---|--- 
    28673 H | 6 | -9 | -6 
    28674 S |  | 6 | -6 
    28675 O |  |  | 4 
    28676 Iteration cutoff | 2 
    28677  
    28678 Matchmaker 3j0c.pdb1, chain H (#1.11) with AF3 E2 353-438.pdb, chain B (#655),
    28679 sequence alignment score = 329.4 
    28680 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    28681 8.151) 
    28682  
    28683 
    28684 > hide sel cartoons
    28685 
    28686 > select #1.11/I
    28687 
    28688 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    28689 
    28690 > show sel cartoons
    28691 
    28692 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    28693 
    28694 Chain information for AF3 CA.pdb #656 
    28695 --- 
    28696 Chain | Description 
    28697 A | No description available 
    28698  
    28699 
    28700 > matchmaker #656 to #1.11 & sel
    28701 
    28702 Parameters 
    28703 --- 
    28704 Chain pairing | bb 
    28705 Alignment algorithm | Needleman-Wunsch 
    28706 Similarity matrix | BLOSUM-62 
    28707 SS fraction | 0.3 
    28708 Gap open (HH/SS/other) | 18/18/6 
    28709 Gap extend | 1 
    28710 SS matrix |  |  | H | S | O 
    28711 ---|---|---|--- 
    28712 H | 6 | -9 | -6 
    28713 S |  | 6 | -6 
    28714 O |  |  | 4 
    28715 Iteration cutoff | 2 
    28716  
    28717 Matchmaker 3j0c.pdb1, chain I (#1.11) with AF3 CA.pdb, chain A (#656),
    28718 sequence alignment score = 306.5 
    28719 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    28720 2.689) 
    28721  
    28722 
    28723 > hide sel cartoons
    28724 
    28725 > color #652 dodgerblue
    28726 
    28727 > color #653 dodgerblue
    28728 
    28729 > color #654 #00b305ff
    28730 
    28731 > color #655 #00b305ff
    28732 
    28733 > color #656 #f15839ff
    28734 
    28735 > select #1.12/G
    28736 
    28737 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    28738 
    28739 > show sel cartoons
    28740 
    28741 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    28742 
    28743 Chain information for AF3 E1 1-421.pdb #657 
    28744 --- 
    28745 Chain | Description 
    28746 A | No description available 
    28747  
    28748 
    28749 > matchmaker #657 to #1.12 & sel
    28750 
    28751 Parameters 
    28752 --- 
    28753 Chain pairing | bb 
    28754 Alignment algorithm | Needleman-Wunsch 
    28755 Similarity matrix | BLOSUM-62 
    28756 SS fraction | 0.3 
    28757 Gap open (HH/SS/other) | 18/18/6 
    28758 Gap extend | 1 
    28759 SS matrix |  |  | H | S | O 
    28760 ---|---|---|--- 
    28761 H | 6 | -9 | -6 
    28762 S |  | 6 | -6 
    28763 O |  |  | 4 
    28764 Iteration cutoff | 2 
    28765  
    28766 Matchmaker 3j0c.pdb1, chain G (#1.12) with AF3 E1 1-421.pdb, chain A (#657),
    28767 sequence alignment score = 1060.7 
    28768 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    28769 2.985) 
    28770  
    28771 
    28772 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    28773 
    28774 Chain information for AF3 E1 422-461.pdb #658 
    28775 --- 
    28776 Chain | Description 
    28777 A | No description available 
    28778  
    28779 
    28780 > matchmaker #658 to #1.12 & sel
    28781 
    28782 Parameters 
    28783 --- 
    28784 Chain pairing | bb 
    28785 Alignment algorithm | Needleman-Wunsch 
    28786 Similarity matrix | BLOSUM-62 
    28787 SS fraction | 0.3 
    28788 Gap open (HH/SS/other) | 18/18/6 
    28789 Gap extend | 1 
    28790 SS matrix |  |  | H | S | O 
    28791 ---|---|---|--- 
    28792 H | 6 | -9 | -6 
    28793 S |  | 6 | -6 
    28794 O |  |  | 4 
    28795 Iteration cutoff | 2 
    28796  
    28797 Matchmaker 3j0c.pdb1, chain G (#1.12) with AF3 E1 422-461.pdb, chain A (#658),
    28798 sequence alignment score = 626.9 
    28799 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    28800 2.997) 
    28801  
    28802 
    28803 > hide sel cartoons
    28804 
    28805 > select #1.12/H
    28806 
    28807 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    28808 
    28809 > show sel cartoons
    28810 
    28811 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    28812 
    28813 Chain information for AF3 E2 1-352.pdb #659 
    28814 --- 
    28815 Chain | Description 
    28816 B | No description available 
    28817  
    28818 
    28819 > matchmaker #659 to #1.12 & sel
    28820 
    28821 Parameters 
    28822 --- 
    28823 Chain pairing | bb 
    28824 Alignment algorithm | Needleman-Wunsch 
    28825 Similarity matrix | BLOSUM-62 
    28826 SS fraction | 0.3 
    28827 Gap open (HH/SS/other) | 18/18/6 
    28828 Gap extend | 1 
    28829 SS matrix |  |  | H | S | O 
    28830 ---|---|---|--- 
    28831 H | 6 | -9 | -6 
    28832 S |  | 6 | -6 
    28833 O |  |  | 4 
    28834 Iteration cutoff | 2 
    28835  
    28836 Matchmaker 3j0c.pdb1, chain H (#1.12) with AF3 E2 1-352.pdb, chain B (#659),
    28837 sequence alignment score = 590.9 
    28838 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    28839 6.107) 
    28840  
    28841 
    28842 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    28843 
    28844 Chain information for AF3 E2 353-438.pdb #660 
    28845 --- 
    28846 Chain | Description 
    28847 B | No description available 
    28848  
    28849 
    28850 > matchmaker #660 to #1.12 & sel
    28851 
    28852 Parameters 
    28853 --- 
    28854 Chain pairing | bb 
    28855 Alignment algorithm | Needleman-Wunsch 
    28856 Similarity matrix | BLOSUM-62 
    28857 SS fraction | 0.3 
    28858 Gap open (HH/SS/other) | 18/18/6 
    28859 Gap extend | 1 
    28860 SS matrix |  |  | H | S | O 
    28861 ---|---|---|--- 
    28862 H | 6 | -9 | -6 
    28863 S |  | 6 | -6 
    28864 O |  |  | 4 
    28865 Iteration cutoff | 2 
    28866  
    28867 Matchmaker 3j0c.pdb1, chain H (#1.12) with AF3 E2 353-438.pdb, chain B (#660),
    28868 sequence alignment score = 329.4 
    28869 RMSD between 40 pruned atom pairs is 0.937 angstroms; (across all 84 pairs:
    28870 8.150) 
    28871  
    28872 
    28873 > hide sel cartoons
    28874 
    28875 > select #1.12/I
    28876 
    28877 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    28878 
    28879 > show sel cartoons
    28880 
    28881 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    28882 
    28883 Chain information for AF3 CA.pdb #661 
    28884 --- 
    28885 Chain | Description 
    28886 A | No description available 
    28887  
    28888 
    28889 > matchmaker #661 to #1.12 & sel
    28890 
    28891 Parameters 
    28892 --- 
    28893 Chain pairing | bb 
    28894 Alignment algorithm | Needleman-Wunsch 
    28895 Similarity matrix | BLOSUM-62 
    28896 SS fraction | 0.3 
    28897 Gap open (HH/SS/other) | 18/18/6 
    28898 Gap extend | 1 
    28899 SS matrix |  |  | H | S | O 
    28900 ---|---|---|--- 
    28901 H | 6 | -9 | -6 
    28902 S |  | 6 | -6 
    28903 O |  |  | 4 
    28904 Iteration cutoff | 2 
    28905  
    28906 Matchmaker 3j0c.pdb1, chain I (#1.12) with AF3 CA.pdb, chain A (#661),
    28907 sequence alignment score = 306.5 
    28908 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    28909 2.689) 
    28910  
    28911 
    28912 > hide sel cartoons
    28913 
    28914 > color #657 dodgerblue
    28915 
    28916 > color #658 dodgerblue
    28917 
    28918 > color #659 #00b305ff
    28919 
    28920 > color #660 #00b305ff
    28921 
    28922 > color #661 #f15839ff
    28923 
    28924 > select #1.13/G
    28925 
    28926 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    28927 
    28928 > show sel cartoons
    28929 
    28930 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    28931 
    28932 Chain information for AF3 E1 1-421.pdb #662 
    28933 --- 
    28934 Chain | Description 
    28935 A | No description available 
    28936  
    28937 
    28938 > matchmaker #662 to #1.13 & sel
    28939 
    28940 Parameters 
    28941 --- 
    28942 Chain pairing | bb 
    28943 Alignment algorithm | Needleman-Wunsch 
    28944 Similarity matrix | BLOSUM-62 
    28945 SS fraction | 0.3 
    28946 Gap open (HH/SS/other) | 18/18/6 
    28947 Gap extend | 1 
    28948 SS matrix |  |  | H | S | O 
    28949 ---|---|---|--- 
    28950 H | 6 | -9 | -6 
    28951 S |  | 6 | -6 
    28952 O |  |  | 4 
    28953 Iteration cutoff | 2 
    28954  
    28955 Matchmaker 3j0c.pdb1, chain G (#1.13) with AF3 E1 1-421.pdb, chain A (#662),
    28956 sequence alignment score = 1060.7 
    28957 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    28958 2.985) 
    28959  
    28960 
    28961 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    28962 
    28963 Chain information for AF3 E1 422-461.pdb #663 
    28964 --- 
    28965 Chain | Description 
    28966 A | No description available 
    28967  
    28968 
    28969 > matchmaker #663 to #1.13 & sel
    28970 
    28971 Parameters 
    28972 --- 
    28973 Chain pairing | bb 
    28974 Alignment algorithm | Needleman-Wunsch 
    28975 Similarity matrix | BLOSUM-62 
    28976 SS fraction | 0.3 
    28977 Gap open (HH/SS/other) | 18/18/6 
    28978 Gap extend | 1 
    28979 SS matrix |  |  | H | S | O 
    28980 ---|---|---|--- 
    28981 H | 6 | -9 | -6 
    28982 S |  | 6 | -6 
    28983 O |  |  | 4 
    28984 Iteration cutoff | 2 
    28985  
    28986 Matchmaker 3j0c.pdb1, chain G (#1.13) with AF3 E1 422-461.pdb, chain A (#663),
    28987 sequence alignment score = 626.9 
    28988 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    28989 2.997) 
    28990  
    28991 
    28992 > hide sel cartoons
    28993 
    28994 > select #1.13/I
    28995 
    28996 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    28997 
    28998 > show sel cartoons
    28999 
    29000 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    29001 
    29002 Chain information for AF3 CA.pdb #664 
    29003 --- 
    29004 Chain | Description 
    29005 A | No description available 
    29006  
    29007 
    29008 > matchmaker #664 to #1.13 & sel
    29009 
    29010 Parameters 
    29011 --- 
    29012 Chain pairing | bb 
    29013 Alignment algorithm | Needleman-Wunsch 
    29014 Similarity matrix | BLOSUM-62 
    29015 SS fraction | 0.3 
    29016 Gap open (HH/SS/other) | 18/18/6 
    29017 Gap extend | 1 
    29018 SS matrix |  |  | H | S | O 
    29019 ---|---|---|--- 
    29020 H | 6 | -9 | -6 
    29021 S |  | 6 | -6 
    29022 O |  |  | 4 
    29023 Iteration cutoff | 2 
    29024  
    29025 Matchmaker 3j0c.pdb1, chain I (#1.13) with AF3 CA.pdb, chain A (#664),
    29026 sequence alignment score = 306.5 
    29027 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    29028 2.689) 
    29029  
    29030 
    29031 > hide sel cartoons
    29032 
    29033 > select #1.13/H
    29034 
    29035 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    29036 
    29037 > show sel cartoons
    29038 
    29039 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    29040 
    29041 Chain information for AF3 E2 1-352.pdb #665 
    29042 --- 
    29043 Chain | Description 
    29044 B | No description available 
    29045  
    29046 
    29047 > matchmaker #665 to #1.13 & sel
    29048 
    29049 Parameters 
    29050 --- 
    29051 Chain pairing | bb 
    29052 Alignment algorithm | Needleman-Wunsch 
    29053 Similarity matrix | BLOSUM-62 
    29054 SS fraction | 0.3 
    29055 Gap open (HH/SS/other) | 18/18/6 
    29056 Gap extend | 1 
    29057 SS matrix |  |  | H | S | O 
    29058 ---|---|---|--- 
    29059 H | 6 | -9 | -6 
    29060 S |  | 6 | -6 
    29061 O |  |  | 4 
    29062 Iteration cutoff | 2 
    29063  
    29064 Matchmaker 3j0c.pdb1, chain H (#1.13) with AF3 E2 1-352.pdb, chain B (#665),
    29065 sequence alignment score = 590.9 
    29066 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    29067 6.107) 
    29068  
    29069 
    29070 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    29071 
    29072 Chain information for AF3 E2 353-438.pdb #666 
    29073 --- 
    29074 Chain | Description 
    29075 B | No description available 
    29076  
    29077 
    29078 > matchmaker #666 to #1.13 & sel
    29079 
    29080 Parameters 
    29081 --- 
    29082 Chain pairing | bb 
    29083 Alignment algorithm | Needleman-Wunsch 
    29084 Similarity matrix | BLOSUM-62 
    29085 SS fraction | 0.3 
    29086 Gap open (HH/SS/other) | 18/18/6 
    29087 Gap extend | 1 
    29088 SS matrix |  |  | H | S | O 
    29089 ---|---|---|--- 
    29090 H | 6 | -9 | -6 
    29091 S |  | 6 | -6 
    29092 O |  |  | 4 
    29093 Iteration cutoff | 2 
    29094  
    29095 Matchmaker 3j0c.pdb1, chain H (#1.13) with AF3 E2 353-438.pdb, chain B (#666),
    29096 sequence alignment score = 329.4 
    29097 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    29098 8.150) 
    29099  
    29100 
    29101 > hide sel cartoons
    29102 
    29103 > close #664
    29104 
    29105 > select #1.13/I
    29106 
    29107 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    29108 
    29109 > show sel cartoons
    29110 
    29111 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    29112 
    29113 Chain information for AF3 CA.pdb #664 
    29114 --- 
    29115 Chain | Description 
    29116 A | No description available 
    29117  
    29118 
    29119 > close #666
    29120 
    29121 > close #665
    29122 
    29123 > close #664
    29124 
    29125 > hide sel cartoons
    29126 
    29127 > select #1.13/H
    29128 
    29129 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    29130 
    29131 > show sel cartoons
    29132 
    29133 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    29134 
    29135 Chain information for AF3 E2 1-352.pdb #664 
    29136 --- 
    29137 Chain | Description 
    29138 B | No description available 
    29139  
    29140 
    29141 > matchmaker #664 to #1.13 & sel
    29142 
    29143 Parameters 
    29144 --- 
    29145 Chain pairing | bb 
    29146 Alignment algorithm | Needleman-Wunsch 
    29147 Similarity matrix | BLOSUM-62 
    29148 SS fraction | 0.3 
    29149 Gap open (HH/SS/other) | 18/18/6 
    29150 Gap extend | 1 
    29151 SS matrix |  |  | H | S | O 
    29152 ---|---|---|--- 
    29153 H | 6 | -9 | -6 
    29154 S |  | 6 | -6 
    29155 O |  |  | 4 
    29156 Iteration cutoff | 2 
    29157  
    29158 Matchmaker 3j0c.pdb1, chain H (#1.13) with AF3 E2 1-352.pdb, chain B (#664),
    29159 sequence alignment score = 590.9 
    29160 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    29161 6.107) 
    29162  
    29163 
    29164 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    29165 
    29166 Chain information for AF3 E2 353-438.pdb #665 
    29167 --- 
    29168 Chain | Description 
    29169 B | No description available 
    29170  
    29171 
    29172 > matchmaker #665 to #1.13 & sel
    29173 
    29174 Parameters 
    29175 --- 
    29176 Chain pairing | bb 
    29177 Alignment algorithm | Needleman-Wunsch 
    29178 Similarity matrix | BLOSUM-62 
    29179 SS fraction | 0.3 
    29180 Gap open (HH/SS/other) | 18/18/6 
    29181 Gap extend | 1 
    29182 SS matrix |  |  | H | S | O 
    29183 ---|---|---|--- 
    29184 H | 6 | -9 | -6 
    29185 S |  | 6 | -6 
    29186 O |  |  | 4 
    29187 Iteration cutoff | 2 
    29188  
    29189 Matchmaker 3j0c.pdb1, chain H (#1.13) with AF3 E2 353-438.pdb, chain B (#665),
    29190 sequence alignment score = 329.4 
    29191 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    29192 8.150) 
    29193  
    29194 
    29195 > hide sel cartoons
    29196 
    29197 > select #1.13/I
    29198 
    29199 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    29200 
    29201 > show sel cartoons
    29202 
    29203 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    29204 
    29205 Chain information for AF3 CA.pdb #666 
    29206 --- 
    29207 Chain | Description 
    29208 A | No description available 
    29209  
    29210 
    29211 > matchmaker #666 to #1.13 & sel
    29212 
    29213 Parameters 
    29214 --- 
    29215 Chain pairing | bb 
    29216 Alignment algorithm | Needleman-Wunsch 
    29217 Similarity matrix | BLOSUM-62 
    29218 SS fraction | 0.3 
    29219 Gap open (HH/SS/other) | 18/18/6 
    29220 Gap extend | 1 
    29221 SS matrix |  |  | H | S | O 
    29222 ---|---|---|--- 
    29223 H | 6 | -9 | -6 
    29224 S |  | 6 | -6 
    29225 O |  |  | 4 
    29226 Iteration cutoff | 2 
    29227  
    29228 Matchmaker 3j0c.pdb1, chain I (#1.13) with AF3 CA.pdb, chain A (#666),
    29229 sequence alignment score = 306.5 
    29230 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    29231 2.689) 
    29232  
    29233 
    29234 > hide sel cartoons
    29235 
    29236 > color #662 dodgerblue
    29237 
    29238 > color #663 dodgerblue
    29239 
    29240 > color #664 #00b305ff
    29241 
    29242 > color #665 #00b305ff
    29243 
    29244 > color #666 #f15839ff
    29245 
    29246 > select #1.14/G
    29247 
    29248 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    29249 
    29250 > show sel cartoons
    29251 
    29252 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    29253 
    29254 Chain information for AF3 E1 1-421.pdb #667 
    29255 --- 
    29256 Chain | Description 
    29257 A | No description available 
    29258  
    29259 
    29260 > matchmaker #667 to #1.13 & sel
    29261 
    29262 No 'to' model specified 
    29263 
    29264 > matchmaker #667 to #1.14 & sel
    29265 
    29266 Parameters 
    29267 --- 
    29268 Chain pairing | bb 
    29269 Alignment algorithm | Needleman-Wunsch 
    29270 Similarity matrix | BLOSUM-62 
    29271 SS fraction | 0.3 
    29272 Gap open (HH/SS/other) | 18/18/6 
    29273 Gap extend | 1 
    29274 SS matrix |  |  | H | S | O 
    29275 ---|---|---|--- 
    29276 H | 6 | -9 | -6 
    29277 S |  | 6 | -6 
    29278 O |  |  | 4 
    29279 Iteration cutoff | 2 
    29280  
    29281 Matchmaker 3j0c.pdb1, chain G (#1.14) with AF3 E1 1-421.pdb, chain A (#667),
    29282 sequence alignment score = 1060.7 
    29283 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    29284 2.985) 
    29285  
    29286 
    29287 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    29288 
    29289 Chain information for AF3 E1 422-461.pdb #668 
    29290 --- 
    29291 Chain | Description 
    29292 A | No description available 
    29293  
    29294 
    29295 > matchmaker #668 to #1.14 & sel
    29296 
    29297 Parameters 
    29298 --- 
    29299 Chain pairing | bb 
    29300 Alignment algorithm | Needleman-Wunsch 
    29301 Similarity matrix | BLOSUM-62 
    29302 SS fraction | 0.3 
    29303 Gap open (HH/SS/other) | 18/18/6 
    29304 Gap extend | 1 
    29305 SS matrix |  |  | H | S | O 
    29306 ---|---|---|--- 
    29307 H | 6 | -9 | -6 
    29308 S |  | 6 | -6 
    29309 O |  |  | 4 
    29310 Iteration cutoff | 2 
    29311  
    29312 Matchmaker 3j0c.pdb1, chain G (#1.14) with AF3 E1 422-461.pdb, chain A (#668),
    29313 sequence alignment score = 626.9 
    29314 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    29315 2.997) 
    29316  
    29317 
    29318 > hide sel cartoons
    29319 
    29320 > select #1.13/H
    29321 
    29322 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    29323 
    29324 > show sel cartoons
    29325 
    29326 > select #1.14/H
    29327 
    29328 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    29329 
    29330 > show sel cartoons
    29331 
    29332 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    29333 
    29334 Chain information for AF3 E2 1-352.pdb #669 
    29335 --- 
    29336 Chain | Description 
    29337 B | No description available 
    29338  
    29339 
    29340 > matchmaker #669 to #1.14 & sel
    29341 
    29342 Parameters 
    29343 --- 
    29344 Chain pairing | bb 
    29345 Alignment algorithm | Needleman-Wunsch 
    29346 Similarity matrix | BLOSUM-62 
    29347 SS fraction | 0.3 
    29348 Gap open (HH/SS/other) | 18/18/6 
    29349 Gap extend | 1 
    29350 SS matrix |  |  | H | S | O 
    29351 ---|---|---|--- 
    29352 H | 6 | -9 | -6 
    29353 S |  | 6 | -6 
    29354 O |  |  | 4 
    29355 Iteration cutoff | 2 
    29356  
    29357 Matchmaker 3j0c.pdb1, chain H (#1.14) with AF3 E2 1-352.pdb, chain B (#669),
    29358 sequence alignment score = 590.9 
    29359 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    29360 6.107) 
    29361  
    29362 
    29363 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    29364 
    29365 Chain information for AF3 E2 353-438.pdb #670 
    29366 --- 
    29367 Chain | Description 
    29368 B | No description available 
    29369  
    29370 
    29371 > matchmaker #670 to #1.14 & sel
    29372 
    29373 Parameters 
    29374 --- 
    29375 Chain pairing | bb 
    29376 Alignment algorithm | Needleman-Wunsch 
    29377 Similarity matrix | BLOSUM-62 
    29378 SS fraction | 0.3 
    29379 Gap open (HH/SS/other) | 18/18/6 
    29380 Gap extend | 1 
    29381 SS matrix |  |  | H | S | O 
    29382 ---|---|---|--- 
    29383 H | 6 | -9 | -6 
    29384 S |  | 6 | -6 
    29385 O |  |  | 4 
    29386 Iteration cutoff | 2 
    29387  
    29388 Matchmaker 3j0c.pdb1, chain H (#1.14) with AF3 E2 353-438.pdb, chain B (#670),
    29389 sequence alignment score = 329.4 
    29390 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    29391 8.150) 
    29392  
    29393 
    29394 > hide sel cartoons
    29395 
    29396 > select #1.14/I
    29397 
    29398 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    29399 
    29400 > show sel cartoons
    29401 
    29402 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    29403 
    29404 Chain information for AF3 CA.pdb #671 
    29405 --- 
    29406 Chain | Description 
    29407 A | No description available 
    29408  
    29409 
    29410 > matchmaker #671 to #1.14 & sel
    29411 
    29412 Parameters 
    29413 --- 
    29414 Chain pairing | bb 
    29415 Alignment algorithm | Needleman-Wunsch 
    29416 Similarity matrix | BLOSUM-62 
    29417 SS fraction | 0.3 
    29418 Gap open (HH/SS/other) | 18/18/6 
    29419 Gap extend | 1 
    29420 SS matrix |  |  | H | S | O 
    29421 ---|---|---|--- 
    29422 H | 6 | -9 | -6 
    29423 S |  | 6 | -6 
    29424 O |  |  | 4 
    29425 Iteration cutoff | 2 
    29426  
    29427 Matchmaker 3j0c.pdb1, chain I (#1.14) with AF3 CA.pdb, chain A (#671),
    29428 sequence alignment score = 306.5 
    29429 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    29430 2.689) 
    29431  
    29432 
    29433 > hide sel cartoons
    29434 
    29435 > color #667 dodgerblue
    29436 
    29437 > color #668 dodgerblue
    29438 
    29439 > color #669 #00b305ff
    29440 
    29441 > color #670 #00b305ff
    29442 
    29443 > color #671 #f15839ff
    29444 
    29445 > select #1.13/H
    29446 
    29447 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    29448 
    29449 > hide sel cartoons
    29450 
    29451 > select #1.14/G
    29452 
    29453 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    29454 
    29455 > show sel cartoons
    29456 
    29457 > hide sel cartoons
    29458 
    29459 > select #1.15/G
    29460 
    29461 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    29462 
    29463 > show sel cartoons
    29464 
    29465 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    29466 
    29467 Chain information for AF3 E1 1-421.pdb #672 
    29468 --- 
    29469 Chain | Description 
    29470 A | No description available 
    29471  
    29472 
    29473 > matchmaker #672 to #1.15 & sel
    29474 
    29475 Parameters 
    29476 --- 
    29477 Chain pairing | bb 
    29478 Alignment algorithm | Needleman-Wunsch 
    29479 Similarity matrix | BLOSUM-62 
    29480 SS fraction | 0.3 
    29481 Gap open (HH/SS/other) | 18/18/6 
    29482 Gap extend | 1 
    29483 SS matrix |  |  | H | S | O 
    29484 ---|---|---|--- 
    29485 H | 6 | -9 | -6 
    29486 S |  | 6 | -6 
    29487 O |  |  | 4 
    29488 Iteration cutoff | 2 
    29489  
    29490 Matchmaker 3j0c.pdb1, chain G (#1.15) with AF3 E1 1-421.pdb, chain A (#672),
    29491 sequence alignment score = 1060.7 
    29492 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    29493 2.985) 
    29494  
    29495 
    29496 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    29497 
    29498 Chain information for AF3 E1 422-461.pdb #673 
    29499 --- 
    29500 Chain | Description 
    29501 A | No description available 
    29502  
    29503 
    29504 > matchmaker #673 to #1.15 & sel
    29505 
    29506 Parameters 
    29507 --- 
    29508 Chain pairing | bb 
    29509 Alignment algorithm | Needleman-Wunsch 
    29510 Similarity matrix | BLOSUM-62 
    29511 SS fraction | 0.3 
    29512 Gap open (HH/SS/other) | 18/18/6 
    29513 Gap extend | 1 
    29514 SS matrix |  |  | H | S | O 
    29515 ---|---|---|--- 
    29516 H | 6 | -9 | -6 
    29517 S |  | 6 | -6 
    29518 O |  |  | 4 
    29519 Iteration cutoff | 2 
    29520  
    29521 Matchmaker 3j0c.pdb1, chain G (#1.15) with AF3 E1 422-461.pdb, chain A (#673),
    29522 sequence alignment score = 626.9 
    29523 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    29524 2.997) 
    29525  
    29526 
    29527 > hide sel cartoons
    29528 
    29529 > select #1.15/H
    29530 
    29531 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    29532 
    29533 > show sel cartoons
    29534 
    29535 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    29536 
    29537 Chain information for AF3 E2 1-352.pdb #674 
    29538 --- 
    29539 Chain | Description 
    29540 B | No description available 
    29541  
    29542 
    29543 > matchmaker #674 to #1.15 & sel
    29544 
    29545 Parameters 
    29546 --- 
    29547 Chain pairing | bb 
    29548 Alignment algorithm | Needleman-Wunsch 
    29549 Similarity matrix | BLOSUM-62 
    29550 SS fraction | 0.3 
    29551 Gap open (HH/SS/other) | 18/18/6 
    29552 Gap extend | 1 
    29553 SS matrix |  |  | H | S | O 
    29554 ---|---|---|--- 
    29555 H | 6 | -9 | -6 
    29556 S |  | 6 | -6 
    29557 O |  |  | 4 
    29558 Iteration cutoff | 2 
    29559  
    29560 Matchmaker 3j0c.pdb1, chain H (#1.15) with AF3 E2 1-352.pdb, chain B (#674),
    29561 sequence alignment score = 590.9 
    29562 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    29563 6.107) 
    29564  
    29565 
    29566 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    29567 
    29568 Chain information for AF3 E2 353-438.pdb #675 
    29569 --- 
    29570 Chain | Description 
    29571 B | No description available 
    29572  
    29573 
    29574 > matchmaker #675 to #1.15 & sel
    29575 
    29576 Parameters 
    29577 --- 
    29578 Chain pairing | bb 
    29579 Alignment algorithm | Needleman-Wunsch 
    29580 Similarity matrix | BLOSUM-62 
    29581 SS fraction | 0.3 
    29582 Gap open (HH/SS/other) | 18/18/6 
    29583 Gap extend | 1 
    29584 SS matrix |  |  | H | S | O 
    29585 ---|---|---|--- 
    29586 H | 6 | -9 | -6 
    29587 S |  | 6 | -6 
    29588 O |  |  | 4 
    29589 Iteration cutoff | 2 
    29590  
    29591 Matchmaker 3j0c.pdb1, chain H (#1.15) with AF3 E2 353-438.pdb, chain B (#675),
    29592 sequence alignment score = 329.4 
    29593 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    29594 8.150) 
    29595  
    29596 
    29597 > hide sel cartoons
    29598 
    29599 > select #1.15/I
    29600 
    29601 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    29602 
    29603 > show sel cartoons
    29604 
    29605 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    29606 
    29607 Chain information for AF3 CA.pdb #676 
    29608 --- 
    29609 Chain | Description 
    29610 A | No description available 
    29611  
    29612 
    29613 > matchmaker #676 to #1.15 & sel
    29614 
    29615 Parameters 
    29616 --- 
    29617 Chain pairing | bb 
    29618 Alignment algorithm | Needleman-Wunsch 
    29619 Similarity matrix | BLOSUM-62 
    29620 SS fraction | 0.3 
    29621 Gap open (HH/SS/other) | 18/18/6 
    29622 Gap extend | 1 
    29623 SS matrix |  |  | H | S | O 
    29624 ---|---|---|--- 
    29625 H | 6 | -9 | -6 
    29626 S |  | 6 | -6 
    29627 O |  |  | 4 
    29628 Iteration cutoff | 2 
    29629  
    29630 Matchmaker 3j0c.pdb1, chain I (#1.15) with AF3 CA.pdb, chain A (#676),
    29631 sequence alignment score = 306.5 
    29632 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    29633 2.689) 
    29634  
    29635 
    29636 > hide sel cartoons
    29637 
    29638 > color #672 dodgerblue
    29639 
    29640 > color #673 dodgerblue
    29641 
    29642 > color #674 #00b305ff
    29643 
    29644 > color #675 #00b305ff
    29645 
    29646 > color #676 #f15839ff
    29647 
    29648 > select #1.16/G
    29649 
    29650 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    29651 
    29652 > show sel cartoons
    29653 
    29654 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    29655 
    29656 Chain information for AF3 E1 1-421.pdb #677 
    29657 --- 
    29658 Chain | Description 
    29659 A | No description available 
    29660  
    29661 
    29662 > matchmaker #677 to #1.15 & sel
    29663 
    29664 No 'to' model specified 
    29665 
    29666 > matchmaker #677 to #1.16 & sel
    29667 
    29668 Parameters 
    29669 --- 
    29670 Chain pairing | bb 
    29671 Alignment algorithm | Needleman-Wunsch 
    29672 Similarity matrix | BLOSUM-62 
    29673 SS fraction | 0.3 
    29674 Gap open (HH/SS/other) | 18/18/6 
    29675 Gap extend | 1 
    29676 SS matrix |  |  | H | S | O 
    29677 ---|---|---|--- 
    29678 H | 6 | -9 | -6 
    29679 S |  | 6 | -6 
    29680 O |  |  | 4 
    29681 Iteration cutoff | 2 
    29682  
    29683 Matchmaker 3j0c.pdb1, chain G (#1.16) with AF3 E1 1-421.pdb, chain A (#677),
    29684 sequence alignment score = 1060.7 
    29685 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    29686 2.985) 
    29687  
    29688 
    29689 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    29690 
    29691 Chain information for AF3 E1 422-461.pdb #678 
    29692 --- 
    29693 Chain | Description 
    29694 A | No description available 
    29695  
    29696 
    29697 > matchmaker #678 to #1.16 & sel
    29698 
    29699 Parameters 
    29700 --- 
    29701 Chain pairing | bb 
    29702 Alignment algorithm | Needleman-Wunsch 
    29703 Similarity matrix | BLOSUM-62 
    29704 SS fraction | 0.3 
    29705 Gap open (HH/SS/other) | 18/18/6 
    29706 Gap extend | 1 
    29707 SS matrix |  |  | H | S | O 
    29708 ---|---|---|--- 
    29709 H | 6 | -9 | -6 
    29710 S |  | 6 | -6 
    29711 O |  |  | 4 
    29712 Iteration cutoff | 2 
    29713  
    29714 Matchmaker 3j0c.pdb1, chain G (#1.16) with AF3 E1 422-461.pdb, chain A (#678),
    29715 sequence alignment score = 626.9 
    29716 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    29717 2.997) 
    29718  
    29719 
    29720 > hide sel cartoons
    29721 
    29722 > select #1.16/H
    29723 
    29724 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    29725 
    29726 > show sel cartoons
    29727 
    29728 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    29729 
    29730 Chain information for AF3 E2 1-352.pdb #679 
    29731 --- 
    29732 Chain | Description 
    29733 B | No description available 
    29734  
    29735 
    29736 > matchmaker #679 to #1.16 & sel
    29737 
    29738 Parameters 
    29739 --- 
    29740 Chain pairing | bb 
    29741 Alignment algorithm | Needleman-Wunsch 
    29742 Similarity matrix | BLOSUM-62 
    29743 SS fraction | 0.3 
    29744 Gap open (HH/SS/other) | 18/18/6 
    29745 Gap extend | 1 
    29746 SS matrix |  |  | H | S | O 
    29747 ---|---|---|--- 
    29748 H | 6 | -9 | -6 
    29749 S |  | 6 | -6 
    29750 O |  |  | 4 
    29751 Iteration cutoff | 2 
    29752  
    29753 Matchmaker 3j0c.pdb1, chain H (#1.16) with AF3 E2 1-352.pdb, chain B (#679),
    29754 sequence alignment score = 590.9 
    29755 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    29756 6.107) 
    29757  
    29758 
    29759 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    29760 
    29761 Chain information for AF3 E2 353-438.pdb #680 
    29762 --- 
    29763 Chain | Description 
    29764 B | No description available 
    29765  
    29766 
    29767 > matchmaker #680 to #1.16 & sel
    29768 
    29769 Parameters 
    29770 --- 
    29771 Chain pairing | bb 
    29772 Alignment algorithm | Needleman-Wunsch 
    29773 Similarity matrix | BLOSUM-62 
    29774 SS fraction | 0.3 
    29775 Gap open (HH/SS/other) | 18/18/6 
    29776 Gap extend | 1 
    29777 SS matrix |  |  | H | S | O 
    29778 ---|---|---|--- 
    29779 H | 6 | -9 | -6 
    29780 S |  | 6 | -6 
    29781 O |  |  | 4 
    29782 Iteration cutoff | 2 
    29783  
    29784 Matchmaker 3j0c.pdb1, chain H (#1.16) with AF3 E2 353-438.pdb, chain B (#680),
    29785 sequence alignment score = 329.4 
    29786 RMSD between 40 pruned atom pairs is 0.937 angstroms; (across all 84 pairs:
    29787 8.150) 
    29788  
    29789 
    29790 > hide sel cartoons
    29791 
    29792 > select #1.16/I
    29793 
    29794 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    29795 
    29796 > show sel cartoons
    29797 
    29798 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    29799 
    29800 Chain information for AF3 CA.pdb #681 
    29801 --- 
    29802 Chain | Description 
    29803 A | No description available 
    29804  
    29805 
    29806 > matchmaker #681 to #1.16 & sel
    29807 
    29808 Parameters 
    29809 --- 
    29810 Chain pairing | bb 
    29811 Alignment algorithm | Needleman-Wunsch 
    29812 Similarity matrix | BLOSUM-62 
    29813 SS fraction | 0.3 
    29814 Gap open (HH/SS/other) | 18/18/6 
    29815 Gap extend | 1 
    29816 SS matrix |  |  | H | S | O 
    29817 ---|---|---|--- 
    29818 H | 6 | -9 | -6 
    29819 S |  | 6 | -6 
    29820 O |  |  | 4 
    29821 Iteration cutoff | 2 
    29822  
    29823 Matchmaker 3j0c.pdb1, chain I (#1.16) with AF3 CA.pdb, chain A (#681),
    29824 sequence alignment score = 306.5 
    29825 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    29826 2.689) 
    29827  
    29828 
    29829 > hide sel cartoons
    29830 
    29831 > color #677 dodgerblue
    29832 
    29833 > color #678 dodgerblue
    29834 
    29835 > color #679 #00b305ff
    29836 
    29837 > color #680 dodgerblue
    29838 
    29839 > color #680 #00b305ff
    29840 
    29841 > color #681 #f15839ff
    29842 
    29843 > select #1.17/G
    29844 
    29845 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    29846 
    29847 > show sel cartoons
    29848 
    29849 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    29850 
    29851 Chain information for AF3 E1 1-421.pdb #682 
    29852 --- 
    29853 Chain | Description 
    29854 A | No description available 
    29855  
    29856 
    29857 > matchmaker #682 to #1.16 & sel
    29858 
    29859 No 'to' model specified 
    29860 
    29861 > matchmaker #682 to #1.17 & sel
    29862 
    29863 Parameters 
    29864 --- 
    29865 Chain pairing | bb 
    29866 Alignment algorithm | Needleman-Wunsch 
    29867 Similarity matrix | BLOSUM-62 
    29868 SS fraction | 0.3 
    29869 Gap open (HH/SS/other) | 18/18/6 
    29870 Gap extend | 1 
    29871 SS matrix |  |  | H | S | O 
    29872 ---|---|---|--- 
    29873 H | 6 | -9 | -6 
    29874 S |  | 6 | -6 
    29875 O |  |  | 4 
    29876 Iteration cutoff | 2 
    29877  
    29878 Matchmaker 3j0c.pdb1, chain G (#1.17) with AF3 E1 1-421.pdb, chain A (#682),
    29879 sequence alignment score = 1060.7 
    29880 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    29881 2.985) 
    29882  
    29883 
    29884 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    29885 
    29886 Chain information for AF3 E1 422-461.pdb #683 
    29887 --- 
    29888 Chain | Description 
    29889 A | No description available 
    29890  
    29891 
    29892 > matchmaker #683 to #1.17 & sel
    29893 
    29894 Parameters 
    29895 --- 
    29896 Chain pairing | bb 
    29897 Alignment algorithm | Needleman-Wunsch 
    29898 Similarity matrix | BLOSUM-62 
    29899 SS fraction | 0.3 
    29900 Gap open (HH/SS/other) | 18/18/6 
    29901 Gap extend | 1 
    29902 SS matrix |  |  | H | S | O 
    29903 ---|---|---|--- 
    29904 H | 6 | -9 | -6 
    29905 S |  | 6 | -6 
    29906 O |  |  | 4 
    29907 Iteration cutoff | 2 
    29908  
    29909 Matchmaker 3j0c.pdb1, chain G (#1.17) with AF3 E1 422-461.pdb, chain A (#683),
    29910 sequence alignment score = 626.9 
    29911 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    29912 2.997) 
    29913  
    29914 
    29915 > hide sel cartoons
    29916 
    29917 > select #1.17/H
    29918 
    29919 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    29920 
    29921 > show sel cartoons
    29922 
    29923 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    29924 
    29925 Chain information for AF3 E2 1-352.pdb #684 
    29926 --- 
    29927 Chain | Description 
    29928 B | No description available 
    29929  
    29930 
    29931 > matchmaker #684 to #1.17 & sel
    29932 
    29933 Parameters 
    29934 --- 
    29935 Chain pairing | bb 
    29936 Alignment algorithm | Needleman-Wunsch 
    29937 Similarity matrix | BLOSUM-62 
    29938 SS fraction | 0.3 
    29939 Gap open (HH/SS/other) | 18/18/6 
    29940 Gap extend | 1 
    29941 SS matrix |  |  | H | S | O 
    29942 ---|---|---|--- 
    29943 H | 6 | -9 | -6 
    29944 S |  | 6 | -6 
    29945 O |  |  | 4 
    29946 Iteration cutoff | 2 
    29947  
    29948 Matchmaker 3j0c.pdb1, chain H (#1.17) with AF3 E2 1-352.pdb, chain B (#684),
    29949 sequence alignment score = 590.9 
    29950 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    29951 6.107) 
    29952  
    29953 
    29954 > hide sel cartoons
    29955 
    29956 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    29957 
    29958 Chain information for AF3 E2 353-438.pdb #685 
    29959 --- 
    29960 Chain | Description 
    29961 B | No description available 
    29962  
    29963 
    29964 > matchmaker #685 to #1.17 & sel
    29965 
    29966 Parameters 
    29967 --- 
    29968 Chain pairing | bb 
    29969 Alignment algorithm | Needleman-Wunsch 
    29970 Similarity matrix | BLOSUM-62 
    29971 SS fraction | 0.3 
    29972 Gap open (HH/SS/other) | 18/18/6 
    29973 Gap extend | 1 
    29974 SS matrix |  |  | H | S | O 
    29975 ---|---|---|--- 
    29976 H | 6 | -9 | -6 
    29977 S |  | 6 | -6 
    29978 O |  |  | 4 
    29979 Iteration cutoff | 2 
    29980  
    29981 Matchmaker 3j0c.pdb1, chain H (#1.17) with AF3 E2 353-438.pdb, chain B (#685),
    29982 sequence alignment score = 329.4 
    29983 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    29984 8.150) 
    29985  
    29986 
    29987 > select #1.17/I
    29988 
    29989 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    29990 
    29991 > show sel cartoons
    29992 
    29993 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    29994 
    29995 Chain information for AF3 CA.pdb #686 
    29996 --- 
    29997 Chain | Description 
    29998 A | No description available 
    29999  
    30000 
    30001 > matchmaker #686 to #1.17 & sel
    30002 
    30003 Parameters 
    30004 --- 
    30005 Chain pairing | bb 
    30006 Alignment algorithm | Needleman-Wunsch 
    30007 Similarity matrix | BLOSUM-62 
    30008 SS fraction | 0.3 
    30009 Gap open (HH/SS/other) | 18/18/6 
    30010 Gap extend | 1 
    30011 SS matrix |  |  | H | S | O 
    30012 ---|---|---|--- 
    30013 H | 6 | -9 | -6 
    30014 S |  | 6 | -6 
    30015 O |  |  | 4 
    30016 Iteration cutoff | 2 
    30017  
    30018 Matchmaker 3j0c.pdb1, chain I (#1.17) with AF3 CA.pdb, chain A (#686),
    30019 sequence alignment score = 306.5 
    30020 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    30021 2.689) 
    30022  
    30023 
    30024 > hide sel cartoons
    30025 
    30026 > color #682 dodgerblue
    30027 
    30028 > color #683 dodgerblue
    30029 
    30030 > color #684 #00b305ff
    30031 
    30032 > color #685 #00b305ff
    30033 
    30034 > color #686 #f15839ff
    30035 
    30036 > select #1.18/G
    30037 
    30038 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    30039 
    30040 > show sel cartoons
    30041 
    30042 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    30043 
    30044 Chain information for AF3 E1 1-421.pdb #687 
    30045 --- 
    30046 Chain | Description 
    30047 A | No description available 
    30048  
    30049 
    30050 > matchmaker #687 to #1.18 & sel
    30051 
    30052 Parameters 
    30053 --- 
    30054 Chain pairing | bb 
    30055 Alignment algorithm | Needleman-Wunsch 
    30056 Similarity matrix | BLOSUM-62 
    30057 SS fraction | 0.3 
    30058 Gap open (HH/SS/other) | 18/18/6 
    30059 Gap extend | 1 
    30060 SS matrix |  |  | H | S | O 
    30061 ---|---|---|--- 
    30062 H | 6 | -9 | -6 
    30063 S |  | 6 | -6 
    30064 O |  |  | 4 
    30065 Iteration cutoff | 2 
    30066  
    30067 Matchmaker 3j0c.pdb1, chain G (#1.18) with AF3 E1 1-421.pdb, chain A (#687),
    30068 sequence alignment score = 1060.7 
    30069 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    30070 2.985) 
    30071  
    30072 
    30073 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    30074 
    30075 Chain information for AF3 E1 422-461.pdb #688 
    30076 --- 
    30077 Chain | Description 
    30078 A | No description available 
    30079  
    30080 
    30081 > matchmaker #688 to #1.18 & sel
    30082 
    30083 Parameters 
    30084 --- 
    30085 Chain pairing | bb 
    30086 Alignment algorithm | Needleman-Wunsch 
    30087 Similarity matrix | BLOSUM-62 
    30088 SS fraction | 0.3 
    30089 Gap open (HH/SS/other) | 18/18/6 
    30090 Gap extend | 1 
    30091 SS matrix |  |  | H | S | O 
    30092 ---|---|---|--- 
    30093 H | 6 | -9 | -6 
    30094 S |  | 6 | -6 
    30095 O |  |  | 4 
    30096 Iteration cutoff | 2 
    30097  
    30098 Matchmaker 3j0c.pdb1, chain G (#1.18) with AF3 E1 422-461.pdb, chain A (#688),
    30099 sequence alignment score = 626.9 
    30100 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    30101 2.997) 
    30102  
    30103 
    30104 > hide sel cartoons
    30105 
    30106 > select #1.18/H
    30107 
    30108 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    30109 
    30110 > show sel cartoons
    30111 
    30112 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    30113 
    30114 Chain information for AF3 E2 1-352.pdb #689 
    30115 --- 
    30116 Chain | Description 
    30117 B | No description available 
    30118  
    30119 
    30120 > matchmaker #689 to #1.18 & sel
    30121 
    30122 Parameters 
    30123 --- 
    30124 Chain pairing | bb 
    30125 Alignment algorithm | Needleman-Wunsch 
    30126 Similarity matrix | BLOSUM-62 
    30127 SS fraction | 0.3 
    30128 Gap open (HH/SS/other) | 18/18/6 
    30129 Gap extend | 1 
    30130 SS matrix |  |  | H | S | O 
    30131 ---|---|---|--- 
    30132 H | 6 | -9 | -6 
    30133 S |  | 6 | -6 
    30134 O |  |  | 4 
    30135 Iteration cutoff | 2 
    30136  
    30137 Matchmaker 3j0c.pdb1, chain H (#1.18) with AF3 E2 1-352.pdb, chain B (#689),
    30138 sequence alignment score = 590.9 
    30139 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    30140 6.107) 
    30141  
    30142 
    30143 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    30144 
    30145 Chain information for AF3 E2 353-438.pdb #690 
    30146 --- 
    30147 Chain | Description 
    30148 B | No description available 
    30149  
    30150 
    30151 > matchmaker #690 to #1.18 & sel
    30152 
    30153 Parameters 
    30154 --- 
    30155 Chain pairing | bb 
    30156 Alignment algorithm | Needleman-Wunsch 
    30157 Similarity matrix | BLOSUM-62 
    30158 SS fraction | 0.3 
    30159 Gap open (HH/SS/other) | 18/18/6 
    30160 Gap extend | 1 
    30161 SS matrix |  |  | H | S | O 
    30162 ---|---|---|--- 
    30163 H | 6 | -9 | -6 
    30164 S |  | 6 | -6 
    30165 O |  |  | 4 
    30166 Iteration cutoff | 2 
    30167  
    30168 Matchmaker 3j0c.pdb1, chain H (#1.18) with AF3 E2 353-438.pdb, chain B (#690),
    30169 sequence alignment score = 329.4 
    30170 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    30171 8.150) 
    30172  
    30173 
    30174 > hide sel cartoons
    30175 
    30176 > select #1.18/I
    30177 
    30178 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    30179 
    30180 > show sel cartoons
    30181 
    30182 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    30183 
    30184 Chain information for AF3 CA.pdb #691 
    30185 --- 
    30186 Chain | Description 
    30187 A | No description available 
    30188  
    30189 
    30190 > matchmaker #691 to #1.18 & sel
    30191 
    30192 Parameters 
    30193 --- 
    30194 Chain pairing | bb 
    30195 Alignment algorithm | Needleman-Wunsch 
    30196 Similarity matrix | BLOSUM-62 
    30197 SS fraction | 0.3 
    30198 Gap open (HH/SS/other) | 18/18/6 
    30199 Gap extend | 1 
    30200 SS matrix |  |  | H | S | O 
    30201 ---|---|---|--- 
    30202 H | 6 | -9 | -6 
    30203 S |  | 6 | -6 
    30204 O |  |  | 4 
    30205 Iteration cutoff | 2 
    30206  
    30207 Matchmaker 3j0c.pdb1, chain I (#1.18) with AF3 CA.pdb, chain A (#691),
    30208 sequence alignment score = 306.5 
    30209 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    30210 2.689) 
    30211  
    30212 
    30213 > hide sel cartoons
    30214 
    30215 > color #687 dodgerblue
    30216 
    30217 > color #688 dodgerblue
    30218 
    30219 > color #689 #00b305ff
    30220 
    30221 > color #690 #00b305ff
    30222 
    30223 > color #691 #f15839ff
    30224 
    30225 > select #1.19/G
    30226 
    30227 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    30228 
    30229 > show sel cartoons
    30230 
    30231 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    30232 
    30233 Chain information for AF3 E1 1-421.pdb #692 
    30234 --- 
    30235 Chain | Description 
    30236 A | No description available 
    30237  
    30238 
    30239 > matchmaker #692 to #1.18 & sel
    30240 
    30241 No 'to' model specified 
    30242 
    30243 > matchmaker #692 to #1.19 & sel
    30244 
    30245 Parameters 
    30246 --- 
    30247 Chain pairing | bb 
    30248 Alignment algorithm | Needleman-Wunsch 
    30249 Similarity matrix | BLOSUM-62 
    30250 SS fraction | 0.3 
    30251 Gap open (HH/SS/other) | 18/18/6 
    30252 Gap extend | 1 
    30253 SS matrix |  |  | H | S | O 
    30254 ---|---|---|--- 
    30255 H | 6 | -9 | -6 
    30256 S |  | 6 | -6 
    30257 O |  |  | 4 
    30258 Iteration cutoff | 2 
    30259  
    30260 Matchmaker 3j0c.pdb1, chain G (#1.19) with AF3 E1 1-421.pdb, chain A (#692),
    30261 sequence alignment score = 1060.7 
    30262 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    30263 2.985) 
    30264  
    30265 
    30266 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    30267 
    30268 Chain information for AF3 E1 422-461.pdb #693 
    30269 --- 
    30270 Chain | Description 
    30271 A | No description available 
    30272  
    30273 
    30274 > matchmaker #693 to #1.19 & sel
    30275 
    30276 Parameters 
    30277 --- 
    30278 Chain pairing | bb 
    30279 Alignment algorithm | Needleman-Wunsch 
    30280 Similarity matrix | BLOSUM-62 
    30281 SS fraction | 0.3 
    30282 Gap open (HH/SS/other) | 18/18/6 
    30283 Gap extend | 1 
    30284 SS matrix |  |  | H | S | O 
    30285 ---|---|---|--- 
    30286 H | 6 | -9 | -6 
    30287 S |  | 6 | -6 
    30288 O |  |  | 4 
    30289 Iteration cutoff | 2 
    30290  
    30291 Matchmaker 3j0c.pdb1, chain G (#1.19) with AF3 E1 422-461.pdb, chain A (#693),
    30292 sequence alignment score = 626.9 
    30293 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    30294 2.997) 
    30295  
    30296 
    30297 > hide sel cartoons
    30298 
    30299 > select #1.19/H
    30300 
    30301 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    30302 
    30303 > show sel cartoons
    30304 
    30305 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    30306 
    30307 Chain information for AF3 E2 1-352.pdb #694 
    30308 --- 
    30309 Chain | Description 
    30310 B | No description available 
    30311  
    30312 
    30313 > matchmaker #694 to #1.19 & sel
    30314 
    30315 Parameters 
    30316 --- 
    30317 Chain pairing | bb 
    30318 Alignment algorithm | Needleman-Wunsch 
    30319 Similarity matrix | BLOSUM-62 
    30320 SS fraction | 0.3 
    30321 Gap open (HH/SS/other) | 18/18/6 
    30322 Gap extend | 1 
    30323 SS matrix |  |  | H | S | O 
    30324 ---|---|---|--- 
    30325 H | 6 | -9 | -6 
    30326 S |  | 6 | -6 
    30327 O |  |  | 4 
    30328 Iteration cutoff | 2 
    30329  
    30330 Matchmaker 3j0c.pdb1, chain H (#1.19) with AF3 E2 1-352.pdb, chain B (#694),
    30331 sequence alignment score = 590.9 
    30332 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    30333 6.107) 
    30334  
    30335 
    30336 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    30337 
    30338 Chain information for AF3 E2 353-438.pdb #695 
    30339 --- 
    30340 Chain | Description 
    30341 B | No description available 
    30342  
    30343 
    30344 > matchmaker #695 to #1.19 & sel
    30345 
    30346 Parameters 
    30347 --- 
    30348 Chain pairing | bb 
    30349 Alignment algorithm | Needleman-Wunsch 
    30350 Similarity matrix | BLOSUM-62 
    30351 SS fraction | 0.3 
    30352 Gap open (HH/SS/other) | 18/18/6 
    30353 Gap extend | 1 
    30354 SS matrix |  |  | H | S | O 
    30355 ---|---|---|--- 
    30356 H | 6 | -9 | -6 
    30357 S |  | 6 | -6 
    30358 O |  |  | 4 
    30359 Iteration cutoff | 2 
    30360  
    30361 Matchmaker 3j0c.pdb1, chain H (#1.19) with AF3 E2 353-438.pdb, chain B (#695),
    30362 sequence alignment score = 329.4 
    30363 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    30364 8.150) 
    30365  
    30366 
    30367 > hide sel cartoons
    30368 
    30369 > select #1.19/I
    30370 
    30371 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    30372 
    30373 > show sel cartoons
    30374 
    30375 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    30376 
    30377 Chain information for AF3 CA.pdb #696 
    30378 --- 
    30379 Chain | Description 
    30380 A | No description available 
    30381  
    30382 
    30383 > matchmaker #696 to #1.19 & sel
    30384 
    30385 Parameters 
    30386 --- 
    30387 Chain pairing | bb 
    30388 Alignment algorithm | Needleman-Wunsch 
    30389 Similarity matrix | BLOSUM-62 
    30390 SS fraction | 0.3 
    30391 Gap open (HH/SS/other) | 18/18/6 
    30392 Gap extend | 1 
    30393 SS matrix |  |  | H | S | O 
    30394 ---|---|---|--- 
    30395 H | 6 | -9 | -6 
    30396 S |  | 6 | -6 
    30397 O |  |  | 4 
    30398 Iteration cutoff | 2 
    30399  
    30400 Matchmaker 3j0c.pdb1, chain I (#1.19) with AF3 CA.pdb, chain A (#696),
    30401 sequence alignment score = 306.5 
    30402 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    30403 2.689) 
    30404  
    30405 
    30406 > hide sel cartoons
    30407 
    30408 > color #692 dodgerblue
    30409 
    30410 > color #693 dodgerblue
    30411 
    30412 > color #694 #00b305ff
    30413 
    30414 > color #695 #00b305ff
    30415 
    30416 > color #696 #f15839ff
    30417 
    30418 > select #1.20/G
    30419 
    30420 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    30421 
    30422 > show sel cartoons
    30423 
    30424 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    30425 
    30426 Chain information for AF3 E1 1-421.pdb #697 
    30427 --- 
    30428 Chain | Description 
    30429 A | No description available 
    30430  
    30431 
    30432 > matchmaker #697 to #1.20 & sel
    30433 
    30434 Parameters 
    30435 --- 
    30436 Chain pairing | bb 
    30437 Alignment algorithm | Needleman-Wunsch 
    30438 Similarity matrix | BLOSUM-62 
    30439 SS fraction | 0.3 
    30440 Gap open (HH/SS/other) | 18/18/6 
    30441 Gap extend | 1 
    30442 SS matrix |  |  | H | S | O 
    30443 ---|---|---|--- 
    30444 H | 6 | -9 | -6 
    30445 S |  | 6 | -6 
    30446 O |  |  | 4 
    30447 Iteration cutoff | 2 
    30448  
    30449 Matchmaker 3j0c.pdb1, chain G (#1.20) with AF3 E1 1-421.pdb, chain A (#697),
    30450 sequence alignment score = 1060.7 
    30451 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    30452 2.985) 
    30453  
    30454 
    30455 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    30456 
    30457 Chain information for AF3 E1 422-461.pdb #698 
    30458 --- 
    30459 Chain | Description 
    30460 A | No description available 
    30461  
    30462 
    30463 > matchmaker #698 to #1.20 & sel
    30464 
    30465 Parameters 
    30466 --- 
    30467 Chain pairing | bb 
    30468 Alignment algorithm | Needleman-Wunsch 
    30469 Similarity matrix | BLOSUM-62 
    30470 SS fraction | 0.3 
    30471 Gap open (HH/SS/other) | 18/18/6 
    30472 Gap extend | 1 
    30473 SS matrix |  |  | H | S | O 
    30474 ---|---|---|--- 
    30475 H | 6 | -9 | -6 
    30476 S |  | 6 | -6 
    30477 O |  |  | 4 
    30478 Iteration cutoff | 2 
    30479  
    30480 Matchmaker 3j0c.pdb1, chain G (#1.20) with AF3 E1 422-461.pdb, chain A (#698),
    30481 sequence alignment score = 626.9 
    30482 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    30483 2.997) 
    30484  
    30485 
    30486 > hide sel cartoons
    30487 
    30488 > select #1.20/H
    30489 
    30490 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    30491 
    30492 > show sel cartoons
    30493 
    30494 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    30495 
    30496 Chain information for AF3 E2 1-352.pdb #699 
    30497 --- 
    30498 Chain | Description 
    30499 B | No description available 
    30500  
    30501 
    30502 > matchmaker #699 to #1.20 & sel
    30503 
    30504 Parameters 
    30505 --- 
    30506 Chain pairing | bb 
    30507 Alignment algorithm | Needleman-Wunsch 
    30508 Similarity matrix | BLOSUM-62 
    30509 SS fraction | 0.3 
    30510 Gap open (HH/SS/other) | 18/18/6 
    30511 Gap extend | 1 
    30512 SS matrix |  |  | H | S | O 
    30513 ---|---|---|--- 
    30514 H | 6 | -9 | -6 
    30515 S |  | 6 | -6 
    30516 O |  |  | 4 
    30517 Iteration cutoff | 2 
    30518  
    30519 Matchmaker 3j0c.pdb1, chain H (#1.20) with AF3 E2 1-352.pdb, chain B (#699),
    30520 sequence alignment score = 590.9 
    30521 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    30522 6.107) 
    30523  
    30524 
    30525 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    30526 
    30527 Chain information for AF3 E2 353-438.pdb #700 
    30528 --- 
    30529 Chain | Description 
    30530 B | No description available 
    30531  
    30532 
    30533 > matchmaker #700 to #1.20 & sel
    30534 
    30535 Parameters 
    30536 --- 
    30537 Chain pairing | bb 
    30538 Alignment algorithm | Needleman-Wunsch 
    30539 Similarity matrix | BLOSUM-62 
    30540 SS fraction | 0.3 
    30541 Gap open (HH/SS/other) | 18/18/6 
    30542 Gap extend | 1 
    30543 SS matrix |  |  | H | S | O 
    30544 ---|---|---|--- 
    30545 H | 6 | -9 | -6 
    30546 S |  | 6 | -6 
    30547 O |  |  | 4 
    30548 Iteration cutoff | 2 
    30549  
    30550 Matchmaker 3j0c.pdb1, chain H (#1.20) with AF3 E2 353-438.pdb, chain B (#700),
    30551 sequence alignment score = 329.4 
    30552 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    30553 8.150) 
    30554  
    30555 
    30556 > hide sel cartoons
    30557 
    30558 > select #1.20/I
    30559 
    30560 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    30561 
    30562 > show sel cartoons
    30563 
    30564 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    30565 
    30566 Chain information for AF3 CA.pdb #701 
    30567 --- 
    30568 Chain | Description 
    30569 A | No description available 
    30570  
    30571 
    30572 > matchmaker #701 to #1.20 & sel
    30573 
    30574 Parameters 
    30575 --- 
    30576 Chain pairing | bb 
    30577 Alignment algorithm | Needleman-Wunsch 
    30578 Similarity matrix | BLOSUM-62 
    30579 SS fraction | 0.3 
    30580 Gap open (HH/SS/other) | 18/18/6 
    30581 Gap extend | 1 
    30582 SS matrix |  |  | H | S | O 
    30583 ---|---|---|--- 
    30584 H | 6 | -9 | -6 
    30585 S |  | 6 | -6 
    30586 O |  |  | 4 
    30587 Iteration cutoff | 2 
    30588  
    30589 Matchmaker 3j0c.pdb1, chain I (#1.20) with AF3 CA.pdb, chain A (#701),
    30590 sequence alignment score = 306.5 
    30591 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    30592 2.689) 
    30593  
    30594 
    30595 > hide sel cartoons
    30596 
    30597 > color #697 dodgerblue
    30598 
    30599 > color #698 dodgerblue
    30600 
    30601 > color #699 #00b305ff
    30602 
    30603 > color #700 #00b305ff
    30604 
    30605 > color #701 #f15839ff
    30606 
    30607 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    30608 
    30609 > hide #652 models
    30610 
    30611 > hide #653 models
    30612 
    30613 > hide #654 models
    30614 
    30615 > hide #655 models
    30616 
    30617 > hide #656 models
    30618 
    30619 > hide #657 models
    30620 
    30621 > hide #658 models
    30622 
    30623 > hide #660 models
    30624 
    30625 > hide #661 models
    30626 
    30627 > hide #659 models
    30628 
    30629 > hide #662 models
    30630 
    30631 > hide #663 models
    30632 
    30633 > hide #664 models
    30634 
    30635 > hide #665 models
    30636 
    30637 > hide #666 models
    30638 
    30639 > hide #667 models
    30640 
    30641 > hide #668 models
    30642 
    30643 > hide #669 models
    30644 
    30645 > hide #670 models
    30646 
    30647 > hide #671 models
    30648 
    30649 > hide #672 models
    30650 
    30651 > hide #673 models
    30652 
    30653 > hide #674 models
    30654 
    30655 > hide #675 models
    30656 
    30657 > hide #676 models
    30658 
    30659 > hide #677 models
    30660 
    30661 > hide #678 models
    30662 
    30663 > hide #679 models
    30664 
    30665 > hide #680 models
    30666 
    30667 > hide #681 models
    30668 
    30669 > hide #682 models
    30670 
    30671 > hide #683 models
    30672 
    30673 > hide #684 models
    30674 
    30675 > hide #685 models
    30676 
    30677 > hide #686 models
    30678 
    30679 > hide #687 models
    30680 
    30681 > hide #688 models
    30682 
    30683 > hide #689 models
    30684 
    30685 > hide #690 models
    30686 
    30687 > hide #691 models
    30688 
    30689 > hide #692 models
    30690 
    30691 > hide #693 models
    30692 
    30693 > hide #694 models
    30694 
    30695 > hide #695 models
    30696 
    30697 > hide #696 models
    30698 
    30699 > hide #697 models
    30700 
    30701 > hide #698 models
    30702 
    30703 > hide #699 models
    30704 
    30705 > hide #700 models
    30706 
    30707 > hide #701 models
    30708 
    30709 > select #1.21/G
    30710 
    30711 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    30712 
    30713 > show sel cartoons
    30714 
    30715 > view
    30716 
    30717 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    30718 
    30719 Chain information for AF3 E1 1-421.pdb #702 
    30720 --- 
    30721 Chain | Description 
    30722 A | No description available 
    30723  
    30724 
    30725 > matchmaker #702 to #1.21 & sel
    30726 
    30727 Parameters 
    30728 --- 
    30729 Chain pairing | bb 
    30730 Alignment algorithm | Needleman-Wunsch 
    30731 Similarity matrix | BLOSUM-62 
    30732 SS fraction | 0.3 
    30733 Gap open (HH/SS/other) | 18/18/6 
    30734 Gap extend | 1 
    30735 SS matrix |  |  | H | S | O 
    30736 ---|---|---|--- 
    30737 H | 6 | -9 | -6 
    30738 S |  | 6 | -6 
    30739 O |  |  | 4 
    30740 Iteration cutoff | 2 
    30741  
    30742 Matchmaker 3j0c.pdb1, chain G (#1.21) with AF3 E1 1-421.pdb, chain A (#702),
    30743 sequence alignment score = 1060.7 
    30744 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    30745 2.985) 
    30746  
    30747 
    30748 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    30749 
    30750 Chain information for AF3 E1 422-461.pdb #703 
    30751 --- 
    30752 Chain | Description 
    30753 A | No description available 
    30754  
    30755 
    30756 > matchmaker #703 to #1.21 & sel
    30757 
    30758 Parameters 
    30759 --- 
    30760 Chain pairing | bb 
    30761 Alignment algorithm | Needleman-Wunsch 
    30762 Similarity matrix | BLOSUM-62 
    30763 SS fraction | 0.3 
    30764 Gap open (HH/SS/other) | 18/18/6 
    30765 Gap extend | 1 
    30766 SS matrix |  |  | H | S | O 
    30767 ---|---|---|--- 
    30768 H | 6 | -9 | -6 
    30769 S |  | 6 | -6 
    30770 O |  |  | 4 
    30771 Iteration cutoff | 2 
    30772  
    30773 Matchmaker 3j0c.pdb1, chain G (#1.21) with AF3 E1 422-461.pdb, chain A (#703),
    30774 sequence alignment score = 626.9 
    30775 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    30776 2.997) 
    30777  
    30778 
    30779 > select #1.21/H
    30780 
    30781 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    30782 
    30783 > show sel cartoons
    30784 
    30785 [Repeated 1 time(s)]
    30786 
    30787 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    30788 
    30789 Chain information for AF3 E2 1-352.pdb #704 
    30790 --- 
    30791 Chain | Description 
    30792 B | No description available 
    30793  
    30794 
    30795 > matchmaker #704 to #1.21 & sel
    30796 
    30797 Parameters 
    30798 --- 
    30799 Chain pairing | bb 
    30800 Alignment algorithm | Needleman-Wunsch 
    30801 Similarity matrix | BLOSUM-62 
    30802 SS fraction | 0.3 
    30803 Gap open (HH/SS/other) | 18/18/6 
    30804 Gap extend | 1 
    30805 SS matrix |  |  | H | S | O 
    30806 ---|---|---|--- 
    30807 H | 6 | -9 | -6 
    30808 S |  | 6 | -6 
    30809 O |  |  | 4 
    30810 Iteration cutoff | 2 
    30811  
    30812 Matchmaker 3j0c.pdb1, chain H (#1.21) with AF3 E2 1-352.pdb, chain B (#704),
    30813 sequence alignment score = 590.9 
    30814 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    30815 6.107) 
    30816  
    30817 
    30818 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    30819 
    30820 Chain information for AF3 E2 353-438.pdb #705 
    30821 --- 
    30822 Chain | Description 
    30823 B | No description available 
    30824  
    30825 
    30826 > matchmaker #705 to #1.21 & sel
    30827 
    30828 Parameters 
    30829 --- 
    30830 Chain pairing | bb 
    30831 Alignment algorithm | Needleman-Wunsch 
    30832 Similarity matrix | BLOSUM-62 
    30833 SS fraction | 0.3 
    30834 Gap open (HH/SS/other) | 18/18/6 
    30835 Gap extend | 1 
    30836 SS matrix |  |  | H | S | O 
    30837 ---|---|---|--- 
    30838 H | 6 | -9 | -6 
    30839 S |  | 6 | -6 
    30840 O |  |  | 4 
    30841 Iteration cutoff | 2 
    30842  
    30843 Matchmaker 3j0c.pdb1, chain H (#1.21) with AF3 E2 353-438.pdb, chain B (#705),
    30844 sequence alignment score = 329.4 
    30845 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    30846 8.150) 
    30847  
    30848 
    30849 > hide sel cartoons
    30850 
    30851 > select #1.21/G
    30852 
    30853 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    30854 
    30855 > hide sel cartoons
    30856 
    30857 > select #1.21/I
    30858 
    30859 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    30860 
    30861 > show sel cartoons
    30862 
    30863 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    30864 
    30865 Chain information for AF3 CA.pdb #706 
    30866 --- 
    30867 Chain | Description 
    30868 A | No description available 
    30869  
    30870 
    30871 > matchmaker #706 to #1.21 & sel
    30872 
    30873 Parameters 
    30874 --- 
    30875 Chain pairing | bb 
    30876 Alignment algorithm | Needleman-Wunsch 
    30877 Similarity matrix | BLOSUM-62 
    30878 SS fraction | 0.3 
    30879 Gap open (HH/SS/other) | 18/18/6 
    30880 Gap extend | 1 
    30881 SS matrix |  |  | H | S | O 
    30882 ---|---|---|--- 
    30883 H | 6 | -9 | -6 
    30884 S |  | 6 | -6 
    30885 O |  |  | 4 
    30886 Iteration cutoff | 2 
    30887  
    30888 Matchmaker 3j0c.pdb1, chain I (#1.21) with AF3 CA.pdb, chain A (#706),
    30889 sequence alignment score = 306.5 
    30890 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    30891 2.689) 
    30892  
    30893 
    30894 > hide sel cartoons
    30895 
    30896 > color #702 dodgerblue
    30897 
    30898 > color #703 dodgerblue
    30899 
    30900 > color #704 #00b305ff
    30901 
    30902 > color #705 #00b305ff
    30903 
    30904 > color #706 #f15839ff
    30905 
    30906 > select #1.22/G
    30907 
    30908 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    30909 
    30910 > show sel cartoons
    30911 
    30912 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    30913 
    30914 Chain information for AF3 E1 1-421.pdb #707 
    30915 --- 
    30916 Chain | Description 
    30917 A | No description available 
    30918  
    30919 
    30920 > matchmaker #707 to #1.22 & sel
    30921 
    30922 Parameters 
    30923 --- 
    30924 Chain pairing | bb 
    30925 Alignment algorithm | Needleman-Wunsch 
    30926 Similarity matrix | BLOSUM-62 
    30927 SS fraction | 0.3 
    30928 Gap open (HH/SS/other) | 18/18/6 
    30929 Gap extend | 1 
    30930 SS matrix |  |  | H | S | O 
    30931 ---|---|---|--- 
    30932 H | 6 | -9 | -6 
    30933 S |  | 6 | -6 
    30934 O |  |  | 4 
    30935 Iteration cutoff | 2 
    30936  
    30937 Matchmaker 3j0c.pdb1, chain G (#1.22) with AF3 E1 1-421.pdb, chain A (#707),
    30938 sequence alignment score = 1060.7 
    30939 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    30940 2.985) 
    30941  
    30942 
    30943 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    30944 
    30945 Chain information for AF3 E1 422-461.pdb #708 
    30946 --- 
    30947 Chain | Description 
    30948 A | No description available 
    30949  
    30950 
    30951 > matchmaker #708 to #1.22 & sel
    30952 
    30953 Parameters 
    30954 --- 
    30955 Chain pairing | bb 
    30956 Alignment algorithm | Needleman-Wunsch 
    30957 Similarity matrix | BLOSUM-62 
    30958 SS fraction | 0.3 
    30959 Gap open (HH/SS/other) | 18/18/6 
    30960 Gap extend | 1 
    30961 SS matrix |  |  | H | S | O 
    30962 ---|---|---|--- 
    30963 H | 6 | -9 | -6 
    30964 S |  | 6 | -6 
    30965 O |  |  | 4 
    30966 Iteration cutoff | 2 
    30967  
    30968 Matchmaker 3j0c.pdb1, chain G (#1.22) with AF3 E1 422-461.pdb, chain A (#708),
    30969 sequence alignment score = 626.9 
    30970 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    30971 2.996) 
    30972  
    30973 
    30974 > hide sel cartoons
    30975 
    30976 > select #1.21/H
    30977 
    30978 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    30979 
    30980 > show sel cartoons
    30981 
    30982 > hide sel cartoons
    30983 
    30984 > select #1.22/H
    30985 
    30986 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    30987 
    30988 > show sel cartoons
    30989 
    30990 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    30991 
    30992 Chain information for AF3 E2 1-352.pdb #709 
    30993 --- 
    30994 Chain | Description 
    30995 B | No description available 
    30996  
    30997 
    30998 > matchmaker #709 to #1.22 & sel
    30999 
    31000 Parameters 
    31001 --- 
    31002 Chain pairing | bb 
    31003 Alignment algorithm | Needleman-Wunsch 
    31004 Similarity matrix | BLOSUM-62 
    31005 SS fraction | 0.3 
    31006 Gap open (HH/SS/other) | 18/18/6 
    31007 Gap extend | 1 
    31008 SS matrix |  |  | H | S | O 
    31009 ---|---|---|--- 
    31010 H | 6 | -9 | -6 
    31011 S |  | 6 | -6 
    31012 O |  |  | 4 
    31013 Iteration cutoff | 2 
    31014  
    31015 Matchmaker 3j0c.pdb1, chain H (#1.22) with AF3 E2 1-352.pdb, chain B (#709),
    31016 sequence alignment score = 590.9 
    31017 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    31018 6.107) 
    31019  
    31020 
    31021 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    31022 
    31023 Chain information for AF3 E2 353-438.pdb #710 
    31024 --- 
    31025 Chain | Description 
    31026 B | No description available 
    31027  
    31028 
    31029 > matchmaker #710 to #1.22 & sel
    31030 
    31031 Parameters 
    31032 --- 
    31033 Chain pairing | bb 
    31034 Alignment algorithm | Needleman-Wunsch 
    31035 Similarity matrix | BLOSUM-62 
    31036 SS fraction | 0.3 
    31037 Gap open (HH/SS/other) | 18/18/6 
    31038 Gap extend | 1 
    31039 SS matrix |  |  | H | S | O 
    31040 ---|---|---|--- 
    31041 H | 6 | -9 | -6 
    31042 S |  | 6 | -6 
    31043 O |  |  | 4 
    31044 Iteration cutoff | 2 
    31045  
    31046 Matchmaker 3j0c.pdb1, chain H (#1.22) with AF3 E2 353-438.pdb, chain B (#710),
    31047 sequence alignment score = 329.4 
    31048 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    31049 8.151) 
    31050  
    31051 
    31052 > hide sel cartoons
    31053 
    31054 > select #1.22/I
    31055 
    31056 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    31057 
    31058 > show sel cartoons
    31059 
    31060 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    31061 
    31062 Chain information for AF3 CA.pdb #711 
    31063 --- 
    31064 Chain | Description 
    31065 A | No description available 
    31066  
    31067 
    31068 > matchmaker #711 to #1.22 & sel
    31069 
    31070 Parameters 
    31071 --- 
    31072 Chain pairing | bb 
    31073 Alignment algorithm | Needleman-Wunsch 
    31074 Similarity matrix | BLOSUM-62 
    31075 SS fraction | 0.3 
    31076 Gap open (HH/SS/other) | 18/18/6 
    31077 Gap extend | 1 
    31078 SS matrix |  |  | H | S | O 
    31079 ---|---|---|--- 
    31080 H | 6 | -9 | -6 
    31081 S |  | 6 | -6 
    31082 O |  |  | 4 
    31083 Iteration cutoff | 2 
    31084  
    31085 Matchmaker 3j0c.pdb1, chain I (#1.22) with AF3 CA.pdb, chain A (#711),
    31086 sequence alignment score = 306.5 
    31087 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    31088 2.689) 
    31089  
    31090 
    31091 > hide sel cartoons
    31092 
    31093 > color #707 dodgerblue
    31094 
    31095 > color #708 dodgerblue
    31096 
    31097 > color #709 #00b305ff
    31098 
    31099 > color #710 #00b305ff
    31100 
    31101 > color #711 #f15839ff
    31102 
    31103 > select #1.23/G
    31104 
    31105 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    31106 
    31107 > show sel cartoons
    31108 
    31109 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    31110 
    31111 Chain information for AF3 E1 1-421.pdb #712 
    31112 --- 
    31113 Chain | Description 
    31114 A | No description available 
    31115  
    31116 
    31117 > matchmaker #712 to #1.23 & sel
    31118 
    31119 Parameters 
    31120 --- 
    31121 Chain pairing | bb 
    31122 Alignment algorithm | Needleman-Wunsch 
    31123 Similarity matrix | BLOSUM-62 
    31124 SS fraction | 0.3 
    31125 Gap open (HH/SS/other) | 18/18/6 
    31126 Gap extend | 1 
    31127 SS matrix |  |  | H | S | O 
    31128 ---|---|---|--- 
    31129 H | 6 | -9 | -6 
    31130 S |  | 6 | -6 
    31131 O |  |  | 4 
    31132 Iteration cutoff | 2 
    31133  
    31134 Matchmaker 3j0c.pdb1, chain G (#1.23) with AF3 E1 1-421.pdb, chain A (#712),
    31135 sequence alignment score = 1060.7 
    31136 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    31137 2.985) 
    31138  
    31139 
    31140 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    31141 
    31142 Chain information for AF3 E1 422-461.pdb #713 
    31143 --- 
    31144 Chain | Description 
    31145 A | No description available 
    31146  
    31147 
    31148 > matchmaker #713 to #1.23 & sel
    31149 
    31150 Parameters 
    31151 --- 
    31152 Chain pairing | bb 
    31153 Alignment algorithm | Needleman-Wunsch 
    31154 Similarity matrix | BLOSUM-62 
    31155 SS fraction | 0.3 
    31156 Gap open (HH/SS/other) | 18/18/6 
    31157 Gap extend | 1 
    31158 SS matrix |  |  | H | S | O 
    31159 ---|---|---|--- 
    31160 H | 6 | -9 | -6 
    31161 S |  | 6 | -6 
    31162 O |  |  | 4 
    31163 Iteration cutoff | 2 
    31164  
    31165 Matchmaker 3j0c.pdb1, chain G (#1.23) with AF3 E1 422-461.pdb, chain A (#713),
    31166 sequence alignment score = 626.9 
    31167 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    31168 2.997) 
    31169  
    31170 
    31171 > hide sel cartoons
    31172 
    31173 > select #1.23/H
    31174 
    31175 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    31176 
    31177 > show sel cartoons
    31178 
    31179 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    31180 
    31181 Chain information for AF3 E2 1-352.pdb #714 
    31182 --- 
    31183 Chain | Description 
    31184 B | No description available 
    31185  
    31186 
    31187 > matchmaker #714 to #1.23 & sel
    31188 
    31189 Parameters 
    31190 --- 
    31191 Chain pairing | bb 
    31192 Alignment algorithm | Needleman-Wunsch 
    31193 Similarity matrix | BLOSUM-62 
    31194 SS fraction | 0.3 
    31195 Gap open (HH/SS/other) | 18/18/6 
    31196 Gap extend | 1 
    31197 SS matrix |  |  | H | S | O 
    31198 ---|---|---|--- 
    31199 H | 6 | -9 | -6 
    31200 S |  | 6 | -6 
    31201 O |  |  | 4 
    31202 Iteration cutoff | 2 
    31203  
    31204 Matchmaker 3j0c.pdb1, chain H (#1.23) with AF3 E2 1-352.pdb, chain B (#714),
    31205 sequence alignment score = 590.9 
    31206 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    31207 6.107) 
    31208  
    31209 
    31210 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    31211 
    31212 Chain information for AF3 E2 353-438.pdb #715 
    31213 --- 
    31214 Chain | Description 
    31215 B | No description available 
    31216  
    31217 
    31218 > matchmaker #715 to #1.23 & sel
    31219 
    31220 Parameters 
    31221 --- 
    31222 Chain pairing | bb 
    31223 Alignment algorithm | Needleman-Wunsch 
    31224 Similarity matrix | BLOSUM-62 
    31225 SS fraction | 0.3 
    31226 Gap open (HH/SS/other) | 18/18/6 
    31227 Gap extend | 1 
    31228 SS matrix |  |  | H | S | O 
    31229 ---|---|---|--- 
    31230 H | 6 | -9 | -6 
    31231 S |  | 6 | -6 
    31232 O |  |  | 4 
    31233 Iteration cutoff | 2 
    31234  
    31235 Matchmaker 3j0c.pdb1, chain H (#1.23) with AF3 E2 353-438.pdb, chain B (#715),
    31236 sequence alignment score = 329.4 
    31237 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    31238 8.150) 
    31239  
    31240 
    31241 > hide sel cartoons
    31242 
    31243 > select #1.23/I
    31244 
    31245 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    31246 
    31247 > show sel cartoons
    31248 
    31249 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    31250 
    31251 Chain information for AF3 CA.pdb #716 
    31252 --- 
    31253 Chain | Description 
    31254 A | No description available 
    31255  
    31256 
    31257 > matchmaker #716 to #1.23 & sel
    31258 
    31259 Parameters 
    31260 --- 
    31261 Chain pairing | bb 
    31262 Alignment algorithm | Needleman-Wunsch 
    31263 Similarity matrix | BLOSUM-62 
    31264 SS fraction | 0.3 
    31265 Gap open (HH/SS/other) | 18/18/6 
    31266 Gap extend | 1 
    31267 SS matrix |  |  | H | S | O 
    31268 ---|---|---|--- 
    31269 H | 6 | -9 | -6 
    31270 S |  | 6 | -6 
    31271 O |  |  | 4 
    31272 Iteration cutoff | 2 
    31273  
    31274 Matchmaker 3j0c.pdb1, chain I (#1.23) with AF3 CA.pdb, chain A (#716),
    31275 sequence alignment score = 306.5 
    31276 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    31277 2.689) 
    31278  
    31279 
    31280 > hide sel cartoons
    31281 
    31282 > color #712 dodgerblue
    31283 
    31284 > color #713 dodgerblue
    31285 
    31286 > color #714 #00b305ff
    31287 
    31288 > color #715 #00b305ff
    31289 
    31290 > color #716 #f15839ff
    31291 
    31292 > select #1.24/G
    31293 
    31294 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    31295 
    31296 > show sel cartoons
    31297 
    31298 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    31299 
    31300 Chain information for AF3 E1 1-421.pdb #717 
    31301 --- 
    31302 Chain | Description 
    31303 A | No description available 
    31304  
    31305 
    31306 > matchmaker #717 to #1.23 & sel
    31307 
    31308 No 'to' model specified 
    31309 
    31310 > matchmaker #717 to #1.24 & sel
    31311 
    31312 Parameters 
    31313 --- 
    31314 Chain pairing | bb 
    31315 Alignment algorithm | Needleman-Wunsch 
    31316 Similarity matrix | BLOSUM-62 
    31317 SS fraction | 0.3 
    31318 Gap open (HH/SS/other) | 18/18/6 
    31319 Gap extend | 1 
    31320 SS matrix |  |  | H | S | O 
    31321 ---|---|---|--- 
    31322 H | 6 | -9 | -6 
    31323 S |  | 6 | -6 
    31324 O |  |  | 4 
    31325 Iteration cutoff | 2 
    31326  
    31327 Matchmaker 3j0c.pdb1, chain G (#1.24) with AF3 E1 1-421.pdb, chain A (#717),
    31328 sequence alignment score = 1060.7 
    31329 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    31330 2.985) 
    31331  
    31332 
    31333 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    31334 
    31335 Chain information for AF3 E1 422-461.pdb #718 
    31336 --- 
    31337 Chain | Description 
    31338 A | No description available 
    31339  
    31340 
    31341 > matchmaker #718 to #1.24 & sel
    31342 
    31343 Parameters 
    31344 --- 
    31345 Chain pairing | bb 
    31346 Alignment algorithm | Needleman-Wunsch 
    31347 Similarity matrix | BLOSUM-62 
    31348 SS fraction | 0.3 
    31349 Gap open (HH/SS/other) | 18/18/6 
    31350 Gap extend | 1 
    31351 SS matrix |  |  | H | S | O 
    31352 ---|---|---|--- 
    31353 H | 6 | -9 | -6 
    31354 S |  | 6 | -6 
    31355 O |  |  | 4 
    31356 Iteration cutoff | 2 
    31357  
    31358 Matchmaker 3j0c.pdb1, chain G (#1.24) with AF3 E1 422-461.pdb, chain A (#718),
    31359 sequence alignment score = 626.9 
    31360 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    31361 2.997) 
    31362  
    31363 
    31364 > hide sel cartoons
    31365 
    31366 > select #1.24/H
    31367 
    31368 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    31369 
    31370 > show sel cartoons
    31371 
    31372 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    31373 
    31374 Chain information for AF3 E2 1-352.pdb #719 
    31375 --- 
    31376 Chain | Description 
    31377 B | No description available 
    31378  
    31379 
    31380 > matchmaker #719 to #1.24 & sel
    31381 
    31382 Parameters 
    31383 --- 
    31384 Chain pairing | bb 
    31385 Alignment algorithm | Needleman-Wunsch 
    31386 Similarity matrix | BLOSUM-62 
    31387 SS fraction | 0.3 
    31388 Gap open (HH/SS/other) | 18/18/6 
    31389 Gap extend | 1 
    31390 SS matrix |  |  | H | S | O 
    31391 ---|---|---|--- 
    31392 H | 6 | -9 | -6 
    31393 S |  | 6 | -6 
    31394 O |  |  | 4 
    31395 Iteration cutoff | 2 
    31396  
    31397 Matchmaker 3j0c.pdb1, chain H (#1.24) with AF3 E2 1-352.pdb, chain B (#719),
    31398 sequence alignment score = 590.9 
    31399 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    31400 6.107) 
    31401  
    31402 
    31403 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    31404 
    31405 Chain information for AF3 E2 353-438.pdb #720 
    31406 --- 
    31407 Chain | Description 
    31408 B | No description available 
    31409  
    31410 
    31411 > matchmaker #720 to #1.24 & sel
    31412 
    31413 Parameters 
    31414 --- 
    31415 Chain pairing | bb 
    31416 Alignment algorithm | Needleman-Wunsch 
    31417 Similarity matrix | BLOSUM-62 
    31418 SS fraction | 0.3 
    31419 Gap open (HH/SS/other) | 18/18/6 
    31420 Gap extend | 1 
    31421 SS matrix |  |  | H | S | O 
    31422 ---|---|---|--- 
    31423 H | 6 | -9 | -6 
    31424 S |  | 6 | -6 
    31425 O |  |  | 4 
    31426 Iteration cutoff | 2 
    31427  
    31428 Matchmaker 3j0c.pdb1, chain H (#1.24) with AF3 E2 353-438.pdb, chain B (#720),
    31429 sequence alignment score = 329.4 
    31430 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    31431 8.150) 
    31432  
    31433 
    31434 > hide sel cartoons
    31435 
    31436 > select #1.24/I
    31437 
    31438 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    31439 
    31440 > show sel cartoons
    31441 
    31442 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    31443 
    31444 Chain information for AF3 CA.pdb #721 
    31445 --- 
    31446 Chain | Description 
    31447 A | No description available 
    31448  
    31449 
    31450 > matchmaker #721 to #1.24 & sel
    31451 
    31452 Parameters 
    31453 --- 
    31454 Chain pairing | bb 
    31455 Alignment algorithm | Needleman-Wunsch 
    31456 Similarity matrix | BLOSUM-62 
    31457 SS fraction | 0.3 
    31458 Gap open (HH/SS/other) | 18/18/6 
    31459 Gap extend | 1 
    31460 SS matrix |  |  | H | S | O 
    31461 ---|---|---|--- 
    31462 H | 6 | -9 | -6 
    31463 S |  | 6 | -6 
    31464 O |  |  | 4 
    31465 Iteration cutoff | 2 
    31466  
    31467 Matchmaker 3j0c.pdb1, chain I (#1.24) with AF3 CA.pdb, chain A (#721),
    31468 sequence alignment score = 306.5 
    31469 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    31470 2.689) 
    31471  
    31472 
    31473 > hide sel cartoons
    31474 
    31475 > color #717 dodgerblue
    31476 
    31477 > color #718 dodgerblue
    31478 
    31479 > color #719 #00b305ff
    31480 
    31481 > color #720 #00b305ff
    31482 
    31483 > color #721 #f15839ff
    31484 
    31485 > select #1.25/G
    31486 
    31487 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    31488 
    31489 > show sel cartoons
    31490 
    31491 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    31492 
    31493 Chain information for AF3 E1 1-421.pdb #722 
    31494 --- 
    31495 Chain | Description 
    31496 A | No description available 
    31497  
    31498 
    31499 > matchmaker #722 to #1.25 & sel
    31500 
    31501 Parameters 
    31502 --- 
    31503 Chain pairing | bb 
    31504 Alignment algorithm | Needleman-Wunsch 
    31505 Similarity matrix | BLOSUM-62 
    31506 SS fraction | 0.3 
    31507 Gap open (HH/SS/other) | 18/18/6 
    31508 Gap extend | 1 
    31509 SS matrix |  |  | H | S | O 
    31510 ---|---|---|--- 
    31511 H | 6 | -9 | -6 
    31512 S |  | 6 | -6 
    31513 O |  |  | 4 
    31514 Iteration cutoff | 2 
    31515  
    31516 Matchmaker 3j0c.pdb1, chain G (#1.25) with AF3 E1 1-421.pdb, chain A (#722),
    31517 sequence alignment score = 1060.7 
    31518 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    31519 2.985) 
    31520  
    31521 
    31522 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    31523 
    31524 Chain information for AF3 E1 422-461.pdb #723 
    31525 --- 
    31526 Chain | Description 
    31527 A | No description available 
    31528  
    31529 
    31530 > matchmaker #723 to #1.25 & sel
    31531 
    31532 Parameters 
    31533 --- 
    31534 Chain pairing | bb 
    31535 Alignment algorithm | Needleman-Wunsch 
    31536 Similarity matrix | BLOSUM-62 
    31537 SS fraction | 0.3 
    31538 Gap open (HH/SS/other) | 18/18/6 
    31539 Gap extend | 1 
    31540 SS matrix |  |  | H | S | O 
    31541 ---|---|---|--- 
    31542 H | 6 | -9 | -6 
    31543 S |  | 6 | -6 
    31544 O |  |  | 4 
    31545 Iteration cutoff | 2 
    31546  
    31547 Matchmaker 3j0c.pdb1, chain G (#1.25) with AF3 E1 422-461.pdb, chain A (#723),
    31548 sequence alignment score = 626.9 
    31549 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    31550 2.997) 
    31551  
    31552 
    31553 > hide sel cartoons
    31554 
    31555 > select #1.25/H
    31556 
    31557 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    31558 
    31559 > show sel cartoons
    31560 
    31561 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    31562 
    31563 Chain information for AF3 E2 1-352.pdb #724 
    31564 --- 
    31565 Chain | Description 
    31566 B | No description available 
    31567  
    31568 
    31569 > matchmaker #724 to #1.25 & sel
    31570 
    31571 Parameters 
    31572 --- 
    31573 Chain pairing | bb 
    31574 Alignment algorithm | Needleman-Wunsch 
    31575 Similarity matrix | BLOSUM-62 
    31576 SS fraction | 0.3 
    31577 Gap open (HH/SS/other) | 18/18/6 
    31578 Gap extend | 1 
    31579 SS matrix |  |  | H | S | O 
    31580 ---|---|---|--- 
    31581 H | 6 | -9 | -6 
    31582 S |  | 6 | -6 
    31583 O |  |  | 4 
    31584 Iteration cutoff | 2 
    31585  
    31586 Matchmaker 3j0c.pdb1, chain H (#1.25) with AF3 E2 1-352.pdb, chain B (#724),
    31587 sequence alignment score = 590.9 
    31588 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    31589 6.107) 
    31590  
    31591 
    31592 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    31593 
    31594 Chain information for AF3 E2 353-438.pdb #725 
    31595 --- 
    31596 Chain | Description 
    31597 B | No description available 
    31598  
    31599 
    31600 > matchmaker #725 to #1.25 & sel
    31601 
    31602 Parameters 
    31603 --- 
    31604 Chain pairing | bb 
    31605 Alignment algorithm | Needleman-Wunsch 
    31606 Similarity matrix | BLOSUM-62 
    31607 SS fraction | 0.3 
    31608 Gap open (HH/SS/other) | 18/18/6 
    31609 Gap extend | 1 
    31610 SS matrix |  |  | H | S | O 
    31611 ---|---|---|--- 
    31612 H | 6 | -9 | -6 
    31613 S |  | 6 | -6 
    31614 O |  |  | 4 
    31615 Iteration cutoff | 2 
    31616  
    31617 Matchmaker 3j0c.pdb1, chain H (#1.25) with AF3 E2 353-438.pdb, chain B (#725),
    31618 sequence alignment score = 329.4 
    31619 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    31620 8.150) 
    31621  
    31622 
    31623 > hide sel cartoons
    31624 
    31625 > select #1.25/I
    31626 
    31627 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    31628 
    31629 > show sel cartoons
    31630 
    31631 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    31632 
    31633 Chain information for AF3 CA.pdb #726 
    31634 --- 
    31635 Chain | Description 
    31636 A | No description available 
    31637  
    31638 
    31639 > matchmaker #726 to #1.25 & sel
    31640 
    31641 Parameters 
    31642 --- 
    31643 Chain pairing | bb 
    31644 Alignment algorithm | Needleman-Wunsch 
    31645 Similarity matrix | BLOSUM-62 
    31646 SS fraction | 0.3 
    31647 Gap open (HH/SS/other) | 18/18/6 
    31648 Gap extend | 1 
    31649 SS matrix |  |  | H | S | O 
    31650 ---|---|---|--- 
    31651 H | 6 | -9 | -6 
    31652 S |  | 6 | -6 
    31653 O |  |  | 4 
    31654 Iteration cutoff | 2 
    31655  
    31656 Matchmaker 3j0c.pdb1, chain I (#1.25) with AF3 CA.pdb, chain A (#726),
    31657 sequence alignment score = 306.5 
    31658 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    31659 2.689) 
    31660  
    31661 
    31662 > hide sel cartoons
    31663 
    31664 > color #722 dodgerblue
    31665 
    31666 > color #723 dodgerblue
    31667 
    31668 > color #724 #00b305ff
    31669 
    31670 > color #725 #00b305ff
    31671 
    31672 > color #726 #f15839ff
    31673 
    31674 > select #1.26/G
    31675 
    31676 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    31677 
    31678 > show sel cartoons
    31679 
    31680 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    31681 
    31682 Chain information for AF3 E1 1-421.pdb #727 
    31683 --- 
    31684 Chain | Description 
    31685 A | No description available 
    31686  
    31687 
    31688 > matchmaker #727 to #1.25 & sel
    31689 
    31690 No 'to' model specified 
    31691 
    31692 > matchmaker #727 to #1.26 & sel
    31693 
    31694 Parameters 
    31695 --- 
    31696 Chain pairing | bb 
    31697 Alignment algorithm | Needleman-Wunsch 
    31698 Similarity matrix | BLOSUM-62 
    31699 SS fraction | 0.3 
    31700 Gap open (HH/SS/other) | 18/18/6 
    31701 Gap extend | 1 
    31702 SS matrix |  |  | H | S | O 
    31703 ---|---|---|--- 
    31704 H | 6 | -9 | -6 
    31705 S |  | 6 | -6 
    31706 O |  |  | 4 
    31707 Iteration cutoff | 2 
    31708  
    31709 Matchmaker 3j0c.pdb1, chain G (#1.26) with AF3 E1 1-421.pdb, chain A (#727),
    31710 sequence alignment score = 1060.7 
    31711 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    31712 2.985) 
    31713  
    31714 
    31715 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    31716 
    31717 Chain information for AF3 E1 422-461.pdb #728 
    31718 --- 
    31719 Chain | Description 
    31720 A | No description available 
    31721  
    31722 
    31723 > matchmaker #728 to #1.26 & sel
    31724 
    31725 Parameters 
    31726 --- 
    31727 Chain pairing | bb 
    31728 Alignment algorithm | Needleman-Wunsch 
    31729 Similarity matrix | BLOSUM-62 
    31730 SS fraction | 0.3 
    31731 Gap open (HH/SS/other) | 18/18/6 
    31732 Gap extend | 1 
    31733 SS matrix |  |  | H | S | O 
    31734 ---|---|---|--- 
    31735 H | 6 | -9 | -6 
    31736 S |  | 6 | -6 
    31737 O |  |  | 4 
    31738 Iteration cutoff | 2 
    31739  
    31740 Matchmaker 3j0c.pdb1, chain G (#1.26) with AF3 E1 422-461.pdb, chain A (#728),
    31741 sequence alignment score = 626.9 
    31742 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    31743 2.997) 
    31744  
    31745 
    31746 > hide sel cartoons
    31747 
    31748 > select #1.26/H
    31749 
    31750 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    31751 
    31752 > show sel cartoons
    31753 
    31754 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    31755 
    31756 Chain information for AF3 E2 1-352.pdb #729 
    31757 --- 
    31758 Chain | Description 
    31759 B | No description available 
    31760  
    31761 
    31762 > matchmaker #729 to #1.26 & sel
    31763 
    31764 Parameters 
    31765 --- 
    31766 Chain pairing | bb 
    31767 Alignment algorithm | Needleman-Wunsch 
    31768 Similarity matrix | BLOSUM-62 
    31769 SS fraction | 0.3 
    31770 Gap open (HH/SS/other) | 18/18/6 
    31771 Gap extend | 1 
    31772 SS matrix |  |  | H | S | O 
    31773 ---|---|---|--- 
    31774 H | 6 | -9 | -6 
    31775 S |  | 6 | -6 
    31776 O |  |  | 4 
    31777 Iteration cutoff | 2 
    31778  
    31779 Matchmaker 3j0c.pdb1, chain H (#1.26) with AF3 E2 1-352.pdb, chain B (#729),
    31780 sequence alignment score = 590.9 
    31781 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    31782 6.107) 
    31783  
    31784 
    31785 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    31786 
    31787 Chain information for AF3 E2 353-438.pdb #730 
    31788 --- 
    31789 Chain | Description 
    31790 B | No description available 
    31791  
    31792 
    31793 > matchmaker #730 to #1.26 & sel
    31794 
    31795 Parameters 
    31796 --- 
    31797 Chain pairing | bb 
    31798 Alignment algorithm | Needleman-Wunsch 
    31799 Similarity matrix | BLOSUM-62 
    31800 SS fraction | 0.3 
    31801 Gap open (HH/SS/other) | 18/18/6 
    31802 Gap extend | 1 
    31803 SS matrix |  |  | H | S | O 
    31804 ---|---|---|--- 
    31805 H | 6 | -9 | -6 
    31806 S |  | 6 | -6 
    31807 O |  |  | 4 
    31808 Iteration cutoff | 2 
    31809  
    31810 Matchmaker 3j0c.pdb1, chain H (#1.26) with AF3 E2 353-438.pdb, chain B (#730),
    31811 sequence alignment score = 329.4 
    31812 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    31813 8.150) 
    31814  
    31815 
    31816 > hide sel cartoons
    31817 
    31818 > select #1.27/I
    31819 
    31820 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    31821 
    31822 > show sel cartoons
    31823 
    31824 > hide sel cartoons
    31825 
    31826 > select #1.26/F
    31827 
    31828 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    31829 
    31830 > show sel cartoons
    31831 
    31832 > hide sel cartoons
    31833 
    31834 > select #1.25/H
    31835 
    31836 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    31837 
    31838 > show sel cartoons
    31839 
    31840 > hide sel cartoons
    31841 
    31842 > select #1.25/I
    31843 
    31844 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    31845 
    31846 > select #1.26/I
    31847 
    31848 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    31849 
    31850 > show sel cartoons
    31851 
    31852 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    31853 
    31854 Chain information for AF3 CA.pdb #731 
    31855 --- 
    31856 Chain | Description 
    31857 A | No description available 
    31858  
    31859 
    31860 > matchmaker #731 to #1.26 & sel
    31861 
    31862 Parameters 
    31863 --- 
    31864 Chain pairing | bb 
    31865 Alignment algorithm | Needleman-Wunsch 
    31866 Similarity matrix | BLOSUM-62 
    31867 SS fraction | 0.3 
    31868 Gap open (HH/SS/other) | 18/18/6 
    31869 Gap extend | 1 
    31870 SS matrix |  |  | H | S | O 
    31871 ---|---|---|--- 
    31872 H | 6 | -9 | -6 
    31873 S |  | 6 | -6 
    31874 O |  |  | 4 
    31875 Iteration cutoff | 2 
    31876  
    31877 Matchmaker 3j0c.pdb1, chain I (#1.26) with AF3 CA.pdb, chain A (#731),
    31878 sequence alignment score = 306.5 
    31879 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    31880 2.689) 
    31881  
    31882 
    31883 > hide sel cartoons
    31884 
    31885 > color #727 dodgerblue
    31886 
    31887 > color #728 dodgerblue
    31888 
    31889 > color #729 #00b305ff
    31890 
    31891 > color #730 #00b305ff
    31892 
    31893 > color #731 #f15839ff
    31894 
    31895 > select #1.27/G
    31896 
    31897 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    31898 
    31899 > show sel cartoons
    31900 
    31901 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    31902 
    31903 Chain information for AF3 E1 1-421.pdb #732 
    31904 --- 
    31905 Chain | Description 
    31906 A | No description available 
    31907  
    31908 
    31909 > matchmaker #732 to #1.27 & sel
    31910 
    31911 Parameters 
    31912 --- 
    31913 Chain pairing | bb 
    31914 Alignment algorithm | Needleman-Wunsch 
    31915 Similarity matrix | BLOSUM-62 
    31916 SS fraction | 0.3 
    31917 Gap open (HH/SS/other) | 18/18/6 
    31918 Gap extend | 1 
    31919 SS matrix |  |  | H | S | O 
    31920 ---|---|---|--- 
    31921 H | 6 | -9 | -6 
    31922 S |  | 6 | -6 
    31923 O |  |  | 4 
    31924 Iteration cutoff | 2 
    31925  
    31926 Matchmaker 3j0c.pdb1, chain G (#1.27) with AF3 E1 1-421.pdb, chain A (#732),
    31927 sequence alignment score = 1060.7 
    31928 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    31929 2.985) 
    31930  
    31931 
    31932 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    31933 
    31934 Chain information for AF3 E1 422-461.pdb #733 
    31935 --- 
    31936 Chain | Description 
    31937 A | No description available 
    31938  
    31939 
    31940 > matchmaker #733 to #1.27 & sel
    31941 
    31942 Parameters 
    31943 --- 
    31944 Chain pairing | bb 
    31945 Alignment algorithm | Needleman-Wunsch 
    31946 Similarity matrix | BLOSUM-62 
    31947 SS fraction | 0.3 
    31948 Gap open (HH/SS/other) | 18/18/6 
    31949 Gap extend | 1 
    31950 SS matrix |  |  | H | S | O 
    31951 ---|---|---|--- 
    31952 H | 6 | -9 | -6 
    31953 S |  | 6 | -6 
    31954 O |  |  | 4 
    31955 Iteration cutoff | 2 
    31956  
    31957 Matchmaker 3j0c.pdb1, chain G (#1.27) with AF3 E1 422-461.pdb, chain A (#733),
    31958 sequence alignment score = 626.9 
    31959 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    31960 2.997) 
    31961  
    31962 
    31963 > hide sel cartoons
    31964 
    31965 > select #1.27/H
    31966 
    31967 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    31968 
    31969 > show sel cartoons
    31970 
    31971 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    31972 
    31973 Chain information for AF3 E2 1-352.pdb #734 
    31974 --- 
    31975 Chain | Description 
    31976 B | No description available 
    31977  
    31978 
    31979 > matchmaker #734 to #1.27 & sel
    31980 
    31981 Parameters 
    31982 --- 
    31983 Chain pairing | bb 
    31984 Alignment algorithm | Needleman-Wunsch 
    31985 Similarity matrix | BLOSUM-62 
    31986 SS fraction | 0.3 
    31987 Gap open (HH/SS/other) | 18/18/6 
    31988 Gap extend | 1 
    31989 SS matrix |  |  | H | S | O 
    31990 ---|---|---|--- 
    31991 H | 6 | -9 | -6 
    31992 S |  | 6 | -6 
    31993 O |  |  | 4 
    31994 Iteration cutoff | 2 
    31995  
    31996 Matchmaker 3j0c.pdb1, chain H (#1.27) with AF3 E2 1-352.pdb, chain B (#734),
    31997 sequence alignment score = 590.9 
    31998 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    31999 6.107) 
    32000  
    32001 
    32002 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    32003 
    32004 Chain information for AF3 E2 353-438.pdb #735 
    32005 --- 
    32006 Chain | Description 
    32007 B | No description available 
    32008  
    32009 
    32010 > matchmaker #735 to #1.27 & sel
    32011 
    32012 Parameters 
    32013 --- 
    32014 Chain pairing | bb 
    32015 Alignment algorithm | Needleman-Wunsch 
    32016 Similarity matrix | BLOSUM-62 
    32017 SS fraction | 0.3 
    32018 Gap open (HH/SS/other) | 18/18/6 
    32019 Gap extend | 1 
    32020 SS matrix |  |  | H | S | O 
    32021 ---|---|---|--- 
    32022 H | 6 | -9 | -6 
    32023 S |  | 6 | -6 
    32024 O |  |  | 4 
    32025 Iteration cutoff | 2 
    32026  
    32027 Matchmaker 3j0c.pdb1, chain H (#1.27) with AF3 E2 353-438.pdb, chain B (#735),
    32028 sequence alignment score = 329.4 
    32029 RMSD between 40 pruned atom pairs is 0.937 angstroms; (across all 84 pairs:
    32030 8.151) 
    32031  
    32032 
    32033 > hide sel cartoons
    32034 
    32035 > select #1.27/I
    32036 
    32037 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    32038 
    32039 > show sel cartoons
    32040 
    32041 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    32042 
    32043 Chain information for AF3 CA.pdb #736 
    32044 --- 
    32045 Chain | Description 
    32046 A | No description available 
    32047  
    32048 
    32049 > matchmaker #736 to #1.27 & sel
    32050 
    32051 Parameters 
    32052 --- 
    32053 Chain pairing | bb 
    32054 Alignment algorithm | Needleman-Wunsch 
    32055 Similarity matrix | BLOSUM-62 
    32056 SS fraction | 0.3 
    32057 Gap open (HH/SS/other) | 18/18/6 
    32058 Gap extend | 1 
    32059 SS matrix |  |  | H | S | O 
    32060 ---|---|---|--- 
    32061 H | 6 | -9 | -6 
    32062 S |  | 6 | -6 
    32063 O |  |  | 4 
    32064 Iteration cutoff | 2 
    32065  
    32066 Matchmaker 3j0c.pdb1, chain I (#1.27) with AF3 CA.pdb, chain A (#736),
    32067 sequence alignment score = 306.5 
    32068 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    32069 2.689) 
    32070  
    32071 
    32072 > hide sel cartoons
    32073 
    32074 > color #732 dodgerblue
    32075 
    32076 > color #733 dodgerblue
    32077 
    32078 > color #734 #00b305ff
    32079 
    32080 > color #735 #00b305ff
    32081 
    32082 > color #736 #f15839ff
    32083 
    32084 > select #1.28/G
    32085 
    32086 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    32087 
    32088 > show sel cartoons
    32089 
    32090 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    32091 
    32092 Chain information for AF3 E1 1-421.pdb #737 
    32093 --- 
    32094 Chain | Description 
    32095 A | No description available 
    32096  
    32097 
    32098 > matchmaker #737 to #1.28 & sel
    32099 
    32100 Parameters 
    32101 --- 
    32102 Chain pairing | bb 
    32103 Alignment algorithm | Needleman-Wunsch 
    32104 Similarity matrix | BLOSUM-62 
    32105 SS fraction | 0.3 
    32106 Gap open (HH/SS/other) | 18/18/6 
    32107 Gap extend | 1 
    32108 SS matrix |  |  | H | S | O 
    32109 ---|---|---|--- 
    32110 H | 6 | -9 | -6 
    32111 S |  | 6 | -6 
    32112 O |  |  | 4 
    32113 Iteration cutoff | 2 
    32114  
    32115 Matchmaker 3j0c.pdb1, chain G (#1.28) with AF3 E1 1-421.pdb, chain A (#737),
    32116 sequence alignment score = 1060.7 
    32117 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    32118 2.985) 
    32119  
    32120 
    32121 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    32122 
    32123 Chain information for AF3 E1 422-461.pdb #738 
    32124 --- 
    32125 Chain | Description 
    32126 A | No description available 
    32127  
    32128 
    32129 > matchmaker #738 to #1.28 & sel
    32130 
    32131 Parameters 
    32132 --- 
    32133 Chain pairing | bb 
    32134 Alignment algorithm | Needleman-Wunsch 
    32135 Similarity matrix | BLOSUM-62 
    32136 SS fraction | 0.3 
    32137 Gap open (HH/SS/other) | 18/18/6 
    32138 Gap extend | 1 
    32139 SS matrix |  |  | H | S | O 
    32140 ---|---|---|--- 
    32141 H | 6 | -9 | -6 
    32142 S |  | 6 | -6 
    32143 O |  |  | 4 
    32144 Iteration cutoff | 2 
    32145  
    32146 Matchmaker 3j0c.pdb1, chain G (#1.28) with AF3 E1 422-461.pdb, chain A (#738),
    32147 sequence alignment score = 626.9 
    32148 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    32149 2.997) 
    32150  
    32151 
    32152 > hide sel cartoons
    32153 
    32154 > select #1.28/H
    32155 
    32156 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    32157 
    32158 > show sel cartoons
    32159 
    32160 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    32161 
    32162 Chain information for AF3 E2 1-352.pdb #739 
    32163 --- 
    32164 Chain | Description 
    32165 B | No description available 
    32166  
    32167 
    32168 > matchmaker #739 to #1.28 & sel
    32169 
    32170 Parameters 
    32171 --- 
    32172 Chain pairing | bb 
    32173 Alignment algorithm | Needleman-Wunsch 
    32174 Similarity matrix | BLOSUM-62 
    32175 SS fraction | 0.3 
    32176 Gap open (HH/SS/other) | 18/18/6 
    32177 Gap extend | 1 
    32178 SS matrix |  |  | H | S | O 
    32179 ---|---|---|--- 
    32180 H | 6 | -9 | -6 
    32181 S |  | 6 | -6 
    32182 O |  |  | 4 
    32183 Iteration cutoff | 2 
    32184  
    32185 Matchmaker 3j0c.pdb1, chain H (#1.28) with AF3 E2 1-352.pdb, chain B (#739),
    32186 sequence alignment score = 590.9 
    32187 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    32188 6.107) 
    32189  
    32190 
    32191 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    32192 
    32193 Chain information for AF3 E2 353-438.pdb #740 
    32194 --- 
    32195 Chain | Description 
    32196 B | No description available 
    32197  
    32198 
    32199 > matchmaker #740 to #1.28 & sel
    32200 
    32201 Parameters 
    32202 --- 
    32203 Chain pairing | bb 
    32204 Alignment algorithm | Needleman-Wunsch 
    32205 Similarity matrix | BLOSUM-62 
    32206 SS fraction | 0.3 
    32207 Gap open (HH/SS/other) | 18/18/6 
    32208 Gap extend | 1 
    32209 SS matrix |  |  | H | S | O 
    32210 ---|---|---|--- 
    32211 H | 6 | -9 | -6 
    32212 S |  | 6 | -6 
    32213 O |  |  | 4 
    32214 Iteration cutoff | 2 
    32215  
    32216 Matchmaker 3j0c.pdb1, chain H (#1.28) with AF3 E2 353-438.pdb, chain B (#740),
    32217 sequence alignment score = 329.4 
    32218 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    32219 8.150) 
    32220  
    32221 
    32222 > hide sel cartoons
    32223 
    32224 > select #1.28/I
    32225 
    32226 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    32227 
    32228 > show sel cartoons
    32229 
    32230 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    32231 
    32232 Chain information for AF3 CA.pdb #741 
    32233 --- 
    32234 Chain | Description 
    32235 A | No description available 
    32236  
    32237 
    32238 > matchmaker #741 to #1.28 & sel
    32239 
    32240 Parameters 
    32241 --- 
    32242 Chain pairing | bb 
    32243 Alignment algorithm | Needleman-Wunsch 
    32244 Similarity matrix | BLOSUM-62 
    32245 SS fraction | 0.3 
    32246 Gap open (HH/SS/other) | 18/18/6 
    32247 Gap extend | 1 
    32248 SS matrix |  |  | H | S | O 
    32249 ---|---|---|--- 
    32250 H | 6 | -9 | -6 
    32251 S |  | 6 | -6 
    32252 O |  |  | 4 
    32253 Iteration cutoff | 2 
    32254  
    32255 Matchmaker 3j0c.pdb1, chain I (#1.28) with AF3 CA.pdb, chain A (#741),
    32256 sequence alignment score = 306.5 
    32257 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    32258 2.689) 
    32259  
    32260 
    32261 > hide sel cartoons
    32262 
    32263 > color #737 dodgerblue
    32264 
    32265 > color #738 dodgerblue
    32266 
    32267 > color #739 #00b305ff
    32268 
    32269 > color #740 #00b305ff
    32270 
    32271 > color #741 #f15839ff
    32272 
    32273 > select #1.29/G
    32274 
    32275 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    32276 
    32277 > show sel cartoons
    32278 
    32279 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    32280 
    32281 Chain information for AF3 E1 1-421.pdb #742 
    32282 --- 
    32283 Chain | Description 
    32284 A | No description available 
    32285  
    32286 
    32287 > matchmaker #742 to #1.29 & sel
    32288 
    32289 Parameters 
    32290 --- 
    32291 Chain pairing | bb 
    32292 Alignment algorithm | Needleman-Wunsch 
    32293 Similarity matrix | BLOSUM-62 
    32294 SS fraction | 0.3 
    32295 Gap open (HH/SS/other) | 18/18/6 
    32296 Gap extend | 1 
    32297 SS matrix |  |  | H | S | O 
    32298 ---|---|---|--- 
    32299 H | 6 | -9 | -6 
    32300 S |  | 6 | -6 
    32301 O |  |  | 4 
    32302 Iteration cutoff | 2 
    32303  
    32304 Matchmaker 3j0c.pdb1, chain G (#1.29) with AF3 E1 1-421.pdb, chain A (#742),
    32305 sequence alignment score = 1060.7 
    32306 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    32307 2.985) 
    32308  
    32309 
    32310 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    32311 
    32312 Chain information for AF3 E1 422-461.pdb #743 
    32313 --- 
    32314 Chain | Description 
    32315 A | No description available 
    32316  
    32317 
    32318 > matchmaker #743 to #1.29 & sel
    32319 
    32320 Parameters 
    32321 --- 
    32322 Chain pairing | bb 
    32323 Alignment algorithm | Needleman-Wunsch 
    32324 Similarity matrix | BLOSUM-62 
    32325 SS fraction | 0.3 
    32326 Gap open (HH/SS/other) | 18/18/6 
    32327 Gap extend | 1 
    32328 SS matrix |  |  | H | S | O 
    32329 ---|---|---|--- 
    32330 H | 6 | -9 | -6 
    32331 S |  | 6 | -6 
    32332 O |  |  | 4 
    32333 Iteration cutoff | 2 
    32334  
    32335 Matchmaker 3j0c.pdb1, chain G (#1.29) with AF3 E1 422-461.pdb, chain A (#743),
    32336 sequence alignment score = 626.9 
    32337 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    32338 2.997) 
    32339  
    32340 
    32341 > hide sel cartoons
    32342 
    32343 > select #1.29/H
    32344 
    32345 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    32346 
    32347 > show sel cartoons
    32348 
    32349 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    32350 
    32351 Chain information for AF3 E2 1-352.pdb #744 
    32352 --- 
    32353 Chain | Description 
    32354 B | No description available 
    32355  
    32356 
    32357 > matchmaker #744 to #1.29 & sel
    32358 
    32359 Parameters 
    32360 --- 
    32361 Chain pairing | bb 
    32362 Alignment algorithm | Needleman-Wunsch 
    32363 Similarity matrix | BLOSUM-62 
    32364 SS fraction | 0.3 
    32365 Gap open (HH/SS/other) | 18/18/6 
    32366 Gap extend | 1 
    32367 SS matrix |  |  | H | S | O 
    32368 ---|---|---|--- 
    32369 H | 6 | -9 | -6 
    32370 S |  | 6 | -6 
    32371 O |  |  | 4 
    32372 Iteration cutoff | 2 
    32373  
    32374 Matchmaker 3j0c.pdb1, chain H (#1.29) with AF3 E2 1-352.pdb, chain B (#744),
    32375 sequence alignment score = 590.9 
    32376 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    32377 6.107) 
    32378  
    32379 
    32380 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    32381 
    32382 Chain information for AF3 E2 353-438.pdb #745 
    32383 --- 
    32384 Chain | Description 
    32385 B | No description available 
    32386  
    32387 
    32388 > matchmaker #745 to #1.29 & sel
    32389 
    32390 Parameters 
    32391 --- 
    32392 Chain pairing | bb 
    32393 Alignment algorithm | Needleman-Wunsch 
    32394 Similarity matrix | BLOSUM-62 
    32395 SS fraction | 0.3 
    32396 Gap open (HH/SS/other) | 18/18/6 
    32397 Gap extend | 1 
    32398 SS matrix |  |  | H | S | O 
    32399 ---|---|---|--- 
    32400 H | 6 | -9 | -6 
    32401 S |  | 6 | -6 
    32402 O |  |  | 4 
    32403 Iteration cutoff | 2 
    32404  
    32405 Matchmaker 3j0c.pdb1, chain H (#1.29) with AF3 E2 353-438.pdb, chain B (#745),
    32406 sequence alignment score = 329.4 
    32407 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    32408 8.150) 
    32409  
    32410 
    32411 > hide sel cartoons
    32412 
    32413 > select #1.29/I
    32414 
    32415 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    32416 
    32417 > show sel cartoons
    32418 
    32419 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    32420 
    32421 Chain information for AF3 CA.pdb #746 
    32422 --- 
    32423 Chain | Description 
    32424 A | No description available 
    32425  
    32426 
    32427 > matchmaker #746 to #1.29 & sel
    32428 
    32429 Parameters 
    32430 --- 
    32431 Chain pairing | bb 
    32432 Alignment algorithm | Needleman-Wunsch 
    32433 Similarity matrix | BLOSUM-62 
    32434 SS fraction | 0.3 
    32435 Gap open (HH/SS/other) | 18/18/6 
    32436 Gap extend | 1 
    32437 SS matrix |  |  | H | S | O 
    32438 ---|---|---|--- 
    32439 H | 6 | -9 | -6 
    32440 S |  | 6 | -6 
    32441 O |  |  | 4 
    32442 Iteration cutoff | 2 
    32443  
    32444 Matchmaker 3j0c.pdb1, chain I (#1.29) with AF3 CA.pdb, chain A (#746),
    32445 sequence alignment score = 306.5 
    32446 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    32447 2.689) 
    32448  
    32449 
    32450 > hide sel cartoons
    32451 
    32452 > color #742 dodgerblue
    32453 
    32454 > color #743 dodgerblue
    32455 
    32456 > color #744 #00b305ff
    32457 
    32458 > color #745 #00b305ff
    32459 
    32460 > color #746 #f15839ff
    32461 
    32462 > select #1.30/G
    32463 
    32464 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    32465 
    32466 > show sel cartoons
    32467 
    32468 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    32469 
    32470 Chain information for AF3 E1 1-421.pdb #747 
    32471 --- 
    32472 Chain | Description 
    32473 A | No description available 
    32474  
    32475 
    32476 > matchmaker #747 to #1.30 & sel
    32477 
    32478 Parameters 
    32479 --- 
    32480 Chain pairing | bb 
    32481 Alignment algorithm | Needleman-Wunsch 
    32482 Similarity matrix | BLOSUM-62 
    32483 SS fraction | 0.3 
    32484 Gap open (HH/SS/other) | 18/18/6 
    32485 Gap extend | 1 
    32486 SS matrix |  |  | H | S | O 
    32487 ---|---|---|--- 
    32488 H | 6 | -9 | -6 
    32489 S |  | 6 | -6 
    32490 O |  |  | 4 
    32491 Iteration cutoff | 2 
    32492  
    32493 Matchmaker 3j0c.pdb1, chain G (#1.30) with AF3 E1 1-421.pdb, chain A (#747),
    32494 sequence alignment score = 1060.7 
    32495 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    32496 2.985) 
    32497  
    32498 
    32499 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    32500 
    32501 Chain information for AF3 E1 422-461.pdb #748 
    32502 --- 
    32503 Chain | Description 
    32504 A | No description available 
    32505  
    32506 
    32507 > matchmaker #748 to #1.30 & sel
    32508 
    32509 Parameters 
    32510 --- 
    32511 Chain pairing | bb 
    32512 Alignment algorithm | Needleman-Wunsch 
    32513 Similarity matrix | BLOSUM-62 
    32514 SS fraction | 0.3 
    32515 Gap open (HH/SS/other) | 18/18/6 
    32516 Gap extend | 1 
    32517 SS matrix |  |  | H | S | O 
    32518 ---|---|---|--- 
    32519 H | 6 | -9 | -6 
    32520 S |  | 6 | -6 
    32521 O |  |  | 4 
    32522 Iteration cutoff | 2 
    32523  
    32524 Matchmaker 3j0c.pdb1, chain G (#1.30) with AF3 E1 422-461.pdb, chain A (#748),
    32525 sequence alignment score = 626.9 
    32526 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    32527 2.997) 
    32528  
    32529 
    32530 > hide sel cartoons
    32531 
    32532 > select #1.30/H
    32533 
    32534 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    32535 
    32536 > show sel cartoons
    32537 
    32538 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    32539 
    32540 Chain information for AF3 E2 1-352.pdb #749 
    32541 --- 
    32542 Chain | Description 
    32543 B | No description available 
    32544  
    32545 
    32546 > matchmaker #749 to #1.30 & sel
    32547 
    32548 Parameters 
    32549 --- 
    32550 Chain pairing | bb 
    32551 Alignment algorithm | Needleman-Wunsch 
    32552 Similarity matrix | BLOSUM-62 
    32553 SS fraction | 0.3 
    32554 Gap open (HH/SS/other) | 18/18/6 
    32555 Gap extend | 1 
    32556 SS matrix |  |  | H | S | O 
    32557 ---|---|---|--- 
    32558 H | 6 | -9 | -6 
    32559 S |  | 6 | -6 
    32560 O |  |  | 4 
    32561 Iteration cutoff | 2 
    32562  
    32563 Matchmaker 3j0c.pdb1, chain H (#1.30) with AF3 E2 1-352.pdb, chain B (#749),
    32564 sequence alignment score = 590.9 
    32565 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    32566 6.107) 
    32567  
    32568 
    32569 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    32570 
    32571 Chain information for AF3 E2 353-438.pdb #750 
    32572 --- 
    32573 Chain | Description 
    32574 B | No description available 
    32575  
    32576 
    32577 > matchmaker #750 to #1.30 & sel
    32578 
    32579 Parameters 
    32580 --- 
    32581 Chain pairing | bb 
    32582 Alignment algorithm | Needleman-Wunsch 
    32583 Similarity matrix | BLOSUM-62 
    32584 SS fraction | 0.3 
    32585 Gap open (HH/SS/other) | 18/18/6 
    32586 Gap extend | 1 
    32587 SS matrix |  |  | H | S | O 
    32588 ---|---|---|--- 
    32589 H | 6 | -9 | -6 
    32590 S |  | 6 | -6 
    32591 O |  |  | 4 
    32592 Iteration cutoff | 2 
    32593  
    32594 Matchmaker 3j0c.pdb1, chain H (#1.30) with AF3 E2 353-438.pdb, chain B (#750),
    32595 sequence alignment score = 329.4 
    32596 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    32597 8.150) 
    32598  
    32599 
    32600 > hide sel cartoons
    32601 
    32602 > select #1.30/H
    32603 
    32604 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    32605 
    32606 > show sel cartoons
    32607 
    32608 > hide sel cartoons
    32609 
    32610 > select #1.30/I
    32611 
    32612 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    32613 
    32614 > show sel cartoons
    32615 
    32616 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    32617 
    32618 Chain information for AF3 CA.pdb #751 
    32619 --- 
    32620 Chain | Description 
    32621 A | No description available 
    32622  
    32623 
    32624 > matchmaker #751 to #1.30 & sel
    32625 
    32626 Parameters 
    32627 --- 
    32628 Chain pairing | bb 
    32629 Alignment algorithm | Needleman-Wunsch 
    32630 Similarity matrix | BLOSUM-62 
    32631 SS fraction | 0.3 
    32632 Gap open (HH/SS/other) | 18/18/6 
    32633 Gap extend | 1 
    32634 SS matrix |  |  | H | S | O 
    32635 ---|---|---|--- 
    32636 H | 6 | -9 | -6 
    32637 S |  | 6 | -6 
    32638 O |  |  | 4 
    32639 Iteration cutoff | 2 
    32640  
    32641 Matchmaker 3j0c.pdb1, chain I (#1.30) with AF3 CA.pdb, chain A (#751),
    32642 sequence alignment score = 306.5 
    32643 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    32644 2.689) 
    32645  
    32646 
    32647 > hide sel cartoons
    32648 
    32649 > color #747 dodgerblue
    32650 
    32651 > color #748 dodgerblue
    32652 
    32653 > color #749 #00b305ff
    32654 
    32655 > color #750 #00b305ff
    32656 
    32657 > color #751 #f15839ff
    32658 
    32659 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    32660 
    32661 ——— End of log from Wed Jul 17 13:58:06 2024 ———
    32662 
    32663 opened ChimeraX session 
    32664 
    32665 > ui tool show Matchmaker
    32666 
    32667 The cached device pixel ratio value was stale on window expose. Please file a
    32668 QTBUG which explains how to reproduce. 
    32669 
    32670 > hide #702 models
    32671 
    32672 > hide #703 models
    32673 
    32674 > hide #704 models
    32675 
    32676 > hide #705 models
    32677 
    32678 > hide #706 models
    32679 
    32680 > hide #707 models
    32681 
    32682 > hide #708 models
    32683 
    32684 > hide #709 models
    32685 
    32686 > hide #710 models
    32687 
    32688 > hide #711 models
    32689 
    32690 > hide #712 models
    32691 
    32692 > hide #713 models
    32693 
    32694 > hide #714 models
    32695 
    32696 > hide #715 models
    32697 
    32698 > hide #716 models
    32699 
    32700 > hide #717 models
    32701 
    32702 > hide #718 models
    32703 
    32704 > hide #719 models
    32705 
    32706 > hide #720 models
    32707 
    32708 > hide #721 models
    32709 
    32710 > hide #722 models
    32711 
    32712 > hide #723 models
    32713 
    32714 > hide #724 models
    32715 
    32716 > hide #725 models
    32717 
    32718 > hide #726 models
    32719 
    32720 > hide #727 models
    32721 
    32722 > hide #728 models
    32723 
    32724 > hide #729 models
    32725 
    32726 > hide #730 models
    32727 
    32728 > hide #731 models
    32729 
    32730 > hide #732 models
    32731 
    32732 > hide #733 models
    32733 
    32734 > hide #734 models
    32735 
    32736 > hide #735 models
    32737 
    32738 > hide #736 models
    32739 
    32740 > hide #737 models
    32741 
    32742 > hide #738 models
    32743 
    32744 > hide #739 models
    32745 
    32746 > hide #740 models
    32747 
    32748 > hide #741 models
    32749 
    32750 > hide #742 models
    32751 
    32752 > hide #743 models
    32753 
    32754 > hide #744 models
    32755 
    32756 > hide #745 models
    32757 
    32758 > hide #746 models
    32759 
    32760 > hide #747 models
    32761 
    32762 > hide #748 models
    32763 
    32764 > hide #749 models
    32765 
    32766 > hide #750 models
    32767 
    32768 > hide #751 models
    32769 
    32770 > select #1.31/G
    32771 
    32772 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    32773 
    32774 > show sel cartoons
    32775 
    32776 > view
    32777 
    32778 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    32779 
    32780 Chain information for AF3 E1 1-421.pdb #752 
    32781 --- 
    32782 Chain | Description 
    32783 A | No description available 
    32784  
    32785 
    32786 > matchmaker #752 to #1.1
    32787 
    32788 Parameters 
    32789 --- 
    32790 Chain pairing | bb 
    32791 Alignment algorithm | Needleman-Wunsch 
    32792 Similarity matrix | BLOSUM-62 
    32793 SS fraction | 0.3 
    32794 Gap open (HH/SS/other) | 18/18/6 
    32795 Gap extend | 1 
    32796 SS matrix |  |  | H | S | O 
    32797 ---|---|---|--- 
    32798 H | 6 | -9 | -6 
    32799 S |  | 6 | -6 
    32800 O |  |  | 4 
    32801 Iteration cutoff | 2 
    32802  
    32803 Matchmaker 3j0c.pdb1, chain A (#1.1) with AF3 E1 1-421.pdb, chain A (#752),
    32804 sequence alignment score = 1060.7 
    32805 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    32806 3.020) 
    32807  
    32808 
    32809 > matchmaker #752 to #1.1 & sel
    32810 
    32811 No 'to' model specified 
    32812 
    32813 > matchmaker #752 to #1.1 & sel
    32814 
    32815 No 'to' model specified 
    32816 
    32817 > close #752
    32818 
    32819 > hide sel cartoons
    32820 
    32821 > select #1.31/G
    32822 
    32823 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    32824 
    32825 > show sel cartoons
    32826 
    32827 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    32828 
    32829 Chain information for AF3 E1 1-421.pdb #752 
    32830 --- 
    32831 Chain | Description 
    32832 A | No description available 
    32833  
    32834 
    32835 > matchmaker #752 to #1.1 & sel
    32836 
    32837 No 'to' model specified 
    32838 
    32839 > matchmaker #752 & sel to #1.1 & sel
    32840 
    32841 No 'to' model specified 
    32842 
    32843 > select #1.1/H
    32844 
    32845 3304 atoms, 3400 bonds, 423 residues, 1 model selected 
    32846 
    32847 > show sel cartoons
    32848 
    32849 > hide sel cartoons
    32850 
    32851 > select #1.31/G
    32852 
    32853 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    32854 
    32855 > show sel cartoons
    32856 
    32857 > matchmaker #752 to #1.1 & sel
    32858 
    32859 No 'to' model specified 
    32860 
    32861 > show #751 models
    32862 
    32863 > show #750 models
    32864 
    32865 > show #749 models
    32866 
    32867 > show #748 models
    32868 
    32869 > show #747 models
    32870 
    32871 > select #1.30/H
    32872 
    32873 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    32874 
    32875 > hide sel cartoons
    32876 
    32877 > show sel cartoons
    32878 
    32879 > hide sel cartoons
    32880 
    32881 > select #1.30/G
    32882 
    32883 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    32884 
    32885 > show sel cartoons
    32886 
    32887 > hide sel cartoons
    32888 
    32889 > matchmaker #752 to #1.31 & sel
    32890 
    32891 No 'to' model specified 
    32892 
    32893 > select #1.31/G
    32894 
    32895 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    32896 
    32897 > show sel cartoons
    32898 
    32899 > matchmaker #752 to #1.31 & sel
    32900 
    32901 Parameters 
    32902 --- 
    32903 Chain pairing | bb 
    32904 Alignment algorithm | Needleman-Wunsch 
    32905 Similarity matrix | BLOSUM-62 
    32906 SS fraction | 0.3 
    32907 Gap open (HH/SS/other) | 18/18/6 
    32908 Gap extend | 1 
    32909 SS matrix |  |  | H | S | O 
    32910 ---|---|---|--- 
    32911 H | 6 | -9 | -6 
    32912 S |  | 6 | -6 
    32913 O |  |  | 4 
    32914 Iteration cutoff | 2 
    32915  
    32916 Matchmaker 3j0c.pdb1, chain G (#1.31) with AF3 E1 1-421.pdb, chain A (#752),
    32917 sequence alignment score = 1060.7 
    32918 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    32919 2.985) 
    32920  
    32921 
    32922 > view
    32923 
    32924 > hide sel cartoons
    32925 
    32926 > show sel cartoons
    32927 
    32928 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    32929 
    32930 Chain information for AF3 E1 422-461.pdb #753 
    32931 --- 
    32932 Chain | Description 
    32933 A | No description available 
    32934  
    32935 
    32936 > matchmaker #753 to #1.31 & sel
    32937 
    32938 Parameters 
    32939 --- 
    32940 Chain pairing | bb 
    32941 Alignment algorithm | Needleman-Wunsch 
    32942 Similarity matrix | BLOSUM-62 
    32943 SS fraction | 0.3 
    32944 Gap open (HH/SS/other) | 18/18/6 
    32945 Gap extend | 1 
    32946 SS matrix |  |  | H | S | O 
    32947 ---|---|---|--- 
    32948 H | 6 | -9 | -6 
    32949 S |  | 6 | -6 
    32950 O |  |  | 4 
    32951 Iteration cutoff | 2 
    32952  
    32953 Matchmaker 3j0c.pdb1, chain G (#1.31) with AF3 E1 422-461.pdb, chain A (#753),
    32954 sequence alignment score = 626.9 
    32955 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    32956 2.997) 
    32957  
    32958 
    32959 > hide sel cartoons
    32960 
    32961 > select #1.31/H
    32962 
    32963 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    32964 
    32965 > show sel cartoons
    32966 
    32967 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    32968 
    32969 Chain information for AF3 E2 1-352.pdb #754 
    32970 --- 
    32971 Chain | Description 
    32972 B | No description available 
    32973  
    32974 
    32975 > matchmaker #754 to #1.31 & sel
    32976 
    32977 Parameters 
    32978 --- 
    32979 Chain pairing | bb 
    32980 Alignment algorithm | Needleman-Wunsch 
    32981 Similarity matrix | BLOSUM-62 
    32982 SS fraction | 0.3 
    32983 Gap open (HH/SS/other) | 18/18/6 
    32984 Gap extend | 1 
    32985 SS matrix |  |  | H | S | O 
    32986 ---|---|---|--- 
    32987 H | 6 | -9 | -6 
    32988 S |  | 6 | -6 
    32989 O |  |  | 4 
    32990 Iteration cutoff | 2 
    32991  
    32992 Matchmaker 3j0c.pdb1, chain H (#1.31) with AF3 E2 1-352.pdb, chain B (#754),
    32993 sequence alignment score = 590.9 
    32994 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    32995 6.107) 
    32996  
    32997 
    32998 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    32999 
    33000 Chain information for AF3 E2 353-438.pdb #755 
    33001 --- 
    33002 Chain | Description 
    33003 B | No description available 
    33004  
    33005 
    33006 > matchmaker #755 to #1.31 & sel
    33007 
    33008 Parameters 
    33009 --- 
    33010 Chain pairing | bb 
    33011 Alignment algorithm | Needleman-Wunsch 
    33012 Similarity matrix | BLOSUM-62 
    33013 SS fraction | 0.3 
    33014 Gap open (HH/SS/other) | 18/18/6 
    33015 Gap extend | 1 
    33016 SS matrix |  |  | H | S | O 
    33017 ---|---|---|--- 
    33018 H | 6 | -9 | -6 
    33019 S |  | 6 | -6 
    33020 O |  |  | 4 
    33021 Iteration cutoff | 2 
    33022  
    33023 Matchmaker 3j0c.pdb1, chain H (#1.31) with AF3 E2 353-438.pdb, chain B (#755),
    33024 sequence alignment score = 329.4 
    33025 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    33026 8.150) 
    33027  
    33028 
    33029 > hide sel cartoons
    33030 
    33031 > select #1.31/I
    33032 
    33033 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    33034 
    33035 > show sel cartoons
    33036 
    33037 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    33038 
    33039 Chain information for AF3 CA.pdb #756 
    33040 --- 
    33041 Chain | Description 
    33042 A | No description available 
    33043  
    33044 
    33045 > matchmaker #756 to #1.31 & sel
    33046 
    33047 Parameters 
    33048 --- 
    33049 Chain pairing | bb 
    33050 Alignment algorithm | Needleman-Wunsch 
    33051 Similarity matrix | BLOSUM-62 
    33052 SS fraction | 0.3 
    33053 Gap open (HH/SS/other) | 18/18/6 
    33054 Gap extend | 1 
    33055 SS matrix |  |  | H | S | O 
    33056 ---|---|---|--- 
    33057 H | 6 | -9 | -6 
    33058 S |  | 6 | -6 
    33059 O |  |  | 4 
    33060 Iteration cutoff | 2 
    33061  
    33062 Matchmaker 3j0c.pdb1, chain I (#1.31) with AF3 CA.pdb, chain A (#756),
    33063 sequence alignment score = 306.5 
    33064 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    33065 2.689) 
    33066  
    33067 
    33068 > hide sel cartoons
    33069 
    33070 > hide #747 models
    33071 
    33072 > hide #748 models
    33073 
    33074 > hide #749 models
    33075 
    33076 > hide #750 models
    33077 
    33078 > hide #751 models
    33079 
    33080 > color #752 dodgerblue
    33081 
    33082 > color #753 dodgerblue
    33083 
    33084 > color #754 #00b305ff
    33085 
    33086 > color #755 #00b305ff
    33087 
    33088 > color #756 #f15839ff
    33089 
    33090 > select #1.32/G
    33091 
    33092 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    33093 
    33094 > show sel cartoons
    33095 
    33096 [Repeated 1 time(s)]
    33097 
    33098 > view
    33099 
    33100 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    33101 
    33102 Chain information for AF3 E1 1-421.pdb #757 
    33103 --- 
    33104 Chain | Description 
    33105 A | No description available 
    33106  
    33107 
    33108 > matchmaker #757 to #1.32 & sel
    33109 
    33110 Parameters 
    33111 --- 
    33112 Chain pairing | bb 
    33113 Alignment algorithm | Needleman-Wunsch 
    33114 Similarity matrix | BLOSUM-62 
    33115 SS fraction | 0.3 
    33116 Gap open (HH/SS/other) | 18/18/6 
    33117 Gap extend | 1 
    33118 SS matrix |  |  | H | S | O 
    33119 ---|---|---|--- 
    33120 H | 6 | -9 | -6 
    33121 S |  | 6 | -6 
    33122 O |  |  | 4 
    33123 Iteration cutoff | 2 
    33124  
    33125 Matchmaker 3j0c.pdb1, chain G (#1.32) with AF3 E1 1-421.pdb, chain A (#757),
    33126 sequence alignment score = 1060.7 
    33127 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    33128 2.985) 
    33129  
    33130 
    33131 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    33132 
    33133 Chain information for AF3 E1 422-461.pdb #758 
    33134 --- 
    33135 Chain | Description 
    33136 A | No description available 
    33137  
    33138 
    33139 > matchmaker #758 to #1.32 & sel
    33140 
    33141 Parameters 
    33142 --- 
    33143 Chain pairing | bb 
    33144 Alignment algorithm | Needleman-Wunsch 
    33145 Similarity matrix | BLOSUM-62 
    33146 SS fraction | 0.3 
    33147 Gap open (HH/SS/other) | 18/18/6 
    33148 Gap extend | 1 
    33149 SS matrix |  |  | H | S | O 
    33150 ---|---|---|--- 
    33151 H | 6 | -9 | -6 
    33152 S |  | 6 | -6 
    33153 O |  |  | 4 
    33154 Iteration cutoff | 2 
    33155  
    33156 Matchmaker 3j0c.pdb1, chain G (#1.32) with AF3 E1 422-461.pdb, chain A (#758),
    33157 sequence alignment score = 626.9 
    33158 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    33159 2.997) 
    33160  
    33161 
    33162 > hide sel cartoons
    33163 
    33164 > select #1.32/H
    33165 
    33166 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    33167 
    33168 > show sel cartoons
    33169 
    33170 [Repeated 1 time(s)]
    33171 
    33172 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    33173 
    33174 Chain information for AF3 E2 1-352.pdb #759 
    33175 --- 
    33176 Chain | Description 
    33177 B | No description available 
    33178  
    33179 
    33180 > matchmaker #759 to #1.32 & sel
    33181 
    33182 Parameters 
    33183 --- 
    33184 Chain pairing | bb 
    33185 Alignment algorithm | Needleman-Wunsch 
    33186 Similarity matrix | BLOSUM-62 
    33187 SS fraction | 0.3 
    33188 Gap open (HH/SS/other) | 18/18/6 
    33189 Gap extend | 1 
    33190 SS matrix |  |  | H | S | O 
    33191 ---|---|---|--- 
    33192 H | 6 | -9 | -6 
    33193 S |  | 6 | -6 
    33194 O |  |  | 4 
    33195 Iteration cutoff | 2 
    33196  
    33197 Matchmaker 3j0c.pdb1, chain H (#1.32) with AF3 E2 1-352.pdb, chain B (#759),
    33198 sequence alignment score = 590.9 
    33199 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    33200 6.107) 
    33201  
    33202 
    33203 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    33204 
    33205 Chain information for AF3 E2 353-438.pdb #760 
    33206 --- 
    33207 Chain | Description 
    33208 B | No description available 
    33209  
    33210 
    33211 > matchmaker #760 to #1.32 & sel
    33212 
    33213 Parameters 
    33214 --- 
    33215 Chain pairing | bb 
    33216 Alignment algorithm | Needleman-Wunsch 
    33217 Similarity matrix | BLOSUM-62 
    33218 SS fraction | 0.3 
    33219 Gap open (HH/SS/other) | 18/18/6 
    33220 Gap extend | 1 
    33221 SS matrix |  |  | H | S | O 
    33222 ---|---|---|--- 
    33223 H | 6 | -9 | -6 
    33224 S |  | 6 | -6 
    33225 O |  |  | 4 
    33226 Iteration cutoff | 2 
    33227  
    33228 Matchmaker 3j0c.pdb1, chain H (#1.32) with AF3 E2 353-438.pdb, chain B (#760),
    33229 sequence alignment score = 329.4 
    33230 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    33231 8.150) 
    33232  
    33233 
    33234 > hide sel cartoons
    33235 
    33236 > select #1.32/I
    33237 
    33238 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    33239 
    33240 > show sel cartoons
    33241 
    33242 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    33243 
    33244 Chain information for AF3 CA.pdb #761 
    33245 --- 
    33246 Chain | Description 
    33247 A | No description available 
    33248  
    33249 
    33250 > matchmaker #761 to #1.32 & sel
    33251 
    33252 Parameters 
    33253 --- 
    33254 Chain pairing | bb 
    33255 Alignment algorithm | Needleman-Wunsch 
    33256 Similarity matrix | BLOSUM-62 
    33257 SS fraction | 0.3 
    33258 Gap open (HH/SS/other) | 18/18/6 
    33259 Gap extend | 1 
    33260 SS matrix |  |  | H | S | O 
    33261 ---|---|---|--- 
    33262 H | 6 | -9 | -6 
    33263 S |  | 6 | -6 
    33264 O |  |  | 4 
    33265 Iteration cutoff | 2 
    33266  
    33267 Matchmaker 3j0c.pdb1, chain I (#1.32) with AF3 CA.pdb, chain A (#761),
    33268 sequence alignment score = 306.5 
    33269 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    33270 2.689) 
    33271  
    33272 
    33273 > hide sel cartoons
    33274 
    33275 > color #757 dodgerblue
    33276 
    33277 > color #758 dodgerblue
    33278 
    33279 > color #759 #00b305ff
    33280 
    33281 > color #760 #00b305ff
    33282 
    33283 > color #761 #f15839ff
    33284 
    33285 > select #1.33/G
    33286 
    33287 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    33288 
    33289 > show sel cartoons
    33290 
    33291 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    33292 
    33293 Chain information for AF3 E1 1-421.pdb #762 
    33294 --- 
    33295 Chain | Description 
    33296 A | No description available 
    33297  
    33298 
    33299 > matchmaker #762 to #1.33 & sel
    33300 
    33301 Parameters 
    33302 --- 
    33303 Chain pairing | bb 
    33304 Alignment algorithm | Needleman-Wunsch 
    33305 Similarity matrix | BLOSUM-62 
    33306 SS fraction | 0.3 
    33307 Gap open (HH/SS/other) | 18/18/6 
    33308 Gap extend | 1 
    33309 SS matrix |  |  | H | S | O 
    33310 ---|---|---|--- 
    33311 H | 6 | -9 | -6 
    33312 S |  | 6 | -6 
    33313 O |  |  | 4 
    33314 Iteration cutoff | 2 
    33315  
    33316 Matchmaker 3j0c.pdb1, chain G (#1.33) with AF3 E1 1-421.pdb, chain A (#762),
    33317 sequence alignment score = 1060.7 
    33318 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    33319 2.985) 
    33320  
    33321 
    33322 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    33323 
    33324 Chain information for AF3 E1 422-461.pdb #763 
    33325 --- 
    33326 Chain | Description 
    33327 A | No description available 
    33328  
    33329 
    33330 > matchmaker #763 to #1.33 & sel
    33331 
    33332 Parameters 
    33333 --- 
    33334 Chain pairing | bb 
    33335 Alignment algorithm | Needleman-Wunsch 
    33336 Similarity matrix | BLOSUM-62 
    33337 SS fraction | 0.3 
    33338 Gap open (HH/SS/other) | 18/18/6 
    33339 Gap extend | 1 
    33340 SS matrix |  |  | H | S | O 
    33341 ---|---|---|--- 
    33342 H | 6 | -9 | -6 
    33343 S |  | 6 | -6 
    33344 O |  |  | 4 
    33345 Iteration cutoff | 2 
    33346  
    33347 Matchmaker 3j0c.pdb1, chain G (#1.33) with AF3 E1 422-461.pdb, chain A (#763),
    33348 sequence alignment score = 626.9 
    33349 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    33350 2.997) 
    33351  
    33352 
    33353 > select #1.32/H
    33354 
    33355 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    33356 
    33357 > show sel cartoons
    33358 
    33359 > hide sel cartoons
    33360 
    33361 > select #1.33/H
    33362 
    33363 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    33364 
    33365 > show sel cartoons
    33366 
    33367 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    33368 
    33369 Chain information for AF3 E2 1-352.pdb #764 
    33370 --- 
    33371 Chain | Description 
    33372 B | No description available 
    33373  
    33374 
    33375 > matchmaker #764 to #1.33 & sel
    33376 
    33377 Parameters 
    33378 --- 
    33379 Chain pairing | bb 
    33380 Alignment algorithm | Needleman-Wunsch 
    33381 Similarity matrix | BLOSUM-62 
    33382 SS fraction | 0.3 
    33383 Gap open (HH/SS/other) | 18/18/6 
    33384 Gap extend | 1 
    33385 SS matrix |  |  | H | S | O 
    33386 ---|---|---|--- 
    33387 H | 6 | -9 | -6 
    33388 S |  | 6 | -6 
    33389 O |  |  | 4 
    33390 Iteration cutoff | 2 
    33391  
    33392 Matchmaker 3j0c.pdb1, chain H (#1.33) with AF3 E2 1-352.pdb, chain B (#764),
    33393 sequence alignment score = 590.9 
    33394 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    33395 6.107) 
    33396  
    33397 
    33398 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    33399 
    33400 Chain information for AF3 E2 353-438.pdb #765 
    33401 --- 
    33402 Chain | Description 
    33403 B | No description available 
    33404  
    33405 
    33406 > matchmaker #765 to #1.33 & sel
    33407 
    33408 Parameters 
    33409 --- 
    33410 Chain pairing | bb 
    33411 Alignment algorithm | Needleman-Wunsch 
    33412 Similarity matrix | BLOSUM-62 
    33413 SS fraction | 0.3 
    33414 Gap open (HH/SS/other) | 18/18/6 
    33415 Gap extend | 1 
    33416 SS matrix |  |  | H | S | O 
    33417 ---|---|---|--- 
    33418 H | 6 | -9 | -6 
    33419 S |  | 6 | -6 
    33420 O |  |  | 4 
    33421 Iteration cutoff | 2 
    33422  
    33423 Matchmaker 3j0c.pdb1, chain H (#1.33) with AF3 E2 353-438.pdb, chain B (#765),
    33424 sequence alignment score = 329.4 
    33425 RMSD between 40 pruned atom pairs is 0.937 angstroms; (across all 84 pairs:
    33426 8.151) 
    33427  
    33428 
    33429 > hide sel cartoons
    33430 
    33431 > select #1.33/I
    33432 
    33433 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    33434 
    33435 > show sel cartoons
    33436 
    33437 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    33438 
    33439 Chain information for AF3 CA.pdb #766 
    33440 --- 
    33441 Chain | Description 
    33442 A | No description available 
    33443  
    33444 
    33445 > matchmaker #766 to #1.33 & sel
    33446 
    33447 Parameters 
    33448 --- 
    33449 Chain pairing | bb 
    33450 Alignment algorithm | Needleman-Wunsch 
    33451 Similarity matrix | BLOSUM-62 
    33452 SS fraction | 0.3 
    33453 Gap open (HH/SS/other) | 18/18/6 
    33454 Gap extend | 1 
    33455 SS matrix |  |  | H | S | O 
    33456 ---|---|---|--- 
    33457 H | 6 | -9 | -6 
    33458 S |  | 6 | -6 
    33459 O |  |  | 4 
    33460 Iteration cutoff | 2 
    33461  
    33462 Matchmaker 3j0c.pdb1, chain I (#1.33) with AF3 CA.pdb, chain A (#766),
    33463 sequence alignment score = 306.5 
    33464 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    33465 2.689) 
    33466  
    33467 
    33468 > hide sel cartoons
    33469 
    33470 > color #762 dodgerblue
    33471 
    33472 > color #763 dodgerblue
    33473 
    33474 > color #764 #00b305ff
    33475 
    33476 > color #765 #00b305ff
    33477 
    33478 > color #766 #f15839ff
    33479 
    33480 > select #1.33/G
    33481 
    33482 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    33483 
    33484 > hide sel cartoons
    33485 
    33486 > select #1.34/G
    33487 
    33488 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    33489 
    33490 > show sel cartoons
    33491 
    33492 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    33493 
    33494 Chain information for AF3 E1 1-421.pdb #767 
    33495 --- 
    33496 Chain | Description 
    33497 A | No description available 
    33498  
    33499 
    33500 > matchmaker #767 to #1.34 & sel
    33501 
    33502 Parameters 
    33503 --- 
    33504 Chain pairing | bb 
    33505 Alignment algorithm | Needleman-Wunsch 
    33506 Similarity matrix | BLOSUM-62 
    33507 SS fraction | 0.3 
    33508 Gap open (HH/SS/other) | 18/18/6 
    33509 Gap extend | 1 
    33510 SS matrix |  |  | H | S | O 
    33511 ---|---|---|--- 
    33512 H | 6 | -9 | -6 
    33513 S |  | 6 | -6 
    33514 O |  |  | 4 
    33515 Iteration cutoff | 2 
    33516  
    33517 Matchmaker 3j0c.pdb1, chain G (#1.34) with AF3 E1 1-421.pdb, chain A (#767),
    33518 sequence alignment score = 1060.7 
    33519 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    33520 2.985) 
    33521  
    33522 
    33523 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    33524 
    33525 Chain information for AF3 E1 422-461.pdb #768 
    33526 --- 
    33527 Chain | Description 
    33528 A | No description available 
    33529  
    33530 
    33531 > matchmaker #768 to #1.34 & sel
    33532 
    33533 Parameters 
    33534 --- 
    33535 Chain pairing | bb 
    33536 Alignment algorithm | Needleman-Wunsch 
    33537 Similarity matrix | BLOSUM-62 
    33538 SS fraction | 0.3 
    33539 Gap open (HH/SS/other) | 18/18/6 
    33540 Gap extend | 1 
    33541 SS matrix |  |  | H | S | O 
    33542 ---|---|---|--- 
    33543 H | 6 | -9 | -6 
    33544 S |  | 6 | -6 
    33545 O |  |  | 4 
    33546 Iteration cutoff | 2 
    33547  
    33548 Matchmaker 3j0c.pdb1, chain G (#1.34) with AF3 E1 422-461.pdb, chain A (#768),
    33549 sequence alignment score = 626.9 
    33550 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    33551 2.997) 
    33552  
    33553 
    33554 > hide sel cartoons
    33555 
    33556 > select #1.34/H
    33557 
    33558 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    33559 
    33560 > show sel cartoons
    33561 
    33562 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    33563 
    33564 Chain information for AF3 E2 1-352.pdb #769 
    33565 --- 
    33566 Chain | Description 
    33567 B | No description available 
    33568  
    33569 
    33570 > matchmaker #769 to #1.34 & sel
    33571 
    33572 Parameters 
    33573 --- 
    33574 Chain pairing | bb 
    33575 Alignment algorithm | Needleman-Wunsch 
    33576 Similarity matrix | BLOSUM-62 
    33577 SS fraction | 0.3 
    33578 Gap open (HH/SS/other) | 18/18/6 
    33579 Gap extend | 1 
    33580 SS matrix |  |  | H | S | O 
    33581 ---|---|---|--- 
    33582 H | 6 | -9 | -6 
    33583 S |  | 6 | -6 
    33584 O |  |  | 4 
    33585 Iteration cutoff | 2 
    33586  
    33587 Matchmaker 3j0c.pdb1, chain H (#1.34) with AF3 E2 1-352.pdb, chain B (#769),
    33588 sequence alignment score = 590.9 
    33589 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    33590 6.107) 
    33591  
    33592 
    33593 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    33594 
    33595 Chain information for AF3 E2 353-438.pdb #770 
    33596 --- 
    33597 Chain | Description 
    33598 B | No description available 
    33599  
    33600 
    33601 > matchmaker #770 to #1.34 & sel
    33602 
    33603 Parameters 
    33604 --- 
    33605 Chain pairing | bb 
    33606 Alignment algorithm | Needleman-Wunsch 
    33607 Similarity matrix | BLOSUM-62 
    33608 SS fraction | 0.3 
    33609 Gap open (HH/SS/other) | 18/18/6 
    33610 Gap extend | 1 
    33611 SS matrix |  |  | H | S | O 
    33612 ---|---|---|--- 
    33613 H | 6 | -9 | -6 
    33614 S |  | 6 | -6 
    33615 O |  |  | 4 
    33616 Iteration cutoff | 2 
    33617  
    33618 Matchmaker 3j0c.pdb1, chain H (#1.34) with AF3 E2 353-438.pdb, chain B (#770),
    33619 sequence alignment score = 329.4 
    33620 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    33621 8.150) 
    33622  
    33623 
    33624 > hide sel cartoons
    33625 
    33626 > select #1.34/I
    33627 
    33628 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    33629 
    33630 > show sel cartoons
    33631 
    33632 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    33633 
    33634 Chain information for AF3 CA.pdb #771 
    33635 --- 
    33636 Chain | Description 
    33637 A | No description available 
    33638  
    33639 
    33640 > matchmaker #771 to #1.34 & sel
    33641 
    33642 Parameters 
    33643 --- 
    33644 Chain pairing | bb 
    33645 Alignment algorithm | Needleman-Wunsch 
    33646 Similarity matrix | BLOSUM-62 
    33647 SS fraction | 0.3 
    33648 Gap open (HH/SS/other) | 18/18/6 
    33649 Gap extend | 1 
    33650 SS matrix |  |  | H | S | O 
    33651 ---|---|---|--- 
    33652 H | 6 | -9 | -6 
    33653 S |  | 6 | -6 
    33654 O |  |  | 4 
    33655 Iteration cutoff | 2 
    33656  
    33657 Matchmaker 3j0c.pdb1, chain I (#1.34) with AF3 CA.pdb, chain A (#771),
    33658 sequence alignment score = 306.5 
    33659 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    33660 2.689) 
    33661  
    33662 
    33663 > hide sel cartoons
    33664 
    33665 > color #767 dodgerblue
    33666 
    33667 > color #768 dodgerblue
    33668 
    33669 > color #769 #00b305ff
    33670 
    33671 > color #770 #00b305ff
    33672 
    33673 > color #771 #f15839ff
    33674 
    33675 > select #1.35/G
    33676 
    33677 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    33678 
    33679 > show sel cartoons
    33680 
    33681 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    33682 
    33683 Chain information for AF3 E1 1-421.pdb #772 
    33684 --- 
    33685 Chain | Description 
    33686 A | No description available 
    33687  
    33688 
    33689 > matchmaker #772 to #1.34 & sel
    33690 
    33691 No 'to' model specified 
    33692 
    33693 > matchmaker #772 to #1.35 & sel
    33694 
    33695 Parameters 
    33696 --- 
    33697 Chain pairing | bb 
    33698 Alignment algorithm | Needleman-Wunsch 
    33699 Similarity matrix | BLOSUM-62 
    33700 SS fraction | 0.3 
    33701 Gap open (HH/SS/other) | 18/18/6 
    33702 Gap extend | 1 
    33703 SS matrix |  |  | H | S | O 
    33704 ---|---|---|--- 
    33705 H | 6 | -9 | -6 
    33706 S |  | 6 | -6 
    33707 O |  |  | 4 
    33708 Iteration cutoff | 2 
    33709  
    33710 Matchmaker 3j0c.pdb1, chain G (#1.35) with AF3 E1 1-421.pdb, chain A (#772),
    33711 sequence alignment score = 1060.7 
    33712 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    33713 2.985) 
    33714  
    33715 
    33716 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    33717 
    33718 Chain information for AF3 E1 422-461.pdb #773 
    33719 --- 
    33720 Chain | Description 
    33721 A | No description available 
    33722  
    33723 
    33724 > matchmaker #773 to #1.35 & sel
    33725 
    33726 Parameters 
    33727 --- 
    33728 Chain pairing | bb 
    33729 Alignment algorithm | Needleman-Wunsch 
    33730 Similarity matrix | BLOSUM-62 
    33731 SS fraction | 0.3 
    33732 Gap open (HH/SS/other) | 18/18/6 
    33733 Gap extend | 1 
    33734 SS matrix |  |  | H | S | O 
    33735 ---|---|---|--- 
    33736 H | 6 | -9 | -6 
    33737 S |  | 6 | -6 
    33738 O |  |  | 4 
    33739 Iteration cutoff | 2 
    33740  
    33741 Matchmaker 3j0c.pdb1, chain G (#1.35) with AF3 E1 422-461.pdb, chain A (#773),
    33742 sequence alignment score = 626.9 
    33743 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    33744 2.997) 
    33745  
    33746 
    33747 > hide sel cartoons
    33748 
    33749 > select #1.35/H
    33750 
    33751 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    33752 
    33753 > show sel cartoons
    33754 
    33755 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    33756 
    33757 Chain information for AF3 E2 1-352.pdb #774 
    33758 --- 
    33759 Chain | Description 
    33760 B | No description available 
    33761  
    33762 
    33763 > matchmaker #774 to #1.35 & sel
    33764 
    33765 Parameters 
    33766 --- 
    33767 Chain pairing | bb 
    33768 Alignment algorithm | Needleman-Wunsch 
    33769 Similarity matrix | BLOSUM-62 
    33770 SS fraction | 0.3 
    33771 Gap open (HH/SS/other) | 18/18/6 
    33772 Gap extend | 1 
    33773 SS matrix |  |  | H | S | O 
    33774 ---|---|---|--- 
    33775 H | 6 | -9 | -6 
    33776 S |  | 6 | -6 
    33777 O |  |  | 4 
    33778 Iteration cutoff | 2 
    33779  
    33780 Matchmaker 3j0c.pdb1, chain H (#1.35) with AF3 E2 1-352.pdb, chain B (#774),
    33781 sequence alignment score = 590.9 
    33782 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    33783 6.107) 
    33784  
    33785 
    33786 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    33787 
    33788 Chain information for AF3 E2 353-438.pdb #775 
    33789 --- 
    33790 Chain | Description 
    33791 B | No description available 
    33792  
    33793 
    33794 > matchmaker #775 to #1.35 & sel
    33795 
    33796 Parameters 
    33797 --- 
    33798 Chain pairing | bb 
    33799 Alignment algorithm | Needleman-Wunsch 
    33800 Similarity matrix | BLOSUM-62 
    33801 SS fraction | 0.3 
    33802 Gap open (HH/SS/other) | 18/18/6 
    33803 Gap extend | 1 
    33804 SS matrix |  |  | H | S | O 
    33805 ---|---|---|--- 
    33806 H | 6 | -9 | -6 
    33807 S |  | 6 | -6 
    33808 O |  |  | 4 
    33809 Iteration cutoff | 2 
    33810  
    33811 Matchmaker 3j0c.pdb1, chain H (#1.35) with AF3 E2 353-438.pdb, chain B (#775),
    33812 sequence alignment score = 329.4 
    33813 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    33814 8.150) 
    33815  
    33816 
    33817 > hide sel cartoons
    33818 
    33819 > select #1.35/I
    33820 
    33821 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    33822 
    33823 > show sel cartoons
    33824 
    33825 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    33826 
    33827 Chain information for AF3 CA.pdb #776 
    33828 --- 
    33829 Chain | Description 
    33830 A | No description available 
    33831  
    33832 
    33833 > matchmaker #776 to #1.35 & sel
    33834 
    33835 Parameters 
    33836 --- 
    33837 Chain pairing | bb 
    33838 Alignment algorithm | Needleman-Wunsch 
    33839 Similarity matrix | BLOSUM-62 
    33840 SS fraction | 0.3 
    33841 Gap open (HH/SS/other) | 18/18/6 
    33842 Gap extend | 1 
    33843 SS matrix |  |  | H | S | O 
    33844 ---|---|---|--- 
    33845 H | 6 | -9 | -6 
    33846 S |  | 6 | -6 
    33847 O |  |  | 4 
    33848 Iteration cutoff | 2 
    33849  
    33850 Matchmaker 3j0c.pdb1, chain I (#1.35) with AF3 CA.pdb, chain A (#776),
    33851 sequence alignment score = 306.5 
    33852 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    33853 2.689) 
    33854  
    33855 
    33856 > hide sel cartoons
    33857 
    33858 > color #772 dodgerblue
    33859 
    33860 > color #773 dodgerblue
    33861 
    33862 > color #774 #00b305ff
    33863 
    33864 > color #775 #00b305ff
    33865 
    33866 > color #776 #f15839ff
    33867 
    33868 > select #1.36/G
    33869 
    33870 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    33871 
    33872 > show sel cartoons
    33873 
    33874 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    33875 
    33876 Chain information for AF3 E1 1-421.pdb #777 
    33877 --- 
    33878 Chain | Description 
    33879 A | No description available 
    33880  
    33881 
    33882 > matchmaker #777 to #1.36 & sel
    33883 
    33884 Parameters 
    33885 --- 
    33886 Chain pairing | bb 
    33887 Alignment algorithm | Needleman-Wunsch 
    33888 Similarity matrix | BLOSUM-62 
    33889 SS fraction | 0.3 
    33890 Gap open (HH/SS/other) | 18/18/6 
    33891 Gap extend | 1 
    33892 SS matrix |  |  | H | S | O 
    33893 ---|---|---|--- 
    33894 H | 6 | -9 | -6 
    33895 S |  | 6 | -6 
    33896 O |  |  | 4 
    33897 Iteration cutoff | 2 
    33898  
    33899 Matchmaker 3j0c.pdb1, chain G (#1.36) with AF3 E1 1-421.pdb, chain A (#777),
    33900 sequence alignment score = 1060.7 
    33901 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    33902 2.985) 
    33903  
    33904 
    33905 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    33906 
    33907 Chain information for AF3 E1 422-461.pdb #778 
    33908 --- 
    33909 Chain | Description 
    33910 A | No description available 
    33911  
    33912 
    33913 > matchmaker #778 to #1.36 & sel
    33914 
    33915 Parameters 
    33916 --- 
    33917 Chain pairing | bb 
    33918 Alignment algorithm | Needleman-Wunsch 
    33919 Similarity matrix | BLOSUM-62 
    33920 SS fraction | 0.3 
    33921 Gap open (HH/SS/other) | 18/18/6 
    33922 Gap extend | 1 
    33923 SS matrix |  |  | H | S | O 
    33924 ---|---|---|--- 
    33925 H | 6 | -9 | -6 
    33926 S |  | 6 | -6 
    33927 O |  |  | 4 
    33928 Iteration cutoff | 2 
    33929  
    33930 Matchmaker 3j0c.pdb1, chain G (#1.36) with AF3 E1 422-461.pdb, chain A (#778),
    33931 sequence alignment score = 626.9 
    33932 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    33933 2.997) 
    33934  
    33935 
    33936 > hide sel cartoons
    33937 
    33938 > select #1.36/H
    33939 
    33940 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    33941 
    33942 > show sel cartoons
    33943 
    33944 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    33945 
    33946 Chain information for AF3 E2 1-352.pdb #779 
    33947 --- 
    33948 Chain | Description 
    33949 B | No description available 
    33950  
    33951 
    33952 > matchmaker #779 to #1.36 & sel
    33953 
    33954 Parameters 
    33955 --- 
    33956 Chain pairing | bb 
    33957 Alignment algorithm | Needleman-Wunsch 
    33958 Similarity matrix | BLOSUM-62 
    33959 SS fraction | 0.3 
    33960 Gap open (HH/SS/other) | 18/18/6 
    33961 Gap extend | 1 
    33962 SS matrix |  |  | H | S | O 
    33963 ---|---|---|--- 
    33964 H | 6 | -9 | -6 
    33965 S |  | 6 | -6 
    33966 O |  |  | 4 
    33967 Iteration cutoff | 2 
    33968  
    33969 Matchmaker 3j0c.pdb1, chain H (#1.36) with AF3 E2 1-352.pdb, chain B (#779),
    33970 sequence alignment score = 590.9 
    33971 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    33972 6.107) 
    33973  
    33974 
    33975 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    33976 
    33977 Chain information for AF3 E2 353-438.pdb #780 
    33978 --- 
    33979 Chain | Description 
    33980 B | No description available 
    33981  
    33982 
    33983 > matchmaker #780 to #1.36 & sel
    33984 
    33985 Parameters 
    33986 --- 
    33987 Chain pairing | bb 
    33988 Alignment algorithm | Needleman-Wunsch 
    33989 Similarity matrix | BLOSUM-62 
    33990 SS fraction | 0.3 
    33991 Gap open (HH/SS/other) | 18/18/6 
    33992 Gap extend | 1 
    33993 SS matrix |  |  | H | S | O 
    33994 ---|---|---|--- 
    33995 H | 6 | -9 | -6 
    33996 S |  | 6 | -6 
    33997 O |  |  | 4 
    33998 Iteration cutoff | 2 
    33999  
    34000 Matchmaker 3j0c.pdb1, chain H (#1.36) with AF3 E2 353-438.pdb, chain B (#780),
    34001 sequence alignment score = 329.4 
    34002 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    34003 8.151) 
    34004  
    34005 
    34006 > hide sel cartoons
    34007 
    34008 > select #1.36/I
    34009 
    34010 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    34011 
    34012 > show sel cartoons
    34013 
    34014 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    34015 
    34016 Chain information for AF3 CA.pdb #781 
    34017 --- 
    34018 Chain | Description 
    34019 A | No description available 
    34020  
    34021 
    34022 > matchmaker #781 to #1.36 & sel
    34023 
    34024 Parameters 
    34025 --- 
    34026 Chain pairing | bb 
    34027 Alignment algorithm | Needleman-Wunsch 
    34028 Similarity matrix | BLOSUM-62 
    34029 SS fraction | 0.3 
    34030 Gap open (HH/SS/other) | 18/18/6 
    34031 Gap extend | 1 
    34032 SS matrix |  |  | H | S | O 
    34033 ---|---|---|--- 
    34034 H | 6 | -9 | -6 
    34035 S |  | 6 | -6 
    34036 O |  |  | 4 
    34037 Iteration cutoff | 2 
    34038  
    34039 Matchmaker 3j0c.pdb1, chain I (#1.36) with AF3 CA.pdb, chain A (#781),
    34040 sequence alignment score = 306.5 
    34041 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    34042 2.689) 
    34043  
    34044 
    34045 > hide sel cartoons
    34046 
    34047 > color #777 dodgerblue
    34048 
    34049 > color #778 dodgerblue
    34050 
    34051 > color #779 #00b305ff
    34052 
    34053 > color #780 #00b305ff
    34054 
    34055 > color #781 #f15839ff
    34056 
    34057 > select #1.38/G
    34058 
    34059 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    34060 
    34061 > show sel cartoons
    34062 
    34063 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    34064 
    34065 Chain information for AF3 E1 1-421.pdb #782 
    34066 --- 
    34067 Chain | Description 
    34068 A | No description available 
    34069  
    34070 
    34071 > matchmaker #782 to #1.36 & sel
    34072 
    34073 No 'to' model specified 
    34074 
    34075 > matchmaker #782 to #1.37 & sel
    34076 
    34077 No 'to' model specified 
    34078 
    34079 > matchmaker #782 to #1.37 & sel
    34080 
    34081 No 'to' model specified 
    34082 
    34083 > hide sel cartoons
    34084 
    34085 > select #1.38/G
    34086 
    34087 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    34088 
    34089 > show sel cartoons
    34090 
    34091 > matchmaker #782 to #1.38 & sel
    34092 
    34093 Parameters 
    34094 --- 
    34095 Chain pairing | bb 
    34096 Alignment algorithm | Needleman-Wunsch 
    34097 Similarity matrix | BLOSUM-62 
    34098 SS fraction | 0.3 
    34099 Gap open (HH/SS/other) | 18/18/6 
    34100 Gap extend | 1 
    34101 SS matrix |  |  | H | S | O 
    34102 ---|---|---|--- 
    34103 H | 6 | -9 | -6 
    34104 S |  | 6 | -6 
    34105 O |  |  | 4 
    34106 Iteration cutoff | 2 
    34107  
    34108 Matchmaker 3j0c.pdb1, chain G (#1.38) with AF3 E1 1-421.pdb, chain A (#782),
    34109 sequence alignment score = 1060.7 
    34110 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    34111 2.985) 
    34112  
    34113 
    34114 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    34115 
    34116 Chain information for AF3 E1 422-461.pdb #783 
    34117 --- 
    34118 Chain | Description 
    34119 A | No description available 
    34120  
    34121 
    34122 > matchmaker #783 to #1.38 & sel
    34123 
    34124 Parameters 
    34125 --- 
    34126 Chain pairing | bb 
    34127 Alignment algorithm | Needleman-Wunsch 
    34128 Similarity matrix | BLOSUM-62 
    34129 SS fraction | 0.3 
    34130 Gap open (HH/SS/other) | 18/18/6 
    34131 Gap extend | 1 
    34132 SS matrix |  |  | H | S | O 
    34133 ---|---|---|--- 
    34134 H | 6 | -9 | -6 
    34135 S |  | 6 | -6 
    34136 O |  |  | 4 
    34137 Iteration cutoff | 2 
    34138  
    34139 Matchmaker 3j0c.pdb1, chain G (#1.38) with AF3 E1 422-461.pdb, chain A (#783),
    34140 sequence alignment score = 626.9 
    34141 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    34142 2.997) 
    34143  
    34144 
    34145 > hide sel cartoons
    34146 
    34147 > select #1.38/H
    34148 
    34149 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    34150 
    34151 > show sel cartoons
    34152 
    34153 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    34154 
    34155 Chain information for AF3 E2 1-352.pdb #784 
    34156 --- 
    34157 Chain | Description 
    34158 B | No description available 
    34159  
    34160 
    34161 > matchmaker #784 to #1.38 & sel
    34162 
    34163 Parameters 
    34164 --- 
    34165 Chain pairing | bb 
    34166 Alignment algorithm | Needleman-Wunsch 
    34167 Similarity matrix | BLOSUM-62 
    34168 SS fraction | 0.3 
    34169 Gap open (HH/SS/other) | 18/18/6 
    34170 Gap extend | 1 
    34171 SS matrix |  |  | H | S | O 
    34172 ---|---|---|--- 
    34173 H | 6 | -9 | -6 
    34174 S |  | 6 | -6 
    34175 O |  |  | 4 
    34176 Iteration cutoff | 2 
    34177  
    34178 Matchmaker 3j0c.pdb1, chain H (#1.38) with AF3 E2 1-352.pdb, chain B (#784),
    34179 sequence alignment score = 590.9 
    34180 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    34181 6.107) 
    34182  
    34183 
    34184 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    34185 
    34186 Chain information for AF3 E2 353-438.pdb #785 
    34187 --- 
    34188 Chain | Description 
    34189 B | No description available 
    34190  
    34191 
    34192 > matchmaker #785 to #1.38 & sel
    34193 
    34194 Parameters 
    34195 --- 
    34196 Chain pairing | bb 
    34197 Alignment algorithm | Needleman-Wunsch 
    34198 Similarity matrix | BLOSUM-62 
    34199 SS fraction | 0.3 
    34200 Gap open (HH/SS/other) | 18/18/6 
    34201 Gap extend | 1 
    34202 SS matrix |  |  | H | S | O 
    34203 ---|---|---|--- 
    34204 H | 6 | -9 | -6 
    34205 S |  | 6 | -6 
    34206 O |  |  | 4 
    34207 Iteration cutoff | 2 
    34208  
    34209 Matchmaker 3j0c.pdb1, chain H (#1.38) with AF3 E2 353-438.pdb, chain B (#785),
    34210 sequence alignment score = 329.4 
    34211 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    34212 8.150) 
    34213  
    34214 
    34215 > hide sel cartoons
    34216 
    34217 > select #1.38/I
    34218 
    34219 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    34220 
    34221 > show sel cartoons
    34222 
    34223 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    34224 
    34225 Chain information for AF3 CA.pdb #786 
    34226 --- 
    34227 Chain | Description 
    34228 A | No description available 
    34229  
    34230 
    34231 > matchmaker #786 to #1.38 & sel
    34232 
    34233 Parameters 
    34234 --- 
    34235 Chain pairing | bb 
    34236 Alignment algorithm | Needleman-Wunsch 
    34237 Similarity matrix | BLOSUM-62 
    34238 SS fraction | 0.3 
    34239 Gap open (HH/SS/other) | 18/18/6 
    34240 Gap extend | 1 
    34241 SS matrix |  |  | H | S | O 
    34242 ---|---|---|--- 
    34243 H | 6 | -9 | -6 
    34244 S |  | 6 | -6 
    34245 O |  |  | 4 
    34246 Iteration cutoff | 2 
    34247  
    34248 Matchmaker 3j0c.pdb1, chain I (#1.38) with AF3 CA.pdb, chain A (#786),
    34249 sequence alignment score = 306.5 
    34250 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    34251 2.689) 
    34252  
    34253 
    34254 > hide sel cartoons
    34255 
    34256 > color #782 dodgerblue
    34257 
    34258 > color #783 dodgerblue
    34259 
    34260 > color #784 #00b305ff
    34261 
    34262 > color #785 #00b305ff
    34263 
    34264 > color #786 #f15839ff
    34265 
    34266 > select #1.39/G
    34267 
    34268 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    34269 
    34270 > show sel cartoons
    34271 
    34272 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    34273 
    34274 Chain information for AF3 E1 1-421.pdb #787 
    34275 --- 
    34276 Chain | Description 
    34277 A | No description available 
    34278  
    34279 
    34280 > matchmaker #787 to #1.38 & sel
    34281 
    34282 No 'to' model specified 
    34283 
    34284 > matchmaker #787 to #1.39 & sel
    34285 
    34286 Parameters 
    34287 --- 
    34288 Chain pairing | bb 
    34289 Alignment algorithm | Needleman-Wunsch 
    34290 Similarity matrix | BLOSUM-62 
    34291 SS fraction | 0.3 
    34292 Gap open (HH/SS/other) | 18/18/6 
    34293 Gap extend | 1 
    34294 SS matrix |  |  | H | S | O 
    34295 ---|---|---|--- 
    34296 H | 6 | -9 | -6 
    34297 S |  | 6 | -6 
    34298 O |  |  | 4 
    34299 Iteration cutoff | 2 
    34300  
    34301 Matchmaker 3j0c.pdb1, chain G (#1.39) with AF3 E1 1-421.pdb, chain A (#787),
    34302 sequence alignment score = 1060.7 
    34303 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    34304 2.985) 
    34305  
    34306 
    34307 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    34308 
    34309 Chain information for AF3 E1 422-461.pdb #788 
    34310 --- 
    34311 Chain | Description 
    34312 A | No description available 
    34313  
    34314 
    34315 > matchmaker #788 to #1.39 & sel
    34316 
    34317 Parameters 
    34318 --- 
    34319 Chain pairing | bb 
    34320 Alignment algorithm | Needleman-Wunsch 
    34321 Similarity matrix | BLOSUM-62 
    34322 SS fraction | 0.3 
    34323 Gap open (HH/SS/other) | 18/18/6 
    34324 Gap extend | 1 
    34325 SS matrix |  |  | H | S | O 
    34326 ---|---|---|--- 
    34327 H | 6 | -9 | -6 
    34328 S |  | 6 | -6 
    34329 O |  |  | 4 
    34330 Iteration cutoff | 2 
    34331  
    34332 Matchmaker 3j0c.pdb1, chain G (#1.39) with AF3 E1 422-461.pdb, chain A (#788),
    34333 sequence alignment score = 626.9 
    34334 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    34335 2.997) 
    34336  
    34337 
    34338 > hide sel cartoons
    34339 
    34340 > select #1.39/H
    34341 
    34342 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    34343 
    34344 > show sel cartoons
    34345 
    34346 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    34347 
    34348 Chain information for AF3 E2 1-352.pdb #789 
    34349 --- 
    34350 Chain | Description 
    34351 B | No description available 
    34352  
    34353 
    34354 > matchmaker #789 to #1.39 & sel
    34355 
    34356 Parameters 
    34357 --- 
    34358 Chain pairing | bb 
    34359 Alignment algorithm | Needleman-Wunsch 
    34360 Similarity matrix | BLOSUM-62 
    34361 SS fraction | 0.3 
    34362 Gap open (HH/SS/other) | 18/18/6 
    34363 Gap extend | 1 
    34364 SS matrix |  |  | H | S | O 
    34365 ---|---|---|--- 
    34366 H | 6 | -9 | -6 
    34367 S |  | 6 | -6 
    34368 O |  |  | 4 
    34369 Iteration cutoff | 2 
    34370  
    34371 Matchmaker 3j0c.pdb1, chain H (#1.39) with AF3 E2 1-352.pdb, chain B (#789),
    34372 sequence alignment score = 590.9 
    34373 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    34374 6.107) 
    34375  
    34376 
    34377 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    34378 
    34379 Chain information for AF3 E2 353-438.pdb #790 
    34380 --- 
    34381 Chain | Description 
    34382 B | No description available 
    34383  
    34384 
    34385 > matchmaker #790 to #1.39 & sel
    34386 
    34387 Parameters 
    34388 --- 
    34389 Chain pairing | bb 
    34390 Alignment algorithm | Needleman-Wunsch 
    34391 Similarity matrix | BLOSUM-62 
    34392 SS fraction | 0.3 
    34393 Gap open (HH/SS/other) | 18/18/6 
    34394 Gap extend | 1 
    34395 SS matrix |  |  | H | S | O 
    34396 ---|---|---|--- 
    34397 H | 6 | -9 | -6 
    34398 S |  | 6 | -6 
    34399 O |  |  | 4 
    34400 Iteration cutoff | 2 
    34401  
    34402 Matchmaker 3j0c.pdb1, chain H (#1.39) with AF3 E2 353-438.pdb, chain B (#790),
    34403 sequence alignment score = 329.4 
    34404 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    34405 8.151) 
    34406  
    34407 
    34408 > hide sel cartoons
    34409 
    34410 > select #1.39/I
    34411 
    34412 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    34413 
    34414 > show sel cartoons
    34415 
    34416 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    34417 
    34418 Chain information for AF3 CA.pdb #791 
    34419 --- 
    34420 Chain | Description 
    34421 A | No description available 
    34422  
    34423 
    34424 > matchmaker #791 to #1.39 & sel
    34425 
    34426 Parameters 
    34427 --- 
    34428 Chain pairing | bb 
    34429 Alignment algorithm | Needleman-Wunsch 
    34430 Similarity matrix | BLOSUM-62 
    34431 SS fraction | 0.3 
    34432 Gap open (HH/SS/other) | 18/18/6 
    34433 Gap extend | 1 
    34434 SS matrix |  |  | H | S | O 
    34435 ---|---|---|--- 
    34436 H | 6 | -9 | -6 
    34437 S |  | 6 | -6 
    34438 O |  |  | 4 
    34439 Iteration cutoff | 2 
    34440  
    34441 Matchmaker 3j0c.pdb1, chain I (#1.39) with AF3 CA.pdb, chain A (#791),
    34442 sequence alignment score = 306.5 
    34443 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    34444 2.689) 
    34445  
    34446 
    34447 > hide sel cartoons
    34448 
    34449 > color #787 dodgerblue
    34450 
    34451 > color #788 dodgerblue
    34452 
    34453 > color #789 #00b305ff
    34454 
    34455 > color #790 #00b305ff
    34456 
    34457 > color #791 #f15839ff
    34458 
    34459 > select #1.40/G
    34460 
    34461 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    34462 
    34463 > show sel cartoons
    34464 
    34465 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    34466 
    34467 Chain information for AF3 E1 1-421.pdb #792 
    34468 --- 
    34469 Chain | Description 
    34470 A | No description available 
    34471  
    34472 
    34473 > matchmaker #792 to #1.39 & sel
    34474 
    34475 No 'to' model specified 
    34476 
    34477 > matchmaker #792 to #1.40 & sel
    34478 
    34479 Parameters 
    34480 --- 
    34481 Chain pairing | bb 
    34482 Alignment algorithm | Needleman-Wunsch 
    34483 Similarity matrix | BLOSUM-62 
    34484 SS fraction | 0.3 
    34485 Gap open (HH/SS/other) | 18/18/6 
    34486 Gap extend | 1 
    34487 SS matrix |  |  | H | S | O 
    34488 ---|---|---|--- 
    34489 H | 6 | -9 | -6 
    34490 S |  | 6 | -6 
    34491 O |  |  | 4 
    34492 Iteration cutoff | 2 
    34493  
    34494 Matchmaker 3j0c.pdb1, chain G (#1.40) with AF3 E1 1-421.pdb, chain A (#792),
    34495 sequence alignment score = 1060.7 
    34496 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    34497 2.985) 
    34498  
    34499 
    34500 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    34501 
    34502 Chain information for AF3 E1 422-461.pdb #793 
    34503 --- 
    34504 Chain | Description 
    34505 A | No description available 
    34506  
    34507 
    34508 > matchmaker #793 to #1.40 & sel
    34509 
    34510 Parameters 
    34511 --- 
    34512 Chain pairing | bb 
    34513 Alignment algorithm | Needleman-Wunsch 
    34514 Similarity matrix | BLOSUM-62 
    34515 SS fraction | 0.3 
    34516 Gap open (HH/SS/other) | 18/18/6 
    34517 Gap extend | 1 
    34518 SS matrix |  |  | H | S | O 
    34519 ---|---|---|--- 
    34520 H | 6 | -9 | -6 
    34521 S |  | 6 | -6 
    34522 O |  |  | 4 
    34523 Iteration cutoff | 2 
    34524  
    34525 Matchmaker 3j0c.pdb1, chain G (#1.40) with AF3 E1 422-461.pdb, chain A (#793),
    34526 sequence alignment score = 626.9 
    34527 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    34528 2.997) 
    34529  
    34530 
    34531 > hide sel cartoons
    34532 
    34533 > select #1.40/H
    34534 
    34535 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    34536 
    34537 > show sel cartoons
    34538 
    34539 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    34540 
    34541 Chain information for AF3 E2 1-352.pdb #794 
    34542 --- 
    34543 Chain | Description 
    34544 B | No description available 
    34545  
    34546 
    34547 > matchmaker #794 to #1.40 & sel
    34548 
    34549 Parameters 
    34550 --- 
    34551 Chain pairing | bb 
    34552 Alignment algorithm | Needleman-Wunsch 
    34553 Similarity matrix | BLOSUM-62 
    34554 SS fraction | 0.3 
    34555 Gap open (HH/SS/other) | 18/18/6 
    34556 Gap extend | 1 
    34557 SS matrix |  |  | H | S | O 
    34558 ---|---|---|--- 
    34559 H | 6 | -9 | -6 
    34560 S |  | 6 | -6 
    34561 O |  |  | 4 
    34562 Iteration cutoff | 2 
    34563  
    34564 Matchmaker 3j0c.pdb1, chain H (#1.40) with AF3 E2 1-352.pdb, chain B (#794),
    34565 sequence alignment score = 590.9 
    34566 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    34567 6.107) 
    34568  
    34569 
    34570 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    34571 
    34572 Chain information for AF3 E2 353-438.pdb #795 
    34573 --- 
    34574 Chain | Description 
    34575 B | No description available 
    34576  
    34577 
    34578 > matchmaker #795 to #1.40 & sel
    34579 
    34580 Parameters 
    34581 --- 
    34582 Chain pairing | bb 
    34583 Alignment algorithm | Needleman-Wunsch 
    34584 Similarity matrix | BLOSUM-62 
    34585 SS fraction | 0.3 
    34586 Gap open (HH/SS/other) | 18/18/6 
    34587 Gap extend | 1 
    34588 SS matrix |  |  | H | S | O 
    34589 ---|---|---|--- 
    34590 H | 6 | -9 | -6 
    34591 S |  | 6 | -6 
    34592 O |  |  | 4 
    34593 Iteration cutoff | 2 
    34594  
    34595 Matchmaker 3j0c.pdb1, chain H (#1.40) with AF3 E2 353-438.pdb, chain B (#795),
    34596 sequence alignment score = 329.4 
    34597 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    34598 8.150) 
    34599  
    34600 
    34601 > hide sel cartoons
    34602 
    34603 > select #1.40/I
    34604 
    34605 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    34606 
    34607 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    34608 
    34609 Chain information for AF3 CA.pdb #796 
    34610 --- 
    34611 Chain | Description 
    34612 A | No description available 
    34613  
    34614 
    34615 > matchmaker #796 to #1.40 & sel
    34616 
    34617 Parameters 
    34618 --- 
    34619 Chain pairing | bb 
    34620 Alignment algorithm | Needleman-Wunsch 
    34621 Similarity matrix | BLOSUM-62 
    34622 SS fraction | 0.3 
    34623 Gap open (HH/SS/other) | 18/18/6 
    34624 Gap extend | 1 
    34625 SS matrix |  |  | H | S | O 
    34626 ---|---|---|--- 
    34627 H | 6 | -9 | -6 
    34628 S |  | 6 | -6 
    34629 O |  |  | 4 
    34630 Iteration cutoff | 2 
    34631  
    34632 Matchmaker 3j0c.pdb1, chain I (#1.40) with AF3 CA.pdb, chain A (#796),
    34633 sequence alignment score = 306.5 
    34634 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    34635 2.689) 
    34636  
    34637 
    34638 > color #792 dodgerblue
    34639 
    34640 > color #793 dodgerblue
    34641 
    34642 > color #794 #00b305ff
    34643 
    34644 > color #795 #00b305ff
    34645 
    34646 > color #796 #f15839ff
    34647 
    34648 > show #751 models
    34649 
    34650 > show #750 models
    34651 
    34652 > show #749 models
    34653 
    34654 > show #748 models
    34655 
    34656 > show #747 models
    34657 
    34658 > hide #747 models
    34659 
    34660 > hide #748 models
    34661 
    34662 > hide #749 models
    34663 
    34664 > hide #750 models
    34665 
    34666 > hide #751 models
    34667 
    34668 > select #1.37/G
    34669 
    34670 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    34671 
    34672 > show sel cartoons
    34673 
    34674 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    34675 
    34676 Chain information for AF3 E1 1-421.pdb #797 
    34677 --- 
    34678 Chain | Description 
    34679 A | No description available 
    34680  
    34681 
    34682 > matchmaker #796 to #1.37 & sel
    34683 
    34684 Parameters 
    34685 --- 
    34686 Chain pairing | bb 
    34687 Alignment algorithm | Needleman-Wunsch 
    34688 Similarity matrix | BLOSUM-62 
    34689 SS fraction | 0.3 
    34690 Gap open (HH/SS/other) | 18/18/6 
    34691 Gap extend | 1 
    34692 SS matrix |  |  | H | S | O 
    34693 ---|---|---|--- 
    34694 H | 6 | -9 | -6 
    34695 S |  | 6 | -6 
    34696 O |  |  | 4 
    34697 Iteration cutoff | 2 
    34698  
    34699 Matchmaker 3j0c.pdb1, chain G (#1.37) with AF3 CA.pdb, chain A (#796),
    34700 sequence alignment score = 32.6 
    34701 RMSD between 10 pruned atom pairs is 1.151 angstroms; (across all 110 pairs:
    34702 22.900) 
    34703  
    34704 
    34705 > matchmaker #796 to #1.40 & sel
    34706 
    34707 No 'to' model specified 
    34708 
    34709 > select #1.40/I
    34710 
    34711 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    34712 
    34713 > show sel cartoons
    34714 
    34715 > matchmaker #796 to #1.40 & sel
    34716 
    34717 Parameters 
    34718 --- 
    34719 Chain pairing | bb 
    34720 Alignment algorithm | Needleman-Wunsch 
    34721 Similarity matrix | BLOSUM-62 
    34722 SS fraction | 0.3 
    34723 Gap open (HH/SS/other) | 18/18/6 
    34724 Gap extend | 1 
    34725 SS matrix |  |  | H | S | O 
    34726 ---|---|---|--- 
    34727 H | 6 | -9 | -6 
    34728 S |  | 6 | -6 
    34729 O |  |  | 4 
    34730 Iteration cutoff | 2 
    34731  
    34732 Matchmaker 3j0c.pdb1, chain I (#1.40) with AF3 CA.pdb, chain A (#796),
    34733 sequence alignment score = 306.5 
    34734 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    34735 2.689) 
    34736  
    34737 
    34738 > hide sel cartoons
    34739 
    34740 > select #1.37/G
    34741 
    34742 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    34743 
    34744 > matchmaker #797 to #1.37 & sel
    34745 
    34746 Parameters 
    34747 --- 
    34748 Chain pairing | bb 
    34749 Alignment algorithm | Needleman-Wunsch 
    34750 Similarity matrix | BLOSUM-62 
    34751 SS fraction | 0.3 
    34752 Gap open (HH/SS/other) | 18/18/6 
    34753 Gap extend | 1 
    34754 SS matrix |  |  | H | S | O 
    34755 ---|---|---|--- 
    34756 H | 6 | -9 | -6 
    34757 S |  | 6 | -6 
    34758 O |  |  | 4 
    34759 Iteration cutoff | 2 
    34760  
    34761 Matchmaker 3j0c.pdb1, chain G (#1.37) with AF3 E1 1-421.pdb, chain A (#797),
    34762 sequence alignment score = 1060.7 
    34763 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    34764 2.985) 
    34765  
    34766 
    34767 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    34768 
    34769 Chain information for AF3 E1 422-461.pdb #798 
    34770 --- 
    34771 Chain | Description 
    34772 A | No description available 
    34773  
    34774 
    34775 > matchmaker #798 to #1.37 & sel
    34776 
    34777 Parameters 
    34778 --- 
    34779 Chain pairing | bb 
    34780 Alignment algorithm | Needleman-Wunsch 
    34781 Similarity matrix | BLOSUM-62 
    34782 SS fraction | 0.3 
    34783 Gap open (HH/SS/other) | 18/18/6 
    34784 Gap extend | 1 
    34785 SS matrix |  |  | H | S | O 
    34786 ---|---|---|--- 
    34787 H | 6 | -9 | -6 
    34788 S |  | 6 | -6 
    34789 O |  |  | 4 
    34790 Iteration cutoff | 2 
    34791  
    34792 Matchmaker 3j0c.pdb1, chain G (#1.37) with AF3 E1 422-461.pdb, chain A (#798),
    34793 sequence alignment score = 626.9 
    34794 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    34795 2.997) 
    34796  
    34797 
    34798 > hide sel cartoons
    34799 
    34800 > select #1.37/H
    34801 
    34802 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    34803 
    34804 > show sel cartoons
    34805 
    34806 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    34807 
    34808 Chain information for AF3 E2 1-352.pdb #799 
    34809 --- 
    34810 Chain | Description 
    34811 B | No description available 
    34812  
    34813 
    34814 > matchmaker #799 to #1.37 & sel
    34815 
    34816 Parameters 
    34817 --- 
    34818 Chain pairing | bb 
    34819 Alignment algorithm | Needleman-Wunsch 
    34820 Similarity matrix | BLOSUM-62 
    34821 SS fraction | 0.3 
    34822 Gap open (HH/SS/other) | 18/18/6 
    34823 Gap extend | 1 
    34824 SS matrix |  |  | H | S | O 
    34825 ---|---|---|--- 
    34826 H | 6 | -9 | -6 
    34827 S |  | 6 | -6 
    34828 O |  |  | 4 
    34829 Iteration cutoff | 2 
    34830  
    34831 Matchmaker 3j0c.pdb1, chain H (#1.37) with AF3 E2 1-352.pdb, chain B (#799),
    34832 sequence alignment score = 590.9 
    34833 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    34834 6.107) 
    34835  
    34836 
    34837 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    34838 
    34839 Chain information for AF3 E2 353-438.pdb #800 
    34840 --- 
    34841 Chain | Description 
    34842 B | No description available 
    34843  
    34844 
    34845 > matchmaker #800 to #1.37 & sel
    34846 
    34847 Parameters 
    34848 --- 
    34849 Chain pairing | bb 
    34850 Alignment algorithm | Needleman-Wunsch 
    34851 Similarity matrix | BLOSUM-62 
    34852 SS fraction | 0.3 
    34853 Gap open (HH/SS/other) | 18/18/6 
    34854 Gap extend | 1 
    34855 SS matrix |  |  | H | S | O 
    34856 ---|---|---|--- 
    34857 H | 6 | -9 | -6 
    34858 S |  | 6 | -6 
    34859 O |  |  | 4 
    34860 Iteration cutoff | 2 
    34861  
    34862 Matchmaker 3j0c.pdb1, chain H (#1.37) with AF3 E2 353-438.pdb, chain B (#800),
    34863 sequence alignment score = 329.4 
    34864 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    34865 8.150) 
    34866  
    34867 
    34868 > hide sel cartoons
    34869 
    34870 > select #1.37/I
    34871 
    34872 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    34873 
    34874 > show sel cartoons
    34875 
    34876 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    34877 
    34878 Chain information for AF3 CA.pdb #801 
    34879 --- 
    34880 Chain | Description 
    34881 A | No description available 
    34882  
    34883 
    34884 > matchmaker #801 to #1.37 & sel
    34885 
    34886 Parameters 
    34887 --- 
    34888 Chain pairing | bb 
    34889 Alignment algorithm | Needleman-Wunsch 
    34890 Similarity matrix | BLOSUM-62 
    34891 SS fraction | 0.3 
    34892 Gap open (HH/SS/other) | 18/18/6 
    34893 Gap extend | 1 
    34894 SS matrix |  |  | H | S | O 
    34895 ---|---|---|--- 
    34896 H | 6 | -9 | -6 
    34897 S |  | 6 | -6 
    34898 O |  |  | 4 
    34899 Iteration cutoff | 2 
    34900  
    34901 Matchmaker 3j0c.pdb1, chain I (#1.37) with AF3 CA.pdb, chain A (#801),
    34902 sequence alignment score = 306.5 
    34903 RMSD between 119 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    34904 2.689) 
    34905  
    34906 
    34907 > hide sel cartoons
    34908 
    34909 > color #797 dodgerblue
    34910 
    34911 > color #798 dodgerblue
    34912 
    34913 > color #799 #00b305ff
    34914 
    34915 > color #800 #00b305ff
    34916 
    34917 > color #801 #f15839ff
    34918 
    34919 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    34920 
    34921 > hide #752 models
    34922 
    34923 > hide #753 models
    34924 
    34925 > hide #754 models
    34926 
    34927 > hide #755 models
    34928 
    34929 > hide #756 models
    34930 
    34931 > hide #757 models
    34932 
    34933 > hide #758 models
    34934 
    34935 > hide #759 models
    34936 
    34937 > hide #760 models
    34938 
    34939 > hide #761 models
    34940 
    34941 > hide #762 models
    34942 
    34943 > hide #763 models
    34944 
    34945 > hide #764 models
    34946 
    34947 > hide #765 models
    34948 
    34949 > hide #766 models
    34950 
    34951 > hide #767 models
    34952 
    34953 > hide #768 models
    34954 
    34955 > hide #769 models
    34956 
    34957 > hide #770 models
    34958 
    34959 > hide #771 models
    34960 
    34961 > hide #772 models
    34962 
    34963 > hide #773 models
    34964 
    34965 > hide #774 models
    34966 
    34967 > hide #776 models
    34968 
    34969 > hide #775 models
    34970 
    34971 > hide #777 models
    34972 
    34973 > hide #778 models
    34974 
    34975 > hide #779 models
    34976 
    34977 > hide #780 models
    34978 
    34979 > hide #781 models
    34980 
    34981 > hide #782 models
    34982 
    34983 > hide #783 models
    34984 
    34985 > hide #784 models
    34986 
    34987 > hide #785 models
    34988 
    34989 > hide #786 models
    34990 
    34991 > hide #787 models
    34992 
    34993 > hide #788 models
    34994 
    34995 > hide #789 models
    34996 
    34997 > hide #790 models
    34998 
    34999 > hide #791 models
    35000 
    35001 > hide #792 models
    35002 
    35003 > hide #793 models
    35004 
    35005 > hide #794 models
    35006 
    35007 > hide #795 models
    35008 
    35009 > hide #796 models
    35010 
    35011 > hide #797 models
    35012 
    35013 > hide #798 models
    35014 
    35015 > hide #799 models
    35016 
    35017 > hide #800 models
    35018 
    35019 > hide #801 models
    35020 
    35021 > select #1.38/G
    35022 
    35023 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    35024 
    35025 > show sel cartoons
    35026 
    35027 > hide sel cartoons
    35028 
    35029 > select #1.41/G
    35030 
    35031 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    35032 
    35033 > show sel cartoons
    35034 
    35035 > view
    35036 
    35037 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    35038 
    35039 Chain information for AF3 E1 1-421.pdb #802 
    35040 --- 
    35041 Chain | Description 
    35042 A | No description available 
    35043  
    35044 
    35045 > matchmaker #802 to #1.41 & sel
    35046 
    35047 Parameters 
    35048 --- 
    35049 Chain pairing | bb 
    35050 Alignment algorithm | Needleman-Wunsch 
    35051 Similarity matrix | BLOSUM-62 
    35052 SS fraction | 0.3 
    35053 Gap open (HH/SS/other) | 18/18/6 
    35054 Gap extend | 1 
    35055 SS matrix |  |  | H | S | O 
    35056 ---|---|---|--- 
    35057 H | 6 | -9 | -6 
    35058 S |  | 6 | -6 
    35059 O |  |  | 4 
    35060 Iteration cutoff | 2 
    35061  
    35062 Matchmaker 3j0c.pdb1, chain G (#1.41) with AF3 E1 1-421.pdb, chain A (#802),
    35063 sequence alignment score = 1060.7 
    35064 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    35065 2.985) 
    35066  
    35067 
    35068 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    35069 
    35070 Chain information for AF3 E1 422-461.pdb #803 
    35071 --- 
    35072 Chain | Description 
    35073 A | No description available 
    35074  
    35075 
    35076 > matchmaker #803 to #1.41 & sel
    35077 
    35078 Parameters 
    35079 --- 
    35080 Chain pairing | bb 
    35081 Alignment algorithm | Needleman-Wunsch 
    35082 Similarity matrix | BLOSUM-62 
    35083 SS fraction | 0.3 
    35084 Gap open (HH/SS/other) | 18/18/6 
    35085 Gap extend | 1 
    35086 SS matrix |  |  | H | S | O 
    35087 ---|---|---|--- 
    35088 H | 6 | -9 | -6 
    35089 S |  | 6 | -6 
    35090 O |  |  | 4 
    35091 Iteration cutoff | 2 
    35092  
    35093 Matchmaker 3j0c.pdb1, chain G (#1.41) with AF3 E1 422-461.pdb, chain A (#803),
    35094 sequence alignment score = 626.9 
    35095 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    35096 2.997) 
    35097  
    35098 
    35099 > hide sel cartoons
    35100 
    35101 > select #1.41/H
    35102 
    35103 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    35104 
    35105 > show sel cartoons
    35106 
    35107 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    35108 
    35109 Chain information for AF3 E2 1-352.pdb #804 
    35110 --- 
    35111 Chain | Description 
    35112 B | No description available 
    35113  
    35114 
    35115 > matchmaker #804 to #1.41 & sel
    35116 
    35117 Parameters 
    35118 --- 
    35119 Chain pairing | bb 
    35120 Alignment algorithm | Needleman-Wunsch 
    35121 Similarity matrix | BLOSUM-62 
    35122 SS fraction | 0.3 
    35123 Gap open (HH/SS/other) | 18/18/6 
    35124 Gap extend | 1 
    35125 SS matrix |  |  | H | S | O 
    35126 ---|---|---|--- 
    35127 H | 6 | -9 | -6 
    35128 S |  | 6 | -6 
    35129 O |  |  | 4 
    35130 Iteration cutoff | 2 
    35131  
    35132 Matchmaker 3j0c.pdb1, chain H (#1.41) with AF3 E2 1-352.pdb, chain B (#804),
    35133 sequence alignment score = 590.9 
    35134 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    35135 6.107) 
    35136  
    35137 
    35138 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    35139 
    35140 Chain information for AF3 E2 353-438.pdb #805 
    35141 --- 
    35142 Chain | Description 
    35143 B | No description available 
    35144  
    35145 
    35146 > matchmaker #805 to #1.41 & sel
    35147 
    35148 Parameters 
    35149 --- 
    35150 Chain pairing | bb 
    35151 Alignment algorithm | Needleman-Wunsch 
    35152 Similarity matrix | BLOSUM-62 
    35153 SS fraction | 0.3 
    35154 Gap open (HH/SS/other) | 18/18/6 
    35155 Gap extend | 1 
    35156 SS matrix |  |  | H | S | O 
    35157 ---|---|---|--- 
    35158 H | 6 | -9 | -6 
    35159 S |  | 6 | -6 
    35160 O |  |  | 4 
    35161 Iteration cutoff | 2 
    35162  
    35163 Matchmaker 3j0c.pdb1, chain H (#1.41) with AF3 E2 353-438.pdb, chain B (#805),
    35164 sequence alignment score = 329.4 
    35165 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    35166 8.150) 
    35167  
    35168 
    35169 > hide sel cartoons
    35170 
    35171 > select #1.41/I
    35172 
    35173 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    35174 
    35175 > show sel cartoons
    35176 
    35177 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    35178 
    35179 Chain information for AF3 CA.pdb #806 
    35180 --- 
    35181 Chain | Description 
    35182 A | No description available 
    35183  
    35184 
    35185 > matchmaker #806 to #1.41 & sel
    35186 
    35187 Parameters 
    35188 --- 
    35189 Chain pairing | bb 
    35190 Alignment algorithm | Needleman-Wunsch 
    35191 Similarity matrix | BLOSUM-62 
    35192 SS fraction | 0.3 
    35193 Gap open (HH/SS/other) | 18/18/6 
    35194 Gap extend | 1 
    35195 SS matrix |  |  | H | S | O 
    35196 ---|---|---|--- 
    35197 H | 6 | -9 | -6 
    35198 S |  | 6 | -6 
    35199 O |  |  | 4 
    35200 Iteration cutoff | 2 
    35201  
    35202 Matchmaker 3j0c.pdb1, chain I (#1.41) with AF3 CA.pdb, chain A (#806),
    35203 sequence alignment score = 306.5 
    35204 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    35205 2.689) 
    35206  
    35207 
    35208 > hide sel cartoons
    35209 
    35210 > color #802 dodgerblue
    35211 
    35212 > color #803 dodgerblue
    35213 
    35214 > color #804 #00b305ff
    35215 
    35216 > color #805 #00b305ff
    35217 
    35218 > color #806 #f15839ff
    35219 
    35220 > select #1.42/G
    35221 
    35222 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    35223 
    35224 > show sel cartoons
    35225 
    35226 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    35227 
    35228 Chain information for AF3 E1 1-421.pdb #807 
    35229 --- 
    35230 Chain | Description 
    35231 A | No description available 
    35232  
    35233 
    35234 > matchmaker #807 to #1.42 & sel
    35235 
    35236 Parameters 
    35237 --- 
    35238 Chain pairing | bb 
    35239 Alignment algorithm | Needleman-Wunsch 
    35240 Similarity matrix | BLOSUM-62 
    35241 SS fraction | 0.3 
    35242 Gap open (HH/SS/other) | 18/18/6 
    35243 Gap extend | 1 
    35244 SS matrix |  |  | H | S | O 
    35245 ---|---|---|--- 
    35246 H | 6 | -9 | -6 
    35247 S |  | 6 | -6 
    35248 O |  |  | 4 
    35249 Iteration cutoff | 2 
    35250  
    35251 Matchmaker 3j0c.pdb1, chain G (#1.42) with AF3 E1 1-421.pdb, chain A (#807),
    35252 sequence alignment score = 1060.7 
    35253 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    35254 2.985) 
    35255  
    35256 
    35257 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    35258 
    35259 Chain information for AF3 E1 422-461.pdb #808 
    35260 --- 
    35261 Chain | Description 
    35262 A | No description available 
    35263  
    35264 
    35265 > matchmaker #808 to #1.42 & sel
    35266 
    35267 Parameters 
    35268 --- 
    35269 Chain pairing | bb 
    35270 Alignment algorithm | Needleman-Wunsch 
    35271 Similarity matrix | BLOSUM-62 
    35272 SS fraction | 0.3 
    35273 Gap open (HH/SS/other) | 18/18/6 
    35274 Gap extend | 1 
    35275 SS matrix |  |  | H | S | O 
    35276 ---|---|---|--- 
    35277 H | 6 | -9 | -6 
    35278 S |  | 6 | -6 
    35279 O |  |  | 4 
    35280 Iteration cutoff | 2 
    35281  
    35282 Matchmaker 3j0c.pdb1, chain G (#1.42) with AF3 E1 422-461.pdb, chain A (#808),
    35283 sequence alignment score = 626.9 
    35284 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    35285 2.997) 
    35286  
    35287 
    35288 > hide sel cartoons
    35289 
    35290 > select #1.42/H
    35291 
    35292 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    35293 
    35294 > show sel cartoons
    35295 
    35296 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    35297 
    35298 Chain information for AF3 E2 1-352.pdb #809 
    35299 --- 
    35300 Chain | Description 
    35301 B | No description available 
    35302  
    35303 
    35304 > matchmaker #809 to #1.42 & sel
    35305 
    35306 Parameters 
    35307 --- 
    35308 Chain pairing | bb 
    35309 Alignment algorithm | Needleman-Wunsch 
    35310 Similarity matrix | BLOSUM-62 
    35311 SS fraction | 0.3 
    35312 Gap open (HH/SS/other) | 18/18/6 
    35313 Gap extend | 1 
    35314 SS matrix |  |  | H | S | O 
    35315 ---|---|---|--- 
    35316 H | 6 | -9 | -6 
    35317 S |  | 6 | -6 
    35318 O |  |  | 4 
    35319 Iteration cutoff | 2 
    35320  
    35321 Matchmaker 3j0c.pdb1, chain H (#1.42) with AF3 E2 1-352.pdb, chain B (#809),
    35322 sequence alignment score = 590.9 
    35323 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    35324 6.107) 
    35325  
    35326 
    35327 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    35328 
    35329 Chain information for AF3 E2 353-438.pdb #810 
    35330 --- 
    35331 Chain | Description 
    35332 B | No description available 
    35333  
    35334 
    35335 > matchmaker #810 to #1.42 & sel
    35336 
    35337 Parameters 
    35338 --- 
    35339 Chain pairing | bb 
    35340 Alignment algorithm | Needleman-Wunsch 
    35341 Similarity matrix | BLOSUM-62 
    35342 SS fraction | 0.3 
    35343 Gap open (HH/SS/other) | 18/18/6 
    35344 Gap extend | 1 
    35345 SS matrix |  |  | H | S | O 
    35346 ---|---|---|--- 
    35347 H | 6 | -9 | -6 
    35348 S |  | 6 | -6 
    35349 O |  |  | 4 
    35350 Iteration cutoff | 2 
    35351  
    35352 Matchmaker 3j0c.pdb1, chain H (#1.42) with AF3 E2 353-438.pdb, chain B (#810),
    35353 sequence alignment score = 329.4 
    35354 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    35355 8.151) 
    35356  
    35357 
    35358 > hide sel cartoons
    35359 
    35360 > select #1.42/I
    35361 
    35362 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    35363 
    35364 > show sel cartoons
    35365 
    35366 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    35367 
    35368 Chain information for AF3 CA.pdb #811 
    35369 --- 
    35370 Chain | Description 
    35371 A | No description available 
    35372  
    35373 
    35374 > matchmaker #811 to #1.42 & sel
    35375 
    35376 Parameters 
    35377 --- 
    35378 Chain pairing | bb 
    35379 Alignment algorithm | Needleman-Wunsch 
    35380 Similarity matrix | BLOSUM-62 
    35381 SS fraction | 0.3 
    35382 Gap open (HH/SS/other) | 18/18/6 
    35383 Gap extend | 1 
    35384 SS matrix |  |  | H | S | O 
    35385 ---|---|---|--- 
    35386 H | 6 | -9 | -6 
    35387 S |  | 6 | -6 
    35388 O |  |  | 4 
    35389 Iteration cutoff | 2 
    35390  
    35391 Matchmaker 3j0c.pdb1, chain I (#1.42) with AF3 CA.pdb, chain A (#811),
    35392 sequence alignment score = 306.5 
    35393 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    35394 2.689) 
    35395  
    35396 
    35397 > hide sel cartoons
    35398 
    35399 > color #807 dodgerblue
    35400 
    35401 > color #808 dodgerblue
    35402 
    35403 > color #809 #00b305ff
    35404 
    35405 > color #810 #00b305ff
    35406 
    35407 > color #811 #f15839ff
    35408 
    35409 > select #1.43/G
    35410 
    35411 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    35412 
    35413 > show sel cartoons
    35414 
    35415 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    35416 
    35417 Chain information for AF3 E1 1-421.pdb #812 
    35418 --- 
    35419 Chain | Description 
    35420 A | No description available 
    35421  
    35422 
    35423 > matchmaker #812 to #1.42 & sel
    35424 
    35425 No 'to' model specified 
    35426 
    35427 > matchmaker #812 to #1.43 & sel
    35428 
    35429 Parameters 
    35430 --- 
    35431 Chain pairing | bb 
    35432 Alignment algorithm | Needleman-Wunsch 
    35433 Similarity matrix | BLOSUM-62 
    35434 SS fraction | 0.3 
    35435 Gap open (HH/SS/other) | 18/18/6 
    35436 Gap extend | 1 
    35437 SS matrix |  |  | H | S | O 
    35438 ---|---|---|--- 
    35439 H | 6 | -9 | -6 
    35440 S |  | 6 | -6 
    35441 O |  |  | 4 
    35442 Iteration cutoff | 2 
    35443  
    35444 Matchmaker 3j0c.pdb1, chain G (#1.43) with AF3 E1 1-421.pdb, chain A (#812),
    35445 sequence alignment score = 1060.7 
    35446 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    35447 2.985) 
    35448  
    35449 
    35450 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    35451 
    35452 Chain information for AF3 E1 422-461.pdb #813 
    35453 --- 
    35454 Chain | Description 
    35455 A | No description available 
    35456  
    35457 
    35458 > matchmaker #813 to #1.43 & sel
    35459 
    35460 Parameters 
    35461 --- 
    35462 Chain pairing | bb 
    35463 Alignment algorithm | Needleman-Wunsch 
    35464 Similarity matrix | BLOSUM-62 
    35465 SS fraction | 0.3 
    35466 Gap open (HH/SS/other) | 18/18/6 
    35467 Gap extend | 1 
    35468 SS matrix |  |  | H | S | O 
    35469 ---|---|---|--- 
    35470 H | 6 | -9 | -6 
    35471 S |  | 6 | -6 
    35472 O |  |  | 4 
    35473 Iteration cutoff | 2 
    35474  
    35475 Matchmaker 3j0c.pdb1, chain G (#1.43) with AF3 E1 422-461.pdb, chain A (#813),
    35476 sequence alignment score = 626.9 
    35477 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    35478 2.997) 
    35479  
    35480 
    35481 > hide sel cartoons
    35482 
    35483 > select #1.43/H
    35484 
    35485 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    35486 
    35487 > show sel cartoons
    35488 
    35489 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    35490 
    35491 Chain information for AF3 E2 1-352.pdb #814 
    35492 --- 
    35493 Chain | Description 
    35494 B | No description available 
    35495  
    35496 
    35497 > matchmaker #814 to #1.43 & sel
    35498 
    35499 Parameters 
    35500 --- 
    35501 Chain pairing | bb 
    35502 Alignment algorithm | Needleman-Wunsch 
    35503 Similarity matrix | BLOSUM-62 
    35504 SS fraction | 0.3 
    35505 Gap open (HH/SS/other) | 18/18/6 
    35506 Gap extend | 1 
    35507 SS matrix |  |  | H | S | O 
    35508 ---|---|---|--- 
    35509 H | 6 | -9 | -6 
    35510 S |  | 6 | -6 
    35511 O |  |  | 4 
    35512 Iteration cutoff | 2 
    35513  
    35514 Matchmaker 3j0c.pdb1, chain H (#1.43) with AF3 E2 1-352.pdb, chain B (#814),
    35515 sequence alignment score = 590.9 
    35516 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    35517 6.107) 
    35518  
    35519 
    35520 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    35521 
    35522 Chain information for AF3 E2 353-438.pdb #815 
    35523 --- 
    35524 Chain | Description 
    35525 B | No description available 
    35526  
    35527 
    35528 > matchmaker #815 to #1.43 & sel
    35529 
    35530 Parameters 
    35531 --- 
    35532 Chain pairing | bb 
    35533 Alignment algorithm | Needleman-Wunsch 
    35534 Similarity matrix | BLOSUM-62 
    35535 SS fraction | 0.3 
    35536 Gap open (HH/SS/other) | 18/18/6 
    35537 Gap extend | 1 
    35538 SS matrix |  |  | H | S | O 
    35539 ---|---|---|--- 
    35540 H | 6 | -9 | -6 
    35541 S |  | 6 | -6 
    35542 O |  |  | 4 
    35543 Iteration cutoff | 2 
    35544  
    35545 Matchmaker 3j0c.pdb1, chain H (#1.43) with AF3 E2 353-438.pdb, chain B (#815),
    35546 sequence alignment score = 329.4 
    35547 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    35548 8.150) 
    35549  
    35550 
    35551 > hide sel cartoons
    35552 
    35553 > select #1.43/I
    35554 
    35555 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    35556 
    35557 > show sel cartoons
    35558 
    35559 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    35560 
    35561 Chain information for AF3 CA.pdb #816 
    35562 --- 
    35563 Chain | Description 
    35564 A | No description available 
    35565  
    35566 
    35567 > matchmaker #816 to #1.43 & sel
    35568 
    35569 Parameters 
    35570 --- 
    35571 Chain pairing | bb 
    35572 Alignment algorithm | Needleman-Wunsch 
    35573 Similarity matrix | BLOSUM-62 
    35574 SS fraction | 0.3 
    35575 Gap open (HH/SS/other) | 18/18/6 
    35576 Gap extend | 1 
    35577 SS matrix |  |  | H | S | O 
    35578 ---|---|---|--- 
    35579 H | 6 | -9 | -6 
    35580 S |  | 6 | -6 
    35581 O |  |  | 4 
    35582 Iteration cutoff | 2 
    35583  
    35584 Matchmaker 3j0c.pdb1, chain I (#1.43) with AF3 CA.pdb, chain A (#816),
    35585 sequence alignment score = 306.5 
    35586 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    35587 2.689) 
    35588  
    35589 
    35590 > hide sel cartoons
    35591 
    35592 > color #812 dodgerblue
    35593 
    35594 > color #813 dodgerblue
    35595 
    35596 > color #814 #00b305ff
    35597 
    35598 > color #815 #00b305ff
    35599 
    35600 > color #816 #f15839ff
    35601 
    35602 > select #1.43/G
    35603 
    35604 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    35605 
    35606 > show sel cartoons
    35607 
    35608 > hide sel cartoons
    35609 
    35610 > select #1.44/G
    35611 
    35612 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    35613 
    35614 > show sel cartoons
    35615 
    35616 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    35617 
    35618 Chain information for AF3 E1 1-421.pdb #817 
    35619 --- 
    35620 Chain | Description 
    35621 A | No description available 
    35622  
    35623 
    35624 > matchmaker #817 to #1.44 & sel
    35625 
    35626 Parameters 
    35627 --- 
    35628 Chain pairing | bb 
    35629 Alignment algorithm | Needleman-Wunsch 
    35630 Similarity matrix | BLOSUM-62 
    35631 SS fraction | 0.3 
    35632 Gap open (HH/SS/other) | 18/18/6 
    35633 Gap extend | 1 
    35634 SS matrix |  |  | H | S | O 
    35635 ---|---|---|--- 
    35636 H | 6 | -9 | -6 
    35637 S |  | 6 | -6 
    35638 O |  |  | 4 
    35639 Iteration cutoff | 2 
    35640  
    35641 Matchmaker 3j0c.pdb1, chain G (#1.44) with AF3 E1 1-421.pdb, chain A (#817),
    35642 sequence alignment score = 1060.7 
    35643 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    35644 2.985) 
    35645  
    35646 
    35647 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    35648 
    35649 Chain information for AF3 E1 422-461.pdb #818 
    35650 --- 
    35651 Chain | Description 
    35652 A | No description available 
    35653  
    35654 
    35655 > matchmaker #818 to #1.44 & sel
    35656 
    35657 Parameters 
    35658 --- 
    35659 Chain pairing | bb 
    35660 Alignment algorithm | Needleman-Wunsch 
    35661 Similarity matrix | BLOSUM-62 
    35662 SS fraction | 0.3 
    35663 Gap open (HH/SS/other) | 18/18/6 
    35664 Gap extend | 1 
    35665 SS matrix |  |  | H | S | O 
    35666 ---|---|---|--- 
    35667 H | 6 | -9 | -6 
    35668 S |  | 6 | -6 
    35669 O |  |  | 4 
    35670 Iteration cutoff | 2 
    35671  
    35672 Matchmaker 3j0c.pdb1, chain G (#1.44) with AF3 E1 422-461.pdb, chain A (#818),
    35673 sequence alignment score = 626.9 
    35674 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    35675 2.997) 
    35676  
    35677 
    35678 > hide sel cartoons
    35679 
    35680 > select #1.44/H
    35681 
    35682 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    35683 
    35684 > show sel cartoons
    35685 
    35686 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    35687 
    35688 Chain information for AF3 E2 1-352.pdb #819 
    35689 --- 
    35690 Chain | Description 
    35691 B | No description available 
    35692  
    35693 
    35694 > matchmaker #819 to #1.44 & sel
    35695 
    35696 Parameters 
    35697 --- 
    35698 Chain pairing | bb 
    35699 Alignment algorithm | Needleman-Wunsch 
    35700 Similarity matrix | BLOSUM-62 
    35701 SS fraction | 0.3 
    35702 Gap open (HH/SS/other) | 18/18/6 
    35703 Gap extend | 1 
    35704 SS matrix |  |  | H | S | O 
    35705 ---|---|---|--- 
    35706 H | 6 | -9 | -6 
    35707 S |  | 6 | -6 
    35708 O |  |  | 4 
    35709 Iteration cutoff | 2 
    35710  
    35711 Matchmaker 3j0c.pdb1, chain H (#1.44) with AF3 E2 1-352.pdb, chain B (#819),
    35712 sequence alignment score = 590.9 
    35713 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    35714 6.107) 
    35715  
    35716 
    35717 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    35718 
    35719 Chain information for AF3 E2 353-438.pdb #820 
    35720 --- 
    35721 Chain | Description 
    35722 B | No description available 
    35723  
    35724 
    35725 > matchmaker #820 to #1.44 & sel
    35726 
    35727 Parameters 
    35728 --- 
    35729 Chain pairing | bb 
    35730 Alignment algorithm | Needleman-Wunsch 
    35731 Similarity matrix | BLOSUM-62 
    35732 SS fraction | 0.3 
    35733 Gap open (HH/SS/other) | 18/18/6 
    35734 Gap extend | 1 
    35735 SS matrix |  |  | H | S | O 
    35736 ---|---|---|--- 
    35737 H | 6 | -9 | -6 
    35738 S |  | 6 | -6 
    35739 O |  |  | 4 
    35740 Iteration cutoff | 2 
    35741  
    35742 Matchmaker 3j0c.pdb1, chain H (#1.44) with AF3 E2 353-438.pdb, chain B (#820),
    35743 sequence alignment score = 329.4 
    35744 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    35745 8.151) 
    35746  
    35747 
    35748 > show sel cartoons
    35749 
    35750 > hide sel cartoons
    35751 
    35752 > select #1.44/I
    35753 
    35754 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    35755 
    35756 > show sel cartoons
    35757 
    35758 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    35759 
    35760 Chain information for AF3 CA.pdb #821 
    35761 --- 
    35762 Chain | Description 
    35763 A | No description available 
    35764  
    35765 
    35766 > matchmaker #821 to #1.44 & sel
    35767 
    35768 Parameters 
    35769 --- 
    35770 Chain pairing | bb 
    35771 Alignment algorithm | Needleman-Wunsch 
    35772 Similarity matrix | BLOSUM-62 
    35773 SS fraction | 0.3 
    35774 Gap open (HH/SS/other) | 18/18/6 
    35775 Gap extend | 1 
    35776 SS matrix |  |  | H | S | O 
    35777 ---|---|---|--- 
    35778 H | 6 | -9 | -6 
    35779 S |  | 6 | -6 
    35780 O |  |  | 4 
    35781 Iteration cutoff | 2 
    35782  
    35783 Matchmaker 3j0c.pdb1, chain I (#1.44) with AF3 CA.pdb, chain A (#821),
    35784 sequence alignment score = 306.5 
    35785 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    35786 2.689) 
    35787  
    35788 
    35789 > hide sel cartoons
    35790 
    35791 > color #817 dodgerblue
    35792 
    35793 > color #818 dodgerblue
    35794 
    35795 > color #819 #00b305ff
    35796 
    35797 > color #820 #00b305ff
    35798 
    35799 > color #821 #f15839ff
    35800 
    35801 > select #1.45/G
    35802 
    35803 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    35804 
    35805 > show sel cartoons
    35806 
    35807 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    35808 
    35809 Chain information for AF3 E1 1-421.pdb #822 
    35810 --- 
    35811 Chain | Description 
    35812 A | No description available 
    35813  
    35814 
    35815 > matchmaker #822 to #1.45 & sel
    35816 
    35817 Parameters 
    35818 --- 
    35819 Chain pairing | bb 
    35820 Alignment algorithm | Needleman-Wunsch 
    35821 Similarity matrix | BLOSUM-62 
    35822 SS fraction | 0.3 
    35823 Gap open (HH/SS/other) | 18/18/6 
    35824 Gap extend | 1 
    35825 SS matrix |  |  | H | S | O 
    35826 ---|---|---|--- 
    35827 H | 6 | -9 | -6 
    35828 S |  | 6 | -6 
    35829 O |  |  | 4 
    35830 Iteration cutoff | 2 
    35831  
    35832 Matchmaker 3j0c.pdb1, chain G (#1.45) with AF3 E1 1-421.pdb, chain A (#822),
    35833 sequence alignment score = 1060.7 
    35834 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    35835 2.985) 
    35836  
    35837 
    35838 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    35839 
    35840 Chain information for AF3 E1 422-461.pdb #823 
    35841 --- 
    35842 Chain | Description 
    35843 A | No description available 
    35844  
    35845 
    35846 > matchmaker #823 to #1.45 & sel
    35847 
    35848 Parameters 
    35849 --- 
    35850 Chain pairing | bb 
    35851 Alignment algorithm | Needleman-Wunsch 
    35852 Similarity matrix | BLOSUM-62 
    35853 SS fraction | 0.3 
    35854 Gap open (HH/SS/other) | 18/18/6 
    35855 Gap extend | 1 
    35856 SS matrix |  |  | H | S | O 
    35857 ---|---|---|--- 
    35858 H | 6 | -9 | -6 
    35859 S |  | 6 | -6 
    35860 O |  |  | 4 
    35861 Iteration cutoff | 2 
    35862  
    35863 Matchmaker 3j0c.pdb1, chain G (#1.45) with AF3 E1 422-461.pdb, chain A (#823),
    35864 sequence alignment score = 626.9 
    35865 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    35866 2.997) 
    35867  
    35868 
    35869 > hide sel cartoons
    35870 
    35871 > select #1.45/H
    35872 
    35873 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    35874 
    35875 > show sel cartoons
    35876 
    35877 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    35878 
    35879 Chain information for AF3 E2 1-352.pdb #824 
    35880 --- 
    35881 Chain | Description 
    35882 B | No description available 
    35883  
    35884 
    35885 > matchmaker #824 to #1.45 & sel
    35886 
    35887 Parameters 
    35888 --- 
    35889 Chain pairing | bb 
    35890 Alignment algorithm | Needleman-Wunsch 
    35891 Similarity matrix | BLOSUM-62 
    35892 SS fraction | 0.3 
    35893 Gap open (HH/SS/other) | 18/18/6 
    35894 Gap extend | 1 
    35895 SS matrix |  |  | H | S | O 
    35896 ---|---|---|--- 
    35897 H | 6 | -9 | -6 
    35898 S |  | 6 | -6 
    35899 O |  |  | 4 
    35900 Iteration cutoff | 2 
    35901  
    35902 Matchmaker 3j0c.pdb1, chain H (#1.45) with AF3 E2 1-352.pdb, chain B (#824),
    35903 sequence alignment score = 590.9 
    35904 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    35905 6.107) 
    35906  
    35907 
    35908 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    35909 
    35910 Chain information for AF3 E2 353-438.pdb #825 
    35911 --- 
    35912 Chain | Description 
    35913 B | No description available 
    35914  
    35915 
    35916 > matchmaker #825 to #1.45 & sel
    35917 
    35918 Parameters 
    35919 --- 
    35920 Chain pairing | bb 
    35921 Alignment algorithm | Needleman-Wunsch 
    35922 Similarity matrix | BLOSUM-62 
    35923 SS fraction | 0.3 
    35924 Gap open (HH/SS/other) | 18/18/6 
    35925 Gap extend | 1 
    35926 SS matrix |  |  | H | S | O 
    35927 ---|---|---|--- 
    35928 H | 6 | -9 | -6 
    35929 S |  | 6 | -6 
    35930 O |  |  | 4 
    35931 Iteration cutoff | 2 
    35932  
    35933 Matchmaker 3j0c.pdb1, chain H (#1.45) with AF3 E2 353-438.pdb, chain B (#825),
    35934 sequence alignment score = 329.4 
    35935 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    35936 8.150) 
    35937  
    35938 
    35939 > hide sel cartoons
    35940 
    35941 > select #1.45/I
    35942 
    35943 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    35944 
    35945 > show sel cartoons
    35946 
    35947 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    35948 
    35949 Chain information for AF3 CA.pdb #826 
    35950 --- 
    35951 Chain | Description 
    35952 A | No description available 
    35953  
    35954 
    35955 > matchmaker #826 to #1.45 & sel
    35956 
    35957 Parameters 
    35958 --- 
    35959 Chain pairing | bb 
    35960 Alignment algorithm | Needleman-Wunsch 
    35961 Similarity matrix | BLOSUM-62 
    35962 SS fraction | 0.3 
    35963 Gap open (HH/SS/other) | 18/18/6 
    35964 Gap extend | 1 
    35965 SS matrix |  |  | H | S | O 
    35966 ---|---|---|--- 
    35967 H | 6 | -9 | -6 
    35968 S |  | 6 | -6 
    35969 O |  |  | 4 
    35970 Iteration cutoff | 2 
    35971  
    35972 Matchmaker 3j0c.pdb1, chain I (#1.45) with AF3 CA.pdb, chain A (#826),
    35973 sequence alignment score = 306.5 
    35974 RMSD between 119 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    35975 2.689) 
    35976  
    35977 
    35978 > hide sel cartoons
    35979 
    35980 > color #822 dodgerblue
    35981 
    35982 > color #823 dodgerblue
    35983 
    35984 > color #824 #00b305ff
    35985 
    35986 > color #825 #00b305ff
    35987 
    35988 > color #826 #f15839ff
    35989 
    35990 > select #1.46/G
    35991 
    35992 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    35993 
    35994 > show sel cartoons
    35995 
    35996 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    35997 
    35998 Chain information for AF3 E1 1-421.pdb #827 
    35999 --- 
    36000 Chain | Description 
    36001 A | No description available 
    36002  
    36003 
    36004 > matchmaker #827 to #1.46 & sel
    36005 
    36006 Parameters 
    36007 --- 
    36008 Chain pairing | bb 
    36009 Alignment algorithm | Needleman-Wunsch 
    36010 Similarity matrix | BLOSUM-62 
    36011 SS fraction | 0.3 
    36012 Gap open (HH/SS/other) | 18/18/6 
    36013 Gap extend | 1 
    36014 SS matrix |  |  | H | S | O 
    36015 ---|---|---|--- 
    36016 H | 6 | -9 | -6 
    36017 S |  | 6 | -6 
    36018 O |  |  | 4 
    36019 Iteration cutoff | 2 
    36020  
    36021 Matchmaker 3j0c.pdb1, chain G (#1.46) with AF3 E1 1-421.pdb, chain A (#827),
    36022 sequence alignment score = 1060.7 
    36023 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    36024 2.985) 
    36025  
    36026 
    36027 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    36028 
    36029 Chain information for AF3 E1 422-461.pdb #828 
    36030 --- 
    36031 Chain | Description 
    36032 A | No description available 
    36033  
    36034 
    36035 > matchmaker #828 to #1.46 & sel
    36036 
    36037 Parameters 
    36038 --- 
    36039 Chain pairing | bb 
    36040 Alignment algorithm | Needleman-Wunsch 
    36041 Similarity matrix | BLOSUM-62 
    36042 SS fraction | 0.3 
    36043 Gap open (HH/SS/other) | 18/18/6 
    36044 Gap extend | 1 
    36045 SS matrix |  |  | H | S | O 
    36046 ---|---|---|--- 
    36047 H | 6 | -9 | -6 
    36048 S |  | 6 | -6 
    36049 O |  |  | 4 
    36050 Iteration cutoff | 2 
    36051  
    36052 Matchmaker 3j0c.pdb1, chain G (#1.46) with AF3 E1 422-461.pdb, chain A (#828),
    36053 sequence alignment score = 626.9 
    36054 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    36055 2.997) 
    36056  
    36057 
    36058 > hide sel cartoons
    36059 
    36060 > select #1.46/H
    36061 
    36062 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    36063 
    36064 > show sel cartoons
    36065 
    36066 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    36067 
    36068 Chain information for AF3 E2 1-352.pdb #829 
    36069 --- 
    36070 Chain | Description 
    36071 B | No description available 
    36072  
    36073 
    36074 > matchmaker #829 to #1.46 & sel
    36075 
    36076 Parameters 
    36077 --- 
    36078 Chain pairing | bb 
    36079 Alignment algorithm | Needleman-Wunsch 
    36080 Similarity matrix | BLOSUM-62 
    36081 SS fraction | 0.3 
    36082 Gap open (HH/SS/other) | 18/18/6 
    36083 Gap extend | 1 
    36084 SS matrix |  |  | H | S | O 
    36085 ---|---|---|--- 
    36086 H | 6 | -9 | -6 
    36087 S |  | 6 | -6 
    36088 O |  |  | 4 
    36089 Iteration cutoff | 2 
    36090  
    36091 Matchmaker 3j0c.pdb1, chain H (#1.46) with AF3 E2 1-352.pdb, chain B (#829),
    36092 sequence alignment score = 590.9 
    36093 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    36094 6.107) 
    36095  
    36096 
    36097 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    36098 
    36099 Chain information for AF3 E2 353-438.pdb #830 
    36100 --- 
    36101 Chain | Description 
    36102 B | No description available 
    36103  
    36104 
    36105 > matchmaker #830 to #1.46 & sel
    36106 
    36107 Parameters 
    36108 --- 
    36109 Chain pairing | bb 
    36110 Alignment algorithm | Needleman-Wunsch 
    36111 Similarity matrix | BLOSUM-62 
    36112 SS fraction | 0.3 
    36113 Gap open (HH/SS/other) | 18/18/6 
    36114 Gap extend | 1 
    36115 SS matrix |  |  | H | S | O 
    36116 ---|---|---|--- 
    36117 H | 6 | -9 | -6 
    36118 S |  | 6 | -6 
    36119 O |  |  | 4 
    36120 Iteration cutoff | 2 
    36121  
    36122 Matchmaker 3j0c.pdb1, chain H (#1.46) with AF3 E2 353-438.pdb, chain B (#830),
    36123 sequence alignment score = 329.4 
    36124 RMSD between 40 pruned atom pairs is 0.937 angstroms; (across all 84 pairs:
    36125 8.150) 
    36126  
    36127 
    36128 > hide sel cartoons
    36129 
    36130 > select #1.46/I
    36131 
    36132 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    36133 
    36134 > show sel cartoons
    36135 
    36136 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    36137 
    36138 Chain information for AF3 CA.pdb #831 
    36139 --- 
    36140 Chain | Description 
    36141 A | No description available 
    36142  
    36143 
    36144 > matchmaker #831 to #1.46 & sel
    36145 
    36146 Parameters 
    36147 --- 
    36148 Chain pairing | bb 
    36149 Alignment algorithm | Needleman-Wunsch 
    36150 Similarity matrix | BLOSUM-62 
    36151 SS fraction | 0.3 
    36152 Gap open (HH/SS/other) | 18/18/6 
    36153 Gap extend | 1 
    36154 SS matrix |  |  | H | S | O 
    36155 ---|---|---|--- 
    36156 H | 6 | -9 | -6 
    36157 S |  | 6 | -6 
    36158 O |  |  | 4 
    36159 Iteration cutoff | 2 
    36160  
    36161 Matchmaker 3j0c.pdb1, chain I (#1.46) with AF3 CA.pdb, chain A (#831),
    36162 sequence alignment score = 306.5 
    36163 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    36164 2.689) 
    36165  
    36166 
    36167 > hide sel cartoons
    36168 
    36169 > color #827 dodgerblue
    36170 
    36171 > color #828 dodgerblue
    36172 
    36173 > color #829 #00b305ff
    36174 
    36175 > color #830 #00b305ff
    36176 
    36177 > color #831 #f15839ff
    36178 
    36179 > select #1.47/G
    36180 
    36181 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    36182 
    36183 > show sel cartoons
    36184 
    36185 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    36186 
    36187 Chain information for AF3 E1 1-421.pdb #832 
    36188 --- 
    36189 Chain | Description 
    36190 A | No description available 
    36191  
    36192 
    36193 > matchmaker #832 to #1.47 & sel
    36194 
    36195 Parameters 
    36196 --- 
    36197 Chain pairing | bb 
    36198 Alignment algorithm | Needleman-Wunsch 
    36199 Similarity matrix | BLOSUM-62 
    36200 SS fraction | 0.3 
    36201 Gap open (HH/SS/other) | 18/18/6 
    36202 Gap extend | 1 
    36203 SS matrix |  |  | H | S | O 
    36204 ---|---|---|--- 
    36205 H | 6 | -9 | -6 
    36206 S |  | 6 | -6 
    36207 O |  |  | 4 
    36208 Iteration cutoff | 2 
    36209  
    36210 Matchmaker 3j0c.pdb1, chain G (#1.47) with AF3 E1 1-421.pdb, chain A (#832),
    36211 sequence alignment score = 1060.7 
    36212 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    36213 2.985) 
    36214  
    36215 
    36216 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    36217 
    36218 Chain information for AF3 E1 422-461.pdb #833 
    36219 --- 
    36220 Chain | Description 
    36221 A | No description available 
    36222  
    36223 
    36224 > matchmaker #833 to #1.47 & sel
    36225 
    36226 Parameters 
    36227 --- 
    36228 Chain pairing | bb 
    36229 Alignment algorithm | Needleman-Wunsch 
    36230 Similarity matrix | BLOSUM-62 
    36231 SS fraction | 0.3 
    36232 Gap open (HH/SS/other) | 18/18/6 
    36233 Gap extend | 1 
    36234 SS matrix |  |  | H | S | O 
    36235 ---|---|---|--- 
    36236 H | 6 | -9 | -6 
    36237 S |  | 6 | -6 
    36238 O |  |  | 4 
    36239 Iteration cutoff | 2 
    36240  
    36241 Matchmaker 3j0c.pdb1, chain G (#1.47) with AF3 E1 422-461.pdb, chain A (#833),
    36242 sequence alignment score = 626.9 
    36243 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    36244 2.997) 
    36245  
    36246 
    36247 > hide sel cartoons
    36248 
    36249 > select #1.47/H
    36250 
    36251 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    36252 
    36253 > show sel cartoons
    36254 
    36255 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    36256 
    36257 Chain information for AF3 E2 1-352.pdb #834 
    36258 --- 
    36259 Chain | Description 
    36260 B | No description available 
    36261  
    36262 
    36263 > matchmaker #834 to #1.47 & sel
    36264 
    36265 Parameters 
    36266 --- 
    36267 Chain pairing | bb 
    36268 Alignment algorithm | Needleman-Wunsch 
    36269 Similarity matrix | BLOSUM-62 
    36270 SS fraction | 0.3 
    36271 Gap open (HH/SS/other) | 18/18/6 
    36272 Gap extend | 1 
    36273 SS matrix |  |  | H | S | O 
    36274 ---|---|---|--- 
    36275 H | 6 | -9 | -6 
    36276 S |  | 6 | -6 
    36277 O |  |  | 4 
    36278 Iteration cutoff | 2 
    36279  
    36280 Matchmaker 3j0c.pdb1, chain H (#1.47) with AF3 E2 1-352.pdb, chain B (#834),
    36281 sequence alignment score = 590.9 
    36282 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    36283 6.107) 
    36284  
    36285 
    36286 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    36287 
    36288 Chain information for AF3 E2 353-438.pdb #835 
    36289 --- 
    36290 Chain | Description 
    36291 B | No description available 
    36292  
    36293 
    36294 > matchmaker #835 to #1.47 & sel
    36295 
    36296 Parameters 
    36297 --- 
    36298 Chain pairing | bb 
    36299 Alignment algorithm | Needleman-Wunsch 
    36300 Similarity matrix | BLOSUM-62 
    36301 SS fraction | 0.3 
    36302 Gap open (HH/SS/other) | 18/18/6 
    36303 Gap extend | 1 
    36304 SS matrix |  |  | H | S | O 
    36305 ---|---|---|--- 
    36306 H | 6 | -9 | -6 
    36307 S |  | 6 | -6 
    36308 O |  |  | 4 
    36309 Iteration cutoff | 2 
    36310  
    36311 Matchmaker 3j0c.pdb1, chain H (#1.47) with AF3 E2 353-438.pdb, chain B (#835),
    36312 sequence alignment score = 329.4 
    36313 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    36314 8.150) 
    36315  
    36316 
    36317 > hide sel cartoons
    36318 
    36319 > select #1.47/I
    36320 
    36321 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    36322 
    36323 > show sel cartoons
    36324 
    36325 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    36326 
    36327 Chain information for AF3 CA.pdb #836 
    36328 --- 
    36329 Chain | Description 
    36330 A | No description available 
    36331  
    36332 
    36333 > matchmaker #836 to #1.47 & sel
    36334 
    36335 Parameters 
    36336 --- 
    36337 Chain pairing | bb 
    36338 Alignment algorithm | Needleman-Wunsch 
    36339 Similarity matrix | BLOSUM-62 
    36340 SS fraction | 0.3 
    36341 Gap open (HH/SS/other) | 18/18/6 
    36342 Gap extend | 1 
    36343 SS matrix |  |  | H | S | O 
    36344 ---|---|---|--- 
    36345 H | 6 | -9 | -6 
    36346 S |  | 6 | -6 
    36347 O |  |  | 4 
    36348 Iteration cutoff | 2 
    36349  
    36350 Matchmaker 3j0c.pdb1, chain I (#1.47) with AF3 CA.pdb, chain A (#836),
    36351 sequence alignment score = 306.5 
    36352 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    36353 2.689) 
    36354  
    36355 
    36356 > hide sel cartoons
    36357 
    36358 > color #832 dodgerblue
    36359 
    36360 > color #833 dodgerblue
    36361 
    36362 > color #834 #00b305ff
    36363 
    36364 > color #835 #00b305ff
    36365 
    36366 > color #836 #f15839ff
    36367 
    36368 > select #1.48/G
    36369 
    36370 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    36371 
    36372 > show sel cartoons
    36373 
    36374 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    36375 
    36376 Chain information for AF3 E1 1-421.pdb #837 
    36377 --- 
    36378 Chain | Description 
    36379 A | No description available 
    36380  
    36381 
    36382 > matchmaker #837 to #1.48 & sel
    36383 
    36384 Parameters 
    36385 --- 
    36386 Chain pairing | bb 
    36387 Alignment algorithm | Needleman-Wunsch 
    36388 Similarity matrix | BLOSUM-62 
    36389 SS fraction | 0.3 
    36390 Gap open (HH/SS/other) | 18/18/6 
    36391 Gap extend | 1 
    36392 SS matrix |  |  | H | S | O 
    36393 ---|---|---|--- 
    36394 H | 6 | -9 | -6 
    36395 S |  | 6 | -6 
    36396 O |  |  | 4 
    36397 Iteration cutoff | 2 
    36398  
    36399 Matchmaker 3j0c.pdb1, chain G (#1.48) with AF3 E1 1-421.pdb, chain A (#837),
    36400 sequence alignment score = 1060.7 
    36401 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    36402 2.985) 
    36403  
    36404 
    36405 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    36406 
    36407 Chain information for AF3 E1 422-461.pdb #838 
    36408 --- 
    36409 Chain | Description 
    36410 A | No description available 
    36411  
    36412 
    36413 > matchmaker #838 to #1.48 & sel
    36414 
    36415 Parameters 
    36416 --- 
    36417 Chain pairing | bb 
    36418 Alignment algorithm | Needleman-Wunsch 
    36419 Similarity matrix | BLOSUM-62 
    36420 SS fraction | 0.3 
    36421 Gap open (HH/SS/other) | 18/18/6 
    36422 Gap extend | 1 
    36423 SS matrix |  |  | H | S | O 
    36424 ---|---|---|--- 
    36425 H | 6 | -9 | -6 
    36426 S |  | 6 | -6 
    36427 O |  |  | 4 
    36428 Iteration cutoff | 2 
    36429  
    36430 Matchmaker 3j0c.pdb1, chain G (#1.48) with AF3 E1 422-461.pdb, chain A (#838),
    36431 sequence alignment score = 626.9 
    36432 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    36433 2.997) 
    36434  
    36435 
    36436 > hide sel cartoons
    36437 
    36438 > select #1.48/H
    36439 
    36440 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    36441 
    36442 > show sel cartoons
    36443 
    36444 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    36445 
    36446 Chain information for AF3 E2 1-352.pdb #839 
    36447 --- 
    36448 Chain | Description 
    36449 B | No description available 
    36450  
    36451 
    36452 > matchmaker #839 to #1.48 & sel
    36453 
    36454 Parameters 
    36455 --- 
    36456 Chain pairing | bb 
    36457 Alignment algorithm | Needleman-Wunsch 
    36458 Similarity matrix | BLOSUM-62 
    36459 SS fraction | 0.3 
    36460 Gap open (HH/SS/other) | 18/18/6 
    36461 Gap extend | 1 
    36462 SS matrix |  |  | H | S | O 
    36463 ---|---|---|--- 
    36464 H | 6 | -9 | -6 
    36465 S |  | 6 | -6 
    36466 O |  |  | 4 
    36467 Iteration cutoff | 2 
    36468  
    36469 Matchmaker 3j0c.pdb1, chain H (#1.48) with AF3 E2 1-352.pdb, chain B (#839),
    36470 sequence alignment score = 590.9 
    36471 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    36472 6.107) 
    36473  
    36474 
    36475 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    36476 
    36477 Chain information for AF3 E2 353-438.pdb #840 
    36478 --- 
    36479 Chain | Description 
    36480 B | No description available 
    36481  
    36482 
    36483 > matchmaker #840 to #1.48 & sel
    36484 
    36485 Parameters 
    36486 --- 
    36487 Chain pairing | bb 
    36488 Alignment algorithm | Needleman-Wunsch 
    36489 Similarity matrix | BLOSUM-62 
    36490 SS fraction | 0.3 
    36491 Gap open (HH/SS/other) | 18/18/6 
    36492 Gap extend | 1 
    36493 SS matrix |  |  | H | S | O 
    36494 ---|---|---|--- 
    36495 H | 6 | -9 | -6 
    36496 S |  | 6 | -6 
    36497 O |  |  | 4 
    36498 Iteration cutoff | 2 
    36499  
    36500 Matchmaker 3j0c.pdb1, chain H (#1.48) with AF3 E2 353-438.pdb, chain B (#840),
    36501 sequence alignment score = 329.4 
    36502 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    36503 8.150) 
    36504  
    36505 
    36506 > hide sel cartoons
    36507 
    36508 > select #1.48/I
    36509 
    36510 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    36511 
    36512 > show sel cartoons
    36513 
    36514 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    36515 
    36516 Chain information for AF3 CA.pdb #841 
    36517 --- 
    36518 Chain | Description 
    36519 A | No description available 
    36520  
    36521 
    36522 > matchmaker #841 to #1.48 & sel
    36523 
    36524 Parameters 
    36525 --- 
    36526 Chain pairing | bb 
    36527 Alignment algorithm | Needleman-Wunsch 
    36528 Similarity matrix | BLOSUM-62 
    36529 SS fraction | 0.3 
    36530 Gap open (HH/SS/other) | 18/18/6 
    36531 Gap extend | 1 
    36532 SS matrix |  |  | H | S | O 
    36533 ---|---|---|--- 
    36534 H | 6 | -9 | -6 
    36535 S |  | 6 | -6 
    36536 O |  |  | 4 
    36537 Iteration cutoff | 2 
    36538  
    36539 Matchmaker 3j0c.pdb1, chain I (#1.48) with AF3 CA.pdb, chain A (#841),
    36540 sequence alignment score = 306.5 
    36541 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    36542 2.689) 
    36543  
    36544 
    36545 > hide sel cartoons
    36546 
    36547 > color #837 dodgerblue
    36548 
    36549 > color #838 dodgerblue
    36550 
    36551 > color #839 #00b305ff
    36552 
    36553 > color #840 #00b305ff
    36554 
    36555 > color #841 #f15839ff
    36556 
    36557 > select #1.49/G
    36558 
    36559 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    36560 
    36561 > show sel cartoons
    36562 
    36563 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    36564 
    36565 Chain information for AF3 E1 1-421.pdb #842 
    36566 --- 
    36567 Chain | Description 
    36568 A | No description available 
    36569  
    36570 
    36571 > matchmaker #842 to #1.49 & sel
    36572 
    36573 Parameters 
    36574 --- 
    36575 Chain pairing | bb 
    36576 Alignment algorithm | Needleman-Wunsch 
    36577 Similarity matrix | BLOSUM-62 
    36578 SS fraction | 0.3 
    36579 Gap open (HH/SS/other) | 18/18/6 
    36580 Gap extend | 1 
    36581 SS matrix |  |  | H | S | O 
    36582 ---|---|---|--- 
    36583 H | 6 | -9 | -6 
    36584 S |  | 6 | -6 
    36585 O |  |  | 4 
    36586 Iteration cutoff | 2 
    36587  
    36588 Matchmaker 3j0c.pdb1, chain G (#1.49) with AF3 E1 1-421.pdb, chain A (#842),
    36589 sequence alignment score = 1060.7 
    36590 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    36591 2.985) 
    36592  
    36593 
    36594 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    36595 
    36596 Chain information for AF3 E1 422-461.pdb #843 
    36597 --- 
    36598 Chain | Description 
    36599 A | No description available 
    36600  
    36601 
    36602 > matchmaker #843 to #1.49 & sel
    36603 
    36604 Parameters 
    36605 --- 
    36606 Chain pairing | bb 
    36607 Alignment algorithm | Needleman-Wunsch 
    36608 Similarity matrix | BLOSUM-62 
    36609 SS fraction | 0.3 
    36610 Gap open (HH/SS/other) | 18/18/6 
    36611 Gap extend | 1 
    36612 SS matrix |  |  | H | S | O 
    36613 ---|---|---|--- 
    36614 H | 6 | -9 | -6 
    36615 S |  | 6 | -6 
    36616 O |  |  | 4 
    36617 Iteration cutoff | 2 
    36618  
    36619 Matchmaker 3j0c.pdb1, chain G (#1.49) with AF3 E1 422-461.pdb, chain A (#843),
    36620 sequence alignment score = 626.9 
    36621 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    36622 2.997) 
    36623  
    36624 
    36625 > hide sel cartoons
    36626 
    36627 > select #1.49/H
    36628 
    36629 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    36630 
    36631 > show sel cartoons
    36632 
    36633 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    36634 
    36635 Chain information for AF3 E2 1-352.pdb #844 
    36636 --- 
    36637 Chain | Description 
    36638 B | No description available 
    36639  
    36640 
    36641 > matchmaker #844 to #1.49 & sel
    36642 
    36643 Parameters 
    36644 --- 
    36645 Chain pairing | bb 
    36646 Alignment algorithm | Needleman-Wunsch 
    36647 Similarity matrix | BLOSUM-62 
    36648 SS fraction | 0.3 
    36649 Gap open (HH/SS/other) | 18/18/6 
    36650 Gap extend | 1 
    36651 SS matrix |  |  | H | S | O 
    36652 ---|---|---|--- 
    36653 H | 6 | -9 | -6 
    36654 S |  | 6 | -6 
    36655 O |  |  | 4 
    36656 Iteration cutoff | 2 
    36657  
    36658 Matchmaker 3j0c.pdb1, chain H (#1.49) with AF3 E2 1-352.pdb, chain B (#844),
    36659 sequence alignment score = 590.9 
    36660 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    36661 6.107) 
    36662  
    36663 
    36664 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    36665 
    36666 Chain information for AF3 E2 353-438.pdb #845 
    36667 --- 
    36668 Chain | Description 
    36669 B | No description available 
    36670  
    36671 
    36672 > matchmaker #845 to #1.49 & sel
    36673 
    36674 Parameters 
    36675 --- 
    36676 Chain pairing | bb 
    36677 Alignment algorithm | Needleman-Wunsch 
    36678 Similarity matrix | BLOSUM-62 
    36679 SS fraction | 0.3 
    36680 Gap open (HH/SS/other) | 18/18/6 
    36681 Gap extend | 1 
    36682 SS matrix |  |  | H | S | O 
    36683 ---|---|---|--- 
    36684 H | 6 | -9 | -6 
    36685 S |  | 6 | -6 
    36686 O |  |  | 4 
    36687 Iteration cutoff | 2 
    36688  
    36689 Matchmaker 3j0c.pdb1, chain H (#1.49) with AF3 E2 353-438.pdb, chain B (#845),
    36690 sequence alignment score = 329.4 
    36691 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    36692 8.150) 
    36693  
    36694 
    36695 > hide sel cartoons
    36696 
    36697 > select #1.39/I
    36698 
    36699 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    36700 
    36701 > select #1.49/I
    36702 
    36703 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    36704 
    36705 > show sel cartoons
    36706 
    36707 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    36708 
    36709 Chain information for AF3 CA.pdb #846 
    36710 --- 
    36711 Chain | Description 
    36712 A | No description available 
    36713  
    36714 
    36715 > matchmaker #846 to #1.49 & sel
    36716 
    36717 Parameters 
    36718 --- 
    36719 Chain pairing | bb 
    36720 Alignment algorithm | Needleman-Wunsch 
    36721 Similarity matrix | BLOSUM-62 
    36722 SS fraction | 0.3 
    36723 Gap open (HH/SS/other) | 18/18/6 
    36724 Gap extend | 1 
    36725 SS matrix |  |  | H | S | O 
    36726 ---|---|---|--- 
    36727 H | 6 | -9 | -6 
    36728 S |  | 6 | -6 
    36729 O |  |  | 4 
    36730 Iteration cutoff | 2 
    36731  
    36732 Matchmaker 3j0c.pdb1, chain I (#1.49) with AF3 CA.pdb, chain A (#846),
    36733 sequence alignment score = 306.5 
    36734 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    36735 2.689) 
    36736  
    36737 
    36738 > hide sel cartoons
    36739 
    36740 > color #842 dodgerblue
    36741 
    36742 > color #843 dodgerblue
    36743 
    36744 > color #844 #00b305ff
    36745 
    36746 > color #845 #00b305ff
    36747 
    36748 > color #846 #f15839ff
    36749 
    36750 > select #1.50/G
    36751 
    36752 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    36753 
    36754 > show sel cartoons
    36755 
    36756 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    36757 
    36758 Chain information for AF3 E1 1-421.pdb #847 
    36759 --- 
    36760 Chain | Description 
    36761 A | No description available 
    36762  
    36763 
    36764 > matchmaker #847 to #1.50 & sel
    36765 
    36766 Parameters 
    36767 --- 
    36768 Chain pairing | bb 
    36769 Alignment algorithm | Needleman-Wunsch 
    36770 Similarity matrix | BLOSUM-62 
    36771 SS fraction | 0.3 
    36772 Gap open (HH/SS/other) | 18/18/6 
    36773 Gap extend | 1 
    36774 SS matrix |  |  | H | S | O 
    36775 ---|---|---|--- 
    36776 H | 6 | -9 | -6 
    36777 S |  | 6 | -6 
    36778 O |  |  | 4 
    36779 Iteration cutoff | 2 
    36780  
    36781 Matchmaker 3j0c.pdb1, chain G (#1.50) with AF3 E1 1-421.pdb, chain A (#847),
    36782 sequence alignment score = 1060.7 
    36783 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    36784 2.985) 
    36785  
    36786 
    36787 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    36788 
    36789 Chain information for AF3 E1 422-461.pdb #848 
    36790 --- 
    36791 Chain | Description 
    36792 A | No description available 
    36793  
    36794 
    36795 > matchmaker #848 to #1.50 & sel
    36796 
    36797 Parameters 
    36798 --- 
    36799 Chain pairing | bb 
    36800 Alignment algorithm | Needleman-Wunsch 
    36801 Similarity matrix | BLOSUM-62 
    36802 SS fraction | 0.3 
    36803 Gap open (HH/SS/other) | 18/18/6 
    36804 Gap extend | 1 
    36805 SS matrix |  |  | H | S | O 
    36806 ---|---|---|--- 
    36807 H | 6 | -9 | -6 
    36808 S |  | 6 | -6 
    36809 O |  |  | 4 
    36810 Iteration cutoff | 2 
    36811  
    36812 Matchmaker 3j0c.pdb1, chain G (#1.50) with AF3 E1 422-461.pdb, chain A (#848),
    36813 sequence alignment score = 626.9 
    36814 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    36815 2.997) 
    36816  
    36817 
    36818 > hide sel cartoons
    36819 
    36820 [Repeated 1 time(s)]
    36821 
    36822 > select #1.50/H
    36823 
    36824 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    36825 
    36826 > show sel cartoons
    36827 
    36828 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    36829 
    36830 Chain information for AF3 E2 1-352.pdb #849 
    36831 --- 
    36832 Chain | Description 
    36833 B | No description available 
    36834  
    36835 
    36836 > matchmaker #849 to #1.50 & sel
    36837 
    36838 Parameters 
    36839 --- 
    36840 Chain pairing | bb 
    36841 Alignment algorithm | Needleman-Wunsch 
    36842 Similarity matrix | BLOSUM-62 
    36843 SS fraction | 0.3 
    36844 Gap open (HH/SS/other) | 18/18/6 
    36845 Gap extend | 1 
    36846 SS matrix |  |  | H | S | O 
    36847 ---|---|---|--- 
    36848 H | 6 | -9 | -6 
    36849 S |  | 6 | -6 
    36850 O |  |  | 4 
    36851 Iteration cutoff | 2 
    36852  
    36853 Matchmaker 3j0c.pdb1, chain H (#1.50) with AF3 E2 1-352.pdb, chain B (#849),
    36854 sequence alignment score = 590.9 
    36855 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    36856 6.107) 
    36857  
    36858 
    36859 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    36860 
    36861 Chain information for AF3 E2 353-438.pdb #850 
    36862 --- 
    36863 Chain | Description 
    36864 B | No description available 
    36865  
    36866 
    36867 > matchmaker #850 to #1.50 & sel
    36868 
    36869 Parameters 
    36870 --- 
    36871 Chain pairing | bb 
    36872 Alignment algorithm | Needleman-Wunsch 
    36873 Similarity matrix | BLOSUM-62 
    36874 SS fraction | 0.3 
    36875 Gap open (HH/SS/other) | 18/18/6 
    36876 Gap extend | 1 
    36877 SS matrix |  |  | H | S | O 
    36878 ---|---|---|--- 
    36879 H | 6 | -9 | -6 
    36880 S |  | 6 | -6 
    36881 O |  |  | 4 
    36882 Iteration cutoff | 2 
    36883  
    36884 Matchmaker 3j0c.pdb1, chain H (#1.50) with AF3 E2 353-438.pdb, chain B (#850),
    36885 sequence alignment score = 329.4 
    36886 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    36887 8.151) 
    36888  
    36889 
    36890 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    36891 
    36892 Chain information for AF3 CA.pdb #851 
    36893 --- 
    36894 Chain | Description 
    36895 A | No description available 
    36896  
    36897 
    36898 > hide sel cartoons
    36899 
    36900 > select #1.50/I
    36901 
    36902 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    36903 
    36904 > show sel cartoons
    36905 
    36906 > matchmaker #851 to #1.50 & sel
    36907 
    36908 Parameters 
    36909 --- 
    36910 Chain pairing | bb 
    36911 Alignment algorithm | Needleman-Wunsch 
    36912 Similarity matrix | BLOSUM-62 
    36913 SS fraction | 0.3 
    36914 Gap open (HH/SS/other) | 18/18/6 
    36915 Gap extend | 1 
    36916 SS matrix |  |  | H | S | O 
    36917 ---|---|---|--- 
    36918 H | 6 | -9 | -6 
    36919 S |  | 6 | -6 
    36920 O |  |  | 4 
    36921 Iteration cutoff | 2 
    36922  
    36923 Matchmaker 3j0c.pdb1, chain I (#1.50) with AF3 CA.pdb, chain A (#851),
    36924 sequence alignment score = 306.5 
    36925 RMSD between 119 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    36926 2.689) 
    36927  
    36928 
    36929 > hide sel cartoons
    36930 
    36931 > color #847 dodgerblue
    36932 
    36933 > color #848 dodgerblue
    36934 
    36935 > color #849 #00b305ff
    36936 
    36937 > color #850 #00b305ff
    36938 
    36939 > color #851 #f15839ff
    36940 
    36941 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    36942 
    36943 > hide #802 models
    36944 
    36945 > hide #803 models
    36946 
    36947 > hide #804 models
    36948 
    36949 > hide #805 models
    36950 
    36951 > hide #806 models
    36952 
    36953 > hide #807 models
    36954 
    36955 > hide #808 models
    36956 
    36957 > hide #809 models
    36958 
    36959 > hide #810 models
    36960 
    36961 > hide #811 models
    36962 
    36963 > hide #812 models
    36964 
    36965 > hide #813 models
    36966 
    36967 > hide #814 models
    36968 
    36969 > hide #815 models
    36970 
    36971 > hide #816 models
    36972 
    36973 > hide #817 models
    36974 
    36975 > hide #818 models
    36976 
    36977 > hide #819 models
    36978 
    36979 > hide #820 models
    36980 
    36981 > hide #821 models
    36982 
    36983 > hide #822 models
    36984 
    36985 > hide #823 models
    36986 
    36987 > hide #824 models
    36988 
    36989 > hide #825 models
    36990 
    36991 > hide #826 models
    36992 
    36993 > hide #827 models
    36994 
    36995 > hide #828 models
    36996 
    36997 > hide #829 models
    36998 
    36999 > hide #830 models
    37000 
    37001 > hide #831 models
    37002 
    37003 > hide #832 models
    37004 
    37005 > hide #833 models
    37006 
    37007 > hide #834 models
    37008 
    37009 > hide #835 models
    37010 
    37011 > hide #836 models
    37012 
    37013 > hide #837 models
    37014 
    37015 > hide #838 models
    37016 
    37017 > hide #839 models
    37018 
    37019 > hide #840 models
    37020 
    37021 > hide #841 models
    37022 
    37023 > hide #842 models
    37024 
    37025 > hide #844 models
    37026 
    37027 > hide #843 models
    37028 
    37029 > hide #845 models
    37030 
    37031 > hide #846 models
    37032 
    37033 > hide #847 models
    37034 
    37035 > hide #848 models
    37036 
    37037 > hide #849 models
    37038 
    37039 > hide #850 models
    37040 
    37041 > hide #851 models
    37042 
    37043 > select #1.51/G
    37044 
    37045 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    37046 
    37047 > show sel cartoons
    37048 
    37049 [Repeated 1 time(s)]
    37050 
    37051 > view
    37052 
    37053 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    37054 
    37055 Chain information for AF3 E1 1-421.pdb #852 
    37056 --- 
    37057 Chain | Description 
    37058 A | No description available 
    37059  
    37060 
    37061 > matchmaker #852 to #1.50 & sel
    37062 
    37063 No 'to' model specified 
    37064 
    37065 > matchmaker #852 to #1.51 & sel
    37066 
    37067 Parameters 
    37068 --- 
    37069 Chain pairing | bb 
    37070 Alignment algorithm | Needleman-Wunsch 
    37071 Similarity matrix | BLOSUM-62 
    37072 SS fraction | 0.3 
    37073 Gap open (HH/SS/other) | 18/18/6 
    37074 Gap extend | 1 
    37075 SS matrix |  |  | H | S | O 
    37076 ---|---|---|--- 
    37077 H | 6 | -9 | -6 
    37078 S |  | 6 | -6 
    37079 O |  |  | 4 
    37080 Iteration cutoff | 2 
    37081  
    37082 Matchmaker 3j0c.pdb1, chain G (#1.51) with AF3 E1 1-421.pdb, chain A (#852),
    37083 sequence alignment score = 1060.7 
    37084 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    37085 2.985) 
    37086  
    37087 
    37088 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    37089 
    37090 Chain information for AF3 E1 422-461.pdb #853 
    37091 --- 
    37092 Chain | Description 
    37093 A | No description available 
    37094  
    37095 
    37096 > matchmaker #853 to #1.51 & sel
    37097 
    37098 Parameters 
    37099 --- 
    37100 Chain pairing | bb 
    37101 Alignment algorithm | Needleman-Wunsch 
    37102 Similarity matrix | BLOSUM-62 
    37103 SS fraction | 0.3 
    37104 Gap open (HH/SS/other) | 18/18/6 
    37105 Gap extend | 1 
    37106 SS matrix |  |  | H | S | O 
    37107 ---|---|---|--- 
    37108 H | 6 | -9 | -6 
    37109 S |  | 6 | -6 
    37110 O |  |  | 4 
    37111 Iteration cutoff | 2 
    37112  
    37113 Matchmaker 3j0c.pdb1, chain G (#1.51) with AF3 E1 422-461.pdb, chain A (#853),
    37114 sequence alignment score = 626.9 
    37115 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    37116 2.996) 
    37117  
    37118 
    37119 > hide sel cartoons
    37120 
    37121 > select #1.51/H
    37122 
    37123 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    37124 
    37125 > show sel cartoons
    37126 
    37127 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    37128 
    37129 Chain information for AF3 E2 1-352.pdb #854 
    37130 --- 
    37131 Chain | Description 
    37132 B | No description available 
    37133  
    37134 
    37135 > matchmaker #854 to #1.51 & sel
    37136 
    37137 Parameters 
    37138 --- 
    37139 Chain pairing | bb 
    37140 Alignment algorithm | Needleman-Wunsch 
    37141 Similarity matrix | BLOSUM-62 
    37142 SS fraction | 0.3 
    37143 Gap open (HH/SS/other) | 18/18/6 
    37144 Gap extend | 1 
    37145 SS matrix |  |  | H | S | O 
    37146 ---|---|---|--- 
    37147 H | 6 | -9 | -6 
    37148 S |  | 6 | -6 
    37149 O |  |  | 4 
    37150 Iteration cutoff | 2 
    37151  
    37152 Matchmaker 3j0c.pdb1, chain H (#1.51) with AF3 E2 1-352.pdb, chain B (#854),
    37153 sequence alignment score = 590.9 
    37154 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    37155 6.107) 
    37156  
    37157 
    37158 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    37159 
    37160 Chain information for AF3 E2 353-438.pdb #855 
    37161 --- 
    37162 Chain | Description 
    37163 B | No description available 
    37164  
    37165 
    37166 > matchmaker #855 to #1.51 & sel
    37167 
    37168 Parameters 
    37169 --- 
    37170 Chain pairing | bb 
    37171 Alignment algorithm | Needleman-Wunsch 
    37172 Similarity matrix | BLOSUM-62 
    37173 SS fraction | 0.3 
    37174 Gap open (HH/SS/other) | 18/18/6 
    37175 Gap extend | 1 
    37176 SS matrix |  |  | H | S | O 
    37177 ---|---|---|--- 
    37178 H | 6 | -9 | -6 
    37179 S |  | 6 | -6 
    37180 O |  |  | 4 
    37181 Iteration cutoff | 2 
    37182  
    37183 Matchmaker 3j0c.pdb1, chain H (#1.51) with AF3 E2 353-438.pdb, chain B (#855),
    37184 sequence alignment score = 329.4 
    37185 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    37186 8.151) 
    37187  
    37188 
    37189 > hide sel cartoons
    37190 
    37191 > select #1.51/I
    37192 
    37193 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    37194 
    37195 > show sel cartoons
    37196 
    37197 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    37198 
    37199 Chain information for AF3 CA.pdb #856 
    37200 --- 
    37201 Chain | Description 
    37202 A | No description available 
    37203  
    37204 
    37205 > matchmaker #856 to #1.51 & sel
    37206 
    37207 Parameters 
    37208 --- 
    37209 Chain pairing | bb 
    37210 Alignment algorithm | Needleman-Wunsch 
    37211 Similarity matrix | BLOSUM-62 
    37212 SS fraction | 0.3 
    37213 Gap open (HH/SS/other) | 18/18/6 
    37214 Gap extend | 1 
    37215 SS matrix |  |  | H | S | O 
    37216 ---|---|---|--- 
    37217 H | 6 | -9 | -6 
    37218 S |  | 6 | -6 
    37219 O |  |  | 4 
    37220 Iteration cutoff | 2 
    37221  
    37222 Matchmaker 3j0c.pdb1, chain I (#1.51) with AF3 CA.pdb, chain A (#856),
    37223 sequence alignment score = 306.5 
    37224 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    37225 2.689) 
    37226  
    37227 
    37228 > hide sel cartoons
    37229 
    37230 > color #852 dodgerblue
    37231 
    37232 > color #853 dodgerblue
    37233 
    37234 > color #854 #00b305ff
    37235 
    37236 > color #855 #00b305ff
    37237 
    37238 > color #856 #f15839ff
    37239 
    37240 > select #1.52/G
    37241 
    37242 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    37243 
    37244 > show sel cartoons
    37245 
    37246 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    37247 
    37248 Chain information for AF3 E1 1-421.pdb #857 
    37249 --- 
    37250 Chain | Description 
    37251 A | No description available 
    37252  
    37253 
    37254 > matchmaker #857 to #1.52 & sel
    37255 
    37256 Parameters 
    37257 --- 
    37258 Chain pairing | bb 
    37259 Alignment algorithm | Needleman-Wunsch 
    37260 Similarity matrix | BLOSUM-62 
    37261 SS fraction | 0.3 
    37262 Gap open (HH/SS/other) | 18/18/6 
    37263 Gap extend | 1 
    37264 SS matrix |  |  | H | S | O 
    37265 ---|---|---|--- 
    37266 H | 6 | -9 | -6 
    37267 S |  | 6 | -6 
    37268 O |  |  | 4 
    37269 Iteration cutoff | 2 
    37270  
    37271 Matchmaker 3j0c.pdb1, chain G (#1.52) with AF3 E1 1-421.pdb, chain A (#857),
    37272 sequence alignment score = 1060.7 
    37273 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    37274 2.985) 
    37275  
    37276 
    37277 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    37278 
    37279 Chain information for AF3 E1 422-461.pdb #858 
    37280 --- 
    37281 Chain | Description 
    37282 A | No description available 
    37283  
    37284 
    37285 > matchmaker #858 to #1.52 & sel
    37286 
    37287 Parameters 
    37288 --- 
    37289 Chain pairing | bb 
    37290 Alignment algorithm | Needleman-Wunsch 
    37291 Similarity matrix | BLOSUM-62 
    37292 SS fraction | 0.3 
    37293 Gap open (HH/SS/other) | 18/18/6 
    37294 Gap extend | 1 
    37295 SS matrix |  |  | H | S | O 
    37296 ---|---|---|--- 
    37297 H | 6 | -9 | -6 
    37298 S |  | 6 | -6 
    37299 O |  |  | 4 
    37300 Iteration cutoff | 2 
    37301  
    37302 Matchmaker 3j0c.pdb1, chain G (#1.52) with AF3 E1 422-461.pdb, chain A (#858),
    37303 sequence alignment score = 626.9 
    37304 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    37305 2.997) 
    37306  
    37307 
    37308 > hide sel cartoons
    37309 
    37310 > select #1.52/H
    37311 
    37312 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    37313 
    37314 > show sel cartoons
    37315 
    37316 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    37317 
    37318 Chain information for AF3 E2 1-352.pdb #859 
    37319 --- 
    37320 Chain | Description 
    37321 B | No description available 
    37322  
    37323 
    37324 > matchmaker #859 to #1.52 & sel
    37325 
    37326 Parameters 
    37327 --- 
    37328 Chain pairing | bb 
    37329 Alignment algorithm | Needleman-Wunsch 
    37330 Similarity matrix | BLOSUM-62 
    37331 SS fraction | 0.3 
    37332 Gap open (HH/SS/other) | 18/18/6 
    37333 Gap extend | 1 
    37334 SS matrix |  |  | H | S | O 
    37335 ---|---|---|--- 
    37336 H | 6 | -9 | -6 
    37337 S |  | 6 | -6 
    37338 O |  |  | 4 
    37339 Iteration cutoff | 2 
    37340  
    37341 Matchmaker 3j0c.pdb1, chain H (#1.52) with AF3 E2 1-352.pdb, chain B (#859),
    37342 sequence alignment score = 590.9 
    37343 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    37344 6.107) 
    37345  
    37346 
    37347 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    37348 
    37349 Chain information for AF3 E2 353-438.pdb #860 
    37350 --- 
    37351 Chain | Description 
    37352 B | No description available 
    37353  
    37354 
    37355 > matchmaker #860 to #1.52 & sel
    37356 
    37357 Parameters 
    37358 --- 
    37359 Chain pairing | bb 
    37360 Alignment algorithm | Needleman-Wunsch 
    37361 Similarity matrix | BLOSUM-62 
    37362 SS fraction | 0.3 
    37363 Gap open (HH/SS/other) | 18/18/6 
    37364 Gap extend | 1 
    37365 SS matrix |  |  | H | S | O 
    37366 ---|---|---|--- 
    37367 H | 6 | -9 | -6 
    37368 S |  | 6 | -6 
    37369 O |  |  | 4 
    37370 Iteration cutoff | 2 
    37371  
    37372 Matchmaker 3j0c.pdb1, chain H (#1.52) with AF3 E2 353-438.pdb, chain B (#860),
    37373 sequence alignment score = 329.4 
    37374 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    37375 8.150) 
    37376  
    37377 
    37378 > hide sel cartoons
    37379 
    37380 > select #1.52/I
    37381 
    37382 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    37383 
    37384 > show sel cartoons
    37385 
    37386 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    37387 
    37388 Chain information for AF3 CA.pdb #861 
    37389 --- 
    37390 Chain | Description 
    37391 A | No description available 
    37392  
    37393 
    37394 > matchmaker #861 to #1.52 & sel
    37395 
    37396 Parameters 
    37397 --- 
    37398 Chain pairing | bb 
    37399 Alignment algorithm | Needleman-Wunsch 
    37400 Similarity matrix | BLOSUM-62 
    37401 SS fraction | 0.3 
    37402 Gap open (HH/SS/other) | 18/18/6 
    37403 Gap extend | 1 
    37404 SS matrix |  |  | H | S | O 
    37405 ---|---|---|--- 
    37406 H | 6 | -9 | -6 
    37407 S |  | 6 | -6 
    37408 O |  |  | 4 
    37409 Iteration cutoff | 2 
    37410  
    37411 Matchmaker 3j0c.pdb1, chain I (#1.52) with AF3 CA.pdb, chain A (#861),
    37412 sequence alignment score = 306.5 
    37413 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    37414 2.689) 
    37415  
    37416 
    37417 > hide sel cartoons
    37418 
    37419 > color #857 dodgerblue
    37420 
    37421 > color #858 dodgerblue
    37422 
    37423 > color #859 #00b305ff
    37424 
    37425 > color #860 #00b305ff
    37426 
    37427 > color #861 #f15839ff
    37428 
    37429 > select #1.53/G
    37430 
    37431 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    37432 
    37433 > show sel cartoons
    37434 
    37435 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    37436 
    37437 Chain information for AF3 E1 1-421.pdb #862 
    37438 --- 
    37439 Chain | Description 
    37440 A | No description available 
    37441  
    37442 
    37443 > matchmaker #862 to #1.53 & sel
    37444 
    37445 Parameters 
    37446 --- 
    37447 Chain pairing | bb 
    37448 Alignment algorithm | Needleman-Wunsch 
    37449 Similarity matrix | BLOSUM-62 
    37450 SS fraction | 0.3 
    37451 Gap open (HH/SS/other) | 18/18/6 
    37452 Gap extend | 1 
    37453 SS matrix |  |  | H | S | O 
    37454 ---|---|---|--- 
    37455 H | 6 | -9 | -6 
    37456 S |  | 6 | -6 
    37457 O |  |  | 4 
    37458 Iteration cutoff | 2 
    37459  
    37460 Matchmaker 3j0c.pdb1, chain G (#1.53) with AF3 E1 1-421.pdb, chain A (#862),
    37461 sequence alignment score = 1060.7 
    37462 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    37463 2.985) 
    37464  
    37465 
    37466 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    37467 
    37468 Chain information for AF3 E1 422-461.pdb #863 
    37469 --- 
    37470 Chain | Description 
    37471 A | No description available 
    37472  
    37473 
    37474 > matchmaker #863 to #1.53 & sel
    37475 
    37476 Parameters 
    37477 --- 
    37478 Chain pairing | bb 
    37479 Alignment algorithm | Needleman-Wunsch 
    37480 Similarity matrix | BLOSUM-62 
    37481 SS fraction | 0.3 
    37482 Gap open (HH/SS/other) | 18/18/6 
    37483 Gap extend | 1 
    37484 SS matrix |  |  | H | S | O 
    37485 ---|---|---|--- 
    37486 H | 6 | -9 | -6 
    37487 S |  | 6 | -6 
    37488 O |  |  | 4 
    37489 Iteration cutoff | 2 
    37490  
    37491 Matchmaker 3j0c.pdb1, chain G (#1.53) with AF3 E1 422-461.pdb, chain A (#863),
    37492 sequence alignment score = 626.9 
    37493 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    37494 2.997) 
    37495  
    37496 
    37497 > hide sel cartoons
    37498 
    37499 > select #1.53/H
    37500 
    37501 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    37502 
    37503 > show sel cartoons
    37504 
    37505 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    37506 
    37507 Chain information for AF3 E2 1-352.pdb #864 
    37508 --- 
    37509 Chain | Description 
    37510 B | No description available 
    37511  
    37512 
    37513 > matchmaker #864 to #1.53 & sel
    37514 
    37515 Parameters 
    37516 --- 
    37517 Chain pairing | bb 
    37518 Alignment algorithm | Needleman-Wunsch 
    37519 Similarity matrix | BLOSUM-62 
    37520 SS fraction | 0.3 
    37521 Gap open (HH/SS/other) | 18/18/6 
    37522 Gap extend | 1 
    37523 SS matrix |  |  | H | S | O 
    37524 ---|---|---|--- 
    37525 H | 6 | -9 | -6 
    37526 S |  | 6 | -6 
    37527 O |  |  | 4 
    37528 Iteration cutoff | 2 
    37529  
    37530 Matchmaker 3j0c.pdb1, chain H (#1.53) with AF3 E2 1-352.pdb, chain B (#864),
    37531 sequence alignment score = 590.9 
    37532 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    37533 6.107) 
    37534  
    37535 
    37536 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    37537 
    37538 Chain information for AF3 E2 353-438.pdb #865 
    37539 --- 
    37540 Chain | Description 
    37541 B | No description available 
    37542  
    37543 
    37544 > matchmaker #865 to #1.53 & sel
    37545 
    37546 Parameters 
    37547 --- 
    37548 Chain pairing | bb 
    37549 Alignment algorithm | Needleman-Wunsch 
    37550 Similarity matrix | BLOSUM-62 
    37551 SS fraction | 0.3 
    37552 Gap open (HH/SS/other) | 18/18/6 
    37553 Gap extend | 1 
    37554 SS matrix |  |  | H | S | O 
    37555 ---|---|---|--- 
    37556 H | 6 | -9 | -6 
    37557 S |  | 6 | -6 
    37558 O |  |  | 4 
    37559 Iteration cutoff | 2 
    37560  
    37561 Matchmaker 3j0c.pdb1, chain H (#1.53) with AF3 E2 353-438.pdb, chain B (#865),
    37562 sequence alignment score = 329.4 
    37563 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    37564 8.150) 
    37565  
    37566 
    37567 > hide sel cartoons
    37568 
    37569 > select #1.53/I
    37570 
    37571 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    37572 
    37573 > show sel cartoons
    37574 
    37575 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    37576 
    37577 Chain information for AF3 CA.pdb #866 
    37578 --- 
    37579 Chain | Description 
    37580 A | No description available 
    37581  
    37582 
    37583 > matchmaker #866 to #1.53 & sel
    37584 
    37585 Parameters 
    37586 --- 
    37587 Chain pairing | bb 
    37588 Alignment algorithm | Needleman-Wunsch 
    37589 Similarity matrix | BLOSUM-62 
    37590 SS fraction | 0.3 
    37591 Gap open (HH/SS/other) | 18/18/6 
    37592 Gap extend | 1 
    37593 SS matrix |  |  | H | S | O 
    37594 ---|---|---|--- 
    37595 H | 6 | -9 | -6 
    37596 S |  | 6 | -6 
    37597 O |  |  | 4 
    37598 Iteration cutoff | 2 
    37599  
    37600 Matchmaker 3j0c.pdb1, chain I (#1.53) with AF3 CA.pdb, chain A (#866),
    37601 sequence alignment score = 306.5 
    37602 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    37603 2.689) 
    37604  
    37605 
    37606 > hide sel cartoons
    37607 
    37608 > color #862 dodgerblue
    37609 
    37610 > color #863 dodgerblue
    37611 
    37612 > color #864 #00b305ff
    37613 
    37614 > color #865 #00b305ff
    37615 
    37616 > color #866 #f15839ff
    37617 
    37618 > select #1.54/G
    37619 
    37620 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    37621 
    37622 > show sel cartoons
    37623 
    37624 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    37625 
    37626 Chain information for AF3 E1 1-421.pdb #867 
    37627 --- 
    37628 Chain | Description 
    37629 A | No description available 
    37630  
    37631 
    37632 > matchmaker #867 to #1.54 & sel
    37633 
    37634 Parameters 
    37635 --- 
    37636 Chain pairing | bb 
    37637 Alignment algorithm | Needleman-Wunsch 
    37638 Similarity matrix | BLOSUM-62 
    37639 SS fraction | 0.3 
    37640 Gap open (HH/SS/other) | 18/18/6 
    37641 Gap extend | 1 
    37642 SS matrix |  |  | H | S | O 
    37643 ---|---|---|--- 
    37644 H | 6 | -9 | -6 
    37645 S |  | 6 | -6 
    37646 O |  |  | 4 
    37647 Iteration cutoff | 2 
    37648  
    37649 Matchmaker 3j0c.pdb1, chain G (#1.54) with AF3 E1 1-421.pdb, chain A (#867),
    37650 sequence alignment score = 1060.7 
    37651 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    37652 2.985) 
    37653  
    37654 
    37655 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    37656 
    37657 Chain information for AF3 E1 422-461.pdb #868 
    37658 --- 
    37659 Chain | Description 
    37660 A | No description available 
    37661  
    37662 
    37663 > matchmaker #868 to #1.54 & sel
    37664 
    37665 Parameters 
    37666 --- 
    37667 Chain pairing | bb 
    37668 Alignment algorithm | Needleman-Wunsch 
    37669 Similarity matrix | BLOSUM-62 
    37670 SS fraction | 0.3 
    37671 Gap open (HH/SS/other) | 18/18/6 
    37672 Gap extend | 1 
    37673 SS matrix |  |  | H | S | O 
    37674 ---|---|---|--- 
    37675 H | 6 | -9 | -6 
    37676 S |  | 6 | -6 
    37677 O |  |  | 4 
    37678 Iteration cutoff | 2 
    37679  
    37680 Matchmaker 3j0c.pdb1, chain G (#1.54) with AF3 E1 422-461.pdb, chain A (#868),
    37681 sequence alignment score = 626.9 
    37682 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    37683 2.997) 
    37684  
    37685 
    37686 > hide sel cartoons
    37687 
    37688 > select #1.54/H
    37689 
    37690 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    37691 
    37692 > show sel cartoons
    37693 
    37694 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    37695 
    37696 Chain information for AF3 E2 1-352.pdb #869 
    37697 --- 
    37698 Chain | Description 
    37699 B | No description available 
    37700  
    37701 
    37702 > matchmaker #869 to #1.54 & sel
    37703 
    37704 Parameters 
    37705 --- 
    37706 Chain pairing | bb 
    37707 Alignment algorithm | Needleman-Wunsch 
    37708 Similarity matrix | BLOSUM-62 
    37709 SS fraction | 0.3 
    37710 Gap open (HH/SS/other) | 18/18/6 
    37711 Gap extend | 1 
    37712 SS matrix |  |  | H | S | O 
    37713 ---|---|---|--- 
    37714 H | 6 | -9 | -6 
    37715 S |  | 6 | -6 
    37716 O |  |  | 4 
    37717 Iteration cutoff | 2 
    37718  
    37719 Matchmaker 3j0c.pdb1, chain H (#1.54) with AF3 E2 1-352.pdb, chain B (#869),
    37720 sequence alignment score = 590.9 
    37721 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    37722 6.107) 
    37723  
    37724 
    37725 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    37726 
    37727 Chain information for AF3 E2 353-438.pdb #870 
    37728 --- 
    37729 Chain | Description 
    37730 B | No description available 
    37731  
    37732 
    37733 > matchmaker #870 to #1.54 & sel
    37734 
    37735 Parameters 
    37736 --- 
    37737 Chain pairing | bb 
    37738 Alignment algorithm | Needleman-Wunsch 
    37739 Similarity matrix | BLOSUM-62 
    37740 SS fraction | 0.3 
    37741 Gap open (HH/SS/other) | 18/18/6 
    37742 Gap extend | 1 
    37743 SS matrix |  |  | H | S | O 
    37744 ---|---|---|--- 
    37745 H | 6 | -9 | -6 
    37746 S |  | 6 | -6 
    37747 O |  |  | 4 
    37748 Iteration cutoff | 2 
    37749  
    37750 Matchmaker 3j0c.pdb1, chain H (#1.54) with AF3 E2 353-438.pdb, chain B (#870),
    37751 sequence alignment score = 329.4 
    37752 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    37753 8.150) 
    37754  
    37755 
    37756 > hide sel cartoons
    37757 
    37758 > select #1.54/I
    37759 
    37760 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    37761 
    37762 > show sel cartoons
    37763 
    37764 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    37765 
    37766 Chain information for AF3 CA.pdb #871 
    37767 --- 
    37768 Chain | Description 
    37769 A | No description available 
    37770  
    37771 
    37772 > matchmaker #871 to #1.54 & sel
    37773 
    37774 Parameters 
    37775 --- 
    37776 Chain pairing | bb 
    37777 Alignment algorithm | Needleman-Wunsch 
    37778 Similarity matrix | BLOSUM-62 
    37779 SS fraction | 0.3 
    37780 Gap open (HH/SS/other) | 18/18/6 
    37781 Gap extend | 1 
    37782 SS matrix |  |  | H | S | O 
    37783 ---|---|---|--- 
    37784 H | 6 | -9 | -6 
    37785 S |  | 6 | -6 
    37786 O |  |  | 4 
    37787 Iteration cutoff | 2 
    37788  
    37789 Matchmaker 3j0c.pdb1, chain I (#1.54) with AF3 CA.pdb, chain A (#871),
    37790 sequence alignment score = 306.5 
    37791 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    37792 2.689) 
    37793  
    37794 
    37795 > hide sel cartoons
    37796 
    37797 > color #867 dodgerblue
    37798 
    37799 > color #868 dodgerblue
    37800 
    37801 > color #869 #00b305ff
    37802 
    37803 > color #870 #00b305ff
    37804 
    37805 > color #871 #f15839ff
    37806 
    37807 > select #1.55/G
    37808 
    37809 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    37810 
    37811 > show sel cartoons
    37812 
    37813 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    37814 
    37815 Chain information for AF3 E1 1-421.pdb #872 
    37816 --- 
    37817 Chain | Description 
    37818 A | No description available 
    37819  
    37820 
    37821 > matchmaker #872 to #1.55 & sel
    37822 
    37823 Parameters 
    37824 --- 
    37825 Chain pairing | bb 
    37826 Alignment algorithm | Needleman-Wunsch 
    37827 Similarity matrix | BLOSUM-62 
    37828 SS fraction | 0.3 
    37829 Gap open (HH/SS/other) | 18/18/6 
    37830 Gap extend | 1 
    37831 SS matrix |  |  | H | S | O 
    37832 ---|---|---|--- 
    37833 H | 6 | -9 | -6 
    37834 S |  | 6 | -6 
    37835 O |  |  | 4 
    37836 Iteration cutoff | 2 
    37837  
    37838 Matchmaker 3j0c.pdb1, chain G (#1.55) with AF3 E1 1-421.pdb, chain A (#872),
    37839 sequence alignment score = 1060.7 
    37840 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    37841 2.985) 
    37842  
    37843 
    37844 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    37845 
    37846 Chain information for AF3 E1 422-461.pdb #873 
    37847 --- 
    37848 Chain | Description 
    37849 A | No description available 
    37850  
    37851 
    37852 > matchmaker #873 to #1.55 & sel
    37853 
    37854 Parameters 
    37855 --- 
    37856 Chain pairing | bb 
    37857 Alignment algorithm | Needleman-Wunsch 
    37858 Similarity matrix | BLOSUM-62 
    37859 SS fraction | 0.3 
    37860 Gap open (HH/SS/other) | 18/18/6 
    37861 Gap extend | 1 
    37862 SS matrix |  |  | H | S | O 
    37863 ---|---|---|--- 
    37864 H | 6 | -9 | -6 
    37865 S |  | 6 | -6 
    37866 O |  |  | 4 
    37867 Iteration cutoff | 2 
    37868  
    37869 Matchmaker 3j0c.pdb1, chain G (#1.55) with AF3 E1 422-461.pdb, chain A (#873),
    37870 sequence alignment score = 626.9 
    37871 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    37872 2.997) 
    37873  
    37874 
    37875 > hide sel cartoons
    37876 
    37877 [Repeated 1 time(s)]
    37878 
    37879 > select #1.55/H
    37880 
    37881 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    37882 
    37883 > show sel cartoons
    37884 
    37885 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    37886 
    37887 Chain information for AF3 E2 1-352.pdb #874 
    37888 --- 
    37889 Chain | Description 
    37890 B | No description available 
    37891  
    37892 
    37893 > matchmaker #874 to #1.55 & sel
    37894 
    37895 Parameters 
    37896 --- 
    37897 Chain pairing | bb 
    37898 Alignment algorithm | Needleman-Wunsch 
    37899 Similarity matrix | BLOSUM-62 
    37900 SS fraction | 0.3 
    37901 Gap open (HH/SS/other) | 18/18/6 
    37902 Gap extend | 1 
    37903 SS matrix |  |  | H | S | O 
    37904 ---|---|---|--- 
    37905 H | 6 | -9 | -6 
    37906 S |  | 6 | -6 
    37907 O |  |  | 4 
    37908 Iteration cutoff | 2 
    37909  
    37910 Matchmaker 3j0c.pdb1, chain H (#1.55) with AF3 E2 1-352.pdb, chain B (#874),
    37911 sequence alignment score = 590.9 
    37912 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    37913 6.107) 
    37914  
    37915 
    37916 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    37917 
    37918 Chain information for AF3 E2 353-438.pdb #875 
    37919 --- 
    37920 Chain | Description 
    37921 B | No description available 
    37922  
    37923 
    37924 > matchmaker #875 to #1.55 & sel
    37925 
    37926 Parameters 
    37927 --- 
    37928 Chain pairing | bb 
    37929 Alignment algorithm | Needleman-Wunsch 
    37930 Similarity matrix | BLOSUM-62 
    37931 SS fraction | 0.3 
    37932 Gap open (HH/SS/other) | 18/18/6 
    37933 Gap extend | 1 
    37934 SS matrix |  |  | H | S | O 
    37935 ---|---|---|--- 
    37936 H | 6 | -9 | -6 
    37937 S |  | 6 | -6 
    37938 O |  |  | 4 
    37939 Iteration cutoff | 2 
    37940  
    37941 Matchmaker 3j0c.pdb1, chain H (#1.55) with AF3 E2 353-438.pdb, chain B (#875),
    37942 sequence alignment score = 329.4 
    37943 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    37944 8.150) 
    37945  
    37946 
    37947 > hide sel cartoons
    37948 
    37949 > select #1.55/I
    37950 
    37951 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    37952 
    37953 > show sel cartoons
    37954 
    37955 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    37956 
    37957 Chain information for AF3 CA.pdb #876 
    37958 --- 
    37959 Chain | Description 
    37960 A | No description available 
    37961  
    37962 
    37963 > matchmaker #876 to #1.55 & sel
    37964 
    37965 Parameters 
    37966 --- 
    37967 Chain pairing | bb 
    37968 Alignment algorithm | Needleman-Wunsch 
    37969 Similarity matrix | BLOSUM-62 
    37970 SS fraction | 0.3 
    37971 Gap open (HH/SS/other) | 18/18/6 
    37972 Gap extend | 1 
    37973 SS matrix |  |  | H | S | O 
    37974 ---|---|---|--- 
    37975 H | 6 | -9 | -6 
    37976 S |  | 6 | -6 
    37977 O |  |  | 4 
    37978 Iteration cutoff | 2 
    37979  
    37980 Matchmaker 3j0c.pdb1, chain I (#1.55) with AF3 CA.pdb, chain A (#876),
    37981 sequence alignment score = 306.5 
    37982 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    37983 2.689) 
    37984  
    37985 
    37986 > hide sel cartoons
    37987 
    37988 > color #872 dodgerblue
    37989 
    37990 > color #873 dodgerblue
    37991 
    37992 > color #874 #00b305ff
    37993 
    37994 > color #875 #00b305ff
    37995 
    37996 > color #876 #f15839ff
    37997 
    37998 > select #1.56/G
    37999 
    38000 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    38001 
    38002 > show sel cartoons
    38003 
    38004 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    38005 
    38006 Chain information for AF3 E1 1-421.pdb #877 
    38007 --- 
    38008 Chain | Description 
    38009 A | No description available 
    38010  
    38011 
    38012 > matchmaker #877 to #1.56 & sel
    38013 
    38014 Parameters 
    38015 --- 
    38016 Chain pairing | bb 
    38017 Alignment algorithm | Needleman-Wunsch 
    38018 Similarity matrix | BLOSUM-62 
    38019 SS fraction | 0.3 
    38020 Gap open (HH/SS/other) | 18/18/6 
    38021 Gap extend | 1 
    38022 SS matrix |  |  | H | S | O 
    38023 ---|---|---|--- 
    38024 H | 6 | -9 | -6 
    38025 S |  | 6 | -6 
    38026 O |  |  | 4 
    38027 Iteration cutoff | 2 
    38028  
    38029 Matchmaker 3j0c.pdb1, chain G (#1.56) with AF3 E1 1-421.pdb, chain A (#877),
    38030 sequence alignment score = 1060.7 
    38031 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    38032 2.985) 
    38033  
    38034 
    38035 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    38036 
    38037 Chain information for AF3 E1 422-461.pdb #878 
    38038 --- 
    38039 Chain | Description 
    38040 A | No description available 
    38041  
    38042 
    38043 > matchmaker #878 to #1.56 & sel
    38044 
    38045 Parameters 
    38046 --- 
    38047 Chain pairing | bb 
    38048 Alignment algorithm | Needleman-Wunsch 
    38049 Similarity matrix | BLOSUM-62 
    38050 SS fraction | 0.3 
    38051 Gap open (HH/SS/other) | 18/18/6 
    38052 Gap extend | 1 
    38053 SS matrix |  |  | H | S | O 
    38054 ---|---|---|--- 
    38055 H | 6 | -9 | -6 
    38056 S |  | 6 | -6 
    38057 O |  |  | 4 
    38058 Iteration cutoff | 2 
    38059  
    38060 Matchmaker 3j0c.pdb1, chain G (#1.56) with AF3 E1 422-461.pdb, chain A (#878),
    38061 sequence alignment score = 626.9 
    38062 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    38063 2.997) 
    38064  
    38065 
    38066 > hide sel cartoons
    38067 
    38068 [Repeated 1 time(s)]
    38069 
    38070 > select #1.56/H
    38071 
    38072 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    38073 
    38074 > show sel cartoons
    38075 
    38076 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    38077 
    38078 Chain information for AF3 E2 1-352.pdb #879 
    38079 --- 
    38080 Chain | Description 
    38081 B | No description available 
    38082  
    38083 
    38084 > matchmaker #879 to #1.56 & sel
    38085 
    38086 Parameters 
    38087 --- 
    38088 Chain pairing | bb 
    38089 Alignment algorithm | Needleman-Wunsch 
    38090 Similarity matrix | BLOSUM-62 
    38091 SS fraction | 0.3 
    38092 Gap open (HH/SS/other) | 18/18/6 
    38093 Gap extend | 1 
    38094 SS matrix |  |  | H | S | O 
    38095 ---|---|---|--- 
    38096 H | 6 | -9 | -6 
    38097 S |  | 6 | -6 
    38098 O |  |  | 4 
    38099 Iteration cutoff | 2 
    38100  
    38101 Matchmaker 3j0c.pdb1, chain H (#1.56) with AF3 E2 1-352.pdb, chain B (#879),
    38102 sequence alignment score = 590.9 
    38103 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    38104 6.107) 
    38105  
    38106 
    38107 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    38108 
    38109 Chain information for AF3 E2 353-438.pdb #880 
    38110 --- 
    38111 Chain | Description 
    38112 B | No description available 
    38113  
    38114 
    38115 > matchmaker #880 to #1.56 & sel
    38116 
    38117 Parameters 
    38118 --- 
    38119 Chain pairing | bb 
    38120 Alignment algorithm | Needleman-Wunsch 
    38121 Similarity matrix | BLOSUM-62 
    38122 SS fraction | 0.3 
    38123 Gap open (HH/SS/other) | 18/18/6 
    38124 Gap extend | 1 
    38125 SS matrix |  |  | H | S | O 
    38126 ---|---|---|--- 
    38127 H | 6 | -9 | -6 
    38128 S |  | 6 | -6 
    38129 O |  |  | 4 
    38130 Iteration cutoff | 2 
    38131  
    38132 Matchmaker 3j0c.pdb1, chain H (#1.56) with AF3 E2 353-438.pdb, chain B (#880),
    38133 sequence alignment score = 329.4 
    38134 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    38135 8.150) 
    38136  
    38137 
    38138 > hide sel cartoons
    38139 
    38140 > select #1.56/I
    38141 
    38142 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    38143 
    38144 > show sel cartoons
    38145 
    38146 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    38147 
    38148 Chain information for AF3 CA.pdb #881 
    38149 --- 
    38150 Chain | Description 
    38151 A | No description available 
    38152  
    38153 
    38154 > matchmaker #881 to #1.56 & sel
    38155 
    38156 Parameters 
    38157 --- 
    38158 Chain pairing | bb 
    38159 Alignment algorithm | Needleman-Wunsch 
    38160 Similarity matrix | BLOSUM-62 
    38161 SS fraction | 0.3 
    38162 Gap open (HH/SS/other) | 18/18/6 
    38163 Gap extend | 1 
    38164 SS matrix |  |  | H | S | O 
    38165 ---|---|---|--- 
    38166 H | 6 | -9 | -6 
    38167 S |  | 6 | -6 
    38168 O |  |  | 4 
    38169 Iteration cutoff | 2 
    38170  
    38171 Matchmaker 3j0c.pdb1, chain I (#1.56) with AF3 CA.pdb, chain A (#881),
    38172 sequence alignment score = 306.5 
    38173 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    38174 2.689) 
    38175  
    38176 
    38177 > hide sel cartoons
    38178 
    38179 > color #877 dodgerblue
    38180 
    38181 > color #878 dodgerblue
    38182 
    38183 > color #879 #00b305ff
    38184 
    38185 > color #880 #00b305ff
    38186 
    38187 > color #881 #f15839ff
    38188 
    38189 > select #1.57/G
    38190 
    38191 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    38192 
    38193 > show sel cartoons
    38194 
    38195 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    38196 
    38197 Chain information for AF3 E1 1-421.pdb #882 
    38198 --- 
    38199 Chain | Description 
    38200 A | No description available 
    38201  
    38202 
    38203 > matchmaker #882 to #1.57 & sel
    38204 
    38205 Parameters 
    38206 --- 
    38207 Chain pairing | bb 
    38208 Alignment algorithm | Needleman-Wunsch 
    38209 Similarity matrix | BLOSUM-62 
    38210 SS fraction | 0.3 
    38211 Gap open (HH/SS/other) | 18/18/6 
    38212 Gap extend | 1 
    38213 SS matrix |  |  | H | S | O 
    38214 ---|---|---|--- 
    38215 H | 6 | -9 | -6 
    38216 S |  | 6 | -6 
    38217 O |  |  | 4 
    38218 Iteration cutoff | 2 
    38219  
    38220 Matchmaker 3j0c.pdb1, chain G (#1.57) with AF3 E1 1-421.pdb, chain A (#882),
    38221 sequence alignment score = 1060.7 
    38222 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    38223 2.985) 
    38224  
    38225 
    38226 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    38227 
    38228 Chain information for AF3 E1 422-461.pdb #883 
    38229 --- 
    38230 Chain | Description 
    38231 A | No description available 
    38232  
    38233 
    38234 > matchmaker #883 to #1.57 & sel
    38235 
    38236 Parameters 
    38237 --- 
    38238 Chain pairing | bb 
    38239 Alignment algorithm | Needleman-Wunsch 
    38240 Similarity matrix | BLOSUM-62 
    38241 SS fraction | 0.3 
    38242 Gap open (HH/SS/other) | 18/18/6 
    38243 Gap extend | 1 
    38244 SS matrix |  |  | H | S | O 
    38245 ---|---|---|--- 
    38246 H | 6 | -9 | -6 
    38247 S |  | 6 | -6 
    38248 O |  |  | 4 
    38249 Iteration cutoff | 2 
    38250  
    38251 Matchmaker 3j0c.pdb1, chain G (#1.57) with AF3 E1 422-461.pdb, chain A (#883),
    38252 sequence alignment score = 626.9 
    38253 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    38254 2.997) 
    38255  
    38256 
    38257 > hide sel cartoons
    38258 
    38259 > select #1.57/H
    38260 
    38261 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    38262 
    38263 > show sel cartoons
    38264 
    38265 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    38266 
    38267 Chain information for AF3 E2 1-352.pdb #884 
    38268 --- 
    38269 Chain | Description 
    38270 B | No description available 
    38271  
    38272 
    38273 > matchmaker #884 to #1.57 & sel
    38274 
    38275 Parameters 
    38276 --- 
    38277 Chain pairing | bb 
    38278 Alignment algorithm | Needleman-Wunsch 
    38279 Similarity matrix | BLOSUM-62 
    38280 SS fraction | 0.3 
    38281 Gap open (HH/SS/other) | 18/18/6 
    38282 Gap extend | 1 
    38283 SS matrix |  |  | H | S | O 
    38284 ---|---|---|--- 
    38285 H | 6 | -9 | -6 
    38286 S |  | 6 | -6 
    38287 O |  |  | 4 
    38288 Iteration cutoff | 2 
    38289  
    38290 Matchmaker 3j0c.pdb1, chain H (#1.57) with AF3 E2 1-352.pdb, chain B (#884),
    38291 sequence alignment score = 590.9 
    38292 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    38293 6.107) 
    38294  
    38295 
    38296 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    38297 
    38298 Chain information for AF3 E2 353-438.pdb #885 
    38299 --- 
    38300 Chain | Description 
    38301 B | No description available 
    38302  
    38303 
    38304 > matchmaker #885 to #1.57 & sel
    38305 
    38306 Parameters 
    38307 --- 
    38308 Chain pairing | bb 
    38309 Alignment algorithm | Needleman-Wunsch 
    38310 Similarity matrix | BLOSUM-62 
    38311 SS fraction | 0.3 
    38312 Gap open (HH/SS/other) | 18/18/6 
    38313 Gap extend | 1 
    38314 SS matrix |  |  | H | S | O 
    38315 ---|---|---|--- 
    38316 H | 6 | -9 | -6 
    38317 S |  | 6 | -6 
    38318 O |  |  | 4 
    38319 Iteration cutoff | 2 
    38320  
    38321 Matchmaker 3j0c.pdb1, chain H (#1.57) with AF3 E2 353-438.pdb, chain B (#885),
    38322 sequence alignment score = 329.4 
    38323 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    38324 8.150) 
    38325  
    38326 
    38327 > hide sel cartoons
    38328 
    38329 > select #1.57/I
    38330 
    38331 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    38332 
    38333 > show sel cartoons
    38334 
    38335 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    38336 
    38337 Chain information for AF3 CA.pdb #886 
    38338 --- 
    38339 Chain | Description 
    38340 A | No description available 
    38341  
    38342 
    38343 > matchmaker #886 to #1.57 & sel
    38344 
    38345 Parameters 
    38346 --- 
    38347 Chain pairing | bb 
    38348 Alignment algorithm | Needleman-Wunsch 
    38349 Similarity matrix | BLOSUM-62 
    38350 SS fraction | 0.3 
    38351 Gap open (HH/SS/other) | 18/18/6 
    38352 Gap extend | 1 
    38353 SS matrix |  |  | H | S | O 
    38354 ---|---|---|--- 
    38355 H | 6 | -9 | -6 
    38356 S |  | 6 | -6 
    38357 O |  |  | 4 
    38358 Iteration cutoff | 2 
    38359  
    38360 Matchmaker 3j0c.pdb1, chain I (#1.57) with AF3 CA.pdb, chain A (#886),
    38361 sequence alignment score = 306.5 
    38362 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    38363 2.689) 
    38364  
    38365 
    38366 > hide sel cartoons
    38367 
    38368 > color #882 dodgerblue
    38369 
    38370 > color #883 dodgerblue
    38371 
    38372 > color #884 #00b305ff
    38373 
    38374 > color #885 #00b305ff
    38375 
    38376 > color #886 #f15839ff
    38377 
    38378 > select #1.58/G
    38379 
    38380 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    38381 
    38382 > show sel cartoons
    38383 
    38384 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    38385 
    38386 Chain information for AF3 E1 1-421.pdb #887 
    38387 --- 
    38388 Chain | Description 
    38389 A | No description available 
    38390  
    38391 
    38392 > matchmaker #887 to #1.58 & sel
    38393 
    38394 Parameters 
    38395 --- 
    38396 Chain pairing | bb 
    38397 Alignment algorithm | Needleman-Wunsch 
    38398 Similarity matrix | BLOSUM-62 
    38399 SS fraction | 0.3 
    38400 Gap open (HH/SS/other) | 18/18/6 
    38401 Gap extend | 1 
    38402 SS matrix |  |  | H | S | O 
    38403 ---|---|---|--- 
    38404 H | 6 | -9 | -6 
    38405 S |  | 6 | -6 
    38406 O |  |  | 4 
    38407 Iteration cutoff | 2 
    38408  
    38409 Matchmaker 3j0c.pdb1, chain G (#1.58) with AF3 E1 1-421.pdb, chain A (#887),
    38410 sequence alignment score = 1060.7 
    38411 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    38412 2.985) 
    38413  
    38414 
    38415 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    38416 
    38417 Chain information for AF3 E1 422-461.pdb #888 
    38418 --- 
    38419 Chain | Description 
    38420 A | No description available 
    38421  
    38422 
    38423 > matchmaker #888 to #1.58 & sel
    38424 
    38425 Parameters 
    38426 --- 
    38427 Chain pairing | bb 
    38428 Alignment algorithm | Needleman-Wunsch 
    38429 Similarity matrix | BLOSUM-62 
    38430 SS fraction | 0.3 
    38431 Gap open (HH/SS/other) | 18/18/6 
    38432 Gap extend | 1 
    38433 SS matrix |  |  | H | S | O 
    38434 ---|---|---|--- 
    38435 H | 6 | -9 | -6 
    38436 S |  | 6 | -6 
    38437 O |  |  | 4 
    38438 Iteration cutoff | 2 
    38439  
    38440 Matchmaker 3j0c.pdb1, chain G (#1.58) with AF3 E1 422-461.pdb, chain A (#888),
    38441 sequence alignment score = 626.9 
    38442 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    38443 2.997) 
    38444  
    38445 
    38446 > hide sel cartoons
    38447 
    38448 > select #1.58/H
    38449 
    38450 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    38451 
    38452 > show sel cartoons
    38453 
    38454 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    38455 
    38456 Chain information for AF3 E2 1-352.pdb #889 
    38457 --- 
    38458 Chain | Description 
    38459 B | No description available 
    38460  
    38461 
    38462 > matchmaker #889 to #1.58 & sel
    38463 
    38464 Parameters 
    38465 --- 
    38466 Chain pairing | bb 
    38467 Alignment algorithm | Needleman-Wunsch 
    38468 Similarity matrix | BLOSUM-62 
    38469 SS fraction | 0.3 
    38470 Gap open (HH/SS/other) | 18/18/6 
    38471 Gap extend | 1 
    38472 SS matrix |  |  | H | S | O 
    38473 ---|---|---|--- 
    38474 H | 6 | -9 | -6 
    38475 S |  | 6 | -6 
    38476 O |  |  | 4 
    38477 Iteration cutoff | 2 
    38478  
    38479 Matchmaker 3j0c.pdb1, chain H (#1.58) with AF3 E2 1-352.pdb, chain B (#889),
    38480 sequence alignment score = 590.9 
    38481 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    38482 6.107) 
    38483  
    38484 
    38485 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    38486 
    38487 Chain information for AF3 E2 353-438.pdb #890 
    38488 --- 
    38489 Chain | Description 
    38490 B | No description available 
    38491  
    38492 
    38493 > matchmaker #890 to #1.58 & sel
    38494 
    38495 Parameters 
    38496 --- 
    38497 Chain pairing | bb 
    38498 Alignment algorithm | Needleman-Wunsch 
    38499 Similarity matrix | BLOSUM-62 
    38500 SS fraction | 0.3 
    38501 Gap open (HH/SS/other) | 18/18/6 
    38502 Gap extend | 1 
    38503 SS matrix |  |  | H | S | O 
    38504 ---|---|---|--- 
    38505 H | 6 | -9 | -6 
    38506 S |  | 6 | -6 
    38507 O |  |  | 4 
    38508 Iteration cutoff | 2 
    38509  
    38510 Matchmaker 3j0c.pdb1, chain H (#1.58) with AF3 E2 353-438.pdb, chain B (#890),
    38511 sequence alignment score = 329.4 
    38512 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    38513 8.150) 
    38514  
    38515 
    38516 > hide sel cartoons
    38517 
    38518 > select #1.58/I
    38519 
    38520 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    38521 
    38522 > show sel cartoons
    38523 
    38524 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    38525 
    38526 Chain information for AF3 CA.pdb #891 
    38527 --- 
    38528 Chain | Description 
    38529 A | No description available 
    38530  
    38531 
    38532 > matchmaker #891 to #1.58 & sel
    38533 
    38534 Parameters 
    38535 --- 
    38536 Chain pairing | bb 
    38537 Alignment algorithm | Needleman-Wunsch 
    38538 Similarity matrix | BLOSUM-62 
    38539 SS fraction | 0.3 
    38540 Gap open (HH/SS/other) | 18/18/6 
    38541 Gap extend | 1 
    38542 SS matrix |  |  | H | S | O 
    38543 ---|---|---|--- 
    38544 H | 6 | -9 | -6 
    38545 S |  | 6 | -6 
    38546 O |  |  | 4 
    38547 Iteration cutoff | 2 
    38548  
    38549 Matchmaker 3j0c.pdb1, chain I (#1.58) with AF3 CA.pdb, chain A (#891),
    38550 sequence alignment score = 306.5 
    38551 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    38552 2.689) 
    38553  
    38554 
    38555 > hide sel cartoons
    38556 
    38557 > color #887 dodgerblue
    38558 
    38559 > color #888 dodgerblue
    38560 
    38561 > color #889 #00b305ff
    38562 
    38563 > color #890 #00b305ff
    38564 
    38565 > color #891 #f15839ff
    38566 
    38567 > select #1.59/G
    38568 
    38569 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    38570 
    38571 > show sel cartoons
    38572 
    38573 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    38574 
    38575 Chain information for AF3 E1 1-421.pdb #892 
    38576 --- 
    38577 Chain | Description 
    38578 A | No description available 
    38579  
    38580 
    38581 > matchmaker #892 to #1.59 & sel
    38582 
    38583 Parameters 
    38584 --- 
    38585 Chain pairing | bb 
    38586 Alignment algorithm | Needleman-Wunsch 
    38587 Similarity matrix | BLOSUM-62 
    38588 SS fraction | 0.3 
    38589 Gap open (HH/SS/other) | 18/18/6 
    38590 Gap extend | 1 
    38591 SS matrix |  |  | H | S | O 
    38592 ---|---|---|--- 
    38593 H | 6 | -9 | -6 
    38594 S |  | 6 | -6 
    38595 O |  |  | 4 
    38596 Iteration cutoff | 2 
    38597  
    38598 Matchmaker 3j0c.pdb1, chain G (#1.59) with AF3 E1 1-421.pdb, chain A (#892),
    38599 sequence alignment score = 1060.7 
    38600 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    38601 2.985) 
    38602  
    38603 
    38604 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    38605 
    38606 Chain information for AF3 E1 422-461.pdb #893 
    38607 --- 
    38608 Chain | Description 
    38609 A | No description available 
    38610  
    38611 
    38612 > matchmaker #893 to #1.59 & sel
    38613 
    38614 Parameters 
    38615 --- 
    38616 Chain pairing | bb 
    38617 Alignment algorithm | Needleman-Wunsch 
    38618 Similarity matrix | BLOSUM-62 
    38619 SS fraction | 0.3 
    38620 Gap open (HH/SS/other) | 18/18/6 
    38621 Gap extend | 1 
    38622 SS matrix |  |  | H | S | O 
    38623 ---|---|---|--- 
    38624 H | 6 | -9 | -6 
    38625 S |  | 6 | -6 
    38626 O |  |  | 4 
    38627 Iteration cutoff | 2 
    38628  
    38629 Matchmaker 3j0c.pdb1, chain G (#1.59) with AF3 E1 422-461.pdb, chain A (#893),
    38630 sequence alignment score = 626.9 
    38631 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    38632 2.996) 
    38633  
    38634 
    38635 > hide sel cartoons
    38636 
    38637 > select #1.59/H
    38638 
    38639 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    38640 
    38641 > show sel cartoons
    38642 
    38643 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    38644 
    38645 Chain information for AF3 E2 1-352.pdb #894 
    38646 --- 
    38647 Chain | Description 
    38648 B | No description available 
    38649  
    38650 
    38651 > matchmaker #894 to #1.59 & sel
    38652 
    38653 Parameters 
    38654 --- 
    38655 Chain pairing | bb 
    38656 Alignment algorithm | Needleman-Wunsch 
    38657 Similarity matrix | BLOSUM-62 
    38658 SS fraction | 0.3 
    38659 Gap open (HH/SS/other) | 18/18/6 
    38660 Gap extend | 1 
    38661 SS matrix |  |  | H | S | O 
    38662 ---|---|---|--- 
    38663 H | 6 | -9 | -6 
    38664 S |  | 6 | -6 
    38665 O |  |  | 4 
    38666 Iteration cutoff | 2 
    38667  
    38668 Matchmaker 3j0c.pdb1, chain H (#1.59) with AF3 E2 1-352.pdb, chain B (#894),
    38669 sequence alignment score = 590.9 
    38670 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    38671 6.107) 
    38672  
    38673 
    38674 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    38675 
    38676 Chain information for AF3 E2 353-438.pdb #895 
    38677 --- 
    38678 Chain | Description 
    38679 B | No description available 
    38680  
    38681 
    38682 > matchmaker #895 to #1.59 & sel
    38683 
    38684 Parameters 
    38685 --- 
    38686 Chain pairing | bb 
    38687 Alignment algorithm | Needleman-Wunsch 
    38688 Similarity matrix | BLOSUM-62 
    38689 SS fraction | 0.3 
    38690 Gap open (HH/SS/other) | 18/18/6 
    38691 Gap extend | 1 
    38692 SS matrix |  |  | H | S | O 
    38693 ---|---|---|--- 
    38694 H | 6 | -9 | -6 
    38695 S |  | 6 | -6 
    38696 O |  |  | 4 
    38697 Iteration cutoff | 2 
    38698  
    38699 Matchmaker 3j0c.pdb1, chain H (#1.59) with AF3 E2 353-438.pdb, chain B (#895),
    38700 sequence alignment score = 329.4 
    38701 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    38702 8.151) 
    38703  
    38704 
    38705 > hide sel cartoons
    38706 
    38707 > select #1.59/I
    38708 
    38709 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    38710 
    38711 > show sel cartoons
    38712 
    38713 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    38714 
    38715 Chain information for AF3 CA.pdb #896 
    38716 --- 
    38717 Chain | Description 
    38718 A | No description available 
    38719  
    38720 
    38721 > matchmaker #896 to #1.59 & sel
    38722 
    38723 Parameters 
    38724 --- 
    38725 Chain pairing | bb 
    38726 Alignment algorithm | Needleman-Wunsch 
    38727 Similarity matrix | BLOSUM-62 
    38728 SS fraction | 0.3 
    38729 Gap open (HH/SS/other) | 18/18/6 
    38730 Gap extend | 1 
    38731 SS matrix |  |  | H | S | O 
    38732 ---|---|---|--- 
    38733 H | 6 | -9 | -6 
    38734 S |  | 6 | -6 
    38735 O |  |  | 4 
    38736 Iteration cutoff | 2 
    38737  
    38738 Matchmaker 3j0c.pdb1, chain I (#1.59) with AF3 CA.pdb, chain A (#896),
    38739 sequence alignment score = 306.5 
    38740 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    38741 2.689) 
    38742  
    38743 
    38744 > hide sel cartoons
    38745 
    38746 > color #892 dodgerblue
    38747 
    38748 > color #893 dodgerblue
    38749 
    38750 > color #894 #00b305ff
    38751 
    38752 > color #895 #00b305ff
    38753 
    38754 > color #896 #f15839ff
    38755 
    38756 > select #1.60/G
    38757 
    38758 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    38759 
    38760 > show sel cartoons
    38761 
    38762 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    38763 
    38764 Chain information for AF3 E1 1-421.pdb #897 
    38765 --- 
    38766 Chain | Description 
    38767 A | No description available 
    38768  
    38769 
    38770 > matchmaker #897 to #1.60 & sel
    38771 
    38772 Parameters 
    38773 --- 
    38774 Chain pairing | bb 
    38775 Alignment algorithm | Needleman-Wunsch 
    38776 Similarity matrix | BLOSUM-62 
    38777 SS fraction | 0.3 
    38778 Gap open (HH/SS/other) | 18/18/6 
    38779 Gap extend | 1 
    38780 SS matrix |  |  | H | S | O 
    38781 ---|---|---|--- 
    38782 H | 6 | -9 | -6 
    38783 S |  | 6 | -6 
    38784 O |  |  | 4 
    38785 Iteration cutoff | 2 
    38786  
    38787 Matchmaker 3j0c.pdb1, chain G (#1.60) with AF3 E1 1-421.pdb, chain A (#897),
    38788 sequence alignment score = 1060.7 
    38789 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    38790 2.985) 
    38791  
    38792 
    38793 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    38794 
    38795 Chain information for AF3 E1 422-461.pdb #898 
    38796 --- 
    38797 Chain | Description 
    38798 A | No description available 
    38799  
    38800 
    38801 > matchmaker #898 to #1.60 & sel
    38802 
    38803 Parameters 
    38804 --- 
    38805 Chain pairing | bb 
    38806 Alignment algorithm | Needleman-Wunsch 
    38807 Similarity matrix | BLOSUM-62 
    38808 SS fraction | 0.3 
    38809 Gap open (HH/SS/other) | 18/18/6 
    38810 Gap extend | 1 
    38811 SS matrix |  |  | H | S | O 
    38812 ---|---|---|--- 
    38813 H | 6 | -9 | -6 
    38814 S |  | 6 | -6 
    38815 O |  |  | 4 
    38816 Iteration cutoff | 2 
    38817  
    38818 Matchmaker 3j0c.pdb1, chain G (#1.60) with AF3 E1 422-461.pdb, chain A (#898),
    38819 sequence alignment score = 626.9 
    38820 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    38821 2.997) 
    38822  
    38823 
    38824 > hide sel cartoons
    38825 
    38826 > select #1.60/H
    38827 
    38828 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    38829 
    38830 > show sel cartoons
    38831 
    38832 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    38833 
    38834 Chain information for AF3 E2 1-352.pdb #899 
    38835 --- 
    38836 Chain | Description 
    38837 B | No description available 
    38838  
    38839 
    38840 > matchmaker #899 to #1.60 & sel
    38841 
    38842 Parameters 
    38843 --- 
    38844 Chain pairing | bb 
    38845 Alignment algorithm | Needleman-Wunsch 
    38846 Similarity matrix | BLOSUM-62 
    38847 SS fraction | 0.3 
    38848 Gap open (HH/SS/other) | 18/18/6 
    38849 Gap extend | 1 
    38850 SS matrix |  |  | H | S | O 
    38851 ---|---|---|--- 
    38852 H | 6 | -9 | -6 
    38853 S |  | 6 | -6 
    38854 O |  |  | 4 
    38855 Iteration cutoff | 2 
    38856  
    38857 Matchmaker 3j0c.pdb1, chain H (#1.60) with AF3 E2 1-352.pdb, chain B (#899),
    38858 sequence alignment score = 590.9 
    38859 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    38860 6.107) 
    38861  
    38862 
    38863 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    38864 
    38865 Chain information for AF3 E2 353-438.pdb #900 
    38866 --- 
    38867 Chain | Description 
    38868 B | No description available 
    38869  
    38870 
    38871 > matchmaker #900 to #1.60 & sel
    38872 
    38873 Parameters 
    38874 --- 
    38875 Chain pairing | bb 
    38876 Alignment algorithm | Needleman-Wunsch 
    38877 Similarity matrix | BLOSUM-62 
    38878 SS fraction | 0.3 
    38879 Gap open (HH/SS/other) | 18/18/6 
    38880 Gap extend | 1 
    38881 SS matrix |  |  | H | S | O 
    38882 ---|---|---|--- 
    38883 H | 6 | -9 | -6 
    38884 S |  | 6 | -6 
    38885 O |  |  | 4 
    38886 Iteration cutoff | 2 
    38887  
    38888 Matchmaker 3j0c.pdb1, chain H (#1.60) with AF3 E2 353-438.pdb, chain B (#900),
    38889 sequence alignment score = 329.4 
    38890 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    38891 8.150) 
    38892  
    38893 
    38894 > hide sel cartoons
    38895 
    38896 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    38897 
    38898 Chain information for AF3 CA.pdb #901 
    38899 --- 
    38900 Chain | Description 
    38901 A | No description available 
    38902  
    38903 
    38904 > select #1.60/I
    38905 
    38906 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    38907 
    38908 > show sel cartoons
    38909 
    38910 > matchmaker #901 to #1.60 & sel
    38911 
    38912 Parameters 
    38913 --- 
    38914 Chain pairing | bb 
    38915 Alignment algorithm | Needleman-Wunsch 
    38916 Similarity matrix | BLOSUM-62 
    38917 SS fraction | 0.3 
    38918 Gap open (HH/SS/other) | 18/18/6 
    38919 Gap extend | 1 
    38920 SS matrix |  |  | H | S | O 
    38921 ---|---|---|--- 
    38922 H | 6 | -9 | -6 
    38923 S |  | 6 | -6 
    38924 O |  |  | 4 
    38925 Iteration cutoff | 2 
    38926  
    38927 Matchmaker 3j0c.pdb1, chain I (#1.60) with AF3 CA.pdb, chain A (#901),
    38928 sequence alignment score = 306.5 
    38929 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    38930 2.689) 
    38931  
    38932 
    38933 > hide sel cartoons
    38934 
    38935 > color #897 dodgerblue
    38936 
    38937 > color #898 dodgerblue
    38938 
    38939 > color #899 #00b305ff
    38940 
    38941 > color #901 #f15839ff
    38942 
    38943 > color #900 #00b305ff
    38944 
    38945 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    38946 
    38947 ——— End of log from Wed Jul 17 16:12:00 2024 ———
    38948 
    38949 opened ChimeraX session 
    38950 
    38951 > ui tool show Matchmaker
    38952 
    38953 
    38954 ===== Log before crash end =====
    38955 
    38956 Log:
    38957 UCSF ChimeraX version: 1.8 (2024-06-10) 
    38958 © 2016-2024 Regents of the University of California. All rights reserved. 
    38959 
    38960 > open "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs"
    38961 
    38962 Log from Wed Jul 17 16:12:00 2024UCSF ChimeraX version: 1.8 (2024-06-10) 
    38963 © 2016-2024 Regents of the University of California. All rights reserved. 
    38964 
    38965 > open "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs"
    38966 
    38967 Log from Wed Jul 17 13:58:06 2024UCSF ChimeraX version: 1.8 (2024-06-10) 
    38968 © 2016-2024 Regents of the University of California. All rights reserved. 
    38969 
    38970 > open "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs"
    38971 
    38972 Log from Tue Jul 16 18:02:55 2024UCSF ChimeraX version: 1.8 (2024-06-10) 
    38973 © 2016-2024 Regents of the University of California. All rights reserved. 
    38974 
    38975 > open "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs"
    38976 
    38977 Log from Mon Jul 15 16:59:09 2024UCSF ChimeraX version: 1.8 (2024-06-10) 
    38978 © 2016-2024 Regents of the University of California. All rights reserved. 
    38979 
    38980 > open "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs"
    38981 
    38982 Log from Mon Jul 15 16:48:15 2024UCSF ChimeraX version: 1.8 (2024-06-10) 
    38983 © 2016-2024 Regents of the University of California. All rights reserved. 
    38984 
    38985 > open "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs"
    38986 
    38987 Log from Mon Jul 15 14:11:54 2024UCSF ChimeraX version: 1.8 (2024-06-10) 
    38988 © 2016-2024 Regents of the University of California. All rights reserved. 
    38989 
    38990 > open "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs"
    38991 
    38992 Log from Sun Jul 14 15:37:22 2024UCSF ChimeraX version: 1.8 (2024-06-10) 
    38993 © 2016-2024 Regents of the University of California. All rights reserved. 
    38994 
    38995 > open "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs"
    38996 
    38997 Log from Sun Jul 14 15:13:35 2024UCSF ChimeraX version: 1.8 (2024-06-10) 
    38998 © 2016-2024 Regents of the University of California. All rights reserved. 
    38999 
    39000 > open "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" format session
    39001 
    39002 Log from Sun Jul 14 14:55:26 2024 Startup Messages 
    39003 --- 
    39004 note | available bundle cache has not been initialized yet 
    39005  
    39006 UCSF ChimeraX version: 1.8 (2024-06-10) 
    39007 © 2016-2024 Regents of the University of California. All rights reserved. 
    39008 How to cite UCSF ChimeraX 
    39009 
    39010 > open /Users/Jean/Desktop/3j0c.pdb1
    39011 
    39012 3j0c.pdb1 title: 
    39013 Models of E1, E2 and CP of venezuelan equine encephalitis virus Tc-83 strain
    39014 restrained by A near atomic resolution cryo-em map [more info...] 
    39015  
    39016 Chain information for 3j0c.pdb1 
    39017 --- 
    39018 Chain | Description 
    39019 1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A 1.13/A 1.14/A 1.15/A 1.16/A 1.17/A 1.18/A 1.19/A 1.20/A 1.21/A 1.22/A 1.23/A 1.24/A 1.25/A 1.26/A 1.27/A 1.28/A 1.29/A 1.30/A 1.31/A 1.32/A 1.33/A 1.34/A 1.35/A 1.36/A 1.37/A 1.38/A 1.39/A 1.40/A 1.41/A 1.42/A 1.43/A 1.44/A 1.45/A 1.46/A 1.47/A 1.48/A 1.49/A 1.50/A 1.51/A 1.52/A 1.53/A 1.54/A 1.55/A 1.56/A 1.57/A 1.58/A 1.59/A 1.60/A 1.1/D 1.2/D 1.3/D 1.4/D 1.5/D 1.6/D 1.7/D 1.8/D 1.9/D 1.10/D 1.11/D 1.12/D 1.13/D 1.14/D 1.15/D 1.16/D 1.17/D 1.18/D 1.19/D 1.20/D 1.21/D 1.22/D 1.23/D 1.24/D 1.25/D 1.26/D 1.27/D 1.28/D 1.29/D 1.30/D 1.31/D 1.32/D 1.33/D 1.34/D 1.35/D 1.36/D 1.37/D 1.38/D 1.39/D 1.40/D 1.41/D 1.42/D 1.43/D 1.44/D 1.45/D 1.46/D 1.47/D 1.48/D 1.49/D 1.50/D 1.51/D 1.52/D 1.53/D 1.54/D 1.55/D 1.56/D 1.57/D 1.58/D 1.59/D 1.60/D 1.1/G 1.2/G 1.3/G 1.4/G 1.5/G 1.6/G 1.7/G 1.8/G 1.9/G 1.10/G 1.11/G 1.12/G 1.13/G 1.14/G 1.15/G 1.16/G 1.17/G 1.18/G 1.19/G 1.20/G 1.21/G 1.22/G 1.23/G 1.24/G 1.25/G 1.26/G 1.27/G 1.28/G 1.29/G 1.30/G 1.31/G 1.32/G 1.33/G 1.34/G 1.35/G 1.36/G 1.37/G 1.38/G 1.39/G 1.40/G 1.41/G 1.42/G 1.43/G 1.44/G 1.45/G 1.46/G 1.47/G 1.48/G 1.49/G 1.50/G 1.51/G 1.52/G 1.53/G 1.54/G 1.55/G 1.56/G 1.57/G 1.58/G 1.59/G 1.60/G 1.1/J 1.2/J 1.3/J 1.4/J 1.5/J 1.6/J 1.7/J 1.8/J 1.9/J 1.10/J 1.11/J 1.12/J 1.13/J 1.14/J 1.15/J 1.16/J 1.17/J 1.18/J 1.19/J 1.20/J 1.21/J 1.22/J 1.23/J 1.24/J 1.25/J 1.26/J 1.27/J 1.28/J 1.29/J 1.30/J 1.31/J 1.32/J 1.33/J 1.34/J 1.35/J 1.36/J 1.37/J 1.38/J 1.39/J 1.40/J 1.41/J 1.42/J 1.43/J 1.44/J 1.45/J 1.46/J 1.47/J 1.48/J 1.49/J 1.50/J 1.51/J 1.52/J 1.53/J 1.54/J 1.55/J 1.56/J 1.57/J 1.58/J 1.59/J 1.60/J | No description available 
    39020 1.1/B 1.2/B 1.3/B 1.4/B 1.5/B 1.6/B 1.7/B 1.8/B 1.9/B 1.10/B 1.11/B 1.12/B 1.13/B 1.14/B 1.15/B 1.16/B 1.17/B 1.18/B 1.19/B 1.20/B 1.21/B 1.22/B 1.23/B 1.24/B 1.25/B 1.26/B 1.27/B 1.28/B 1.29/B 1.30/B 1.31/B 1.32/B 1.33/B 1.34/B 1.35/B 1.36/B 1.37/B 1.38/B 1.39/B 1.40/B 1.41/B 1.42/B 1.43/B 1.44/B 1.45/B 1.46/B 1.47/B 1.48/B 1.49/B 1.50/B 1.51/B 1.52/B 1.53/B 1.54/B 1.55/B 1.56/B 1.57/B 1.58/B 1.59/B 1.60/B 1.1/E 1.2/E 1.3/E 1.4/E 1.5/E 1.6/E 1.7/E 1.8/E 1.9/E 1.10/E 1.11/E 1.12/E 1.13/E 1.14/E 1.15/E 1.16/E 1.17/E 1.18/E 1.19/E 1.20/E 1.21/E 1.22/E 1.23/E 1.24/E 1.25/E 1.26/E 1.27/E 1.28/E 1.29/E 1.30/E 1.31/E 1.32/E 1.33/E 1.34/E 1.35/E 1.36/E 1.37/E 1.38/E 1.39/E 1.40/E 1.41/E 1.42/E 1.43/E 1.44/E 1.45/E 1.46/E 1.47/E 1.48/E 1.49/E 1.50/E 1.51/E 1.52/E 1.53/E 1.54/E 1.55/E 1.56/E 1.57/E 1.58/E 1.59/E 1.60/E 1.1/H 1.2/H 1.3/H 1.4/H 1.5/H 1.6/H 1.7/H 1.8/H 1.9/H 1.10/H 1.11/H 1.12/H 1.13/H 1.14/H 1.15/H 1.16/H 1.17/H 1.18/H 1.19/H 1.20/H 1.21/H 1.22/H 1.23/H 1.24/H 1.25/H 1.26/H 1.27/H 1.28/H 1.29/H 1.30/H 1.31/H 1.32/H 1.33/H 1.34/H 1.35/H 1.36/H 1.37/H 1.38/H 1.39/H 1.40/H 1.41/H 1.42/H 1.43/H 1.44/H 1.45/H 1.46/H 1.47/H 1.48/H 1.49/H 1.50/H 1.51/H 1.52/H 1.53/H 1.54/H 1.55/H 1.56/H 1.57/H 1.58/H 1.59/H 1.60/H 1.1/K 1.2/K 1.3/K 1.4/K 1.5/K 1.6/K 1.7/K 1.8/K 1.9/K 1.10/K 1.11/K 1.12/K 1.13/K 1.14/K 1.15/K 1.16/K 1.17/K 1.18/K 1.19/K 1.20/K 1.21/K 1.22/K 1.23/K 1.24/K 1.25/K 1.26/K 1.27/K 1.28/K 1.29/K 1.30/K 1.31/K 1.32/K 1.33/K 1.34/K 1.35/K 1.36/K 1.37/K 1.38/K 1.39/K 1.40/K 1.41/K 1.42/K 1.43/K 1.44/K 1.45/K 1.46/K 1.47/K 1.48/K 1.49/K 1.50/K 1.51/K 1.52/K 1.53/K 1.54/K 1.55/K 1.56/K 1.57/K 1.58/K 1.59/K 1.60/K | No description available 
    39021 1.1/C 1.2/C 1.3/C 1.4/C 1.5/C 1.6/C 1.7/C 1.8/C 1.9/C 1.10/C 1.11/C 1.12/C 1.13/C 1.14/C 1.15/C 1.16/C 1.17/C 1.18/C 1.19/C 1.20/C 1.21/C 1.22/C 1.23/C 1.24/C 1.25/C 1.26/C 1.27/C 1.28/C 1.29/C 1.30/C 1.31/C 1.32/C 1.33/C 1.34/C 1.35/C 1.36/C 1.37/C 1.38/C 1.39/C 1.40/C 1.41/C 1.42/C 1.43/C 1.44/C 1.45/C 1.46/C 1.47/C 1.48/C 1.49/C 1.50/C 1.51/C 1.52/C 1.53/C 1.54/C 1.55/C 1.56/C 1.57/C 1.58/C 1.59/C 1.60/C 1.1/F 1.2/F 1.3/F 1.4/F 1.5/F 1.6/F 1.7/F 1.8/F 1.9/F 1.10/F 1.11/F 1.12/F 1.13/F 1.14/F 1.15/F 1.16/F 1.17/F 1.18/F 1.19/F 1.20/F 1.21/F 1.22/F 1.23/F 1.24/F 1.25/F 1.26/F 1.27/F 1.28/F 1.29/F 1.30/F 1.31/F 1.32/F 1.33/F 1.34/F 1.35/F 1.36/F 1.37/F 1.38/F 1.39/F 1.40/F 1.41/F 1.42/F 1.43/F 1.44/F 1.45/F 1.46/F 1.47/F 1.48/F 1.49/F 1.50/F 1.51/F 1.52/F 1.53/F 1.54/F 1.55/F 1.56/F 1.57/F 1.58/F 1.59/F 1.60/F 1.1/I 1.2/I 1.3/I 1.4/I 1.5/I 1.6/I 1.7/I 1.8/I 1.9/I 1.10/I 1.11/I 1.12/I 1.13/I 1.14/I 1.15/I 1.16/I 1.17/I 1.18/I 1.19/I 1.20/I 1.21/I 1.22/I 1.23/I 1.24/I 1.25/I 1.26/I 1.27/I 1.28/I 1.29/I 1.30/I 1.31/I 1.32/I 1.33/I 1.34/I 1.35/I 1.36/I 1.37/I 1.38/I 1.39/I 1.40/I 1.41/I 1.42/I 1.43/I 1.44/I 1.45/I 1.46/I 1.47/I 1.48/I 1.49/I 1.50/I 1.51/I 1.52/I 1.53/I 1.54/I 1.55/I 1.56/I 1.57/I 1.58/I 1.59/I 1.60/I 1.1/L 1.2/L 1.3/L 1.4/L 1.5/L 1.6/L 1.7/L 1.8/L 1.9/L 1.10/L 1.11/L 1.12/L 1.13/L 1.14/L 1.15/L 1.16/L 1.17/L 1.18/L 1.19/L 1.20/L 1.21/L 1.22/L 1.23/L 1.24/L 1.25/L 1.26/L 1.27/L 1.28/L 1.29/L 1.30/L 1.31/L 1.32/L 1.33/L 1.34/L 1.35/L 1.36/L 1.37/L 1.38/L 1.39/L 1.40/L 1.41/L 1.42/L 1.43/L 1.44/L 1.45/L 1.46/L 1.47/L 1.48/L 1.49/L 1.50/L 1.51/L 1.52/L 1.53/L 1.54/L 1.55/L 1.56/L 1.57/L 1.58/L 1.59/L 1.60/L | No description available 
    39022  
    39023 
    39024 > set bgColor white
    39025 
    39026 > save /Users/Jean/Desktop/image1.png supersample 3
    39027 
    39028 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    39029 
    39030 ——— End of log from Sun Jul 14 14:55:26 2024 ———
    39031 
    39032 opened ChimeraX session 
    39033 
    39034 > hide cartoons
    39035 
    39036 > hide atoms
    39037 
    39038 > select #1.1/A
    39039 
    39040 3370 atoms, 3467 bonds, 442 residues, 1 model selected 
    39041 
    39042 > ui tool show Matchmaker
    39043 
    39044 > show sel cartoons
    39045 
    39046 > view sel
    39047 
    39048 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    39049 
    39050 Chain information for AF3 E1 1-421.pdb #2 
    39051 --- 
    39052 Chain | Description 
    39053 A | No description available 
    39054  
    39055 
    39056 > matchmaker #2 to #1.1 & sel
    39057 
    39058 Parameters 
    39059 --- 
    39060 Chain pairing | bb 
    39061 Alignment algorithm | Needleman-Wunsch 
    39062 Similarity matrix | BLOSUM-62 
    39063 SS fraction | 0.3 
    39064 Gap open (HH/SS/other) | 18/18/6 
    39065 Gap extend | 1 
    39066 SS matrix |  |  | H | S | O 
    39067 ---|---|---|--- 
    39068 H | 6 | -9 | -6 
    39069 S |  | 6 | -6 
    39070 O |  |  | 4 
    39071 Iteration cutoff | 2 
    39072  
    39073 Matchmaker 3j0c.pdb1, chain A (#1.1) with AF3 E1 1-421.pdb, chain A (#2),
    39074 sequence alignment score = 1060.7 
    39075 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    39076 3.020) 
    39077  
    39078 
    39079 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    39080 
    39081 Chain information for AF3 E1 422-461.pdb #3 
    39082 --- 
    39083 Chain | Description 
    39084 A | No description available 
    39085  
    39086 
    39087 > matchmaker #3 to #1.1 & sel
    39088 
    39089 Parameters 
    39090 --- 
    39091 Chain pairing | bb 
    39092 Alignment algorithm | Needleman-Wunsch 
    39093 Similarity matrix | BLOSUM-62 
    39094 SS fraction | 0.3 
    39095 Gap open (HH/SS/other) | 18/18/6 
    39096 Gap extend | 1 
    39097 SS matrix |  |  | H | S | O 
    39098 ---|---|---|--- 
    39099 H | 6 | -9 | -6 
    39100 S |  | 6 | -6 
    39101 O |  |  | 4 
    39102 Iteration cutoff | 2 
    39103  
    39104 Matchmaker 3j0c.pdb1, chain A (#1.1) with AF3 E1 422-461.pdb, chain A (#3),
    39105 sequence alignment score = 626.9 
    39106 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    39107 2.776) 
    39108  
    39109 
    39110 > select #1.1/B
    39111 
    39112 3304 atoms, 3400 bonds, 423 residues, 1 model selected 
    39113 
    39114 > show sel cartoons
    39115 
    39116 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    39117 
    39118 Chain information for AF3 E2 1-352.pdb #4 
    39119 --- 
    39120 Chain | Description 
    39121 B | No description available 
    39122  
    39123 
    39124 > matchmaker #4 to #1.1 & sel
    39125 
    39126 Parameters 
    39127 --- 
    39128 Chain pairing | bb 
    39129 Alignment algorithm | Needleman-Wunsch 
    39130 Similarity matrix | BLOSUM-62 
    39131 SS fraction | 0.3 
    39132 Gap open (HH/SS/other) | 18/18/6 
    39133 Gap extend | 1 
    39134 SS matrix |  |  | H | S | O 
    39135 ---|---|---|--- 
    39136 H | 6 | -9 | -6 
    39137 S |  | 6 | -6 
    39138 O |  |  | 4 
    39139 Iteration cutoff | 2 
    39140  
    39141 Matchmaker 3j0c.pdb1, chain B (#1.1) with AF3 E2 1-352.pdb, chain B (#4),
    39142 sequence alignment score = 583.7 
    39143 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    39144 5.933) 
    39145  
    39146 
    39147 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    39148 
    39149 Chain information for AF3 E2 353-438.pdb #5 
    39150 --- 
    39151 Chain | Description 
    39152 B | No description available 
    39153  
    39154 
    39155 > matchmaker #5 to #1.1 & sel
    39156 
    39157 Parameters 
    39158 --- 
    39159 Chain pairing | bb 
    39160 Alignment algorithm | Needleman-Wunsch 
    39161 Similarity matrix | BLOSUM-62 
    39162 SS fraction | 0.3 
    39163 Gap open (HH/SS/other) | 18/18/6 
    39164 Gap extend | 1 
    39165 SS matrix |  |  | H | S | O 
    39166 ---|---|---|--- 
    39167 H | 6 | -9 | -6 
    39168 S |  | 6 | -6 
    39169 O |  |  | 4 
    39170 Iteration cutoff | 2 
    39171  
    39172 Matchmaker 3j0c.pdb1, chain B (#1.1) with AF3 E2 353-438.pdb, chain B (#5),
    39173 sequence alignment score = 333.4 
    39174 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    39175 8.411) 
    39176  
    39177 
    39178 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    39179 
    39180 ——— End of log from Sun Jul 14 15:13:35 2024 ———
    39181 
    39182 opened ChimeraX session 
    39183 
    39184 > select #1.1/C
    39185 
    39186 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    39187 
    39188 > show sel cartoons
    39189 
    39190 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    39191 
    39192 Chain information for AF3 CA.pdb #6 
    39193 --- 
    39194 Chain | Description 
    39195 A | No description available 
    39196  
    39197 
    39198 > ui tool show Matchmaker
    39199 
    39200 > matchmaker #6 to #1.1
    39201 
    39202 Parameters 
    39203 --- 
    39204 Chain pairing | bb 
    39205 Alignment algorithm | Needleman-Wunsch 
    39206 Similarity matrix | BLOSUM-62 
    39207 SS fraction | 0.3 
    39208 Gap open (HH/SS/other) | 18/18/6 
    39209 Gap extend | 1 
    39210 SS matrix |  |  | H | S | O 
    39211 ---|---|---|--- 
    39212 H | 6 | -9 | -6 
    39213 S |  | 6 | -6 
    39214 O |  |  | 4 
    39215 Iteration cutoff | 2 
    39216  
    39217 Matchmaker 3j0c.pdb1, chain F (#1.1) with AF3 CA.pdb, chain A (#6), sequence
    39218 alignment score = 335.3 
    39219 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    39220 2.550) 
    39221  
    39222 
    39223 > matchmaker #6 to #1.1 & sel
    39224 
    39225 Parameters 
    39226 --- 
    39227 Chain pairing | bb 
    39228 Alignment algorithm | Needleman-Wunsch 
    39229 Similarity matrix | BLOSUM-62 
    39230 SS fraction | 0.3 
    39231 Gap open (HH/SS/other) | 18/18/6 
    39232 Gap extend | 1 
    39233 SS matrix |  |  | H | S | O 
    39234 ---|---|---|--- 
    39235 H | 6 | -9 | -6 
    39236 S |  | 6 | -6 
    39237 O |  |  | 4 
    39238 Iteration cutoff | 2 
    39239  
    39240 Matchmaker 3j0c.pdb1, chain C (#1.1) with AF3 CA.pdb, chain A (#6), sequence
    39241 alignment score = 328.1 
    39242 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    39243 2.714) 
    39244  
    39245 
    39246 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    39247 
    39248 ——— End of log from Sun Jul 14 15:37:22 2024 ———
    39249 
    39250 opened ChimeraX session 
    39251 
    39252 > color #2 dodgerblue
    39253 
    39254 > color #3 dodgerblue
    39255 
    39256 > color #4 #00b305ff
    39257 
    39258 > color #5 #00b305ff
    39259 
    39260 > color #6 #f15839ff
    39261 
    39262 > select #1.1/A
    39263 
    39264 3370 atoms, 3467 bonds, 442 residues, 1 model selected 
    39265 
    39266 > hide sel cartoons
    39267 
    39268 > select #1.1/B
    39269 
    39270 3304 atoms, 3400 bonds, 423 residues, 1 model selected 
    39271 
    39272 > hide sel cartoons
    39273 
    39274 > select #1.1/C
    39275 
    39276 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    39277 
    39278 > hide sel cartoons
    39279 
    39280 > ui tool show Matchmaker
    39281 
    39282 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    39283 
    39284 Chain information for AF3 E1 1-421.pdb #7 
    39285 --- 
    39286 Chain | Description 
    39287 A | No description available 
    39288  
    39289 
    39290 > select #1.2/A
    39291 
    39292 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    39293 
    39294 > show sel cartoons
    39295 
    39296 > matchmaker #7 to #1.2 & sel
    39297 
    39298 Parameters 
    39299 --- 
    39300 Chain pairing | bb 
    39301 Alignment algorithm | Needleman-Wunsch 
    39302 Similarity matrix | BLOSUM-62 
    39303 SS fraction | 0.3 
    39304 Gap open (HH/SS/other) | 18/18/6 
    39305 Gap extend | 1 
    39306 SS matrix |  |  | H | S | O 
    39307 ---|---|---|--- 
    39308 H | 6 | -9 | -6 
    39309 S |  | 6 | -6 
    39310 O |  |  | 4 
    39311 Iteration cutoff | 2 
    39312  
    39313 Matchmaker 3j0c.pdb1, chain A (#1.2) with AF3 E1 1-421.pdb, chain A (#7),
    39314 sequence alignment score = 1060.7 
    39315 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    39316 3.020) 
    39317  
    39318 
    39319 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    39320 
    39321 Chain information for AF3 E1 422-461.pdb #8 
    39322 --- 
    39323 Chain | Description 
    39324 A | No description available 
    39325  
    39326 
    39327 > matchmaker #8 to #1.2 & sel
    39328 
    39329 Parameters 
    39330 --- 
    39331 Chain pairing | bb 
    39332 Alignment algorithm | Needleman-Wunsch 
    39333 Similarity matrix | BLOSUM-62 
    39334 SS fraction | 0.3 
    39335 Gap open (HH/SS/other) | 18/18/6 
    39336 Gap extend | 1 
    39337 SS matrix |  |  | H | S | O 
    39338 ---|---|---|--- 
    39339 H | 6 | -9 | -6 
    39340 S |  | 6 | -6 
    39341 O |  |  | 4 
    39342 Iteration cutoff | 2 
    39343  
    39344 Matchmaker 3j0c.pdb1, chain A (#1.2) with AF3 E1 422-461.pdb, chain A (#8),
    39345 sequence alignment score = 626.9 
    39346 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    39347 2.775) 
    39348  
    39349 
    39350 > select #1.2/B
    39351 
    39352 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    39353 
    39354 > show sel cartoons
    39355 
    39356 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    39357 
    39358 Chain information for AF3 E2 1-352.pdb #9 
    39359 --- 
    39360 Chain | Description 
    39361 B | No description available 
    39362  
    39363 
    39364 > matchmaker #9 to #1.2 & sel
    39365 
    39366 Parameters 
    39367 --- 
    39368 Chain pairing | bb 
    39369 Alignment algorithm | Needleman-Wunsch 
    39370 Similarity matrix | BLOSUM-62 
    39371 SS fraction | 0.3 
    39372 Gap open (HH/SS/other) | 18/18/6 
    39373 Gap extend | 1 
    39374 SS matrix |  |  | H | S | O 
    39375 ---|---|---|--- 
    39376 H | 6 | -9 | -6 
    39377 S |  | 6 | -6 
    39378 O |  |  | 4 
    39379 Iteration cutoff | 2 
    39380  
    39381 Matchmaker 3j0c.pdb1, chain B (#1.2) with AF3 E2 1-352.pdb, chain B (#9),
    39382 sequence alignment score = 583.7 
    39383 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    39384 5.933) 
    39385  
    39386 
    39387 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    39388 
    39389 Chain information for AF3 E2 353-438.pdb #10 
    39390 --- 
    39391 Chain | Description 
    39392 B | No description available 
    39393  
    39394 
    39395 > matchmaker #10 to #1.2 & sel
    39396 
    39397 Parameters 
    39398 --- 
    39399 Chain pairing | bb 
    39400 Alignment algorithm | Needleman-Wunsch 
    39401 Similarity matrix | BLOSUM-62 
    39402 SS fraction | 0.3 
    39403 Gap open (HH/SS/other) | 18/18/6 
    39404 Gap extend | 1 
    39405 SS matrix |  |  | H | S | O 
    39406 ---|---|---|--- 
    39407 H | 6 | -9 | -6 
    39408 S |  | 6 | -6 
    39409 O |  |  | 4 
    39410 Iteration cutoff | 2 
    39411  
    39412 Matchmaker 3j0c.pdb1, chain B (#1.2) with AF3 E2 353-438.pdb, chain B (#10),
    39413 sequence alignment score = 322.6 
    39414 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    39415 8.411) 
    39416  
    39417 
    39418 > select #1.3/A
    39419 
    39420 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    39421 
    39422 > select clear
    39423 
    39424 > select #1.2/C
    39425 
    39426 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    39427 
    39428 > show sel cartoons
    39429 
    39430 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    39431 
    39432 Chain information for AF3 CA.pdb #11 
    39433 --- 
    39434 Chain | Description 
    39435 A | No description available 
    39436  
    39437 
    39438 > matchmaker #10 to #1.2 & sel
    39439 
    39440 Parameters 
    39441 --- 
    39442 Chain pairing | bb 
    39443 Alignment algorithm | Needleman-Wunsch 
    39444 Similarity matrix | BLOSUM-62 
    39445 SS fraction | 0.3 
    39446 Gap open (HH/SS/other) | 18/18/6 
    39447 Gap extend | 1 
    39448 SS matrix |  |  | H | S | O 
    39449 ---|---|---|--- 
    39450 H | 6 | -9 | -6 
    39451 S |  | 6 | -6 
    39452 O |  |  | 4 
    39453 Iteration cutoff | 2 
    39454  
    39455 Matchmaker 3j0c.pdb1, chain C (#1.2) with AF3 E2 353-438.pdb, chain B (#10),
    39456 sequence alignment score = 16.2 
    39457 RMSD between 8 pruned atom pairs is 0.563 angstroms; (across all 28 pairs:
    39458 19.587) 
    39459  
    39460 
    39461 > select #1.2/B
    39462 
    39463 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    39464 
    39465 > matchmaker #10 to #1.2 & sel
    39466 
    39467 Parameters 
    39468 --- 
    39469 Chain pairing | bb 
    39470 Alignment algorithm | Needleman-Wunsch 
    39471 Similarity matrix | BLOSUM-62 
    39472 SS fraction | 0.3 
    39473 Gap open (HH/SS/other) | 18/18/6 
    39474 Gap extend | 1 
    39475 SS matrix |  |  | H | S | O 
    39476 ---|---|---|--- 
    39477 H | 6 | -9 | -6 
    39478 S |  | 6 | -6 
    39479 O |  |  | 4 
    39480 Iteration cutoff | 2 
    39481  
    39482 Matchmaker 3j0c.pdb1, chain B (#1.2) with AF3 E2 353-438.pdb, chain B (#10),
    39483 sequence alignment score = 322.6 
    39484 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    39485 8.411) 
    39486  
    39487 
    39488 > select #1.3/C
    39489 
    39490 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    39491 
    39492 > show sel cartoons
    39493 
    39494 > hide sel cartoons
    39495 
    39496 > select #1.2/C
    39497 
    39498 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    39499 
    39500 > show sel cartoons
    39501 
    39502 > matchmaker #11 to #1.2 & sel
    39503 
    39504 Parameters 
    39505 --- 
    39506 Chain pairing | bb 
    39507 Alignment algorithm | Needleman-Wunsch 
    39508 Similarity matrix | BLOSUM-62 
    39509 SS fraction | 0.3 
    39510 Gap open (HH/SS/other) | 18/18/6 
    39511 Gap extend | 1 
    39512 SS matrix |  |  | H | S | O 
    39513 ---|---|---|--- 
    39514 H | 6 | -9 | -6 
    39515 S |  | 6 | -6 
    39516 O |  |  | 4 
    39517 Iteration cutoff | 2 
    39518  
    39519 Matchmaker 3j0c.pdb1, chain C (#1.2) with AF3 CA.pdb, chain A (#11), sequence
    39520 alignment score = 328.1 
    39521 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    39522 2.714) 
    39523  
    39524 
    39525 > hide sel cartoons
    39526 
    39527 > select #1.2/A
    39528 
    39529 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    39530 
    39531 > hide sel cartoons
    39532 
    39533 > select #1.2/B
    39534 
    39535 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    39536 
    39537 > hide sel cartoons
    39538 
    39539 > color #7 dodgerblue
    39540 
    39541 > color #8 dodgerblue
    39542 
    39543 > color #9 #00b305ff
    39544 
    39545 > color #10 #00b305ff
    39546 
    39547 > color #11 #f15839ff
    39548 
    39549 > select #1.3/A
    39550 
    39551 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    39552 
    39553 > show sel cartoons
    39554 
    39555 [Repeated 1 time(s)]
    39556 
    39557 > select #1.3/A
    39558 
    39559 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    39560 
    39561 > show sel cartoons
    39562 
    39563 > hide sel cartoons
    39564 
    39565 > select #1.3/A
    39566 
    39567 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    39568 
    39569 > show sel cartoons
    39570 
    39571 > select #1.3/B
    39572 
    39573 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    39574 
    39575 > show sel cartoons
    39576 
    39577 > select #1.3/C
    39578 
    39579 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    39580 
    39581 > show sel cartoons
    39582 
    39583 > select #1.4/A
    39584 
    39585 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    39586 
    39587 > show sel cartoons
    39588 
    39589 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    39590 
    39591 ——— End of log from Mon Jul 15 14:11:54 2024 ———
    39592 
    39593 opened ChimeraX session 
    39594 
    39595 > select #1.3/A
    39596 
    39597 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    39598 
    39599 > show sel cartoons
    39600 
    39601 > view sel
    39602 
    39603 > lighting soft
    39604 
    39605 > set bgColor black
    39606 
    39607 > lighting full
    39608 
    39609 > lighting soft
    39610 
    39611 > lighting simple
    39612 
    39613 > lighting soft
    39614 
    39615 > lighting full
    39616 
    39617 > view sel
    39618 
    39619 > view
    39620 
    39621 > select #1.4/A
    39622 
    39623 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    39624 
    39625 > hide sel cartoons
    39626 
    39627 > select #1.3/C
    39628 
    39629 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    39630 
    39631 > hide sel cartoons
    39632 
    39633 > show sel cartoons
    39634 
    39635 > select #1.3/A
    39636 
    39637 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    39638 
    39639 > ui tool show Matchmaker
    39640 
    39641 The cached device pixel ratio value was stale on window expose. Please file a
    39642 QTBUG which explains how to reproduce. 
    39643 
    39644 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    39645 
    39646 Chain information for AF3 E1 1-421.pdb #12 
    39647 --- 
    39648 Chain | Description 
    39649 A | No description available 
    39650  
    39651 
    39652 > matchmaker #12 to #1.3
    39653 
    39654 Parameters 
    39655 --- 
    39656 Chain pairing | bb 
    39657 Alignment algorithm | Needleman-Wunsch 
    39658 Similarity matrix | BLOSUM-62 
    39659 SS fraction | 0.3 
    39660 Gap open (HH/SS/other) | 18/18/6 
    39661 Gap extend | 1 
    39662 SS matrix |  |  | H | S | O 
    39663 ---|---|---|--- 
    39664 H | 6 | -9 | -6 
    39665 S |  | 6 | -6 
    39666 O |  |  | 4 
    39667 Iteration cutoff | 2 
    39668  
    39669 Matchmaker 3j0c.pdb1, chain A (#1.3) with AF3 E1 1-421.pdb, chain A (#12),
    39670 sequence alignment score = 1060.7 
    39671 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    39672 3.020) 
    39673  
    39674 
    39675 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    39676 
    39677 Chain information for AF3 E1 422-461.pdb #13 
    39678 --- 
    39679 Chain | Description 
    39680 A | No description available 
    39681  
    39682 
    39683 > matchmaker #12 to #1.3
    39684 
    39685 Parameters 
    39686 --- 
    39687 Chain pairing | bb 
    39688 Alignment algorithm | Needleman-Wunsch 
    39689 Similarity matrix | BLOSUM-62 
    39690 SS fraction | 0.3 
    39691 Gap open (HH/SS/other) | 18/18/6 
    39692 Gap extend | 1 
    39693 SS matrix |  |  | H | S | O 
    39694 ---|---|---|--- 
    39695 H | 6 | -9 | -6 
    39696 S |  | 6 | -6 
    39697 O |  |  | 4 
    39698 Iteration cutoff | 2 
    39699  
    39700 Matchmaker 3j0c.pdb1, chain A (#1.3) with AF3 E1 1-421.pdb, chain A (#12),
    39701 sequence alignment score = 1060.7 
    39702 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    39703 3.020) 
    39704  
    39705 
    39706 The cached device pixel ratio value was stale on window expose. Please file a
    39707 QTBUG which explains how to reproduce. 
    39708 
    39709 > matchmaker #13 to #1.3
    39710 
    39711 Parameters 
    39712 --- 
    39713 Chain pairing | bb 
    39714 Alignment algorithm | Needleman-Wunsch 
    39715 Similarity matrix | BLOSUM-62 
    39716 SS fraction | 0.3 
    39717 Gap open (HH/SS/other) | 18/18/6 
    39718 Gap extend | 1 
    39719 SS matrix |  |  | H | S | O 
    39720 ---|---|---|--- 
    39721 H | 6 | -9 | -6 
    39722 S |  | 6 | -6 
    39723 O |  |  | 4 
    39724 Iteration cutoff | 2 
    39725  
    39726 Matchmaker 3j0c.pdb1, chain A (#1.3) with AF3 E1 422-461.pdb, chain A (#13),
    39727 sequence alignment score = 626.9 
    39728 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    39729 2.775) 
    39730  
    39731 
    39732 > select #1.3/B
    39733 
    39734 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    39735 
    39736 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    39737 
    39738 Chain information for AF3 E2 1-352.pdb #14 
    39739 --- 
    39740 Chain | Description 
    39741 B | No description available 
    39742  
    39743 
    39744 > matchmaker #14 to #1.3
    39745 
    39746 Parameters 
    39747 --- 
    39748 Chain pairing | bb 
    39749 Alignment algorithm | Needleman-Wunsch 
    39750 Similarity matrix | BLOSUM-62 
    39751 SS fraction | 0.3 
    39752 Gap open (HH/SS/other) | 18/18/6 
    39753 Gap extend | 1 
    39754 SS matrix |  |  | H | S | O 
    39755 ---|---|---|--- 
    39756 H | 6 | -9 | -6 
    39757 S |  | 6 | -6 
    39758 O |  |  | 4 
    39759 Iteration cutoff | 2 
    39760  
    39761 Matchmaker 3j0c.pdb1, chain E (#1.3) with AF3 E2 1-352.pdb, chain B (#14),
    39762 sequence alignment score = 594.5 
    39763 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    39764 6.147) 
    39765  
    39766 
    39767 > matchmaker #14 to #1.3 & sel
    39768 
    39769 Parameters 
    39770 --- 
    39771 Chain pairing | bb 
    39772 Alignment algorithm | Needleman-Wunsch 
    39773 Similarity matrix | BLOSUM-62 
    39774 SS fraction | 0.3 
    39775 Gap open (HH/SS/other) | 18/18/6 
    39776 Gap extend | 1 
    39777 SS matrix |  |  | H | S | O 
    39778 ---|---|---|--- 
    39779 H | 6 | -9 | -6 
    39780 S |  | 6 | -6 
    39781 O |  |  | 4 
    39782 Iteration cutoff | 2 
    39783  
    39784 Matchmaker 3j0c.pdb1, chain B (#1.3) with AF3 E2 1-352.pdb, chain B (#14),
    39785 sequence alignment score = 583.7 
    39786 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    39787 5.933) 
    39788  
    39789 
    39790 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    39791 
    39792 Chain information for AF3 E2 353-438.pdb #15 
    39793 --- 
    39794 Chain | Description 
    39795 B | No description available 
    39796  
    39797 
    39798 > matchmaker #15 to #1.3 & sel
    39799 
    39800 Parameters 
    39801 --- 
    39802 Chain pairing | bb 
    39803 Alignment algorithm | Needleman-Wunsch 
    39804 Similarity matrix | BLOSUM-62 
    39805 SS fraction | 0.3 
    39806 Gap open (HH/SS/other) | 18/18/6 
    39807 Gap extend | 1 
    39808 SS matrix |  |  | H | S | O 
    39809 ---|---|---|--- 
    39810 H | 6 | -9 | -6 
    39811 S |  | 6 | -6 
    39812 O |  |  | 4 
    39813 Iteration cutoff | 2 
    39814  
    39815 Matchmaker 3j0c.pdb1, chain B (#1.3) with AF3 E2 353-438.pdb, chain B (#15),
    39816 sequence alignment score = 322.6 
    39817 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    39818 8.411) 
    39819  
    39820 
    39821 > hide sel cartoons
    39822 
    39823 > select #1.3/C
    39824 
    39825 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    39826 
    39827 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    39828 
    39829 Chain information for AF3 CA.pdb #16 
    39830 --- 
    39831 Chain | Description 
    39832 A | No description available 
    39833  
    39834 
    39835 > matchmaker #16 to #1.3 & sel
    39836 
    39837 Parameters 
    39838 --- 
    39839 Chain pairing | bb 
    39840 Alignment algorithm | Needleman-Wunsch 
    39841 Similarity matrix | BLOSUM-62 
    39842 SS fraction | 0.3 
    39843 Gap open (HH/SS/other) | 18/18/6 
    39844 Gap extend | 1 
    39845 SS matrix |  |  | H | S | O 
    39846 ---|---|---|--- 
    39847 H | 6 | -9 | -6 
    39848 S |  | 6 | -6 
    39849 O |  |  | 4 
    39850 Iteration cutoff | 2 
    39851  
    39852 Matchmaker 3j0c.pdb1, chain C (#1.3) with AF3 CA.pdb, chain A (#16), sequence
    39853 alignment score = 328.1 
    39854 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    39855 2.714) 
    39856  
    39857 
    39858 > hide sel cartoons
    39859 
    39860 > select #1.3/A
    39861 
    39862 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    39863 
    39864 > hide sel cartoons
    39865 
    39866 > hide #12 models
    39867 
    39868 > show #12 models
    39869 
    39870 > color #12 dodgerblue
    39871 
    39872 > color #13 dodgerblue
    39873 
    39874 > color #14 #00b305ff
    39875 
    39876 > color #15 #00b305ff
    39877 
    39878 > color #16 #f15839ff
    39879 
    39880 > select #1.4/A
    39881 
    39882 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    39883 
    39884 > show sel cartoons
    39885 
    39886 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    39887 
    39888 Chain information for AF3 E1 1-421.pdb #17 
    39889 --- 
    39890 Chain | Description 
    39891 A | No description available 
    39892  
    39893 
    39894 > matchmaker #17 to #1.4 & sel
    39895 
    39896 Parameters 
    39897 --- 
    39898 Chain pairing | bb 
    39899 Alignment algorithm | Needleman-Wunsch 
    39900 Similarity matrix | BLOSUM-62 
    39901 SS fraction | 0.3 
    39902 Gap open (HH/SS/other) | 18/18/6 
    39903 Gap extend | 1 
    39904 SS matrix |  |  | H | S | O 
    39905 ---|---|---|--- 
    39906 H | 6 | -9 | -6 
    39907 S |  | 6 | -6 
    39908 O |  |  | 4 
    39909 Iteration cutoff | 2 
    39910  
    39911 Matchmaker 3j0c.pdb1, chain A (#1.4) with AF3 E1 1-421.pdb, chain A (#17),
    39912 sequence alignment score = 1060.7 
    39913 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    39914 3.020) 
    39915  
    39916 
    39917 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    39918 
    39919 Chain information for AF3 E1 422-461.pdb #18 
    39920 --- 
    39921 Chain | Description 
    39922 A | No description available 
    39923  
    39924 
    39925 > matchmaker #18 to #1.4 & sel
    39926 
    39927 Parameters 
    39928 --- 
    39929 Chain pairing | bb 
    39930 Alignment algorithm | Needleman-Wunsch 
    39931 Similarity matrix | BLOSUM-62 
    39932 SS fraction | 0.3 
    39933 Gap open (HH/SS/other) | 18/18/6 
    39934 Gap extend | 1 
    39935 SS matrix |  |  | H | S | O 
    39936 ---|---|---|--- 
    39937 H | 6 | -9 | -6 
    39938 S |  | 6 | -6 
    39939 O |  |  | 4 
    39940 Iteration cutoff | 2 
    39941  
    39942 Matchmaker 3j0c.pdb1, chain A (#1.4) with AF3 E1 422-461.pdb, chain A (#18),
    39943 sequence alignment score = 626.9 
    39944 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    39945 2.775) 
    39946  
    39947 
    39948 > hide sel cartoons
    39949 
    39950 > select #1.4/B
    39951 
    39952 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    39953 
    39954 > show sel cartoons
    39955 
    39956 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    39957 
    39958 Chain information for AF3 E2 1-352.pdb #19 
    39959 --- 
    39960 Chain | Description 
    39961 B | No description available 
    39962  
    39963 
    39964 > matchmaker #19 to #1.4 & sel
    39965 
    39966 Parameters 
    39967 --- 
    39968 Chain pairing | bb 
    39969 Alignment algorithm | Needleman-Wunsch 
    39970 Similarity matrix | BLOSUM-62 
    39971 SS fraction | 0.3 
    39972 Gap open (HH/SS/other) | 18/18/6 
    39973 Gap extend | 1 
    39974 SS matrix |  |  | H | S | O 
    39975 ---|---|---|--- 
    39976 H | 6 | -9 | -6 
    39977 S |  | 6 | -6 
    39978 O |  |  | 4 
    39979 Iteration cutoff | 2 
    39980  
    39981 Matchmaker 3j0c.pdb1, chain B (#1.4) with AF3 E2 1-352.pdb, chain B (#19),
    39982 sequence alignment score = 583.7 
    39983 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    39984 5.933) 
    39985  
    39986 
    39987 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    39988 
    39989 Chain information for AF3 E2 353-438.pdb #20 
    39990 --- 
    39991 Chain | Description 
    39992 B | No description available 
    39993  
    39994 
    39995 > matchmaker #20 to #1.4 & sel
    39996 
    39997 Parameters 
    39998 --- 
    39999 Chain pairing | bb 
    40000 Alignment algorithm | Needleman-Wunsch 
    40001 Similarity matrix | BLOSUM-62 
    40002 SS fraction | 0.3 
    40003 Gap open (HH/SS/other) | 18/18/6 
    40004 Gap extend | 1 
    40005 SS matrix |  |  | H | S | O 
    40006 ---|---|---|--- 
    40007 H | 6 | -9 | -6 
    40008 S |  | 6 | -6 
    40009 O |  |  | 4 
    40010 Iteration cutoff | 2 
    40011  
    40012 Matchmaker 3j0c.pdb1, chain B (#1.4) with AF3 E2 353-438.pdb, chain B (#20),
    40013 sequence alignment score = 322.6 
    40014 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    40015 8.411) 
    40016  
    40017 
    40018 > select #1.4/C
    40019 
    40020 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    40021 
    40022 > show sel cartoons
    40023 
    40024 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    40025 
    40026 Chain information for AF3 CA.pdb #21 
    40027 --- 
    40028 Chain | Description 
    40029 A | No description available 
    40030  
    40031 
    40032 > matchmaker #21 to #1.4 & sel
    40033 
    40034 Parameters 
    40035 --- 
    40036 Chain pairing | bb 
    40037 Alignment algorithm | Needleman-Wunsch 
    40038 Similarity matrix | BLOSUM-62 
    40039 SS fraction | 0.3 
    40040 Gap open (HH/SS/other) | 18/18/6 
    40041 Gap extend | 1 
    40042 SS matrix |  |  | H | S | O 
    40043 ---|---|---|--- 
    40044 H | 6 | -9 | -6 
    40045 S |  | 6 | -6 
    40046 O |  |  | 4 
    40047 Iteration cutoff | 2 
    40048  
    40049 Matchmaker 3j0c.pdb1, chain C (#1.4) with AF3 CA.pdb, chain A (#21), sequence
    40050 alignment score = 328.1 
    40051 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    40052 2.714) 
    40053  
    40054 
    40055 > hide sel cartoons
    40056 
    40057 > select #1.4/B
    40058 
    40059 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    40060 
    40061 > hide sel cartoons
    40062 
    40063 > color #17 dodgerblue
    40064 
    40065 > color #18 dodgerblue
    40066 
    40067 > color #19 #00b305ff
    40068 
    40069 > color #20 #00b305ff
    40070 
    40071 > color #21 #f15839ff
    40072 
    40073 > select #1.5/A
    40074 
    40075 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    40076 
    40077 > show sel cartoons
    40078 
    40079 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    40080 
    40081 Chain information for AF3 E1 1-421.pdb #22 
    40082 --- 
    40083 Chain | Description 
    40084 A | No description available 
    40085  
    40086 
    40087 > matchmaker #22 to #1.5 & sel
    40088 
    40089 Parameters 
    40090 --- 
    40091 Chain pairing | bb 
    40092 Alignment algorithm | Needleman-Wunsch 
    40093 Similarity matrix | BLOSUM-62 
    40094 SS fraction | 0.3 
    40095 Gap open (HH/SS/other) | 18/18/6 
    40096 Gap extend | 1 
    40097 SS matrix |  |  | H | S | O 
    40098 ---|---|---|--- 
    40099 H | 6 | -9 | -6 
    40100 S |  | 6 | -6 
    40101 O |  |  | 4 
    40102 Iteration cutoff | 2 
    40103  
    40104 Matchmaker 3j0c.pdb1, chain A (#1.5) with AF3 E1 1-421.pdb, chain A (#22),
    40105 sequence alignment score = 1060.7 
    40106 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    40107 3.020) 
    40108  
    40109 
    40110 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    40111 
    40112 Chain information for AF3 E1 422-461.pdb #23 
    40113 --- 
    40114 Chain | Description 
    40115 A | No description available 
    40116  
    40117 
    40118 > matchmaker #23 to #1.5 & sel
    40119 
    40120 Parameters 
    40121 --- 
    40122 Chain pairing | bb 
    40123 Alignment algorithm | Needleman-Wunsch 
    40124 Similarity matrix | BLOSUM-62 
    40125 SS fraction | 0.3 
    40126 Gap open (HH/SS/other) | 18/18/6 
    40127 Gap extend | 1 
    40128 SS matrix |  |  | H | S | O 
    40129 ---|---|---|--- 
    40130 H | 6 | -9 | -6 
    40131 S |  | 6 | -6 
    40132 O |  |  | 4 
    40133 Iteration cutoff | 2 
    40134  
    40135 Matchmaker 3j0c.pdb1, chain A (#1.5) with AF3 E1 422-461.pdb, chain A (#23),
    40136 sequence alignment score = 626.9 
    40137 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    40138 2.776) 
    40139  
    40140 
    40141 > select #1.5/B
    40142 
    40143 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    40144 
    40145 > show sel cartoons
    40146 
    40147 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    40148 
    40149 Chain information for AF3 E2 1-352.pdb #24 
    40150 --- 
    40151 Chain | Description 
    40152 B | No description available 
    40153  
    40154 
    40155 > matchmaker #24 to #1.5 & sel
    40156 
    40157 Parameters 
    40158 --- 
    40159 Chain pairing | bb 
    40160 Alignment algorithm | Needleman-Wunsch 
    40161 Similarity matrix | BLOSUM-62 
    40162 SS fraction | 0.3 
    40163 Gap open (HH/SS/other) | 18/18/6 
    40164 Gap extend | 1 
    40165 SS matrix |  |  | H | S | O 
    40166 ---|---|---|--- 
    40167 H | 6 | -9 | -6 
    40168 S |  | 6 | -6 
    40169 O |  |  | 4 
    40170 Iteration cutoff | 2 
    40171  
    40172 Matchmaker 3j0c.pdb1, chain B (#1.5) with AF3 E2 1-352.pdb, chain B (#24),
    40173 sequence alignment score = 583.7 
    40174 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    40175 5.933) 
    40176  
    40177 
    40178 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    40179 
    40180 Chain information for AF3 E2 353-438.pdb #25 
    40181 --- 
    40182 Chain | Description 
    40183 B | No description available 
    40184  
    40185 
    40186 > matchmaker #25 to #1.5 & sel
    40187 
    40188 Parameters 
    40189 --- 
    40190 Chain pairing | bb 
    40191 Alignment algorithm | Needleman-Wunsch 
    40192 Similarity matrix | BLOSUM-62 
    40193 SS fraction | 0.3 
    40194 Gap open (HH/SS/other) | 18/18/6 
    40195 Gap extend | 1 
    40196 SS matrix |  |  | H | S | O 
    40197 ---|---|---|--- 
    40198 H | 6 | -9 | -6 
    40199 S |  | 6 | -6 
    40200 O |  |  | 4 
    40201 Iteration cutoff | 2 
    40202  
    40203 Matchmaker 3j0c.pdb1, chain B (#1.5) with AF3 E2 353-438.pdb, chain B (#25),
    40204 sequence alignment score = 322.6 
    40205 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    40206 8.411) 
    40207  
    40208 
    40209 > hide sel cartoons
    40210 
    40211 > select #1.5/A
    40212 
    40213 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    40214 
    40215 > hide sel cartoons
    40216 
    40217 > select #1.5/C
    40218 
    40219 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    40220 
    40221 > show sel cartoons
    40222 
    40223 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    40224 
    40225 Chain information for AF3 CA.pdb #26 
    40226 --- 
    40227 Chain | Description 
    40228 A | No description available 
    40229  
    40230 
    40231 > matchmaker #26 to #1.5 & sel
    40232 
    40233 Parameters 
    40234 --- 
    40235 Chain pairing | bb 
    40236 Alignment algorithm | Needleman-Wunsch 
    40237 Similarity matrix | BLOSUM-62 
    40238 SS fraction | 0.3 
    40239 Gap open (HH/SS/other) | 18/18/6 
    40240 Gap extend | 1 
    40241 SS matrix |  |  | H | S | O 
    40242 ---|---|---|--- 
    40243 H | 6 | -9 | -6 
    40244 S |  | 6 | -6 
    40245 O |  |  | 4 
    40246 Iteration cutoff | 2 
    40247  
    40248 Matchmaker 3j0c.pdb1, chain C (#1.5) with AF3 CA.pdb, chain A (#26), sequence
    40249 alignment score = 328.1 
    40250 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    40251 2.714) 
    40252  
    40253 
    40254 > hide sel cartoons
    40255 
    40256 > color #22 dodgerblue
    40257 
    40258 > color #23 dodgerblue
    40259 
    40260 > color #24 #00b305ff
    40261 
    40262 > color #25 #00b305ff
    40263 
    40264 > color #26 #f15839ff
    40265 
    40266 > select #1.6/A
    40267 
    40268 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    40269 
    40270 > show sel cartoons
    40271 
    40272 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    40273 
    40274 Chain information for AF3 E1 1-421.pdb #27 
    40275 --- 
    40276 Chain | Description 
    40277 A | No description available 
    40278  
    40279 
    40280 > matchmaker #27 to #1.6 & sel
    40281 
    40282 Parameters 
    40283 --- 
    40284 Chain pairing | bb 
    40285 Alignment algorithm | Needleman-Wunsch 
    40286 Similarity matrix | BLOSUM-62 
    40287 SS fraction | 0.3 
    40288 Gap open (HH/SS/other) | 18/18/6 
    40289 Gap extend | 1 
    40290 SS matrix |  |  | H | S | O 
    40291 ---|---|---|--- 
    40292 H | 6 | -9 | -6 
    40293 S |  | 6 | -6 
    40294 O |  |  | 4 
    40295 Iteration cutoff | 2 
    40296  
    40297 Matchmaker 3j0c.pdb1, chain A (#1.6) with AF3 E1 1-421.pdb, chain A (#27),
    40298 sequence alignment score = 1060.7 
    40299 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    40300 3.020) 
    40301  
    40302 
    40303 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    40304 
    40305 Chain information for AF3 E1 422-461.pdb #28 
    40306 --- 
    40307 Chain | Description 
    40308 A | No description available 
    40309  
    40310 
    40311 > matchmaker #28 to #1.6 & sel
    40312 
    40313 Parameters 
    40314 --- 
    40315 Chain pairing | bb 
    40316 Alignment algorithm | Needleman-Wunsch 
    40317 Similarity matrix | BLOSUM-62 
    40318 SS fraction | 0.3 
    40319 Gap open (HH/SS/other) | 18/18/6 
    40320 Gap extend | 1 
    40321 SS matrix |  |  | H | S | O 
    40322 ---|---|---|--- 
    40323 H | 6 | -9 | -6 
    40324 S |  | 6 | -6 
    40325 O |  |  | 4 
    40326 Iteration cutoff | 2 
    40327  
    40328 Matchmaker 3j0c.pdb1, chain A (#1.6) with AF3 E1 422-461.pdb, chain A (#28),
    40329 sequence alignment score = 626.9 
    40330 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    40331 2.775) 
    40332  
    40333 
    40334 > hide sel cartoons
    40335 
    40336 > select #1.6/B
    40337 
    40338 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    40339 
    40340 > show sel cartoons
    40341 
    40342 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    40343 
    40344 Chain information for AF3 E2 1-352.pdb #29 
    40345 --- 
    40346 Chain | Description 
    40347 B | No description available 
    40348  
    40349 
    40350 > matchmaker #29 to #1.6 & sel
    40351 
    40352 Parameters 
    40353 --- 
    40354 Chain pairing | bb 
    40355 Alignment algorithm | Needleman-Wunsch 
    40356 Similarity matrix | BLOSUM-62 
    40357 SS fraction | 0.3 
    40358 Gap open (HH/SS/other) | 18/18/6 
    40359 Gap extend | 1 
    40360 SS matrix |  |  | H | S | O 
    40361 ---|---|---|--- 
    40362 H | 6 | -9 | -6 
    40363 S |  | 6 | -6 
    40364 O |  |  | 4 
    40365 Iteration cutoff | 2 
    40366  
    40367 Matchmaker 3j0c.pdb1, chain B (#1.6) with AF3 E2 1-352.pdb, chain B (#29),
    40368 sequence alignment score = 583.7 
    40369 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    40370 5.933) 
    40371  
    40372 
    40373 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    40374 
    40375 Chain information for AF3 E2 353-438.pdb #30 
    40376 --- 
    40377 Chain | Description 
    40378 B | No description available 
    40379  
    40380 
    40381 > matchmaker #30 to #1.6 & sel
    40382 
    40383 Parameters 
    40384 --- 
    40385 Chain pairing | bb 
    40386 Alignment algorithm | Needleman-Wunsch 
    40387 Similarity matrix | BLOSUM-62 
    40388 SS fraction | 0.3 
    40389 Gap open (HH/SS/other) | 18/18/6 
    40390 Gap extend | 1 
    40391 SS matrix |  |  | H | S | O 
    40392 ---|---|---|--- 
    40393 H | 6 | -9 | -6 
    40394 S |  | 6 | -6 
    40395 O |  |  | 4 
    40396 Iteration cutoff | 2 
    40397  
    40398 Matchmaker 3j0c.pdb1, chain B (#1.6) with AF3 E2 353-438.pdb, chain B (#30),
    40399 sequence alignment score = 333.4 
    40400 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    40401 8.411) 
    40402  
    40403 
    40404 > hide sel cartoons
    40405 
    40406 > select #1.6/C
    40407 
    40408 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    40409 
    40410 > show sel cartoons
    40411 
    40412 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    40413 
    40414 Chain information for AF3 CA.pdb #31 
    40415 --- 
    40416 Chain | Description 
    40417 A | No description available 
    40418  
    40419 
    40420 > matchmaker #31 to #1.6 & sel
    40421 
    40422 Parameters 
    40423 --- 
    40424 Chain pairing | bb 
    40425 Alignment algorithm | Needleman-Wunsch 
    40426 Similarity matrix | BLOSUM-62 
    40427 SS fraction | 0.3 
    40428 Gap open (HH/SS/other) | 18/18/6 
    40429 Gap extend | 1 
    40430 SS matrix |  |  | H | S | O 
    40431 ---|---|---|--- 
    40432 H | 6 | -9 | -6 
    40433 S |  | 6 | -6 
    40434 O |  |  | 4 
    40435 Iteration cutoff | 2 
    40436  
    40437 Matchmaker 3j0c.pdb1, chain C (#1.6) with AF3 CA.pdb, chain A (#31), sequence
    40438 alignment score = 328.1 
    40439 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    40440 2.714) 
    40441  
    40442 
    40443 > hide sel cartoons
    40444 
    40445 > color #27 dodgerblue
    40446 
    40447 > color #28 dodgerblue
    40448 
    40449 > color #29 #00b305ff
    40450 
    40451 > color #30 #00b305ff
    40452 
    40453 > color #31 #f15839ff
    40454 
    40455 > select #1.7/A
    40456 
    40457 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    40458 
    40459 > show sel cartoons
    40460 
    40461 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    40462 
    40463 Chain information for AF3 E1 1-421.pdb #32 
    40464 --- 
    40465 Chain | Description 
    40466 A | No description available 
    40467  
    40468 
    40469 > matchmaker #32 to #1.7 & sel
    40470 
    40471 Parameters 
    40472 --- 
    40473 Chain pairing | bb 
    40474 Alignment algorithm | Needleman-Wunsch 
    40475 Similarity matrix | BLOSUM-62 
    40476 SS fraction | 0.3 
    40477 Gap open (HH/SS/other) | 18/18/6 
    40478 Gap extend | 1 
    40479 SS matrix |  |  | H | S | O 
    40480 ---|---|---|--- 
    40481 H | 6 | -9 | -6 
    40482 S |  | 6 | -6 
    40483 O |  |  | 4 
    40484 Iteration cutoff | 2 
    40485  
    40486 Matchmaker 3j0c.pdb1, chain A (#1.7) with AF3 E1 1-421.pdb, chain A (#32),
    40487 sequence alignment score = 1060.7 
    40488 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    40489 3.020) 
    40490  
    40491 
    40492 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    40493 
    40494 Chain information for AF3 E1 422-461.pdb #33 
    40495 --- 
    40496 Chain | Description 
    40497 A | No description available 
    40498  
    40499 
    40500 > matchmaker #33 to #1.7 & sel
    40501 
    40502 Parameters 
    40503 --- 
    40504 Chain pairing | bb 
    40505 Alignment algorithm | Needleman-Wunsch 
    40506 Similarity matrix | BLOSUM-62 
    40507 SS fraction | 0.3 
    40508 Gap open (HH/SS/other) | 18/18/6 
    40509 Gap extend | 1 
    40510 SS matrix |  |  | H | S | O 
    40511 ---|---|---|--- 
    40512 H | 6 | -9 | -6 
    40513 S |  | 6 | -6 
    40514 O |  |  | 4 
    40515 Iteration cutoff | 2 
    40516  
    40517 Matchmaker 3j0c.pdb1, chain A (#1.7) with AF3 E1 422-461.pdb, chain A (#33),
    40518 sequence alignment score = 626.9 
    40519 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    40520 2.775) 
    40521  
    40522 
    40523 > hide sel cartoons
    40524 
    40525 > select #1.7/B
    40526 
    40527 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    40528 
    40529 > show sel cartoons
    40530 
    40531 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    40532 
    40533 Chain information for AF3 E2 1-352.pdb #34 
    40534 --- 
    40535 Chain | Description 
    40536 B | No description available 
    40537  
    40538 
    40539 > matchmaker #34 to #1.7 & sel
    40540 
    40541 Parameters 
    40542 --- 
    40543 Chain pairing | bb 
    40544 Alignment algorithm | Needleman-Wunsch 
    40545 Similarity matrix | BLOSUM-62 
    40546 SS fraction | 0.3 
    40547 Gap open (HH/SS/other) | 18/18/6 
    40548 Gap extend | 1 
    40549 SS matrix |  |  | H | S | O 
    40550 ---|---|---|--- 
    40551 H | 6 | -9 | -6 
    40552 S |  | 6 | -6 
    40553 O |  |  | 4 
    40554 Iteration cutoff | 2 
    40555  
    40556 Matchmaker 3j0c.pdb1, chain B (#1.7) with AF3 E2 1-352.pdb, chain B (#34),
    40557 sequence alignment score = 583.7 
    40558 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    40559 5.933) 
    40560  
    40561 
    40562 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    40563 
    40564 Chain information for AF3 E2 353-438.pdb #35 
    40565 --- 
    40566 Chain | Description 
    40567 B | No description available 
    40568  
    40569 
    40570 > matchmaker #35 to #1.7 & sel
    40571 
    40572 Parameters 
    40573 --- 
    40574 Chain pairing | bb 
    40575 Alignment algorithm | Needleman-Wunsch 
    40576 Similarity matrix | BLOSUM-62 
    40577 SS fraction | 0.3 
    40578 Gap open (HH/SS/other) | 18/18/6 
    40579 Gap extend | 1 
    40580 SS matrix |  |  | H | S | O 
    40581 ---|---|---|--- 
    40582 H | 6 | -9 | -6 
    40583 S |  | 6 | -6 
    40584 O |  |  | 4 
    40585 Iteration cutoff | 2 
    40586  
    40587 Matchmaker 3j0c.pdb1, chain B (#1.7) with AF3 E2 353-438.pdb, chain B (#35),
    40588 sequence alignment score = 333.4 
    40589 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    40590 8.411) 
    40591  
    40592 
    40593 > hide sel cartoons
    40594 
    40595 > select #1.7/C
    40596 
    40597 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    40598 
    40599 > show sel cartoons
    40600 
    40601 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    40602 
    40603 Chain information for AF3 CA.pdb #36 
    40604 --- 
    40605 Chain | Description 
    40606 A | No description available 
    40607  
    40608 
    40609 > matchmaker #36 to #1.7 & sel
    40610 
    40611 Parameters 
    40612 --- 
    40613 Chain pairing | bb 
    40614 Alignment algorithm | Needleman-Wunsch 
    40615 Similarity matrix | BLOSUM-62 
    40616 SS fraction | 0.3 
    40617 Gap open (HH/SS/other) | 18/18/6 
    40618 Gap extend | 1 
    40619 SS matrix |  |  | H | S | O 
    40620 ---|---|---|--- 
    40621 H | 6 | -9 | -6 
    40622 S |  | 6 | -6 
    40623 O |  |  | 4 
    40624 Iteration cutoff | 2 
    40625  
    40626 Matchmaker 3j0c.pdb1, chain C (#1.7) with AF3 CA.pdb, chain A (#36), sequence
    40627 alignment score = 328.1 
    40628 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    40629 2.714) 
    40630  
    40631 
    40632 > hide sel cartoons
    40633 
    40634 > hide #32 models
    40635 
    40636 > color #32 dodgerblue
    40637 
    40638 > color #33 dodgerblue
    40639 
    40640 > color #34 #00b305ff
    40641 
    40642 > color #35 #00b305ff
    40643 
    40644 > color #36 #f15839ff
    40645 
    40646 > select #1.8/A
    40647 
    40648 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    40649 
    40650 > show sel cartoons
    40651 
    40652 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    40653 
    40654 Chain information for AF3 E1 1-421.pdb #37 
    40655 --- 
    40656 Chain | Description 
    40657 A | No description available 
    40658  
    40659 
    40660 > matchmaker #37 to #1.8 & sel
    40661 
    40662 Parameters 
    40663 --- 
    40664 Chain pairing | bb 
    40665 Alignment algorithm | Needleman-Wunsch 
    40666 Similarity matrix | BLOSUM-62 
    40667 SS fraction | 0.3 
    40668 Gap open (HH/SS/other) | 18/18/6 
    40669 Gap extend | 1 
    40670 SS matrix |  |  | H | S | O 
    40671 ---|---|---|--- 
    40672 H | 6 | -9 | -6 
    40673 S |  | 6 | -6 
    40674 O |  |  | 4 
    40675 Iteration cutoff | 2 
    40676  
    40677 Matchmaker 3j0c.pdb1, chain A (#1.8) with AF3 E1 1-421.pdb, chain A (#37),
    40678 sequence alignment score = 1060.7 
    40679 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    40680 3.020) 
    40681  
    40682 
    40683 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    40684 
    40685 Chain information for AF3 E1 422-461.pdb #38 
    40686 --- 
    40687 Chain | Description 
    40688 A | No description available 
    40689  
    40690 
    40691 > matchmaker #38 to #1.8 & sel
    40692 
    40693 Parameters 
    40694 --- 
    40695 Chain pairing | bb 
    40696 Alignment algorithm | Needleman-Wunsch 
    40697 Similarity matrix | BLOSUM-62 
    40698 SS fraction | 0.3 
    40699 Gap open (HH/SS/other) | 18/18/6 
    40700 Gap extend | 1 
    40701 SS matrix |  |  | H | S | O 
    40702 ---|---|---|--- 
    40703 H | 6 | -9 | -6 
    40704 S |  | 6 | -6 
    40705 O |  |  | 4 
    40706 Iteration cutoff | 2 
    40707  
    40708 Matchmaker 3j0c.pdb1, chain A (#1.8) with AF3 E1 422-461.pdb, chain A (#38),
    40709 sequence alignment score = 626.9 
    40710 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    40711 2.775) 
    40712  
    40713 
    40714 > hide sel cartoons
    40715 
    40716 > select #1.8/B
    40717 
    40718 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    40719 
    40720 > show sel cartoons
    40721 
    40722 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    40723 
    40724 Chain information for AF3 E2 1-352.pdb #39 
    40725 --- 
    40726 Chain | Description 
    40727 B | No description available 
    40728  
    40729 
    40730 > matchmaker #39 to #1.8 & sel
    40731 
    40732 Parameters 
    40733 --- 
    40734 Chain pairing | bb 
    40735 Alignment algorithm | Needleman-Wunsch 
    40736 Similarity matrix | BLOSUM-62 
    40737 SS fraction | 0.3 
    40738 Gap open (HH/SS/other) | 18/18/6 
    40739 Gap extend | 1 
    40740 SS matrix |  |  | H | S | O 
    40741 ---|---|---|--- 
    40742 H | 6 | -9 | -6 
    40743 S |  | 6 | -6 
    40744 O |  |  | 4 
    40745 Iteration cutoff | 2 
    40746  
    40747 Matchmaker 3j0c.pdb1, chain B (#1.8) with AF3 E2 1-352.pdb, chain B (#39),
    40748 sequence alignment score = 583.7 
    40749 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    40750 5.933) 
    40751  
    40752 
    40753 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    40754 
    40755 Chain information for AF3 E2 353-438.pdb #40 
    40756 --- 
    40757 Chain | Description 
    40758 B | No description available 
    40759  
    40760 
    40761 > matchmaker #40 to #1.8 & sel
    40762 
    40763 Parameters 
    40764 --- 
    40765 Chain pairing | bb 
    40766 Alignment algorithm | Needleman-Wunsch 
    40767 Similarity matrix | BLOSUM-62 
    40768 SS fraction | 0.3 
    40769 Gap open (HH/SS/other) | 18/18/6 
    40770 Gap extend | 1 
    40771 SS matrix |  |  | H | S | O 
    40772 ---|---|---|--- 
    40773 H | 6 | -9 | -6 
    40774 S |  | 6 | -6 
    40775 O |  |  | 4 
    40776 Iteration cutoff | 2 
    40777  
    40778 Matchmaker 3j0c.pdb1, chain B (#1.8) with AF3 E2 353-438.pdb, chain B (#40),
    40779 sequence alignment score = 333.4 
    40780 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    40781 8.411) 
    40782  
    40783 
    40784 > hide sel cartoons
    40785 
    40786 [Repeated 1 time(s)]
    40787 
    40788 > select #1.8/C
    40789 
    40790 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    40791 
    40792 > show sel cartoons
    40793 
    40794 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    40795 
    40796 Chain information for AF3 CA.pdb #41 
    40797 --- 
    40798 Chain | Description 
    40799 A | No description available 
    40800  
    40801 
    40802 > matchmaker #41 to #1.8 & sel
    40803 
    40804 Parameters 
    40805 --- 
    40806 Chain pairing | bb 
    40807 Alignment algorithm | Needleman-Wunsch 
    40808 Similarity matrix | BLOSUM-62 
    40809 SS fraction | 0.3 
    40810 Gap open (HH/SS/other) | 18/18/6 
    40811 Gap extend | 1 
    40812 SS matrix |  |  | H | S | O 
    40813 ---|---|---|--- 
    40814 H | 6 | -9 | -6 
    40815 S |  | 6 | -6 
    40816 O |  |  | 4 
    40817 Iteration cutoff | 2 
    40818  
    40819 Matchmaker 3j0c.pdb1, chain C (#1.8) with AF3 CA.pdb, chain A (#41), sequence
    40820 alignment score = 328.1 
    40821 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    40822 2.714) 
    40823  
    40824 
    40825 > hide sel cartoons
    40826 
    40827 > show #32 models
    40828 
    40829 > color #37 dodgerblue
    40830 
    40831 > color #38 dodgerblue
    40832 
    40833 > color #39 #00b305ff
    40834 
    40835 > color #40 #00b305ff
    40836 
    40837 > color #41 #f15839ff
    40838 
    40839 > select #1.9/A
    40840 
    40841 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    40842 
    40843 > show sel cartoons
    40844 
    40845 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    40846 
    40847 Chain information for AF3 E1 1-421.pdb #42 
    40848 --- 
    40849 Chain | Description 
    40850 A | No description available 
    40851  
    40852 
    40853 > matchmaker #42 to #1.8 & sel
    40854 
    40855 No 'to' model specified 
    40856 
    40857 > matchmaker #42 to #1.9 & sel
    40858 
    40859 Parameters 
    40860 --- 
    40861 Chain pairing | bb 
    40862 Alignment algorithm | Needleman-Wunsch 
    40863 Similarity matrix | BLOSUM-62 
    40864 SS fraction | 0.3 
    40865 Gap open (HH/SS/other) | 18/18/6 
    40866 Gap extend | 1 
    40867 SS matrix |  |  | H | S | O 
    40868 ---|---|---|--- 
    40869 H | 6 | -9 | -6 
    40870 S |  | 6 | -6 
    40871 O |  |  | 4 
    40872 Iteration cutoff | 2 
    40873  
    40874 Matchmaker 3j0c.pdb1, chain A (#1.9) with AF3 E1 1-421.pdb, chain A (#42),
    40875 sequence alignment score = 1060.7 
    40876 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    40877 3.020) 
    40878  
    40879 
    40880 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    40881 
    40882 Chain information for AF3 E1 422-461.pdb #43 
    40883 --- 
    40884 Chain | Description 
    40885 A | No description available 
    40886  
    40887 
    40888 > matchmaker #43 to #1.9 & sel
    40889 
    40890 Parameters 
    40891 --- 
    40892 Chain pairing | bb 
    40893 Alignment algorithm | Needleman-Wunsch 
    40894 Similarity matrix | BLOSUM-62 
    40895 SS fraction | 0.3 
    40896 Gap open (HH/SS/other) | 18/18/6 
    40897 Gap extend | 1 
    40898 SS matrix |  |  | H | S | O 
    40899 ---|---|---|--- 
    40900 H | 6 | -9 | -6 
    40901 S |  | 6 | -6 
    40902 O |  |  | 4 
    40903 Iteration cutoff | 2 
    40904  
    40905 Matchmaker 3j0c.pdb1, chain A (#1.9) with AF3 E1 422-461.pdb, chain A (#43),
    40906 sequence alignment score = 626.9 
    40907 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    40908 2.775) 
    40909  
    40910 
    40911 > hide sel cartoons
    40912 
    40913 > select #1.9/B
    40914 
    40915 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    40916 
    40917 > show sel cartoons
    40918 
    40919 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    40920 
    40921 Chain information for AF3 E2 1-352.pdb #44 
    40922 --- 
    40923 Chain | Description 
    40924 B | No description available 
    40925  
    40926 
    40927 > matchmaker #44 to #1.9 & sel
    40928 
    40929 Parameters 
    40930 --- 
    40931 Chain pairing | bb 
    40932 Alignment algorithm | Needleman-Wunsch 
    40933 Similarity matrix | BLOSUM-62 
    40934 SS fraction | 0.3 
    40935 Gap open (HH/SS/other) | 18/18/6 
    40936 Gap extend | 1 
    40937 SS matrix |  |  | H | S | O 
    40938 ---|---|---|--- 
    40939 H | 6 | -9 | -6 
    40940 S |  | 6 | -6 
    40941 O |  |  | 4 
    40942 Iteration cutoff | 2 
    40943  
    40944 Matchmaker 3j0c.pdb1, chain B (#1.9) with AF3 E2 1-352.pdb, chain B (#44),
    40945 sequence alignment score = 583.7 
    40946 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    40947 5.933) 
    40948  
    40949 
    40950 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    40951 
    40952 Chain information for AF3 E2 353-438.pdb #45 
    40953 --- 
    40954 Chain | Description 
    40955 B | No description available 
    40956  
    40957 
    40958 > matchmaker #45 to #1.9 & sel
    40959 
    40960 Parameters 
    40961 --- 
    40962 Chain pairing | bb 
    40963 Alignment algorithm | Needleman-Wunsch 
    40964 Similarity matrix | BLOSUM-62 
    40965 SS fraction | 0.3 
    40966 Gap open (HH/SS/other) | 18/18/6 
    40967 Gap extend | 1 
    40968 SS matrix |  |  | H | S | O 
    40969 ---|---|---|--- 
    40970 H | 6 | -9 | -6 
    40971 S |  | 6 | -6 
    40972 O |  |  | 4 
    40973 Iteration cutoff | 2 
    40974  
    40975 Matchmaker 3j0c.pdb1, chain B (#1.9) with AF3 E2 353-438.pdb, chain B (#45),
    40976 sequence alignment score = 322.6 
    40977 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    40978 8.411) 
    40979  
    40980 
    40981 > hide sel cartoons
    40982 
    40983 > select #1.9/C
    40984 
    40985 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    40986 
    40987 > show sel cartoons
    40988 
    40989 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    40990 
    40991 Chain information for AF3 CA.pdb #46 
    40992 --- 
    40993 Chain | Description 
    40994 A | No description available 
    40995  
    40996 
    40997 > matchmaker #46 to #1.9 & sel
    40998 
    40999 Parameters 
    41000 --- 
    41001 Chain pairing | bb 
    41002 Alignment algorithm | Needleman-Wunsch 
    41003 Similarity matrix | BLOSUM-62 
    41004 SS fraction | 0.3 
    41005 Gap open (HH/SS/other) | 18/18/6 
    41006 Gap extend | 1 
    41007 SS matrix |  |  | H | S | O 
    41008 ---|---|---|--- 
    41009 H | 6 | -9 | -6 
    41010 S |  | 6 | -6 
    41011 O |  |  | 4 
    41012 Iteration cutoff | 2 
    41013  
    41014 Matchmaker 3j0c.pdb1, chain C (#1.9) with AF3 CA.pdb, chain A (#46), sequence
    41015 alignment score = 328.1 
    41016 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    41017 2.714) 
    41018  
    41019 
    41020 > hide sel cartoons
    41021 
    41022 > hide #42 models
    41023 
    41024 > show #42 models
    41025 
    41026 > color #42 dodgerblue
    41027 
    41028 > color #43 dodgerblue
    41029 
    41030 > color #44 #00b305ff
    41031 
    41032 > color #45 #00b305ff
    41033 
    41034 > color #46 #f15839ff
    41035 
    41036 > select #1.10/A
    41037 
    41038 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    41039 
    41040 > show sel cartoons
    41041 
    41042 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    41043 
    41044 Chain information for AF3 E1 1-421.pdb #47 
    41045 --- 
    41046 Chain | Description 
    41047 A | No description available 
    41048  
    41049 
    41050 > matchmaker #47 to #1.10 & sel
    41051 
    41052 Parameters 
    41053 --- 
    41054 Chain pairing | bb 
    41055 Alignment algorithm | Needleman-Wunsch 
    41056 Similarity matrix | BLOSUM-62 
    41057 SS fraction | 0.3 
    41058 Gap open (HH/SS/other) | 18/18/6 
    41059 Gap extend | 1 
    41060 SS matrix |  |  | H | S | O 
    41061 ---|---|---|--- 
    41062 H | 6 | -9 | -6 
    41063 S |  | 6 | -6 
    41064 O |  |  | 4 
    41065 Iteration cutoff | 2 
    41066  
    41067 Matchmaker 3j0c.pdb1, chain A (#1.10) with AF3 E1 1-421.pdb, chain A (#47),
    41068 sequence alignment score = 1060.7 
    41069 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    41070 3.020) 
    41071  
    41072 
    41073 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    41074 
    41075 Chain information for AF3 E1 422-461.pdb #48 
    41076 --- 
    41077 Chain | Description 
    41078 A | No description available 
    41079  
    41080 
    41081 > matchmaker #47 to #1.10 & sel
    41082 
    41083 Parameters 
    41084 --- 
    41085 Chain pairing | bb 
    41086 Alignment algorithm | Needleman-Wunsch 
    41087 Similarity matrix | BLOSUM-62 
    41088 SS fraction | 0.3 
    41089 Gap open (HH/SS/other) | 18/18/6 
    41090 Gap extend | 1 
    41091 SS matrix |  |  | H | S | O 
    41092 ---|---|---|--- 
    41093 H | 6 | -9 | -6 
    41094 S |  | 6 | -6 
    41095 O |  |  | 4 
    41096 Iteration cutoff | 2 
    41097  
    41098 Matchmaker 3j0c.pdb1, chain A (#1.10) with AF3 E1 1-421.pdb, chain A (#47),
    41099 sequence alignment score = 1060.7 
    41100 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    41101 3.020) 
    41102  
    41103 
    41104 > matchmaker #47 to #1.10 & sel
    41105 
    41106 Parameters 
    41107 --- 
    41108 Chain pairing | bb 
    41109 Alignment algorithm | Needleman-Wunsch 
    41110 Similarity matrix | BLOSUM-62 
    41111 SS fraction | 0.3 
    41112 Gap open (HH/SS/other) | 18/18/6 
    41113 Gap extend | 1 
    41114 SS matrix |  |  | H | S | O 
    41115 ---|---|---|--- 
    41116 H | 6 | -9 | -6 
    41117 S |  | 6 | -6 
    41118 O |  |  | 4 
    41119 Iteration cutoff | 2 
    41120  
    41121 Matchmaker 3j0c.pdb1, chain A (#1.10) with AF3 E1 1-421.pdb, chain A (#47),
    41122 sequence alignment score = 1060.7 
    41123 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    41124 3.020) 
    41125  
    41126 
    41127 > matchmaker #48 to #1.10 & sel
    41128 
    41129 Parameters 
    41130 --- 
    41131 Chain pairing | bb 
    41132 Alignment algorithm | Needleman-Wunsch 
    41133 Similarity matrix | BLOSUM-62 
    41134 SS fraction | 0.3 
    41135 Gap open (HH/SS/other) | 18/18/6 
    41136 Gap extend | 1 
    41137 SS matrix |  |  | H | S | O 
    41138 ---|---|---|--- 
    41139 H | 6 | -9 | -6 
    41140 S |  | 6 | -6 
    41141 O |  |  | 4 
    41142 Iteration cutoff | 2 
    41143  
    41144 Matchmaker 3j0c.pdb1, chain A (#1.10) with AF3 E1 422-461.pdb, chain A (#48),
    41145 sequence alignment score = 626.9 
    41146 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    41147 2.776) 
    41148  
    41149 
    41150 > hide sel cartoons
    41151 
    41152 > select #1.10/B
    41153 
    41154 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    41155 
    41156 > show sel cartoons
    41157 
    41158 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    41159 
    41160 Chain information for AF3 E2 1-352.pdb #49 
    41161 --- 
    41162 Chain | Description 
    41163 B | No description available 
    41164  
    41165 
    41166 > matchmaker #49 to #1.10 & sel
    41167 
    41168 Parameters 
    41169 --- 
    41170 Chain pairing | bb 
    41171 Alignment algorithm | Needleman-Wunsch 
    41172 Similarity matrix | BLOSUM-62 
    41173 SS fraction | 0.3 
    41174 Gap open (HH/SS/other) | 18/18/6 
    41175 Gap extend | 1 
    41176 SS matrix |  |  | H | S | O 
    41177 ---|---|---|--- 
    41178 H | 6 | -9 | -6 
    41179 S |  | 6 | -6 
    41180 O |  |  | 4 
    41181 Iteration cutoff | 2 
    41182  
    41183 Matchmaker 3j0c.pdb1, chain B (#1.10) with AF3 E2 1-352.pdb, chain B (#49),
    41184 sequence alignment score = 583.7 
    41185 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    41186 5.933) 
    41187  
    41188 
    41189 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    41190 
    41191 Chain information for AF3 E2 353-438.pdb #50 
    41192 --- 
    41193 Chain | Description 
    41194 B | No description available 
    41195  
    41196 
    41197 > matchmaker #50 to #1.10 & sel
    41198 
    41199 Parameters 
    41200 --- 
    41201 Chain pairing | bb 
    41202 Alignment algorithm | Needleman-Wunsch 
    41203 Similarity matrix | BLOSUM-62 
    41204 SS fraction | 0.3 
    41205 Gap open (HH/SS/other) | 18/18/6 
    41206 Gap extend | 1 
    41207 SS matrix |  |  | H | S | O 
    41208 ---|---|---|--- 
    41209 H | 6 | -9 | -6 
    41210 S |  | 6 | -6 
    41211 O |  |  | 4 
    41212 Iteration cutoff | 2 
    41213  
    41214 Matchmaker 3j0c.pdb1, chain B (#1.10) with AF3 E2 353-438.pdb, chain B (#50),
    41215 sequence alignment score = 322.6 
    41216 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    41217 8.411) 
    41218  
    41219 
    41220 > hide sel cartoons
    41221 
    41222 > select #1.10/C
    41223 
    41224 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    41225 
    41226 > show sel cartoons
    41227 
    41228 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    41229 
    41230 Chain information for AF3 CA.pdb #51 
    41231 --- 
    41232 Chain | Description 
    41233 A | No description available 
    41234  
    41235 
    41236 > matchmaker #51 to #1.10 & sel
    41237 
    41238 Parameters 
    41239 --- 
    41240 Chain pairing | bb 
    41241 Alignment algorithm | Needleman-Wunsch 
    41242 Similarity matrix | BLOSUM-62 
    41243 SS fraction | 0.3 
    41244 Gap open (HH/SS/other) | 18/18/6 
    41245 Gap extend | 1 
    41246 SS matrix |  |  | H | S | O 
    41247 ---|---|---|--- 
    41248 H | 6 | -9 | -6 
    41249 S |  | 6 | -6 
    41250 O |  |  | 4 
    41251 Iteration cutoff | 2 
    41252  
    41253 Matchmaker 3j0c.pdb1, chain C (#1.10) with AF3 CA.pdb, chain A (#51), sequence
    41254 alignment score = 328.1 
    41255 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    41256 2.714) 
    41257  
    41258 
    41259 > hide sel cartoons
    41260 
    41261 > color #47 dodgerblue
    41262 
    41263 > color #48 dodgerblue
    41264 
    41265 > color #49 #00b305ff
    41266 
    41267 > color #50 #00b305ff
    41268 
    41269 > color #51 #f15839ff
    41270 
    41271 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    41272 
    41273 > select #1.11/A
    41274 
    41275 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    41276 
    41277 > show sel cartoons
    41278 
    41279 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    41280 
    41281 Chain information for AF3 E1 1-421.pdb #52 
    41282 --- 
    41283 Chain | Description 
    41284 A | No description available 
    41285  
    41286 
    41287 > matchmaker #52 to #1.11 & sel
    41288 
    41289 Parameters 
    41290 --- 
    41291 Chain pairing | bb 
    41292 Alignment algorithm | Needleman-Wunsch 
    41293 Similarity matrix | BLOSUM-62 
    41294 SS fraction | 0.3 
    41295 Gap open (HH/SS/other) | 18/18/6 
    41296 Gap extend | 1 
    41297 SS matrix |  |  | H | S | O 
    41298 ---|---|---|--- 
    41299 H | 6 | -9 | -6 
    41300 S |  | 6 | -6 
    41301 O |  |  | 4 
    41302 Iteration cutoff | 2 
    41303  
    41304 Matchmaker 3j0c.pdb1, chain A (#1.11) with AF3 E1 1-421.pdb, chain A (#52),
    41305 sequence alignment score = 1060.7 
    41306 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    41307 3.020) 
    41308  
    41309 
    41310 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    41311 
    41312 Chain information for AF3 E1 422-461.pdb #53 
    41313 --- 
    41314 Chain | Description 
    41315 A | No description available 
    41316  
    41317 
    41318 > matchmaker #53 to #1.11 & sel
    41319 
    41320 Parameters 
    41321 --- 
    41322 Chain pairing | bb 
    41323 Alignment algorithm | Needleman-Wunsch 
    41324 Similarity matrix | BLOSUM-62 
    41325 SS fraction | 0.3 
    41326 Gap open (HH/SS/other) | 18/18/6 
    41327 Gap extend | 1 
    41328 SS matrix |  |  | H | S | O 
    41329 ---|---|---|--- 
    41330 H | 6 | -9 | -6 
    41331 S |  | 6 | -6 
    41332 O |  |  | 4 
    41333 Iteration cutoff | 2 
    41334  
    41335 Matchmaker 3j0c.pdb1, chain A (#1.11) with AF3 E1 422-461.pdb, chain A (#53),
    41336 sequence alignment score = 626.9 
    41337 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    41338 2.776) 
    41339  
    41340 
    41341 > hide sel cartoons
    41342 
    41343 > select #1.11/B
    41344 
    41345 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    41346 
    41347 > show sel cartoons
    41348 
    41349 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    41350 
    41351 Chain information for AF3 E2 1-352.pdb #54 
    41352 --- 
    41353 Chain | Description 
    41354 B | No description available 
    41355  
    41356 
    41357 > matchmaker #54 to #1.11 & sel
    41358 
    41359 Parameters 
    41360 --- 
    41361 Chain pairing | bb 
    41362 Alignment algorithm | Needleman-Wunsch 
    41363 Similarity matrix | BLOSUM-62 
    41364 SS fraction | 0.3 
    41365 Gap open (HH/SS/other) | 18/18/6 
    41366 Gap extend | 1 
    41367 SS matrix |  |  | H | S | O 
    41368 ---|---|---|--- 
    41369 H | 6 | -9 | -6 
    41370 S |  | 6 | -6 
    41371 O |  |  | 4 
    41372 Iteration cutoff | 2 
    41373  
    41374 Matchmaker 3j0c.pdb1, chain B (#1.11) with AF3 E2 1-352.pdb, chain B (#54),
    41375 sequence alignment score = 583.7 
    41376 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    41377 5.933) 
    41378  
    41379 
    41380 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    41381 
    41382 Chain information for AF3 E2 353-438.pdb #55 
    41383 --- 
    41384 Chain | Description 
    41385 B | No description available 
    41386  
    41387 
    41388 > matchmaker #55 to #1.11 & sel
    41389 
    41390 Parameters 
    41391 --- 
    41392 Chain pairing | bb 
    41393 Alignment algorithm | Needleman-Wunsch 
    41394 Similarity matrix | BLOSUM-62 
    41395 SS fraction | 0.3 
    41396 Gap open (HH/SS/other) | 18/18/6 
    41397 Gap extend | 1 
    41398 SS matrix |  |  | H | S | O 
    41399 ---|---|---|--- 
    41400 H | 6 | -9 | -6 
    41401 S |  | 6 | -6 
    41402 O |  |  | 4 
    41403 Iteration cutoff | 2 
    41404  
    41405 Matchmaker 3j0c.pdb1, chain B (#1.11) with AF3 E2 353-438.pdb, chain B (#55),
    41406 sequence alignment score = 333.4 
    41407 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    41408 8.411) 
    41409  
    41410 
    41411 > hide sel cartoons
    41412 
    41413 > select #1.11/C
    41414 
    41415 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    41416 
    41417 > show sel cartoons
    41418 
    41419 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    41420 
    41421 Chain information for AF3 CA.pdb #56 
    41422 --- 
    41423 Chain | Description 
    41424 A | No description available 
    41425  
    41426 
    41427 > matchmaker #56 to #1.11 & sel
    41428 
    41429 Parameters 
    41430 --- 
    41431 Chain pairing | bb 
    41432 Alignment algorithm | Needleman-Wunsch 
    41433 Similarity matrix | BLOSUM-62 
    41434 SS fraction | 0.3 
    41435 Gap open (HH/SS/other) | 18/18/6 
    41436 Gap extend | 1 
    41437 SS matrix |  |  | H | S | O 
    41438 ---|---|---|--- 
    41439 H | 6 | -9 | -6 
    41440 S |  | 6 | -6 
    41441 O |  |  | 4 
    41442 Iteration cutoff | 2 
    41443  
    41444 Matchmaker 3j0c.pdb1, chain C (#1.11) with AF3 CA.pdb, chain A (#56), sequence
    41445 alignment score = 328.1 
    41446 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    41447 2.714) 
    41448  
    41449 
    41450 > hide sel cartoons
    41451 
    41452 > color #52 dodgerblue
    41453 
    41454 > color #53 dodgerblue
    41455 
    41456 > color #54 #00b305ff
    41457 
    41458 > color #55 #00b305ff
    41459 
    41460 > color #56 #f15839ff
    41461 
    41462 > select #1.12/A
    41463 
    41464 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    41465 
    41466 > show sel cartoons
    41467 
    41468 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    41469 
    41470 Chain information for AF3 E1 1-421.pdb #57 
    41471 --- 
    41472 Chain | Description 
    41473 A | No description available 
    41474  
    41475 
    41476 > matchmaker #57 to #1.12 & sel
    41477 
    41478 Parameters 
    41479 --- 
    41480 Chain pairing | bb 
    41481 Alignment algorithm | Needleman-Wunsch 
    41482 Similarity matrix | BLOSUM-62 
    41483 SS fraction | 0.3 
    41484 Gap open (HH/SS/other) | 18/18/6 
    41485 Gap extend | 1 
    41486 SS matrix |  |  | H | S | O 
    41487 ---|---|---|--- 
    41488 H | 6 | -9 | -6 
    41489 S |  | 6 | -6 
    41490 O |  |  | 4 
    41491 Iteration cutoff | 2 
    41492  
    41493 Matchmaker 3j0c.pdb1, chain A (#1.12) with AF3 E1 1-421.pdb, chain A (#57),
    41494 sequence alignment score = 1060.7 
    41495 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    41496 3.020) 
    41497  
    41498 
    41499 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    41500 
    41501 Chain information for AF3 E1 422-461.pdb #58 
    41502 --- 
    41503 Chain | Description 
    41504 A | No description available 
    41505  
    41506 
    41507 > matchmaker #58 to #1.12 & sel
    41508 
    41509 Parameters 
    41510 --- 
    41511 Chain pairing | bb 
    41512 Alignment algorithm | Needleman-Wunsch 
    41513 Similarity matrix | BLOSUM-62 
    41514 SS fraction | 0.3 
    41515 Gap open (HH/SS/other) | 18/18/6 
    41516 Gap extend | 1 
    41517 SS matrix |  |  | H | S | O 
    41518 ---|---|---|--- 
    41519 H | 6 | -9 | -6 
    41520 S |  | 6 | -6 
    41521 O |  |  | 4 
    41522 Iteration cutoff | 2 
    41523  
    41524 Matchmaker 3j0c.pdb1, chain A (#1.12) with AF3 E1 422-461.pdb, chain A (#58),
    41525 sequence alignment score = 626.9 
    41526 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    41527 2.776) 
    41528  
    41529 
    41530 > hide sel cartoons
    41531 
    41532 > select #1.12/B
    41533 
    41534 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    41535 
    41536 > show sel cartoons
    41537 
    41538 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    41539 
    41540 Chain information for AF3 E2 1-352.pdb #59 
    41541 --- 
    41542 Chain | Description 
    41543 B | No description available 
    41544  
    41545 
    41546 > matchmaker #59 to #1.12 & sel
    41547 
    41548 Parameters 
    41549 --- 
    41550 Chain pairing | bb 
    41551 Alignment algorithm | Needleman-Wunsch 
    41552 Similarity matrix | BLOSUM-62 
    41553 SS fraction | 0.3 
    41554 Gap open (HH/SS/other) | 18/18/6 
    41555 Gap extend | 1 
    41556 SS matrix |  |  | H | S | O 
    41557 ---|---|---|--- 
    41558 H | 6 | -9 | -6 
    41559 S |  | 6 | -6 
    41560 O |  |  | 4 
    41561 Iteration cutoff | 2 
    41562  
    41563 Matchmaker 3j0c.pdb1, chain B (#1.12) with AF3 E2 1-352.pdb, chain B (#59),
    41564 sequence alignment score = 583.7 
    41565 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    41566 5.933) 
    41567  
    41568 
    41569 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    41570 
    41571 Chain information for AF3 E2 353-438.pdb #60 
    41572 --- 
    41573 Chain | Description 
    41574 B | No description available 
    41575  
    41576 
    41577 > matchmaker #60 to #1.12 & sel
    41578 
    41579 Parameters 
    41580 --- 
    41581 Chain pairing | bb 
    41582 Alignment algorithm | Needleman-Wunsch 
    41583 Similarity matrix | BLOSUM-62 
    41584 SS fraction | 0.3 
    41585 Gap open (HH/SS/other) | 18/18/6 
    41586 Gap extend | 1 
    41587 SS matrix |  |  | H | S | O 
    41588 ---|---|---|--- 
    41589 H | 6 | -9 | -6 
    41590 S |  | 6 | -6 
    41591 O |  |  | 4 
    41592 Iteration cutoff | 2 
    41593  
    41594 Matchmaker 3j0c.pdb1, chain B (#1.12) with AF3 E2 353-438.pdb, chain B (#60),
    41595 sequence alignment score = 333.4 
    41596 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    41597 8.411) 
    41598  
    41599 
    41600 > hide sel cartoons
    41601 
    41602 > select #1.12/C
    41603 
    41604 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    41605 
    41606 > show sel cartoons
    41607 
    41608 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    41609 
    41610 Chain information for AF3 CA.pdb #61 
    41611 --- 
    41612 Chain | Description 
    41613 A | No description available 
    41614  
    41615 
    41616 > matchmaker #61 to #1.12 & sel
    41617 
    41618 Parameters 
    41619 --- 
    41620 Chain pairing | bb 
    41621 Alignment algorithm | Needleman-Wunsch 
    41622 Similarity matrix | BLOSUM-62 
    41623 SS fraction | 0.3 
    41624 Gap open (HH/SS/other) | 18/18/6 
    41625 Gap extend | 1 
    41626 SS matrix |  |  | H | S | O 
    41627 ---|---|---|--- 
    41628 H | 6 | -9 | -6 
    41629 S |  | 6 | -6 
    41630 O |  |  | 4 
    41631 Iteration cutoff | 2 
    41632  
    41633 Matchmaker 3j0c.pdb1, chain C (#1.12) with AF3 CA.pdb, chain A (#61), sequence
    41634 alignment score = 328.1 
    41635 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    41636 2.714) 
    41637  
    41638 
    41639 > hide sel cartoons
    41640 
    41641 > hide #57 models
    41642 
    41643 > show #57 models
    41644 
    41645 > color #57 dodgerblue
    41646 
    41647 > color #58 dodgerblue
    41648 
    41649 > color #59 #00b305ff
    41650 
    41651 > color #60 #00b305ff
    41652 
    41653 > color #61 #f15839ff
    41654 
    41655 > select #1.13/A
    41656 
    41657 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    41658 
    41659 > show sel cartoons
    41660 
    41661 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    41662 
    41663 Chain information for AF3 E1 1-421.pdb #62 
    41664 --- 
    41665 Chain | Description 
    41666 A | No description available 
    41667  
    41668 
    41669 > matchmaker #62 to #1.12 & sel
    41670 
    41671 No 'to' model specified 
    41672 
    41673 > matchmaker #62 to #1.13 & sel
    41674 
    41675 Parameters 
    41676 --- 
    41677 Chain pairing | bb 
    41678 Alignment algorithm | Needleman-Wunsch 
    41679 Similarity matrix | BLOSUM-62 
    41680 SS fraction | 0.3 
    41681 Gap open (HH/SS/other) | 18/18/6 
    41682 Gap extend | 1 
    41683 SS matrix |  |  | H | S | O 
    41684 ---|---|---|--- 
    41685 H | 6 | -9 | -6 
    41686 S |  | 6 | -6 
    41687 O |  |  | 4 
    41688 Iteration cutoff | 2 
    41689  
    41690 Matchmaker 3j0c.pdb1, chain A (#1.13) with AF3 E1 1-421.pdb, chain A (#62),
    41691 sequence alignment score = 1060.7 
    41692 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    41693 3.020) 
    41694  
    41695 
    41696 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    41697 
    41698 Chain information for AF3 E1 422-461.pdb #63 
    41699 --- 
    41700 Chain | Description 
    41701 A | No description available 
    41702  
    41703 
    41704 > matchmaker #63 to #1.13 & sel
    41705 
    41706 Parameters 
    41707 --- 
    41708 Chain pairing | bb 
    41709 Alignment algorithm | Needleman-Wunsch 
    41710 Similarity matrix | BLOSUM-62 
    41711 SS fraction | 0.3 
    41712 Gap open (HH/SS/other) | 18/18/6 
    41713 Gap extend | 1 
    41714 SS matrix |  |  | H | S | O 
    41715 ---|---|---|--- 
    41716 H | 6 | -9 | -6 
    41717 S |  | 6 | -6 
    41718 O |  |  | 4 
    41719 Iteration cutoff | 2 
    41720  
    41721 Matchmaker 3j0c.pdb1, chain A (#1.13) with AF3 E1 422-461.pdb, chain A (#63),
    41722 sequence alignment score = 626.9 
    41723 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    41724 2.775) 
    41725  
    41726 
    41727 > hide sel cartoons
    41728 
    41729 > select #1.13/B
    41730 
    41731 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    41732 
    41733 > show sel cartoons
    41734 
    41735 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    41736 
    41737 Chain information for AF3 E2 1-352.pdb #64 
    41738 --- 
    41739 Chain | Description 
    41740 B | No description available 
    41741  
    41742 
    41743 > matchmaker #64 to #1.13 & sel
    41744 
    41745 Parameters 
    41746 --- 
    41747 Chain pairing | bb 
    41748 Alignment algorithm | Needleman-Wunsch 
    41749 Similarity matrix | BLOSUM-62 
    41750 SS fraction | 0.3 
    41751 Gap open (HH/SS/other) | 18/18/6 
    41752 Gap extend | 1 
    41753 SS matrix |  |  | H | S | O 
    41754 ---|---|---|--- 
    41755 H | 6 | -9 | -6 
    41756 S |  | 6 | -6 
    41757 O |  |  | 4 
    41758 Iteration cutoff | 2 
    41759  
    41760 Matchmaker 3j0c.pdb1, chain B (#1.13) with AF3 E2 1-352.pdb, chain B (#64),
    41761 sequence alignment score = 583.7 
    41762 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    41763 5.933) 
    41764  
    41765 
    41766 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    41767 
    41768 Chain information for AF3 E2 353-438.pdb #65 
    41769 --- 
    41770 Chain | Description 
    41771 B | No description available 
    41772  
    41773 
    41774 > matchmaker #65 to #1.13 & sel
    41775 
    41776 Parameters 
    41777 --- 
    41778 Chain pairing | bb 
    41779 Alignment algorithm | Needleman-Wunsch 
    41780 Similarity matrix | BLOSUM-62 
    41781 SS fraction | 0.3 
    41782 Gap open (HH/SS/other) | 18/18/6 
    41783 Gap extend | 1 
    41784 SS matrix |  |  | H | S | O 
    41785 ---|---|---|--- 
    41786 H | 6 | -9 | -6 
    41787 S |  | 6 | -6 
    41788 O |  |  | 4 
    41789 Iteration cutoff | 2 
    41790  
    41791 Matchmaker 3j0c.pdb1, chain B (#1.13) with AF3 E2 353-438.pdb, chain B (#65),
    41792 sequence alignment score = 322.6 
    41793 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    41794 8.411) 
    41795  
    41796 
    41797 > select #1.13/C
    41798 
    41799 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    41800 
    41801 > show sel cartoons
    41802 
    41803 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    41804 
    41805 Chain information for AF3 CA.pdb #66 
    41806 --- 
    41807 Chain | Description 
    41808 A | No description available 
    41809  
    41810 
    41811 > matchmaker #66 to #1.13 & sel
    41812 
    41813 Parameters 
    41814 --- 
    41815 Chain pairing | bb 
    41816 Alignment algorithm | Needleman-Wunsch 
    41817 Similarity matrix | BLOSUM-62 
    41818 SS fraction | 0.3 
    41819 Gap open (HH/SS/other) | 18/18/6 
    41820 Gap extend | 1 
    41821 SS matrix |  |  | H | S | O 
    41822 ---|---|---|--- 
    41823 H | 6 | -9 | -6 
    41824 S |  | 6 | -6 
    41825 O |  |  | 4 
    41826 Iteration cutoff | 2 
    41827  
    41828 Matchmaker 3j0c.pdb1, chain C (#1.13) with AF3 CA.pdb, chain A (#66), sequence
    41829 alignment score = 328.1 
    41830 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    41831 2.714) 
    41832  
    41833 
    41834 > hide sel cartoons
    41835 
    41836 > select #1.13/B
    41837 
    41838 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    41839 
    41840 > hide sel cartoons
    41841 
    41842 > color #62 dodgerblue
    41843 
    41844 > color #63 dodgerblue
    41845 
    41846 > color #64 #00b305ff
    41847 
    41848 > color #65 #00b305ff
    41849 
    41850 > color #66 #f15839ff
    41851 
    41852 > select #1.14/A
    41853 
    41854 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    41855 
    41856 > show sel cartoons
    41857 
    41858 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    41859 
    41860 Chain information for AF3 E1 1-421.pdb #67 
    41861 --- 
    41862 Chain | Description 
    41863 A | No description available 
    41864  
    41865 
    41866 > matchmaker #67 to #1.13 & sel
    41867 
    41868 No 'to' model specified 
    41869 
    41870 > matchmaker #67 to #1.14 & sel
    41871 
    41872 Parameters 
    41873 --- 
    41874 Chain pairing | bb 
    41875 Alignment algorithm | Needleman-Wunsch 
    41876 Similarity matrix | BLOSUM-62 
    41877 SS fraction | 0.3 
    41878 Gap open (HH/SS/other) | 18/18/6 
    41879 Gap extend | 1 
    41880 SS matrix |  |  | H | S | O 
    41881 ---|---|---|--- 
    41882 H | 6 | -9 | -6 
    41883 S |  | 6 | -6 
    41884 O |  |  | 4 
    41885 Iteration cutoff | 2 
    41886  
    41887 Matchmaker 3j0c.pdb1, chain A (#1.14) with AF3 E1 1-421.pdb, chain A (#67),
    41888 sequence alignment score = 1060.7 
    41889 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    41890 3.020) 
    41891  
    41892 
    41893 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    41894 
    41895 Chain information for AF3 E1 422-461.pdb #68 
    41896 --- 
    41897 Chain | Description 
    41898 A | No description available 
    41899  
    41900 
    41901 > matchmaker #68 to #1.14 & sel
    41902 
    41903 Parameters 
    41904 --- 
    41905 Chain pairing | bb 
    41906 Alignment algorithm | Needleman-Wunsch 
    41907 Similarity matrix | BLOSUM-62 
    41908 SS fraction | 0.3 
    41909 Gap open (HH/SS/other) | 18/18/6 
    41910 Gap extend | 1 
    41911 SS matrix |  |  | H | S | O 
    41912 ---|---|---|--- 
    41913 H | 6 | -9 | -6 
    41914 S |  | 6 | -6 
    41915 O |  |  | 4 
    41916 Iteration cutoff | 2 
    41917  
    41918 Matchmaker 3j0c.pdb1, chain A (#1.14) with AF3 E1 422-461.pdb, chain A (#68),
    41919 sequence alignment score = 626.9 
    41920 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    41921 2.775) 
    41922  
    41923 
    41924 > hide sel cartoons
    41925 
    41926 > select #1.14/B
    41927 
    41928 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    41929 
    41930 > show sel cartoons
    41931 
    41932 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    41933 
    41934 Chain information for AF3 E2 1-352.pdb #69 
    41935 --- 
    41936 Chain | Description 
    41937 B | No description available 
    41938  
    41939 
    41940 > matchmaker #69 to #1.14 & sel
    41941 
    41942 Parameters 
    41943 --- 
    41944 Chain pairing | bb 
    41945 Alignment algorithm | Needleman-Wunsch 
    41946 Similarity matrix | BLOSUM-62 
    41947 SS fraction | 0.3 
    41948 Gap open (HH/SS/other) | 18/18/6 
    41949 Gap extend | 1 
    41950 SS matrix |  |  | H | S | O 
    41951 ---|---|---|--- 
    41952 H | 6 | -9 | -6 
    41953 S |  | 6 | -6 
    41954 O |  |  | 4 
    41955 Iteration cutoff | 2 
    41956  
    41957 Matchmaker 3j0c.pdb1, chain B (#1.14) with AF3 E2 1-352.pdb, chain B (#69),
    41958 sequence alignment score = 583.7 
    41959 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    41960 5.933) 
    41961  
    41962 
    41963 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    41964 
    41965 Chain information for AF3 E2 353-438.pdb #70 
    41966 --- 
    41967 Chain | Description 
    41968 B | No description available 
    41969  
    41970 
    41971 > matchmaker #70 to #1.14 & sel
    41972 
    41973 Parameters 
    41974 --- 
    41975 Chain pairing | bb 
    41976 Alignment algorithm | Needleman-Wunsch 
    41977 Similarity matrix | BLOSUM-62 
    41978 SS fraction | 0.3 
    41979 Gap open (HH/SS/other) | 18/18/6 
    41980 Gap extend | 1 
    41981 SS matrix |  |  | H | S | O 
    41982 ---|---|---|--- 
    41983 H | 6 | -9 | -6 
    41984 S |  | 6 | -6 
    41985 O |  |  | 4 
    41986 Iteration cutoff | 2 
    41987  
    41988 Matchmaker 3j0c.pdb1, chain B (#1.14) with AF3 E2 353-438.pdb, chain B (#70),
    41989 sequence alignment score = 322.6 
    41990 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    41991 8.411) 
    41992  
    41993 
    41994 > hide sel cartoons
    41995 
    41996 > select #1.14/C
    41997 
    41998 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    41999 
    42000 > show sel cartoons
    42001 
    42002 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    42003 
    42004 Chain information for AF3 CA.pdb #71 
    42005 --- 
    42006 Chain | Description 
    42007 A | No description available 
    42008  
    42009 
    42010 > matchmaker #71 to #1.14 & sel
    42011 
    42012 Parameters 
    42013 --- 
    42014 Chain pairing | bb 
    42015 Alignment algorithm | Needleman-Wunsch 
    42016 Similarity matrix | BLOSUM-62 
    42017 SS fraction | 0.3 
    42018 Gap open (HH/SS/other) | 18/18/6 
    42019 Gap extend | 1 
    42020 SS matrix |  |  | H | S | O 
    42021 ---|---|---|--- 
    42022 H | 6 | -9 | -6 
    42023 S |  | 6 | -6 
    42024 O |  |  | 4 
    42025 Iteration cutoff | 2 
    42026  
    42027 Matchmaker 3j0c.pdb1, chain C (#1.14) with AF3 CA.pdb, chain A (#71), sequence
    42028 alignment score = 328.1 
    42029 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    42030 2.714) 
    42031  
    42032 
    42033 > hide sel cartoons
    42034 
    42035 > color #67 dodgerblue
    42036 
    42037 > color #68 dodgerblue
    42038 
    42039 > color #69 #00b305ff
    42040 
    42041 > color #70 #00b305ff
    42042 
    42043 > color #71 #f15839ff
    42044 
    42045 > select #1.15/A
    42046 
    42047 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    42048 
    42049 > show sel cartoons
    42050 
    42051 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    42052 
    42053 Chain information for AF3 E1 1-421.pdb #72 
    42054 --- 
    42055 Chain | Description 
    42056 A | No description available 
    42057  
    42058 
    42059 > matchmaker #72 to #1.15 & sel
    42060 
    42061 Parameters 
    42062 --- 
    42063 Chain pairing | bb 
    42064 Alignment algorithm | Needleman-Wunsch 
    42065 Similarity matrix | BLOSUM-62 
    42066 SS fraction | 0.3 
    42067 Gap open (HH/SS/other) | 18/18/6 
    42068 Gap extend | 1 
    42069 SS matrix |  |  | H | S | O 
    42070 ---|---|---|--- 
    42071 H | 6 | -9 | -6 
    42072 S |  | 6 | -6 
    42073 O |  |  | 4 
    42074 Iteration cutoff | 2 
    42075  
    42076 Matchmaker 3j0c.pdb1, chain A (#1.15) with AF3 E1 1-421.pdb, chain A (#72),
    42077 sequence alignment score = 1060.7 
    42078 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    42079 3.020) 
    42080  
    42081 
    42082 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    42083 
    42084 Chain information for AF3 E1 422-461.pdb #73 
    42085 --- 
    42086 Chain | Description 
    42087 A | No description available 
    42088  
    42089 
    42090 > matchmaker #73 to #1.15 & sel
    42091 
    42092 Parameters 
    42093 --- 
    42094 Chain pairing | bb 
    42095 Alignment algorithm | Needleman-Wunsch 
    42096 Similarity matrix | BLOSUM-62 
    42097 SS fraction | 0.3 
    42098 Gap open (HH/SS/other) | 18/18/6 
    42099 Gap extend | 1 
    42100 SS matrix |  |  | H | S | O 
    42101 ---|---|---|--- 
    42102 H | 6 | -9 | -6 
    42103 S |  | 6 | -6 
    42104 O |  |  | 4 
    42105 Iteration cutoff | 2 
    42106  
    42107 Matchmaker 3j0c.pdb1, chain A (#1.15) with AF3 E1 422-461.pdb, chain A (#73),
    42108 sequence alignment score = 626.9 
    42109 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    42110 2.776) 
    42111  
    42112 
    42113 > hide sel cartoons
    42114 
    42115 > select #1.15/B
    42116 
    42117 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    42118 
    42119 > show sel cartoons
    42120 
    42121 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    42122 
    42123 Chain information for AF3 E2 1-352.pdb #74 
    42124 --- 
    42125 Chain | Description 
    42126 B | No description available 
    42127  
    42128 
    42129 > matchmaker #74 to #1.15 & sel
    42130 
    42131 Parameters 
    42132 --- 
    42133 Chain pairing | bb 
    42134 Alignment algorithm | Needleman-Wunsch 
    42135 Similarity matrix | BLOSUM-62 
    42136 SS fraction | 0.3 
    42137 Gap open (HH/SS/other) | 18/18/6 
    42138 Gap extend | 1 
    42139 SS matrix |  |  | H | S | O 
    42140 ---|---|---|--- 
    42141 H | 6 | -9 | -6 
    42142 S |  | 6 | -6 
    42143 O |  |  | 4 
    42144 Iteration cutoff | 2 
    42145  
    42146 Matchmaker 3j0c.pdb1, chain B (#1.15) with AF3 E2 1-352.pdb, chain B (#74),
    42147 sequence alignment score = 583.7 
    42148 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    42149 5.933) 
    42150  
    42151 
    42152 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    42153 
    42154 Chain information for AF3 E2 353-438.pdb #75 
    42155 --- 
    42156 Chain | Description 
    42157 B | No description available 
    42158  
    42159 
    42160 > matchmaker #75 to #1.15 & sel
    42161 
    42162 Parameters 
    42163 --- 
    42164 Chain pairing | bb 
    42165 Alignment algorithm | Needleman-Wunsch 
    42166 Similarity matrix | BLOSUM-62 
    42167 SS fraction | 0.3 
    42168 Gap open (HH/SS/other) | 18/18/6 
    42169 Gap extend | 1 
    42170 SS matrix |  |  | H | S | O 
    42171 ---|---|---|--- 
    42172 H | 6 | -9 | -6 
    42173 S |  | 6 | -6 
    42174 O |  |  | 4 
    42175 Iteration cutoff | 2 
    42176  
    42177 Matchmaker 3j0c.pdb1, chain B (#1.15) with AF3 E2 353-438.pdb, chain B (#75),
    42178 sequence alignment score = 333.4 
    42179 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    42180 8.411) 
    42181  
    42182 
    42183 > hide sel cartoons
    42184 
    42185 > select #1.15/C
    42186 
    42187 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    42188 
    42189 > show sel cartoons
    42190 
    42191 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    42192 
    42193 Chain information for AF3 CA.pdb #76 
    42194 --- 
    42195 Chain | Description 
    42196 A | No description available 
    42197  
    42198 
    42199 > matchmaker #76 to #1.15 & sel
    42200 
    42201 Parameters 
    42202 --- 
    42203 Chain pairing | bb 
    42204 Alignment algorithm | Needleman-Wunsch 
    42205 Similarity matrix | BLOSUM-62 
    42206 SS fraction | 0.3 
    42207 Gap open (HH/SS/other) | 18/18/6 
    42208 Gap extend | 1 
    42209 SS matrix |  |  | H | S | O 
    42210 ---|---|---|--- 
    42211 H | 6 | -9 | -6 
    42212 S |  | 6 | -6 
    42213 O |  |  | 4 
    42214 Iteration cutoff | 2 
    42215  
    42216 Matchmaker 3j0c.pdb1, chain C (#1.15) with AF3 CA.pdb, chain A (#76), sequence
    42217 alignment score = 328.1 
    42218 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    42219 2.714) 
    42220  
    42221 
    42222 > hide sel cartoons
    42223 
    42224 > color #72 dodgerblue
    42225 
    42226 > color #73 dodgerblue
    42227 
    42228 > color #74 #00b305ff
    42229 
    42230 > color #75 #00b305ff
    42231 
    42232 > color #76 #f15839ff
    42233 
    42234 > select #1.16/A
    42235 
    42236 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    42237 
    42238 > show sel cartoons
    42239 
    42240 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    42241 
    42242 Chain information for AF3 E1 1-421.pdb #77 
    42243 --- 
    42244 Chain | Description 
    42245 A | No description available 
    42246  
    42247 
    42248 > matchmaker #77 to #1.16 & sel
    42249 
    42250 Parameters 
    42251 --- 
    42252 Chain pairing | bb 
    42253 Alignment algorithm | Needleman-Wunsch 
    42254 Similarity matrix | BLOSUM-62 
    42255 SS fraction | 0.3 
    42256 Gap open (HH/SS/other) | 18/18/6 
    42257 Gap extend | 1 
    42258 SS matrix |  |  | H | S | O 
    42259 ---|---|---|--- 
    42260 H | 6 | -9 | -6 
    42261 S |  | 6 | -6 
    42262 O |  |  | 4 
    42263 Iteration cutoff | 2 
    42264  
    42265 Matchmaker 3j0c.pdb1, chain A (#1.16) with AF3 E1 1-421.pdb, chain A (#77),
    42266 sequence alignment score = 1060.7 
    42267 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    42268 3.020) 
    42269  
    42270 
    42271 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    42272 
    42273 Chain information for AF3 E1 422-461.pdb #78 
    42274 --- 
    42275 Chain | Description 
    42276 A | No description available 
    42277  
    42278 
    42279 > matchmaker #78 to #1.16 & sel
    42280 
    42281 Parameters 
    42282 --- 
    42283 Chain pairing | bb 
    42284 Alignment algorithm | Needleman-Wunsch 
    42285 Similarity matrix | BLOSUM-62 
    42286 SS fraction | 0.3 
    42287 Gap open (HH/SS/other) | 18/18/6 
    42288 Gap extend | 1 
    42289 SS matrix |  |  | H | S | O 
    42290 ---|---|---|--- 
    42291 H | 6 | -9 | -6 
    42292 S |  | 6 | -6 
    42293 O |  |  | 4 
    42294 Iteration cutoff | 2 
    42295  
    42296 Matchmaker 3j0c.pdb1, chain A (#1.16) with AF3 E1 422-461.pdb, chain A (#78),
    42297 sequence alignment score = 626.9 
    42298 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    42299 2.775) 
    42300  
    42301 
    42302 > hide sel cartoons
    42303 
    42304 > select #1.16/B
    42305 
    42306 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    42307 
    42308 > show sel cartoons
    42309 
    42310 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    42311 
    42312 Chain information for AF3 E2 1-352.pdb #79 
    42313 --- 
    42314 Chain | Description 
    42315 B | No description available 
    42316  
    42317 
    42318 > matchmaker #79 to #1.16 & sel
    42319 
    42320 Parameters 
    42321 --- 
    42322 Chain pairing | bb 
    42323 Alignment algorithm | Needleman-Wunsch 
    42324 Similarity matrix | BLOSUM-62 
    42325 SS fraction | 0.3 
    42326 Gap open (HH/SS/other) | 18/18/6 
    42327 Gap extend | 1 
    42328 SS matrix |  |  | H | S | O 
    42329 ---|---|---|--- 
    42330 H | 6 | -9 | -6 
    42331 S |  | 6 | -6 
    42332 O |  |  | 4 
    42333 Iteration cutoff | 2 
    42334  
    42335 Matchmaker 3j0c.pdb1, chain B (#1.16) with AF3 E2 1-352.pdb, chain B (#79),
    42336 sequence alignment score = 583.7 
    42337 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    42338 5.933) 
    42339  
    42340 
    42341 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    42342 
    42343 Chain information for AF3 E2 353-438.pdb #80 
    42344 --- 
    42345 Chain | Description 
    42346 B | No description available 
    42347  
    42348 
    42349 > matchmaker #80 to #1.16 & sel
    42350 
    42351 Parameters 
    42352 --- 
    42353 Chain pairing | bb 
    42354 Alignment algorithm | Needleman-Wunsch 
    42355 Similarity matrix | BLOSUM-62 
    42356 SS fraction | 0.3 
    42357 Gap open (HH/SS/other) | 18/18/6 
    42358 Gap extend | 1 
    42359 SS matrix |  |  | H | S | O 
    42360 ---|---|---|--- 
    42361 H | 6 | -9 | -6 
    42362 S |  | 6 | -6 
    42363 O |  |  | 4 
    42364 Iteration cutoff | 2 
    42365  
    42366 Matchmaker 3j0c.pdb1, chain B (#1.16) with AF3 E2 353-438.pdb, chain B (#80),
    42367 sequence alignment score = 322.6 
    42368 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    42369 8.411) 
    42370  
    42371 
    42372 > hide sel cartoons
    42373 
    42374 > select #1.16/C
    42375 
    42376 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    42377 
    42378 > show sel cartoons
    42379 
    42380 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    42381 
    42382 Chain information for AF3 CA.pdb #81 
    42383 --- 
    42384 Chain | Description 
    42385 A | No description available 
    42386  
    42387 
    42388 > matchmaker #81 to #1.16 & sel
    42389 
    42390 Parameters 
    42391 --- 
    42392 Chain pairing | bb 
    42393 Alignment algorithm | Needleman-Wunsch 
    42394 Similarity matrix | BLOSUM-62 
    42395 SS fraction | 0.3 
    42396 Gap open (HH/SS/other) | 18/18/6 
    42397 Gap extend | 1 
    42398 SS matrix |  |  | H | S | O 
    42399 ---|---|---|--- 
    42400 H | 6 | -9 | -6 
    42401 S |  | 6 | -6 
    42402 O |  |  | 4 
    42403 Iteration cutoff | 2 
    42404  
    42405 Matchmaker 3j0c.pdb1, chain C (#1.16) with AF3 CA.pdb, chain A (#81), sequence
    42406 alignment score = 328.1 
    42407 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    42408 2.714) 
    42409  
    42410 
    42411 > hide sel cartoons
    42412 
    42413 > color #77 dodgerblue
    42414 
    42415 > color #78 dodgerblue
    42416 
    42417 > color #79 #00b305ff
    42418 
    42419 > color #80 #00b305ff
    42420 
    42421 > color #81 #f15839ff
    42422 
    42423 > select #1.17/A
    42424 
    42425 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    42426 
    42427 > show sel cartoons
    42428 
    42429 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    42430 
    42431 Chain information for AF3 E1 1-421.pdb #82 
    42432 --- 
    42433 Chain | Description 
    42434 A | No description available 
    42435  
    42436 
    42437 > matchmaker #82 to #1.17 & sel
    42438 
    42439 Parameters 
    42440 --- 
    42441 Chain pairing | bb 
    42442 Alignment algorithm | Needleman-Wunsch 
    42443 Similarity matrix | BLOSUM-62 
    42444 SS fraction | 0.3 
    42445 Gap open (HH/SS/other) | 18/18/6 
    42446 Gap extend | 1 
    42447 SS matrix |  |  | H | S | O 
    42448 ---|---|---|--- 
    42449 H | 6 | -9 | -6 
    42450 S |  | 6 | -6 
    42451 O |  |  | 4 
    42452 Iteration cutoff | 2 
    42453  
    42454 Matchmaker 3j0c.pdb1, chain A (#1.17) with AF3 E1 1-421.pdb, chain A (#82),
    42455 sequence alignment score = 1060.7 
    42456 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    42457 3.020) 
    42458  
    42459 
    42460 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    42461 
    42462 Chain information for AF3 E1 422-461.pdb #83 
    42463 --- 
    42464 Chain | Description 
    42465 A | No description available 
    42466  
    42467 
    42468 > matchmaker #83 to #1.17 & sel
    42469 
    42470 Parameters 
    42471 --- 
    42472 Chain pairing | bb 
    42473 Alignment algorithm | Needleman-Wunsch 
    42474 Similarity matrix | BLOSUM-62 
    42475 SS fraction | 0.3 
    42476 Gap open (HH/SS/other) | 18/18/6 
    42477 Gap extend | 1 
    42478 SS matrix |  |  | H | S | O 
    42479 ---|---|---|--- 
    42480 H | 6 | -9 | -6 
    42481 S |  | 6 | -6 
    42482 O |  |  | 4 
    42483 Iteration cutoff | 2 
    42484  
    42485 Matchmaker 3j0c.pdb1, chain A (#1.17) with AF3 E1 422-461.pdb, chain A (#83),
    42486 sequence alignment score = 626.9 
    42487 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    42488 2.776) 
    42489  
    42490 
    42491 > hide sel cartoons
    42492 
    42493 > select #1.17/B
    42494 
    42495 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    42496 
    42497 > show sel cartoons
    42498 
    42499 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    42500 
    42501 Chain information for AF3 E2 1-352.pdb #84 
    42502 --- 
    42503 Chain | Description 
    42504 B | No description available 
    42505  
    42506 
    42507 > matchmaker #84 to #1.17 & sel
    42508 
    42509 Parameters 
    42510 --- 
    42511 Chain pairing | bb 
    42512 Alignment algorithm | Needleman-Wunsch 
    42513 Similarity matrix | BLOSUM-62 
    42514 SS fraction | 0.3 
    42515 Gap open (HH/SS/other) | 18/18/6 
    42516 Gap extend | 1 
    42517 SS matrix |  |  | H | S | O 
    42518 ---|---|---|--- 
    42519 H | 6 | -9 | -6 
    42520 S |  | 6 | -6 
    42521 O |  |  | 4 
    42522 Iteration cutoff | 2 
    42523  
    42524 Matchmaker 3j0c.pdb1, chain B (#1.17) with AF3 E2 1-352.pdb, chain B (#84),
    42525 sequence alignment score = 583.7 
    42526 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    42527 5.933) 
    42528  
    42529 
    42530 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    42531 
    42532 Chain information for AF3 E2 353-438.pdb #85 
    42533 --- 
    42534 Chain | Description 
    42535 B | No description available 
    42536  
    42537 
    42538 > matchmaker #85 to #1.17 & sel
    42539 
    42540 Parameters 
    42541 --- 
    42542 Chain pairing | bb 
    42543 Alignment algorithm | Needleman-Wunsch 
    42544 Similarity matrix | BLOSUM-62 
    42545 SS fraction | 0.3 
    42546 Gap open (HH/SS/other) | 18/18/6 
    42547 Gap extend | 1 
    42548 SS matrix |  |  | H | S | O 
    42549 ---|---|---|--- 
    42550 H | 6 | -9 | -6 
    42551 S |  | 6 | -6 
    42552 O |  |  | 4 
    42553 Iteration cutoff | 2 
    42554  
    42555 Matchmaker 3j0c.pdb1, chain B (#1.17) with AF3 E2 353-438.pdb, chain B (#85),
    42556 sequence alignment score = 322.6 
    42557 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    42558 8.411) 
    42559  
    42560 
    42561 > hide sel cartoons
    42562 
    42563 > select #1.17/C
    42564 
    42565 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    42566 
    42567 > show sel cartoons
    42568 
    42569 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    42570 
    42571 Chain information for AF3 CA.pdb #86 
    42572 --- 
    42573 Chain | Description 
    42574 A | No description available 
    42575  
    42576 
    42577 > matchmaker #86 to #1.17 & sel
    42578 
    42579 Parameters 
    42580 --- 
    42581 Chain pairing | bb 
    42582 Alignment algorithm | Needleman-Wunsch 
    42583 Similarity matrix | BLOSUM-62 
    42584 SS fraction | 0.3 
    42585 Gap open (HH/SS/other) | 18/18/6 
    42586 Gap extend | 1 
    42587 SS matrix |  |  | H | S | O 
    42588 ---|---|---|--- 
    42589 H | 6 | -9 | -6 
    42590 S |  | 6 | -6 
    42591 O |  |  | 4 
    42592 Iteration cutoff | 2 
    42593  
    42594 Matchmaker 3j0c.pdb1, chain C (#1.17) with AF3 CA.pdb, chain A (#86), sequence
    42595 alignment score = 328.1 
    42596 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    42597 2.714) 
    42598  
    42599 
    42600 > hide sel cartoons
    42601 
    42602 > color #82 dodgerblue
    42603 
    42604 > color #83 dodgerblue
    42605 
    42606 > color #84 #00b305ff
    42607 
    42608 > color #85 #00b305ff
    42609 
    42610 > color #86 #f15839ff
    42611 
    42612 > select #1.18/A
    42613 
    42614 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    42615 
    42616 > show sel cartoons
    42617 
    42618 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    42619 
    42620 Chain information for AF3 E1 1-421.pdb #87 
    42621 --- 
    42622 Chain | Description 
    42623 A | No description available 
    42624  
    42625 
    42626 > matchmaker #87 to #1.18 & sel
    42627 
    42628 Parameters 
    42629 --- 
    42630 Chain pairing | bb 
    42631 Alignment algorithm | Needleman-Wunsch 
    42632 Similarity matrix | BLOSUM-62 
    42633 SS fraction | 0.3 
    42634 Gap open (HH/SS/other) | 18/18/6 
    42635 Gap extend | 1 
    42636 SS matrix |  |  | H | S | O 
    42637 ---|---|---|--- 
    42638 H | 6 | -9 | -6 
    42639 S |  | 6 | -6 
    42640 O |  |  | 4 
    42641 Iteration cutoff | 2 
    42642  
    42643 Matchmaker 3j0c.pdb1, chain A (#1.18) with AF3 E1 1-421.pdb, chain A (#87),
    42644 sequence alignment score = 1060.7 
    42645 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    42646 3.020) 
    42647  
    42648 
    42649 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    42650 
    42651 Chain information for AF3 E1 422-461.pdb #88 
    42652 --- 
    42653 Chain | Description 
    42654 A | No description available 
    42655  
    42656 
    42657 > matchmaker #88 to #1.18 & sel
    42658 
    42659 Parameters 
    42660 --- 
    42661 Chain pairing | bb 
    42662 Alignment algorithm | Needleman-Wunsch 
    42663 Similarity matrix | BLOSUM-62 
    42664 SS fraction | 0.3 
    42665 Gap open (HH/SS/other) | 18/18/6 
    42666 Gap extend | 1 
    42667 SS matrix |  |  | H | S | O 
    42668 ---|---|---|--- 
    42669 H | 6 | -9 | -6 
    42670 S |  | 6 | -6 
    42671 O |  |  | 4 
    42672 Iteration cutoff | 2 
    42673  
    42674 Matchmaker 3j0c.pdb1, chain A (#1.18) with AF3 E1 422-461.pdb, chain A (#88),
    42675 sequence alignment score = 626.9 
    42676 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    42677 2.776) 
    42678  
    42679 
    42680 > hide sel cartoons
    42681 
    42682 > select #1.18/B
    42683 
    42684 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    42685 
    42686 > show sel cartoons
    42687 
    42688 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    42689 
    42690 Chain information for AF3 E2 1-352.pdb #89 
    42691 --- 
    42692 Chain | Description 
    42693 B | No description available 
    42694  
    42695 
    42696 > matchmaker #89 to #1.18 & sel
    42697 
    42698 Parameters 
    42699 --- 
    42700 Chain pairing | bb 
    42701 Alignment algorithm | Needleman-Wunsch 
    42702 Similarity matrix | BLOSUM-62 
    42703 SS fraction | 0.3 
    42704 Gap open (HH/SS/other) | 18/18/6 
    42705 Gap extend | 1 
    42706 SS matrix |  |  | H | S | O 
    42707 ---|---|---|--- 
    42708 H | 6 | -9 | -6 
    42709 S |  | 6 | -6 
    42710 O |  |  | 4 
    42711 Iteration cutoff | 2 
    42712  
    42713 Matchmaker 3j0c.pdb1, chain B (#1.18) with AF3 E2 1-352.pdb, chain B (#89),
    42714 sequence alignment score = 583.7 
    42715 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    42716 5.933) 
    42717  
    42718 
    42719 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    42720 
    42721 Chain information for AF3 E2 353-438.pdb #90 
    42722 --- 
    42723 Chain | Description 
    42724 B | No description available 
    42725  
    42726 
    42727 > matchmaker #90 to #1.18 & sel
    42728 
    42729 Parameters 
    42730 --- 
    42731 Chain pairing | bb 
    42732 Alignment algorithm | Needleman-Wunsch 
    42733 Similarity matrix | BLOSUM-62 
    42734 SS fraction | 0.3 
    42735 Gap open (HH/SS/other) | 18/18/6 
    42736 Gap extend | 1 
    42737 SS matrix |  |  | H | S | O 
    42738 ---|---|---|--- 
    42739 H | 6 | -9 | -6 
    42740 S |  | 6 | -6 
    42741 O |  |  | 4 
    42742 Iteration cutoff | 2 
    42743  
    42744 Matchmaker 3j0c.pdb1, chain B (#1.18) with AF3 E2 353-438.pdb, chain B (#90),
    42745 sequence alignment score = 333.4 
    42746 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    42747 8.411) 
    42748  
    42749 
    42750 > hide sel cartoons
    42751 
    42752 > select #1.18/C
    42753 
    42754 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    42755 
    42756 > show sel cartoons
    42757 
    42758 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    42759 
    42760 Chain information for AF3 CA.pdb #91 
    42761 --- 
    42762 Chain | Description 
    42763 A | No description available 
    42764  
    42765 
    42766 > matchmaker #91 to #1.18 & sel
    42767 
    42768 Parameters 
    42769 --- 
    42770 Chain pairing | bb 
    42771 Alignment algorithm | Needleman-Wunsch 
    42772 Similarity matrix | BLOSUM-62 
    42773 SS fraction | 0.3 
    42774 Gap open (HH/SS/other) | 18/18/6 
    42775 Gap extend | 1 
    42776 SS matrix |  |  | H | S | O 
    42777 ---|---|---|--- 
    42778 H | 6 | -9 | -6 
    42779 S |  | 6 | -6 
    42780 O |  |  | 4 
    42781 Iteration cutoff | 2 
    42782  
    42783 Matchmaker 3j0c.pdb1, chain C (#1.18) with AF3 CA.pdb, chain A (#91), sequence
    42784 alignment score = 328.1 
    42785 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    42786 2.714) 
    42787  
    42788 
    42789 > hide sel cartoons
    42790 
    42791 > color #87 dodgerblue
    42792 
    42793 > color #88 dodgerblue
    42794 
    42795 > color #89 #00b305ff
    42796 
    42797 > color #90 #00b305ff
    42798 
    42799 > color #91 #f15839ff
    42800 
    42801 > select #1.19/A
    42802 
    42803 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    42804 
    42805 > show sel cartoons
    42806 
    42807 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    42808 
    42809 Chain information for AF3 E1 1-421.pdb #92 
    42810 --- 
    42811 Chain | Description 
    42812 A | No description available 
    42813  
    42814 
    42815 > matchmaker #92 to #1.19 & sel
    42816 
    42817 Parameters 
    42818 --- 
    42819 Chain pairing | bb 
    42820 Alignment algorithm | Needleman-Wunsch 
    42821 Similarity matrix | BLOSUM-62 
    42822 SS fraction | 0.3 
    42823 Gap open (HH/SS/other) | 18/18/6 
    42824 Gap extend | 1 
    42825 SS matrix |  |  | H | S | O 
    42826 ---|---|---|--- 
    42827 H | 6 | -9 | -6 
    42828 S |  | 6 | -6 
    42829 O |  |  | 4 
    42830 Iteration cutoff | 2 
    42831  
    42832 Matchmaker 3j0c.pdb1, chain A (#1.19) with AF3 E1 1-421.pdb, chain A (#92),
    42833 sequence alignment score = 1060.7 
    42834 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    42835 3.020) 
    42836  
    42837 
    42838 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    42839 
    42840 Chain information for AF3 E1 422-461.pdb #93 
    42841 --- 
    42842 Chain | Description 
    42843 A | No description available 
    42844  
    42845 
    42846 > matchmaker #93 to #1.19 & sel
    42847 
    42848 Parameters 
    42849 --- 
    42850 Chain pairing | bb 
    42851 Alignment algorithm | Needleman-Wunsch 
    42852 Similarity matrix | BLOSUM-62 
    42853 SS fraction | 0.3 
    42854 Gap open (HH/SS/other) | 18/18/6 
    42855 Gap extend | 1 
    42856 SS matrix |  |  | H | S | O 
    42857 ---|---|---|--- 
    42858 H | 6 | -9 | -6 
    42859 S |  | 6 | -6 
    42860 O |  |  | 4 
    42861 Iteration cutoff | 2 
    42862  
    42863 Matchmaker 3j0c.pdb1, chain A (#1.19) with AF3 E1 422-461.pdb, chain A (#93),
    42864 sequence alignment score = 626.9 
    42865 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    42866 2.775) 
    42867  
    42868 
    42869 > hide sel cartoons
    42870 
    42871 > select #1.19/B
    42872 
    42873 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    42874 
    42875 > show sel cartoons
    42876 
    42877 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    42878 
    42879 Chain information for AF3 E2 1-352.pdb #94 
    42880 --- 
    42881 Chain | Description 
    42882 B | No description available 
    42883  
    42884 
    42885 > matchmaker #94 to #1.19 & sel
    42886 
    42887 Parameters 
    42888 --- 
    42889 Chain pairing | bb 
    42890 Alignment algorithm | Needleman-Wunsch 
    42891 Similarity matrix | BLOSUM-62 
    42892 SS fraction | 0.3 
    42893 Gap open (HH/SS/other) | 18/18/6 
    42894 Gap extend | 1 
    42895 SS matrix |  |  | H | S | O 
    42896 ---|---|---|--- 
    42897 H | 6 | -9 | -6 
    42898 S |  | 6 | -6 
    42899 O |  |  | 4 
    42900 Iteration cutoff | 2 
    42901  
    42902 Matchmaker 3j0c.pdb1, chain B (#1.19) with AF3 E2 1-352.pdb, chain B (#94),
    42903 sequence alignment score = 583.7 
    42904 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    42905 5.933) 
    42906  
    42907 
    42908 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    42909 
    42910 Chain information for AF3 E2 353-438.pdb #95 
    42911 --- 
    42912 Chain | Description 
    42913 B | No description available 
    42914  
    42915 
    42916 > matchmaker #95 to #1.19 & sel
    42917 
    42918 Parameters 
    42919 --- 
    42920 Chain pairing | bb 
    42921 Alignment algorithm | Needleman-Wunsch 
    42922 Similarity matrix | BLOSUM-62 
    42923 SS fraction | 0.3 
    42924 Gap open (HH/SS/other) | 18/18/6 
    42925 Gap extend | 1 
    42926 SS matrix |  |  | H | S | O 
    42927 ---|---|---|--- 
    42928 H | 6 | -9 | -6 
    42929 S |  | 6 | -6 
    42930 O |  |  | 4 
    42931 Iteration cutoff | 2 
    42932  
    42933 Matchmaker 3j0c.pdb1, chain B (#1.19) with AF3 E2 353-438.pdb, chain B (#95),
    42934 sequence alignment score = 322.6 
    42935 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    42936 8.411) 
    42937  
    42938 
    42939 > hide sel cartoons
    42940 
    42941 > select #1.19/C
    42942 
    42943 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    42944 
    42945 > show sel cartoons
    42946 
    42947 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    42948 
    42949 Chain information for AF3 CA.pdb #96 
    42950 --- 
    42951 Chain | Description 
    42952 A | No description available 
    42953  
    42954 
    42955 > matchmaker #96 to #1.19 & sel
    42956 
    42957 Parameters 
    42958 --- 
    42959 Chain pairing | bb 
    42960 Alignment algorithm | Needleman-Wunsch 
    42961 Similarity matrix | BLOSUM-62 
    42962 SS fraction | 0.3 
    42963 Gap open (HH/SS/other) | 18/18/6 
    42964 Gap extend | 1 
    42965 SS matrix |  |  | H | S | O 
    42966 ---|---|---|--- 
    42967 H | 6 | -9 | -6 
    42968 S |  | 6 | -6 
    42969 O |  |  | 4 
    42970 Iteration cutoff | 2 
    42971  
    42972 Matchmaker 3j0c.pdb1, chain C (#1.19) with AF3 CA.pdb, chain A (#96), sequence
    42973 alignment score = 328.1 
    42974 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    42975 2.714) 
    42976  
    42977 
    42978 > hide sel cartoons
    42979 
    42980 > color #92 dodgerblue
    42981 
    42982 > color #93 dodgerblue
    42983 
    42984 > color #94 dodgerblue
    42985 
    42986 > color #94 #00b305ff
    42987 
    42988 > color #95 #00b305ff
    42989 
    42990 > color #96 #f15839ff
    42991 
    42992 > select #1.20/A
    42993 
    42994 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    42995 
    42996 > show sel cartoons
    42997 
    42998 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    42999 
    43000 Chain information for AF3 E1 1-421.pdb #97 
    43001 --- 
    43002 Chain | Description 
    43003 A | No description available 
    43004  
    43005 
    43006 > matchmaker #97 to #1.20 & sel
    43007 
    43008 Parameters 
    43009 --- 
    43010 Chain pairing | bb 
    43011 Alignment algorithm | Needleman-Wunsch 
    43012 Similarity matrix | BLOSUM-62 
    43013 SS fraction | 0.3 
    43014 Gap open (HH/SS/other) | 18/18/6 
    43015 Gap extend | 1 
    43016 SS matrix |  |  | H | S | O 
    43017 ---|---|---|--- 
    43018 H | 6 | -9 | -6 
    43019 S |  | 6 | -6 
    43020 O |  |  | 4 
    43021 Iteration cutoff | 2 
    43022  
    43023 Matchmaker 3j0c.pdb1, chain A (#1.20) with AF3 E1 1-421.pdb, chain A (#97),
    43024 sequence alignment score = 1060.7 
    43025 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    43026 3.020) 
    43027  
    43028 
    43029 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    43030 
    43031 Chain information for AF3 E1 422-461.pdb #98 
    43032 --- 
    43033 Chain | Description 
    43034 A | No description available 
    43035  
    43036 
    43037 > matchmaker #98 to #1.20 & sel
    43038 
    43039 Parameters 
    43040 --- 
    43041 Chain pairing | bb 
    43042 Alignment algorithm | Needleman-Wunsch 
    43043 Similarity matrix | BLOSUM-62 
    43044 SS fraction | 0.3 
    43045 Gap open (HH/SS/other) | 18/18/6 
    43046 Gap extend | 1 
    43047 SS matrix |  |  | H | S | O 
    43048 ---|---|---|--- 
    43049 H | 6 | -9 | -6 
    43050 S |  | 6 | -6 
    43051 O |  |  | 4 
    43052 Iteration cutoff | 2 
    43053  
    43054 Matchmaker 3j0c.pdb1, chain A (#1.20) with AF3 E1 422-461.pdb, chain A (#98),
    43055 sequence alignment score = 626.9 
    43056 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    43057 2.775) 
    43058  
    43059 
    43060 > hide sel cartoons
    43061 
    43062 > select #1.20/B
    43063 
    43064 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    43065 
    43066 > show sel cartoons
    43067 
    43068 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    43069 
    43070 Chain information for AF3 E2 1-352.pdb #99 
    43071 --- 
    43072 Chain | Description 
    43073 B | No description available 
    43074  
    43075 
    43076 > matchmaker #99 to #1.20 & sel
    43077 
    43078 Parameters 
    43079 --- 
    43080 Chain pairing | bb 
    43081 Alignment algorithm | Needleman-Wunsch 
    43082 Similarity matrix | BLOSUM-62 
    43083 SS fraction | 0.3 
    43084 Gap open (HH/SS/other) | 18/18/6 
    43085 Gap extend | 1 
    43086 SS matrix |  |  | H | S | O 
    43087 ---|---|---|--- 
    43088 H | 6 | -9 | -6 
    43089 S |  | 6 | -6 
    43090 O |  |  | 4 
    43091 Iteration cutoff | 2 
    43092  
    43093 Matchmaker 3j0c.pdb1, chain B (#1.20) with AF3 E2 1-352.pdb, chain B (#99),
    43094 sequence alignment score = 583.7 
    43095 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    43096 5.933) 
    43097  
    43098 
    43099 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    43100 
    43101 Chain information for AF3 E2 353-438.pdb #100 
    43102 --- 
    43103 Chain | Description 
    43104 B | No description available 
    43105  
    43106 
    43107 > matchmaker #100 to #1.20 & sel
    43108 
    43109 Parameters 
    43110 --- 
    43111 Chain pairing | bb 
    43112 Alignment algorithm | Needleman-Wunsch 
    43113 Similarity matrix | BLOSUM-62 
    43114 SS fraction | 0.3 
    43115 Gap open (HH/SS/other) | 18/18/6 
    43116 Gap extend | 1 
    43117 SS matrix |  |  | H | S | O 
    43118 ---|---|---|--- 
    43119 H | 6 | -9 | -6 
    43120 S |  | 6 | -6 
    43121 O |  |  | 4 
    43122 Iteration cutoff | 2 
    43123  
    43124 Matchmaker 3j0c.pdb1, chain B (#1.20) with AF3 E2 353-438.pdb, chain B (#100),
    43125 sequence alignment score = 322.6 
    43126 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    43127 8.411) 
    43128  
    43129 
    43130 > hide sel cartoons
    43131 
    43132 > select #1.20/C
    43133 
    43134 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    43135 
    43136 > show sel cartoons
    43137 
    43138 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    43139 
    43140 Chain information for AF3 CA.pdb #101 
    43141 --- 
    43142 Chain | Description 
    43143 A | No description available 
    43144  
    43145 
    43146 > matchmaker #101 to #1.20 & sel
    43147 
    43148 Parameters 
    43149 --- 
    43150 Chain pairing | bb 
    43151 Alignment algorithm | Needleman-Wunsch 
    43152 Similarity matrix | BLOSUM-62 
    43153 SS fraction | 0.3 
    43154 Gap open (HH/SS/other) | 18/18/6 
    43155 Gap extend | 1 
    43156 SS matrix |  |  | H | S | O 
    43157 ---|---|---|--- 
    43158 H | 6 | -9 | -6 
    43159 S |  | 6 | -6 
    43160 O |  |  | 4 
    43161 Iteration cutoff | 2 
    43162  
    43163 Matchmaker 3j0c.pdb1, chain C (#1.20) with AF3 CA.pdb, chain A (#101),
    43164 sequence alignment score = 328.1 
    43165 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    43166 2.714) 
    43167  
    43168 
    43169 > hide sel cartoons
    43170 
    43171 > color #97 dodgerblue
    43172 
    43173 > color #98 dodgerblue
    43174 
    43175 > color #99 #00b305ff
    43176 
    43177 > color #100 #00b305ff
    43178 
    43179 > color #101 #f15839ff
    43180 
    43181 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    43182 
    43183 > select #1.21/A
    43184 
    43185 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    43186 
    43187 > show sel cartoons
    43188 
    43189 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    43190 
    43191 Chain information for AF3 E1 1-421.pdb #102 
    43192 --- 
    43193 Chain | Description 
    43194 A | No description available 
    43195  
    43196 
    43197 > matchmaker #102 to #1.21 & sel
    43198 
    43199 Parameters 
    43200 --- 
    43201 Chain pairing | bb 
    43202 Alignment algorithm | Needleman-Wunsch 
    43203 Similarity matrix | BLOSUM-62 
    43204 SS fraction | 0.3 
    43205 Gap open (HH/SS/other) | 18/18/6 
    43206 Gap extend | 1 
    43207 SS matrix |  |  | H | S | O 
    43208 ---|---|---|--- 
    43209 H | 6 | -9 | -6 
    43210 S |  | 6 | -6 
    43211 O |  |  | 4 
    43212 Iteration cutoff | 2 
    43213  
    43214 Matchmaker 3j0c.pdb1, chain A (#1.21) with AF3 E1 1-421.pdb, chain A (#102),
    43215 sequence alignment score = 1060.7 
    43216 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    43217 3.020) 
    43218  
    43219 
    43220 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    43221 
    43222 Chain information for AF3 E1 422-461.pdb #103 
    43223 --- 
    43224 Chain | Description 
    43225 A | No description available 
    43226  
    43227 
    43228 > matchmaker #103 to #1.21 & sel
    43229 
    43230 Parameters 
    43231 --- 
    43232 Chain pairing | bb 
    43233 Alignment algorithm | Needleman-Wunsch 
    43234 Similarity matrix | BLOSUM-62 
    43235 SS fraction | 0.3 
    43236 Gap open (HH/SS/other) | 18/18/6 
    43237 Gap extend | 1 
    43238 SS matrix |  |  | H | S | O 
    43239 ---|---|---|--- 
    43240 H | 6 | -9 | -6 
    43241 S |  | 6 | -6 
    43242 O |  |  | 4 
    43243 Iteration cutoff | 2 
    43244  
    43245 Matchmaker 3j0c.pdb1, chain A (#1.21) with AF3 E1 422-461.pdb, chain A (#103),
    43246 sequence alignment score = 626.9 
    43247 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    43248 2.775) 
    43249  
    43250 
    43251 > hide sel cartoons
    43252 
    43253 > select #1.21/B
    43254 
    43255 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    43256 
    43257 > show sel cartoons
    43258 
    43259 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    43260 
    43261 Chain information for AF3 E2 1-352.pdb #104 
    43262 --- 
    43263 Chain | Description 
    43264 B | No description available 
    43265  
    43266 
    43267 > matchmaker #104 to #1.21 & sel
    43268 
    43269 Parameters 
    43270 --- 
    43271 Chain pairing | bb 
    43272 Alignment algorithm | Needleman-Wunsch 
    43273 Similarity matrix | BLOSUM-62 
    43274 SS fraction | 0.3 
    43275 Gap open (HH/SS/other) | 18/18/6 
    43276 Gap extend | 1 
    43277 SS matrix |  |  | H | S | O 
    43278 ---|---|---|--- 
    43279 H | 6 | -9 | -6 
    43280 S |  | 6 | -6 
    43281 O |  |  | 4 
    43282 Iteration cutoff | 2 
    43283  
    43284 Matchmaker 3j0c.pdb1, chain B (#1.21) with AF3 E2 1-352.pdb, chain B (#104),
    43285 sequence alignment score = 583.7 
    43286 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    43287 5.933) 
    43288  
    43289 
    43290 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    43291 
    43292 Chain information for AF3 E2 353-438.pdb #105 
    43293 --- 
    43294 Chain | Description 
    43295 B | No description available 
    43296  
    43297 
    43298 > matchmaker #105 to #1.21 & sel
    43299 
    43300 Parameters 
    43301 --- 
    43302 Chain pairing | bb 
    43303 Alignment algorithm | Needleman-Wunsch 
    43304 Similarity matrix | BLOSUM-62 
    43305 SS fraction | 0.3 
    43306 Gap open (HH/SS/other) | 18/18/6 
    43307 Gap extend | 1 
    43308 SS matrix |  |  | H | S | O 
    43309 ---|---|---|--- 
    43310 H | 6 | -9 | -6 
    43311 S |  | 6 | -6 
    43312 O |  |  | 4 
    43313 Iteration cutoff | 2 
    43314  
    43315 Matchmaker 3j0c.pdb1, chain B (#1.21) with AF3 E2 353-438.pdb, chain B (#105),
    43316 sequence alignment score = 322.6 
    43317 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    43318 8.411) 
    43319  
    43320 
    43321 > hide sel cartoons
    43322 
    43323 > select #1.21/C
    43324 
    43325 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    43326 
    43327 > show sel cartoons
    43328 
    43329 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    43330 
    43331 Chain information for AF3 CA.pdb #106 
    43332 --- 
    43333 Chain | Description 
    43334 A | No description available 
    43335  
    43336 
    43337 > matchmaker #106 to #1.21 & sel
    43338 
    43339 Parameters 
    43340 --- 
    43341 Chain pairing | bb 
    43342 Alignment algorithm | Needleman-Wunsch 
    43343 Similarity matrix | BLOSUM-62 
    43344 SS fraction | 0.3 
    43345 Gap open (HH/SS/other) | 18/18/6 
    43346 Gap extend | 1 
    43347 SS matrix |  |  | H | S | O 
    43348 ---|---|---|--- 
    43349 H | 6 | -9 | -6 
    43350 S |  | 6 | -6 
    43351 O |  |  | 4 
    43352 Iteration cutoff | 2 
    43353  
    43354 Matchmaker 3j0c.pdb1, chain C (#1.21) with AF3 CA.pdb, chain A (#106),
    43355 sequence alignment score = 328.1 
    43356 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    43357 2.714) 
    43358  
    43359 
    43360 > hide sel cartoons
    43361 
    43362 > color #102 dodgerblue
    43363 
    43364 > color #103 dodgerblue
    43365 
    43366 > color #104 #00b305ff
    43367 
    43368 > color #105 #00b305ff
    43369 
    43370 > color #106 #f15839ff
    43371 
    43372 > select #1.22/A
    43373 
    43374 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    43375 
    43376 > show sel cartoons
    43377 
    43378 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    43379 
    43380 Chain information for AF3 E1 1-421.pdb #107 
    43381 --- 
    43382 Chain | Description 
    43383 A | No description available 
    43384  
    43385 
    43386 > matchmaker #107 to #1.22 & sel
    43387 
    43388 Parameters 
    43389 --- 
    43390 Chain pairing | bb 
    43391 Alignment algorithm | Needleman-Wunsch 
    43392 Similarity matrix | BLOSUM-62 
    43393 SS fraction | 0.3 
    43394 Gap open (HH/SS/other) | 18/18/6 
    43395 Gap extend | 1 
    43396 SS matrix |  |  | H | S | O 
    43397 ---|---|---|--- 
    43398 H | 6 | -9 | -6 
    43399 S |  | 6 | -6 
    43400 O |  |  | 4 
    43401 Iteration cutoff | 2 
    43402  
    43403 Matchmaker 3j0c.pdb1, chain A (#1.22) with AF3 E1 1-421.pdb, chain A (#107),
    43404 sequence alignment score = 1060.7 
    43405 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    43406 3.020) 
    43407  
    43408 
    43409 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    43410 
    43411 Chain information for AF3 E1 422-461.pdb #108 
    43412 --- 
    43413 Chain | Description 
    43414 A | No description available 
    43415  
    43416 
    43417 > matchmaker #108 to #1.22 & sel
    43418 
    43419 Parameters 
    43420 --- 
    43421 Chain pairing | bb 
    43422 Alignment algorithm | Needleman-Wunsch 
    43423 Similarity matrix | BLOSUM-62 
    43424 SS fraction | 0.3 
    43425 Gap open (HH/SS/other) | 18/18/6 
    43426 Gap extend | 1 
    43427 SS matrix |  |  | H | S | O 
    43428 ---|---|---|--- 
    43429 H | 6 | -9 | -6 
    43430 S |  | 6 | -6 
    43431 O |  |  | 4 
    43432 Iteration cutoff | 2 
    43433  
    43434 Matchmaker 3j0c.pdb1, chain A (#1.22) with AF3 E1 422-461.pdb, chain A (#108),
    43435 sequence alignment score = 626.9 
    43436 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    43437 2.776) 
    43438  
    43439 
    43440 > hide sel cartoons
    43441 
    43442 > select #1.22/B
    43443 
    43444 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    43445 
    43446 > show sel cartoons
    43447 
    43448 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    43449 
    43450 Chain information for AF3 E2 1-352.pdb #109 
    43451 --- 
    43452 Chain | Description 
    43453 B | No description available 
    43454  
    43455 
    43456 > matchmaker #109 to #1.22 & sel
    43457 
    43458 Parameters 
    43459 --- 
    43460 Chain pairing | bb 
    43461 Alignment algorithm | Needleman-Wunsch 
    43462 Similarity matrix | BLOSUM-62 
    43463 SS fraction | 0.3 
    43464 Gap open (HH/SS/other) | 18/18/6 
    43465 Gap extend | 1 
    43466 SS matrix |  |  | H | S | O 
    43467 ---|---|---|--- 
    43468 H | 6 | -9 | -6 
    43469 S |  | 6 | -6 
    43470 O |  |  | 4 
    43471 Iteration cutoff | 2 
    43472  
    43473 Matchmaker 3j0c.pdb1, chain B (#1.22) with AF3 E2 1-352.pdb, chain B (#109),
    43474 sequence alignment score = 583.7 
    43475 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    43476 5.933) 
    43477  
    43478 
    43479 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    43480 
    43481 Chain information for AF3 E2 353-438.pdb #110 
    43482 --- 
    43483 Chain | Description 
    43484 B | No description available 
    43485  
    43486 
    43487 > matchmaker #110 to #1.22 & sel
    43488 
    43489 Parameters 
    43490 --- 
    43491 Chain pairing | bb 
    43492 Alignment algorithm | Needleman-Wunsch 
    43493 Similarity matrix | BLOSUM-62 
    43494 SS fraction | 0.3 
    43495 Gap open (HH/SS/other) | 18/18/6 
    43496 Gap extend | 1 
    43497 SS matrix |  |  | H | S | O 
    43498 ---|---|---|--- 
    43499 H | 6 | -9 | -6 
    43500 S |  | 6 | -6 
    43501 O |  |  | 4 
    43502 Iteration cutoff | 2 
    43503  
    43504 Matchmaker 3j0c.pdb1, chain B (#1.22) with AF3 E2 353-438.pdb, chain B (#110),
    43505 sequence alignment score = 322.6 
    43506 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    43507 8.411) 
    43508  
    43509 
    43510 > hide sel cartoons
    43511 
    43512 > select #1.22/C
    43513 
    43514 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    43515 
    43516 > show sel cartoons
    43517 
    43518 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    43519 
    43520 Chain information for AF3 CA.pdb #111 
    43521 --- 
    43522 Chain | Description 
    43523 A | No description available 
    43524  
    43525 
    43526 > matchmaker #111 to #1.22 & sel
    43527 
    43528 Parameters 
    43529 --- 
    43530 Chain pairing | bb 
    43531 Alignment algorithm | Needleman-Wunsch 
    43532 Similarity matrix | BLOSUM-62 
    43533 SS fraction | 0.3 
    43534 Gap open (HH/SS/other) | 18/18/6 
    43535 Gap extend | 1 
    43536 SS matrix |  |  | H | S | O 
    43537 ---|---|---|--- 
    43538 H | 6 | -9 | -6 
    43539 S |  | 6 | -6 
    43540 O |  |  | 4 
    43541 Iteration cutoff | 2 
    43542  
    43543 Matchmaker 3j0c.pdb1, chain C (#1.22) with AF3 CA.pdb, chain A (#111),
    43544 sequence alignment score = 328.1 
    43545 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    43546 2.714) 
    43547  
    43548 
    43549 > hide sel cartoons
    43550 
    43551 > color #107 dodgerblue
    43552 
    43553 > color #108 dodgerblue
    43554 
    43555 > color #109 #00b305ff
    43556 
    43557 > color #110 #00b305ff
    43558 
    43559 > color #111 #f15839ff
    43560 
    43561 > select #1.23/A
    43562 
    43563 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    43564 
    43565 > show sel cartoons
    43566 
    43567 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    43568 
    43569 Chain information for AF3 E1 1-421.pdb #112 
    43570 --- 
    43571 Chain | Description 
    43572 A | No description available 
    43573  
    43574 
    43575 > matchmaker #112 to #1.23 & sel
    43576 
    43577 Parameters 
    43578 --- 
    43579 Chain pairing | bb 
    43580 Alignment algorithm | Needleman-Wunsch 
    43581 Similarity matrix | BLOSUM-62 
    43582 SS fraction | 0.3 
    43583 Gap open (HH/SS/other) | 18/18/6 
    43584 Gap extend | 1 
    43585 SS matrix |  |  | H | S | O 
    43586 ---|---|---|--- 
    43587 H | 6 | -9 | -6 
    43588 S |  | 6 | -6 
    43589 O |  |  | 4 
    43590 Iteration cutoff | 2 
    43591  
    43592 Matchmaker 3j0c.pdb1, chain A (#1.23) with AF3 E1 1-421.pdb, chain A (#112),
    43593 sequence alignment score = 1060.7 
    43594 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    43595 3.020) 
    43596  
    43597 
    43598 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    43599 
    43600 Chain information for AF3 E1 422-461.pdb #113 
    43601 --- 
    43602 Chain | Description 
    43603 A | No description available 
    43604  
    43605 
    43606 > matchmaker #113 to #1.23 & sel
    43607 
    43608 Parameters 
    43609 --- 
    43610 Chain pairing | bb 
    43611 Alignment algorithm | Needleman-Wunsch 
    43612 Similarity matrix | BLOSUM-62 
    43613 SS fraction | 0.3 
    43614 Gap open (HH/SS/other) | 18/18/6 
    43615 Gap extend | 1 
    43616 SS matrix |  |  | H | S | O 
    43617 ---|---|---|--- 
    43618 H | 6 | -9 | -6 
    43619 S |  | 6 | -6 
    43620 O |  |  | 4 
    43621 Iteration cutoff | 2 
    43622  
    43623 Matchmaker 3j0c.pdb1, chain A (#1.23) with AF3 E1 422-461.pdb, chain A (#113),
    43624 sequence alignment score = 626.9 
    43625 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    43626 2.776) 
    43627  
    43628 
    43629 > hide sel cartoons
    43630 
    43631 [Repeated 1 time(s)]
    43632 
    43633 > select #1.23/B
    43634 
    43635 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    43636 
    43637 > show sel cartoons
    43638 
    43639 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    43640 
    43641 Chain information for AF3 E2 1-352.pdb #114 
    43642 --- 
    43643 Chain | Description 
    43644 B | No description available 
    43645  
    43646 
    43647 > matchmaker #114 to #1.23 & sel
    43648 
    43649 Parameters 
    43650 --- 
    43651 Chain pairing | bb 
    43652 Alignment algorithm | Needleman-Wunsch 
    43653 Similarity matrix | BLOSUM-62 
    43654 SS fraction | 0.3 
    43655 Gap open (HH/SS/other) | 18/18/6 
    43656 Gap extend | 1 
    43657 SS matrix |  |  | H | S | O 
    43658 ---|---|---|--- 
    43659 H | 6 | -9 | -6 
    43660 S |  | 6 | -6 
    43661 O |  |  | 4 
    43662 Iteration cutoff | 2 
    43663  
    43664 Matchmaker 3j0c.pdb1, chain B (#1.23) with AF3 E2 1-352.pdb, chain B (#114),
    43665 sequence alignment score = 583.7 
    43666 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    43667 5.933) 
    43668  
    43669 
    43670 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    43671 
    43672 Chain information for AF3 E2 353-438.pdb #115 
    43673 --- 
    43674 Chain | Description 
    43675 B | No description available 
    43676  
    43677 
    43678 > matchmaker #115 to #1.23 & sel
    43679 
    43680 Parameters 
    43681 --- 
    43682 Chain pairing | bb 
    43683 Alignment algorithm | Needleman-Wunsch 
    43684 Similarity matrix | BLOSUM-62 
    43685 SS fraction | 0.3 
    43686 Gap open (HH/SS/other) | 18/18/6 
    43687 Gap extend | 1 
    43688 SS matrix |  |  | H | S | O 
    43689 ---|---|---|--- 
    43690 H | 6 | -9 | -6 
    43691 S |  | 6 | -6 
    43692 O |  |  | 4 
    43693 Iteration cutoff | 2 
    43694  
    43695 Matchmaker 3j0c.pdb1, chain B (#1.23) with AF3 E2 353-438.pdb, chain B (#115),
    43696 sequence alignment score = 333.4 
    43697 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    43698 8.411) 
    43699  
    43700 
    43701 > hide sel cartoons
    43702 
    43703 > select #1.23/C
    43704 
    43705 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    43706 
    43707 > show sel cartoons
    43708 
    43709 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    43710 
    43711 Chain information for AF3 CA.pdb #116 
    43712 --- 
    43713 Chain | Description 
    43714 A | No description available 
    43715  
    43716 
    43717 > matchmaker #116 to #1.23 & sel
    43718 
    43719 Parameters 
    43720 --- 
    43721 Chain pairing | bb 
    43722 Alignment algorithm | Needleman-Wunsch 
    43723 Similarity matrix | BLOSUM-62 
    43724 SS fraction | 0.3 
    43725 Gap open (HH/SS/other) | 18/18/6 
    43726 Gap extend | 1 
    43727 SS matrix |  |  | H | S | O 
    43728 ---|---|---|--- 
    43729 H | 6 | -9 | -6 
    43730 S |  | 6 | -6 
    43731 O |  |  | 4 
    43732 Iteration cutoff | 2 
    43733  
    43734 Matchmaker 3j0c.pdb1, chain C (#1.23) with AF3 CA.pdb, chain A (#116),
    43735 sequence alignment score = 328.1 
    43736 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    43737 2.714) 
    43738  
    43739 
    43740 > hide sel cartoons
    43741 
    43742 > color #112 dodgerblue
    43743 
    43744 > color #113 dodgerblue
    43745 
    43746 > color #114 #00b305ff
    43747 
    43748 > color #115 #00b305ff
    43749 
    43750 > color #116 #f15839ff
    43751 
    43752 > select #1.24/A
    43753 
    43754 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    43755 
    43756 > show sel cartoons
    43757 
    43758 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    43759 
    43760 Chain information for AF3 E1 1-421.pdb #117 
    43761 --- 
    43762 Chain | Description 
    43763 A | No description available 
    43764  
    43765 
    43766 > matchmaker #117 to #1.24 & sel
    43767 
    43768 Parameters 
    43769 --- 
    43770 Chain pairing | bb 
    43771 Alignment algorithm | Needleman-Wunsch 
    43772 Similarity matrix | BLOSUM-62 
    43773 SS fraction | 0.3 
    43774 Gap open (HH/SS/other) | 18/18/6 
    43775 Gap extend | 1 
    43776 SS matrix |  |  | H | S | O 
    43777 ---|---|---|--- 
    43778 H | 6 | -9 | -6 
    43779 S |  | 6 | -6 
    43780 O |  |  | 4 
    43781 Iteration cutoff | 2 
    43782  
    43783 Matchmaker 3j0c.pdb1, chain A (#1.24) with AF3 E1 1-421.pdb, chain A (#117),
    43784 sequence alignment score = 1060.7 
    43785 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    43786 3.020) 
    43787  
    43788 
    43789 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    43790 
    43791 Chain information for AF3 E1 422-461.pdb #118 
    43792 --- 
    43793 Chain | Description 
    43794 A | No description available 
    43795  
    43796 
    43797 > matchmaker #118 to #1.24 & sel
    43798 
    43799 Parameters 
    43800 --- 
    43801 Chain pairing | bb 
    43802 Alignment algorithm | Needleman-Wunsch 
    43803 Similarity matrix | BLOSUM-62 
    43804 SS fraction | 0.3 
    43805 Gap open (HH/SS/other) | 18/18/6 
    43806 Gap extend | 1 
    43807 SS matrix |  |  | H | S | O 
    43808 ---|---|---|--- 
    43809 H | 6 | -9 | -6 
    43810 S |  | 6 | -6 
    43811 O |  |  | 4 
    43812 Iteration cutoff | 2 
    43813  
    43814 Matchmaker 3j0c.pdb1, chain A (#1.24) with AF3 E1 422-461.pdb, chain A (#118),
    43815 sequence alignment score = 626.9 
    43816 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    43817 2.775) 
    43818  
    43819 
    43820 > hide sel cartoons
    43821 
    43822 > select #1.24/B
    43823 
    43824 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    43825 
    43826 > show sel cartoons
    43827 
    43828 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    43829 
    43830 Chain information for AF3 E2 1-352.pdb #119 
    43831 --- 
    43832 Chain | Description 
    43833 B | No description available 
    43834  
    43835 
    43836 > matchmaker #119 to #1.24 & sel
    43837 
    43838 Parameters 
    43839 --- 
    43840 Chain pairing | bb 
    43841 Alignment algorithm | Needleman-Wunsch 
    43842 Similarity matrix | BLOSUM-62 
    43843 SS fraction | 0.3 
    43844 Gap open (HH/SS/other) | 18/18/6 
    43845 Gap extend | 1 
    43846 SS matrix |  |  | H | S | O 
    43847 ---|---|---|--- 
    43848 H | 6 | -9 | -6 
    43849 S |  | 6 | -6 
    43850 O |  |  | 4 
    43851 Iteration cutoff | 2 
    43852  
    43853 Matchmaker 3j0c.pdb1, chain B (#1.24) with AF3 E2 1-352.pdb, chain B (#119),
    43854 sequence alignment score = 583.7 
    43855 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    43856 5.933) 
    43857  
    43858 
    43859 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    43860 
    43861 Chain information for AF3 E2 353-438.pdb #120 
    43862 --- 
    43863 Chain | Description 
    43864 B | No description available 
    43865  
    43866 
    43867 > matchmaker #120 to #1.24 & sel
    43868 
    43869 Parameters 
    43870 --- 
    43871 Chain pairing | bb 
    43872 Alignment algorithm | Needleman-Wunsch 
    43873 Similarity matrix | BLOSUM-62 
    43874 SS fraction | 0.3 
    43875 Gap open (HH/SS/other) | 18/18/6 
    43876 Gap extend | 1 
    43877 SS matrix |  |  | H | S | O 
    43878 ---|---|---|--- 
    43879 H | 6 | -9 | -6 
    43880 S |  | 6 | -6 
    43881 O |  |  | 4 
    43882 Iteration cutoff | 2 
    43883  
    43884 Matchmaker 3j0c.pdb1, chain B (#1.24) with AF3 E2 353-438.pdb, chain B (#120),
    43885 sequence alignment score = 333.4 
    43886 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    43887 8.411) 
    43888  
    43889 
    43890 > hide sel cartoons
    43891 
    43892 > select #1.24/C
    43893 
    43894 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    43895 
    43896 > show sel cartoons
    43897 
    43898 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    43899 
    43900 Chain information for AF3 CA.pdb #121 
    43901 --- 
    43902 Chain | Description 
    43903 A | No description available 
    43904  
    43905 
    43906 > matchmaker #121 to #1.24 & sel
    43907 
    43908 Parameters 
    43909 --- 
    43910 Chain pairing | bb 
    43911 Alignment algorithm | Needleman-Wunsch 
    43912 Similarity matrix | BLOSUM-62 
    43913 SS fraction | 0.3 
    43914 Gap open (HH/SS/other) | 18/18/6 
    43915 Gap extend | 1 
    43916 SS matrix |  |  | H | S | O 
    43917 ---|---|---|--- 
    43918 H | 6 | -9 | -6 
    43919 S |  | 6 | -6 
    43920 O |  |  | 4 
    43921 Iteration cutoff | 2 
    43922  
    43923 Matchmaker 3j0c.pdb1, chain C (#1.24) with AF3 CA.pdb, chain A (#121),
    43924 sequence alignment score = 328.1 
    43925 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    43926 2.714) 
    43927  
    43928 
    43929 > hide sel cartoons
    43930 
    43931 > color #117 dodgerblue
    43932 
    43933 > color #118 dodgerblue
    43934 
    43935 > color #119 #00b305ff
    43936 
    43937 > color #120 #00b305ff
    43938 
    43939 > color #121 #f15839ff
    43940 
    43941 > select #1.25/A
    43942 
    43943 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    43944 
    43945 > show sel cartoons
    43946 
    43947 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    43948 
    43949 Chain information for AF3 E1 1-421.pdb #122 
    43950 --- 
    43951 Chain | Description 
    43952 A | No description available 
    43953  
    43954 
    43955 > matchmaker #122 to #1.25 & sel
    43956 
    43957 Parameters 
    43958 --- 
    43959 Chain pairing | bb 
    43960 Alignment algorithm | Needleman-Wunsch 
    43961 Similarity matrix | BLOSUM-62 
    43962 SS fraction | 0.3 
    43963 Gap open (HH/SS/other) | 18/18/6 
    43964 Gap extend | 1 
    43965 SS matrix |  |  | H | S | O 
    43966 ---|---|---|--- 
    43967 H | 6 | -9 | -6 
    43968 S |  | 6 | -6 
    43969 O |  |  | 4 
    43970 Iteration cutoff | 2 
    43971  
    43972 Matchmaker 3j0c.pdb1, chain A (#1.25) with AF3 E1 1-421.pdb, chain A (#122),
    43973 sequence alignment score = 1060.7 
    43974 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    43975 3.020) 
    43976  
    43977 
    43978 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    43979 
    43980 Chain information for AF3 E1 422-461.pdb #123 
    43981 --- 
    43982 Chain | Description 
    43983 A | No description available 
    43984  
    43985 
    43986 > matchmaker #123 to #1.25 & sel
    43987 
    43988 Parameters 
    43989 --- 
    43990 Chain pairing | bb 
    43991 Alignment algorithm | Needleman-Wunsch 
    43992 Similarity matrix | BLOSUM-62 
    43993 SS fraction | 0.3 
    43994 Gap open (HH/SS/other) | 18/18/6 
    43995 Gap extend | 1 
    43996 SS matrix |  |  | H | S | O 
    43997 ---|---|---|--- 
    43998 H | 6 | -9 | -6 
    43999 S |  | 6 | -6 
    44000 O |  |  | 4 
    44001 Iteration cutoff | 2 
    44002  
    44003 Matchmaker 3j0c.pdb1, chain A (#1.25) with AF3 E1 422-461.pdb, chain A (#123),
    44004 sequence alignment score = 626.9 
    44005 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    44006 2.776) 
    44007  
    44008 
    44009 > hide sel cartoons
    44010 
    44011 > select #1.25/B
    44012 
    44013 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    44014 
    44015 > show sel cartoons
    44016 
    44017 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    44018 
    44019 Chain information for AF3 E2 1-352.pdb #124 
    44020 --- 
    44021 Chain | Description 
    44022 B | No description available 
    44023  
    44024 
    44025 > matchmaker #124 to #1.25 & sel
    44026 
    44027 Parameters 
    44028 --- 
    44029 Chain pairing | bb 
    44030 Alignment algorithm | Needleman-Wunsch 
    44031 Similarity matrix | BLOSUM-62 
    44032 SS fraction | 0.3 
    44033 Gap open (HH/SS/other) | 18/18/6 
    44034 Gap extend | 1 
    44035 SS matrix |  |  | H | S | O 
    44036 ---|---|---|--- 
    44037 H | 6 | -9 | -6 
    44038 S |  | 6 | -6 
    44039 O |  |  | 4 
    44040 Iteration cutoff | 2 
    44041  
    44042 Matchmaker 3j0c.pdb1, chain B (#1.25) with AF3 E2 1-352.pdb, chain B (#124),
    44043 sequence alignment score = 583.7 
    44044 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    44045 5.933) 
    44046  
    44047 
    44048 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    44049 
    44050 Chain information for AF3 E2 353-438.pdb #125 
    44051 --- 
    44052 Chain | Description 
    44053 B | No description available 
    44054  
    44055 
    44056 > matchmaker #125 to #1.25 & sel
    44057 
    44058 Parameters 
    44059 --- 
    44060 Chain pairing | bb 
    44061 Alignment algorithm | Needleman-Wunsch 
    44062 Similarity matrix | BLOSUM-62 
    44063 SS fraction | 0.3 
    44064 Gap open (HH/SS/other) | 18/18/6 
    44065 Gap extend | 1 
    44066 SS matrix |  |  | H | S | O 
    44067 ---|---|---|--- 
    44068 H | 6 | -9 | -6 
    44069 S |  | 6 | -6 
    44070 O |  |  | 4 
    44071 Iteration cutoff | 2 
    44072  
    44073 Matchmaker 3j0c.pdb1, chain B (#1.25) with AF3 E2 353-438.pdb, chain B (#125),
    44074 sequence alignment score = 333.4 
    44075 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    44076 8.411) 
    44077  
    44078 
    44079 > hide sel cartoons
    44080 
    44081 > select #1.25/C
    44082 
    44083 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    44084 
    44085 > show sel cartoons
    44086 
    44087 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    44088 
    44089 Chain information for AF3 CA.pdb #126 
    44090 --- 
    44091 Chain | Description 
    44092 A | No description available 
    44093  
    44094 
    44095 > matchmaker #126 to #1.25 & sel
    44096 
    44097 Parameters 
    44098 --- 
    44099 Chain pairing | bb 
    44100 Alignment algorithm | Needleman-Wunsch 
    44101 Similarity matrix | BLOSUM-62 
    44102 SS fraction | 0.3 
    44103 Gap open (HH/SS/other) | 18/18/6 
    44104 Gap extend | 1 
    44105 SS matrix |  |  | H | S | O 
    44106 ---|---|---|--- 
    44107 H | 6 | -9 | -6 
    44108 S |  | 6 | -6 
    44109 O |  |  | 4 
    44110 Iteration cutoff | 2 
    44111  
    44112 Matchmaker 3j0c.pdb1, chain C (#1.25) with AF3 CA.pdb, chain A (#126),
    44113 sequence alignment score = 328.1 
    44114 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    44115 2.714) 
    44116  
    44117 
    44118 > hide sel cartoons
    44119 
    44120 > color #122 dodgerblue
    44121 
    44122 > color #123 dodgerblue
    44123 
    44124 > color #124 #00b305ff
    44125 
    44126 > color #125 #00b305ff
    44127 
    44128 > color #126 #f15839ff
    44129 
    44130 > select #1.26/A
    44131 
    44132 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    44133 
    44134 > show sel cartoons
    44135 
    44136 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    44137 
    44138 Chain information for AF3 E1 1-421.pdb #127 
    44139 --- 
    44140 Chain | Description 
    44141 A | No description available 
    44142  
    44143 
    44144 > matchmaker #127 to #1.26 & sel
    44145 
    44146 Parameters 
    44147 --- 
    44148 Chain pairing | bb 
    44149 Alignment algorithm | Needleman-Wunsch 
    44150 Similarity matrix | BLOSUM-62 
    44151 SS fraction | 0.3 
    44152 Gap open (HH/SS/other) | 18/18/6 
    44153 Gap extend | 1 
    44154 SS matrix |  |  | H | S | O 
    44155 ---|---|---|--- 
    44156 H | 6 | -9 | -6 
    44157 S |  | 6 | -6 
    44158 O |  |  | 4 
    44159 Iteration cutoff | 2 
    44160  
    44161 Matchmaker 3j0c.pdb1, chain A (#1.26) with AF3 E1 1-421.pdb, chain A (#127),
    44162 sequence alignment score = 1060.7 
    44163 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    44164 3.020) 
    44165  
    44166 
    44167 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    44168 
    44169 Chain information for AF3 E1 422-461.pdb #128 
    44170 --- 
    44171 Chain | Description 
    44172 A | No description available 
    44173  
    44174 
    44175 > matchmaker #128 to #1.26 & sel
    44176 
    44177 Parameters 
    44178 --- 
    44179 Chain pairing | bb 
    44180 Alignment algorithm | Needleman-Wunsch 
    44181 Similarity matrix | BLOSUM-62 
    44182 SS fraction | 0.3 
    44183 Gap open (HH/SS/other) | 18/18/6 
    44184 Gap extend | 1 
    44185 SS matrix |  |  | H | S | O 
    44186 ---|---|---|--- 
    44187 H | 6 | -9 | -6 
    44188 S |  | 6 | -6 
    44189 O |  |  | 4 
    44190 Iteration cutoff | 2 
    44191  
    44192 Matchmaker 3j0c.pdb1, chain A (#1.26) with AF3 E1 422-461.pdb, chain A (#128),
    44193 sequence alignment score = 626.9 
    44194 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    44195 2.775) 
    44196  
    44197 
    44198 > hide sel cartoons
    44199 
    44200 > select #1.26/B
    44201 
    44202 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    44203 
    44204 > show sel cartoons
    44205 
    44206 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    44207 
    44208 Chain information for AF3 E2 1-352.pdb #129 
    44209 --- 
    44210 Chain | Description 
    44211 B | No description available 
    44212  
    44213 
    44214 > matchmaker #129 to #1.26 & sel
    44215 
    44216 Parameters 
    44217 --- 
    44218 Chain pairing | bb 
    44219 Alignment algorithm | Needleman-Wunsch 
    44220 Similarity matrix | BLOSUM-62 
    44221 SS fraction | 0.3 
    44222 Gap open (HH/SS/other) | 18/18/6 
    44223 Gap extend | 1 
    44224 SS matrix |  |  | H | S | O 
    44225 ---|---|---|--- 
    44226 H | 6 | -9 | -6 
    44227 S |  | 6 | -6 
    44228 O |  |  | 4 
    44229 Iteration cutoff | 2 
    44230  
    44231 Matchmaker 3j0c.pdb1, chain B (#1.26) with AF3 E2 1-352.pdb, chain B (#129),
    44232 sequence alignment score = 583.7 
    44233 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    44234 5.933) 
    44235  
    44236 
    44237 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    44238 
    44239 Chain information for AF3 E2 353-438.pdb #130 
    44240 --- 
    44241 Chain | Description 
    44242 B | No description available 
    44243  
    44244 
    44245 > matchmaker #130 to #1.26 & sel
    44246 
    44247 Parameters 
    44248 --- 
    44249 Chain pairing | bb 
    44250 Alignment algorithm | Needleman-Wunsch 
    44251 Similarity matrix | BLOSUM-62 
    44252 SS fraction | 0.3 
    44253 Gap open (HH/SS/other) | 18/18/6 
    44254 Gap extend | 1 
    44255 SS matrix |  |  | H | S | O 
    44256 ---|---|---|--- 
    44257 H | 6 | -9 | -6 
    44258 S |  | 6 | -6 
    44259 O |  |  | 4 
    44260 Iteration cutoff | 2 
    44261  
    44262 Matchmaker 3j0c.pdb1, chain B (#1.26) with AF3 E2 353-438.pdb, chain B (#130),
    44263 sequence alignment score = 322.6 
    44264 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    44265 8.411) 
    44266  
    44267 
    44268 > hide sel cartoons
    44269 
    44270 > select #1.26/C
    44271 
    44272 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    44273 
    44274 > show sel cartoons
    44275 
    44276 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    44277 
    44278 Chain information for AF3 CA.pdb #131 
    44279 --- 
    44280 Chain | Description 
    44281 A | No description available 
    44282  
    44283 
    44284 > matchmaker #131 to #1.26 & sel
    44285 
    44286 Parameters 
    44287 --- 
    44288 Chain pairing | bb 
    44289 Alignment algorithm | Needleman-Wunsch 
    44290 Similarity matrix | BLOSUM-62 
    44291 SS fraction | 0.3 
    44292 Gap open (HH/SS/other) | 18/18/6 
    44293 Gap extend | 1 
    44294 SS matrix |  |  | H | S | O 
    44295 ---|---|---|--- 
    44296 H | 6 | -9 | -6 
    44297 S |  | 6 | -6 
    44298 O |  |  | 4 
    44299 Iteration cutoff | 2 
    44300  
    44301 Matchmaker 3j0c.pdb1, chain C (#1.26) with AF3 CA.pdb, chain A (#131),
    44302 sequence alignment score = 328.1 
    44303 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    44304 2.714) 
    44305  
    44306 
    44307 > hide sel cartoons
    44308 
    44309 > color #127 dodgerblue
    44310 
    44311 > color #128 dodgerblue
    44312 
    44313 > color #129 #00b305ff
    44314 
    44315 > color #130 #00b305ff
    44316 
    44317 > color #131 #f15839ff
    44318 
    44319 > select #1.27/A
    44320 
    44321 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    44322 
    44323 > show sel cartoons
    44324 
    44325 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    44326 
    44327 Chain information for AF3 E1 1-421.pdb #132 
    44328 --- 
    44329 Chain | Description 
    44330 A | No description available 
    44331  
    44332 
    44333 > matchmaker #132 to #1.27 & sel
    44334 
    44335 Parameters 
    44336 --- 
    44337 Chain pairing | bb 
    44338 Alignment algorithm | Needleman-Wunsch 
    44339 Similarity matrix | BLOSUM-62 
    44340 SS fraction | 0.3 
    44341 Gap open (HH/SS/other) | 18/18/6 
    44342 Gap extend | 1 
    44343 SS matrix |  |  | H | S | O 
    44344 ---|---|---|--- 
    44345 H | 6 | -9 | -6 
    44346 S |  | 6 | -6 
    44347 O |  |  | 4 
    44348 Iteration cutoff | 2 
    44349  
    44350 Matchmaker 3j0c.pdb1, chain A (#1.27) with AF3 E1 1-421.pdb, chain A (#132),
    44351 sequence alignment score = 1060.7 
    44352 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    44353 3.020) 
    44354  
    44355 
    44356 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    44357 
    44358 Chain information for AF3 E1 422-461.pdb #133 
    44359 --- 
    44360 Chain | Description 
    44361 A | No description available 
    44362  
    44363 
    44364 > matchmaker #133 to #1.27 & sel
    44365 
    44366 Parameters 
    44367 --- 
    44368 Chain pairing | bb 
    44369 Alignment algorithm | Needleman-Wunsch 
    44370 Similarity matrix | BLOSUM-62 
    44371 SS fraction | 0.3 
    44372 Gap open (HH/SS/other) | 18/18/6 
    44373 Gap extend | 1 
    44374 SS matrix |  |  | H | S | O 
    44375 ---|---|---|--- 
    44376 H | 6 | -9 | -6 
    44377 S |  | 6 | -6 
    44378 O |  |  | 4 
    44379 Iteration cutoff | 2 
    44380  
    44381 Matchmaker 3j0c.pdb1, chain A (#1.27) with AF3 E1 422-461.pdb, chain A (#133),
    44382 sequence alignment score = 626.9 
    44383 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    44384 2.775) 
    44385  
    44386 
    44387 > hide sel cartoons
    44388 
    44389 > select #1.27/B
    44390 
    44391 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    44392 
    44393 > show sel cartoons
    44394 
    44395 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    44396 
    44397 Chain information for AF3 E2 1-352.pdb #134 
    44398 --- 
    44399 Chain | Description 
    44400 B | No description available 
    44401  
    44402 
    44403 > matchmaker #134 to #1.27 & sel
    44404 
    44405 Parameters 
    44406 --- 
    44407 Chain pairing | bb 
    44408 Alignment algorithm | Needleman-Wunsch 
    44409 Similarity matrix | BLOSUM-62 
    44410 SS fraction | 0.3 
    44411 Gap open (HH/SS/other) | 18/18/6 
    44412 Gap extend | 1 
    44413 SS matrix |  |  | H | S | O 
    44414 ---|---|---|--- 
    44415 H | 6 | -9 | -6 
    44416 S |  | 6 | -6 
    44417 O |  |  | 4 
    44418 Iteration cutoff | 2 
    44419  
    44420 Matchmaker 3j0c.pdb1, chain B (#1.27) with AF3 E2 1-352.pdb, chain B (#134),
    44421 sequence alignment score = 583.7 
    44422 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    44423 5.933) 
    44424  
    44425 
    44426 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    44427 
    44428 Chain information for AF3 E2 353-438.pdb #135 
    44429 --- 
    44430 Chain | Description 
    44431 B | No description available 
    44432  
    44433 
    44434 > matchmaker #135 to #1.27 & sel
    44435 
    44436 Parameters 
    44437 --- 
    44438 Chain pairing | bb 
    44439 Alignment algorithm | Needleman-Wunsch 
    44440 Similarity matrix | BLOSUM-62 
    44441 SS fraction | 0.3 
    44442 Gap open (HH/SS/other) | 18/18/6 
    44443 Gap extend | 1 
    44444 SS matrix |  |  | H | S | O 
    44445 ---|---|---|--- 
    44446 H | 6 | -9 | -6 
    44447 S |  | 6 | -6 
    44448 O |  |  | 4 
    44449 Iteration cutoff | 2 
    44450  
    44451 Matchmaker 3j0c.pdb1, chain B (#1.27) with AF3 E2 353-438.pdb, chain B (#135),
    44452 sequence alignment score = 333.4 
    44453 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    44454 8.411) 
    44455  
    44456 
    44457 > hide sel cartoons
    44458 
    44459 > select #1.27/C
    44460 
    44461 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    44462 
    44463 > show sel cartoons
    44464 
    44465 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    44466 
    44467 Chain information for AF3 CA.pdb #136 
    44468 --- 
    44469 Chain | Description 
    44470 A | No description available 
    44471  
    44472 
    44473 > matchmaker #136 to #1.27 & sel
    44474 
    44475 Parameters 
    44476 --- 
    44477 Chain pairing | bb 
    44478 Alignment algorithm | Needleman-Wunsch 
    44479 Similarity matrix | BLOSUM-62 
    44480 SS fraction | 0.3 
    44481 Gap open (HH/SS/other) | 18/18/6 
    44482 Gap extend | 1 
    44483 SS matrix |  |  | H | S | O 
    44484 ---|---|---|--- 
    44485 H | 6 | -9 | -6 
    44486 S |  | 6 | -6 
    44487 O |  |  | 4 
    44488 Iteration cutoff | 2 
    44489  
    44490 Matchmaker 3j0c.pdb1, chain C (#1.27) with AF3 CA.pdb, chain A (#136),
    44491 sequence alignment score = 328.1 
    44492 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    44493 2.714) 
    44494  
    44495 
    44496 > hide sel cartoons
    44497 
    44498 > color #132 dodgerblue
    44499 
    44500 > color #133 dodgerblue
    44501 
    44502 > color #134 #00b305ff
    44503 
    44504 > color #135 #00b305ff
    44505 
    44506 > color #136 #f15839ff
    44507 
    44508 > select #1.28/A
    44509 
    44510 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    44511 
    44512 > show sel cartoons
    44513 
    44514 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    44515 
    44516 Chain information for AF3 E1 1-421.pdb #137 
    44517 --- 
    44518 Chain | Description 
    44519 A | No description available 
    44520  
    44521 
    44522 > matchmaker #137 to #1.28 & sel
    44523 
    44524 Parameters 
    44525 --- 
    44526 Chain pairing | bb 
    44527 Alignment algorithm | Needleman-Wunsch 
    44528 Similarity matrix | BLOSUM-62 
    44529 SS fraction | 0.3 
    44530 Gap open (HH/SS/other) | 18/18/6 
    44531 Gap extend | 1 
    44532 SS matrix |  |  | H | S | O 
    44533 ---|---|---|--- 
    44534 H | 6 | -9 | -6 
    44535 S |  | 6 | -6 
    44536 O |  |  | 4 
    44537 Iteration cutoff | 2 
    44538  
    44539 Matchmaker 3j0c.pdb1, chain A (#1.28) with AF3 E1 1-421.pdb, chain A (#137),
    44540 sequence alignment score = 1060.7 
    44541 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    44542 3.020) 
    44543  
    44544 
    44545 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    44546 
    44547 Chain information for AF3 E1 422-461.pdb #138 
    44548 --- 
    44549 Chain | Description 
    44550 A | No description available 
    44551  
    44552 
    44553 > matchmaker #138 to #1.28 & sel
    44554 
    44555 Parameters 
    44556 --- 
    44557 Chain pairing | bb 
    44558 Alignment algorithm | Needleman-Wunsch 
    44559 Similarity matrix | BLOSUM-62 
    44560 SS fraction | 0.3 
    44561 Gap open (HH/SS/other) | 18/18/6 
    44562 Gap extend | 1 
    44563 SS matrix |  |  | H | S | O 
    44564 ---|---|---|--- 
    44565 H | 6 | -9 | -6 
    44566 S |  | 6 | -6 
    44567 O |  |  | 4 
    44568 Iteration cutoff | 2 
    44569  
    44570 Matchmaker 3j0c.pdb1, chain A (#1.28) with AF3 E1 422-461.pdb, chain A (#138),
    44571 sequence alignment score = 626.9 
    44572 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    44573 2.776) 
    44574  
    44575 
    44576 > hide sel cartoons
    44577 
    44578 > select #1.28/B
    44579 
    44580 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    44581 
    44582 > show sel cartoons
    44583 
    44584 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    44585 
    44586 Chain information for AF3 E2 1-352.pdb #139 
    44587 --- 
    44588 Chain | Description 
    44589 B | No description available 
    44590  
    44591 
    44592 > matchmaker #139 to #1.28 & sel
    44593 
    44594 Parameters 
    44595 --- 
    44596 Chain pairing | bb 
    44597 Alignment algorithm | Needleman-Wunsch 
    44598 Similarity matrix | BLOSUM-62 
    44599 SS fraction | 0.3 
    44600 Gap open (HH/SS/other) | 18/18/6 
    44601 Gap extend | 1 
    44602 SS matrix |  |  | H | S | O 
    44603 ---|---|---|--- 
    44604 H | 6 | -9 | -6 
    44605 S |  | 6 | -6 
    44606 O |  |  | 4 
    44607 Iteration cutoff | 2 
    44608  
    44609 Matchmaker 3j0c.pdb1, chain B (#1.28) with AF3 E2 1-352.pdb, chain B (#139),
    44610 sequence alignment score = 583.7 
    44611 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    44612 5.933) 
    44613  
    44614 
    44615 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    44616 
    44617 Chain information for AF3 E2 353-438.pdb #140 
    44618 --- 
    44619 Chain | Description 
    44620 B | No description available 
    44621  
    44622 
    44623 > matchmaker #140 to #1.28 & sel
    44624 
    44625 Parameters 
    44626 --- 
    44627 Chain pairing | bb 
    44628 Alignment algorithm | Needleman-Wunsch 
    44629 Similarity matrix | BLOSUM-62 
    44630 SS fraction | 0.3 
    44631 Gap open (HH/SS/other) | 18/18/6 
    44632 Gap extend | 1 
    44633 SS matrix |  |  | H | S | O 
    44634 ---|---|---|--- 
    44635 H | 6 | -9 | -6 
    44636 S |  | 6 | -6 
    44637 O |  |  | 4 
    44638 Iteration cutoff | 2 
    44639  
    44640 Matchmaker 3j0c.pdb1, chain B (#1.28) with AF3 E2 353-438.pdb, chain B (#140),
    44641 sequence alignment score = 333.4 
    44642 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    44643 8.411) 
    44644  
    44645 
    44646 > hide sel cartoons
    44647 
    44648 > select #1.28/C
    44649 
    44650 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    44651 
    44652 > show sel cartoons
    44653 
    44654 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    44655 
    44656 Chain information for AF3 CA.pdb #141 
    44657 --- 
    44658 Chain | Description 
    44659 A | No description available 
    44660  
    44661 
    44662 > matchmaker #141 to #1.28 & sel
    44663 
    44664 Parameters 
    44665 --- 
    44666 Chain pairing | bb 
    44667 Alignment algorithm | Needleman-Wunsch 
    44668 Similarity matrix | BLOSUM-62 
    44669 SS fraction | 0.3 
    44670 Gap open (HH/SS/other) | 18/18/6 
    44671 Gap extend | 1 
    44672 SS matrix |  |  | H | S | O 
    44673 ---|---|---|--- 
    44674 H | 6 | -9 | -6 
    44675 S |  | 6 | -6 
    44676 O |  |  | 4 
    44677 Iteration cutoff | 2 
    44678  
    44679 Matchmaker 3j0c.pdb1, chain C (#1.28) with AF3 CA.pdb, chain A (#141),
    44680 sequence alignment score = 328.1 
    44681 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    44682 2.714) 
    44683  
    44684 
    44685 > hide sel cartoons
    44686 
    44687 > color #137 dodgerblue
    44688 
    44689 > color #138 dodgerblue
    44690 
    44691 > color #139 #00b305ff
    44692 
    44693 > color #140 #00b305ff
    44694 
    44695 > color #141 #f15839ff
    44696 
    44697 > select #1.29/A
    44698 
    44699 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    44700 
    44701 > show sel cartoons
    44702 
    44703 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    44704 
    44705 Chain information for AF3 E1 1-421.pdb #142 
    44706 --- 
    44707 Chain | Description 
    44708 A | No description available 
    44709  
    44710 
    44711 > matchmaker #142 to #1.29 & sel
    44712 
    44713 Parameters 
    44714 --- 
    44715 Chain pairing | bb 
    44716 Alignment algorithm | Needleman-Wunsch 
    44717 Similarity matrix | BLOSUM-62 
    44718 SS fraction | 0.3 
    44719 Gap open (HH/SS/other) | 18/18/6 
    44720 Gap extend | 1 
    44721 SS matrix |  |  | H | S | O 
    44722 ---|---|---|--- 
    44723 H | 6 | -9 | -6 
    44724 S |  | 6 | -6 
    44725 O |  |  | 4 
    44726 Iteration cutoff | 2 
    44727  
    44728 Matchmaker 3j0c.pdb1, chain A (#1.29) with AF3 E1 1-421.pdb, chain A (#142),
    44729 sequence alignment score = 1060.7 
    44730 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    44731 3.020) 
    44732  
    44733 
    44734 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    44735 
    44736 Chain information for AF3 E1 422-461.pdb #143 
    44737 --- 
    44738 Chain | Description 
    44739 A | No description available 
    44740  
    44741 
    44742 > matchmaker #143 to #1.29 & sel
    44743 
    44744 Parameters 
    44745 --- 
    44746 Chain pairing | bb 
    44747 Alignment algorithm | Needleman-Wunsch 
    44748 Similarity matrix | BLOSUM-62 
    44749 SS fraction | 0.3 
    44750 Gap open (HH/SS/other) | 18/18/6 
    44751 Gap extend | 1 
    44752 SS matrix |  |  | H | S | O 
    44753 ---|---|---|--- 
    44754 H | 6 | -9 | -6 
    44755 S |  | 6 | -6 
    44756 O |  |  | 4 
    44757 Iteration cutoff | 2 
    44758  
    44759 Matchmaker 3j0c.pdb1, chain A (#1.29) with AF3 E1 422-461.pdb, chain A (#143),
    44760 sequence alignment score = 626.9 
    44761 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    44762 2.775) 
    44763  
    44764 
    44765 > hide sel cartoons
    44766 
    44767 > select #1.29/B
    44768 
    44769 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    44770 
    44771 > show sel cartoons
    44772 
    44773 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    44774 
    44775 Chain information for AF3 E2 1-352.pdb #144 
    44776 --- 
    44777 Chain | Description 
    44778 B | No description available 
    44779  
    44780 
    44781 > matchmaker #144 to #1.29 & sel
    44782 
    44783 Parameters 
    44784 --- 
    44785 Chain pairing | bb 
    44786 Alignment algorithm | Needleman-Wunsch 
    44787 Similarity matrix | BLOSUM-62 
    44788 SS fraction | 0.3 
    44789 Gap open (HH/SS/other) | 18/18/6 
    44790 Gap extend | 1 
    44791 SS matrix |  |  | H | S | O 
    44792 ---|---|---|--- 
    44793 H | 6 | -9 | -6 
    44794 S |  | 6 | -6 
    44795 O |  |  | 4 
    44796 Iteration cutoff | 2 
    44797  
    44798 Matchmaker 3j0c.pdb1, chain B (#1.29) with AF3 E2 1-352.pdb, chain B (#144),
    44799 sequence alignment score = 583.7 
    44800 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    44801 5.933) 
    44802  
    44803 
    44804 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    44805 
    44806 Chain information for AF3 E2 353-438.pdb #145 
    44807 --- 
    44808 Chain | Description 
    44809 B | No description available 
    44810  
    44811 
    44812 > matchmaker #145 to #1.29 & sel
    44813 
    44814 Parameters 
    44815 --- 
    44816 Chain pairing | bb 
    44817 Alignment algorithm | Needleman-Wunsch 
    44818 Similarity matrix | BLOSUM-62 
    44819 SS fraction | 0.3 
    44820 Gap open (HH/SS/other) | 18/18/6 
    44821 Gap extend | 1 
    44822 SS matrix |  |  | H | S | O 
    44823 ---|---|---|--- 
    44824 H | 6 | -9 | -6 
    44825 S |  | 6 | -6 
    44826 O |  |  | 4 
    44827 Iteration cutoff | 2 
    44828  
    44829 Matchmaker 3j0c.pdb1, chain B (#1.29) with AF3 E2 353-438.pdb, chain B (#145),
    44830 sequence alignment score = 333.4 
    44831 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    44832 8.411) 
    44833  
    44834 
    44835 > hide sel cartoons
    44836 
    44837 > select #1.29/C
    44838 
    44839 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    44840 
    44841 > show sel cartoons
    44842 
    44843 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    44844 
    44845 Chain information for AF3 CA.pdb #146 
    44846 --- 
    44847 Chain | Description 
    44848 A | No description available 
    44849  
    44850 
    44851 > matchmaker #146 to #1.29 & sel
    44852 
    44853 Parameters 
    44854 --- 
    44855 Chain pairing | bb 
    44856 Alignment algorithm | Needleman-Wunsch 
    44857 Similarity matrix | BLOSUM-62 
    44858 SS fraction | 0.3 
    44859 Gap open (HH/SS/other) | 18/18/6 
    44860 Gap extend | 1 
    44861 SS matrix |  |  | H | S | O 
    44862 ---|---|---|--- 
    44863 H | 6 | -9 | -6 
    44864 S |  | 6 | -6 
    44865 O |  |  | 4 
    44866 Iteration cutoff | 2 
    44867  
    44868 Matchmaker 3j0c.pdb1, chain C (#1.29) with AF3 CA.pdb, chain A (#146),
    44869 sequence alignment score = 328.1 
    44870 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    44871 2.714) 
    44872  
    44873 
    44874 > hide sel cartoons
    44875 
    44876 > color #142 dodgerblue
    44877 
    44878 > color #143 dodgerblue
    44879 
    44880 > color #144 #00b305ff
    44881 
    44882 > color #145 #00b305ff
    44883 
    44884 > color #146 #f15839ff
    44885 
    44886 > select #1.30/A
    44887 
    44888 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    44889 
    44890 > show sel cartoons
    44891 
    44892 > select #1.30/B
    44893 
    44894 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    44895 
    44896 > select #1.30/A
    44897 
    44898 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    44899 
    44900 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    44901 
    44902 Chain information for AF3 E1 1-421.pdb #147 
    44903 --- 
    44904 Chain | Description 
    44905 A | No description available 
    44906  
    44907 
    44908 > matchmaker #147 to #1.30 & sel
    44909 
    44910 Parameters 
    44911 --- 
    44912 Chain pairing | bb 
    44913 Alignment algorithm | Needleman-Wunsch 
    44914 Similarity matrix | BLOSUM-62 
    44915 SS fraction | 0.3 
    44916 Gap open (HH/SS/other) | 18/18/6 
    44917 Gap extend | 1 
    44918 SS matrix |  |  | H | S | O 
    44919 ---|---|---|--- 
    44920 H | 6 | -9 | -6 
    44921 S |  | 6 | -6 
    44922 O |  |  | 4 
    44923 Iteration cutoff | 2 
    44924  
    44925 Matchmaker 3j0c.pdb1, chain A (#1.30) with AF3 E1 1-421.pdb, chain A (#147),
    44926 sequence alignment score = 1060.7 
    44927 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    44928 3.020) 
    44929  
    44930 
    44931 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    44932 
    44933 Chain information for AF3 E1 422-461.pdb #148 
    44934 --- 
    44935 Chain | Description 
    44936 A | No description available 
    44937  
    44938 
    44939 > matchmaker #148 to #1.30 & sel
    44940 
    44941 Parameters 
    44942 --- 
    44943 Chain pairing | bb 
    44944 Alignment algorithm | Needleman-Wunsch 
    44945 Similarity matrix | BLOSUM-62 
    44946 SS fraction | 0.3 
    44947 Gap open (HH/SS/other) | 18/18/6 
    44948 Gap extend | 1 
    44949 SS matrix |  |  | H | S | O 
    44950 ---|---|---|--- 
    44951 H | 6 | -9 | -6 
    44952 S |  | 6 | -6 
    44953 O |  |  | 4 
    44954 Iteration cutoff | 2 
    44955  
    44956 Matchmaker 3j0c.pdb1, chain A (#1.30) with AF3 E1 422-461.pdb, chain A (#148),
    44957 sequence alignment score = 626.9 
    44958 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    44959 2.775) 
    44960  
    44961 
    44962 > hide sel cartoons
    44963 
    44964 > select #1.30/B
    44965 
    44966 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    44967 
    44968 > show sel cartoons
    44969 
    44970 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    44971 
    44972 Chain information for AF3 E2 1-352.pdb #149 
    44973 --- 
    44974 Chain | Description 
    44975 B | No description available 
    44976  
    44977 
    44978 > matchmaker #149 to #1.30 & sel
    44979 
    44980 Parameters 
    44981 --- 
    44982 Chain pairing | bb 
    44983 Alignment algorithm | Needleman-Wunsch 
    44984 Similarity matrix | BLOSUM-62 
    44985 SS fraction | 0.3 
    44986 Gap open (HH/SS/other) | 18/18/6 
    44987 Gap extend | 1 
    44988 SS matrix |  |  | H | S | O 
    44989 ---|---|---|--- 
    44990 H | 6 | -9 | -6 
    44991 S |  | 6 | -6 
    44992 O |  |  | 4 
    44993 Iteration cutoff | 2 
    44994  
    44995 Matchmaker 3j0c.pdb1, chain B (#1.30) with AF3 E2 1-352.pdb, chain B (#149),
    44996 sequence alignment score = 583.7 
    44997 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    44998 5.933) 
    44999  
    45000 
    45001 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    45002 
    45003 Chain information for AF3 E2 353-438.pdb #150 
    45004 --- 
    45005 Chain | Description 
    45006 B | No description available 
    45007  
    45008 
    45009 > matchmaker #150 to #1.30 & sel
    45010 
    45011 Parameters 
    45012 --- 
    45013 Chain pairing | bb 
    45014 Alignment algorithm | Needleman-Wunsch 
    45015 Similarity matrix | BLOSUM-62 
    45016 SS fraction | 0.3 
    45017 Gap open (HH/SS/other) | 18/18/6 
    45018 Gap extend | 1 
    45019 SS matrix |  |  | H | S | O 
    45020 ---|---|---|--- 
    45021 H | 6 | -9 | -6 
    45022 S |  | 6 | -6 
    45023 O |  |  | 4 
    45024 Iteration cutoff | 2 
    45025  
    45026 Matchmaker 3j0c.pdb1, chain B (#1.30) with AF3 E2 353-438.pdb, chain B (#150),
    45027 sequence alignment score = 333.4 
    45028 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    45029 8.411) 
    45030  
    45031 
    45032 > hide sel cartoons
    45033 
    45034 > select #1.30/C
    45035 
    45036 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    45037 
    45038 > show sel cartoons
    45039 
    45040 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    45041 
    45042 Chain information for AF3 CA.pdb #151 
    45043 --- 
    45044 Chain | Description 
    45045 A | No description available 
    45046  
    45047 
    45048 > matchmaker #151 to #1.30 & sel
    45049 
    45050 Parameters 
    45051 --- 
    45052 Chain pairing | bb 
    45053 Alignment algorithm | Needleman-Wunsch 
    45054 Similarity matrix | BLOSUM-62 
    45055 SS fraction | 0.3 
    45056 Gap open (HH/SS/other) | 18/18/6 
    45057 Gap extend | 1 
    45058 SS matrix |  |  | H | S | O 
    45059 ---|---|---|--- 
    45060 H | 6 | -9 | -6 
    45061 S |  | 6 | -6 
    45062 O |  |  | 4 
    45063 Iteration cutoff | 2 
    45064  
    45065 Matchmaker 3j0c.pdb1, chain C (#1.30) with AF3 CA.pdb, chain A (#151),
    45066 sequence alignment score = 328.1 
    45067 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    45068 2.714) 
    45069  
    45070 
    45071 > hide sel cartoons
    45072 
    45073 > color #147 dodgerblue
    45074 
    45075 > color #148 dodgerblue
    45076 
    45077 > color #149 #00b305ff
    45078 
    45079 > color #150 #00b305ff
    45080 
    45081 > color #151 #f15839ff
    45082 
    45083 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    45084 
    45085 > select #1.31/A
    45086 
    45087 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    45088 
    45089 > show sel cartoons
    45090 
    45091 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    45092 
    45093 Chain information for AF3 E1 1-421.pdb #152 
    45094 --- 
    45095 Chain | Description 
    45096 A | No description available 
    45097  
    45098 
    45099 > matchmaker #152 to #1.31 & sel
    45100 
    45101 Parameters 
    45102 --- 
    45103 Chain pairing | bb 
    45104 Alignment algorithm | Needleman-Wunsch 
    45105 Similarity matrix | BLOSUM-62 
    45106 SS fraction | 0.3 
    45107 Gap open (HH/SS/other) | 18/18/6 
    45108 Gap extend | 1 
    45109 SS matrix |  |  | H | S | O 
    45110 ---|---|---|--- 
    45111 H | 6 | -9 | -6 
    45112 S |  | 6 | -6 
    45113 O |  |  | 4 
    45114 Iteration cutoff | 2 
    45115  
    45116 Matchmaker 3j0c.pdb1, chain A (#1.31) with AF3 E1 1-421.pdb, chain A (#152),
    45117 sequence alignment score = 1060.7 
    45118 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    45119 3.020) 
    45120  
    45121 
    45122 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    45123 
    45124 Chain information for AF3 E1 422-461.pdb #153 
    45125 --- 
    45126 Chain | Description 
    45127 A | No description available 
    45128  
    45129 
    45130 > matchmaker #153 to #1.31 & sel
    45131 
    45132 Parameters 
    45133 --- 
    45134 Chain pairing | bb 
    45135 Alignment algorithm | Needleman-Wunsch 
    45136 Similarity matrix | BLOSUM-62 
    45137 SS fraction | 0.3 
    45138 Gap open (HH/SS/other) | 18/18/6 
    45139 Gap extend | 1 
    45140 SS matrix |  |  | H | S | O 
    45141 ---|---|---|--- 
    45142 H | 6 | -9 | -6 
    45143 S |  | 6 | -6 
    45144 O |  |  | 4 
    45145 Iteration cutoff | 2 
    45146  
    45147 Matchmaker 3j0c.pdb1, chain A (#1.31) with AF3 E1 422-461.pdb, chain A (#153),
    45148 sequence alignment score = 626.9 
    45149 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    45150 2.775) 
    45151  
    45152 
    45153 > hide sel cartoons
    45154 
    45155 > select #1.31/B
    45156 
    45157 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    45158 
    45159 > show sel cartoons
    45160 
    45161 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    45162 
    45163 Chain information for AF3 E2 1-352.pdb #154 
    45164 --- 
    45165 Chain | Description 
    45166 B | No description available 
    45167  
    45168 
    45169 > matchmaker #154 to #1.31 & sel
    45170 
    45171 Parameters 
    45172 --- 
    45173 Chain pairing | bb 
    45174 Alignment algorithm | Needleman-Wunsch 
    45175 Similarity matrix | BLOSUM-62 
    45176 SS fraction | 0.3 
    45177 Gap open (HH/SS/other) | 18/18/6 
    45178 Gap extend | 1 
    45179 SS matrix |  |  | H | S | O 
    45180 ---|---|---|--- 
    45181 H | 6 | -9 | -6 
    45182 S |  | 6 | -6 
    45183 O |  |  | 4 
    45184 Iteration cutoff | 2 
    45185  
    45186 Matchmaker 3j0c.pdb1, chain B (#1.31) with AF3 E2 1-352.pdb, chain B (#154),
    45187 sequence alignment score = 583.7 
    45188 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    45189 5.933) 
    45190  
    45191 
    45192 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    45193 
    45194 Chain information for AF3 E2 353-438.pdb #155 
    45195 --- 
    45196 Chain | Description 
    45197 B | No description available 
    45198  
    45199 
    45200 > matchmaker #155 to #1.31 & sel
    45201 
    45202 Parameters 
    45203 --- 
    45204 Chain pairing | bb 
    45205 Alignment algorithm | Needleman-Wunsch 
    45206 Similarity matrix | BLOSUM-62 
    45207 SS fraction | 0.3 
    45208 Gap open (HH/SS/other) | 18/18/6 
    45209 Gap extend | 1 
    45210 SS matrix |  |  | H | S | O 
    45211 ---|---|---|--- 
    45212 H | 6 | -9 | -6 
    45213 S |  | 6 | -6 
    45214 O |  |  | 4 
    45215 Iteration cutoff | 2 
    45216  
    45217 Matchmaker 3j0c.pdb1, chain B (#1.31) with AF3 E2 353-438.pdb, chain B (#155),
    45218 sequence alignment score = 333.4 
    45219 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    45220 8.411) 
    45221  
    45222 
    45223 > select #1.31/C
    45224 
    45225 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    45226 
    45227 > show sel cartoons
    45228 
    45229 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    45230 
    45231 Chain information for AF3 CA.pdb #156 
    45232 --- 
    45233 Chain | Description 
    45234 A | No description available 
    45235  
    45236 
    45237 > matchmaker #156 to #1.31 & sel
    45238 
    45239 Parameters 
    45240 --- 
    45241 Chain pairing | bb 
    45242 Alignment algorithm | Needleman-Wunsch 
    45243 Similarity matrix | BLOSUM-62 
    45244 SS fraction | 0.3 
    45245 Gap open (HH/SS/other) | 18/18/6 
    45246 Gap extend | 1 
    45247 SS matrix |  |  | H | S | O 
    45248 ---|---|---|--- 
    45249 H | 6 | -9 | -6 
    45250 S |  | 6 | -6 
    45251 O |  |  | 4 
    45252 Iteration cutoff | 2 
    45253  
    45254 Matchmaker 3j0c.pdb1, chain C (#1.31) with AF3 CA.pdb, chain A (#156),
    45255 sequence alignment score = 328.1 
    45256 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    45257 2.714) 
    45258  
    45259 
    45260 > hide sel cartoons
    45261 
    45262 > select #1.31/B
    45263 
    45264 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    45265 
    45266 > hide sel cartoons
    45267 
    45268 > color #152 dodgerblue
    45269 
    45270 > color #153 dodgerblue
    45271 
    45272 > color #154 #00b305ff
    45273 
    45274 > color #155 #00b305ff
    45275 
    45276 > color #156 #f15839ff
    45277 
    45278 > select #1.32/A
    45279 
    45280 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    45281 
    45282 > show sel cartoons
    45283 
    45284 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    45285 
    45286 Chain information for AF3 E1 1-421.pdb #157 
    45287 --- 
    45288 Chain | Description 
    45289 A | No description available 
    45290  
    45291 
    45292 > matchmaker #157 to #1.32 & sel
    45293 
    45294 Parameters 
    45295 --- 
    45296 Chain pairing | bb 
    45297 Alignment algorithm | Needleman-Wunsch 
    45298 Similarity matrix | BLOSUM-62 
    45299 SS fraction | 0.3 
    45300 Gap open (HH/SS/other) | 18/18/6 
    45301 Gap extend | 1 
    45302 SS matrix |  |  | H | S | O 
    45303 ---|---|---|--- 
    45304 H | 6 | -9 | -6 
    45305 S |  | 6 | -6 
    45306 O |  |  | 4 
    45307 Iteration cutoff | 2 
    45308  
    45309 Matchmaker 3j0c.pdb1, chain A (#1.32) with AF3 E1 1-421.pdb, chain A (#157),
    45310 sequence alignment score = 1060.7 
    45311 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    45312 3.020) 
    45313  
    45314 
    45315 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    45316 
    45317 Chain information for AF3 E1 422-461.pdb #158 
    45318 --- 
    45319 Chain | Description 
    45320 A | No description available 
    45321  
    45322 
    45323 > matchmaker #158 to #1.32 & sel
    45324 
    45325 Parameters 
    45326 --- 
    45327 Chain pairing | bb 
    45328 Alignment algorithm | Needleman-Wunsch 
    45329 Similarity matrix | BLOSUM-62 
    45330 SS fraction | 0.3 
    45331 Gap open (HH/SS/other) | 18/18/6 
    45332 Gap extend | 1 
    45333 SS matrix |  |  | H | S | O 
    45334 ---|---|---|--- 
    45335 H | 6 | -9 | -6 
    45336 S |  | 6 | -6 
    45337 O |  |  | 4 
    45338 Iteration cutoff | 2 
    45339  
    45340 Matchmaker 3j0c.pdb1, chain A (#1.32) with AF3 E1 422-461.pdb, chain A (#158),
    45341 sequence alignment score = 626.9 
    45342 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    45343 2.775) 
    45344  
    45345 
    45346 > hide sel cartoons
    45347 
    45348 > select #1.32/B
    45349 
    45350 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    45351 
    45352 > show sel cartoons
    45353 
    45354 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    45355 
    45356 Chain information for AF3 E2 1-352.pdb #159 
    45357 --- 
    45358 Chain | Description 
    45359 B | No description available 
    45360  
    45361 
    45362 > matchmaker #159 to #1.32 & sel
    45363 
    45364 Parameters 
    45365 --- 
    45366 Chain pairing | bb 
    45367 Alignment algorithm | Needleman-Wunsch 
    45368 Similarity matrix | BLOSUM-62 
    45369 SS fraction | 0.3 
    45370 Gap open (HH/SS/other) | 18/18/6 
    45371 Gap extend | 1 
    45372 SS matrix |  |  | H | S | O 
    45373 ---|---|---|--- 
    45374 H | 6 | -9 | -6 
    45375 S |  | 6 | -6 
    45376 O |  |  | 4 
    45377 Iteration cutoff | 2 
    45378  
    45379 Matchmaker 3j0c.pdb1, chain B (#1.32) with AF3 E2 1-352.pdb, chain B (#159),
    45380 sequence alignment score = 583.7 
    45381 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    45382 5.933) 
    45383  
    45384 
    45385 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    45386 
    45387 Chain information for AF3 E2 353-438.pdb #160 
    45388 --- 
    45389 Chain | Description 
    45390 B | No description available 
    45391  
    45392 
    45393 > matchmaker #160 to #1.32 & sel
    45394 
    45395 Parameters 
    45396 --- 
    45397 Chain pairing | bb 
    45398 Alignment algorithm | Needleman-Wunsch 
    45399 Similarity matrix | BLOSUM-62 
    45400 SS fraction | 0.3 
    45401 Gap open (HH/SS/other) | 18/18/6 
    45402 Gap extend | 1 
    45403 SS matrix |  |  | H | S | O 
    45404 ---|---|---|--- 
    45405 H | 6 | -9 | -6 
    45406 S |  | 6 | -6 
    45407 O |  |  | 4 
    45408 Iteration cutoff | 2 
    45409  
    45410 Matchmaker 3j0c.pdb1, chain B (#1.32) with AF3 E2 353-438.pdb, chain B (#160),
    45411 sequence alignment score = 322.6 
    45412 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    45413 8.411) 
    45414  
    45415 
    45416 > hide sel cartoons
    45417 
    45418 > select #1.32/C
    45419 
    45420 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    45421 
    45422 > show sel cartoons
    45423 
    45424 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    45425 
    45426 Chain information for AF3 CA.pdb #161 
    45427 --- 
    45428 Chain | Description 
    45429 A | No description available 
    45430  
    45431 
    45432 > matchmaker #161 to #1.32 & sel
    45433 
    45434 Parameters 
    45435 --- 
    45436 Chain pairing | bb 
    45437 Alignment algorithm | Needleman-Wunsch 
    45438 Similarity matrix | BLOSUM-62 
    45439 SS fraction | 0.3 
    45440 Gap open (HH/SS/other) | 18/18/6 
    45441 Gap extend | 1 
    45442 SS matrix |  |  | H | S | O 
    45443 ---|---|---|--- 
    45444 H | 6 | -9 | -6 
    45445 S |  | 6 | -6 
    45446 O |  |  | 4 
    45447 Iteration cutoff | 2 
    45448  
    45449 Matchmaker 3j0c.pdb1, chain C (#1.32) with AF3 CA.pdb, chain A (#161),
    45450 sequence alignment score = 328.1 
    45451 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    45452 2.714) 
    45453  
    45454 
    45455 > hide sel cartoons
    45456 
    45457 > color #157 dodgerblue
    45458 
    45459 > color #158 dodgerblue
    45460 
    45461 > color #159 #00b305ff
    45462 
    45463 > color #160 #00b305ff
    45464 
    45465 > color #161 #f15839ff
    45466 
    45467 > select #1.33/A
    45468 
    45469 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    45470 
    45471 > show sel cartoons
    45472 
    45473 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    45474 
    45475 Chain information for AF3 E1 1-421.pdb #162 
    45476 --- 
    45477 Chain | Description 
    45478 A | No description available 
    45479  
    45480 
    45481 > matchmaker #162 to #1.33 & sel
    45482 
    45483 Parameters 
    45484 --- 
    45485 Chain pairing | bb 
    45486 Alignment algorithm | Needleman-Wunsch 
    45487 Similarity matrix | BLOSUM-62 
    45488 SS fraction | 0.3 
    45489 Gap open (HH/SS/other) | 18/18/6 
    45490 Gap extend | 1 
    45491 SS matrix |  |  | H | S | O 
    45492 ---|---|---|--- 
    45493 H | 6 | -9 | -6 
    45494 S |  | 6 | -6 
    45495 O |  |  | 4 
    45496 Iteration cutoff | 2 
    45497  
    45498 Matchmaker 3j0c.pdb1, chain A (#1.33) with AF3 E1 1-421.pdb, chain A (#162),
    45499 sequence alignment score = 1060.7 
    45500 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    45501 3.020) 
    45502  
    45503 
    45504 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    45505 
    45506 Chain information for AF3 E1 422-461.pdb #163 
    45507 --- 
    45508 Chain | Description 
    45509 A | No description available 
    45510  
    45511 
    45512 > matchmaker #163 to #1.33 & sel
    45513 
    45514 Parameters 
    45515 --- 
    45516 Chain pairing | bb 
    45517 Alignment algorithm | Needleman-Wunsch 
    45518 Similarity matrix | BLOSUM-62 
    45519 SS fraction | 0.3 
    45520 Gap open (HH/SS/other) | 18/18/6 
    45521 Gap extend | 1 
    45522 SS matrix |  |  | H | S | O 
    45523 ---|---|---|--- 
    45524 H | 6 | -9 | -6 
    45525 S |  | 6 | -6 
    45526 O |  |  | 4 
    45527 Iteration cutoff | 2 
    45528  
    45529 Matchmaker 3j0c.pdb1, chain A (#1.33) with AF3 E1 422-461.pdb, chain A (#163),
    45530 sequence alignment score = 626.9 
    45531 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    45532 2.775) 
    45533  
    45534 
    45535 > hide sel cartoons
    45536 
    45537 > select #1.33/B
    45538 
    45539 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    45540 
    45541 > show sel cartoons
    45542 
    45543 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    45544 
    45545 Chain information for AF3 E2 1-352.pdb #164 
    45546 --- 
    45547 Chain | Description 
    45548 B | No description available 
    45549  
    45550 
    45551 > matchmaker #164 to #1.33 & sel
    45552 
    45553 Parameters 
    45554 --- 
    45555 Chain pairing | bb 
    45556 Alignment algorithm | Needleman-Wunsch 
    45557 Similarity matrix | BLOSUM-62 
    45558 SS fraction | 0.3 
    45559 Gap open (HH/SS/other) | 18/18/6 
    45560 Gap extend | 1 
    45561 SS matrix |  |  | H | S | O 
    45562 ---|---|---|--- 
    45563 H | 6 | -9 | -6 
    45564 S |  | 6 | -6 
    45565 O |  |  | 4 
    45566 Iteration cutoff | 2 
    45567  
    45568 Matchmaker 3j0c.pdb1, chain B (#1.33) with AF3 E2 1-352.pdb, chain B (#164),
    45569 sequence alignment score = 583.7 
    45570 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    45571 5.933) 
    45572  
    45573 
    45574 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    45575 
    45576 Chain information for AF3 E2 353-438.pdb #165 
    45577 --- 
    45578 Chain | Description 
    45579 B | No description available 
    45580  
    45581 
    45582 > matchmaker #165 to #1.33 & sel
    45583 
    45584 Parameters 
    45585 --- 
    45586 Chain pairing | bb 
    45587 Alignment algorithm | Needleman-Wunsch 
    45588 Similarity matrix | BLOSUM-62 
    45589 SS fraction | 0.3 
    45590 Gap open (HH/SS/other) | 18/18/6 
    45591 Gap extend | 1 
    45592 SS matrix |  |  | H | S | O 
    45593 ---|---|---|--- 
    45594 H | 6 | -9 | -6 
    45595 S |  | 6 | -6 
    45596 O |  |  | 4 
    45597 Iteration cutoff | 2 
    45598  
    45599 Matchmaker 3j0c.pdb1, chain B (#1.33) with AF3 E2 353-438.pdb, chain B (#165),
    45600 sequence alignment score = 322.6 
    45601 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    45602 8.411) 
    45603  
    45604 
    45605 > hide sel cartoons
    45606 
    45607 > select #1.33/C
    45608 
    45609 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    45610 
    45611 > show sel cartoons
    45612 
    45613 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    45614 
    45615 Chain information for AF3 CA.pdb #166 
    45616 --- 
    45617 Chain | Description 
    45618 A | No description available 
    45619  
    45620 
    45621 > matchmaker #166 to #1.33 & sel
    45622 
    45623 Parameters 
    45624 --- 
    45625 Chain pairing | bb 
    45626 Alignment algorithm | Needleman-Wunsch 
    45627 Similarity matrix | BLOSUM-62 
    45628 SS fraction | 0.3 
    45629 Gap open (HH/SS/other) | 18/18/6 
    45630 Gap extend | 1 
    45631 SS matrix |  |  | H | S | O 
    45632 ---|---|---|--- 
    45633 H | 6 | -9 | -6 
    45634 S |  | 6 | -6 
    45635 O |  |  | 4 
    45636 Iteration cutoff | 2 
    45637  
    45638 Matchmaker 3j0c.pdb1, chain C (#1.33) with AF3 CA.pdb, chain A (#166),
    45639 sequence alignment score = 328.1 
    45640 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    45641 2.714) 
    45642  
    45643 
    45644 > hide sel cartoons
    45645 
    45646 > color #162 dodgerblue
    45647 
    45648 > color #163 dodgerblue
    45649 
    45650 > color #164 #00b305ff
    45651 
    45652 > color #165 #00b305ff
    45653 
    45654 > color #166 #f15839ff
    45655 
    45656 > select #1.34/A
    45657 
    45658 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    45659 
    45660 > show sel cartoons
    45661 
    45662 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    45663 
    45664 Chain information for AF3 E1 1-421.pdb #167 
    45665 --- 
    45666 Chain | Description 
    45667 A | No description available 
    45668  
    45669 
    45670 > matchmaker #167 to #1.34 & sel
    45671 
    45672 Parameters 
    45673 --- 
    45674 Chain pairing | bb 
    45675 Alignment algorithm | Needleman-Wunsch 
    45676 Similarity matrix | BLOSUM-62 
    45677 SS fraction | 0.3 
    45678 Gap open (HH/SS/other) | 18/18/6 
    45679 Gap extend | 1 
    45680 SS matrix |  |  | H | S | O 
    45681 ---|---|---|--- 
    45682 H | 6 | -9 | -6 
    45683 S |  | 6 | -6 
    45684 O |  |  | 4 
    45685 Iteration cutoff | 2 
    45686  
    45687 Matchmaker 3j0c.pdb1, chain A (#1.34) with AF3 E1 1-421.pdb, chain A (#167),
    45688 sequence alignment score = 1060.7 
    45689 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    45690 3.020) 
    45691  
    45692 
    45693 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    45694 
    45695 Chain information for AF3 E1 422-461.pdb #168 
    45696 --- 
    45697 Chain | Description 
    45698 A | No description available 
    45699  
    45700 
    45701 > matchmaker #168 to #1.34 & sel
    45702 
    45703 Parameters 
    45704 --- 
    45705 Chain pairing | bb 
    45706 Alignment algorithm | Needleman-Wunsch 
    45707 Similarity matrix | BLOSUM-62 
    45708 SS fraction | 0.3 
    45709 Gap open (HH/SS/other) | 18/18/6 
    45710 Gap extend | 1 
    45711 SS matrix |  |  | H | S | O 
    45712 ---|---|---|--- 
    45713 H | 6 | -9 | -6 
    45714 S |  | 6 | -6 
    45715 O |  |  | 4 
    45716 Iteration cutoff | 2 
    45717  
    45718 Matchmaker 3j0c.pdb1, chain A (#1.34) with AF3 E1 422-461.pdb, chain A (#168),
    45719 sequence alignment score = 626.9 
    45720 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    45721 2.776) 
    45722  
    45723 
    45724 > hide sel cartoons
    45725 
    45726 > select #1.34/B
    45727 
    45728 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    45729 
    45730 > show sel cartoons
    45731 
    45732 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    45733 
    45734 Chain information for AF3 E2 1-352.pdb #169 
    45735 --- 
    45736 Chain | Description 
    45737 B | No description available 
    45738  
    45739 
    45740 > matchmaker #169 to #1.34 & sel
    45741 
    45742 Parameters 
    45743 --- 
    45744 Chain pairing | bb 
    45745 Alignment algorithm | Needleman-Wunsch 
    45746 Similarity matrix | BLOSUM-62 
    45747 SS fraction | 0.3 
    45748 Gap open (HH/SS/other) | 18/18/6 
    45749 Gap extend | 1 
    45750 SS matrix |  |  | H | S | O 
    45751 ---|---|---|--- 
    45752 H | 6 | -9 | -6 
    45753 S |  | 6 | -6 
    45754 O |  |  | 4 
    45755 Iteration cutoff | 2 
    45756  
    45757 Matchmaker 3j0c.pdb1, chain B (#1.34) with AF3 E2 1-352.pdb, chain B (#169),
    45758 sequence alignment score = 583.7 
    45759 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    45760 5.933) 
    45761  
    45762 
    45763 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    45764 
    45765 Chain information for AF3 E2 353-438.pdb #170 
    45766 --- 
    45767 Chain | Description 
    45768 B | No description available 
    45769  
    45770 
    45771 > matchmaker #170 to #1.34 & sel
    45772 
    45773 Parameters 
    45774 --- 
    45775 Chain pairing | bb 
    45776 Alignment algorithm | Needleman-Wunsch 
    45777 Similarity matrix | BLOSUM-62 
    45778 SS fraction | 0.3 
    45779 Gap open (HH/SS/other) | 18/18/6 
    45780 Gap extend | 1 
    45781 SS matrix |  |  | H | S | O 
    45782 ---|---|---|--- 
    45783 H | 6 | -9 | -6 
    45784 S |  | 6 | -6 
    45785 O |  |  | 4 
    45786 Iteration cutoff | 2 
    45787  
    45788 Matchmaker 3j0c.pdb1, chain B (#1.34) with AF3 E2 353-438.pdb, chain B (#170),
    45789 sequence alignment score = 333.4 
    45790 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    45791 8.411) 
    45792  
    45793 
    45794 > hide sel cartoons
    45795 
    45796 > select #1.34/C
    45797 
    45798 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    45799 
    45800 > show sel cartoons
    45801 
    45802 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    45803 
    45804 Chain information for AF3 CA.pdb #171 
    45805 --- 
    45806 Chain | Description 
    45807 A | No description available 
    45808  
    45809 
    45810 > matchmaker #171 to #1.34 & sel
    45811 
    45812 Parameters 
    45813 --- 
    45814 Chain pairing | bb 
    45815 Alignment algorithm | Needleman-Wunsch 
    45816 Similarity matrix | BLOSUM-62 
    45817 SS fraction | 0.3 
    45818 Gap open (HH/SS/other) | 18/18/6 
    45819 Gap extend | 1 
    45820 SS matrix |  |  | H | S | O 
    45821 ---|---|---|--- 
    45822 H | 6 | -9 | -6 
    45823 S |  | 6 | -6 
    45824 O |  |  | 4 
    45825 Iteration cutoff | 2 
    45826  
    45827 Matchmaker 3j0c.pdb1, chain C (#1.34) with AF3 CA.pdb, chain A (#171),
    45828 sequence alignment score = 328.1 
    45829 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    45830 2.714) 
    45831  
    45832 
    45833 > hide sel cartoons
    45834 
    45835 > color #167 dodgerblue
    45836 
    45837 > color #168 dodgerblue
    45838 
    45839 > color #169 #00b305ff
    45840 
    45841 > color #170 #00b305ff
    45842 
    45843 > color #171 #f15839ff
    45844 
    45845 > select #1.35/A
    45846 
    45847 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    45848 
    45849 > show sel cartoons
    45850 
    45851 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    45852 
    45853 Chain information for AF3 E1 1-421.pdb #172 
    45854 --- 
    45855 Chain | Description 
    45856 A | No description available 
    45857  
    45858 
    45859 > matchmaker #172 to #1.35 & sel
    45860 
    45861 Parameters 
    45862 --- 
    45863 Chain pairing | bb 
    45864 Alignment algorithm | Needleman-Wunsch 
    45865 Similarity matrix | BLOSUM-62 
    45866 SS fraction | 0.3 
    45867 Gap open (HH/SS/other) | 18/18/6 
    45868 Gap extend | 1 
    45869 SS matrix |  |  | H | S | O 
    45870 ---|---|---|--- 
    45871 H | 6 | -9 | -6 
    45872 S |  | 6 | -6 
    45873 O |  |  | 4 
    45874 Iteration cutoff | 2 
    45875  
    45876 Matchmaker 3j0c.pdb1, chain A (#1.35) with AF3 E1 1-421.pdb, chain A (#172),
    45877 sequence alignment score = 1060.7 
    45878 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    45879 3.020) 
    45880  
    45881 
    45882 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    45883 
    45884 Chain information for AF3 E1 422-461.pdb #173 
    45885 --- 
    45886 Chain | Description 
    45887 A | No description available 
    45888  
    45889 
    45890 > matchmaker #173 to #1.35 & sel
    45891 
    45892 Parameters 
    45893 --- 
    45894 Chain pairing | bb 
    45895 Alignment algorithm | Needleman-Wunsch 
    45896 Similarity matrix | BLOSUM-62 
    45897 SS fraction | 0.3 
    45898 Gap open (HH/SS/other) | 18/18/6 
    45899 Gap extend | 1 
    45900 SS matrix |  |  | H | S | O 
    45901 ---|---|---|--- 
    45902 H | 6 | -9 | -6 
    45903 S |  | 6 | -6 
    45904 O |  |  | 4 
    45905 Iteration cutoff | 2 
    45906  
    45907 Matchmaker 3j0c.pdb1, chain A (#1.35) with AF3 E1 422-461.pdb, chain A (#173),
    45908 sequence alignment score = 626.9 
    45909 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    45910 2.775) 
    45911  
    45912 
    45913 > hide sel cartoons
    45914 
    45915 > select #1.35/B
    45916 
    45917 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    45918 
    45919 > show sel cartoons
    45920 
    45921 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    45922 
    45923 Chain information for AF3 E2 1-352.pdb #174 
    45924 --- 
    45925 Chain | Description 
    45926 B | No description available 
    45927  
    45928 
    45929 > matchmaker #174 to #1.35 & sel
    45930 
    45931 Parameters 
    45932 --- 
    45933 Chain pairing | bb 
    45934 Alignment algorithm | Needleman-Wunsch 
    45935 Similarity matrix | BLOSUM-62 
    45936 SS fraction | 0.3 
    45937 Gap open (HH/SS/other) | 18/18/6 
    45938 Gap extend | 1 
    45939 SS matrix |  |  | H | S | O 
    45940 ---|---|---|--- 
    45941 H | 6 | -9 | -6 
    45942 S |  | 6 | -6 
    45943 O |  |  | 4 
    45944 Iteration cutoff | 2 
    45945  
    45946 Matchmaker 3j0c.pdb1, chain B (#1.35) with AF3 E2 1-352.pdb, chain B (#174),
    45947 sequence alignment score = 583.7 
    45948 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    45949 5.933) 
    45950  
    45951 
    45952 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    45953 
    45954 Chain information for AF3 E2 353-438.pdb #175 
    45955 --- 
    45956 Chain | Description 
    45957 B | No description available 
    45958  
    45959 
    45960 > matchmaker #175 to #1.35 & sel
    45961 
    45962 Parameters 
    45963 --- 
    45964 Chain pairing | bb 
    45965 Alignment algorithm | Needleman-Wunsch 
    45966 Similarity matrix | BLOSUM-62 
    45967 SS fraction | 0.3 
    45968 Gap open (HH/SS/other) | 18/18/6 
    45969 Gap extend | 1 
    45970 SS matrix |  |  | H | S | O 
    45971 ---|---|---|--- 
    45972 H | 6 | -9 | -6 
    45973 S |  | 6 | -6 
    45974 O |  |  | 4 
    45975 Iteration cutoff | 2 
    45976  
    45977 Matchmaker 3j0c.pdb1, chain B (#1.35) with AF3 E2 353-438.pdb, chain B (#175),
    45978 sequence alignment score = 333.4 
    45979 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    45980 8.411) 
    45981  
    45982 
    45983 > hide sel cartoons
    45984 
    45985 > select #1.35/C
    45986 
    45987 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    45988 
    45989 > show sel cartoons
    45990 
    45991 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    45992 
    45993 Chain information for AF3 CA.pdb #176 
    45994 --- 
    45995 Chain | Description 
    45996 A | No description available 
    45997  
    45998 
    45999 > matchmaker #176 to #1.35 & sel
    46000 
    46001 Parameters 
    46002 --- 
    46003 Chain pairing | bb 
    46004 Alignment algorithm | Needleman-Wunsch 
    46005 Similarity matrix | BLOSUM-62 
    46006 SS fraction | 0.3 
    46007 Gap open (HH/SS/other) | 18/18/6 
    46008 Gap extend | 1 
    46009 SS matrix |  |  | H | S | O 
    46010 ---|---|---|--- 
    46011 H | 6 | -9 | -6 
    46012 S |  | 6 | -6 
    46013 O |  |  | 4 
    46014 Iteration cutoff | 2 
    46015  
    46016 Matchmaker 3j0c.pdb1, chain C (#1.35) with AF3 CA.pdb, chain A (#176),
    46017 sequence alignment score = 328.1 
    46018 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    46019 2.714) 
    46020  
    46021 
    46022 > hide sel cartoons
    46023 
    46024 > color #172 dodgerblue
    46025 
    46026 > color #173 dodgerblue
    46027 
    46028 > color #174 #00b305ff
    46029 
    46030 > color #175 #00b305ff
    46031 
    46032 > color #176 #f15839ff
    46033 
    46034 > select #1.36/A
    46035 
    46036 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    46037 
    46038 > show sel cartoons
    46039 
    46040 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    46041 
    46042 Chain information for AF3 E1 1-421.pdb #177 
    46043 --- 
    46044 Chain | Description 
    46045 A | No description available 
    46046  
    46047 
    46048 > matchmaker #177 to #1.36 & sel
    46049 
    46050 Parameters 
    46051 --- 
    46052 Chain pairing | bb 
    46053 Alignment algorithm | Needleman-Wunsch 
    46054 Similarity matrix | BLOSUM-62 
    46055 SS fraction | 0.3 
    46056 Gap open (HH/SS/other) | 18/18/6 
    46057 Gap extend | 1 
    46058 SS matrix |  |  | H | S | O 
    46059 ---|---|---|--- 
    46060 H | 6 | -9 | -6 
    46061 S |  | 6 | -6 
    46062 O |  |  | 4 
    46063 Iteration cutoff | 2 
    46064  
    46065 Matchmaker 3j0c.pdb1, chain A (#1.36) with AF3 E1 1-421.pdb, chain A (#177),
    46066 sequence alignment score = 1060.7 
    46067 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    46068 3.020) 
    46069  
    46070 
    46071 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    46072 
    46073 Chain information for AF3 E1 422-461.pdb #178 
    46074 --- 
    46075 Chain | Description 
    46076 A | No description available 
    46077  
    46078 
    46079 > matchmaker #178 to #1.36 & sel
    46080 
    46081 Parameters 
    46082 --- 
    46083 Chain pairing | bb 
    46084 Alignment algorithm | Needleman-Wunsch 
    46085 Similarity matrix | BLOSUM-62 
    46086 SS fraction | 0.3 
    46087 Gap open (HH/SS/other) | 18/18/6 
    46088 Gap extend | 1 
    46089 SS matrix |  |  | H | S | O 
    46090 ---|---|---|--- 
    46091 H | 6 | -9 | -6 
    46092 S |  | 6 | -6 
    46093 O |  |  | 4 
    46094 Iteration cutoff | 2 
    46095  
    46096 Matchmaker 3j0c.pdb1, chain A (#1.36) with AF3 E1 422-461.pdb, chain A (#178),
    46097 sequence alignment score = 626.9 
    46098 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    46099 2.776) 
    46100  
    46101 
    46102 > hide sel cartoons
    46103 
    46104 > select #1.36/B
    46105 
    46106 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    46107 
    46108 > show sel cartoons
    46109 
    46110 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    46111 
    46112 Chain information for AF3 E2 1-352.pdb #179 
    46113 --- 
    46114 Chain | Description 
    46115 B | No description available 
    46116  
    46117 
    46118 > matchmaker #179 to #1.36 & sel
    46119 
    46120 Parameters 
    46121 --- 
    46122 Chain pairing | bb 
    46123 Alignment algorithm | Needleman-Wunsch 
    46124 Similarity matrix | BLOSUM-62 
    46125 SS fraction | 0.3 
    46126 Gap open (HH/SS/other) | 18/18/6 
    46127 Gap extend | 1 
    46128 SS matrix |  |  | H | S | O 
    46129 ---|---|---|--- 
    46130 H | 6 | -9 | -6 
    46131 S |  | 6 | -6 
    46132 O |  |  | 4 
    46133 Iteration cutoff | 2 
    46134  
    46135 Matchmaker 3j0c.pdb1, chain B (#1.36) with AF3 E2 1-352.pdb, chain B (#179),
    46136 sequence alignment score = 583.7 
    46137 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    46138 5.933) 
    46139  
    46140 
    46141 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    46142 
    46143 Chain information for AF3 E2 353-438.pdb #180 
    46144 --- 
    46145 Chain | Description 
    46146 B | No description available 
    46147  
    46148 
    46149 > matchmaker #180 to #1.36 & sel
    46150 
    46151 Parameters 
    46152 --- 
    46153 Chain pairing | bb 
    46154 Alignment algorithm | Needleman-Wunsch 
    46155 Similarity matrix | BLOSUM-62 
    46156 SS fraction | 0.3 
    46157 Gap open (HH/SS/other) | 18/18/6 
    46158 Gap extend | 1 
    46159 SS matrix |  |  | H | S | O 
    46160 ---|---|---|--- 
    46161 H | 6 | -9 | -6 
    46162 S |  | 6 | -6 
    46163 O |  |  | 4 
    46164 Iteration cutoff | 2 
    46165  
    46166 Matchmaker 3j0c.pdb1, chain B (#1.36) with AF3 E2 353-438.pdb, chain B (#180),
    46167 sequence alignment score = 333.4 
    46168 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    46169 8.411) 
    46170  
    46171 
    46172 > hide sel cartoons
    46173 
    46174 > select #1.36/C
    46175 
    46176 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    46177 
    46178 > show sel cartoons
    46179 
    46180 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    46181 
    46182 Chain information for AF3 CA.pdb #181 
    46183 --- 
    46184 Chain | Description 
    46185 A | No description available 
    46186  
    46187 
    46188 > matchmaker #181 to #1.36 & sel
    46189 
    46190 Parameters 
    46191 --- 
    46192 Chain pairing | bb 
    46193 Alignment algorithm | Needleman-Wunsch 
    46194 Similarity matrix | BLOSUM-62 
    46195 SS fraction | 0.3 
    46196 Gap open (HH/SS/other) | 18/18/6 
    46197 Gap extend | 1 
    46198 SS matrix |  |  | H | S | O 
    46199 ---|---|---|--- 
    46200 H | 6 | -9 | -6 
    46201 S |  | 6 | -6 
    46202 O |  |  | 4 
    46203 Iteration cutoff | 2 
    46204  
    46205 Matchmaker 3j0c.pdb1, chain C (#1.36) with AF3 CA.pdb, chain A (#181),
    46206 sequence alignment score = 328.1 
    46207 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    46208 2.714) 
    46209  
    46210 
    46211 > hide sel cartoons
    46212 
    46213 > color #177 dodgerblue
    46214 
    46215 > color #178 dodgerblue
    46216 
    46217 > color #179 #00b305ff
    46218 
    46219 > color #180 #00b305ff
    46220 
    46221 > color #181 #f15839ff
    46222 
    46223 > select #1.37/A
    46224 
    46225 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    46226 
    46227 > show sel cartoons
    46228 
    46229 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    46230 
    46231 Chain information for AF3 E1 1-421.pdb #182 
    46232 --- 
    46233 Chain | Description 
    46234 A | No description available 
    46235  
    46236 
    46237 > matchmaker #182 to #1.37 & sel
    46238 
    46239 Parameters 
    46240 --- 
    46241 Chain pairing | bb 
    46242 Alignment algorithm | Needleman-Wunsch 
    46243 Similarity matrix | BLOSUM-62 
    46244 SS fraction | 0.3 
    46245 Gap open (HH/SS/other) | 18/18/6 
    46246 Gap extend | 1 
    46247 SS matrix |  |  | H | S | O 
    46248 ---|---|---|--- 
    46249 H | 6 | -9 | -6 
    46250 S |  | 6 | -6 
    46251 O |  |  | 4 
    46252 Iteration cutoff | 2 
    46253  
    46254 Matchmaker 3j0c.pdb1, chain A (#1.37) with AF3 E1 1-421.pdb, chain A (#182),
    46255 sequence alignment score = 1060.7 
    46256 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    46257 3.020) 
    46258  
    46259 
    46260 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    46261 
    46262 Chain information for AF3 E1 422-461.pdb #183 
    46263 --- 
    46264 Chain | Description 
    46265 A | No description available 
    46266  
    46267 
    46268 > matchmaker #183 to #1.37 & sel
    46269 
    46270 Parameters 
    46271 --- 
    46272 Chain pairing | bb 
    46273 Alignment algorithm | Needleman-Wunsch 
    46274 Similarity matrix | BLOSUM-62 
    46275 SS fraction | 0.3 
    46276 Gap open (HH/SS/other) | 18/18/6 
    46277 Gap extend | 1 
    46278 SS matrix |  |  | H | S | O 
    46279 ---|---|---|--- 
    46280 H | 6 | -9 | -6 
    46281 S |  | 6 | -6 
    46282 O |  |  | 4 
    46283 Iteration cutoff | 2 
    46284  
    46285 Matchmaker 3j0c.pdb1, chain A (#1.37) with AF3 E1 422-461.pdb, chain A (#183),
    46286 sequence alignment score = 626.9 
    46287 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    46288 2.775) 
    46289  
    46290 
    46291 > hide sel cartoons
    46292 
    46293 > select #1.37/B
    46294 
    46295 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    46296 
    46297 > show sel cartoons
    46298 
    46299 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    46300 
    46301 Chain information for AF3 E2 1-352.pdb #184 
    46302 --- 
    46303 Chain | Description 
    46304 B | No description available 
    46305  
    46306 
    46307 > matchmaker #184 to #1.37 & sel
    46308 
    46309 Parameters 
    46310 --- 
    46311 Chain pairing | bb 
    46312 Alignment algorithm | Needleman-Wunsch 
    46313 Similarity matrix | BLOSUM-62 
    46314 SS fraction | 0.3 
    46315 Gap open (HH/SS/other) | 18/18/6 
    46316 Gap extend | 1 
    46317 SS matrix |  |  | H | S | O 
    46318 ---|---|---|--- 
    46319 H | 6 | -9 | -6 
    46320 S |  | 6 | -6 
    46321 O |  |  | 4 
    46322 Iteration cutoff | 2 
    46323  
    46324 Matchmaker 3j0c.pdb1, chain B (#1.37) with AF3 E2 1-352.pdb, chain B (#184),
    46325 sequence alignment score = 583.7 
    46326 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    46327 5.933) 
    46328  
    46329 
    46330 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    46331 
    46332 Chain information for AF3 E2 353-438.pdb #185 
    46333 --- 
    46334 Chain | Description 
    46335 B | No description available 
    46336  
    46337 
    46338 > matchmaker #185 to #1.37 & sel
    46339 
    46340 Parameters 
    46341 --- 
    46342 Chain pairing | bb 
    46343 Alignment algorithm | Needleman-Wunsch 
    46344 Similarity matrix | BLOSUM-62 
    46345 SS fraction | 0.3 
    46346 Gap open (HH/SS/other) | 18/18/6 
    46347 Gap extend | 1 
    46348 SS matrix |  |  | H | S | O 
    46349 ---|---|---|--- 
    46350 H | 6 | -9 | -6 
    46351 S |  | 6 | -6 
    46352 O |  |  | 4 
    46353 Iteration cutoff | 2 
    46354  
    46355 Matchmaker 3j0c.pdb1, chain B (#1.37) with AF3 E2 353-438.pdb, chain B (#185),
    46356 sequence alignment score = 333.4 
    46357 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    46358 8.411) 
    46359  
    46360 
    46361 > hide sel cartoons
    46362 
    46363 > select #1.37/C
    46364 
    46365 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    46366 
    46367 > show sel cartoons
    46368 
    46369 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    46370 
    46371 Chain information for AF3 CA.pdb #186 
    46372 --- 
    46373 Chain | Description 
    46374 A | No description available 
    46375  
    46376 
    46377 > matchmaker #186 to #1.37 & sel
    46378 
    46379 Parameters 
    46380 --- 
    46381 Chain pairing | bb 
    46382 Alignment algorithm | Needleman-Wunsch 
    46383 Similarity matrix | BLOSUM-62 
    46384 SS fraction | 0.3 
    46385 Gap open (HH/SS/other) | 18/18/6 
    46386 Gap extend | 1 
    46387 SS matrix |  |  | H | S | O 
    46388 ---|---|---|--- 
    46389 H | 6 | -9 | -6 
    46390 S |  | 6 | -6 
    46391 O |  |  | 4 
    46392 Iteration cutoff | 2 
    46393  
    46394 Matchmaker 3j0c.pdb1, chain C (#1.37) with AF3 CA.pdb, chain A (#186),
    46395 sequence alignment score = 328.1 
    46396 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    46397 2.714) 
    46398  
    46399 
    46400 > hide sel cartoons
    46401 
    46402 > color #182 dodgerblue
    46403 
    46404 > color #183 dodgerblue
    46405 
    46406 > color #184 #00b305ff
    46407 
    46408 > color #185 #00b305ff
    46409 
    46410 > color #186 #f15839ff
    46411 
    46412 > select #1.38/A
    46413 
    46414 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    46415 
    46416 > show sel cartoons
    46417 
    46418 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    46419 
    46420 Chain information for AF3 E1 1-421.pdb #187 
    46421 --- 
    46422 Chain | Description 
    46423 A | No description available 
    46424  
    46425 
    46426 > matchmaker #187 to #1.38 & sel
    46427 
    46428 Parameters 
    46429 --- 
    46430 Chain pairing | bb 
    46431 Alignment algorithm | Needleman-Wunsch 
    46432 Similarity matrix | BLOSUM-62 
    46433 SS fraction | 0.3 
    46434 Gap open (HH/SS/other) | 18/18/6 
    46435 Gap extend | 1 
    46436 SS matrix |  |  | H | S | O 
    46437 ---|---|---|--- 
    46438 H | 6 | -9 | -6 
    46439 S |  | 6 | -6 
    46440 O |  |  | 4 
    46441 Iteration cutoff | 2 
    46442  
    46443 Matchmaker 3j0c.pdb1, chain A (#1.38) with AF3 E1 1-421.pdb, chain A (#187),
    46444 sequence alignment score = 1060.7 
    46445 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    46446 3.020) 
    46447  
    46448 
    46449 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    46450 
    46451 Chain information for AF3 E1 422-461.pdb #188 
    46452 --- 
    46453 Chain | Description 
    46454 A | No description available 
    46455  
    46456 
    46457 > matchmaker #188 to #1.38 & sel
    46458 
    46459 Parameters 
    46460 --- 
    46461 Chain pairing | bb 
    46462 Alignment algorithm | Needleman-Wunsch 
    46463 Similarity matrix | BLOSUM-62 
    46464 SS fraction | 0.3 
    46465 Gap open (HH/SS/other) | 18/18/6 
    46466 Gap extend | 1 
    46467 SS matrix |  |  | H | S | O 
    46468 ---|---|---|--- 
    46469 H | 6 | -9 | -6 
    46470 S |  | 6 | -6 
    46471 O |  |  | 4 
    46472 Iteration cutoff | 2 
    46473  
    46474 Matchmaker 3j0c.pdb1, chain A (#1.38) with AF3 E1 422-461.pdb, chain A (#188),
    46475 sequence alignment score = 626.9 
    46476 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    46477 2.776) 
    46478  
    46479 
    46480 > hide sel cartoons
    46481 
    46482 > select #1.38/B
    46483 
    46484 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    46485 
    46486 > show sel cartoons
    46487 
    46488 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    46489 
    46490 Chain information for AF3 E2 1-352.pdb #189 
    46491 --- 
    46492 Chain | Description 
    46493 B | No description available 
    46494  
    46495 
    46496 > matchmaker #189 to #1.38 & sel
    46497 
    46498 Parameters 
    46499 --- 
    46500 Chain pairing | bb 
    46501 Alignment algorithm | Needleman-Wunsch 
    46502 Similarity matrix | BLOSUM-62 
    46503 SS fraction | 0.3 
    46504 Gap open (HH/SS/other) | 18/18/6 
    46505 Gap extend | 1 
    46506 SS matrix |  |  | H | S | O 
    46507 ---|---|---|--- 
    46508 H | 6 | -9 | -6 
    46509 S |  | 6 | -6 
    46510 O |  |  | 4 
    46511 Iteration cutoff | 2 
    46512  
    46513 Matchmaker 3j0c.pdb1, chain B (#1.38) with AF3 E2 1-352.pdb, chain B (#189),
    46514 sequence alignment score = 583.7 
    46515 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    46516 5.933) 
    46517  
    46518 
    46519 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    46520 
    46521 Chain information for AF3 E2 353-438.pdb #190 
    46522 --- 
    46523 Chain | Description 
    46524 B | No description available 
    46525  
    46526 
    46527 > matchmaker #190 to #1.38 & sel
    46528 
    46529 Parameters 
    46530 --- 
    46531 Chain pairing | bb 
    46532 Alignment algorithm | Needleman-Wunsch 
    46533 Similarity matrix | BLOSUM-62 
    46534 SS fraction | 0.3 
    46535 Gap open (HH/SS/other) | 18/18/6 
    46536 Gap extend | 1 
    46537 SS matrix |  |  | H | S | O 
    46538 ---|---|---|--- 
    46539 H | 6 | -9 | -6 
    46540 S |  | 6 | -6 
    46541 O |  |  | 4 
    46542 Iteration cutoff | 2 
    46543  
    46544 Matchmaker 3j0c.pdb1, chain B (#1.38) with AF3 E2 353-438.pdb, chain B (#190),
    46545 sequence alignment score = 322.6 
    46546 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    46547 8.411) 
    46548  
    46549 
    46550 > hide sel cartoons
    46551 
    46552 > select #1.38/C
    46553 
    46554 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    46555 
    46556 > show sel cartoons
    46557 
    46558 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    46559 
    46560 Chain information for AF3 CA.pdb #191 
    46561 --- 
    46562 Chain | Description 
    46563 A | No description available 
    46564  
    46565 
    46566 > matchmaker #191 to #1.38 & sel
    46567 
    46568 Parameters 
    46569 --- 
    46570 Chain pairing | bb 
    46571 Alignment algorithm | Needleman-Wunsch 
    46572 Similarity matrix | BLOSUM-62 
    46573 SS fraction | 0.3 
    46574 Gap open (HH/SS/other) | 18/18/6 
    46575 Gap extend | 1 
    46576 SS matrix |  |  | H | S | O 
    46577 ---|---|---|--- 
    46578 H | 6 | -9 | -6 
    46579 S |  | 6 | -6 
    46580 O |  |  | 4 
    46581 Iteration cutoff | 2 
    46582  
    46583 Matchmaker 3j0c.pdb1, chain C (#1.38) with AF3 CA.pdb, chain A (#191),
    46584 sequence alignment score = 328.1 
    46585 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    46586 2.714) 
    46587  
    46588 
    46589 > hide sel cartoons
    46590 
    46591 > color #187 dodgerblue
    46592 
    46593 > color #188 dodgerblue
    46594 
    46595 > color #189 #00b305ff
    46596 
    46597 > color #190 #00b305ff
    46598 
    46599 > color #191 #f15839ff
    46600 
    46601 > select #1.39/A
    46602 
    46603 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    46604 
    46605 > show sel cartoons
    46606 
    46607 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    46608 
    46609 Chain information for AF3 E1 1-421.pdb #192 
    46610 --- 
    46611 Chain | Description 
    46612 A | No description available 
    46613  
    46614 
    46615 > matchmaker #192 to #1.39 & sel
    46616 
    46617 Parameters 
    46618 --- 
    46619 Chain pairing | bb 
    46620 Alignment algorithm | Needleman-Wunsch 
    46621 Similarity matrix | BLOSUM-62 
    46622 SS fraction | 0.3 
    46623 Gap open (HH/SS/other) | 18/18/6 
    46624 Gap extend | 1 
    46625 SS matrix |  |  | H | S | O 
    46626 ---|---|---|--- 
    46627 H | 6 | -9 | -6 
    46628 S |  | 6 | -6 
    46629 O |  |  | 4 
    46630 Iteration cutoff | 2 
    46631  
    46632 Matchmaker 3j0c.pdb1, chain A (#1.39) with AF3 E1 1-421.pdb, chain A (#192),
    46633 sequence alignment score = 1060.7 
    46634 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    46635 3.020) 
    46636  
    46637 
    46638 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    46639 
    46640 Chain information for AF3 E1 422-461.pdb #193 
    46641 --- 
    46642 Chain | Description 
    46643 A | No description available 
    46644  
    46645 
    46646 > matchmaker #193 to #1.39 & sel
    46647 
    46648 Parameters 
    46649 --- 
    46650 Chain pairing | bb 
    46651 Alignment algorithm | Needleman-Wunsch 
    46652 Similarity matrix | BLOSUM-62 
    46653 SS fraction | 0.3 
    46654 Gap open (HH/SS/other) | 18/18/6 
    46655 Gap extend | 1 
    46656 SS matrix |  |  | H | S | O 
    46657 ---|---|---|--- 
    46658 H | 6 | -9 | -6 
    46659 S |  | 6 | -6 
    46660 O |  |  | 4 
    46661 Iteration cutoff | 2 
    46662  
    46663 Matchmaker 3j0c.pdb1, chain A (#1.39) with AF3 E1 422-461.pdb, chain A (#193),
    46664 sequence alignment score = 626.9 
    46665 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    46666 2.776) 
    46667  
    46668 
    46669 > hide sel cartoons
    46670 
    46671 > select #1.39/B
    46672 
    46673 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    46674 
    46675 > show sel cartoons
    46676 
    46677 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    46678 
    46679 Chain information for AF3 E2 1-352.pdb #194 
    46680 --- 
    46681 Chain | Description 
    46682 B | No description available 
    46683  
    46684 
    46685 > matchmaker #194 to #1.39 & sel
    46686 
    46687 Parameters 
    46688 --- 
    46689 Chain pairing | bb 
    46690 Alignment algorithm | Needleman-Wunsch 
    46691 Similarity matrix | BLOSUM-62 
    46692 SS fraction | 0.3 
    46693 Gap open (HH/SS/other) | 18/18/6 
    46694 Gap extend | 1 
    46695 SS matrix |  |  | H | S | O 
    46696 ---|---|---|--- 
    46697 H | 6 | -9 | -6 
    46698 S |  | 6 | -6 
    46699 O |  |  | 4 
    46700 Iteration cutoff | 2 
    46701  
    46702 Matchmaker 3j0c.pdb1, chain B (#1.39) with AF3 E2 1-352.pdb, chain B (#194),
    46703 sequence alignment score = 583.7 
    46704 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    46705 5.933) 
    46706  
    46707 
    46708 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    46709 
    46710 Chain information for AF3 E2 353-438.pdb #195 
    46711 --- 
    46712 Chain | Description 
    46713 B | No description available 
    46714  
    46715 
    46716 > matchmaker #195 to #1.39 & sel
    46717 
    46718 Parameters 
    46719 --- 
    46720 Chain pairing | bb 
    46721 Alignment algorithm | Needleman-Wunsch 
    46722 Similarity matrix | BLOSUM-62 
    46723 SS fraction | 0.3 
    46724 Gap open (HH/SS/other) | 18/18/6 
    46725 Gap extend | 1 
    46726 SS matrix |  |  | H | S | O 
    46727 ---|---|---|--- 
    46728 H | 6 | -9 | -6 
    46729 S |  | 6 | -6 
    46730 O |  |  | 4 
    46731 Iteration cutoff | 2 
    46732  
    46733 Matchmaker 3j0c.pdb1, chain B (#1.39) with AF3 E2 353-438.pdb, chain B (#195),
    46734 sequence alignment score = 322.6 
    46735 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    46736 8.411) 
    46737  
    46738 
    46739 > hide sel cartoons
    46740 
    46741 > select #1.39/C
    46742 
    46743 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    46744 
    46745 > show sel atoms
    46746 
    46747 > hide sel atoms
    46748 
    46749 > show sel cartoons
    46750 
    46751 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    46752 
    46753 Chain information for AF3 CA.pdb #196 
    46754 --- 
    46755 Chain | Description 
    46756 A | No description available 
    46757  
    46758 
    46759 > matchmaker #196 to #1.39 & sel
    46760 
    46761 Parameters 
    46762 --- 
    46763 Chain pairing | bb 
    46764 Alignment algorithm | Needleman-Wunsch 
    46765 Similarity matrix | BLOSUM-62 
    46766 SS fraction | 0.3 
    46767 Gap open (HH/SS/other) | 18/18/6 
    46768 Gap extend | 1 
    46769 SS matrix |  |  | H | S | O 
    46770 ---|---|---|--- 
    46771 H | 6 | -9 | -6 
    46772 S |  | 6 | -6 
    46773 O |  |  | 4 
    46774 Iteration cutoff | 2 
    46775  
    46776 Matchmaker 3j0c.pdb1, chain C (#1.39) with AF3 CA.pdb, chain A (#196),
    46777 sequence alignment score = 328.1 
    46778 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    46779 2.714) 
    46780  
    46781 
    46782 > hide sel cartoons
    46783 
    46784 > color #192 dodgerblue
    46785 
    46786 > color #193 dodgerblue
    46787 
    46788 > color #194 #00b305ff
    46789 
    46790 > color #195 #00b305ff
    46791 
    46792 > color #196 #f15839ff
    46793 
    46794 > select #1.40/A
    46795 
    46796 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    46797 
    46798 > show sel cartoons
    46799 
    46800 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    46801 
    46802 Chain information for AF3 E1 1-421.pdb #197 
    46803 --- 
    46804 Chain | Description 
    46805 A | No description available 
    46806  
    46807 
    46808 > matchmaker #197 to #1.40 & sel
    46809 
    46810 Parameters 
    46811 --- 
    46812 Chain pairing | bb 
    46813 Alignment algorithm | Needleman-Wunsch 
    46814 Similarity matrix | BLOSUM-62 
    46815 SS fraction | 0.3 
    46816 Gap open (HH/SS/other) | 18/18/6 
    46817 Gap extend | 1 
    46818 SS matrix |  |  | H | S | O 
    46819 ---|---|---|--- 
    46820 H | 6 | -9 | -6 
    46821 S |  | 6 | -6 
    46822 O |  |  | 4 
    46823 Iteration cutoff | 2 
    46824  
    46825 Matchmaker 3j0c.pdb1, chain A (#1.40) with AF3 E1 1-421.pdb, chain A (#197),
    46826 sequence alignment score = 1060.7 
    46827 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    46828 3.020) 
    46829  
    46830 
    46831 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    46832 
    46833 Chain information for AF3 E1 422-461.pdb #198 
    46834 --- 
    46835 Chain | Description 
    46836 A | No description available 
    46837  
    46838 
    46839 > matchmaker #198 to #1.40 & sel
    46840 
    46841 Parameters 
    46842 --- 
    46843 Chain pairing | bb 
    46844 Alignment algorithm | Needleman-Wunsch 
    46845 Similarity matrix | BLOSUM-62 
    46846 SS fraction | 0.3 
    46847 Gap open (HH/SS/other) | 18/18/6 
    46848 Gap extend | 1 
    46849 SS matrix |  |  | H | S | O 
    46850 ---|---|---|--- 
    46851 H | 6 | -9 | -6 
    46852 S |  | 6 | -6 
    46853 O |  |  | 4 
    46854 Iteration cutoff | 2 
    46855  
    46856 Matchmaker 3j0c.pdb1, chain A (#1.40) with AF3 E1 422-461.pdb, chain A (#198),
    46857 sequence alignment score = 626.9 
    46858 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    46859 2.775) 
    46860  
    46861 
    46862 > hide sel cartoons
    46863 
    46864 [Repeated 1 time(s)]
    46865 
    46866 > select #1.40/B
    46867 
    46868 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    46869 
    46870 > show sel cartoons
    46871 
    46872 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    46873 
    46874 Chain information for AF3 E2 1-352.pdb #199 
    46875 --- 
    46876 Chain | Description 
    46877 B | No description available 
    46878  
    46879 
    46880 > matchmaker #199 to #1.40 & sel
    46881 
    46882 Parameters 
    46883 --- 
    46884 Chain pairing | bb 
    46885 Alignment algorithm | Needleman-Wunsch 
    46886 Similarity matrix | BLOSUM-62 
    46887 SS fraction | 0.3 
    46888 Gap open (HH/SS/other) | 18/18/6 
    46889 Gap extend | 1 
    46890 SS matrix |  |  | H | S | O 
    46891 ---|---|---|--- 
    46892 H | 6 | -9 | -6 
    46893 S |  | 6 | -6 
    46894 O |  |  | 4 
    46895 Iteration cutoff | 2 
    46896  
    46897 Matchmaker 3j0c.pdb1, chain B (#1.40) with AF3 E2 1-352.pdb, chain B (#199),
    46898 sequence alignment score = 583.7 
    46899 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    46900 5.933) 
    46901  
    46902 
    46903 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    46904 
    46905 Chain information for AF3 E2 353-438.pdb #200 
    46906 --- 
    46907 Chain | Description 
    46908 B | No description available 
    46909  
    46910 
    46911 > matchmaker #200 to #1.40 & sel
    46912 
    46913 Parameters 
    46914 --- 
    46915 Chain pairing | bb 
    46916 Alignment algorithm | Needleman-Wunsch 
    46917 Similarity matrix | BLOSUM-62 
    46918 SS fraction | 0.3 
    46919 Gap open (HH/SS/other) | 18/18/6 
    46920 Gap extend | 1 
    46921 SS matrix |  |  | H | S | O 
    46922 ---|---|---|--- 
    46923 H | 6 | -9 | -6 
    46924 S |  | 6 | -6 
    46925 O |  |  | 4 
    46926 Iteration cutoff | 2 
    46927  
    46928 Matchmaker 3j0c.pdb1, chain B (#1.40) with AF3 E2 353-438.pdb, chain B (#200),
    46929 sequence alignment score = 333.4 
    46930 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    46931 8.411) 
    46932  
    46933 
    46934 > hide sel cartoons
    46935 
    46936 > select #1.40/C
    46937 
    46938 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    46939 
    46940 > show sel cartoons
    46941 
    46942 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    46943 
    46944 Chain information for AF3 CA.pdb #201 
    46945 --- 
    46946 Chain | Description 
    46947 A | No description available 
    46948  
    46949 
    46950 > matchmaker #201 to #1.40 & sel
    46951 
    46952 Parameters 
    46953 --- 
    46954 Chain pairing | bb 
    46955 Alignment algorithm | Needleman-Wunsch 
    46956 Similarity matrix | BLOSUM-62 
    46957 SS fraction | 0.3 
    46958 Gap open (HH/SS/other) | 18/18/6 
    46959 Gap extend | 1 
    46960 SS matrix |  |  | H | S | O 
    46961 ---|---|---|--- 
    46962 H | 6 | -9 | -6 
    46963 S |  | 6 | -6 
    46964 O |  |  | 4 
    46965 Iteration cutoff | 2 
    46966  
    46967 Matchmaker 3j0c.pdb1, chain C (#1.40) with AF3 CA.pdb, chain A (#201),
    46968 sequence alignment score = 328.1 
    46969 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    46970 2.714) 
    46971  
    46972 
    46973 > hide sel cartoons
    46974 
    46975 > color #197 dodgerblue
    46976 
    46977 > color #198 dodgerblue
    46978 
    46979 > color #199 #00b305ff
    46980 
    46981 > color #200 #00b305ff
    46982 
    46983 > color #201 #f15839ff
    46984 
    46985 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    46986 
    46987 > select #1.41/A
    46988 
    46989 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    46990 
    46991 > show sel cartoons
    46992 
    46993 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    46994 
    46995 Chain information for AF3 E1 1-421.pdb #202 
    46996 --- 
    46997 Chain | Description 
    46998 A | No description available 
    46999  
    47000 
    47001 > matchmaker #202 to #1.41 & sel
    47002 
    47003 Parameters 
    47004 --- 
    47005 Chain pairing | bb 
    47006 Alignment algorithm | Needleman-Wunsch 
    47007 Similarity matrix | BLOSUM-62 
    47008 SS fraction | 0.3 
    47009 Gap open (HH/SS/other) | 18/18/6 
    47010 Gap extend | 1 
    47011 SS matrix |  |  | H | S | O 
    47012 ---|---|---|--- 
    47013 H | 6 | -9 | -6 
    47014 S |  | 6 | -6 
    47015 O |  |  | 4 
    47016 Iteration cutoff | 2 
    47017  
    47018 Matchmaker 3j0c.pdb1, chain A (#1.41) with AF3 E1 1-421.pdb, chain A (#202),
    47019 sequence alignment score = 1060.7 
    47020 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    47021 3.020) 
    47022  
    47023 
    47024 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    47025 
    47026 Chain information for AF3 E1 422-461.pdb #203 
    47027 --- 
    47028 Chain | Description 
    47029 A | No description available 
    47030  
    47031 
    47032 > matchmaker #203 to #1.41 & sel
    47033 
    47034 Parameters 
    47035 --- 
    47036 Chain pairing | bb 
    47037 Alignment algorithm | Needleman-Wunsch 
    47038 Similarity matrix | BLOSUM-62 
    47039 SS fraction | 0.3 
    47040 Gap open (HH/SS/other) | 18/18/6 
    47041 Gap extend | 1 
    47042 SS matrix |  |  | H | S | O 
    47043 ---|---|---|--- 
    47044 H | 6 | -9 | -6 
    47045 S |  | 6 | -6 
    47046 O |  |  | 4 
    47047 Iteration cutoff | 2 
    47048  
    47049 Matchmaker 3j0c.pdb1, chain A (#1.41) with AF3 E1 422-461.pdb, chain A (#203),
    47050 sequence alignment score = 626.9 
    47051 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    47052 2.776) 
    47053  
    47054 
    47055 > hide sel cartoons
    47056 
    47057 [Repeated 1 time(s)]
    47058 
    47059 > select #1.41/B
    47060 
    47061 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    47062 
    47063 > show sel cartoons
    47064 
    47065 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    47066 
    47067 Chain information for AF3 E2 1-352.pdb #204 
    47068 --- 
    47069 Chain | Description 
    47070 B | No description available 
    47071  
    47072 
    47073 > matchmaker #204 to #1.41 & sel
    47074 
    47075 Parameters 
    47076 --- 
    47077 Chain pairing | bb 
    47078 Alignment algorithm | Needleman-Wunsch 
    47079 Similarity matrix | BLOSUM-62 
    47080 SS fraction | 0.3 
    47081 Gap open (HH/SS/other) | 18/18/6 
    47082 Gap extend | 1 
    47083 SS matrix |  |  | H | S | O 
    47084 ---|---|---|--- 
    47085 H | 6 | -9 | -6 
    47086 S |  | 6 | -6 
    47087 O |  |  | 4 
    47088 Iteration cutoff | 2 
    47089  
    47090 Matchmaker 3j0c.pdb1, chain B (#1.41) with AF3 E2 1-352.pdb, chain B (#204),
    47091 sequence alignment score = 583.7 
    47092 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    47093 5.933) 
    47094  
    47095 
    47096 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    47097 
    47098 Chain information for AF3 E2 353-438.pdb #205 
    47099 --- 
    47100 Chain | Description 
    47101 B | No description available 
    47102  
    47103 
    47104 > matchmaker #205 to #1.41 & sel
    47105 
    47106 Parameters 
    47107 --- 
    47108 Chain pairing | bb 
    47109 Alignment algorithm | Needleman-Wunsch 
    47110 Similarity matrix | BLOSUM-62 
    47111 SS fraction | 0.3 
    47112 Gap open (HH/SS/other) | 18/18/6 
    47113 Gap extend | 1 
    47114 SS matrix |  |  | H | S | O 
    47115 ---|---|---|--- 
    47116 H | 6 | -9 | -6 
    47117 S |  | 6 | -6 
    47118 O |  |  | 4 
    47119 Iteration cutoff | 2 
    47120  
    47121 Matchmaker 3j0c.pdb1, chain B (#1.41) with AF3 E2 353-438.pdb, chain B (#205),
    47122 sequence alignment score = 322.6 
    47123 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    47124 8.411) 
    47125  
    47126 
    47127 > hide sel cartoons
    47128 
    47129 > select #1.41/C
    47130 
    47131 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    47132 
    47133 > show sel cartoons
    47134 
    47135 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    47136 
    47137 Chain information for AF3 CA.pdb #206 
    47138 --- 
    47139 Chain | Description 
    47140 A | No description available 
    47141  
    47142 
    47143 > matchmaker #206 to #1.41 & sel
    47144 
    47145 Parameters 
    47146 --- 
    47147 Chain pairing | bb 
    47148 Alignment algorithm | Needleman-Wunsch 
    47149 Similarity matrix | BLOSUM-62 
    47150 SS fraction | 0.3 
    47151 Gap open (HH/SS/other) | 18/18/6 
    47152 Gap extend | 1 
    47153 SS matrix |  |  | H | S | O 
    47154 ---|---|---|--- 
    47155 H | 6 | -9 | -6 
    47156 S |  | 6 | -6 
    47157 O |  |  | 4 
    47158 Iteration cutoff | 2 
    47159  
    47160 Matchmaker 3j0c.pdb1, chain C (#1.41) with AF3 CA.pdb, chain A (#206),
    47161 sequence alignment score = 328.1 
    47162 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    47163 2.714) 
    47164  
    47165 
    47166 > hide sel cartoons
    47167 
    47168 > color #202 dodgerblue
    47169 
    47170 > color #203 dodgerblue
    47171 
    47172 > color #204 #00b305ff
    47173 
    47174 > color #205 #00b305ff
    47175 
    47176 > color #206 #f15839ff
    47177 
    47178 > select #1.42/A
    47179 
    47180 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    47181 
    47182 > show sel cartoons
    47183 
    47184 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    47185 
    47186 Chain information for AF3 E1 1-421.pdb #207 
    47187 --- 
    47188 Chain | Description 
    47189 A | No description available 
    47190  
    47191 
    47192 > matchmaker #207 to #1.42 & sel
    47193 
    47194 Parameters 
    47195 --- 
    47196 Chain pairing | bb 
    47197 Alignment algorithm | Needleman-Wunsch 
    47198 Similarity matrix | BLOSUM-62 
    47199 SS fraction | 0.3 
    47200 Gap open (HH/SS/other) | 18/18/6 
    47201 Gap extend | 1 
    47202 SS matrix |  |  | H | S | O 
    47203 ---|---|---|--- 
    47204 H | 6 | -9 | -6 
    47205 S |  | 6 | -6 
    47206 O |  |  | 4 
    47207 Iteration cutoff | 2 
    47208  
    47209 Matchmaker 3j0c.pdb1, chain A (#1.42) with AF3 E1 1-421.pdb, chain A (#207),
    47210 sequence alignment score = 1060.7 
    47211 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    47212 3.020) 
    47213  
    47214 
    47215 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    47216 
    47217 Chain information for AF3 E1 422-461.pdb #208 
    47218 --- 
    47219 Chain | Description 
    47220 A | No description available 
    47221  
    47222 
    47223 > matchmaker #208 to #1.42 & sel
    47224 
    47225 Parameters 
    47226 --- 
    47227 Chain pairing | bb 
    47228 Alignment algorithm | Needleman-Wunsch 
    47229 Similarity matrix | BLOSUM-62 
    47230 SS fraction | 0.3 
    47231 Gap open (HH/SS/other) | 18/18/6 
    47232 Gap extend | 1 
    47233 SS matrix |  |  | H | S | O 
    47234 ---|---|---|--- 
    47235 H | 6 | -9 | -6 
    47236 S |  | 6 | -6 
    47237 O |  |  | 4 
    47238 Iteration cutoff | 2 
    47239  
    47240 Matchmaker 3j0c.pdb1, chain A (#1.42) with AF3 E1 422-461.pdb, chain A (#208),
    47241 sequence alignment score = 626.9 
    47242 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    47243 2.776) 
    47244  
    47245 
    47246 > hide sel cartoons
    47247 
    47248 > select #1.42/B
    47249 
    47250 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    47251 
    47252 > show sel cartoons
    47253 
    47254 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    47255 
    47256 Chain information for AF3 E2 1-352.pdb #209 
    47257 --- 
    47258 Chain | Description 
    47259 B | No description available 
    47260  
    47261 
    47262 > matchmaker #209 to #1.42 & sel
    47263 
    47264 Parameters 
    47265 --- 
    47266 Chain pairing | bb 
    47267 Alignment algorithm | Needleman-Wunsch 
    47268 Similarity matrix | BLOSUM-62 
    47269 SS fraction | 0.3 
    47270 Gap open (HH/SS/other) | 18/18/6 
    47271 Gap extend | 1 
    47272 SS matrix |  |  | H | S | O 
    47273 ---|---|---|--- 
    47274 H | 6 | -9 | -6 
    47275 S |  | 6 | -6 
    47276 O |  |  | 4 
    47277 Iteration cutoff | 2 
    47278  
    47279 Matchmaker 3j0c.pdb1, chain B (#1.42) with AF3 E2 1-352.pdb, chain B (#209),
    47280 sequence alignment score = 583.7 
    47281 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    47282 5.933) 
    47283  
    47284 
    47285 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    47286 
    47287 Chain information for AF3 E2 353-438.pdb #210 
    47288 --- 
    47289 Chain | Description 
    47290 B | No description available 
    47291  
    47292 
    47293 > matchmaker #210 to #1.42 & sel
    47294 
    47295 Parameters 
    47296 --- 
    47297 Chain pairing | bb 
    47298 Alignment algorithm | Needleman-Wunsch 
    47299 Similarity matrix | BLOSUM-62 
    47300 SS fraction | 0.3 
    47301 Gap open (HH/SS/other) | 18/18/6 
    47302 Gap extend | 1 
    47303 SS matrix |  |  | H | S | O 
    47304 ---|---|---|--- 
    47305 H | 6 | -9 | -6 
    47306 S |  | 6 | -6 
    47307 O |  |  | 4 
    47308 Iteration cutoff | 2 
    47309  
    47310 Matchmaker 3j0c.pdb1, chain B (#1.42) with AF3 E2 353-438.pdb, chain B (#210),
    47311 sequence alignment score = 322.6 
    47312 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    47313 8.411) 
    47314  
    47315 
    47316 > hide sel cartoons
    47317 
    47318 > select #1.42/C
    47319 
    47320 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    47321 
    47322 > show sel cartoons
    47323 
    47324 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    47325 
    47326 Chain information for AF3 CA.pdb #211 
    47327 --- 
    47328 Chain | Description 
    47329 A | No description available 
    47330  
    47331 
    47332 > matchmaker #211 to #1.42 & sel
    47333 
    47334 Parameters 
    47335 --- 
    47336 Chain pairing | bb 
    47337 Alignment algorithm | Needleman-Wunsch 
    47338 Similarity matrix | BLOSUM-62 
    47339 SS fraction | 0.3 
    47340 Gap open (HH/SS/other) | 18/18/6 
    47341 Gap extend | 1 
    47342 SS matrix |  |  | H | S | O 
    47343 ---|---|---|--- 
    47344 H | 6 | -9 | -6 
    47345 S |  | 6 | -6 
    47346 O |  |  | 4 
    47347 Iteration cutoff | 2 
    47348  
    47349 Matchmaker 3j0c.pdb1, chain C (#1.42) with AF3 CA.pdb, chain A (#211),
    47350 sequence alignment score = 328.1 
    47351 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    47352 2.714) 
    47353  
    47354 
    47355 > hide sel cartoons
    47356 
    47357 > color #207 dodgerblue
    47358 
    47359 > color #208 dodgerblue
    47360 
    47361 > color #209 #00b305ff
    47362 
    47363 > color #210 #00b305ff
    47364 
    47365 > color #211 #f15839ff
    47366 
    47367 > select #1.43/A
    47368 
    47369 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    47370 
    47371 > show sel cartoons
    47372 
    47373 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    47374 
    47375 Chain information for AF3 E1 1-421.pdb #212 
    47376 --- 
    47377 Chain | Description 
    47378 A | No description available 
    47379  
    47380 
    47381 > matchmaker #212 to #1.43 & sel
    47382 
    47383 Parameters 
    47384 --- 
    47385 Chain pairing | bb 
    47386 Alignment algorithm | Needleman-Wunsch 
    47387 Similarity matrix | BLOSUM-62 
    47388 SS fraction | 0.3 
    47389 Gap open (HH/SS/other) | 18/18/6 
    47390 Gap extend | 1 
    47391 SS matrix |  |  | H | S | O 
    47392 ---|---|---|--- 
    47393 H | 6 | -9 | -6 
    47394 S |  | 6 | -6 
    47395 O |  |  | 4 
    47396 Iteration cutoff | 2 
    47397  
    47398 Matchmaker 3j0c.pdb1, chain A (#1.43) with AF3 E1 1-421.pdb, chain A (#212),
    47399 sequence alignment score = 1060.7 
    47400 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    47401 3.020) 
    47402  
    47403 
    47404 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    47405 
    47406 Chain information for AF3 E1 422-461.pdb #213 
    47407 --- 
    47408 Chain | Description 
    47409 A | No description available 
    47410  
    47411 
    47412 > matchmaker #213 to #1.43 & sel
    47413 
    47414 Parameters 
    47415 --- 
    47416 Chain pairing | bb 
    47417 Alignment algorithm | Needleman-Wunsch 
    47418 Similarity matrix | BLOSUM-62 
    47419 SS fraction | 0.3 
    47420 Gap open (HH/SS/other) | 18/18/6 
    47421 Gap extend | 1 
    47422 SS matrix |  |  | H | S | O 
    47423 ---|---|---|--- 
    47424 H | 6 | -9 | -6 
    47425 S |  | 6 | -6 
    47426 O |  |  | 4 
    47427 Iteration cutoff | 2 
    47428  
    47429 Matchmaker 3j0c.pdb1, chain A (#1.43) with AF3 E1 422-461.pdb, chain A (#213),
    47430 sequence alignment score = 626.9 
    47431 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    47432 2.775) 
    47433  
    47434 
    47435 > hide sel cartoons
    47436 
    47437 > select #1.43/B
    47438 
    47439 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    47440 
    47441 > show sel cartoons
    47442 
    47443 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    47444 
    47445 Chain information for AF3 E2 1-352.pdb #214 
    47446 --- 
    47447 Chain | Description 
    47448 B | No description available 
    47449  
    47450 
    47451 > matchmaker #214 to #1.43 & sel
    47452 
    47453 Parameters 
    47454 --- 
    47455 Chain pairing | bb 
    47456 Alignment algorithm | Needleman-Wunsch 
    47457 Similarity matrix | BLOSUM-62 
    47458 SS fraction | 0.3 
    47459 Gap open (HH/SS/other) | 18/18/6 
    47460 Gap extend | 1 
    47461 SS matrix |  |  | H | S | O 
    47462 ---|---|---|--- 
    47463 H | 6 | -9 | -6 
    47464 S |  | 6 | -6 
    47465 O |  |  | 4 
    47466 Iteration cutoff | 2 
    47467  
    47468 Matchmaker 3j0c.pdb1, chain B (#1.43) with AF3 E2 1-352.pdb, chain B (#214),
    47469 sequence alignment score = 583.7 
    47470 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    47471 5.933) 
    47472  
    47473 
    47474 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    47475 
    47476 Chain information for AF3 E2 353-438.pdb #215 
    47477 --- 
    47478 Chain | Description 
    47479 B | No description available 
    47480  
    47481 
    47482 > matchmaker #215 to #1.43 & sel
    47483 
    47484 Parameters 
    47485 --- 
    47486 Chain pairing | bb 
    47487 Alignment algorithm | Needleman-Wunsch 
    47488 Similarity matrix | BLOSUM-62 
    47489 SS fraction | 0.3 
    47490 Gap open (HH/SS/other) | 18/18/6 
    47491 Gap extend | 1 
    47492 SS matrix |  |  | H | S | O 
    47493 ---|---|---|--- 
    47494 H | 6 | -9 | -6 
    47495 S |  | 6 | -6 
    47496 O |  |  | 4 
    47497 Iteration cutoff | 2 
    47498  
    47499 Matchmaker 3j0c.pdb1, chain B (#1.43) with AF3 E2 353-438.pdb, chain B (#215),
    47500 sequence alignment score = 333.4 
    47501 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    47502 8.411) 
    47503  
    47504 
    47505 > hide sel cartoons
    47506 
    47507 > select #1.43/C
    47508 
    47509 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    47510 
    47511 > show sel cartoons
    47512 
    47513 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    47514 
    47515 Chain information for AF3 CA.pdb #216 
    47516 --- 
    47517 Chain | Description 
    47518 A | No description available 
    47519  
    47520 
    47521 > matchmaker #216 to #1.43 & sel
    47522 
    47523 Parameters 
    47524 --- 
    47525 Chain pairing | bb 
    47526 Alignment algorithm | Needleman-Wunsch 
    47527 Similarity matrix | BLOSUM-62 
    47528 SS fraction | 0.3 
    47529 Gap open (HH/SS/other) | 18/18/6 
    47530 Gap extend | 1 
    47531 SS matrix |  |  | H | S | O 
    47532 ---|---|---|--- 
    47533 H | 6 | -9 | -6 
    47534 S |  | 6 | -6 
    47535 O |  |  | 4 
    47536 Iteration cutoff | 2 
    47537  
    47538 Matchmaker 3j0c.pdb1, chain C (#1.43) with AF3 CA.pdb, chain A (#216),
    47539 sequence alignment score = 328.1 
    47540 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    47541 2.714) 
    47542  
    47543 
    47544 > hide sel cartoons
    47545 
    47546 > color #212 dodgerblue
    47547 
    47548 > color #213 dodgerblue
    47549 
    47550 > color #214 #00b305ff
    47551 
    47552 > color #215 #00b305ff
    47553 
    47554 > color #216 #f15839ff
    47555 
    47556 > select #1.44/A
    47557 
    47558 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    47559 
    47560 > show sel cartoons
    47561 
    47562 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    47563 
    47564 Chain information for AF3 E1 1-421.pdb #217 
    47565 --- 
    47566 Chain | Description 
    47567 A | No description available 
    47568  
    47569 
    47570 > matchmaker #217 to #1.43 & sel
    47571 
    47572 No 'to' model specified 
    47573 
    47574 > matchmaker #217 to #1.44 & sel
    47575 
    47576 Parameters 
    47577 --- 
    47578 Chain pairing | bb 
    47579 Alignment algorithm | Needleman-Wunsch 
    47580 Similarity matrix | BLOSUM-62 
    47581 SS fraction | 0.3 
    47582 Gap open (HH/SS/other) | 18/18/6 
    47583 Gap extend | 1 
    47584 SS matrix |  |  | H | S | O 
    47585 ---|---|---|--- 
    47586 H | 6 | -9 | -6 
    47587 S |  | 6 | -6 
    47588 O |  |  | 4 
    47589 Iteration cutoff | 2 
    47590  
    47591 Matchmaker 3j0c.pdb1, chain A (#1.44) with AF3 E1 1-421.pdb, chain A (#217),
    47592 sequence alignment score = 1060.7 
    47593 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    47594 3.020) 
    47595  
    47596 
    47597 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    47598 
    47599 Chain information for AF3 E1 422-461.pdb #218 
    47600 --- 
    47601 Chain | Description 
    47602 A | No description available 
    47603  
    47604 
    47605 > matchmaker #218 to #1.44 & sel
    47606 
    47607 Parameters 
    47608 --- 
    47609 Chain pairing | bb 
    47610 Alignment algorithm | Needleman-Wunsch 
    47611 Similarity matrix | BLOSUM-62 
    47612 SS fraction | 0.3 
    47613 Gap open (HH/SS/other) | 18/18/6 
    47614 Gap extend | 1 
    47615 SS matrix |  |  | H | S | O 
    47616 ---|---|---|--- 
    47617 H | 6 | -9 | -6 
    47618 S |  | 6 | -6 
    47619 O |  |  | 4 
    47620 Iteration cutoff | 2 
    47621  
    47622 Matchmaker 3j0c.pdb1, chain A (#1.44) with AF3 E1 422-461.pdb, chain A (#218),
    47623 sequence alignment score = 626.9 
    47624 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    47625 2.775) 
    47626  
    47627 
    47628 > hide sel cartoons
    47629 
    47630 > select #1.44/B
    47631 
    47632 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    47633 
    47634 > show sel cartoons
    47635 
    47636 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    47637 
    47638 Chain information for AF3 E2 1-352.pdb #219 
    47639 --- 
    47640 Chain | Description 
    47641 B | No description available 
    47642  
    47643 
    47644 > matchmaker #219 to #1.44 & sel
    47645 
    47646 Parameters 
    47647 --- 
    47648 Chain pairing | bb 
    47649 Alignment algorithm | Needleman-Wunsch 
    47650 Similarity matrix | BLOSUM-62 
    47651 SS fraction | 0.3 
    47652 Gap open (HH/SS/other) | 18/18/6 
    47653 Gap extend | 1 
    47654 SS matrix |  |  | H | S | O 
    47655 ---|---|---|--- 
    47656 H | 6 | -9 | -6 
    47657 S |  | 6 | -6 
    47658 O |  |  | 4 
    47659 Iteration cutoff | 2 
    47660  
    47661 Matchmaker 3j0c.pdb1, chain B (#1.44) with AF3 E2 1-352.pdb, chain B (#219),
    47662 sequence alignment score = 583.7 
    47663 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    47664 5.933) 
    47665  
    47666 
    47667 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    47668 
    47669 Chain information for AF3 E2 353-438.pdb #220 
    47670 --- 
    47671 Chain | Description 
    47672 B | No description available 
    47673  
    47674 
    47675 > matchmaker #220 to #1.44 & sel
    47676 
    47677 Parameters 
    47678 --- 
    47679 Chain pairing | bb 
    47680 Alignment algorithm | Needleman-Wunsch 
    47681 Similarity matrix | BLOSUM-62 
    47682 SS fraction | 0.3 
    47683 Gap open (HH/SS/other) | 18/18/6 
    47684 Gap extend | 1 
    47685 SS matrix |  |  | H | S | O 
    47686 ---|---|---|--- 
    47687 H | 6 | -9 | -6 
    47688 S |  | 6 | -6 
    47689 O |  |  | 4 
    47690 Iteration cutoff | 2 
    47691  
    47692 Matchmaker 3j0c.pdb1, chain B (#1.44) with AF3 E2 353-438.pdb, chain B (#220),
    47693 sequence alignment score = 333.4 
    47694 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    47695 8.411) 
    47696  
    47697 
    47698 > hide sel cartoons
    47699 
    47700 > select #1.44/C
    47701 
    47702 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    47703 
    47704 > show sel cartoons
    47705 
    47706 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    47707 
    47708 Chain information for AF3 CA.pdb #221 
    47709 --- 
    47710 Chain | Description 
    47711 A | No description available 
    47712  
    47713 
    47714 > matchmaker #221 to #1.44 & sel
    47715 
    47716 Parameters 
    47717 --- 
    47718 Chain pairing | bb 
    47719 Alignment algorithm | Needleman-Wunsch 
    47720 Similarity matrix | BLOSUM-62 
    47721 SS fraction | 0.3 
    47722 Gap open (HH/SS/other) | 18/18/6 
    47723 Gap extend | 1 
    47724 SS matrix |  |  | H | S | O 
    47725 ---|---|---|--- 
    47726 H | 6 | -9 | -6 
    47727 S |  | 6 | -6 
    47728 O |  |  | 4 
    47729 Iteration cutoff | 2 
    47730  
    47731 Matchmaker 3j0c.pdb1, chain C (#1.44) with AF3 CA.pdb, chain A (#221),
    47732 sequence alignment score = 328.1 
    47733 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    47734 2.714) 
    47735  
    47736 
    47737 > hide sel cartoons
    47738 
    47739 > color #217 dodgerblue
    47740 
    47741 > color #218 dodgerblue
    47742 
    47743 > color #219 #00b305ff
    47744 
    47745 > color #220 #00b305ff
    47746 
    47747 > color #221 #f15839ff
    47748 
    47749 > select #1.45/A
    47750 
    47751 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    47752 
    47753 > show sel cartoons
    47754 
    47755 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    47756 
    47757 Chain information for AF3 E1 1-421.pdb #222 
    47758 --- 
    47759 Chain | Description 
    47760 A | No description available 
    47761  
    47762 
    47763 > matchmaker #222 to #1.45 & sel
    47764 
    47765 Parameters 
    47766 --- 
    47767 Chain pairing | bb 
    47768 Alignment algorithm | Needleman-Wunsch 
    47769 Similarity matrix | BLOSUM-62 
    47770 SS fraction | 0.3 
    47771 Gap open (HH/SS/other) | 18/18/6 
    47772 Gap extend | 1 
    47773 SS matrix |  |  | H | S | O 
    47774 ---|---|---|--- 
    47775 H | 6 | -9 | -6 
    47776 S |  | 6 | -6 
    47777 O |  |  | 4 
    47778 Iteration cutoff | 2 
    47779  
    47780 Matchmaker 3j0c.pdb1, chain A (#1.45) with AF3 E1 1-421.pdb, chain A (#222),
    47781 sequence alignment score = 1060.7 
    47782 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    47783 3.020) 
    47784  
    47785 
    47786 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    47787 
    47788 Chain information for AF3 E1 422-461.pdb #223 
    47789 --- 
    47790 Chain | Description 
    47791 A | No description available 
    47792  
    47793 
    47794 > matchmaker #223 to #1.45 & sel
    47795 
    47796 Parameters 
    47797 --- 
    47798 Chain pairing | bb 
    47799 Alignment algorithm | Needleman-Wunsch 
    47800 Similarity matrix | BLOSUM-62 
    47801 SS fraction | 0.3 
    47802 Gap open (HH/SS/other) | 18/18/6 
    47803 Gap extend | 1 
    47804 SS matrix |  |  | H | S | O 
    47805 ---|---|---|--- 
    47806 H | 6 | -9 | -6 
    47807 S |  | 6 | -6 
    47808 O |  |  | 4 
    47809 Iteration cutoff | 2 
    47810  
    47811 Matchmaker 3j0c.pdb1, chain A (#1.45) with AF3 E1 422-461.pdb, chain A (#223),
    47812 sequence alignment score = 626.9 
    47813 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    47814 2.775) 
    47815  
    47816 
    47817 > hide sel cartoons
    47818 
    47819 [Repeated 1 time(s)]
    47820 
    47821 > select #1.45/B
    47822 
    47823 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    47824 
    47825 > show sel cartoons
    47826 
    47827 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    47828 
    47829 Chain information for AF3 E2 1-352.pdb #224 
    47830 --- 
    47831 Chain | Description 
    47832 B | No description available 
    47833  
    47834 
    47835 > matchmaker #224 to #1.45 & sel
    47836 
    47837 Parameters 
    47838 --- 
    47839 Chain pairing | bb 
    47840 Alignment algorithm | Needleman-Wunsch 
    47841 Similarity matrix | BLOSUM-62 
    47842 SS fraction | 0.3 
    47843 Gap open (HH/SS/other) | 18/18/6 
    47844 Gap extend | 1 
    47845 SS matrix |  |  | H | S | O 
    47846 ---|---|---|--- 
    47847 H | 6 | -9 | -6 
    47848 S |  | 6 | -6 
    47849 O |  |  | 4 
    47850 Iteration cutoff | 2 
    47851  
    47852 Matchmaker 3j0c.pdb1, chain B (#1.45) with AF3 E2 1-352.pdb, chain B (#224),
    47853 sequence alignment score = 583.7 
    47854 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    47855 5.933) 
    47856  
    47857 
    47858 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    47859 
    47860 Chain information for AF3 E2 353-438.pdb #225 
    47861 --- 
    47862 Chain | Description 
    47863 B | No description available 
    47864  
    47865 
    47866 > matchmaker #225 to #1.45 & sel
    47867 
    47868 Parameters 
    47869 --- 
    47870 Chain pairing | bb 
    47871 Alignment algorithm | Needleman-Wunsch 
    47872 Similarity matrix | BLOSUM-62 
    47873 SS fraction | 0.3 
    47874 Gap open (HH/SS/other) | 18/18/6 
    47875 Gap extend | 1 
    47876 SS matrix |  |  | H | S | O 
    47877 ---|---|---|--- 
    47878 H | 6 | -9 | -6 
    47879 S |  | 6 | -6 
    47880 O |  |  | 4 
    47881 Iteration cutoff | 2 
    47882  
    47883 Matchmaker 3j0c.pdb1, chain B (#1.45) with AF3 E2 353-438.pdb, chain B (#225),
    47884 sequence alignment score = 333.4 
    47885 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    47886 8.411) 
    47887  
    47888 
    47889 > hide sel cartoons
    47890 
    47891 > select #1.45/C
    47892 
    47893 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    47894 
    47895 > show sel cartoons
    47896 
    47897 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    47898 
    47899 Chain information for AF3 CA.pdb #226 
    47900 --- 
    47901 Chain | Description 
    47902 A | No description available 
    47903  
    47904 
    47905 > matchmaker #226 to #1.45 & sel
    47906 
    47907 Parameters 
    47908 --- 
    47909 Chain pairing | bb 
    47910 Alignment algorithm | Needleman-Wunsch 
    47911 Similarity matrix | BLOSUM-62 
    47912 SS fraction | 0.3 
    47913 Gap open (HH/SS/other) | 18/18/6 
    47914 Gap extend | 1 
    47915 SS matrix |  |  | H | S | O 
    47916 ---|---|---|--- 
    47917 H | 6 | -9 | -6 
    47918 S |  | 6 | -6 
    47919 O |  |  | 4 
    47920 Iteration cutoff | 2 
    47921  
    47922 Matchmaker 3j0c.pdb1, chain C (#1.45) with AF3 CA.pdb, chain A (#226),
    47923 sequence alignment score = 328.1 
    47924 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    47925 2.714) 
    47926  
    47927 
    47928 > hide sel cartoons
    47929 
    47930 > color #222 dodgerblue
    47931 
    47932 > color #223 dodgerblue
    47933 
    47934 > color #224 #00b305ff
    47935 
    47936 > color #225 #00b305ff
    47937 
    47938 > color #226 #f15839ff
    47939 
    47940 > select #1.46/A
    47941 
    47942 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    47943 
    47944 > show sel cartoons
    47945 
    47946 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    47947 
    47948 Chain information for AF3 E1 1-421.pdb #227 
    47949 --- 
    47950 Chain | Description 
    47951 A | No description available 
    47952  
    47953 
    47954 > matchmaker #227 to #1.46 & sel
    47955 
    47956 Parameters 
    47957 --- 
    47958 Chain pairing | bb 
    47959 Alignment algorithm | Needleman-Wunsch 
    47960 Similarity matrix | BLOSUM-62 
    47961 SS fraction | 0.3 
    47962 Gap open (HH/SS/other) | 18/18/6 
    47963 Gap extend | 1 
    47964 SS matrix |  |  | H | S | O 
    47965 ---|---|---|--- 
    47966 H | 6 | -9 | -6 
    47967 S |  | 6 | -6 
    47968 O |  |  | 4 
    47969 Iteration cutoff | 2 
    47970  
    47971 Matchmaker 3j0c.pdb1, chain A (#1.46) with AF3 E1 1-421.pdb, chain A (#227),
    47972 sequence alignment score = 1060.7 
    47973 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    47974 3.020) 
    47975  
    47976 
    47977 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    47978 
    47979 Chain information for AF3 E1 422-461.pdb #228 
    47980 --- 
    47981 Chain | Description 
    47982 A | No description available 
    47983  
    47984 
    47985 > matchmaker #228 to #1.46 & sel
    47986 
    47987 Parameters 
    47988 --- 
    47989 Chain pairing | bb 
    47990 Alignment algorithm | Needleman-Wunsch 
    47991 Similarity matrix | BLOSUM-62 
    47992 SS fraction | 0.3 
    47993 Gap open (HH/SS/other) | 18/18/6 
    47994 Gap extend | 1 
    47995 SS matrix |  |  | H | S | O 
    47996 ---|---|---|--- 
    47997 H | 6 | -9 | -6 
    47998 S |  | 6 | -6 
    47999 O |  |  | 4 
    48000 Iteration cutoff | 2 
    48001  
    48002 Matchmaker 3j0c.pdb1, chain A (#1.46) with AF3 E1 422-461.pdb, chain A (#228),
    48003 sequence alignment score = 626.9 
    48004 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    48005 2.776) 
    48006  
    48007 
    48008 > hide sel cartoons
    48009 
    48010 > select #1.46/B
    48011 
    48012 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    48013 
    48014 > show sel cartoons
    48015 
    48016 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    48017 
    48018 Chain information for AF3 E2 1-352.pdb #229 
    48019 --- 
    48020 Chain | Description 
    48021 B | No description available 
    48022  
    48023 
    48024 > matchmaker #229 to #1.46 & sel
    48025 
    48026 Parameters 
    48027 --- 
    48028 Chain pairing | bb 
    48029 Alignment algorithm | Needleman-Wunsch 
    48030 Similarity matrix | BLOSUM-62 
    48031 SS fraction | 0.3 
    48032 Gap open (HH/SS/other) | 18/18/6 
    48033 Gap extend | 1 
    48034 SS matrix |  |  | H | S | O 
    48035 ---|---|---|--- 
    48036 H | 6 | -9 | -6 
    48037 S |  | 6 | -6 
    48038 O |  |  | 4 
    48039 Iteration cutoff | 2 
    48040  
    48041 Matchmaker 3j0c.pdb1, chain B (#1.46) with AF3 E2 1-352.pdb, chain B (#229),
    48042 sequence alignment score = 583.7 
    48043 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    48044 5.933) 
    48045  
    48046 
    48047 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    48048 
    48049 Chain information for AF3 E2 353-438.pdb #230 
    48050 --- 
    48051 Chain | Description 
    48052 B | No description available 
    48053  
    48054 
    48055 > matchmaker #230 to #1.46 & sel
    48056 
    48057 Parameters 
    48058 --- 
    48059 Chain pairing | bb 
    48060 Alignment algorithm | Needleman-Wunsch 
    48061 Similarity matrix | BLOSUM-62 
    48062 SS fraction | 0.3 
    48063 Gap open (HH/SS/other) | 18/18/6 
    48064 Gap extend | 1 
    48065 SS matrix |  |  | H | S | O 
    48066 ---|---|---|--- 
    48067 H | 6 | -9 | -6 
    48068 S |  | 6 | -6 
    48069 O |  |  | 4 
    48070 Iteration cutoff | 2 
    48071  
    48072 Matchmaker 3j0c.pdb1, chain B (#1.46) with AF3 E2 353-438.pdb, chain B (#230),
    48073 sequence alignment score = 333.4 
    48074 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    48075 8.411) 
    48076  
    48077 
    48078 > hide sel cartoons
    48079 
    48080 > select #1.46/C
    48081 
    48082 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    48083 
    48084 > show sel cartoons
    48085 
    48086 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    48087 
    48088 Chain information for AF3 CA.pdb #231 
    48089 --- 
    48090 Chain | Description 
    48091 A | No description available 
    48092  
    48093 
    48094 > matchmaker #231 to #1.46 & sel
    48095 
    48096 Parameters 
    48097 --- 
    48098 Chain pairing | bb 
    48099 Alignment algorithm | Needleman-Wunsch 
    48100 Similarity matrix | BLOSUM-62 
    48101 SS fraction | 0.3 
    48102 Gap open (HH/SS/other) | 18/18/6 
    48103 Gap extend | 1 
    48104 SS matrix |  |  | H | S | O 
    48105 ---|---|---|--- 
    48106 H | 6 | -9 | -6 
    48107 S |  | 6 | -6 
    48108 O |  |  | 4 
    48109 Iteration cutoff | 2 
    48110  
    48111 Matchmaker 3j0c.pdb1, chain C (#1.46) with AF3 CA.pdb, chain A (#231),
    48112 sequence alignment score = 328.1 
    48113 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    48114 2.714) 
    48115  
    48116 
    48117 > hide sel cartoons
    48118 
    48119 > color #227 #408ca2ff
    48120 
    48121 > color #227 dodgerblue
    48122 
    48123 > color #228 dodgerblue
    48124 
    48125 > color #229 #00b305ff
    48126 
    48127 > color #230 #00b305ff
    48128 
    48129 > color #231 #f15839ff
    48130 
    48131 > view sel
    48132 
    48133 No displayed objects specified. 
    48134 
    48135 > select
    48136 > #1.1/A#1.2/A#1.3/A#1.4/A#1.5/A#1.6/A#1.7/A#1.8/A#1.9/A#1.10/A#1.11/A#1.12/A#1.13/A#1.14/A#1.15/A#1.16/A#1.17/A#1.18/A#1.19/A#1.20/A#1.21/A#1.22/A#1.23/A#1.24/A#1.25/A#1.26/A#1.27/A#1.28/A#1.29/A#1.30/A#1.31/A#1.32/A#1.33/A#1.34/A#1.35/A#1.36/A#1.37/A#1.38/A#1.39/A#1.40/A#1.41/A#1.42/A#1.43/A#1.44/A#1.45/A#1.46/A#1.47/A#1.48/A#1.49/A#1.50/A#1.51/A#1.52/A#1.53/A#1.54/A#1.55/A#1.56/A#1.57/A#1.58/A#1.59/A#1.60/A#2/A#3/A#6/A#7/A#8/A#11/A#12/A#13/A#16/A#17/A#18/A#21/A#22/A#23/A#26/A#27/A#28/A#31/A#32/A#33/A#36/A#37/A#38/A#41/A#42/A#43/A#46/A#47/A#48/A#51/A#52/A#53/A#56/A#57/A#58/A#61/A#62/A#63/A#66/A#67/A#68/A#71/A#72/A#73/A#76/A#77/A#78/A#81/A#82/A#83/A#86/A#87/A#88/A#91/A#92/A#93/A#96/A#97/A#98/A#101/A#102/A#103/A#106/A#107/A#108/A#111/A#112/A#113/A#116/A#117/A#118/A#121/A#122/A#123/A#126/A#127/A#128/A#131/A#132/A#133/A#136/A#137/A#138/A#141/A#142/A#143/A#146/A#147/A#148/A#151/A#152/A#153/A#156/A#157/A#158/A#161/A#162/A#163/A#166/A#167/A#168/A#171/A#172/A#173/A#176/A#177/A#178/A#181/A#182/A#183/A#186/A#187/A#188/A#191/A#192/A#193/A#196/A#197/A#198/A#201/A#202/A#203/A#206/A#207/A#208/A#211/A#212/A#213/A#216/A#217/A#218/A#221/A#222/A#223/A#226/A#227/A#228/A#231/A
    48137 
    48138 418952 atoms, 429570 bonds, 55178 residues, 198 models selected 
    48139 
    48140 > view sel
    48141 
    48142 > select clear
    48143 
    48144 > select #1.47/A
    48145 
    48146 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    48147 
    48148 > show sel cartoons
    48149 
    48150 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    48151 
    48152 Chain information for AF3 E1 1-421.pdb #232 
    48153 --- 
    48154 Chain | Description 
    48155 A | No description available 
    48156  
    48157 
    48158 > matchmaker #232 to #1.47 & sel
    48159 
    48160 Parameters 
    48161 --- 
    48162 Chain pairing | bb 
    48163 Alignment algorithm | Needleman-Wunsch 
    48164 Similarity matrix | BLOSUM-62 
    48165 SS fraction | 0.3 
    48166 Gap open (HH/SS/other) | 18/18/6 
    48167 Gap extend | 1 
    48168 SS matrix |  |  | H | S | O 
    48169 ---|---|---|--- 
    48170 H | 6 | -9 | -6 
    48171 S |  | 6 | -6 
    48172 O |  |  | 4 
    48173 Iteration cutoff | 2 
    48174  
    48175 Matchmaker 3j0c.pdb1, chain A (#1.47) with AF3 E1 1-421.pdb, chain A (#232),
    48176 sequence alignment score = 1060.7 
    48177 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    48178 3.020) 
    48179  
    48180 
    48181 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    48182 
    48183 Chain information for AF3 E1 422-461.pdb #233 
    48184 --- 
    48185 Chain | Description 
    48186 A | No description available 
    48187  
    48188 
    48189 > matchmaker #233 to #1.47 & sel
    48190 
    48191 Parameters 
    48192 --- 
    48193 Chain pairing | bb 
    48194 Alignment algorithm | Needleman-Wunsch 
    48195 Similarity matrix | BLOSUM-62 
    48196 SS fraction | 0.3 
    48197 Gap open (HH/SS/other) | 18/18/6 
    48198 Gap extend | 1 
    48199 SS matrix |  |  | H | S | O 
    48200 ---|---|---|--- 
    48201 H | 6 | -9 | -6 
    48202 S |  | 6 | -6 
    48203 O |  |  | 4 
    48204 Iteration cutoff | 2 
    48205  
    48206 Matchmaker 3j0c.pdb1, chain A (#1.47) with AF3 E1 422-461.pdb, chain A (#233),
    48207 sequence alignment score = 626.9 
    48208 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    48209 2.775) 
    48210  
    48211 
    48212 > hide sel cartoons
    48213 
    48214 > select #1.47/B
    48215 
    48216 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    48217 
    48218 > show sel cartoons
    48219 
    48220 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    48221 
    48222 Chain information for AF3 E2 1-352.pdb #234 
    48223 --- 
    48224 Chain | Description 
    48225 B | No description available 
    48226  
    48227 
    48228 > matchmaker #234 to #1.47 & sel
    48229 
    48230 Parameters 
    48231 --- 
    48232 Chain pairing | bb 
    48233 Alignment algorithm | Needleman-Wunsch 
    48234 Similarity matrix | BLOSUM-62 
    48235 SS fraction | 0.3 
    48236 Gap open (HH/SS/other) | 18/18/6 
    48237 Gap extend | 1 
    48238 SS matrix |  |  | H | S | O 
    48239 ---|---|---|--- 
    48240 H | 6 | -9 | -6 
    48241 S |  | 6 | -6 
    48242 O |  |  | 4 
    48243 Iteration cutoff | 2 
    48244  
    48245 Matchmaker 3j0c.pdb1, chain B (#1.47) with AF3 E2 1-352.pdb, chain B (#234),
    48246 sequence alignment score = 583.7 
    48247 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    48248 5.933) 
    48249  
    48250 
    48251 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    48252 
    48253 Chain information for AF3 E2 353-438.pdb #235 
    48254 --- 
    48255 Chain | Description 
    48256 B | No description available 
    48257  
    48258 
    48259 > matchmaker #235 to #1.47 & sel
    48260 
    48261 Parameters 
    48262 --- 
    48263 Chain pairing | bb 
    48264 Alignment algorithm | Needleman-Wunsch 
    48265 Similarity matrix | BLOSUM-62 
    48266 SS fraction | 0.3 
    48267 Gap open (HH/SS/other) | 18/18/6 
    48268 Gap extend | 1 
    48269 SS matrix |  |  | H | S | O 
    48270 ---|---|---|--- 
    48271 H | 6 | -9 | -6 
    48272 S |  | 6 | -6 
    48273 O |  |  | 4 
    48274 Iteration cutoff | 2 
    48275  
    48276 Matchmaker 3j0c.pdb1, chain B (#1.47) with AF3 E2 353-438.pdb, chain B (#235),
    48277 sequence alignment score = 322.6 
    48278 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    48279 8.411) 
    48280  
    48281 
    48282 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    48283 
    48284 Chain information for AF3 CA.pdb #236 
    48285 --- 
    48286 Chain | Description 
    48287 A | No description available 
    48288  
    48289 
    48290 > hide sel cartoons
    48291 
    48292 > select #1.47/C
    48293 
    48294 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    48295 
    48296 > show sel cartoons
    48297 
    48298 > matchmaker #236 to #1.47 & sel
    48299 
    48300 Parameters 
    48301 --- 
    48302 Chain pairing | bb 
    48303 Alignment algorithm | Needleman-Wunsch 
    48304 Similarity matrix | BLOSUM-62 
    48305 SS fraction | 0.3 
    48306 Gap open (HH/SS/other) | 18/18/6 
    48307 Gap extend | 1 
    48308 SS matrix |  |  | H | S | O 
    48309 ---|---|---|--- 
    48310 H | 6 | -9 | -6 
    48311 S |  | 6 | -6 
    48312 O |  |  | 4 
    48313 Iteration cutoff | 2 
    48314  
    48315 Matchmaker 3j0c.pdb1, chain C (#1.47) with AF3 CA.pdb, chain A (#236),
    48316 sequence alignment score = 328.1 
    48317 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    48318 2.714) 
    48319  
    48320 
    48321 > hide sel cartoons
    48322 
    48323 > color #232 dodgerblue
    48324 
    48325 > color #233 dodgerblue
    48326 
    48327 > color #234 #00b305ff
    48328 
    48329 > color #235 #00b305ff
    48330 
    48331 > color #236 #f15839ff
    48332 
    48333 > select #1.48/A
    48334 
    48335 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    48336 
    48337 > show sel cartoons
    48338 
    48339 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    48340 
    48341 Chain information for AF3 E1 1-421.pdb #237 
    48342 --- 
    48343 Chain | Description 
    48344 A | No description available 
    48345  
    48346 
    48347 > matchmaker #237 to #1.48 & sel
    48348 
    48349 Parameters 
    48350 --- 
    48351 Chain pairing | bb 
    48352 Alignment algorithm | Needleman-Wunsch 
    48353 Similarity matrix | BLOSUM-62 
    48354 SS fraction | 0.3 
    48355 Gap open (HH/SS/other) | 18/18/6 
    48356 Gap extend | 1 
    48357 SS matrix |  |  | H | S | O 
    48358 ---|---|---|--- 
    48359 H | 6 | -9 | -6 
    48360 S |  | 6 | -6 
    48361 O |  |  | 4 
    48362 Iteration cutoff | 2 
    48363  
    48364 Matchmaker 3j0c.pdb1, chain A (#1.48) with AF3 E1 1-421.pdb, chain A (#237),
    48365 sequence alignment score = 1060.7 
    48366 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    48367 3.020) 
    48368  
    48369 
    48370 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    48371 
    48372 Chain information for AF3 E1 422-461.pdb #238 
    48373 --- 
    48374 Chain | Description 
    48375 A | No description available 
    48376  
    48377 
    48378 > matchmaker #238 to #1.48 & sel
    48379 
    48380 Parameters 
    48381 --- 
    48382 Chain pairing | bb 
    48383 Alignment algorithm | Needleman-Wunsch 
    48384 Similarity matrix | BLOSUM-62 
    48385 SS fraction | 0.3 
    48386 Gap open (HH/SS/other) | 18/18/6 
    48387 Gap extend | 1 
    48388 SS matrix |  |  | H | S | O 
    48389 ---|---|---|--- 
    48390 H | 6 | -9 | -6 
    48391 S |  | 6 | -6 
    48392 O |  |  | 4 
    48393 Iteration cutoff | 2 
    48394  
    48395 Matchmaker 3j0c.pdb1, chain A (#1.48) with AF3 E1 422-461.pdb, chain A (#238),
    48396 sequence alignment score = 626.9 
    48397 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    48398 2.775) 
    48399  
    48400 
    48401 > hide sel cartoons
    48402 
    48403 > select #1.48/B
    48404 
    48405 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    48406 
    48407 > show sel cartoons
    48408 
    48409 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    48410 
    48411 Chain information for AF3 E2 1-352.pdb #239 
    48412 --- 
    48413 Chain | Description 
    48414 B | No description available 
    48415  
    48416 
    48417 > matchmaker #239 to #1.48 & sel
    48418 
    48419 Parameters 
    48420 --- 
    48421 Chain pairing | bb 
    48422 Alignment algorithm | Needleman-Wunsch 
    48423 Similarity matrix | BLOSUM-62 
    48424 SS fraction | 0.3 
    48425 Gap open (HH/SS/other) | 18/18/6 
    48426 Gap extend | 1 
    48427 SS matrix |  |  | H | S | O 
    48428 ---|---|---|--- 
    48429 H | 6 | -9 | -6 
    48430 S |  | 6 | -6 
    48431 O |  |  | 4 
    48432 Iteration cutoff | 2 
    48433  
    48434 Matchmaker 3j0c.pdb1, chain B (#1.48) with AF3 E2 1-352.pdb, chain B (#239),
    48435 sequence alignment score = 583.7 
    48436 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    48437 5.933) 
    48438  
    48439 
    48440 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    48441 
    48442 Chain information for AF3 E2 353-438.pdb #240 
    48443 --- 
    48444 Chain | Description 
    48445 B | No description available 
    48446  
    48447 
    48448 > matchmaker #240 to #1.48 & sel
    48449 
    48450 Parameters 
    48451 --- 
    48452 Chain pairing | bb 
    48453 Alignment algorithm | Needleman-Wunsch 
    48454 Similarity matrix | BLOSUM-62 
    48455 SS fraction | 0.3 
    48456 Gap open (HH/SS/other) | 18/18/6 
    48457 Gap extend | 1 
    48458 SS matrix |  |  | H | S | O 
    48459 ---|---|---|--- 
    48460 H | 6 | -9 | -6 
    48461 S |  | 6 | -6 
    48462 O |  |  | 4 
    48463 Iteration cutoff | 2 
    48464  
    48465 Matchmaker 3j0c.pdb1, chain B (#1.48) with AF3 E2 353-438.pdb, chain B (#240),
    48466 sequence alignment score = 322.6 
    48467 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    48468 8.411) 
    48469  
    48470 
    48471 > hide sel cartoons
    48472 
    48473 > select #1.48/B
    48474 
    48475 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    48476 
    48477 > show sel cartoons
    48478 
    48479 > hide sel cartoons
    48480 
    48481 > select #1.48/C
    48482 
    48483 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    48484 
    48485 > show sel cartoons
    48486 
    48487 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    48488 
    48489 Chain information for AF3 CA.pdb #241 
    48490 --- 
    48491 Chain | Description 
    48492 A | No description available 
    48493  
    48494 
    48495 > matchmaker #241 to #1.48 & sel
    48496 
    48497 Parameters 
    48498 --- 
    48499 Chain pairing | bb 
    48500 Alignment algorithm | Needleman-Wunsch 
    48501 Similarity matrix | BLOSUM-62 
    48502 SS fraction | 0.3 
    48503 Gap open (HH/SS/other) | 18/18/6 
    48504 Gap extend | 1 
    48505 SS matrix |  |  | H | S | O 
    48506 ---|---|---|--- 
    48507 H | 6 | -9 | -6 
    48508 S |  | 6 | -6 
    48509 O |  |  | 4 
    48510 Iteration cutoff | 2 
    48511  
    48512 Matchmaker 3j0c.pdb1, chain C (#1.48) with AF3 CA.pdb, chain A (#241),
    48513 sequence alignment score = 328.1 
    48514 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    48515 2.714) 
    48516  
    48517 
    48518 > hide sel cartoons
    48519 
    48520 > color #237 dodgerblue
    48521 
    48522 > color #238 dodgerblue
    48523 
    48524 > color #239 #00b305ff
    48525 
    48526 > color #241 #f15839ff
    48527 
    48528 > color #240 #00b305ff
    48529 
    48530 > select #1.49/A
    48531 
    48532 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    48533 
    48534 > show sel cartoons
    48535 
    48536 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    48537 
    48538 Chain information for AF3 E1 1-421.pdb #242 
    48539 --- 
    48540 Chain | Description 
    48541 A | No description available 
    48542  
    48543 
    48544 > matchmaker #242 to #1.49 & sel
    48545 
    48546 Parameters 
    48547 --- 
    48548 Chain pairing | bb 
    48549 Alignment algorithm | Needleman-Wunsch 
    48550 Similarity matrix | BLOSUM-62 
    48551 SS fraction | 0.3 
    48552 Gap open (HH/SS/other) | 18/18/6 
    48553 Gap extend | 1 
    48554 SS matrix |  |  | H | S | O 
    48555 ---|---|---|--- 
    48556 H | 6 | -9 | -6 
    48557 S |  | 6 | -6 
    48558 O |  |  | 4 
    48559 Iteration cutoff | 2 
    48560  
    48561 Matchmaker 3j0c.pdb1, chain A (#1.49) with AF3 E1 1-421.pdb, chain A (#242),
    48562 sequence alignment score = 1060.7 
    48563 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    48564 3.020) 
    48565  
    48566 
    48567 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    48568 
    48569 Chain information for AF3 E1 422-461.pdb #243 
    48570 --- 
    48571 Chain | Description 
    48572 A | No description available 
    48573  
    48574 
    48575 > matchmaker #243 to #1.49 & sel
    48576 
    48577 Parameters 
    48578 --- 
    48579 Chain pairing | bb 
    48580 Alignment algorithm | Needleman-Wunsch 
    48581 Similarity matrix | BLOSUM-62 
    48582 SS fraction | 0.3 
    48583 Gap open (HH/SS/other) | 18/18/6 
    48584 Gap extend | 1 
    48585 SS matrix |  |  | H | S | O 
    48586 ---|---|---|--- 
    48587 H | 6 | -9 | -6 
    48588 S |  | 6 | -6 
    48589 O |  |  | 4 
    48590 Iteration cutoff | 2 
    48591  
    48592 Matchmaker 3j0c.pdb1, chain A (#1.49) with AF3 E1 422-461.pdb, chain A (#243),
    48593 sequence alignment score = 626.9 
    48594 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    48595 2.776) 
    48596  
    48597 
    48598 > hide sel cartoons
    48599 
    48600 > select #1.49/B
    48601 
    48602 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    48603 
    48604 > show sel cartoons
    48605 
    48606 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    48607 
    48608 Chain information for AF3 E2 1-352.pdb #244 
    48609 --- 
    48610 Chain | Description 
    48611 B | No description available 
    48612  
    48613 
    48614 > matchmaker #244 to #1.49 & sel
    48615 
    48616 Parameters 
    48617 --- 
    48618 Chain pairing | bb 
    48619 Alignment algorithm | Needleman-Wunsch 
    48620 Similarity matrix | BLOSUM-62 
    48621 SS fraction | 0.3 
    48622 Gap open (HH/SS/other) | 18/18/6 
    48623 Gap extend | 1 
    48624 SS matrix |  |  | H | S | O 
    48625 ---|---|---|--- 
    48626 H | 6 | -9 | -6 
    48627 S |  | 6 | -6 
    48628 O |  |  | 4 
    48629 Iteration cutoff | 2 
    48630  
    48631 Matchmaker 3j0c.pdb1, chain B (#1.49) with AF3 E2 1-352.pdb, chain B (#244),
    48632 sequence alignment score = 583.7 
    48633 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    48634 5.933) 
    48635  
    48636 
    48637 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    48638 
    48639 Chain information for AF3 E2 353-438.pdb #245 
    48640 --- 
    48641 Chain | Description 
    48642 B | No description available 
    48643  
    48644 
    48645 > matchmaker #245 to #1.49 & sel
    48646 
    48647 Parameters 
    48648 --- 
    48649 Chain pairing | bb 
    48650 Alignment algorithm | Needleman-Wunsch 
    48651 Similarity matrix | BLOSUM-62 
    48652 SS fraction | 0.3 
    48653 Gap open (HH/SS/other) | 18/18/6 
    48654 Gap extend | 1 
    48655 SS matrix |  |  | H | S | O 
    48656 ---|---|---|--- 
    48657 H | 6 | -9 | -6 
    48658 S |  | 6 | -6 
    48659 O |  |  | 4 
    48660 Iteration cutoff | 2 
    48661  
    48662 Matchmaker 3j0c.pdb1, chain B (#1.49) with AF3 E2 353-438.pdb, chain B (#245),
    48663 sequence alignment score = 333.4 
    48664 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    48665 8.411) 
    48666  
    48667 
    48668 > hide sel cartoons
    48669 
    48670 > select #1.49/C
    48671 
    48672 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    48673 
    48674 > show sel cartoons
    48675 
    48676 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    48677 
    48678 Chain information for AF3 CA.pdb #246 
    48679 --- 
    48680 Chain | Description 
    48681 A | No description available 
    48682  
    48683 
    48684 > matchmaker #246 to #1.49 & sel
    48685 
    48686 Parameters 
    48687 --- 
    48688 Chain pairing | bb 
    48689 Alignment algorithm | Needleman-Wunsch 
    48690 Similarity matrix | BLOSUM-62 
    48691 SS fraction | 0.3 
    48692 Gap open (HH/SS/other) | 18/18/6 
    48693 Gap extend | 1 
    48694 SS matrix |  |  | H | S | O 
    48695 ---|---|---|--- 
    48696 H | 6 | -9 | -6 
    48697 S |  | 6 | -6 
    48698 O |  |  | 4 
    48699 Iteration cutoff | 2 
    48700  
    48701 Matchmaker 3j0c.pdb1, chain C (#1.49) with AF3 CA.pdb, chain A (#246),
    48702 sequence alignment score = 328.1 
    48703 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    48704 2.714) 
    48705  
    48706 
    48707 > hide sel cartoons
    48708 
    48709 > color #242 dodgerblue
    48710 
    48711 > color #243 dodgerblue
    48712 
    48713 > color #244 #00b305ff
    48714 
    48715 > color #245 #00b305ff
    48716 
    48717 > color #245 #f15839ff
    48718 
    48719 > color #245 #00b305ff
    48720 
    48721 > color #246 #f15839ff
    48722 
    48723 > select #1.50/A
    48724 
    48725 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    48726 
    48727 > show sel cartoons
    48728 
    48729 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    48730 
    48731 Chain information for AF3 E1 1-421.pdb #247 
    48732 --- 
    48733 Chain | Description 
    48734 A | No description available 
    48735  
    48736 
    48737 > matchmaker #247 to #1.49 & sel
    48738 
    48739 No 'to' model specified 
    48740 
    48741 > matchmaker #247 to #1.50 & sel
    48742 
    48743 Parameters 
    48744 --- 
    48745 Chain pairing | bb 
    48746 Alignment algorithm | Needleman-Wunsch 
    48747 Similarity matrix | BLOSUM-62 
    48748 SS fraction | 0.3 
    48749 Gap open (HH/SS/other) | 18/18/6 
    48750 Gap extend | 1 
    48751 SS matrix |  |  | H | S | O 
    48752 ---|---|---|--- 
    48753 H | 6 | -9 | -6 
    48754 S |  | 6 | -6 
    48755 O |  |  | 4 
    48756 Iteration cutoff | 2 
    48757  
    48758 Matchmaker 3j0c.pdb1, chain A (#1.50) with AF3 E1 1-421.pdb, chain A (#247),
    48759 sequence alignment score = 1060.7 
    48760 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    48761 3.020) 
    48762  
    48763 
    48764 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    48765 
    48766 Chain information for AF3 E1 422-461.pdb #248 
    48767 --- 
    48768 Chain | Description 
    48769 A | No description available 
    48770  
    48771 
    48772 > matchmaker #248 to #1.50 & sel
    48773 
    48774 Parameters 
    48775 --- 
    48776 Chain pairing | bb 
    48777 Alignment algorithm | Needleman-Wunsch 
    48778 Similarity matrix | BLOSUM-62 
    48779 SS fraction | 0.3 
    48780 Gap open (HH/SS/other) | 18/18/6 
    48781 Gap extend | 1 
    48782 SS matrix |  |  | H | S | O 
    48783 ---|---|---|--- 
    48784 H | 6 | -9 | -6 
    48785 S |  | 6 | -6 
    48786 O |  |  | 4 
    48787 Iteration cutoff | 2 
    48788  
    48789 Matchmaker 3j0c.pdb1, chain A (#1.50) with AF3 E1 422-461.pdb, chain A (#248),
    48790 sequence alignment score = 626.9 
    48791 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    48792 2.776) 
    48793  
    48794 
    48795 > hide sel cartoons
    48796 
    48797 > select #1.50/B
    48798 
    48799 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    48800 
    48801 > show sel cartoons
    48802 
    48803 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    48804 
    48805 Chain information for AF3 E2 1-352.pdb #249 
    48806 --- 
    48807 Chain | Description 
    48808 B | No description available 
    48809  
    48810 
    48811 > matchmaker #249 to #1.50 & sel
    48812 
    48813 Parameters 
    48814 --- 
    48815 Chain pairing | bb 
    48816 Alignment algorithm | Needleman-Wunsch 
    48817 Similarity matrix | BLOSUM-62 
    48818 SS fraction | 0.3 
    48819 Gap open (HH/SS/other) | 18/18/6 
    48820 Gap extend | 1 
    48821 SS matrix |  |  | H | S | O 
    48822 ---|---|---|--- 
    48823 H | 6 | -9 | -6 
    48824 S |  | 6 | -6 
    48825 O |  |  | 4 
    48826 Iteration cutoff | 2 
    48827  
    48828 Matchmaker 3j0c.pdb1, chain B (#1.50) with AF3 E2 1-352.pdb, chain B (#249),
    48829 sequence alignment score = 583.7 
    48830 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    48831 5.933) 
    48832  
    48833 
    48834 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    48835 
    48836 Chain information for AF3 E2 353-438.pdb #250 
    48837 --- 
    48838 Chain | Description 
    48839 B | No description available 
    48840  
    48841 
    48842 > matchmaker #250 to #1.50 & sel
    48843 
    48844 Parameters 
    48845 --- 
    48846 Chain pairing | bb 
    48847 Alignment algorithm | Needleman-Wunsch 
    48848 Similarity matrix | BLOSUM-62 
    48849 SS fraction | 0.3 
    48850 Gap open (HH/SS/other) | 18/18/6 
    48851 Gap extend | 1 
    48852 SS matrix |  |  | H | S | O 
    48853 ---|---|---|--- 
    48854 H | 6 | -9 | -6 
    48855 S |  | 6 | -6 
    48856 O |  |  | 4 
    48857 Iteration cutoff | 2 
    48858  
    48859 Matchmaker 3j0c.pdb1, chain B (#1.50) with AF3 E2 353-438.pdb, chain B (#250),
    48860 sequence alignment score = 333.4 
    48861 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    48862 8.411) 
    48863  
    48864 
    48865 > hide sel cartoons
    48866 
    48867 > select #1.50/C
    48868 
    48869 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    48870 
    48871 > show sel cartoons
    48872 
    48873 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    48874 
    48875 Chain information for AF3 CA.pdb #251 
    48876 --- 
    48877 Chain | Description 
    48878 A | No description available 
    48879  
    48880 
    48881 > matchmaker #251 to #1.50 & sel
    48882 
    48883 Parameters 
    48884 --- 
    48885 Chain pairing | bb 
    48886 Alignment algorithm | Needleman-Wunsch 
    48887 Similarity matrix | BLOSUM-62 
    48888 SS fraction | 0.3 
    48889 Gap open (HH/SS/other) | 18/18/6 
    48890 Gap extend | 1 
    48891 SS matrix |  |  | H | S | O 
    48892 ---|---|---|--- 
    48893 H | 6 | -9 | -6 
    48894 S |  | 6 | -6 
    48895 O |  |  | 4 
    48896 Iteration cutoff | 2 
    48897  
    48898 Matchmaker 3j0c.pdb1, chain C (#1.50) with AF3 CA.pdb, chain A (#251),
    48899 sequence alignment score = 328.1 
    48900 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    48901 2.714) 
    48902  
    48903 
    48904 > hide sel cartoons
    48905 
    48906 > color #247 dodgerblue
    48907 
    48908 > color #248 dodgerblue
    48909 
    48910 > color #249 #00b305ff
    48911 
    48912 > color #250 #00b305ff
    48913 
    48914 > color #251 #f15839ff
    48915 
    48916 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    48917 
    48918 > select #1.51/A
    48919 
    48920 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    48921 
    48922 > show sel cartoons
    48923 
    48924 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    48925 
    48926 Chain information for AF3 E1 1-421.pdb #252 
    48927 --- 
    48928 Chain | Description 
    48929 A | No description available 
    48930  
    48931 
    48932 > matchmaker #252 to #1.51 & sel
    48933 
    48934 Parameters 
    48935 --- 
    48936 Chain pairing | bb 
    48937 Alignment algorithm | Needleman-Wunsch 
    48938 Similarity matrix | BLOSUM-62 
    48939 SS fraction | 0.3 
    48940 Gap open (HH/SS/other) | 18/18/6 
    48941 Gap extend | 1 
    48942 SS matrix |  |  | H | S | O 
    48943 ---|---|---|--- 
    48944 H | 6 | -9 | -6 
    48945 S |  | 6 | -6 
    48946 O |  |  | 4 
    48947 Iteration cutoff | 2 
    48948  
    48949 Matchmaker 3j0c.pdb1, chain A (#1.51) with AF3 E1 1-421.pdb, chain A (#252),
    48950 sequence alignment score = 1060.7 
    48951 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    48952 3.020) 
    48953  
    48954 
    48955 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    48956 
    48957 Chain information for AF3 E1 422-461.pdb #253 
    48958 --- 
    48959 Chain | Description 
    48960 A | No description available 
    48961  
    48962 
    48963 > matchmaker #253 to #1.51 & sel
    48964 
    48965 Parameters 
    48966 --- 
    48967 Chain pairing | bb 
    48968 Alignment algorithm | Needleman-Wunsch 
    48969 Similarity matrix | BLOSUM-62 
    48970 SS fraction | 0.3 
    48971 Gap open (HH/SS/other) | 18/18/6 
    48972 Gap extend | 1 
    48973 SS matrix |  |  | H | S | O 
    48974 ---|---|---|--- 
    48975 H | 6 | -9 | -6 
    48976 S |  | 6 | -6 
    48977 O |  |  | 4 
    48978 Iteration cutoff | 2 
    48979  
    48980 Matchmaker 3j0c.pdb1, chain A (#1.51) with AF3 E1 422-461.pdb, chain A (#253),
    48981 sequence alignment score = 626.9 
    48982 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    48983 2.776) 
    48984  
    48985 
    48986 > hide sel cartoons
    48987 
    48988 > select #1.51/B
    48989 
    48990 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    48991 
    48992 > show sel cartoons
    48993 
    48994 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    48995 
    48996 Chain information for AF3 E2 1-352.pdb #254 
    48997 --- 
    48998 Chain | Description 
    48999 B | No description available 
    49000  
    49001 
    49002 > matchmaker #254 to #1.51 & sel
    49003 
    49004 Parameters 
    49005 --- 
    49006 Chain pairing | bb 
    49007 Alignment algorithm | Needleman-Wunsch 
    49008 Similarity matrix | BLOSUM-62 
    49009 SS fraction | 0.3 
    49010 Gap open (HH/SS/other) | 18/18/6 
    49011 Gap extend | 1 
    49012 SS matrix |  |  | H | S | O 
    49013 ---|---|---|--- 
    49014 H | 6 | -9 | -6 
    49015 S |  | 6 | -6 
    49016 O |  |  | 4 
    49017 Iteration cutoff | 2 
    49018  
    49019 Matchmaker 3j0c.pdb1, chain B (#1.51) with AF3 E2 1-352.pdb, chain B (#254),
    49020 sequence alignment score = 583.7 
    49021 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    49022 5.933) 
    49023  
    49024 
    49025 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    49026 
    49027 Chain information for AF3 E2 353-438.pdb #255 
    49028 --- 
    49029 Chain | Description 
    49030 B | No description available 
    49031  
    49032 
    49033 > matchmaker #255 to #1.51 & sel
    49034 
    49035 Parameters 
    49036 --- 
    49037 Chain pairing | bb 
    49038 Alignment algorithm | Needleman-Wunsch 
    49039 Similarity matrix | BLOSUM-62 
    49040 SS fraction | 0.3 
    49041 Gap open (HH/SS/other) | 18/18/6 
    49042 Gap extend | 1 
    49043 SS matrix |  |  | H | S | O 
    49044 ---|---|---|--- 
    49045 H | 6 | -9 | -6 
    49046 S |  | 6 | -6 
    49047 O |  |  | 4 
    49048 Iteration cutoff | 2 
    49049  
    49050 Matchmaker 3j0c.pdb1, chain B (#1.51) with AF3 E2 353-438.pdb, chain B (#255),
    49051 sequence alignment score = 322.6 
    49052 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    49053 8.411) 
    49054  
    49055 
    49056 > hide sel cartoons
    49057 
    49058 > select #1.51/C
    49059 
    49060 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    49061 
    49062 > show sel cartoons
    49063 
    49064 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    49065 
    49066 Chain information for AF3 CA.pdb #256 
    49067 --- 
    49068 Chain | Description 
    49069 A | No description available 
    49070  
    49071 
    49072 > matchmaker #256 to #1.51 & sel
    49073 
    49074 Parameters 
    49075 --- 
    49076 Chain pairing | bb 
    49077 Alignment algorithm | Needleman-Wunsch 
    49078 Similarity matrix | BLOSUM-62 
    49079 SS fraction | 0.3 
    49080 Gap open (HH/SS/other) | 18/18/6 
    49081 Gap extend | 1 
    49082 SS matrix |  |  | H | S | O 
    49083 ---|---|---|--- 
    49084 H | 6 | -9 | -6 
    49085 S |  | 6 | -6 
    49086 O |  |  | 4 
    49087 Iteration cutoff | 2 
    49088  
    49089 Matchmaker 3j0c.pdb1, chain C (#1.51) with AF3 CA.pdb, chain A (#256),
    49090 sequence alignment score = 328.1 
    49091 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    49092 2.714) 
    49093  
    49094 
    49095 > matchmaker #256 to #1.51 & sel
    49096 
    49097 Parameters 
    49098 --- 
    49099 Chain pairing | bb 
    49100 Alignment algorithm | Needleman-Wunsch 
    49101 Similarity matrix | BLOSUM-62 
    49102 SS fraction | 0.3 
    49103 Gap open (HH/SS/other) | 18/18/6 
    49104 Gap extend | 1 
    49105 SS matrix |  |  | H | S | O 
    49106 ---|---|---|--- 
    49107 H | 6 | -9 | -6 
    49108 S |  | 6 | -6 
    49109 O |  |  | 4 
    49110 Iteration cutoff | 2 
    49111  
    49112 Matchmaker 3j0c.pdb1, chain C (#1.51) with AF3 CA.pdb, chain A (#256),
    49113 sequence alignment score = 328.1 
    49114 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    49115 2.714) 
    49116  
    49117 
    49118 > hide sel cartoons
    49119 
    49120 > color #252 dodgerblue
    49121 
    49122 > color #253 dodgerblue
    49123 
    49124 > color #254 #00b305ff
    49125 
    49126 > color #255 #00b305ff
    49127 
    49128 > color #256 #f15839ff
    49129 
    49130 > select #1.52/A
    49131 
    49132 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    49133 
    49134 > show sel cartoons
    49135 
    49136 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    49137 
    49138 Chain information for AF3 E1 1-421.pdb #257 
    49139 --- 
    49140 Chain | Description 
    49141 A | No description available 
    49142  
    49143 
    49144 > matchmaker #257 to #1.52 & sel
    49145 
    49146 Parameters 
    49147 --- 
    49148 Chain pairing | bb 
    49149 Alignment algorithm | Needleman-Wunsch 
    49150 Similarity matrix | BLOSUM-62 
    49151 SS fraction | 0.3 
    49152 Gap open (HH/SS/other) | 18/18/6 
    49153 Gap extend | 1 
    49154 SS matrix |  |  | H | S | O 
    49155 ---|---|---|--- 
    49156 H | 6 | -9 | -6 
    49157 S |  | 6 | -6 
    49158 O |  |  | 4 
    49159 Iteration cutoff | 2 
    49160  
    49161 Matchmaker 3j0c.pdb1, chain A (#1.52) with AF3 E1 1-421.pdb, chain A (#257),
    49162 sequence alignment score = 1060.7 
    49163 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    49164 3.020) 
    49165  
    49166 
    49167 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    49168 
    49169 Chain information for AF3 E1 422-461.pdb #258 
    49170 --- 
    49171 Chain | Description 
    49172 A | No description available 
    49173  
    49174 
    49175 > matchmaker #258 to #1.52 & sel
    49176 
    49177 Parameters 
    49178 --- 
    49179 Chain pairing | bb 
    49180 Alignment algorithm | Needleman-Wunsch 
    49181 Similarity matrix | BLOSUM-62 
    49182 SS fraction | 0.3 
    49183 Gap open (HH/SS/other) | 18/18/6 
    49184 Gap extend | 1 
    49185 SS matrix |  |  | H | S | O 
    49186 ---|---|---|--- 
    49187 H | 6 | -9 | -6 
    49188 S |  | 6 | -6 
    49189 O |  |  | 4 
    49190 Iteration cutoff | 2 
    49191  
    49192 Matchmaker 3j0c.pdb1, chain A (#1.52) with AF3 E1 422-461.pdb, chain A (#258),
    49193 sequence alignment score = 626.9 
    49194 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    49195 2.775) 
    49196  
    49197 
    49198 > hide sel cartoons
    49199 
    49200 > select #1.52/B
    49201 
    49202 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    49203 
    49204 > show sel cartoons
    49205 
    49206 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    49207 
    49208 Chain information for AF3 E2 1-352.pdb #259 
    49209 --- 
    49210 Chain | Description 
    49211 B | No description available 
    49212  
    49213 
    49214 > matchmaker #259 to #1.52 & sel
    49215 
    49216 Parameters 
    49217 --- 
    49218 Chain pairing | bb 
    49219 Alignment algorithm | Needleman-Wunsch 
    49220 Similarity matrix | BLOSUM-62 
    49221 SS fraction | 0.3 
    49222 Gap open (HH/SS/other) | 18/18/6 
    49223 Gap extend | 1 
    49224 SS matrix |  |  | H | S | O 
    49225 ---|---|---|--- 
    49226 H | 6 | -9 | -6 
    49227 S |  | 6 | -6 
    49228 O |  |  | 4 
    49229 Iteration cutoff | 2 
    49230  
    49231 Matchmaker 3j0c.pdb1, chain B (#1.52) with AF3 E2 1-352.pdb, chain B (#259),
    49232 sequence alignment score = 583.7 
    49233 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    49234 5.933) 
    49235  
    49236 
    49237 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    49238 
    49239 Chain information for AF3 E2 353-438.pdb #260 
    49240 --- 
    49241 Chain | Description 
    49242 B | No description available 
    49243  
    49244 
    49245 > matchmaker #260 to #1.52 & sel
    49246 
    49247 Parameters 
    49248 --- 
    49249 Chain pairing | bb 
    49250 Alignment algorithm | Needleman-Wunsch 
    49251 Similarity matrix | BLOSUM-62 
    49252 SS fraction | 0.3 
    49253 Gap open (HH/SS/other) | 18/18/6 
    49254 Gap extend | 1 
    49255 SS matrix |  |  | H | S | O 
    49256 ---|---|---|--- 
    49257 H | 6 | -9 | -6 
    49258 S |  | 6 | -6 
    49259 O |  |  | 4 
    49260 Iteration cutoff | 2 
    49261  
    49262 Matchmaker 3j0c.pdb1, chain B (#1.52) with AF3 E2 353-438.pdb, chain B (#260),
    49263 sequence alignment score = 333.4 
    49264 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    49265 8.411) 
    49266  
    49267 
    49268 > hide sel cartoons
    49269 
    49270 > select #1.52/C
    49271 
    49272 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    49273 
    49274 > show sel cartoons
    49275 
    49276 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    49277 
    49278 Chain information for AF3 CA.pdb #261 
    49279 --- 
    49280 Chain | Description 
    49281 A | No description available 
    49282  
    49283 
    49284 > matchmaker #261 to #1.52 & sel
    49285 
    49286 Parameters 
    49287 --- 
    49288 Chain pairing | bb 
    49289 Alignment algorithm | Needleman-Wunsch 
    49290 Similarity matrix | BLOSUM-62 
    49291 SS fraction | 0.3 
    49292 Gap open (HH/SS/other) | 18/18/6 
    49293 Gap extend | 1 
    49294 SS matrix |  |  | H | S | O 
    49295 ---|---|---|--- 
    49296 H | 6 | -9 | -6 
    49297 S |  | 6 | -6 
    49298 O |  |  | 4 
    49299 Iteration cutoff | 2 
    49300  
    49301 Matchmaker 3j0c.pdb1, chain C (#1.52) with AF3 CA.pdb, chain A (#261),
    49302 sequence alignment score = 328.1 
    49303 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    49304 2.714) 
    49305  
    49306 
    49307 > hide sel cartoons
    49308 
    49309 [Repeated 1 time(s)]
    49310 
    49311 > color #257 dodgerblue
    49312 
    49313 > color #258 dodgerblue
    49314 
    49315 > color #259 #00b305ff
    49316 
    49317 > color #260 #00b305ff
    49318 
    49319 > color #261 #f15839ff
    49320 
    49321 The cached device pixel ratio value was stale on window expose. Please file a
    49322 QTBUG which explains how to reproduce. 
    49323 
    49324 > select
    49325 
    49326 2325488 atoms, 2385760 bonds, 301652 residues, 321 models selected 
    49327 
    49328 > hide sel cartoons
    49329 
    49330 > select up
    49331 
    49332 2325488 atoms, 2385760 bonds, 301652 residues, 321 models selected 
    49333 
    49334 > show #176 target m
    49335 
    49336 > show sel cartoons
    49337 
    49338 > hide #!1 models
    49339 
    49340 > select subtract #1
    49341 
    49342 417248 atoms, 427076 bonds, 55172 residues, 260 models selected 
    49343 
    49344 > select clear
    49345 
    49346 > hide #2 models
    49347 
    49348 > hide #3 models
    49349 
    49350 > hide #4 models
    49351 
    49352 > hide #5 models
    49353 
    49354 > hide #6 models
    49355 
    49356 > hide #7 models
    49357 
    49358 > hide #8 models
    49359 
    49360 > hide #9 models
    49361 
    49362 > hide #10 models
    49363 
    49364 > hide #11 models
    49365 
    49366 > hide #12 models
    49367 
    49368 > hide #13 models
    49369 
    49370 > hide #14 models
    49371 
    49372 > hide #15 models
    49373 
    49374 > hide #16 models
    49375 
    49376 > hide #17 models
    49377 
    49378 > show #16 models
    49379 
    49380 > show #17 models
    49381 
    49382 > hide #18 models
    49383 
    49384 > hide #19 models
    49385 
    49386 > hide #20 models
    49387 
    49388 > hide #21 models
    49389 
    49390 > hide #22 models
    49391 
    49392 > hide #23 models
    49393 
    49394 > hide #24 models
    49395 
    49396 > hide #25 models
    49397 
    49398 > hide #16 models
    49399 
    49400 > hide #17 models
    49401 
    49402 > hide #26 models
    49403 
    49404 > hide #27 models
    49405 
    49406 > hide #28 models
    49407 
    49408 > hide #29 models
    49409 
    49410 > hide #30 models
    49411 
    49412 > hide #31 models
    49413 
    49414 > hide #32 models
    49415 
    49416 > hide #33 models
    49417 
    49418 > hide #34 models
    49419 
    49420 > show #34 models
    49421 
    49422 > hide #35 models
    49423 
    49424 The cached device pixel ratio value was stale on window expose. Please file a
    49425 QTBUG which explains how to reproduce. 
    49426 
    49427 > hide #37 target m
    49428 
    49429 > hide #34 models
    49430 
    49431 > hide #36 models
    49432 
    49433 > hide #38 models
    49434 
    49435 > hide #39 models
    49436 
    49437 > hide #40 models
    49438 
    49439 > hide #41 models
    49440 
    49441 > hide #42 models
    49442 
    49443 > hide #43 models
    49444 
    49445 > hide #44 models
    49446 
    49447 > hide #45 models
    49448 
    49449 > hide #46 models
    49450 
    49451 > hide #47 models
    49452 
    49453 > hide #48 models
    49454 
    49455 > hide #49 models
    49456 
    49457 > hide #50 models
    49458 
    49459 > hide #51 models
    49460 
    49461 > hide #52 models
    49462 
    49463 > hide #53 models
    49464 
    49465 > hide #54 models
    49466 
    49467 > hide #55 models
    49468 
    49469 > hide #56 models
    49470 
    49471 > hide #57 models
    49472 
    49473 > hide #58 models
    49474 
    49475 > hide #59 models
    49476 
    49477 > hide #60 models
    49478 
    49479 > hide #61 models
    49480 
    49481 > hide #62 models
    49482 
    49483 > hide #63 models
    49484 
    49485 > hide #64 models
    49486 
    49487 > hide #65 models
    49488 
    49489 > hide #66 models
    49490 
    49491 > hide #67 models
    49492 
    49493 > hide #68 models
    49494 
    49495 > hide #69 models
    49496 
    49497 > hide #70 models
    49498 
    49499 > hide #71 models
    49500 
    49501 > hide #72 models
    49502 
    49503 > hide #73 models
    49504 
    49505 > hide #74 models
    49506 
    49507 > hide #75 models
    49508 
    49509 > hide #76 models
    49510 
    49511 > hide #77 models
    49512 
    49513 > hide #78 models
    49514 
    49515 > hide #79 models
    49516 
    49517 > hide #80 models
    49518 
    49519 > hide #81 models
    49520 
    49521 > hide #82 models
    49522 
    49523 > hide #83 models
    49524 
    49525 > hide #84 models
    49526 
    49527 > hide #85 models
    49528 
    49529 > hide #86 models
    49530 
    49531 > hide #87 models
    49532 
    49533 > hide #88 models
    49534 
    49535 > hide #89 models
    49536 
    49537 > hide #90 models
    49538 
    49539 > hide #91 models
    49540 
    49541 > hide #92 models
    49542 
    49543 > hide #93 models
    49544 
    49545 > hide #94 models
    49546 
    49547 > hide #95 models
    49548 
    49549 > hide #96 models
    49550 
    49551 > hide #97 models
    49552 
    49553 > hide #98 models
    49554 
    49555 > hide #99 models
    49556 
    49557 > hide #100 models
    49558 
    49559 > hide #101 models
    49560 
    49561 > hide #102 models
    49562 
    49563 > hide #103 models
    49564 
    49565 > hide #104 models
    49566 
    49567 > hide #105 models
    49568 
    49569 > hide #106 models
    49570 
    49571 > hide #107 models
    49572 
    49573 > hide #108 models
    49574 
    49575 > hide #109 models
    49576 
    49577 > hide #110 models
    49578 
    49579 > hide #111 models
    49580 
    49581 > hide #112 models
    49582 
    49583 > hide #113 models
    49584 
    49585 > hide #114 models
    49586 
    49587 > hide #115 models
    49588 
    49589 > hide #116 models
    49590 
    49591 > hide #117 models
    49592 
    49593 > hide #118 models
    49594 
    49595 > hide #119 models
    49596 
    49597 > hide #120 models
    49598 
    49599 > hide #121 models
    49600 
    49601 > hide #122 models
    49602 
    49603 > hide #123 models
    49604 
    49605 > hide #124 models
    49606 
    49607 > hide #125 models
    49608 
    49609 > hide #126 models
    49610 
    49611 > hide #127 models
    49612 
    49613 > hide #128 models
    49614 
    49615 > hide #129 models
    49616 
    49617 > hide #130 models
    49618 
    49619 > hide #131 models
    49620 
    49621 > hide #132 models
    49622 
    49623 > hide #133 models
    49624 
    49625 > hide #134 models
    49626 
    49627 > hide #135 models
    49628 
    49629 > hide #136 models
    49630 
    49631 > hide #137 models
    49632 
    49633 > hide #138 models
    49634 
    49635 > hide #139 models
    49636 
    49637 > hide #140 models
    49638 
    49639 > hide #141 models
    49640 
    49641 > hide #142 models
    49642 
    49643 > hide #143 models
    49644 
    49645 > hide #144 models
    49646 
    49647 > hide #145 models
    49648 
    49649 > hide #146 models
    49650 
    49651 > hide #147 models
    49652 
    49653 > hide #148 models
    49654 
    49655 > hide #149 models
    49656 
    49657 > hide #150 models
    49658 
    49659 > hide #151 models
    49660 
    49661 > hide #152 models
    49662 
    49663 > hide #153 models
    49664 
    49665 > hide #154 models
    49666 
    49667 > hide #155 models
    49668 
    49669 > hide #156 models
    49670 
    49671 > hide #157 models
    49672 
    49673 > hide #158 models
    49674 
    49675 > hide #159 models
    49676 
    49677 > hide #160 models
    49678 
    49679 > hide #161 models
    49680 
    49681 > hide #162 models
    49682 
    49683 > hide #163 models
    49684 
    49685 > hide #164 models
    49686 
    49687 > hide #165 models
    49688 
    49689 > hide #166 models
    49690 
    49691 > hide #167 models
    49692 
    49693 > hide #168 models
    49694 
    49695 > hide #169 models
    49696 
    49697 > hide #170 models
    49698 
    49699 > hide #171 models
    49700 
    49701 > hide #172 models
    49702 
    49703 > hide #173 models
    49704 
    49705 > hide #174 models
    49706 
    49707 > hide #175 models
    49708 
    49709 > hide #176 models
    49710 
    49711 > hide #177 models
    49712 
    49713 > hide #178 models
    49714 
    49715 > hide #179 models
    49716 
    49717 > hide #180 models
    49718 
    49719 > hide #181 models
    49720 
    49721 > hide #182 models
    49722 
    49723 > hide #183 models
    49724 
    49725 > hide #184 models
    49726 
    49727 > hide #185 models
    49728 
    49729 > hide #186 models
    49730 
    49731 > hide #187 models
    49732 
    49733 > hide #188 models
    49734 
    49735 > hide #189 models
    49736 
    49737 > hide #190 models
    49738 
    49739 > hide #191 models
    49740 
    49741 > hide #192 models
    49742 
    49743 > hide #193 models
    49744 
    49745 > hide #194 models
    49746 
    49747 > hide #195 models
    49748 
    49749 > hide #196 models
    49750 
    49751 > hide #197 models
    49752 
    49753 > hide #198 models
    49754 
    49755 > hide #199 models
    49756 
    49757 > hide #200 models
    49758 
    49759 > hide #201 models
    49760 
    49761 > hide #202 models
    49762 
    49763 > hide #203 models
    49764 
    49765 > hide #204 models
    49766 
    49767 > hide #205 models
    49768 
    49769 > hide #206 models
    49770 
    49771 > hide #207 models
    49772 
    49773 > hide #208 models
    49774 
    49775 > hide #209 models
    49776 
    49777 > hide #210 models
    49778 
    49779 > hide #211 models
    49780 
    49781 > hide #212 models
    49782 
    49783 > hide #213 models
    49784 
    49785 > hide #214 models
    49786 
    49787 > hide #215 models
    49788 
    49789 > hide #216 models
    49790 
    49791 > hide #217 models
    49792 
    49793 > hide #218 models
    49794 
    49795 > hide #219 models
    49796 
    49797 > hide #220 models
    49798 
    49799 > hide #221 models
    49800 
    49801 > hide #222 models
    49802 
    49803 > hide #223 models
    49804 
    49805 > hide #224 models
    49806 
    49807 > hide #225 models
    49808 
    49809 > hide #226 models
    49810 
    49811 > hide #227 models
    49812 
    49813 > hide #228 models
    49814 
    49815 > hide #229 models
    49816 
    49817 > hide #230 models
    49818 
    49819 > hide #231 models
    49820 
    49821 > hide #232 models
    49822 
    49823 > hide #233 models
    49824 
    49825 > hide #234 models
    49826 
    49827 > hide #235 models
    49828 
    49829 > hide #236 models
    49830 
    49831 > hide #237 models
    49832 
    49833 > hide #238 models
    49834 
    49835 > hide #239 models
    49836 
    49837 > hide #240 models
    49838 
    49839 > hide #241 models
    49840 
    49841 > hide #242 models
    49842 
    49843 > hide #243 models
    49844 
    49845 > hide #244 models
    49846 
    49847 > hide #245 models
    49848 
    49849 > hide #246 models
    49850 
    49851 > hide #247 models
    49852 
    49853 > hide #248 models
    49854 
    49855 > hide #249 models
    49856 
    49857 > hide #250 models
    49858 
    49859 > hide #251 models
    49860 
    49861 > hide #252 models
    49862 
    49863 > hide #253 models
    49864 
    49865 > hide #254 models
    49866 
    49867 > hide #255 models
    49868 
    49869 > hide #256 models
    49870 
    49871 > hide #257 models
    49872 
    49873 > hide #258 models
    49874 
    49875 > hide #259 models
    49876 
    49877 > hide #260 models
    49878 
    49879 > hide #261 models
    49880 
    49881 > select #1.53/A
    49882 
    49883 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    49884 
    49885 > select #1.52/A
    49886 
    49887 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    49888 
    49889 > view sel
    49890 
    49891 No displayed objects specified. 
    49892 
    49893 > show #!1 models
    49894 
    49895 > select ~sel & ##selected
    49896 
    49897 28434 atoms, 29183 bonds, 3666 residues, 1 model selected 
    49898 
    49899 > hide sel cartoons
    49900 
    49901 > select
    49902 > #1.1/A#1.2/A#1.3/A#1.4/A#1.5/A#1.6/A#1.7/A#1.8/A#1.9/A#1.10/A#1.11/A#1.12/A#1.13/A#1.14/A#1.15/A#1.16/A#1.17/A#1.18/A#1.19/A#1.20/A#1.21/A#1.22/A#1.23/A#1.24/A#1.25/A#1.26/A#1.27/A#1.28/A#1.29/A#1.30/A#1.31/A#1.32/A#1.33/A#1.34/A#1.35/A#1.36/A#1.37/A#1.38/A#1.39/A#1.40/A#1.41/A#1.42/A#1.43/A#1.44/A#1.45/A#1.46/A#1.47/A#1.48/A#1.49/A#1.50/A#1.51/A#1.52/A#1.53/A#1.54/A#1.55/A#1.56/A#1.57/A#1.58/A#1.59/A#1.60/A#2/A#3/A#6/A#7/A#8/A#11/A#12/A#13/A#16/A#17/A#18/A#21/A#22/A#23/A#26/A#27/A#28/A#31/A#32/A#33/A#36/A#37/A#38/A#41/A#42/A#43/A#46/A#47/A#48/A#51/A#52/A#53/A#56/A#57/A#58/A#61/A#62/A#63/A#66/A#67/A#68/A#71/A#72/A#73/A#76/A#77/A#78/A#81/A#82/A#83/A#86/A#87/A#88/A#91/A#92/A#93/A#96/A#97/A#98/A#101/A#102/A#103/A#106/A#107/A#108/A#111/A#112/A#113/A#116/A#117/A#118/A#121/A#122/A#123/A#126/A#127/A#128/A#131/A#132/A#133/A#136/A#137/A#138/A#141/A#142/A#143/A#146/A#147/A#148/A#151/A#152/A#153/A#156/A#157/A#158/A#161/A#162/A#163/A#166/A#167/A#168/A#171/A#172/A#173/A#176/A#177/A#178/A#181/A#182/A#183/A#186/A#187/A#188/A#191/A#192/A#193/A#196/A#197/A#198/A#201/A#202/A#203/A#206/A#207/A#208/A#211/A#212/A#213/A#216/A#217/A#218/A#221/A#222/A#223/A#226/A#227/A#228/A#231/A#232/A#233/A#236/A#237/A#238/A#241/A#242/A#243/A#246/A#247/A#248/A#251/A#252/A#253/A#256/A#257/A#258/A#261/A
    49903 
    49904 447224 atoms, 458514 bonds, 58916 residues, 216 models selected 
    49905 
    49906 > select
    49907 
    49908 2325488 atoms, 2385760 bonds, 301652 residues, 321 models selected 
    49909 
    49910 > hide sel & #1.1-60 cartoons
    49911 
    49912 > select #1.53/A
    49913 
    49914 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    49915 
    49916 > show sel cartoons
    49917 
    49918 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    49919 
    49920 Chain information for AF3 E1 1-421.pdb #262 
    49921 --- 
    49922 Chain | Description 
    49923 A | No description available 
    49924  
    49925 
    49926 > matchmaker #262 to #1.53 & sel
    49927 
    49928 Parameters 
    49929 --- 
    49930 Chain pairing | bb 
    49931 Alignment algorithm | Needleman-Wunsch 
    49932 Similarity matrix | BLOSUM-62 
    49933 SS fraction | 0.3 
    49934 Gap open (HH/SS/other) | 18/18/6 
    49935 Gap extend | 1 
    49936 SS matrix |  |  | H | S | O 
    49937 ---|---|---|--- 
    49938 H | 6 | -9 | -6 
    49939 S |  | 6 | -6 
    49940 O |  |  | 4 
    49941 Iteration cutoff | 2 
    49942  
    49943 Matchmaker 3j0c.pdb1, chain A (#1.53) with AF3 E1 1-421.pdb, chain A (#262),
    49944 sequence alignment score = 1060.7 
    49945 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    49946 3.020) 
    49947  
    49948 
    49949 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    49950 
    49951 Chain information for AF3 E1 422-461.pdb #263 
    49952 --- 
    49953 Chain | Description 
    49954 A | No description available 
    49955  
    49956 
    49957 > matchmaker #263 to #1.53 & sel
    49958 
    49959 Parameters 
    49960 --- 
    49961 Chain pairing | bb 
    49962 Alignment algorithm | Needleman-Wunsch 
    49963 Similarity matrix | BLOSUM-62 
    49964 SS fraction | 0.3 
    49965 Gap open (HH/SS/other) | 18/18/6 
    49966 Gap extend | 1 
    49967 SS matrix |  |  | H | S | O 
    49968 ---|---|---|--- 
    49969 H | 6 | -9 | -6 
    49970 S |  | 6 | -6 
    49971 O |  |  | 4 
    49972 Iteration cutoff | 2 
    49973  
    49974 Matchmaker 3j0c.pdb1, chain A (#1.53) with AF3 E1 422-461.pdb, chain A (#263),
    49975 sequence alignment score = 626.9 
    49976 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    49977 2.775) 
    49978  
    49979 
    49980 > hide sel cartoons
    49981 
    49982 > select #1.53/B
    49983 
    49984 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    49985 
    49986 > show sel cartoons
    49987 
    49988 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    49989 
    49990 Chain information for AF3 E2 1-352.pdb #264 
    49991 --- 
    49992 Chain | Description 
    49993 B | No description available 
    49994  
    49995 
    49996 > matchmaker #264 to #1.53 & sel
    49997 
    49998 Parameters 
    49999 --- 
    50000 Chain pairing | bb 
    50001 Alignment algorithm | Needleman-Wunsch 
    50002 Similarity matrix | BLOSUM-62 
    50003 SS fraction | 0.3 
    50004 Gap open (HH/SS/other) | 18/18/6 
    50005 Gap extend | 1 
    50006 SS matrix |  |  | H | S | O 
    50007 ---|---|---|--- 
    50008 H | 6 | -9 | -6 
    50009 S |  | 6 | -6 
    50010 O |  |  | 4 
    50011 Iteration cutoff | 2 
    50012  
    50013 Matchmaker 3j0c.pdb1, chain B (#1.53) with AF3 E2 1-352.pdb, chain B (#264),
    50014 sequence alignment score = 583.7 
    50015 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    50016 5.933) 
    50017  
    50018 
    50019 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    50020 
    50021 Chain information for AF3 E2 353-438.pdb #265 
    50022 --- 
    50023 Chain | Description 
    50024 B | No description available 
    50025  
    50026 
    50027 > matchmaker #265 to #1.53 & sel
    50028 
    50029 Parameters 
    50030 --- 
    50031 Chain pairing | bb 
    50032 Alignment algorithm | Needleman-Wunsch 
    50033 Similarity matrix | BLOSUM-62 
    50034 SS fraction | 0.3 
    50035 Gap open (HH/SS/other) | 18/18/6 
    50036 Gap extend | 1 
    50037 SS matrix |  |  | H | S | O 
    50038 ---|---|---|--- 
    50039 H | 6 | -9 | -6 
    50040 S |  | 6 | -6 
    50041 O |  |  | 4 
    50042 Iteration cutoff | 2 
    50043  
    50044 Matchmaker 3j0c.pdb1, chain B (#1.53) with AF3 E2 353-438.pdb, chain B (#265),
    50045 sequence alignment score = 333.4 
    50046 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    50047 8.411) 
    50048  
    50049 
    50050 > hide sel cartoons
    50051 
    50052 > select #1.53/C
    50053 
    50054 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    50055 
    50056 > show sel cartoons
    50057 
    50058 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    50059 
    50060 Chain information for AF3 CA.pdb #266 
    50061 --- 
    50062 Chain | Description 
    50063 A | No description available 
    50064  
    50065 
    50066 > matchmaker #266 to #1.53 & sel
    50067 
    50068 Parameters 
    50069 --- 
    50070 Chain pairing | bb 
    50071 Alignment algorithm | Needleman-Wunsch 
    50072 Similarity matrix | BLOSUM-62 
    50073 SS fraction | 0.3 
    50074 Gap open (HH/SS/other) | 18/18/6 
    50075 Gap extend | 1 
    50076 SS matrix |  |  | H | S | O 
    50077 ---|---|---|--- 
    50078 H | 6 | -9 | -6 
    50079 S |  | 6 | -6 
    50080 O |  |  | 4 
    50081 Iteration cutoff | 2 
    50082  
    50083 Matchmaker 3j0c.pdb1, chain C (#1.53) with AF3 CA.pdb, chain A (#266),
    50084 sequence alignment score = 328.1 
    50085 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    50086 2.714) 
    50087  
    50088 
    50089 > hide sel cartoons
    50090 
    50091 > select #1.54/A
    50092 
    50093 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    50094 
    50095 > show sel cartoons
    50096 
    50097 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    50098 
    50099 Chain information for AF3 E1 1-421.pdb #267 
    50100 --- 
    50101 Chain | Description 
    50102 A | No description available 
    50103  
    50104 
    50105 > matchmaker #267 to #1.54 & sel
    50106 
    50107 Parameters 
    50108 --- 
    50109 Chain pairing | bb 
    50110 Alignment algorithm | Needleman-Wunsch 
    50111 Similarity matrix | BLOSUM-62 
    50112 SS fraction | 0.3 
    50113 Gap open (HH/SS/other) | 18/18/6 
    50114 Gap extend | 1 
    50115 SS matrix |  |  | H | S | O 
    50116 ---|---|---|--- 
    50117 H | 6 | -9 | -6 
    50118 S |  | 6 | -6 
    50119 O |  |  | 4 
    50120 Iteration cutoff | 2 
    50121  
    50122 Matchmaker 3j0c.pdb1, chain A (#1.54) with AF3 E1 1-421.pdb, chain A (#267),
    50123 sequence alignment score = 1060.7 
    50124 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    50125 3.020) 
    50126  
    50127 
    50128 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    50129 
    50130 Chain information for AF3 E1 422-461.pdb #268 
    50131 --- 
    50132 Chain | Description 
    50133 A | No description available 
    50134  
    50135 
    50136 > matchmaker #268 to #1.54 & sel
    50137 
    50138 Parameters 
    50139 --- 
    50140 Chain pairing | bb 
    50141 Alignment algorithm | Needleman-Wunsch 
    50142 Similarity matrix | BLOSUM-62 
    50143 SS fraction | 0.3 
    50144 Gap open (HH/SS/other) | 18/18/6 
    50145 Gap extend | 1 
    50146 SS matrix |  |  | H | S | O 
    50147 ---|---|---|--- 
    50148 H | 6 | -9 | -6 
    50149 S |  | 6 | -6 
    50150 O |  |  | 4 
    50151 Iteration cutoff | 2 
    50152  
    50153 Matchmaker 3j0c.pdb1, chain A (#1.54) with AF3 E1 422-461.pdb, chain A (#268),
    50154 sequence alignment score = 626.9 
    50155 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    50156 2.776) 
    50157  
    50158 
    50159 > matchmaker #268 to #1.54 & sel
    50160 
    50161 Parameters 
    50162 --- 
    50163 Chain pairing | bb 
    50164 Alignment algorithm | Needleman-Wunsch 
    50165 Similarity matrix | BLOSUM-62 
    50166 SS fraction | 0.3 
    50167 Gap open (HH/SS/other) | 18/18/6 
    50168 Gap extend | 1 
    50169 SS matrix |  |  | H | S | O 
    50170 ---|---|---|--- 
    50171 H | 6 | -9 | -6 
    50172 S |  | 6 | -6 
    50173 O |  |  | 4 
    50174 Iteration cutoff | 2 
    50175  
    50176 Matchmaker 3j0c.pdb1, chain A (#1.54) with AF3 E1 422-461.pdb, chain A (#268),
    50177 sequence alignment score = 626.9 
    50178 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    50179 2.776) 
    50180  
    50181 
    50182 > hide sel cartoons
    50183 
    50184 > select #1.54/B
    50185 
    50186 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    50187 
    50188 > show sel cartoons
    50189 
    50190 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    50191 
    50192 Chain information for AF3 E2 1-352.pdb #269 
    50193 --- 
    50194 Chain | Description 
    50195 B | No description available 
    50196  
    50197 
    50198 > matchmaker #269 to #1.54 & sel
    50199 
    50200 Parameters 
    50201 --- 
    50202 Chain pairing | bb 
    50203 Alignment algorithm | Needleman-Wunsch 
    50204 Similarity matrix | BLOSUM-62 
    50205 SS fraction | 0.3 
    50206 Gap open (HH/SS/other) | 18/18/6 
    50207 Gap extend | 1 
    50208 SS matrix |  |  | H | S | O 
    50209 ---|---|---|--- 
    50210 H | 6 | -9 | -6 
    50211 S |  | 6 | -6 
    50212 O |  |  | 4 
    50213 Iteration cutoff | 2 
    50214  
    50215 Matchmaker 3j0c.pdb1, chain B (#1.54) with AF3 E2 1-352.pdb, chain B (#269),
    50216 sequence alignment score = 583.7 
    50217 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    50218 5.933) 
    50219  
    50220 
    50221 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    50222 
    50223 Chain information for AF3 E2 353-438.pdb #270 
    50224 --- 
    50225 Chain | Description 
    50226 B | No description available 
    50227  
    50228 
    50229 > matchmaker #270 to #1.54 & sel
    50230 
    50231 Parameters 
    50232 --- 
    50233 Chain pairing | bb 
    50234 Alignment algorithm | Needleman-Wunsch 
    50235 Similarity matrix | BLOSUM-62 
    50236 SS fraction | 0.3 
    50237 Gap open (HH/SS/other) | 18/18/6 
    50238 Gap extend | 1 
    50239 SS matrix |  |  | H | S | O 
    50240 ---|---|---|--- 
    50241 H | 6 | -9 | -6 
    50242 S |  | 6 | -6 
    50243 O |  |  | 4 
    50244 Iteration cutoff | 2 
    50245  
    50246 Matchmaker 3j0c.pdb1, chain B (#1.54) with AF3 E2 353-438.pdb, chain B (#270),
    50247 sequence alignment score = 333.4 
    50248 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    50249 8.411) 
    50250  
    50251 
    50252 > hide sel cartoons
    50253 
    50254 > select #1.54/C
    50255 
    50256 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    50257 
    50258 > show sel cartoons
    50259 
    50260 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    50261 
    50262 Chain information for AF3 CA.pdb #271 
    50263 --- 
    50264 Chain | Description 
    50265 A | No description available 
    50266  
    50267 
    50268 > matchmaker #271 to #1.54 & sel
    50269 
    50270 Parameters 
    50271 --- 
    50272 Chain pairing | bb 
    50273 Alignment algorithm | Needleman-Wunsch 
    50274 Similarity matrix | BLOSUM-62 
    50275 SS fraction | 0.3 
    50276 Gap open (HH/SS/other) | 18/18/6 
    50277 Gap extend | 1 
    50278 SS matrix |  |  | H | S | O 
    50279 ---|---|---|--- 
    50280 H | 6 | -9 | -6 
    50281 S |  | 6 | -6 
    50282 O |  |  | 4 
    50283 Iteration cutoff | 2 
    50284  
    50285 Matchmaker 3j0c.pdb1, chain C (#1.54) with AF3 CA.pdb, chain A (#271),
    50286 sequence alignment score = 328.1 
    50287 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    50288 2.714) 
    50289  
    50290 
    50291 > hide sel cartoons
    50292 
    50293 > color #262 dodgerblue
    50294 
    50295 > color #263 dodgerblue
    50296 
    50297 > color #264 #00b305ff
    50298 
    50299 > color #265 #00b305ff
    50300 
    50301 > color #266 #f15839ff
    50302 
    50303 > color #267 dodgerblue
    50304 
    50305 > color #268 dodgerblue
    50306 
    50307 > color #269 #00b305ff
    50308 
    50309 > color #270 #00b305ff
    50310 
    50311 > color #271 #f15839ff
    50312 
    50313 > select #1.55/A
    50314 
    50315 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    50316 
    50317 > show sel cartoons
    50318 
    50319 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    50320 
    50321 Chain information for AF3 E1 1-421.pdb #272 
    50322 --- 
    50323 Chain | Description 
    50324 A | No description available 
    50325  
    50326 
    50327 > matchmaker #272 to #1.54 & sel
    50328 
    50329 No 'to' model specified 
    50330 
    50331 > matchmaker #272 to #1.55 & sel
    50332 
    50333 Parameters 
    50334 --- 
    50335 Chain pairing | bb 
    50336 Alignment algorithm | Needleman-Wunsch 
    50337 Similarity matrix | BLOSUM-62 
    50338 SS fraction | 0.3 
    50339 Gap open (HH/SS/other) | 18/18/6 
    50340 Gap extend | 1 
    50341 SS matrix |  |  | H | S | O 
    50342 ---|---|---|--- 
    50343 H | 6 | -9 | -6 
    50344 S |  | 6 | -6 
    50345 O |  |  | 4 
    50346 Iteration cutoff | 2 
    50347  
    50348 Matchmaker 3j0c.pdb1, chain A (#1.55) with AF3 E1 1-421.pdb, chain A (#272),
    50349 sequence alignment score = 1060.7 
    50350 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    50351 3.020) 
    50352  
    50353 
    50354 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    50355 
    50356 Chain information for AF3 E1 422-461.pdb #273 
    50357 --- 
    50358 Chain | Description 
    50359 A | No description available 
    50360  
    50361 
    50362 > matchmaker #273 to #1.55 & sel
    50363 
    50364 Parameters 
    50365 --- 
    50366 Chain pairing | bb 
    50367 Alignment algorithm | Needleman-Wunsch 
    50368 Similarity matrix | BLOSUM-62 
    50369 SS fraction | 0.3 
    50370 Gap open (HH/SS/other) | 18/18/6 
    50371 Gap extend | 1 
    50372 SS matrix |  |  | H | S | O 
    50373 ---|---|---|--- 
    50374 H | 6 | -9 | -6 
    50375 S |  | 6 | -6 
    50376 O |  |  | 4 
    50377 Iteration cutoff | 2 
    50378  
    50379 Matchmaker 3j0c.pdb1, chain A (#1.55) with AF3 E1 422-461.pdb, chain A (#273),
    50380 sequence alignment score = 626.9 
    50381 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    50382 2.775) 
    50383  
    50384 
    50385 > hide sel cartoons
    50386 
    50387 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    50388 
    50389 Chain information for AF3 E2 1-352.pdb #274 
    50390 --- 
    50391 Chain | Description 
    50392 B | No description available 
    50393  
    50394 
    50395 > select #1.55/B
    50396 
    50397 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    50398 
    50399 > show sel cartoons
    50400 
    50401 > matchmaker #274 to #1.55 & sel
    50402 
    50403 Parameters 
    50404 --- 
    50405 Chain pairing | bb 
    50406 Alignment algorithm | Needleman-Wunsch 
    50407 Similarity matrix | BLOSUM-62 
    50408 SS fraction | 0.3 
    50409 Gap open (HH/SS/other) | 18/18/6 
    50410 Gap extend | 1 
    50411 SS matrix |  |  | H | S | O 
    50412 ---|---|---|--- 
    50413 H | 6 | -9 | -6 
    50414 S |  | 6 | -6 
    50415 O |  |  | 4 
    50416 Iteration cutoff | 2 
    50417  
    50418 Matchmaker 3j0c.pdb1, chain B (#1.55) with AF3 E2 1-352.pdb, chain B (#274),
    50419 sequence alignment score = 583.7 
    50420 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    50421 5.933) 
    50422  
    50423 
    50424 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    50425 
    50426 Chain information for AF3 E2 353-438.pdb #275 
    50427 --- 
    50428 Chain | Description 
    50429 B | No description available 
    50430  
    50431 
    50432 > matchmaker #275 to #1.55 & sel
    50433 
    50434 Parameters 
    50435 --- 
    50436 Chain pairing | bb 
    50437 Alignment algorithm | Needleman-Wunsch 
    50438 Similarity matrix | BLOSUM-62 
    50439 SS fraction | 0.3 
    50440 Gap open (HH/SS/other) | 18/18/6 
    50441 Gap extend | 1 
    50442 SS matrix |  |  | H | S | O 
    50443 ---|---|---|--- 
    50444 H | 6 | -9 | -6 
    50445 S |  | 6 | -6 
    50446 O |  |  | 4 
    50447 Iteration cutoff | 2 
    50448  
    50449 Matchmaker 3j0c.pdb1, chain B (#1.55) with AF3 E2 353-438.pdb, chain B (#275),
    50450 sequence alignment score = 322.6 
    50451 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    50452 8.411) 
    50453  
    50454 
    50455 > hide sel cartoons
    50456 
    50457 > select #1.55/C
    50458 
    50459 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    50460 
    50461 > show sel cartoons
    50462 
    50463 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    50464 
    50465 Chain information for AF3 CA.pdb #276 
    50466 --- 
    50467 Chain | Description 
    50468 A | No description available 
    50469  
    50470 
    50471 > matchmaker #276 to #1.55 & sel
    50472 
    50473 Parameters 
    50474 --- 
    50475 Chain pairing | bb 
    50476 Alignment algorithm | Needleman-Wunsch 
    50477 Similarity matrix | BLOSUM-62 
    50478 SS fraction | 0.3 
    50479 Gap open (HH/SS/other) | 18/18/6 
    50480 Gap extend | 1 
    50481 SS matrix |  |  | H | S | O 
    50482 ---|---|---|--- 
    50483 H | 6 | -9 | -6 
    50484 S |  | 6 | -6 
    50485 O |  |  | 4 
    50486 Iteration cutoff | 2 
    50487  
    50488 Matchmaker 3j0c.pdb1, chain C (#1.55) with AF3 CA.pdb, chain A (#276),
    50489 sequence alignment score = 328.1 
    50490 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    50491 2.714) 
    50492  
    50493 
    50494 > hide sel cartoons
    50495 
    50496 > color #272 dodgerblue
    50497 
    50498 > color #273 dodgerblue
    50499 
    50500 > color #274 #00b305ff
    50501 
    50502 > color #275 #00b305ff
    50503 
    50504 > color #276 #f15839ff
    50505 
    50506 > select #1.56/A
    50507 
    50508 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    50509 
    50510 > show sel cartoons
    50511 
    50512 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    50513 
    50514 Chain information for AF3 E1 1-421.pdb #277 
    50515 --- 
    50516 Chain | Description 
    50517 A | No description available 
    50518  
    50519 
    50520 > matchmaker #277 to #1.55 & sel
    50521 
    50522 No 'to' model specified 
    50523 
    50524 > matchmaker #277 to #1.56 & sel
    50525 
    50526 Parameters 
    50527 --- 
    50528 Chain pairing | bb 
    50529 Alignment algorithm | Needleman-Wunsch 
    50530 Similarity matrix | BLOSUM-62 
    50531 SS fraction | 0.3 
    50532 Gap open (HH/SS/other) | 18/18/6 
    50533 Gap extend | 1 
    50534 SS matrix |  |  | H | S | O 
    50535 ---|---|---|--- 
    50536 H | 6 | -9 | -6 
    50537 S |  | 6 | -6 
    50538 O |  |  | 4 
    50539 Iteration cutoff | 2 
    50540  
    50541 Matchmaker 3j0c.pdb1, chain A (#1.56) with AF3 E1 1-421.pdb, chain A (#277),
    50542 sequence alignment score = 1060.7 
    50543 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    50544 3.020) 
    50545  
    50546 
    50547 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    50548 
    50549 Chain information for AF3 E1 422-461.pdb #278 
    50550 --- 
    50551 Chain | Description 
    50552 A | No description available 
    50553  
    50554 
    50555 > matchmaker #278 to #1.56 & sel
    50556 
    50557 Parameters 
    50558 --- 
    50559 Chain pairing | bb 
    50560 Alignment algorithm | Needleman-Wunsch 
    50561 Similarity matrix | BLOSUM-62 
    50562 SS fraction | 0.3 
    50563 Gap open (HH/SS/other) | 18/18/6 
    50564 Gap extend | 1 
    50565 SS matrix |  |  | H | S | O 
    50566 ---|---|---|--- 
    50567 H | 6 | -9 | -6 
    50568 S |  | 6 | -6 
    50569 O |  |  | 4 
    50570 Iteration cutoff | 2 
    50571  
    50572 Matchmaker 3j0c.pdb1, chain A (#1.56) with AF3 E1 422-461.pdb, chain A (#278),
    50573 sequence alignment score = 626.9 
    50574 RMSD between 28 pruned atom pairs is 0.572 angstroms; (across all 38 pairs:
    50575 2.775) 
    50576  
    50577 
    50578 > hide sel cartoons
    50579 
    50580 > select #1.56/B
    50581 
    50582 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    50583 
    50584 > show sel cartoons
    50585 
    50586 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    50587 
    50588 Chain information for AF3 E2 1-352.pdb #279 
    50589 --- 
    50590 Chain | Description 
    50591 B | No description available 
    50592  
    50593 
    50594 > matchmaker #279 to #1.56 & sel
    50595 
    50596 Parameters 
    50597 --- 
    50598 Chain pairing | bb 
    50599 Alignment algorithm | Needleman-Wunsch 
    50600 Similarity matrix | BLOSUM-62 
    50601 SS fraction | 0.3 
    50602 Gap open (HH/SS/other) | 18/18/6 
    50603 Gap extend | 1 
    50604 SS matrix |  |  | H | S | O 
    50605 ---|---|---|--- 
    50606 H | 6 | -9 | -6 
    50607 S |  | 6 | -6 
    50608 O |  |  | 4 
    50609 Iteration cutoff | 2 
    50610  
    50611 Matchmaker 3j0c.pdb1, chain B (#1.56) with AF3 E2 1-352.pdb, chain B (#279),
    50612 sequence alignment score = 583.7 
    50613 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    50614 5.933) 
    50615  
    50616 
    50617 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    50618 
    50619 Chain information for AF3 E2 353-438.pdb #280 
    50620 --- 
    50621 Chain | Description 
    50622 B | No description available 
    50623  
    50624 
    50625 > matchmaker #280 to #1.56 & sel
    50626 
    50627 Parameters 
    50628 --- 
    50629 Chain pairing | bb 
    50630 Alignment algorithm | Needleman-Wunsch 
    50631 Similarity matrix | BLOSUM-62 
    50632 SS fraction | 0.3 
    50633 Gap open (HH/SS/other) | 18/18/6 
    50634 Gap extend | 1 
    50635 SS matrix |  |  | H | S | O 
    50636 ---|---|---|--- 
    50637 H | 6 | -9 | -6 
    50638 S |  | 6 | -6 
    50639 O |  |  | 4 
    50640 Iteration cutoff | 2 
    50641  
    50642 Matchmaker 3j0c.pdb1, chain B (#1.56) with AF3 E2 353-438.pdb, chain B (#280),
    50643 sequence alignment score = 333.4 
    50644 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    50645 8.411) 
    50646  
    50647 
    50648 > hide sel cartoons
    50649 
    50650 > select #1.56/C
    50651 
    50652 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    50653 
    50654 > show sel cartoons
    50655 
    50656 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    50657 
    50658 Chain information for AF3 CA.pdb #281 
    50659 --- 
    50660 Chain | Description 
    50661 A | No description available 
    50662  
    50663 
    50664 > matchmaker #281 to #1.56 & sel
    50665 
    50666 Parameters 
    50667 --- 
    50668 Chain pairing | bb 
    50669 Alignment algorithm | Needleman-Wunsch 
    50670 Similarity matrix | BLOSUM-62 
    50671 SS fraction | 0.3 
    50672 Gap open (HH/SS/other) | 18/18/6 
    50673 Gap extend | 1 
    50674 SS matrix |  |  | H | S | O 
    50675 ---|---|---|--- 
    50676 H | 6 | -9 | -6 
    50677 S |  | 6 | -6 
    50678 O |  |  | 4 
    50679 Iteration cutoff | 2 
    50680  
    50681 Matchmaker 3j0c.pdb1, chain C (#1.56) with AF3 CA.pdb, chain A (#281),
    50682 sequence alignment score = 328.1 
    50683 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    50684 2.714) 
    50685  
    50686 
    50687 > hide sel cartoons
    50688 
    50689 > color #277 dodgerblue
    50690 
    50691 > color #278 dodgerblue
    50692 
    50693 > color #279 #00b305ff
    50694 
    50695 > color #280 #00b305ff
    50696 
    50697 > color #281 #f15839ff
    50698 
    50699 > select #1.57/A
    50700 
    50701 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    50702 
    50703 > show sel cartoons
    50704 
    50705 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    50706 
    50707 Chain information for AF3 E1 1-421.pdb #282 
    50708 --- 
    50709 Chain | Description 
    50710 A | No description available 
    50711  
    50712 
    50713 > matchmaker #282 to #1.56 & sel
    50714 
    50715 No 'to' model specified 
    50716 
    50717 > matchmaker #282 to #1.57 & sel
    50718 
    50719 Parameters 
    50720 --- 
    50721 Chain pairing | bb 
    50722 Alignment algorithm | Needleman-Wunsch 
    50723 Similarity matrix | BLOSUM-62 
    50724 SS fraction | 0.3 
    50725 Gap open (HH/SS/other) | 18/18/6 
    50726 Gap extend | 1 
    50727 SS matrix |  |  | H | S | O 
    50728 ---|---|---|--- 
    50729 H | 6 | -9 | -6 
    50730 S |  | 6 | -6 
    50731 O |  |  | 4 
    50732 Iteration cutoff | 2 
    50733  
    50734 Matchmaker 3j0c.pdb1, chain A (#1.57) with AF3 E1 1-421.pdb, chain A (#282),
    50735 sequence alignment score = 1060.7 
    50736 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    50737 3.020) 
    50738  
    50739 
    50740 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    50741 
    50742 Chain information for AF3 E1 422-461.pdb #283 
    50743 --- 
    50744 Chain | Description 
    50745 A | No description available 
    50746  
    50747 
    50748 > matchmaker #283 to #1.57 & sel
    50749 
    50750 Parameters 
    50751 --- 
    50752 Chain pairing | bb 
    50753 Alignment algorithm | Needleman-Wunsch 
    50754 Similarity matrix | BLOSUM-62 
    50755 SS fraction | 0.3 
    50756 Gap open (HH/SS/other) | 18/18/6 
    50757 Gap extend | 1 
    50758 SS matrix |  |  | H | S | O 
    50759 ---|---|---|--- 
    50760 H | 6 | -9 | -6 
    50761 S |  | 6 | -6 
    50762 O |  |  | 4 
    50763 Iteration cutoff | 2 
    50764  
    50765 Matchmaker 3j0c.pdb1, chain A (#1.57) with AF3 E1 422-461.pdb, chain A (#283),
    50766 sequence alignment score = 626.9 
    50767 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    50768 2.776) 
    50769  
    50770 
    50771 > hide sel cartoons
    50772 
    50773 > select #1.57/B
    50774 
    50775 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    50776 
    50777 > show sel cartoons
    50778 
    50779 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    50780 
    50781 Chain information for AF3 E2 1-352.pdb #284 
    50782 --- 
    50783 Chain | Description 
    50784 B | No description available 
    50785  
    50786 
    50787 > matchmaker #284 to #1.57 & sel
    50788 
    50789 Parameters 
    50790 --- 
    50791 Chain pairing | bb 
    50792 Alignment algorithm | Needleman-Wunsch 
    50793 Similarity matrix | BLOSUM-62 
    50794 SS fraction | 0.3 
    50795 Gap open (HH/SS/other) | 18/18/6 
    50796 Gap extend | 1 
    50797 SS matrix |  |  | H | S | O 
    50798 ---|---|---|--- 
    50799 H | 6 | -9 | -6 
    50800 S |  | 6 | -6 
    50801 O |  |  | 4 
    50802 Iteration cutoff | 2 
    50803  
    50804 Matchmaker 3j0c.pdb1, chain B (#1.57) with AF3 E2 1-352.pdb, chain B (#284),
    50805 sequence alignment score = 583.7 
    50806 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    50807 5.933) 
    50808  
    50809 
    50810 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    50811 
    50812 Chain information for AF3 E2 353-438.pdb #285 
    50813 --- 
    50814 Chain | Description 
    50815 B | No description available 
    50816  
    50817 
    50818 > matchmaker #285 to #1.57 & sel
    50819 
    50820 Parameters 
    50821 --- 
    50822 Chain pairing | bb 
    50823 Alignment algorithm | Needleman-Wunsch 
    50824 Similarity matrix | BLOSUM-62 
    50825 SS fraction | 0.3 
    50826 Gap open (HH/SS/other) | 18/18/6 
    50827 Gap extend | 1 
    50828 SS matrix |  |  | H | S | O 
    50829 ---|---|---|--- 
    50830 H | 6 | -9 | -6 
    50831 S |  | 6 | -6 
    50832 O |  |  | 4 
    50833 Iteration cutoff | 2 
    50834  
    50835 Matchmaker 3j0c.pdb1, chain B (#1.57) with AF3 E2 353-438.pdb, chain B (#285),
    50836 sequence alignment score = 333.4 
    50837 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    50838 8.411) 
    50839  
    50840 
    50841 > hide sel cartoons
    50842 
    50843 [Repeated 1 time(s)]
    50844 
    50845 > select #1.57/C
    50846 
    50847 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    50848 
    50849 > show sel cartoons
    50850 
    50851 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    50852 
    50853 Chain information for AF3 CA.pdb #286 
    50854 --- 
    50855 Chain | Description 
    50856 A | No description available 
    50857  
    50858 
    50859 > matchmaker #286 to #1.57 & sel
    50860 
    50861 Parameters 
    50862 --- 
    50863 Chain pairing | bb 
    50864 Alignment algorithm | Needleman-Wunsch 
    50865 Similarity matrix | BLOSUM-62 
    50866 SS fraction | 0.3 
    50867 Gap open (HH/SS/other) | 18/18/6 
    50868 Gap extend | 1 
    50869 SS matrix |  |  | H | S | O 
    50870 ---|---|---|--- 
    50871 H | 6 | -9 | -6 
    50872 S |  | 6 | -6 
    50873 O |  |  | 4 
    50874 Iteration cutoff | 2 
    50875  
    50876 Matchmaker 3j0c.pdb1, chain C (#1.57) with AF3 CA.pdb, chain A (#286),
    50877 sequence alignment score = 328.1 
    50878 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    50879 2.714) 
    50880  
    50881 
    50882 > hide sel cartoons
    50883 
    50884 > color #282 dodgerblue
    50885 
    50886 > color #283 dodgerblue
    50887 
    50888 > color #284 #00b305ff
    50889 
    50890 > color #285 #00b305ff
    50891 
    50892 > color #286 #f15839ff
    50893 
    50894 > select #1.58/A
    50895 
    50896 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    50897 
    50898 > show sel cartoons
    50899 
    50900 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    50901 
    50902 Chain information for AF3 E1 1-421.pdb #287 
    50903 --- 
    50904 Chain | Description 
    50905 A | No description available 
    50906  
    50907 
    50908 > matchmaker #287 to #1.58 & sel
    50909 
    50910 Parameters 
    50911 --- 
    50912 Chain pairing | bb 
    50913 Alignment algorithm | Needleman-Wunsch 
    50914 Similarity matrix | BLOSUM-62 
    50915 SS fraction | 0.3 
    50916 Gap open (HH/SS/other) | 18/18/6 
    50917 Gap extend | 1 
    50918 SS matrix |  |  | H | S | O 
    50919 ---|---|---|--- 
    50920 H | 6 | -9 | -6 
    50921 S |  | 6 | -6 
    50922 O |  |  | 4 
    50923 Iteration cutoff | 2 
    50924  
    50925 Matchmaker 3j0c.pdb1, chain A (#1.58) with AF3 E1 1-421.pdb, chain A (#287),
    50926 sequence alignment score = 1060.7 
    50927 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    50928 3.020) 
    50929  
    50930 
    50931 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    50932 
    50933 Chain information for AF3 E1 422-461.pdb #288 
    50934 --- 
    50935 Chain | Description 
    50936 A | No description available 
    50937  
    50938 
    50939 > matchmaker #288 to #1.58 & sel
    50940 
    50941 Parameters 
    50942 --- 
    50943 Chain pairing | bb 
    50944 Alignment algorithm | Needleman-Wunsch 
    50945 Similarity matrix | BLOSUM-62 
    50946 SS fraction | 0.3 
    50947 Gap open (HH/SS/other) | 18/18/6 
    50948 Gap extend | 1 
    50949 SS matrix |  |  | H | S | O 
    50950 ---|---|---|--- 
    50951 H | 6 | -9 | -6 
    50952 S |  | 6 | -6 
    50953 O |  |  | 4 
    50954 Iteration cutoff | 2 
    50955  
    50956 Matchmaker 3j0c.pdb1, chain A (#1.58) with AF3 E1 422-461.pdb, chain A (#288),
    50957 sequence alignment score = 626.9 
    50958 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    50959 2.775) 
    50960  
    50961 
    50962 > hide sel cartoons
    50963 
    50964 > select #1.58/B
    50965 
    50966 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    50967 
    50968 > show sel cartoons
    50969 
    50970 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    50971 
    50972 Chain information for AF3 E2 1-352.pdb #289 
    50973 --- 
    50974 Chain | Description 
    50975 B | No description available 
    50976  
    50977 
    50978 > matchmaker #289 to #1.58 & sel
    50979 
    50980 Parameters 
    50981 --- 
    50982 Chain pairing | bb 
    50983 Alignment algorithm | Needleman-Wunsch 
    50984 Similarity matrix | BLOSUM-62 
    50985 SS fraction | 0.3 
    50986 Gap open (HH/SS/other) | 18/18/6 
    50987 Gap extend | 1 
    50988 SS matrix |  |  | H | S | O 
    50989 ---|---|---|--- 
    50990 H | 6 | -9 | -6 
    50991 S |  | 6 | -6 
    50992 O |  |  | 4 
    50993 Iteration cutoff | 2 
    50994  
    50995 Matchmaker 3j0c.pdb1, chain B (#1.58) with AF3 E2 1-352.pdb, chain B (#289),
    50996 sequence alignment score = 583.7 
    50997 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    50998 5.933) 
    50999  
    51000 
    51001 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    51002 
    51003 Chain information for AF3 E2 353-438.pdb #290 
    51004 --- 
    51005 Chain | Description 
    51006 B | No description available 
    51007  
    51008 
    51009 > matchmaker #290 to #1.58 & sel
    51010 
    51011 Parameters 
    51012 --- 
    51013 Chain pairing | bb 
    51014 Alignment algorithm | Needleman-Wunsch 
    51015 Similarity matrix | BLOSUM-62 
    51016 SS fraction | 0.3 
    51017 Gap open (HH/SS/other) | 18/18/6 
    51018 Gap extend | 1 
    51019 SS matrix |  |  | H | S | O 
    51020 ---|---|---|--- 
    51021 H | 6 | -9 | -6 
    51022 S |  | 6 | -6 
    51023 O |  |  | 4 
    51024 Iteration cutoff | 2 
    51025  
    51026 Matchmaker 3j0c.pdb1, chain B (#1.58) with AF3 E2 353-438.pdb, chain B (#290),
    51027 sequence alignment score = 322.6 
    51028 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    51029 8.411) 
    51030  
    51031 
    51032 > hide sel cartoons
    51033 
    51034 > select #1.58/C
    51035 
    51036 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    51037 
    51038 > show sel cartoons
    51039 
    51040 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    51041 
    51042 Chain information for AF3 CA.pdb #291 
    51043 --- 
    51044 Chain | Description 
    51045 A | No description available 
    51046  
    51047 
    51048 > matchmaker #291 to #1.58 & sel
    51049 
    51050 Parameters 
    51051 --- 
    51052 Chain pairing | bb 
    51053 Alignment algorithm | Needleman-Wunsch 
    51054 Similarity matrix | BLOSUM-62 
    51055 SS fraction | 0.3 
    51056 Gap open (HH/SS/other) | 18/18/6 
    51057 Gap extend | 1 
    51058 SS matrix |  |  | H | S | O 
    51059 ---|---|---|--- 
    51060 H | 6 | -9 | -6 
    51061 S |  | 6 | -6 
    51062 O |  |  | 4 
    51063 Iteration cutoff | 2 
    51064  
    51065 Matchmaker 3j0c.pdb1, chain C (#1.58) with AF3 CA.pdb, chain A (#291),
    51066 sequence alignment score = 328.1 
    51067 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    51068 2.714) 
    51069  
    51070 
    51071 > hide sel cartoons
    51072 
    51073 > color #287 dodgerblue
    51074 
    51075 > color #288 dodgerblue
    51076 
    51077 > color #289 #00b305ff
    51078 
    51079 > color #290 #00b305ff
    51080 
    51081 > color #291 #f15839ff
    51082 
    51083 > select #1.59/A
    51084 
    51085 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    51086 
    51087 > show sel cartoons
    51088 
    51089 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    51090 
    51091 Chain information for AF3 E1 1-421.pdb #292 
    51092 --- 
    51093 Chain | Description 
    51094 A | No description available 
    51095  
    51096 
    51097 > matchmaker #291 to #1.59 & sel
    51098 
    51099 Parameters 
    51100 --- 
    51101 Chain pairing | bb 
    51102 Alignment algorithm | Needleman-Wunsch 
    51103 Similarity matrix | BLOSUM-62 
    51104 SS fraction | 0.3 
    51105 Gap open (HH/SS/other) | 18/18/6 
    51106 Gap extend | 1 
    51107 SS matrix |  |  | H | S | O 
    51108 ---|---|---|--- 
    51109 H | 6 | -9 | -6 
    51110 S |  | 6 | -6 
    51111 O |  |  | 4 
    51112 Iteration cutoff | 2 
    51113  
    51114 Matchmaker 3j0c.pdb1, chain A (#1.59) with AF3 CA.pdb, chain A (#291),
    51115 sequence alignment score = 32.6 
    51116 RMSD between 11 pruned atom pairs is 1.204 angstroms; (across all 110 pairs:
    51117 22.675) 
    51118  
    51119 
    51120 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    51121 
    51122 Chain information for AF3 E1 422-461.pdb #293 
    51123 --- 
    51124 Chain | Description 
    51125 A | No description available 
    51126  
    51127 
    51128 > matchmaker #291 to #1.58 & sel
    51129 
    51130 No 'to' model specified 
    51131 
    51132 > select #1.58/C
    51133 
    51134 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    51135 
    51136 > show sel cartoons
    51137 
    51138 > matchmaker #291 to #1.58 & sel
    51139 
    51140 Parameters 
    51141 --- 
    51142 Chain pairing | bb 
    51143 Alignment algorithm | Needleman-Wunsch 
    51144 Similarity matrix | BLOSUM-62 
    51145 SS fraction | 0.3 
    51146 Gap open (HH/SS/other) | 18/18/6 
    51147 Gap extend | 1 
    51148 SS matrix |  |  | H | S | O 
    51149 ---|---|---|--- 
    51150 H | 6 | -9 | -6 
    51151 S |  | 6 | -6 
    51152 O |  |  | 4 
    51153 Iteration cutoff | 2 
    51154  
    51155 Matchmaker 3j0c.pdb1, chain C (#1.58) with AF3 CA.pdb, chain A (#291),
    51156 sequence alignment score = 328.1 
    51157 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    51158 2.714) 
    51159  
    51160 
    51161 > hide sel cartoons
    51162 
    51163 > select #1.59/A
    51164 
    51165 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    51166 
    51167 > matchmaker #292 to #1.59 & sel
    51168 
    51169 Parameters 
    51170 --- 
    51171 Chain pairing | bb 
    51172 Alignment algorithm | Needleman-Wunsch 
    51173 Similarity matrix | BLOSUM-62 
    51174 SS fraction | 0.3 
    51175 Gap open (HH/SS/other) | 18/18/6 
    51176 Gap extend | 1 
    51177 SS matrix |  |  | H | S | O 
    51178 ---|---|---|--- 
    51179 H | 6 | -9 | -6 
    51180 S |  | 6 | -6 
    51181 O |  |  | 4 
    51182 Iteration cutoff | 2 
    51183  
    51184 Matchmaker 3j0c.pdb1, chain A (#1.59) with AF3 E1 1-421.pdb, chain A (#292),
    51185 sequence alignment score = 1060.7 
    51186 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    51187 3.020) 
    51188  
    51189 
    51190 > matchmaker #293 to #1.59 & sel
    51191 
    51192 Parameters 
    51193 --- 
    51194 Chain pairing | bb 
    51195 Alignment algorithm | Needleman-Wunsch 
    51196 Similarity matrix | BLOSUM-62 
    51197 SS fraction | 0.3 
    51198 Gap open (HH/SS/other) | 18/18/6 
    51199 Gap extend | 1 
    51200 SS matrix |  |  | H | S | O 
    51201 ---|---|---|--- 
    51202 H | 6 | -9 | -6 
    51203 S |  | 6 | -6 
    51204 O |  |  | 4 
    51205 Iteration cutoff | 2 
    51206  
    51207 Matchmaker 3j0c.pdb1, chain A (#1.59) with AF3 E1 422-461.pdb, chain A (#293),
    51208 sequence alignment score = 626.9 
    51209 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    51210 2.776) 
    51211  
    51212 
    51213 > select #1.39/B
    51214 
    51215 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    51216 
    51217 > select #1.59/A
    51218 
    51219 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    51220 
    51221 > hide sel cartoons
    51222 
    51223 > select #1.59/B
    51224 
    51225 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    51226 
    51227 > show sel cartoons
    51228 
    51229 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    51230 
    51231 Chain information for AF3 E2 1-352.pdb #294 
    51232 --- 
    51233 Chain | Description 
    51234 B | No description available 
    51235  
    51236 
    51237 > matchmaker #294 to #1.59 & sel
    51238 
    51239 Parameters 
    51240 --- 
    51241 Chain pairing | bb 
    51242 Alignment algorithm | Needleman-Wunsch 
    51243 Similarity matrix | BLOSUM-62 
    51244 SS fraction | 0.3 
    51245 Gap open (HH/SS/other) | 18/18/6 
    51246 Gap extend | 1 
    51247 SS matrix |  |  | H | S | O 
    51248 ---|---|---|--- 
    51249 H | 6 | -9 | -6 
    51250 S |  | 6 | -6 
    51251 O |  |  | 4 
    51252 Iteration cutoff | 2 
    51253  
    51254 Matchmaker 3j0c.pdb1, chain B (#1.59) with AF3 E2 1-352.pdb, chain B (#294),
    51255 sequence alignment score = 583.7 
    51256 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    51257 5.933) 
    51258  
    51259 
    51260 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    51261 
    51262 Chain information for AF3 E2 353-438.pdb #295 
    51263 --- 
    51264 Chain | Description 
    51265 B | No description available 
    51266  
    51267 
    51268 > matchmaker #295 to #1.59 & sel
    51269 
    51270 Parameters 
    51271 --- 
    51272 Chain pairing | bb 
    51273 Alignment algorithm | Needleman-Wunsch 
    51274 Similarity matrix | BLOSUM-62 
    51275 SS fraction | 0.3 
    51276 Gap open (HH/SS/other) | 18/18/6 
    51277 Gap extend | 1 
    51278 SS matrix |  |  | H | S | O 
    51279 ---|---|---|--- 
    51280 H | 6 | -9 | -6 
    51281 S |  | 6 | -6 
    51282 O |  |  | 4 
    51283 Iteration cutoff | 2 
    51284  
    51285 Matchmaker 3j0c.pdb1, chain B (#1.59) with AF3 E2 353-438.pdb, chain B (#295),
    51286 sequence alignment score = 322.6 
    51287 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    51288 8.411) 
    51289  
    51290 
    51291 > hide sel cartoons
    51292 
    51293 > select #1.59/C
    51294 
    51295 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    51296 
    51297 > show sel cartoons
    51298 
    51299 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    51300 
    51301 Chain information for AF3 CA.pdb #296 
    51302 --- 
    51303 Chain | Description 
    51304 A | No description available 
    51305  
    51306 
    51307 > matchmaker #296 to #1.59 & sel
    51308 
    51309 Parameters 
    51310 --- 
    51311 Chain pairing | bb 
    51312 Alignment algorithm | Needleman-Wunsch 
    51313 Similarity matrix | BLOSUM-62 
    51314 SS fraction | 0.3 
    51315 Gap open (HH/SS/other) | 18/18/6 
    51316 Gap extend | 1 
    51317 SS matrix |  |  | H | S | O 
    51318 ---|---|---|--- 
    51319 H | 6 | -9 | -6 
    51320 S |  | 6 | -6 
    51321 O |  |  | 4 
    51322 Iteration cutoff | 2 
    51323  
    51324 Matchmaker 3j0c.pdb1, chain C (#1.59) with AF3 CA.pdb, chain A (#296),
    51325 sequence alignment score = 328.1 
    51326 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    51327 2.714) 
    51328  
    51329 
    51330 > hide sel cartoons
    51331 
    51332 > color #292 dodgerblue
    51333 
    51334 > color #293 dodgerblue
    51335 
    51336 > color #294 #00b305ff
    51337 
    51338 > color #295 #00b305ff
    51339 
    51340 > color #296 #f15839ff
    51341 
    51342 > select #1.60/A
    51343 
    51344 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    51345 
    51346 > show sel cartoons
    51347 
    51348 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    51349 
    51350 Chain information for AF3 E1 1-421.pdb #297 
    51351 --- 
    51352 Chain | Description 
    51353 A | No description available 
    51354  
    51355 
    51356 > matchmaker #297 to #1.60 & sel
    51357 
    51358 Parameters 
    51359 --- 
    51360 Chain pairing | bb 
    51361 Alignment algorithm | Needleman-Wunsch 
    51362 Similarity matrix | BLOSUM-62 
    51363 SS fraction | 0.3 
    51364 Gap open (HH/SS/other) | 18/18/6 
    51365 Gap extend | 1 
    51366 SS matrix |  |  | H | S | O 
    51367 ---|---|---|--- 
    51368 H | 6 | -9 | -6 
    51369 S |  | 6 | -6 
    51370 O |  |  | 4 
    51371 Iteration cutoff | 2 
    51372  
    51373 Matchmaker 3j0c.pdb1, chain A (#1.60) with AF3 E1 1-421.pdb, chain A (#297),
    51374 sequence alignment score = 1060.7 
    51375 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    51376 3.020) 
    51377  
    51378 
    51379 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    51380 
    51381 Chain information for AF3 E1 422-461.pdb #298 
    51382 --- 
    51383 Chain | Description 
    51384 A | No description available 
    51385  
    51386 
    51387 > matchmaker #298 to #1.60 & sel
    51388 
    51389 Parameters 
    51390 --- 
    51391 Chain pairing | bb 
    51392 Alignment algorithm | Needleman-Wunsch 
    51393 Similarity matrix | BLOSUM-62 
    51394 SS fraction | 0.3 
    51395 Gap open (HH/SS/other) | 18/18/6 
    51396 Gap extend | 1 
    51397 SS matrix |  |  | H | S | O 
    51398 ---|---|---|--- 
    51399 H | 6 | -9 | -6 
    51400 S |  | 6 | -6 
    51401 O |  |  | 4 
    51402 Iteration cutoff | 2 
    51403  
    51404 Matchmaker 3j0c.pdb1, chain A (#1.60) with AF3 E1 422-461.pdb, chain A (#298),
    51405 sequence alignment score = 626.9 
    51406 RMSD between 28 pruned atom pairs is 0.571 angstroms; (across all 38 pairs:
    51407 2.776) 
    51408  
    51409 
    51410 > hide sel cartoons
    51411 
    51412 > select #1.60/B
    51413 
    51414 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    51415 
    51416 > show sel cartoons
    51417 
    51418 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    51419 
    51420 Chain information for AF3 E2 1-352.pdb #299 
    51421 --- 
    51422 Chain | Description 
    51423 B | No description available 
    51424  
    51425 
    51426 > matchmaker #299 to #1.60 & sel
    51427 
    51428 Parameters 
    51429 --- 
    51430 Chain pairing | bb 
    51431 Alignment algorithm | Needleman-Wunsch 
    51432 Similarity matrix | BLOSUM-62 
    51433 SS fraction | 0.3 
    51434 Gap open (HH/SS/other) | 18/18/6 
    51435 Gap extend | 1 
    51436 SS matrix |  |  | H | S | O 
    51437 ---|---|---|--- 
    51438 H | 6 | -9 | -6 
    51439 S |  | 6 | -6 
    51440 O |  |  | 4 
    51441 Iteration cutoff | 2 
    51442  
    51443 Matchmaker 3j0c.pdb1, chain B (#1.60) with AF3 E2 1-352.pdb, chain B (#299),
    51444 sequence alignment score = 583.7 
    51445 RMSD between 103 pruned atom pairs is 1.056 angstroms; (across all 333 pairs:
    51446 5.933) 
    51447  
    51448 
    51449 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    51450 
    51451 Chain information for AF3 E2 353-438.pdb #300 
    51452 --- 
    51453 Chain | Description 
    51454 B | No description available 
    51455  
    51456 
    51457 > matchmaker #300 to #1.60 & sel
    51458 
    51459 Parameters 
    51460 --- 
    51461 Chain pairing | bb 
    51462 Alignment algorithm | Needleman-Wunsch 
    51463 Similarity matrix | BLOSUM-62 
    51464 SS fraction | 0.3 
    51465 Gap open (HH/SS/other) | 18/18/6 
    51466 Gap extend | 1 
    51467 SS matrix |  |  | H | S | O 
    51468 ---|---|---|--- 
    51469 H | 6 | -9 | -6 
    51470 S |  | 6 | -6 
    51471 O |  |  | 4 
    51472 Iteration cutoff | 2 
    51473  
    51474 Matchmaker 3j0c.pdb1, chain B (#1.60) with AF3 E2 353-438.pdb, chain B (#300),
    51475 sequence alignment score = 333.4 
    51476 RMSD between 37 pruned atom pairs is 0.844 angstroms; (across all 84 pairs:
    51477 8.411) 
    51478  
    51479 
    51480 > hide sel cartoons
    51481 
    51482 > select #1.60/C
    51483 
    51484 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    51485 
    51486 > show sel cartoons
    51487 
    51488 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    51489 
    51490 Chain information for AF3 CA.pdb #301 
    51491 --- 
    51492 Chain | Description 
    51493 A | No description available 
    51494  
    51495 
    51496 > matchmaker #301 to #1.60 & sel
    51497 
    51498 Parameters 
    51499 --- 
    51500 Chain pairing | bb 
    51501 Alignment algorithm | Needleman-Wunsch 
    51502 Similarity matrix | BLOSUM-62 
    51503 SS fraction | 0.3 
    51504 Gap open (HH/SS/other) | 18/18/6 
    51505 Gap extend | 1 
    51506 SS matrix |  |  | H | S | O 
    51507 ---|---|---|--- 
    51508 H | 6 | -9 | -6 
    51509 S |  | 6 | -6 
    51510 O |  |  | 4 
    51511 Iteration cutoff | 2 
    51512  
    51513 Matchmaker 3j0c.pdb1, chain C (#1.60) with AF3 CA.pdb, chain A (#301),
    51514 sequence alignment score = 328.1 
    51515 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    51516 2.714) 
    51517  
    51518 
    51519 > hide sel cartoons
    51520 
    51521 > color #297 dodgerblue
    51522 
    51523 > color #298 dodgerblue
    51524 
    51525 > color #299 #00b305ff
    51526 
    51527 > color #300 #00b305ff
    51528 
    51529 > color #301 #f15839ff
    51530 
    51531 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    51532 
    51533 ——— End of log from Mon Jul 15 16:48:15 2024 ———
    51534 
    51535 opened ChimeraX session 
    51536 
    51537 > show #2 models
    51538 
    51539 > show #3 models
    51540 
    51541 > show #4 models
    51542 
    51543 > show #5 models
    51544 
    51545 > show #6 models
    51546 
    51547 The cached device pixel ratio value was stale on window expose. Please file a
    51548 QTBUG which explains how to reproduce. 
    51549 
    51550 [Repeated 1 time(s)]
    51551 
    51552 > hide #2-6,262-301#1.2-60 target m
    51553 
    51554 > show #1.2 target m
    51555 
    51556 > hide #1.1 target m
    51557 
    51558 > hide #!1 models
    51559 
    51560 > show #2 models
    51561 
    51562 > show #3 models
    51563 
    51564 > show #4 models
    51565 
    51566 The cached device pixel ratio value was stale on window expose. Please file a
    51567 QTBUG which explains how to reproduce. 
    51568 
    51569 > show #5 models
    51570 
    51571 > show #6 models
    51572 
    51573 > show #7 models
    51574 
    51575 > show #8 models
    51576 
    51577 > show #9 models
    51578 
    51579 > show #10 models
    51580 
    51581 > show #11 models
    51582 
    51583 > show #12 models
    51584 
    51585 > show #13 models
    51586 
    51587 > show #14 models
    51588 
    51589 > show #15 models
    51590 
    51591 > show #16 models
    51592 
    51593 > show #17 models
    51594 
    51595 > show #18 models
    51596 
    51597 > show #19 models
    51598 
    51599 > show #20 models
    51600 
    51601 > show #21 models
    51602 
    51603 > show #22 models
    51604 
    51605 > show #23 models
    51606 
    51607 > show #24 models
    51608 
    51609 > show #25 models
    51610 
    51611 > show #26 models
    51612 
    51613 > show #27 models
    51614 
    51615 > show #28 models
    51616 
    51617 > show #29 models
    51618 
    51619 > show #30 models
    51620 
    51621 > show #31 models
    51622 
    51623 > show #32 models
    51624 
    51625 > show #33 models
    51626 
    51627 > show #34 models
    51628 
    51629 > show #35 models
    51630 
    51631 > show #36 models
    51632 
    51633 > show #37 models
    51634 
    51635 > show #38 models
    51636 
    51637 > show #39 models
    51638 
    51639 > show #40 models
    51640 
    51641 > show #41 models
    51642 
    51643 > show #42 models
    51644 
    51645 > show #43 models
    51646 
    51647 > show #44 models
    51648 
    51649 > show #45 models
    51650 
    51651 > show #46 models
    51652 
    51653 > show #47 models
    51654 
    51655 > show #48 models
    51656 
    51657 > show #49 models
    51658 
    51659 > show #50 models
    51660 
    51661 > show #51 models
    51662 
    51663 > show #52 models
    51664 
    51665 > show #53 models
    51666 
    51667 > show #54 models
    51668 
    51669 > show #55 models
    51670 
    51671 > show #56 models
    51672 
    51673 > show #57 models
    51674 
    51675 > show #58 models
    51676 
    51677 > show #59 models
    51678 
    51679 > show #60 models
    51680 
    51681 > show #61 models
    51682 
    51683 > show #62 models
    51684 
    51685 > show #63 models
    51686 
    51687 > show #64 models
    51688 
    51689 > show #65 models
    51690 
    51691 > show #66 models
    51692 
    51693 > show #67 models
    51694 
    51695 > show #68 models
    51696 
    51697 > show #69 models
    51698 
    51699 > show #70 models
    51700 
    51701 > show #71 models
    51702 
    51703 > show #72 models
    51704 
    51705 > show #73 models
    51706 
    51707 > show #74 models
    51708 
    51709 > show #75 models
    51710 
    51711 > show #76 models
    51712 
    51713 > show #77 models
    51714 
    51715 > show #78 models
    51716 
    51717 > show #79 models
    51718 
    51719 > show #80 models
    51720 
    51721 > show #81 models
    51722 
    51723 > show #82 models
    51724 
    51725 The cached device pixel ratio value was stale on window expose. Please file a
    51726 QTBUG which explains how to reproduce. 
    51727 
    51728 > show #82-301 models
    51729 
    51730 > hide #2-301 models
    51731 
    51732 > show #2-301 models
    51733 
    51734 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    51735 
    51736 ——— End of log from Mon Jul 15 16:59:09 2024 ———
    51737 
    51738 opened ChimeraX session 
    51739 
    51740 The cached device pixel ratio value was stale on window expose. Please file a
    51741 QTBUG which explains how to reproduce. 
    51742 
    51743 > select #1.1/D
    51744 
    51745 3370 atoms, 3467 bonds, 442 residues, 1 model selected 
    51746 
    51747 > show #2-301 cartoons
    51748 
    51749 > view sel
    51750 
    51751 No displayed objects specified. 
    51752 
    51753 > select add #1
    51754 
    51755 1908240 atoms, 1958684 bonds, 246480 residues, 61 models selected 
    51756 
    51757 > hide #1.2 models
    51758 
    51759 > show #1.1 models
    51760 
    51761 > hide #1.1 models
    51762 
    51763 > show #1.1 models
    51764 
    51765 > show sel & #1.1 cartoons
    51766 
    51767 > hide #1.1 models
    51768 
    51769 > hide #!1 models
    51770 
    51771 > show #1.1 models
    51772 
    51773 The cached device pixel ratio value was stale on window expose. Please file a
    51774 QTBUG which explains how to reproduce. 
    51775 
    51776 > select subtract #1
    51777 
    51778 Nothing selected 
    51779 
    51780 > hide #!1 models
    51781 
    51782 > hide #1.1 models
    51783 
    51784 > show #1.1 models
    51785 
    51786 > show #1.2 models
    51787 
    51788 > show #1.3 models
    51789 
    51790 > show #1.4 models
    51791 
    51792 > select
    51793 
    51794 2389680 atoms, 2451464 bonds, 310140 residues, 361 models selected 
    51795 
    51796 > show sel & #2-301#1.1-4 cartoons
    51797 
    51798 > hide #!1 models
    51799 
    51800 > show #!1 models
    51801 
    51802 > show #1.5 models
    51803 
    51804 > show #1.6 models
    51805 
    51806 > show #1.7 models
    51807 
    51808 > hide #1.7 models
    51809 
    51810 > show #1.7 models
    51811 
    51812 > show #1.8 models
    51813 
    51814 > ui tool show "Selection Inspector"
    51815 
    51816 The cached device pixel ratio value was stale on window expose. Please file a
    51817 QTBUG which explains how to reproduce. 
    51818 
    51819 [Repeated 1 time(s)]
    51820 
    51821 > setattr sel struct display true
    51822 
    51823 Assigning display attribute to 360 items 
    51824 
    51825 > select #1.1/A
    51826 
    51827 3370 atoms, 3467 bonds, 442 residues, 1 model selected 
    51828 
    51829 > select ~sel & ##selected
    51830 
    51831 28434 atoms, 29221 bonds, 3666 residues, 1 model selected 
    51832 
    51833 > hide sel cartoons
    51834 
    51835 > select
    51836 
    51837 2389680 atoms, 2451464 bonds, 310140 residues, 361 models selected 
    51838 
    51839 > hide sel cartoons
    51840 
    51841 > select #1.1/A
    51842 
    51843 3370 atoms, 3467 bonds, 442 residues, 1 model selected 
    51844 
    51845 > show sel cartoons
    51846 
    51847 > hide sel cartoons
    51848 
    51849 > select #1.1/D
    51850 
    51851 3370 atoms, 3467 bonds, 442 residues, 1 model selected 
    51852 
    51853 > show sel cartoons
    51854 
    51855 > ui tool show Matchmaker
    51856 
    51857 The cached device pixel ratio value was stale on window expose. Please file a
    51858 QTBUG which explains how to reproduce. 
    51859 
    51860 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    51861 
    51862 Chain information for AF3 E1 1-421.pdb #302 
    51863 --- 
    51864 Chain | Description 
    51865 A | No description available 
    51866  
    51867 
    51868 > matchmaker #301 to #1.1 & sel
    51869 
    51870 Parameters 
    51871 --- 
    51872 Chain pairing | bb 
    51873 Alignment algorithm | Needleman-Wunsch 
    51874 Similarity matrix | BLOSUM-62 
    51875 SS fraction | 0.3 
    51876 Gap open (HH/SS/other) | 18/18/6 
    51877 Gap extend | 1 
    51878 SS matrix |  |  | H | S | O 
    51879 ---|---|---|--- 
    51880 H | 6 | -9 | -6 
    51881 S |  | 6 | -6 
    51882 O |  |  | 4 
    51883 Iteration cutoff | 2 
    51884  
    51885 Matchmaker 3j0c.pdb1, chain D (#1.1) with AF3 CA.pdb, chain A (#301), sequence
    51886 alignment score = 32.6 
    51887 RMSD between 11 pruned atom pairs is 1.228 angstroms; (across all 110 pairs:
    51888 22.710) 
    51889  
    51890 
    51891 > select #1.60/C
    51892 
    51893 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    51894 
    51895 > show sel cartoons
    51896 
    51897 > hide #301 models
    51898 
    51899 > show #301 models
    51900 
    51901 > select add #301
    51902 
    51903 2536 atoms, 2591 bonds, 324 residues, 2 models selected 
    51904 
    51905 > hide #301 models
    51906 
    51907 > show #301 models
    51908 
    51909 > color #301 #f15839ff
    51910 
    51911 > show sel cartoons
    51912 
    51913 > select subtract #301
    51914 
    51915 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    51916 
    51917 > matchmaker #301 to #1.60 & sel
    51918 
    51919 Parameters 
    51920 --- 
    51921 Chain pairing | bb 
    51922 Alignment algorithm | Needleman-Wunsch 
    51923 Similarity matrix | BLOSUM-62 
    51924 SS fraction | 0.3 
    51925 Gap open (HH/SS/other) | 18/18/6 
    51926 Gap extend | 1 
    51927 SS matrix |  |  | H | S | O 
    51928 ---|---|---|--- 
    51929 H | 6 | -9 | -6 
    51930 S |  | 6 | -6 
    51931 O |  |  | 4 
    51932 Iteration cutoff | 2 
    51933  
    51934 Matchmaker 3j0c.pdb1, chain C (#1.60) with AF3 CA.pdb, chain A (#301),
    51935 sequence alignment score = 328.1 
    51936 RMSD between 113 pruned atom pairs is 1.224 angstroms; (across all 161 pairs:
    51937 2.714) 
    51938  
    51939 
    51940 > hide sel cartoons
    51941 
    51942 > hide #301 models
    51943 
    51944 > select #1.1/D
    51945 
    51946 3370 atoms, 3467 bonds, 442 residues, 1 model selected 
    51947 
    51948 > matchmaker #302 to #1.1 & sel
    51949 
    51950 Parameters 
    51951 --- 
    51952 Chain pairing | bb 
    51953 Alignment algorithm | Needleman-Wunsch 
    51954 Similarity matrix | BLOSUM-62 
    51955 SS fraction | 0.3 
    51956 Gap open (HH/SS/other) | 18/18/6 
    51957 Gap extend | 1 
    51958 SS matrix |  |  | H | S | O 
    51959 ---|---|---|--- 
    51960 H | 6 | -9 | -6 
    51961 S |  | 6 | -6 
    51962 O |  |  | 4 
    51963 Iteration cutoff | 2 
    51964  
    51965 Matchmaker 3j0c.pdb1, chain D (#1.1) with AF3 E1 1-421.pdb, chain A (#302),
    51966 sequence alignment score = 1060.7 
    51967 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    51968 3.032) 
    51969  
    51970 
    51971 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    51972 
    51973 Chain information for AF3 E1 422-461.pdb #303 
    51974 --- 
    51975 Chain | Description 
    51976 A | No description available 
    51977  
    51978 
    51979 > matchmaker #303 to #1.1 & sel
    51980 
    51981 Parameters 
    51982 --- 
    51983 Chain pairing | bb 
    51984 Alignment algorithm | Needleman-Wunsch 
    51985 Similarity matrix | BLOSUM-62 
    51986 SS fraction | 0.3 
    51987 Gap open (HH/SS/other) | 18/18/6 
    51988 Gap extend | 1 
    51989 SS matrix |  |  | H | S | O 
    51990 ---|---|---|--- 
    51991 H | 6 | -9 | -6 
    51992 S |  | 6 | -6 
    51993 O |  |  | 4 
    51994 Iteration cutoff | 2 
    51995  
    51996 Matchmaker 3j0c.pdb1, chain D (#1.1) with AF3 E1 422-461.pdb, chain A (#303),
    51997 sequence alignment score = 626.9 
    51998 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    51999 2.916) 
    52000  
    52001 
    52002 > select #1.1/E
    52003 
    52004 3304 atoms, 3400 bonds, 423 residues, 1 model selected 
    52005 
    52006 > show sel cartoons
    52007 
    52008 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    52009 
    52010 Chain information for AF3 E2 1-352.pdb #304 
    52011 --- 
    52012 Chain | Description 
    52013 B | No description available 
    52014  
    52015 
    52016 > matchmaker #304 to #1.1 & sel
    52017 
    52018 Parameters 
    52019 --- 
    52020 Chain pairing | bb 
    52021 Alignment algorithm | Needleman-Wunsch 
    52022 Similarity matrix | BLOSUM-62 
    52023 SS fraction | 0.3 
    52024 Gap open (HH/SS/other) | 18/18/6 
    52025 Gap extend | 1 
    52026 SS matrix |  |  | H | S | O 
    52027 ---|---|---|--- 
    52028 H | 6 | -9 | -6 
    52029 S |  | 6 | -6 
    52030 O |  |  | 4 
    52031 Iteration cutoff | 2 
    52032  
    52033 Matchmaker 3j0c.pdb1, chain E (#1.1) with AF3 E2 1-352.pdb, chain B (#304),
    52034 sequence alignment score = 594.5 
    52035 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    52036 6.147) 
    52037  
    52038 
    52039 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    52040 
    52041 Chain information for AF3 E2 353-438.pdb #305 
    52042 --- 
    52043 Chain | Description 
    52044 B | No description available 
    52045  
    52046 
    52047 > matchmaker #305 to #1.1 & sel
    52048 
    52049 Parameters 
    52050 --- 
    52051 Chain pairing | bb 
    52052 Alignment algorithm | Needleman-Wunsch 
    52053 Similarity matrix | BLOSUM-62 
    52054 SS fraction | 0.3 
    52055 Gap open (HH/SS/other) | 18/18/6 
    52056 Gap extend | 1 
    52057 SS matrix |  |  | H | S | O 
    52058 ---|---|---|--- 
    52059 H | 6 | -9 | -6 
    52060 S |  | 6 | -6 
    52061 O |  |  | 4 
    52062 Iteration cutoff | 2 
    52063  
    52064 Matchmaker 3j0c.pdb1, chain E (#1.1) with AF3 E2 353-438.pdb, chain B (#305),
    52065 sequence alignment score = 340.2 
    52066 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    52067 8.673) 
    52068  
    52069 
    52070 > select #1.1/F
    52071 
    52072 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    52073 
    52074 > show sel cartoons
    52075 
    52076 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    52077 
    52078 Chain information for AF3 CA.pdb #306 
    52079 --- 
    52080 Chain | Description 
    52081 A | No description available 
    52082  
    52083 
    52084 > matchmaker #306 to #1.1 & sel
    52085 
    52086 Parameters 
    52087 --- 
    52088 Chain pairing | bb 
    52089 Alignment algorithm | Needleman-Wunsch 
    52090 Similarity matrix | BLOSUM-62 
    52091 SS fraction | 0.3 
    52092 Gap open (HH/SS/other) | 18/18/6 
    52093 Gap extend | 1 
    52094 SS matrix |  |  | H | S | O 
    52095 ---|---|---|--- 
    52096 H | 6 | -9 | -6 
    52097 S |  | 6 | -6 
    52098 O |  |  | 4 
    52099 Iteration cutoff | 2 
    52100  
    52101 Matchmaker 3j0c.pdb1, chain F (#1.1) with AF3 CA.pdb, chain A (#306), sequence
    52102 alignment score = 335.3 
    52103 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    52104 2.550) 
    52105  
    52106 
    52107 > hide sel cartoons
    52108 
    52109 > select #1.1/F
    52110 
    52111 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    52112 
    52113 > show sel cartoons
    52114 
    52115 > hide sel cartoons
    52116 
    52117 > select #1.1/E
    52118 
    52119 3304 atoms, 3400 bonds, 423 residues, 1 model selected 
    52120 
    52121 > hide sel cartoons
    52122 
    52123 > select #1.1/D
    52124 
    52125 3370 atoms, 3467 bonds, 442 residues, 1 model selected 
    52126 
    52127 > hide sel cartoons
    52128 
    52129 > color #302 dodgerblue
    52130 
    52131 > color #303 dodgerblue
    52132 
    52133 > color #304 #00b305ff
    52134 
    52135 > color #305 #00b305ff
    52136 
    52137 > color #306 #f15839ff
    52138 
    52139 > select #1.2/D
    52140 
    52141 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    52142 
    52143 > show sel cartoons
    52144 
    52145 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    52146 
    52147 Chain information for AF3 E1 1-421.pdb #307 
    52148 --- 
    52149 Chain | Description 
    52150 A | No description available 
    52151  
    52152 
    52153 > matchmaker #307 to #1.2 & sel
    52154 
    52155 Parameters 
    52156 --- 
    52157 Chain pairing | bb 
    52158 Alignment algorithm | Needleman-Wunsch 
    52159 Similarity matrix | BLOSUM-62 
    52160 SS fraction | 0.3 
    52161 Gap open (HH/SS/other) | 18/18/6 
    52162 Gap extend | 1 
    52163 SS matrix |  |  | H | S | O 
    52164 ---|---|---|--- 
    52165 H | 6 | -9 | -6 
    52166 S |  | 6 | -6 
    52167 O |  |  | 4 
    52168 Iteration cutoff | 2 
    52169  
    52170 Matchmaker 3j0c.pdb1, chain D (#1.2) with AF3 E1 1-421.pdb, chain A (#307),
    52171 sequence alignment score = 1060.7 
    52172 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    52173 3.032) 
    52174  
    52175 
    52176 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    52177 
    52178 Chain information for AF3 E1 422-461.pdb #308 
    52179 --- 
    52180 Chain | Description 
    52181 A | No description available 
    52182  
    52183 
    52184 > matchmaker #308 to #1.2 & sel
    52185 
    52186 Parameters 
    52187 --- 
    52188 Chain pairing | bb 
    52189 Alignment algorithm | Needleman-Wunsch 
    52190 Similarity matrix | BLOSUM-62 
    52191 SS fraction | 0.3 
    52192 Gap open (HH/SS/other) | 18/18/6 
    52193 Gap extend | 1 
    52194 SS matrix |  |  | H | S | O 
    52195 ---|---|---|--- 
    52196 H | 6 | -9 | -6 
    52197 S |  | 6 | -6 
    52198 O |  |  | 4 
    52199 Iteration cutoff | 2 
    52200  
    52201 Matchmaker 3j0c.pdb1, chain D (#1.2) with AF3 E1 422-461.pdb, chain A (#308),
    52202 sequence alignment score = 626.9 
    52203 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    52204 2.916) 
    52205  
    52206 
    52207 > hide sel cartoons
    52208 
    52209 [Repeated 1 time(s)]
    52210 
    52211 > select #1.2/E
    52212 
    52213 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    52214 
    52215 > show sel cartoons
    52216 
    52217 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    52218 
    52219 Chain information for AF3 E2 1-352.pdb #309 
    52220 --- 
    52221 Chain | Description 
    52222 B | No description available 
    52223  
    52224 
    52225 > matchmaker #309 to #1.2 & sel
    52226 
    52227 Parameters 
    52228 --- 
    52229 Chain pairing | bb 
    52230 Alignment algorithm | Needleman-Wunsch 
    52231 Similarity matrix | BLOSUM-62 
    52232 SS fraction | 0.3 
    52233 Gap open (HH/SS/other) | 18/18/6 
    52234 Gap extend | 1 
    52235 SS matrix |  |  | H | S | O 
    52236 ---|---|---|--- 
    52237 H | 6 | -9 | -6 
    52238 S |  | 6 | -6 
    52239 O |  |  | 4 
    52240 Iteration cutoff | 2 
    52241  
    52242 Matchmaker 3j0c.pdb1, chain E (#1.2) with AF3 E2 1-352.pdb, chain B (#309),
    52243 sequence alignment score = 594.5 
    52244 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    52245 6.147) 
    52246  
    52247 
    52248 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    52249 
    52250 Chain information for AF3 E2 353-438.pdb #310 
    52251 --- 
    52252 Chain | Description 
    52253 B | No description available 
    52254  
    52255 
    52256 > matchmaker #310 to #1.2 & sel
    52257 
    52258 Parameters 
    52259 --- 
    52260 Chain pairing | bb 
    52261 Alignment algorithm | Needleman-Wunsch 
    52262 Similarity matrix | BLOSUM-62 
    52263 SS fraction | 0.3 
    52264 Gap open (HH/SS/other) | 18/18/6 
    52265 Gap extend | 1 
    52266 SS matrix |  |  | H | S | O 
    52267 ---|---|---|--- 
    52268 H | 6 | -9 | -6 
    52269 S |  | 6 | -6 
    52270 O |  |  | 4 
    52271 Iteration cutoff | 2 
    52272  
    52273 Matchmaker 3j0c.pdb1, chain E (#1.2) with AF3 E2 353-438.pdb, chain B (#310),
    52274 sequence alignment score = 340.2 
    52275 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    52276 8.673) 
    52277  
    52278 
    52279 > hide sel cartoons
    52280 
    52281 > select #1.2/F
    52282 
    52283 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    52284 
    52285 > show sel cartoons
    52286 
    52287 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    52288 
    52289 Chain information for AF3 CA.pdb #311 
    52290 --- 
    52291 Chain | Description 
    52292 A | No description available 
    52293  
    52294 
    52295 > matchmaker #311 to #1.2 & sel
    52296 
    52297 Parameters 
    52298 --- 
    52299 Chain pairing | bb 
    52300 Alignment algorithm | Needleman-Wunsch 
    52301 Similarity matrix | BLOSUM-62 
    52302 SS fraction | 0.3 
    52303 Gap open (HH/SS/other) | 18/18/6 
    52304 Gap extend | 1 
    52305 SS matrix |  |  | H | S | O 
    52306 ---|---|---|--- 
    52307 H | 6 | -9 | -6 
    52308 S |  | 6 | -6 
    52309 O |  |  | 4 
    52310 Iteration cutoff | 2 
    52311  
    52312 Matchmaker 3j0c.pdb1, chain F (#1.2) with AF3 CA.pdb, chain A (#311), sequence
    52313 alignment score = 335.3 
    52314 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    52315 2.550) 
    52316  
    52317 
    52318 > hide sel cartoons
    52319 
    52320 > color #307 dodgerblue
    52321 
    52322 > color #308 dodgerblue
    52323 
    52324 > color #309 #00b305ff
    52325 
    52326 > color #310 #00b305ff
    52327 
    52328 > color #311 #f15839ff
    52329 
    52330 > select #1.3/D
    52331 
    52332 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    52333 
    52334 > show sel cartoons
    52335 
    52336 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    52337 
    52338 Chain information for AF3 E1 1-421.pdb #312 
    52339 --- 
    52340 Chain | Description 
    52341 A | No description available 
    52342  
    52343 
    52344 > matchmaker #312 to #1.2 & sel
    52345 
    52346 No 'to' model specified 
    52347 
    52348 > matchmaker #312 to #1.3 & sel
    52349 
    52350 Parameters 
    52351 --- 
    52352 Chain pairing | bb 
    52353 Alignment algorithm | Needleman-Wunsch 
    52354 Similarity matrix | BLOSUM-62 
    52355 SS fraction | 0.3 
    52356 Gap open (HH/SS/other) | 18/18/6 
    52357 Gap extend | 1 
    52358 SS matrix |  |  | H | S | O 
    52359 ---|---|---|--- 
    52360 H | 6 | -9 | -6 
    52361 S |  | 6 | -6 
    52362 O |  |  | 4 
    52363 Iteration cutoff | 2 
    52364  
    52365 Matchmaker 3j0c.pdb1, chain D (#1.3) with AF3 E1 1-421.pdb, chain A (#312),
    52366 sequence alignment score = 1060.7 
    52367 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    52368 3.032) 
    52369  
    52370 
    52371 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    52372 
    52373 Chain information for AF3 E1 422-461.pdb #313 
    52374 --- 
    52375 Chain | Description 
    52376 A | No description available 
    52377  
    52378 
    52379 > matchmaker #313 to #1.3 & sel
    52380 
    52381 Parameters 
    52382 --- 
    52383 Chain pairing | bb 
    52384 Alignment algorithm | Needleman-Wunsch 
    52385 Similarity matrix | BLOSUM-62 
    52386 SS fraction | 0.3 
    52387 Gap open (HH/SS/other) | 18/18/6 
    52388 Gap extend | 1 
    52389 SS matrix |  |  | H | S | O 
    52390 ---|---|---|--- 
    52391 H | 6 | -9 | -6 
    52392 S |  | 6 | -6 
    52393 O |  |  | 4 
    52394 Iteration cutoff | 2 
    52395  
    52396 Matchmaker 3j0c.pdb1, chain D (#1.3) with AF3 E1 422-461.pdb, chain A (#313),
    52397 sequence alignment score = 626.9 
    52398 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    52399 2.916) 
    52400  
    52401 
    52402 > hide sel cartoons
    52403 
    52404 > select #1.3/B
    52405 
    52406 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    52407 
    52408 > select #1.3/E
    52409 
    52410 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    52411 
    52412 > show sel cartoons
    52413 
    52414 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    52415 
    52416 Chain information for AF3 E2 1-352.pdb #314 
    52417 --- 
    52418 Chain | Description 
    52419 B | No description available 
    52420  
    52421 
    52422 > matchmaker #314 to #1.3 & sel
    52423 
    52424 Parameters 
    52425 --- 
    52426 Chain pairing | bb 
    52427 Alignment algorithm | Needleman-Wunsch 
    52428 Similarity matrix | BLOSUM-62 
    52429 SS fraction | 0.3 
    52430 Gap open (HH/SS/other) | 18/18/6 
    52431 Gap extend | 1 
    52432 SS matrix |  |  | H | S | O 
    52433 ---|---|---|--- 
    52434 H | 6 | -9 | -6 
    52435 S |  | 6 | -6 
    52436 O |  |  | 4 
    52437 Iteration cutoff | 2 
    52438  
    52439 Matchmaker 3j0c.pdb1, chain E (#1.3) with AF3 E2 1-352.pdb, chain B (#314),
    52440 sequence alignment score = 594.5 
    52441 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    52442 6.147) 
    52443  
    52444 
    52445 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    52446 
    52447 Chain information for AF3 E2 353-438.pdb #315 
    52448 --- 
    52449 Chain | Description 
    52450 B | No description available 
    52451  
    52452 
    52453 > matchmaker #315 to #1.3 & sel
    52454 
    52455 Parameters 
    52456 --- 
    52457 Chain pairing | bb 
    52458 Alignment algorithm | Needleman-Wunsch 
    52459 Similarity matrix | BLOSUM-62 
    52460 SS fraction | 0.3 
    52461 Gap open (HH/SS/other) | 18/18/6 
    52462 Gap extend | 1 
    52463 SS matrix |  |  | H | S | O 
    52464 ---|---|---|--- 
    52465 H | 6 | -9 | -6 
    52466 S |  | 6 | -6 
    52467 O |  |  | 4 
    52468 Iteration cutoff | 2 
    52469  
    52470 Matchmaker 3j0c.pdb1, chain E (#1.3) with AF3 E2 353-438.pdb, chain B (#315),
    52471 sequence alignment score = 340.2 
    52472 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    52473 8.673) 
    52474  
    52475 
    52476 > hide sel cartoons
    52477 
    52478 > select #1.3/F
    52479 
    52480 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    52481 
    52482 > show sel cartoons
    52483 
    52484 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    52485 
    52486 Chain information for AF3 CA.pdb #316 
    52487 --- 
    52488 Chain | Description 
    52489 A | No description available 
    52490  
    52491 
    52492 > matchmaker #316 to #1.3 & sel
    52493 
    52494 Parameters 
    52495 --- 
    52496 Chain pairing | bb 
    52497 Alignment algorithm | Needleman-Wunsch 
    52498 Similarity matrix | BLOSUM-62 
    52499 SS fraction | 0.3 
    52500 Gap open (HH/SS/other) | 18/18/6 
    52501 Gap extend | 1 
    52502 SS matrix |  |  | H | S | O 
    52503 ---|---|---|--- 
    52504 H | 6 | -9 | -6 
    52505 S |  | 6 | -6 
    52506 O |  |  | 4 
    52507 Iteration cutoff | 2 
    52508  
    52509 Matchmaker 3j0c.pdb1, chain F (#1.3) with AF3 CA.pdb, chain A (#316), sequence
    52510 alignment score = 335.3 
    52511 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    52512 2.550) 
    52513  
    52514 
    52515 > hide sel cartoons
    52516 
    52517 > color #312 dodgerblue
    52518 
    52519 > color #313 dodgerblue
    52520 
    52521 > color #314 #00b305ff
    52522 
    52523 > color #315 #00b305ff
    52524 
    52525 > color #316 #f15839ff
    52526 
    52527 > select #1.4/D
    52528 
    52529 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    52530 
    52531 > show sel cartoons
    52532 
    52533 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    52534 
    52535 Chain information for AF3 E1 1-421.pdb #317 
    52536 --- 
    52537 Chain | Description 
    52538 A | No description available 
    52539  
    52540 
    52541 > matchmaker #317 to #1.4 & sel
    52542 
    52543 Parameters 
    52544 --- 
    52545 Chain pairing | bb 
    52546 Alignment algorithm | Needleman-Wunsch 
    52547 Similarity matrix | BLOSUM-62 
    52548 SS fraction | 0.3 
    52549 Gap open (HH/SS/other) | 18/18/6 
    52550 Gap extend | 1 
    52551 SS matrix |  |  | H | S | O 
    52552 ---|---|---|--- 
    52553 H | 6 | -9 | -6 
    52554 S |  | 6 | -6 
    52555 O |  |  | 4 
    52556 Iteration cutoff | 2 
    52557  
    52558 Matchmaker 3j0c.pdb1, chain D (#1.4) with AF3 E1 1-421.pdb, chain A (#317),
    52559 sequence alignment score = 1060.7 
    52560 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    52561 3.032) 
    52562  
    52563 
    52564 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    52565 
    52566 Chain information for AF3 E1 422-461.pdb #318 
    52567 --- 
    52568 Chain | Description 
    52569 A | No description available 
    52570  
    52571 
    52572 > matchmaker #318 to #1.4 & sel
    52573 
    52574 Parameters 
    52575 --- 
    52576 Chain pairing | bb 
    52577 Alignment algorithm | Needleman-Wunsch 
    52578 Similarity matrix | BLOSUM-62 
    52579 SS fraction | 0.3 
    52580 Gap open (HH/SS/other) | 18/18/6 
    52581 Gap extend | 1 
    52582 SS matrix |  |  | H | S | O 
    52583 ---|---|---|--- 
    52584 H | 6 | -9 | -6 
    52585 S |  | 6 | -6 
    52586 O |  |  | 4 
    52587 Iteration cutoff | 2 
    52588  
    52589 Matchmaker 3j0c.pdb1, chain D (#1.4) with AF3 E1 422-461.pdb, chain A (#318),
    52590 sequence alignment score = 626.9 
    52591 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    52592 2.916) 
    52593  
    52594 
    52595 > hide sel cartoons
    52596 
    52597 > select #1.4/E
    52598 
    52599 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    52600 
    52601 > show sel cartoons
    52602 
    52603 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    52604 
    52605 Chain information for AF3 E2 1-352.pdb #319 
    52606 --- 
    52607 Chain | Description 
    52608 B | No description available 
    52609  
    52610 
    52611 > matchmaker #319 to #1.4 & sel
    52612 
    52613 Parameters 
    52614 --- 
    52615 Chain pairing | bb 
    52616 Alignment algorithm | Needleman-Wunsch 
    52617 Similarity matrix | BLOSUM-62 
    52618 SS fraction | 0.3 
    52619 Gap open (HH/SS/other) | 18/18/6 
    52620 Gap extend | 1 
    52621 SS matrix |  |  | H | S | O 
    52622 ---|---|---|--- 
    52623 H | 6 | -9 | -6 
    52624 S |  | 6 | -6 
    52625 O |  |  | 4 
    52626 Iteration cutoff | 2 
    52627  
    52628 Matchmaker 3j0c.pdb1, chain E (#1.4) with AF3 E2 1-352.pdb, chain B (#319),
    52629 sequence alignment score = 594.5 
    52630 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    52631 6.147) 
    52632  
    52633 
    52634 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    52635 
    52636 Chain information for AF3 E2 353-438.pdb #320 
    52637 --- 
    52638 Chain | Description 
    52639 B | No description available 
    52640  
    52641 
    52642 > matchmaker #320 to #1.4 & sel
    52643 
    52644 Parameters 
    52645 --- 
    52646 Chain pairing | bb 
    52647 Alignment algorithm | Needleman-Wunsch 
    52648 Similarity matrix | BLOSUM-62 
    52649 SS fraction | 0.3 
    52650 Gap open (HH/SS/other) | 18/18/6 
    52651 Gap extend | 1 
    52652 SS matrix |  |  | H | S | O 
    52653 ---|---|---|--- 
    52654 H | 6 | -9 | -6 
    52655 S |  | 6 | -6 
    52656 O |  |  | 4 
    52657 Iteration cutoff | 2 
    52658  
    52659 Matchmaker 3j0c.pdb1, chain E (#1.4) with AF3 E2 353-438.pdb, chain B (#320),
    52660 sequence alignment score = 340.2 
    52661 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    52662 8.673) 
    52663  
    52664 
    52665 > hide sel cartoons
    52666 
    52667 > select #1.4/F
    52668 
    52669 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    52670 
    52671 > show sel cartoons
    52672 
    52673 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    52674 
    52675 Chain information for AF3 CA.pdb #321 
    52676 --- 
    52677 Chain | Description 
    52678 A | No description available 
    52679  
    52680 
    52681 > matchmaker #321 to #1.4 & sel
    52682 
    52683 Parameters 
    52684 --- 
    52685 Chain pairing | bb 
    52686 Alignment algorithm | Needleman-Wunsch 
    52687 Similarity matrix | BLOSUM-62 
    52688 SS fraction | 0.3 
    52689 Gap open (HH/SS/other) | 18/18/6 
    52690 Gap extend | 1 
    52691 SS matrix |  |  | H | S | O 
    52692 ---|---|---|--- 
    52693 H | 6 | -9 | -6 
    52694 S |  | 6 | -6 
    52695 O |  |  | 4 
    52696 Iteration cutoff | 2 
    52697  
    52698 Matchmaker 3j0c.pdb1, chain F (#1.4) with AF3 CA.pdb, chain A (#321), sequence
    52699 alignment score = 335.3 
    52700 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    52701 2.550) 
    52702  
    52703 
    52704 > hide sel cartoons
    52705 
    52706 > color #317 dodgerblue
    52707 
    52708 > color #318 dodgerblue
    52709 
    52710 > color #319 #00b305ff
    52711 
    52712 > color #320 #00b305ff
    52713 
    52714 > color #321 #f15839ff
    52715 
    52716 > select #1.5/D
    52717 
    52718 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    52719 
    52720 > show sel cartoons
    52721 
    52722 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    52723 
    52724 Chain information for AF3 E1 1-421.pdb #322 
    52725 --- 
    52726 Chain | Description 
    52727 A | No description available 
    52728  
    52729 
    52730 > matchmaker #322 to #1.5 & sel
    52731 
    52732 Parameters 
    52733 --- 
    52734 Chain pairing | bb 
    52735 Alignment algorithm | Needleman-Wunsch 
    52736 Similarity matrix | BLOSUM-62 
    52737 SS fraction | 0.3 
    52738 Gap open (HH/SS/other) | 18/18/6 
    52739 Gap extend | 1 
    52740 SS matrix |  |  | H | S | O 
    52741 ---|---|---|--- 
    52742 H | 6 | -9 | -6 
    52743 S |  | 6 | -6 
    52744 O |  |  | 4 
    52745 Iteration cutoff | 2 
    52746  
    52747 Matchmaker 3j0c.pdb1, chain D (#1.5) with AF3 E1 1-421.pdb, chain A (#322),
    52748 sequence alignment score = 1060.7 
    52749 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    52750 3.032) 
    52751  
    52752 
    52753 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    52754 
    52755 Chain information for AF3 E1 422-461.pdb #323 
    52756 --- 
    52757 Chain | Description 
    52758 A | No description available 
    52759  
    52760 
    52761 > matchmaker #323 to #1.5 & sel
    52762 
    52763 Parameters 
    52764 --- 
    52765 Chain pairing | bb 
    52766 Alignment algorithm | Needleman-Wunsch 
    52767 Similarity matrix | BLOSUM-62 
    52768 SS fraction | 0.3 
    52769 Gap open (HH/SS/other) | 18/18/6 
    52770 Gap extend | 1 
    52771 SS matrix |  |  | H | S | O 
    52772 ---|---|---|--- 
    52773 H | 6 | -9 | -6 
    52774 S |  | 6 | -6 
    52775 O |  |  | 4 
    52776 Iteration cutoff | 2 
    52777  
    52778 Matchmaker 3j0c.pdb1, chain D (#1.5) with AF3 E1 422-461.pdb, chain A (#323),
    52779 sequence alignment score = 626.9 
    52780 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    52781 2.915) 
    52782  
    52783 
    52784 > hide sel cartoons
    52785 
    52786 > select #1.5/E
    52787 
    52788 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    52789 
    52790 > show sel cartoons
    52791 
    52792 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    52793 
    52794 Chain information for AF3 E2 1-352.pdb #324 
    52795 --- 
    52796 Chain | Description 
    52797 B | No description available 
    52798  
    52799 
    52800 > matchmaker #324 to #1.5 & sel
    52801 
    52802 Parameters 
    52803 --- 
    52804 Chain pairing | bb 
    52805 Alignment algorithm | Needleman-Wunsch 
    52806 Similarity matrix | BLOSUM-62 
    52807 SS fraction | 0.3 
    52808 Gap open (HH/SS/other) | 18/18/6 
    52809 Gap extend | 1 
    52810 SS matrix |  |  | H | S | O 
    52811 ---|---|---|--- 
    52812 H | 6 | -9 | -6 
    52813 S |  | 6 | -6 
    52814 O |  |  | 4 
    52815 Iteration cutoff | 2 
    52816  
    52817 Matchmaker 3j0c.pdb1, chain E (#1.5) with AF3 E2 1-352.pdb, chain B (#324),
    52818 sequence alignment score = 594.5 
    52819 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    52820 6.147) 
    52821  
    52822 
    52823 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    52824 
    52825 Chain information for AF3 E2 353-438.pdb #325 
    52826 --- 
    52827 Chain | Description 
    52828 B | No description available 
    52829  
    52830 
    52831 > matchmaker #325 to #1.5 & sel
    52832 
    52833 Parameters 
    52834 --- 
    52835 Chain pairing | bb 
    52836 Alignment algorithm | Needleman-Wunsch 
    52837 Similarity matrix | BLOSUM-62 
    52838 SS fraction | 0.3 
    52839 Gap open (HH/SS/other) | 18/18/6 
    52840 Gap extend | 1 
    52841 SS matrix |  |  | H | S | O 
    52842 ---|---|---|--- 
    52843 H | 6 | -9 | -6 
    52844 S |  | 6 | -6 
    52845 O |  |  | 4 
    52846 Iteration cutoff | 2 
    52847  
    52848 Matchmaker 3j0c.pdb1, chain E (#1.5) with AF3 E2 353-438.pdb, chain B (#325),
    52849 sequence alignment score = 340.2 
    52850 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    52851 8.673) 
    52852  
    52853 
    52854 > hide sel cartoons
    52855 
    52856 > select #1.5/F
    52857 
    52858 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    52859 
    52860 > show sel cartoons
    52861 
    52862 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    52863 
    52864 Chain information for AF3 CA.pdb #326 
    52865 --- 
    52866 Chain | Description 
    52867 A | No description available 
    52868  
    52869 
    52870 > matchmaker #326 to #1.5 & sel
    52871 
    52872 Parameters 
    52873 --- 
    52874 Chain pairing | bb 
    52875 Alignment algorithm | Needleman-Wunsch 
    52876 Similarity matrix | BLOSUM-62 
    52877 SS fraction | 0.3 
    52878 Gap open (HH/SS/other) | 18/18/6 
    52879 Gap extend | 1 
    52880 SS matrix |  |  | H | S | O 
    52881 ---|---|---|--- 
    52882 H | 6 | -9 | -6 
    52883 S |  | 6 | -6 
    52884 O |  |  | 4 
    52885 Iteration cutoff | 2 
    52886  
    52887 Matchmaker 3j0c.pdb1, chain F (#1.5) with AF3 CA.pdb, chain A (#326), sequence
    52888 alignment score = 335.3 
    52889 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    52890 2.550) 
    52891  
    52892 
    52893 > hide sel cartoons
    52894 
    52895 > color #322 dodgerblue
    52896 
    52897 > color #323 dodgerblue
    52898 
    52899 > color #324 #00b305ff
    52900 
    52901 > color #325 #00b305ff
    52902 
    52903 > color #326 #f15839ff
    52904 
    52905 > select #1.6/D
    52906 
    52907 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    52908 
    52909 > show sel cartoons
    52910 
    52911 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    52912 
    52913 Chain information for AF3 E1 1-421.pdb #327 
    52914 --- 
    52915 Chain | Description 
    52916 A | No description available 
    52917  
    52918 
    52919 > matchmaker #327 to #1.6 & sel
    52920 
    52921 Parameters 
    52922 --- 
    52923 Chain pairing | bb 
    52924 Alignment algorithm | Needleman-Wunsch 
    52925 Similarity matrix | BLOSUM-62 
    52926 SS fraction | 0.3 
    52927 Gap open (HH/SS/other) | 18/18/6 
    52928 Gap extend | 1 
    52929 SS matrix |  |  | H | S | O 
    52930 ---|---|---|--- 
    52931 H | 6 | -9 | -6 
    52932 S |  | 6 | -6 
    52933 O |  |  | 4 
    52934 Iteration cutoff | 2 
    52935  
    52936 Matchmaker 3j0c.pdb1, chain D (#1.6) with AF3 E1 1-421.pdb, chain A (#327),
    52937 sequence alignment score = 1060.7 
    52938 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    52939 3.032) 
    52940  
    52941 
    52942 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    52943 
    52944 Chain information for AF3 E1 422-461.pdb #328 
    52945 --- 
    52946 Chain | Description 
    52947 A | No description available 
    52948  
    52949 
    52950 > matchmaker #328 to #1.6 & sel
    52951 
    52952 Parameters 
    52953 --- 
    52954 Chain pairing | bb 
    52955 Alignment algorithm | Needleman-Wunsch 
    52956 Similarity matrix | BLOSUM-62 
    52957 SS fraction | 0.3 
    52958 Gap open (HH/SS/other) | 18/18/6 
    52959 Gap extend | 1 
    52960 SS matrix |  |  | H | S | O 
    52961 ---|---|---|--- 
    52962 H | 6 | -9 | -6 
    52963 S |  | 6 | -6 
    52964 O |  |  | 4 
    52965 Iteration cutoff | 2 
    52966  
    52967 Matchmaker 3j0c.pdb1, chain D (#1.6) with AF3 E1 422-461.pdb, chain A (#328),
    52968 sequence alignment score = 626.9 
    52969 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    52970 2.916) 
    52971  
    52972 
    52973 > hide sel cartoons
    52974 
    52975 > select #1.6/E
    52976 
    52977 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    52978 
    52979 > show sel cartoons
    52980 
    52981 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    52982 
    52983 Chain information for AF3 E2 1-352.pdb #329 
    52984 --- 
    52985 Chain | Description 
    52986 B | No description available 
    52987  
    52988 
    52989 > matchmaker #329 to #1.6 & sel
    52990 
    52991 Parameters 
    52992 --- 
    52993 Chain pairing | bb 
    52994 Alignment algorithm | Needleman-Wunsch 
    52995 Similarity matrix | BLOSUM-62 
    52996 SS fraction | 0.3 
    52997 Gap open (HH/SS/other) | 18/18/6 
    52998 Gap extend | 1 
    52999 SS matrix |  |  | H | S | O 
    53000 ---|---|---|--- 
    53001 H | 6 | -9 | -6 
    53002 S |  | 6 | -6 
    53003 O |  |  | 4 
    53004 Iteration cutoff | 2 
    53005  
    53006 Matchmaker 3j0c.pdb1, chain E (#1.6) with AF3 E2 1-352.pdb, chain B (#329),
    53007 sequence alignment score = 594.5 
    53008 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    53009 6.147) 
    53010  
    53011 
    53012 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    53013 
    53014 Chain information for AF3 E2 353-438.pdb #330 
    53015 --- 
    53016 Chain | Description 
    53017 B | No description available 
    53018  
    53019 
    53020 > matchmaker #330 to #1.6 & sel
    53021 
    53022 Parameters 
    53023 --- 
    53024 Chain pairing | bb 
    53025 Alignment algorithm | Needleman-Wunsch 
    53026 Similarity matrix | BLOSUM-62 
    53027 SS fraction | 0.3 
    53028 Gap open (HH/SS/other) | 18/18/6 
    53029 Gap extend | 1 
    53030 SS matrix |  |  | H | S | O 
    53031 ---|---|---|--- 
    53032 H | 6 | -9 | -6 
    53033 S |  | 6 | -6 
    53034 O |  |  | 4 
    53035 Iteration cutoff | 2 
    53036  
    53037 Matchmaker 3j0c.pdb1, chain E (#1.6) with AF3 E2 353-438.pdb, chain B (#330),
    53038 sequence alignment score = 340.2 
    53039 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    53040 8.673) 
    53041  
    53042 
    53043 > hide sel cartoons
    53044 
    53045 > select #1.6/F
    53046 
    53047 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    53048 
    53049 > show sel cartoons
    53050 
    53051 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    53052 
    53053 Chain information for AF3 CA.pdb #331 
    53054 --- 
    53055 Chain | Description 
    53056 A | No description available 
    53057  
    53058 
    53059 > matchmaker #331 to #1.6 & sel
    53060 
    53061 Parameters 
    53062 --- 
    53063 Chain pairing | bb 
    53064 Alignment algorithm | Needleman-Wunsch 
    53065 Similarity matrix | BLOSUM-62 
    53066 SS fraction | 0.3 
    53067 Gap open (HH/SS/other) | 18/18/6 
    53068 Gap extend | 1 
    53069 SS matrix |  |  | H | S | O 
    53070 ---|---|---|--- 
    53071 H | 6 | -9 | -6 
    53072 S |  | 6 | -6 
    53073 O |  |  | 4 
    53074 Iteration cutoff | 2 
    53075  
    53076 Matchmaker 3j0c.pdb1, chain F (#1.6) with AF3 CA.pdb, chain A (#331), sequence
    53077 alignment score = 335.3 
    53078 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    53079 2.550) 
    53080  
    53081 
    53082 > hide sel cartoons
    53083 
    53084 > color #327 dodgerblue
    53085 
    53086 > color #328 dodgerblue
    53087 
    53088 > color #329 #00b305ff
    53089 
    53090 > color #330 #00b305ff
    53091 
    53092 > color #331 #f15839ff
    53093 
    53094 > select #1.7/D
    53095 
    53096 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    53097 
    53098 > show sel cartoons
    53099 
    53100 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    53101 
    53102 Chain information for AF3 E1 1-421.pdb #332 
    53103 --- 
    53104 Chain | Description 
    53105 A | No description available 
    53106  
    53107 
    53108 > matchmaker #332 to #1.7 & sel
    53109 
    53110 Parameters 
    53111 --- 
    53112 Chain pairing | bb 
    53113 Alignment algorithm | Needleman-Wunsch 
    53114 Similarity matrix | BLOSUM-62 
    53115 SS fraction | 0.3 
    53116 Gap open (HH/SS/other) | 18/18/6 
    53117 Gap extend | 1 
    53118 SS matrix |  |  | H | S | O 
    53119 ---|---|---|--- 
    53120 H | 6 | -9 | -6 
    53121 S |  | 6 | -6 
    53122 O |  |  | 4 
    53123 Iteration cutoff | 2 
    53124  
    53125 Matchmaker 3j0c.pdb1, chain D (#1.7) with AF3 E1 1-421.pdb, chain A (#332),
    53126 sequence alignment score = 1060.7 
    53127 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    53128 3.032) 
    53129  
    53130 
    53131 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    53132 
    53133 Chain information for AF3 E1 422-461.pdb #333 
    53134 --- 
    53135 Chain | Description 
    53136 A | No description available 
    53137  
    53138 
    53139 > matchmaker #333 to #1.7 & sel
    53140 
    53141 Parameters 
    53142 --- 
    53143 Chain pairing | bb 
    53144 Alignment algorithm | Needleman-Wunsch 
    53145 Similarity matrix | BLOSUM-62 
    53146 SS fraction | 0.3 
    53147 Gap open (HH/SS/other) | 18/18/6 
    53148 Gap extend | 1 
    53149 SS matrix |  |  | H | S | O 
    53150 ---|---|---|--- 
    53151 H | 6 | -9 | -6 
    53152 S |  | 6 | -6 
    53153 O |  |  | 4 
    53154 Iteration cutoff | 2 
    53155  
    53156 Matchmaker 3j0c.pdb1, chain D (#1.7) with AF3 E1 422-461.pdb, chain A (#333),
    53157 sequence alignment score = 626.9 
    53158 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    53159 2.916) 
    53160  
    53161 
    53162 > hide sel cartoons
    53163 
    53164 > select #1.7/E
    53165 
    53166 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    53167 
    53168 > show sel cartoons
    53169 
    53170 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    53171 
    53172 Chain information for AF3 E2 1-352.pdb #334 
    53173 --- 
    53174 Chain | Description 
    53175 B | No description available 
    53176  
    53177 
    53178 > matchmaker #334 to #1.7 & sel
    53179 
    53180 Parameters 
    53181 --- 
    53182 Chain pairing | bb 
    53183 Alignment algorithm | Needleman-Wunsch 
    53184 Similarity matrix | BLOSUM-62 
    53185 SS fraction | 0.3 
    53186 Gap open (HH/SS/other) | 18/18/6 
    53187 Gap extend | 1 
    53188 SS matrix |  |  | H | S | O 
    53189 ---|---|---|--- 
    53190 H | 6 | -9 | -6 
    53191 S |  | 6 | -6 
    53192 O |  |  | 4 
    53193 Iteration cutoff | 2 
    53194  
    53195 Matchmaker 3j0c.pdb1, chain E (#1.7) with AF3 E2 1-352.pdb, chain B (#334),
    53196 sequence alignment score = 594.5 
    53197 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    53198 6.147) 
    53199  
    53200 
    53201 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    53202 
    53203 Chain information for AF3 E2 353-438.pdb #335 
    53204 --- 
    53205 Chain | Description 
    53206 B | No description available 
    53207  
    53208 
    53209 > matchmaker #335 to #1.7 & sel
    53210 
    53211 Parameters 
    53212 --- 
    53213 Chain pairing | bb 
    53214 Alignment algorithm | Needleman-Wunsch 
    53215 Similarity matrix | BLOSUM-62 
    53216 SS fraction | 0.3 
    53217 Gap open (HH/SS/other) | 18/18/6 
    53218 Gap extend | 1 
    53219 SS matrix |  |  | H | S | O 
    53220 ---|---|---|--- 
    53221 H | 6 | -9 | -6 
    53222 S |  | 6 | -6 
    53223 O |  |  | 4 
    53224 Iteration cutoff | 2 
    53225  
    53226 Matchmaker 3j0c.pdb1, chain E (#1.7) with AF3 E2 353-438.pdb, chain B (#335),
    53227 sequence alignment score = 340.2 
    53228 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    53229 8.673) 
    53230  
    53231 
    53232 > hide sel cartoons
    53233 
    53234 > select #1.7/F
    53235 
    53236 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    53237 
    53238 > show sel cartoons
    53239 
    53240 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    53241 
    53242 Chain information for AF3 CA.pdb #336 
    53243 --- 
    53244 Chain | Description 
    53245 A | No description available 
    53246  
    53247 
    53248 > matchmaker #336 to #1.7 & sel
    53249 
    53250 Parameters 
    53251 --- 
    53252 Chain pairing | bb 
    53253 Alignment algorithm | Needleman-Wunsch 
    53254 Similarity matrix | BLOSUM-62 
    53255 SS fraction | 0.3 
    53256 Gap open (HH/SS/other) | 18/18/6 
    53257 Gap extend | 1 
    53258 SS matrix |  |  | H | S | O 
    53259 ---|---|---|--- 
    53260 H | 6 | -9 | -6 
    53261 S |  | 6 | -6 
    53262 O |  |  | 4 
    53263 Iteration cutoff | 2 
    53264  
    53265 Matchmaker 3j0c.pdb1, chain F (#1.7) with AF3 CA.pdb, chain A (#336), sequence
    53266 alignment score = 335.3 
    53267 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    53268 2.550) 
    53269  
    53270 
    53271 > hide sel cartoons
    53272 
    53273 > color #332 dodgerblue
    53274 
    53275 > color #333 dodgerblue
    53276 
    53277 > color #334 #00b305ff
    53278 
    53279 > color #335 #00b305ff
    53280 
    53281 > color #336 #f15839ff
    53282 
    53283 > select #1.8/D
    53284 
    53285 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    53286 
    53287 > show sel cartoons
    53288 
    53289 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    53290 
    53291 Chain information for AF3 E1 1-421.pdb #337 
    53292 --- 
    53293 Chain | Description 
    53294 A | No description available 
    53295  
    53296 
    53297 > matchmaker #337 to #1.8 & sel
    53298 
    53299 Parameters 
    53300 --- 
    53301 Chain pairing | bb 
    53302 Alignment algorithm | Needleman-Wunsch 
    53303 Similarity matrix | BLOSUM-62 
    53304 SS fraction | 0.3 
    53305 Gap open (HH/SS/other) | 18/18/6 
    53306 Gap extend | 1 
    53307 SS matrix |  |  | H | S | O 
    53308 ---|---|---|--- 
    53309 H | 6 | -9 | -6 
    53310 S |  | 6 | -6 
    53311 O |  |  | 4 
    53312 Iteration cutoff | 2 
    53313  
    53314 Matchmaker 3j0c.pdb1, chain D (#1.8) with AF3 E1 1-421.pdb, chain A (#337),
    53315 sequence alignment score = 1060.7 
    53316 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    53317 3.032) 
    53318  
    53319 
    53320 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    53321 
    53322 Chain information for AF3 E1 422-461.pdb #338 
    53323 --- 
    53324 Chain | Description 
    53325 A | No description available 
    53326  
    53327 
    53328 > matchmaker #338 to #1.8 & sel
    53329 
    53330 Parameters 
    53331 --- 
    53332 Chain pairing | bb 
    53333 Alignment algorithm | Needleman-Wunsch 
    53334 Similarity matrix | BLOSUM-62 
    53335 SS fraction | 0.3 
    53336 Gap open (HH/SS/other) | 18/18/6 
    53337 Gap extend | 1 
    53338 SS matrix |  |  | H | S | O 
    53339 ---|---|---|--- 
    53340 H | 6 | -9 | -6 
    53341 S |  | 6 | -6 
    53342 O |  |  | 4 
    53343 Iteration cutoff | 2 
    53344  
    53345 Matchmaker 3j0c.pdb1, chain D (#1.8) with AF3 E1 422-461.pdb, chain A (#338),
    53346 sequence alignment score = 626.9 
    53347 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    53348 2.916) 
    53349  
    53350 
    53351 > hide sel cartoons
    53352 
    53353 > select #1.8/E
    53354 
    53355 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    53356 
    53357 > show sel cartoons
    53358 
    53359 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    53360 
    53361 Chain information for AF3 E2 1-352.pdb #339 
    53362 --- 
    53363 Chain | Description 
    53364 B | No description available 
    53365  
    53366 
    53367 > matchmaker #339 to #1.8 & sel
    53368 
    53369 Parameters 
    53370 --- 
    53371 Chain pairing | bb 
    53372 Alignment algorithm | Needleman-Wunsch 
    53373 Similarity matrix | BLOSUM-62 
    53374 SS fraction | 0.3 
    53375 Gap open (HH/SS/other) | 18/18/6 
    53376 Gap extend | 1 
    53377 SS matrix |  |  | H | S | O 
    53378 ---|---|---|--- 
    53379 H | 6 | -9 | -6 
    53380 S |  | 6 | -6 
    53381 O |  |  | 4 
    53382 Iteration cutoff | 2 
    53383  
    53384 Matchmaker 3j0c.pdb1, chain E (#1.8) with AF3 E2 1-352.pdb, chain B (#339),
    53385 sequence alignment score = 594.5 
    53386 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    53387 6.147) 
    53388  
    53389 
    53390 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    53391 
    53392 Chain information for AF3 E2 353-438.pdb #340 
    53393 --- 
    53394 Chain | Description 
    53395 B | No description available 
    53396  
    53397 
    53398 > matchmaker #340 to #1.8 & sel
    53399 
    53400 Parameters 
    53401 --- 
    53402 Chain pairing | bb 
    53403 Alignment algorithm | Needleman-Wunsch 
    53404 Similarity matrix | BLOSUM-62 
    53405 SS fraction | 0.3 
    53406 Gap open (HH/SS/other) | 18/18/6 
    53407 Gap extend | 1 
    53408 SS matrix |  |  | H | S | O 
    53409 ---|---|---|--- 
    53410 H | 6 | -9 | -6 
    53411 S |  | 6 | -6 
    53412 O |  |  | 4 
    53413 Iteration cutoff | 2 
    53414  
    53415 Matchmaker 3j0c.pdb1, chain E (#1.8) with AF3 E2 353-438.pdb, chain B (#340),
    53416 sequence alignment score = 340.2 
    53417 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    53418 8.673) 
    53419  
    53420 
    53421 > hide sel cartoons
    53422 
    53423 > select #1.8/F
    53424 
    53425 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    53426 
    53427 > show sel cartoons
    53428 
    53429 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    53430 
    53431 Chain information for AF3 CA.pdb #341 
    53432 --- 
    53433 Chain | Description 
    53434 A | No description available 
    53435  
    53436 
    53437 > matchmaker #341 to #1.8 & sel
    53438 
    53439 Parameters 
    53440 --- 
    53441 Chain pairing | bb 
    53442 Alignment algorithm | Needleman-Wunsch 
    53443 Similarity matrix | BLOSUM-62 
    53444 SS fraction | 0.3 
    53445 Gap open (HH/SS/other) | 18/18/6 
    53446 Gap extend | 1 
    53447 SS matrix |  |  | H | S | O 
    53448 ---|---|---|--- 
    53449 H | 6 | -9 | -6 
    53450 S |  | 6 | -6 
    53451 O |  |  | 4 
    53452 Iteration cutoff | 2 
    53453  
    53454 Matchmaker 3j0c.pdb1, chain F (#1.8) with AF3 CA.pdb, chain A (#341), sequence
    53455 alignment score = 335.3 
    53456 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    53457 2.550) 
    53458  
    53459 
    53460 > hide sel cartoons
    53461 
    53462 > color #337 dodgerblue
    53463 
    53464 > color #338 dodgerblue
    53465 
    53466 > color #339 #00b305ff
    53467 
    53468 > color #340 #00b305ff
    53469 
    53470 > color #341 #f15839ff
    53471 
    53472 > select #1.9/D
    53473 
    53474 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    53475 
    53476 > show sel cartoons
    53477 
    53478 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    53479 
    53480 Chain information for AF3 E1 1-421.pdb #342 
    53481 --- 
    53482 Chain | Description 
    53483 A | No description available 
    53484  
    53485 
    53486 > matchmaker #342 to #1.9 & sel
    53487 
    53488 Parameters 
    53489 --- 
    53490 Chain pairing | bb 
    53491 Alignment algorithm | Needleman-Wunsch 
    53492 Similarity matrix | BLOSUM-62 
    53493 SS fraction | 0.3 
    53494 Gap open (HH/SS/other) | 18/18/6 
    53495 Gap extend | 1 
    53496 SS matrix |  |  | H | S | O 
    53497 ---|---|---|--- 
    53498 H | 6 | -9 | -6 
    53499 S |  | 6 | -6 
    53500 O |  |  | 4 
    53501 Iteration cutoff | 2 
    53502  
    53503 Matchmaker 3j0c.pdb1, chain D (#1.9) with AF3 E1 1-421.pdb, chain A (#342),
    53504 sequence alignment score = 1060.7 
    53505 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    53506 3.032) 
    53507  
    53508 
    53509 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    53510 
    53511 Chain information for AF3 E1 422-461.pdb #343 
    53512 --- 
    53513 Chain | Description 
    53514 A | No description available 
    53515  
    53516 
    53517 > matchmaker #343 to #1.9 & sel
    53518 
    53519 Parameters 
    53520 --- 
    53521 Chain pairing | bb 
    53522 Alignment algorithm | Needleman-Wunsch 
    53523 Similarity matrix | BLOSUM-62 
    53524 SS fraction | 0.3 
    53525 Gap open (HH/SS/other) | 18/18/6 
    53526 Gap extend | 1 
    53527 SS matrix |  |  | H | S | O 
    53528 ---|---|---|--- 
    53529 H | 6 | -9 | -6 
    53530 S |  | 6 | -6 
    53531 O |  |  | 4 
    53532 Iteration cutoff | 2 
    53533  
    53534 Matchmaker 3j0c.pdb1, chain D (#1.9) with AF3 E1 422-461.pdb, chain A (#343),
    53535 sequence alignment score = 626.9 
    53536 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    53537 2.916) 
    53538  
    53539 
    53540 > hide sel cartoons
    53541 
    53542 > select #1.9/E
    53543 
    53544 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    53545 
    53546 > show sel cartoons
    53547 
    53548 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    53549 
    53550 Chain information for AF3 E2 1-352.pdb #344 
    53551 --- 
    53552 Chain | Description 
    53553 B | No description available 
    53554  
    53555 
    53556 > matchmaker #344 to #1.9 & sel
    53557 
    53558 Parameters 
    53559 --- 
    53560 Chain pairing | bb 
    53561 Alignment algorithm | Needleman-Wunsch 
    53562 Similarity matrix | BLOSUM-62 
    53563 SS fraction | 0.3 
    53564 Gap open (HH/SS/other) | 18/18/6 
    53565 Gap extend | 1 
    53566 SS matrix |  |  | H | S | O 
    53567 ---|---|---|--- 
    53568 H | 6 | -9 | -6 
    53569 S |  | 6 | -6 
    53570 O |  |  | 4 
    53571 Iteration cutoff | 2 
    53572  
    53573 Matchmaker 3j0c.pdb1, chain E (#1.9) with AF3 E2 1-352.pdb, chain B (#344),
    53574 sequence alignment score = 594.5 
    53575 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    53576 6.147) 
    53577  
    53578 
    53579 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    53580 
    53581 Chain information for AF3 E2 353-438.pdb #345 
    53582 --- 
    53583 Chain | Description 
    53584 B | No description available 
    53585  
    53586 
    53587 > matchmaker #345 to #1.9 & sel
    53588 
    53589 Parameters 
    53590 --- 
    53591 Chain pairing | bb 
    53592 Alignment algorithm | Needleman-Wunsch 
    53593 Similarity matrix | BLOSUM-62 
    53594 SS fraction | 0.3 
    53595 Gap open (HH/SS/other) | 18/18/6 
    53596 Gap extend | 1 
    53597 SS matrix |  |  | H | S | O 
    53598 ---|---|---|--- 
    53599 H | 6 | -9 | -6 
    53600 S |  | 6 | -6 
    53601 O |  |  | 4 
    53602 Iteration cutoff | 2 
    53603  
    53604 Matchmaker 3j0c.pdb1, chain E (#1.9) with AF3 E2 353-438.pdb, chain B (#345),
    53605 sequence alignment score = 340.2 
    53606 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    53607 8.673) 
    53608  
    53609 
    53610 > hide sel cartoons
    53611 
    53612 > select #1.9/F
    53613 
    53614 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    53615 
    53616 > show sel cartoons
    53617 
    53618 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    53619 
    53620 Chain information for AF3 CA.pdb #346 
    53621 --- 
    53622 Chain | Description 
    53623 A | No description available 
    53624  
    53625 
    53626 > matchmaker #346 to #1.9 & sel
    53627 
    53628 Parameters 
    53629 --- 
    53630 Chain pairing | bb 
    53631 Alignment algorithm | Needleman-Wunsch 
    53632 Similarity matrix | BLOSUM-62 
    53633 SS fraction | 0.3 
    53634 Gap open (HH/SS/other) | 18/18/6 
    53635 Gap extend | 1 
    53636 SS matrix |  |  | H | S | O 
    53637 ---|---|---|--- 
    53638 H | 6 | -9 | -6 
    53639 S |  | 6 | -6 
    53640 O |  |  | 4 
    53641 Iteration cutoff | 2 
    53642  
    53643 Matchmaker 3j0c.pdb1, chain F (#1.9) with AF3 CA.pdb, chain A (#346), sequence
    53644 alignment score = 335.3 
    53645 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    53646 2.550) 
    53647  
    53648 
    53649 > hide sel cartoons
    53650 
    53651 > color #342 dodgerblue
    53652 
    53653 > color #343 dodgerblue
    53654 
    53655 > color #344 #00b305ff
    53656 
    53657 > color #345 #00b305ff
    53658 
    53659 > color #346 #f15839ff
    53660 
    53661 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    53662 
    53663 > hide #302-346 models
    53664 
    53665 > select #1.10/D
    53666 
    53667 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    53668 
    53669 > show sel cartoons
    53670 
    53671 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    53672 
    53673 Chain information for AF3 E1 1-421.pdb #347 
    53674 --- 
    53675 Chain | Description 
    53676 A | No description available 
    53677  
    53678 
    53679 > matchmaker #347 to #1.10 & sel
    53680 
    53681 Parameters 
    53682 --- 
    53683 Chain pairing | bb 
    53684 Alignment algorithm | Needleman-Wunsch 
    53685 Similarity matrix | BLOSUM-62 
    53686 SS fraction | 0.3 
    53687 Gap open (HH/SS/other) | 18/18/6 
    53688 Gap extend | 1 
    53689 SS matrix |  |  | H | S | O 
    53690 ---|---|---|--- 
    53691 H | 6 | -9 | -6 
    53692 S |  | 6 | -6 
    53693 O |  |  | 4 
    53694 Iteration cutoff | 2 
    53695  
    53696 Matchmaker 3j0c.pdb1, chain D (#1.10) with AF3 E1 1-421.pdb, chain A (#347),
    53697 sequence alignment score = 1060.7 
    53698 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    53699 3.032) 
    53700  
    53701 
    53702 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    53703 
    53704 Chain information for AF3 E1 422-461.pdb #348 
    53705 --- 
    53706 Chain | Description 
    53707 A | No description available 
    53708  
    53709 
    53710 > matchmaker #348 to #1.10 & sel
    53711 
    53712 Parameters 
    53713 --- 
    53714 Chain pairing | bb 
    53715 Alignment algorithm | Needleman-Wunsch 
    53716 Similarity matrix | BLOSUM-62 
    53717 SS fraction | 0.3 
    53718 Gap open (HH/SS/other) | 18/18/6 
    53719 Gap extend | 1 
    53720 SS matrix |  |  | H | S | O 
    53721 ---|---|---|--- 
    53722 H | 6 | -9 | -6 
    53723 S |  | 6 | -6 
    53724 O |  |  | 4 
    53725 Iteration cutoff | 2 
    53726  
    53727 Matchmaker 3j0c.pdb1, chain D (#1.10) with AF3 E1 422-461.pdb, chain A (#348),
    53728 sequence alignment score = 626.9 
    53729 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    53730 2.916) 
    53731  
    53732 
    53733 > hide sel cartoons
    53734 
    53735 > select #1.10/E
    53736 
    53737 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    53738 
    53739 > show sel cartoons
    53740 
    53741 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    53742 
    53743 Chain information for AF3 E2 1-352.pdb #349 
    53744 --- 
    53745 Chain | Description 
    53746 B | No description available 
    53747  
    53748 
    53749 > matchmaker #349 to #1.10 & sel
    53750 
    53751 Parameters 
    53752 --- 
    53753 Chain pairing | bb 
    53754 Alignment algorithm | Needleman-Wunsch 
    53755 Similarity matrix | BLOSUM-62 
    53756 SS fraction | 0.3 
    53757 Gap open (HH/SS/other) | 18/18/6 
    53758 Gap extend | 1 
    53759 SS matrix |  |  | H | S | O 
    53760 ---|---|---|--- 
    53761 H | 6 | -9 | -6 
    53762 S |  | 6 | -6 
    53763 O |  |  | 4 
    53764 Iteration cutoff | 2 
    53765  
    53766 Matchmaker 3j0c.pdb1, chain E (#1.10) with AF3 E2 1-352.pdb, chain B (#349),
    53767 sequence alignment score = 594.5 
    53768 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    53769 6.147) 
    53770  
    53771 
    53772 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    53773 
    53774 Chain information for AF3 E2 353-438.pdb #350 
    53775 --- 
    53776 Chain | Description 
    53777 B | No description available 
    53778  
    53779 
    53780 > matchmaker #350 to #1.10 & sel
    53781 
    53782 Parameters 
    53783 --- 
    53784 Chain pairing | bb 
    53785 Alignment algorithm | Needleman-Wunsch 
    53786 Similarity matrix | BLOSUM-62 
    53787 SS fraction | 0.3 
    53788 Gap open (HH/SS/other) | 18/18/6 
    53789 Gap extend | 1 
    53790 SS matrix |  |  | H | S | O 
    53791 ---|---|---|--- 
    53792 H | 6 | -9 | -6 
    53793 S |  | 6 | -6 
    53794 O |  |  | 4 
    53795 Iteration cutoff | 2 
    53796  
    53797 Matchmaker 3j0c.pdb1, chain E (#1.10) with AF3 E2 353-438.pdb, chain B (#350),
    53798 sequence alignment score = 340.2 
    53799 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    53800 8.673) 
    53801  
    53802 
    53803 > hide sel cartoons
    53804 
    53805 > select #1.10/F
    53806 
    53807 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    53808 
    53809 > show sel cartoons
    53810 
    53811 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    53812 
    53813 Chain information for AF3 CA.pdb #351 
    53814 --- 
    53815 Chain | Description 
    53816 A | No description available 
    53817  
    53818 
    53819 > matchmaker #351 to #1.10 & sel
    53820 
    53821 Parameters 
    53822 --- 
    53823 Chain pairing | bb 
    53824 Alignment algorithm | Needleman-Wunsch 
    53825 Similarity matrix | BLOSUM-62 
    53826 SS fraction | 0.3 
    53827 Gap open (HH/SS/other) | 18/18/6 
    53828 Gap extend | 1 
    53829 SS matrix |  |  | H | S | O 
    53830 ---|---|---|--- 
    53831 H | 6 | -9 | -6 
    53832 S |  | 6 | -6 
    53833 O |  |  | 4 
    53834 Iteration cutoff | 2 
    53835  
    53836 Matchmaker 3j0c.pdb1, chain F (#1.10) with AF3 CA.pdb, chain A (#351),
    53837 sequence alignment score = 335.3 
    53838 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    53839 2.550) 
    53840  
    53841 
    53842 > hide sel cartoons
    53843 
    53844 > color #347 dodgerblue
    53845 
    53846 > color #348 dodgerblue
    53847 
    53848 > color #349 #00b305ff
    53849 
    53850 > color #350 #00b305ff
    53851 
    53852 > color #351 #f15839ff
    53853 
    53854 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    53855 
    53856 > select #1.11/D
    53857 
    53858 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    53859 
    53860 > show sel cartoons
    53861 
    53862 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    53863 
    53864 Chain information for AF3 E1 1-421.pdb #352 
    53865 --- 
    53866 Chain | Description 
    53867 A | No description available 
    53868  
    53869 
    53870 > matchmaker #352 to #1.11 & sel
    53871 
    53872 Parameters 
    53873 --- 
    53874 Chain pairing | bb 
    53875 Alignment algorithm | Needleman-Wunsch 
    53876 Similarity matrix | BLOSUM-62 
    53877 SS fraction | 0.3 
    53878 Gap open (HH/SS/other) | 18/18/6 
    53879 Gap extend | 1 
    53880 SS matrix |  |  | H | S | O 
    53881 ---|---|---|--- 
    53882 H | 6 | -9 | -6 
    53883 S |  | 6 | -6 
    53884 O |  |  | 4 
    53885 Iteration cutoff | 2 
    53886  
    53887 Matchmaker 3j0c.pdb1, chain D (#1.11) with AF3 E1 1-421.pdb, chain A (#352),
    53888 sequence alignment score = 1060.7 
    53889 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    53890 3.032) 
    53891  
    53892 
    53893 > view sel
    53894 
    53895 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    53896 
    53897 Chain information for AF3 E1 422-461.pdb #353 
    53898 --- 
    53899 Chain | Description 
    53900 A | No description available 
    53901  
    53902 
    53903 > matchmaker #353 to #1.11 & sel
    53904 
    53905 Parameters 
    53906 --- 
    53907 Chain pairing | bb 
    53908 Alignment algorithm | Needleman-Wunsch 
    53909 Similarity matrix | BLOSUM-62 
    53910 SS fraction | 0.3 
    53911 Gap open (HH/SS/other) | 18/18/6 
    53912 Gap extend | 1 
    53913 SS matrix |  |  | H | S | O 
    53914 ---|---|---|--- 
    53915 H | 6 | -9 | -6 
    53916 S |  | 6 | -6 
    53917 O |  |  | 4 
    53918 Iteration cutoff | 2 
    53919  
    53920 Matchmaker 3j0c.pdb1, chain D (#1.11) with AF3 E1 422-461.pdb, chain A (#353),
    53921 sequence alignment score = 626.9 
    53922 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    53923 2.916) 
    53924  
    53925 
    53926 > hide sel cartoons
    53927 
    53928 > select #1.11/E
    53929 
    53930 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    53931 
    53932 > show sel cartoons
    53933 
    53934 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    53935 
    53936 Chain information for AF3 E2 1-352.pdb #354 
    53937 --- 
    53938 Chain | Description 
    53939 B | No description available 
    53940  
    53941 
    53942 > matchmaker #354 to #1.11 & sel
    53943 
    53944 Parameters 
    53945 --- 
    53946 Chain pairing | bb 
    53947 Alignment algorithm | Needleman-Wunsch 
    53948 Similarity matrix | BLOSUM-62 
    53949 SS fraction | 0.3 
    53950 Gap open (HH/SS/other) | 18/18/6 
    53951 Gap extend | 1 
    53952 SS matrix |  |  | H | S | O 
    53953 ---|---|---|--- 
    53954 H | 6 | -9 | -6 
    53955 S |  | 6 | -6 
    53956 O |  |  | 4 
    53957 Iteration cutoff | 2 
    53958  
    53959 Matchmaker 3j0c.pdb1, chain E (#1.11) with AF3 E2 1-352.pdb, chain B (#354),
    53960 sequence alignment score = 594.5 
    53961 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    53962 6.147) 
    53963  
    53964 
    53965 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    53966 
    53967 Chain information for AF3 E2 353-438.pdb #355 
    53968 --- 
    53969 Chain | Description 
    53970 B | No description available 
    53971  
    53972 
    53973 > matchmaker #355 to #1.11 & sel
    53974 
    53975 Parameters 
    53976 --- 
    53977 Chain pairing | bb 
    53978 Alignment algorithm | Needleman-Wunsch 
    53979 Similarity matrix | BLOSUM-62 
    53980 SS fraction | 0.3 
    53981 Gap open (HH/SS/other) | 18/18/6 
    53982 Gap extend | 1 
    53983 SS matrix |  |  | H | S | O 
    53984 ---|---|---|--- 
    53985 H | 6 | -9 | -6 
    53986 S |  | 6 | -6 
    53987 O |  |  | 4 
    53988 Iteration cutoff | 2 
    53989  
    53990 Matchmaker 3j0c.pdb1, chain E (#1.11) with AF3 E2 353-438.pdb, chain B (#355),
    53991 sequence alignment score = 340.2 
    53992 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    53993 8.673) 
    53994  
    53995 
    53996 > hide sel cartoons
    53997 
    53998 > select #1.11/F
    53999 
    54000 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    54001 
    54002 > show sel cartoons
    54003 
    54004 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    54005 
    54006 Chain information for AF3 CA.pdb #356 
    54007 --- 
    54008 Chain | Description 
    54009 A | No description available 
    54010  
    54011 
    54012 > matchmaker #356 to #1.11 & sel
    54013 
    54014 Parameters 
    54015 --- 
    54016 Chain pairing | bb 
    54017 Alignment algorithm | Needleman-Wunsch 
    54018 Similarity matrix | BLOSUM-62 
    54019 SS fraction | 0.3 
    54020 Gap open (HH/SS/other) | 18/18/6 
    54021 Gap extend | 1 
    54022 SS matrix |  |  | H | S | O 
    54023 ---|---|---|--- 
    54024 H | 6 | -9 | -6 
    54025 S |  | 6 | -6 
    54026 O |  |  | 4 
    54027 Iteration cutoff | 2 
    54028  
    54029 Matchmaker 3j0c.pdb1, chain F (#1.11) with AF3 CA.pdb, chain A (#356),
    54030 sequence alignment score = 335.3 
    54031 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    54032 2.550) 
    54033  
    54034 
    54035 > hide sel cartoons
    54036 
    54037 > color #352 dodgerblue
    54038 
    54039 > color #353 dodgerblue
    54040 
    54041 > color #354 #00b305ff
    54042 
    54043 > color #355 #00b305ff
    54044 
    54045 > color #356 #f15839ff
    54046 
    54047 > select #1.12/D
    54048 
    54049 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    54050 
    54051 > show sel cartoons
    54052 
    54053 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    54054 
    54055 Chain information for AF3 E1 1-421.pdb #357 
    54056 --- 
    54057 Chain | Description 
    54058 A | No description available 
    54059  
    54060 
    54061 > matchmaker #357 to #1.11 & sel
    54062 
    54063 No 'to' model specified 
    54064 
    54065 > matchmaker #357 to #1.12 & sel
    54066 
    54067 Parameters 
    54068 --- 
    54069 Chain pairing | bb 
    54070 Alignment algorithm | Needleman-Wunsch 
    54071 Similarity matrix | BLOSUM-62 
    54072 SS fraction | 0.3 
    54073 Gap open (HH/SS/other) | 18/18/6 
    54074 Gap extend | 1 
    54075 SS matrix |  |  | H | S | O 
    54076 ---|---|---|--- 
    54077 H | 6 | -9 | -6 
    54078 S |  | 6 | -6 
    54079 O |  |  | 4 
    54080 Iteration cutoff | 2 
    54081  
    54082 Matchmaker 3j0c.pdb1, chain D (#1.12) with AF3 E1 1-421.pdb, chain A (#357),
    54083 sequence alignment score = 1060.7 
    54084 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    54085 3.032) 
    54086  
    54087 
    54088 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    54089 
    54090 Chain information for AF3 E1 422-461.pdb #358 
    54091 --- 
    54092 Chain | Description 
    54093 A | No description available 
    54094  
    54095 
    54096 > matchmaker #358 to #1.12 & sel
    54097 
    54098 Parameters 
    54099 --- 
    54100 Chain pairing | bb 
    54101 Alignment algorithm | Needleman-Wunsch 
    54102 Similarity matrix | BLOSUM-62 
    54103 SS fraction | 0.3 
    54104 Gap open (HH/SS/other) | 18/18/6 
    54105 Gap extend | 1 
    54106 SS matrix |  |  | H | S | O 
    54107 ---|---|---|--- 
    54108 H | 6 | -9 | -6 
    54109 S |  | 6 | -6 
    54110 O |  |  | 4 
    54111 Iteration cutoff | 2 
    54112  
    54113 Matchmaker 3j0c.pdb1, chain D (#1.12) with AF3 E1 422-461.pdb, chain A (#358),
    54114 sequence alignment score = 626.9 
    54115 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    54116 2.916) 
    54117  
    54118 
    54119 > hide sel cartoons
    54120 
    54121 > select #1.12/E
    54122 
    54123 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    54124 
    54125 > show sel cartoons
    54126 
    54127 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    54128 
    54129 Chain information for AF3 E2 1-352.pdb #359 
    54130 --- 
    54131 Chain | Description 
    54132 B | No description available 
    54133  
    54134 
    54135 > matchmaker #359 to #1.12 & sel
    54136 
    54137 Parameters 
    54138 --- 
    54139 Chain pairing | bb 
    54140 Alignment algorithm | Needleman-Wunsch 
    54141 Similarity matrix | BLOSUM-62 
    54142 SS fraction | 0.3 
    54143 Gap open (HH/SS/other) | 18/18/6 
    54144 Gap extend | 1 
    54145 SS matrix |  |  | H | S | O 
    54146 ---|---|---|--- 
    54147 H | 6 | -9 | -6 
    54148 S |  | 6 | -6 
    54149 O |  |  | 4 
    54150 Iteration cutoff | 2 
    54151  
    54152 Matchmaker 3j0c.pdb1, chain E (#1.12) with AF3 E2 1-352.pdb, chain B (#359),
    54153 sequence alignment score = 594.5 
    54154 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    54155 6.147) 
    54156  
    54157 
    54158 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    54159 
    54160 Chain information for AF3 E2 353-438.pdb #360 
    54161 --- 
    54162 Chain | Description 
    54163 B | No description available 
    54164  
    54165 
    54166 > matchmaker #360 to #1.12 & sel
    54167 
    54168 Parameters 
    54169 --- 
    54170 Chain pairing | bb 
    54171 Alignment algorithm | Needleman-Wunsch 
    54172 Similarity matrix | BLOSUM-62 
    54173 SS fraction | 0.3 
    54174 Gap open (HH/SS/other) | 18/18/6 
    54175 Gap extend | 1 
    54176 SS matrix |  |  | H | S | O 
    54177 ---|---|---|--- 
    54178 H | 6 | -9 | -6 
    54179 S |  | 6 | -6 
    54180 O |  |  | 4 
    54181 Iteration cutoff | 2 
    54182  
    54183 Matchmaker 3j0c.pdb1, chain E (#1.12) with AF3 E2 353-438.pdb, chain B (#360),
    54184 sequence alignment score = 340.2 
    54185 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    54186 8.673) 
    54187  
    54188 
    54189 > hide sel cartoons
    54190 
    54191 > select #1.12/F
    54192 
    54193 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    54194 
    54195 > show sel cartoons
    54196 
    54197 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    54198 
    54199 Chain information for AF3 CA.pdb #361 
    54200 --- 
    54201 Chain | Description 
    54202 A | No description available 
    54203  
    54204 
    54205 > matchmaker #361 to #1.12 & sel
    54206 
    54207 Parameters 
    54208 --- 
    54209 Chain pairing | bb 
    54210 Alignment algorithm | Needleman-Wunsch 
    54211 Similarity matrix | BLOSUM-62 
    54212 SS fraction | 0.3 
    54213 Gap open (HH/SS/other) | 18/18/6 
    54214 Gap extend | 1 
    54215 SS matrix |  |  | H | S | O 
    54216 ---|---|---|--- 
    54217 H | 6 | -9 | -6 
    54218 S |  | 6 | -6 
    54219 O |  |  | 4 
    54220 Iteration cutoff | 2 
    54221  
    54222 Matchmaker 3j0c.pdb1, chain F (#1.12) with AF3 CA.pdb, chain A (#361),
    54223 sequence alignment score = 335.3 
    54224 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    54225 2.550) 
    54226  
    54227 
    54228 > hide sel cartoons
    54229 
    54230 > color #357 dodgerblue
    54231 
    54232 > color #358 dodgerblue
    54233 
    54234 > color #359 #00b305ff
    54235 
    54236 > color #360 #00b305ff
    54237 
    54238 > color #361 #f15839ff
    54239 
    54240 > select #1.13/D
    54241 
    54242 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    54243 
    54244 > show sel cartoons
    54245 
    54246 > lighting soft
    54247 
    54248 > lighting full
    54249 
    54250 > lighting simple
    54251 
    54252 > lighting soft
    54253 
    54254 [Repeated 1 time(s)]
    54255 
    54256 > view
    54257 
    54258 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    54259 
    54260 Chain information for AF3 E1 1-421.pdb #362 
    54261 --- 
    54262 Chain | Description 
    54263 A | No description available 
    54264  
    54265 
    54266 > matchmaker #362 to #1.13 & sel
    54267 
    54268 Parameters 
    54269 --- 
    54270 Chain pairing | bb 
    54271 Alignment algorithm | Needleman-Wunsch 
    54272 Similarity matrix | BLOSUM-62 
    54273 SS fraction | 0.3 
    54274 Gap open (HH/SS/other) | 18/18/6 
    54275 Gap extend | 1 
    54276 SS matrix |  |  | H | S | O 
    54277 ---|---|---|--- 
    54278 H | 6 | -9 | -6 
    54279 S |  | 6 | -6 
    54280 O |  |  | 4 
    54281 Iteration cutoff | 2 
    54282  
    54283 Matchmaker 3j0c.pdb1, chain D (#1.13) with AF3 E1 1-421.pdb, chain A (#362),
    54284 sequence alignment score = 1060.7 
    54285 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    54286 3.032) 
    54287  
    54288 
    54289 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    54290 
    54291 Chain information for AF3 E1 422-461.pdb #363 
    54292 --- 
    54293 Chain | Description 
    54294 A | No description available 
    54295  
    54296 
    54297 > matchmaker #363 to #1.13 & sel
    54298 
    54299 Parameters 
    54300 --- 
    54301 Chain pairing | bb 
    54302 Alignment algorithm | Needleman-Wunsch 
    54303 Similarity matrix | BLOSUM-62 
    54304 SS fraction | 0.3 
    54305 Gap open (HH/SS/other) | 18/18/6 
    54306 Gap extend | 1 
    54307 SS matrix |  |  | H | S | O 
    54308 ---|---|---|--- 
    54309 H | 6 | -9 | -6 
    54310 S |  | 6 | -6 
    54311 O |  |  | 4 
    54312 Iteration cutoff | 2 
    54313  
    54314 Matchmaker 3j0c.pdb1, chain D (#1.13) with AF3 E1 422-461.pdb, chain A (#363),
    54315 sequence alignment score = 626.9 
    54316 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    54317 2.916) 
    54318  
    54319 
    54320 > hide sel cartoons
    54321 
    54322 > lighting simple
    54323 
    54324 > select #1.13/E
    54325 
    54326 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    54327 
    54328 > show sel cartoons
    54329 
    54330 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    54331 
    54332 Chain information for AF3 E2 1-352.pdb #364 
    54333 --- 
    54334 Chain | Description 
    54335 B | No description available 
    54336  
    54337 
    54338 > matchmaker #364 to #1.13 & sel
    54339 
    54340 Parameters 
    54341 --- 
    54342 Chain pairing | bb 
    54343 Alignment algorithm | Needleman-Wunsch 
    54344 Similarity matrix | BLOSUM-62 
    54345 SS fraction | 0.3 
    54346 Gap open (HH/SS/other) | 18/18/6 
    54347 Gap extend | 1 
    54348 SS matrix |  |  | H | S | O 
    54349 ---|---|---|--- 
    54350 H | 6 | -9 | -6 
    54351 S |  | 6 | -6 
    54352 O |  |  | 4 
    54353 Iteration cutoff | 2 
    54354  
    54355 Matchmaker 3j0c.pdb1, chain E (#1.13) with AF3 E2 1-352.pdb, chain B (#364),
    54356 sequence alignment score = 594.5 
    54357 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    54358 6.147) 
    54359  
    54360 
    54361 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    54362 
    54363 Chain information for AF3 E2 353-438.pdb #365 
    54364 --- 
    54365 Chain | Description 
    54366 B | No description available 
    54367  
    54368 
    54369 > matchmaker #365 to #1.13 & sel
    54370 
    54371 Parameters 
    54372 --- 
    54373 Chain pairing | bb 
    54374 Alignment algorithm | Needleman-Wunsch 
    54375 Similarity matrix | BLOSUM-62 
    54376 SS fraction | 0.3 
    54377 Gap open (HH/SS/other) | 18/18/6 
    54378 Gap extend | 1 
    54379 SS matrix |  |  | H | S | O 
    54380 ---|---|---|--- 
    54381 H | 6 | -9 | -6 
    54382 S |  | 6 | -6 
    54383 O |  |  | 4 
    54384 Iteration cutoff | 2 
    54385  
    54386 Matchmaker 3j0c.pdb1, chain E (#1.13) with AF3 E2 353-438.pdb, chain B (#365),
    54387 sequence alignment score = 340.2 
    54388 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    54389 8.673) 
    54390  
    54391 
    54392 > hide sel cartoons
    54393 
    54394 > select #1.13/F
    54395 
    54396 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    54397 
    54398 > show sel cartoons
    54399 
    54400 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    54401 
    54402 Chain information for AF3 CA.pdb #366 
    54403 --- 
    54404 Chain | Description 
    54405 A | No description available 
    54406  
    54407 
    54408 > matchmaker #366 to #1.13 & sel
    54409 
    54410 Parameters 
    54411 --- 
    54412 Chain pairing | bb 
    54413 Alignment algorithm | Needleman-Wunsch 
    54414 Similarity matrix | BLOSUM-62 
    54415 SS fraction | 0.3 
    54416 Gap open (HH/SS/other) | 18/18/6 
    54417 Gap extend | 1 
    54418 SS matrix |  |  | H | S | O 
    54419 ---|---|---|--- 
    54420 H | 6 | -9 | -6 
    54421 S |  | 6 | -6 
    54422 O |  |  | 4 
    54423 Iteration cutoff | 2 
    54424  
    54425 Matchmaker 3j0c.pdb1, chain F (#1.13) with AF3 CA.pdb, chain A (#366),
    54426 sequence alignment score = 335.3 
    54427 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    54428 2.550) 
    54429  
    54430 
    54431 > hide sel cartoons
    54432 
    54433 > color #362 dodgerblue
    54434 
    54435 > color #363 dodgerblue
    54436 
    54437 > color #364 #00b305ff
    54438 
    54439 > color #365 #00b305ff
    54440 
    54441 > color #366 #f15839ff
    54442 
    54443 > select #1.14/D
    54444 
    54445 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    54446 
    54447 > show sel cartoons
    54448 
    54449 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    54450 
    54451 Chain information for AF3 E1 1-421.pdb #367 
    54452 --- 
    54453 Chain | Description 
    54454 A | No description available 
    54455  
    54456 
    54457 > matchmaker #367 to #1.14 & sel
    54458 
    54459 Parameters 
    54460 --- 
    54461 Chain pairing | bb 
    54462 Alignment algorithm | Needleman-Wunsch 
    54463 Similarity matrix | BLOSUM-62 
    54464 SS fraction | 0.3 
    54465 Gap open (HH/SS/other) | 18/18/6 
    54466 Gap extend | 1 
    54467 SS matrix |  |  | H | S | O 
    54468 ---|---|---|--- 
    54469 H | 6 | -9 | -6 
    54470 S |  | 6 | -6 
    54471 O |  |  | 4 
    54472 Iteration cutoff | 2 
    54473  
    54474 Matchmaker 3j0c.pdb1, chain D (#1.14) with AF3 E1 1-421.pdb, chain A (#367),
    54475 sequence alignment score = 1060.7 
    54476 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    54477 3.032) 
    54478  
    54479 
    54480 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    54481 
    54482 Chain information for AF3 E1 422-461.pdb #368 
    54483 --- 
    54484 Chain | Description 
    54485 A | No description available 
    54486  
    54487 
    54488 > matchmaker #368 to #1.14 & sel
    54489 
    54490 Parameters 
    54491 --- 
    54492 Chain pairing | bb 
    54493 Alignment algorithm | Needleman-Wunsch 
    54494 Similarity matrix | BLOSUM-62 
    54495 SS fraction | 0.3 
    54496 Gap open (HH/SS/other) | 18/18/6 
    54497 Gap extend | 1 
    54498 SS matrix |  |  | H | S | O 
    54499 ---|---|---|--- 
    54500 H | 6 | -9 | -6 
    54501 S |  | 6 | -6 
    54502 O |  |  | 4 
    54503 Iteration cutoff | 2 
    54504  
    54505 Matchmaker 3j0c.pdb1, chain D (#1.14) with AF3 E1 422-461.pdb, chain A (#368),
    54506 sequence alignment score = 626.9 
    54507 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    54508 2.916) 
    54509  
    54510 
    54511 > hide sel cartoons
    54512 
    54513 > select #1.14/E
    54514 
    54515 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    54516 
    54517 > show sel cartoons
    54518 
    54519 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    54520 
    54521 Chain information for AF3 E2 1-352.pdb #369 
    54522 --- 
    54523 Chain | Description 
    54524 B | No description available 
    54525  
    54526 
    54527 > matchmaker #369 to #1.14 & sel
    54528 
    54529 Parameters 
    54530 --- 
    54531 Chain pairing | bb 
    54532 Alignment algorithm | Needleman-Wunsch 
    54533 Similarity matrix | BLOSUM-62 
    54534 SS fraction | 0.3 
    54535 Gap open (HH/SS/other) | 18/18/6 
    54536 Gap extend | 1 
    54537 SS matrix |  |  | H | S | O 
    54538 ---|---|---|--- 
    54539 H | 6 | -9 | -6 
    54540 S |  | 6 | -6 
    54541 O |  |  | 4 
    54542 Iteration cutoff | 2 
    54543  
    54544 Matchmaker 3j0c.pdb1, chain E (#1.14) with AF3 E2 1-352.pdb, chain B (#369),
    54545 sequence alignment score = 594.5 
    54546 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    54547 6.147) 
    54548  
    54549 
    54550 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    54551 
    54552 Chain information for AF3 E2 353-438.pdb #370 
    54553 --- 
    54554 Chain | Description 
    54555 B | No description available 
    54556  
    54557 
    54558 > matchmaker #370 to #1.14 & sel
    54559 
    54560 Parameters 
    54561 --- 
    54562 Chain pairing | bb 
    54563 Alignment algorithm | Needleman-Wunsch 
    54564 Similarity matrix | BLOSUM-62 
    54565 SS fraction | 0.3 
    54566 Gap open (HH/SS/other) | 18/18/6 
    54567 Gap extend | 1 
    54568 SS matrix |  |  | H | S | O 
    54569 ---|---|---|--- 
    54570 H | 6 | -9 | -6 
    54571 S |  | 6 | -6 
    54572 O |  |  | 4 
    54573 Iteration cutoff | 2 
    54574  
    54575 Matchmaker 3j0c.pdb1, chain E (#1.14) with AF3 E2 353-438.pdb, chain B (#370),
    54576 sequence alignment score = 340.2 
    54577 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    54578 8.673) 
    54579  
    54580 
    54581 > hide sel cartoons
    54582 
    54583 > select #1.14/F
    54584 
    54585 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    54586 
    54587 > show sel cartoons
    54588 
    54589 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    54590 
    54591 Chain information for AF3 CA.pdb #371 
    54592 --- 
    54593 Chain | Description 
    54594 A | No description available 
    54595  
    54596 
    54597 > matchmaker #371 to #1.14 & sel
    54598 
    54599 Parameters 
    54600 --- 
    54601 Chain pairing | bb 
    54602 Alignment algorithm | Needleman-Wunsch 
    54603 Similarity matrix | BLOSUM-62 
    54604 SS fraction | 0.3 
    54605 Gap open (HH/SS/other) | 18/18/6 
    54606 Gap extend | 1 
    54607 SS matrix |  |  | H | S | O 
    54608 ---|---|---|--- 
    54609 H | 6 | -9 | -6 
    54610 S |  | 6 | -6 
    54611 O |  |  | 4 
    54612 Iteration cutoff | 2 
    54613  
    54614 Matchmaker 3j0c.pdb1, chain F (#1.14) with AF3 CA.pdb, chain A (#371),
    54615 sequence alignment score = 335.3 
    54616 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    54617 2.550) 
    54618  
    54619 
    54620 > hide sel cartoons
    54621 
    54622 > color #367 dodgerblue
    54623 
    54624 > color #368 dodgerblue
    54625 
    54626 > color #369 #00b305ff
    54627 
    54628 > color #370 #00b305ff
    54629 
    54630 > color #371 #f15839ff
    54631 
    54632 > select #1.16/D
    54633 
    54634 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    54635 
    54636 > show sel cartoons
    54637 
    54638 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    54639 
    54640 Chain information for AF3 E1 1-421.pdb #372 
    54641 --- 
    54642 Chain | Description 
    54643 A | No description available 
    54644  
    54645 
    54646 > hide sel cartoons
    54647 
    54648 > select #1.15/D
    54649 
    54650 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    54651 
    54652 > show sel cartoons
    54653 
    54654 > matchmaker #372 to #1.15 & sel
    54655 
    54656 Parameters 
    54657 --- 
    54658 Chain pairing | bb 
    54659 Alignment algorithm | Needleman-Wunsch 
    54660 Similarity matrix | BLOSUM-62 
    54661 SS fraction | 0.3 
    54662 Gap open (HH/SS/other) | 18/18/6 
    54663 Gap extend | 1 
    54664 SS matrix |  |  | H | S | O 
    54665 ---|---|---|--- 
    54666 H | 6 | -9 | -6 
    54667 S |  | 6 | -6 
    54668 O |  |  | 4 
    54669 Iteration cutoff | 2 
    54670  
    54671 Matchmaker 3j0c.pdb1, chain D (#1.15) with AF3 E1 1-421.pdb, chain A (#372),
    54672 sequence alignment score = 1060.7 
    54673 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    54674 3.032) 
    54675  
    54676 
    54677 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    54678 
    54679 Chain information for AF3 E1 422-461.pdb #373 
    54680 --- 
    54681 Chain | Description 
    54682 A | No description available 
    54683  
    54684 
    54685 > matchmaker #373 to #1.15 & sel
    54686 
    54687 Parameters 
    54688 --- 
    54689 Chain pairing | bb 
    54690 Alignment algorithm | Needleman-Wunsch 
    54691 Similarity matrix | BLOSUM-62 
    54692 SS fraction | 0.3 
    54693 Gap open (HH/SS/other) | 18/18/6 
    54694 Gap extend | 1 
    54695 SS matrix |  |  | H | S | O 
    54696 ---|---|---|--- 
    54697 H | 6 | -9 | -6 
    54698 S |  | 6 | -6 
    54699 O |  |  | 4 
    54700 Iteration cutoff | 2 
    54701  
    54702 Matchmaker 3j0c.pdb1, chain D (#1.15) with AF3 E1 422-461.pdb, chain A (#373),
    54703 sequence alignment score = 626.9 
    54704 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    54705 2.916) 
    54706  
    54707 
    54708 > hide sel cartoons
    54709 
    54710 > select #1.15/E
    54711 
    54712 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    54713 
    54714 > show sel cartoons
    54715 
    54716 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    54717 
    54718 Chain information for AF3 E2 1-352.pdb #374 
    54719 --- 
    54720 Chain | Description 
    54721 B | No description available 
    54722  
    54723 
    54724 > matchmaker #374 to #1.15 & sel
    54725 
    54726 Parameters 
    54727 --- 
    54728 Chain pairing | bb 
    54729 Alignment algorithm | Needleman-Wunsch 
    54730 Similarity matrix | BLOSUM-62 
    54731 SS fraction | 0.3 
    54732 Gap open (HH/SS/other) | 18/18/6 
    54733 Gap extend | 1 
    54734 SS matrix |  |  | H | S | O 
    54735 ---|---|---|--- 
    54736 H | 6 | -9 | -6 
    54737 S |  | 6 | -6 
    54738 O |  |  | 4 
    54739 Iteration cutoff | 2 
    54740  
    54741 Matchmaker 3j0c.pdb1, chain E (#1.15) with AF3 E2 1-352.pdb, chain B (#374),
    54742 sequence alignment score = 594.5 
    54743 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    54744 6.147) 
    54745  
    54746 
    54747 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    54748 
    54749 Chain information for AF3 E2 353-438.pdb #375 
    54750 --- 
    54751 Chain | Description 
    54752 B | No description available 
    54753  
    54754 
    54755 > matchmaker #375 to #1.15 & sel
    54756 
    54757 Parameters 
    54758 --- 
    54759 Chain pairing | bb 
    54760 Alignment algorithm | Needleman-Wunsch 
    54761 Similarity matrix | BLOSUM-62 
    54762 SS fraction | 0.3 
    54763 Gap open (HH/SS/other) | 18/18/6 
    54764 Gap extend | 1 
    54765 SS matrix |  |  | H | S | O 
    54766 ---|---|---|--- 
    54767 H | 6 | -9 | -6 
    54768 S |  | 6 | -6 
    54769 O |  |  | 4 
    54770 Iteration cutoff | 2 
    54771  
    54772 Matchmaker 3j0c.pdb1, chain E (#1.15) with AF3 E2 353-438.pdb, chain B (#375),
    54773 sequence alignment score = 340.2 
    54774 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    54775 8.673) 
    54776  
    54777 
    54778 > hide sel cartoons
    54779 
    54780 > select #1.15/F
    54781 
    54782 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    54783 
    54784 > show sel cartoons
    54785 
    54786 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    54787 
    54788 Chain information for AF3 CA.pdb #376 
    54789 --- 
    54790 Chain | Description 
    54791 A | No description available 
    54792  
    54793 
    54794 > matchmaker #376 to #1.15 & sel
    54795 
    54796 Parameters 
    54797 --- 
    54798 Chain pairing | bb 
    54799 Alignment algorithm | Needleman-Wunsch 
    54800 Similarity matrix | BLOSUM-62 
    54801 SS fraction | 0.3 
    54802 Gap open (HH/SS/other) | 18/18/6 
    54803 Gap extend | 1 
    54804 SS matrix |  |  | H | S | O 
    54805 ---|---|---|--- 
    54806 H | 6 | -9 | -6 
    54807 S |  | 6 | -6 
    54808 O |  |  | 4 
    54809 Iteration cutoff | 2 
    54810  
    54811 Matchmaker 3j0c.pdb1, chain F (#1.15) with AF3 CA.pdb, chain A (#376),
    54812 sequence alignment score = 335.3 
    54813 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    54814 2.550) 
    54815  
    54816 
    54817 > hide sel cartoons
    54818 
    54819 > color #372 dodgerblue
    54820 
    54821 > color #373 dodgerblue
    54822 
    54823 > color #374 #00b305ff
    54824 
    54825 > color #375 #00b305ff
    54826 
    54827 > color #376 #f15839ff
    54828 
    54829 > select #1.16/D
    54830 
    54831 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    54832 
    54833 > show sel cartoons
    54834 
    54835 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    54836 
    54837 Chain information for AF3 E1 1-421.pdb #377 
    54838 --- 
    54839 Chain | Description 
    54840 A | No description available 
    54841  
    54842 
    54843 > matchmaker #377 to #1.15 & sel
    54844 
    54845 No 'to' model specified 
    54846 
    54847 > matchmaker #377 to #1.16 & sel
    54848 
    54849 Parameters 
    54850 --- 
    54851 Chain pairing | bb 
    54852 Alignment algorithm | Needleman-Wunsch 
    54853 Similarity matrix | BLOSUM-62 
    54854 SS fraction | 0.3 
    54855 Gap open (HH/SS/other) | 18/18/6 
    54856 Gap extend | 1 
    54857 SS matrix |  |  | H | S | O 
    54858 ---|---|---|--- 
    54859 H | 6 | -9 | -6 
    54860 S |  | 6 | -6 
    54861 O |  |  | 4 
    54862 Iteration cutoff | 2 
    54863  
    54864 Matchmaker 3j0c.pdb1, chain D (#1.16) with AF3 E1 1-421.pdb, chain A (#377),
    54865 sequence alignment score = 1060.7 
    54866 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    54867 3.032) 
    54868  
    54869 
    54870 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    54871 
    54872 Chain information for AF3 E1 422-461.pdb #378 
    54873 --- 
    54874 Chain | Description 
    54875 A | No description available 
    54876  
    54877 
    54878 > matchmaker #378 to #1.16 & sel
    54879 
    54880 Parameters 
    54881 --- 
    54882 Chain pairing | bb 
    54883 Alignment algorithm | Needleman-Wunsch 
    54884 Similarity matrix | BLOSUM-62 
    54885 SS fraction | 0.3 
    54886 Gap open (HH/SS/other) | 18/18/6 
    54887 Gap extend | 1 
    54888 SS matrix |  |  | H | S | O 
    54889 ---|---|---|--- 
    54890 H | 6 | -9 | -6 
    54891 S |  | 6 | -6 
    54892 O |  |  | 4 
    54893 Iteration cutoff | 2 
    54894  
    54895 Matchmaker 3j0c.pdb1, chain D (#1.16) with AF3 E1 422-461.pdb, chain A (#378),
    54896 sequence alignment score = 626.9 
    54897 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    54898 2.916) 
    54899  
    54900 
    54901 > hide sel cartoons
    54902 
    54903 > select #1.16/E
    54904 
    54905 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    54906 
    54907 > show sel cartoons
    54908 
    54909 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    54910 
    54911 Chain information for AF3 E2 1-352.pdb #379 
    54912 --- 
    54913 Chain | Description 
    54914 B | No description available 
    54915  
    54916 
    54917 > matchmaker #379 to #1.16 & sel
    54918 
    54919 Parameters 
    54920 --- 
    54921 Chain pairing | bb 
    54922 Alignment algorithm | Needleman-Wunsch 
    54923 Similarity matrix | BLOSUM-62 
    54924 SS fraction | 0.3 
    54925 Gap open (HH/SS/other) | 18/18/6 
    54926 Gap extend | 1 
    54927 SS matrix |  |  | H | S | O 
    54928 ---|---|---|--- 
    54929 H | 6 | -9 | -6 
    54930 S |  | 6 | -6 
    54931 O |  |  | 4 
    54932 Iteration cutoff | 2 
    54933  
    54934 Matchmaker 3j0c.pdb1, chain E (#1.16) with AF3 E2 1-352.pdb, chain B (#379),
    54935 sequence alignment score = 594.5 
    54936 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    54937 6.147) 
    54938  
    54939 
    54940 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    54941 
    54942 Chain information for AF3 E2 353-438.pdb #380 
    54943 --- 
    54944 Chain | Description 
    54945 B | No description available 
    54946  
    54947 
    54948 > matchmaker #380 to #1.16 & sel
    54949 
    54950 Parameters 
    54951 --- 
    54952 Chain pairing | bb 
    54953 Alignment algorithm | Needleman-Wunsch 
    54954 Similarity matrix | BLOSUM-62 
    54955 SS fraction | 0.3 
    54956 Gap open (HH/SS/other) | 18/18/6 
    54957 Gap extend | 1 
    54958 SS matrix |  |  | H | S | O 
    54959 ---|---|---|--- 
    54960 H | 6 | -9 | -6 
    54961 S |  | 6 | -6 
    54962 O |  |  | 4 
    54963 Iteration cutoff | 2 
    54964  
    54965 Matchmaker 3j0c.pdb1, chain E (#1.16) with AF3 E2 353-438.pdb, chain B (#380),
    54966 sequence alignment score = 340.2 
    54967 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    54968 8.673) 
    54969  
    54970 
    54971 > hide sel cartoons
    54972 
    54973 > select #1.16/F
    54974 
    54975 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    54976 
    54977 > show sel cartoons
    54978 
    54979 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    54980 
    54981 Chain information for AF3 CA.pdb #381 
    54982 --- 
    54983 Chain | Description 
    54984 A | No description available 
    54985  
    54986 
    54987 > matchmaker #381 to #1.16 & sel
    54988 
    54989 Parameters 
    54990 --- 
    54991 Chain pairing | bb 
    54992 Alignment algorithm | Needleman-Wunsch 
    54993 Similarity matrix | BLOSUM-62 
    54994 SS fraction | 0.3 
    54995 Gap open (HH/SS/other) | 18/18/6 
    54996 Gap extend | 1 
    54997 SS matrix |  |  | H | S | O 
    54998 ---|---|---|--- 
    54999 H | 6 | -9 | -6 
    55000 S |  | 6 | -6 
    55001 O |  |  | 4 
    55002 Iteration cutoff | 2 
    55003  
    55004 Matchmaker 3j0c.pdb1, chain F (#1.16) with AF3 CA.pdb, chain A (#381),
    55005 sequence alignment score = 335.3 
    55006 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    55007 2.550) 
    55008  
    55009 
    55010 > hide sel cartoons
    55011 
    55012 > color #377 dodgerblue
    55013 
    55014 > color #378 dodgerblue
    55015 
    55016 > color #379 #00b305ff
    55017 
    55018 > color #380 #00b305ff
    55019 
    55020 > color #381 #f15839ff
    55021 
    55022 > select #1.17/D
    55023 
    55024 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    55025 
    55026 > show sel cartoons
    55027 
    55028 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    55029 
    55030 Chain information for AF3 E1 1-421.pdb #382 
    55031 --- 
    55032 Chain | Description 
    55033 A | No description available 
    55034  
    55035 
    55036 > matchmaker #382 to #1.17 & sel
    55037 
    55038 Parameters 
    55039 --- 
    55040 Chain pairing | bb 
    55041 Alignment algorithm | Needleman-Wunsch 
    55042 Similarity matrix | BLOSUM-62 
    55043 SS fraction | 0.3 
    55044 Gap open (HH/SS/other) | 18/18/6 
    55045 Gap extend | 1 
    55046 SS matrix |  |  | H | S | O 
    55047 ---|---|---|--- 
    55048 H | 6 | -9 | -6 
    55049 S |  | 6 | -6 
    55050 O |  |  | 4 
    55051 Iteration cutoff | 2 
    55052  
    55053 Matchmaker 3j0c.pdb1, chain D (#1.17) with AF3 E1 1-421.pdb, chain A (#382),
    55054 sequence alignment score = 1060.7 
    55055 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    55056 3.032) 
    55057  
    55058 
    55059 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    55060 
    55061 Chain information for AF3 E1 422-461.pdb #383 
    55062 --- 
    55063 Chain | Description 
    55064 A | No description available 
    55065  
    55066 
    55067 > matchmaker #383 to #1.17 & sel
    55068 
    55069 Parameters 
    55070 --- 
    55071 Chain pairing | bb 
    55072 Alignment algorithm | Needleman-Wunsch 
    55073 Similarity matrix | BLOSUM-62 
    55074 SS fraction | 0.3 
    55075 Gap open (HH/SS/other) | 18/18/6 
    55076 Gap extend | 1 
    55077 SS matrix |  |  | H | S | O 
    55078 ---|---|---|--- 
    55079 H | 6 | -9 | -6 
    55080 S |  | 6 | -6 
    55081 O |  |  | 4 
    55082 Iteration cutoff | 2 
    55083  
    55084 Matchmaker 3j0c.pdb1, chain D (#1.17) with AF3 E1 422-461.pdb, chain A (#383),
    55085 sequence alignment score = 626.9 
    55086 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    55087 2.915) 
    55088  
    55089 
    55090 > hide sel cartoons
    55091 
    55092 > select #1.17/E
    55093 
    55094 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    55095 
    55096 > show sel cartoons
    55097 
    55098 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    55099 
    55100 Chain information for AF3 E2 1-352.pdb #384 
    55101 --- 
    55102 Chain | Description 
    55103 B | No description available 
    55104  
    55105 
    55106 > matchmaker #384 to #1.17 & sel
    55107 
    55108 Parameters 
    55109 --- 
    55110 Chain pairing | bb 
    55111 Alignment algorithm | Needleman-Wunsch 
    55112 Similarity matrix | BLOSUM-62 
    55113 SS fraction | 0.3 
    55114 Gap open (HH/SS/other) | 18/18/6 
    55115 Gap extend | 1 
    55116 SS matrix |  |  | H | S | O 
    55117 ---|---|---|--- 
    55118 H | 6 | -9 | -6 
    55119 S |  | 6 | -6 
    55120 O |  |  | 4 
    55121 Iteration cutoff | 2 
    55122  
    55123 Matchmaker 3j0c.pdb1, chain E (#1.17) with AF3 E2 1-352.pdb, chain B (#384),
    55124 sequence alignment score = 594.5 
    55125 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    55126 6.147) 
    55127  
    55128 
    55129 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    55130 
    55131 Chain information for AF3 E2 353-438.pdb #385 
    55132 --- 
    55133 Chain | Description 
    55134 B | No description available 
    55135  
    55136 
    55137 > matchmaker #385 to #1.17 & sel
    55138 
    55139 Parameters 
    55140 --- 
    55141 Chain pairing | bb 
    55142 Alignment algorithm | Needleman-Wunsch 
    55143 Similarity matrix | BLOSUM-62 
    55144 SS fraction | 0.3 
    55145 Gap open (HH/SS/other) | 18/18/6 
    55146 Gap extend | 1 
    55147 SS matrix |  |  | H | S | O 
    55148 ---|---|---|--- 
    55149 H | 6 | -9 | -6 
    55150 S |  | 6 | -6 
    55151 O |  |  | 4 
    55152 Iteration cutoff | 2 
    55153  
    55154 Matchmaker 3j0c.pdb1, chain E (#1.17) with AF3 E2 353-438.pdb, chain B (#385),
    55155 sequence alignment score = 340.2 
    55156 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    55157 8.673) 
    55158  
    55159 
    55160 > hide sel cartoons
    55161 
    55162 > select #1.17/F
    55163 
    55164 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    55165 
    55166 > show sel cartoons
    55167 
    55168 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    55169 
    55170 Chain information for AF3 CA.pdb #386 
    55171 --- 
    55172 Chain | Description 
    55173 A | No description available 
    55174  
    55175 
    55176 > matchmaker #386 to #1.17 & sel
    55177 
    55178 Parameters 
    55179 --- 
    55180 Chain pairing | bb 
    55181 Alignment algorithm | Needleman-Wunsch 
    55182 Similarity matrix | BLOSUM-62 
    55183 SS fraction | 0.3 
    55184 Gap open (HH/SS/other) | 18/18/6 
    55185 Gap extend | 1 
    55186 SS matrix |  |  | H | S | O 
    55187 ---|---|---|--- 
    55188 H | 6 | -9 | -6 
    55189 S |  | 6 | -6 
    55190 O |  |  | 4 
    55191 Iteration cutoff | 2 
    55192  
    55193 Matchmaker 3j0c.pdb1, chain F (#1.17) with AF3 CA.pdb, chain A (#386),
    55194 sequence alignment score = 335.3 
    55195 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    55196 2.550) 
    55197  
    55198 
    55199 > hide sel cartoons
    55200 
    55201 > color #382 dodgerblue
    55202 
    55203 > color #383 dodgerblue
    55204 
    55205 > color #384 #00b305ff
    55206 
    55207 > color #385 #00b305ff
    55208 
    55209 > color #386 #f15839ff
    55210 
    55211 > select #1.18/D
    55212 
    55213 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    55214 
    55215 > show sel cartoons
    55216 
    55217 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    55218 
    55219 Chain information for AF3 E1 1-421.pdb #387 
    55220 --- 
    55221 Chain | Description 
    55222 A | No description available 
    55223  
    55224 
    55225 > matchmaker #387 to #1.17 & sel
    55226 
    55227 No 'to' model specified 
    55228 
    55229 > matchmaker #387 to #1.18 & sel
    55230 
    55231 Parameters 
    55232 --- 
    55233 Chain pairing | bb 
    55234 Alignment algorithm | Needleman-Wunsch 
    55235 Similarity matrix | BLOSUM-62 
    55236 SS fraction | 0.3 
    55237 Gap open (HH/SS/other) | 18/18/6 
    55238 Gap extend | 1 
    55239 SS matrix |  |  | H | S | O 
    55240 ---|---|---|--- 
    55241 H | 6 | -9 | -6 
    55242 S |  | 6 | -6 
    55243 O |  |  | 4 
    55244 Iteration cutoff | 2 
    55245  
    55246 Matchmaker 3j0c.pdb1, chain D (#1.18) with AF3 E1 1-421.pdb, chain A (#387),
    55247 sequence alignment score = 1060.7 
    55248 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    55249 3.032) 
    55250  
    55251 
    55252 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    55253 
    55254 Chain information for AF3 E1 422-461.pdb #388 
    55255 --- 
    55256 Chain | Description 
    55257 A | No description available 
    55258  
    55259 
    55260 > matchmaker #388 to #1.18 & sel
    55261 
    55262 Parameters 
    55263 --- 
    55264 Chain pairing | bb 
    55265 Alignment algorithm | Needleman-Wunsch 
    55266 Similarity matrix | BLOSUM-62 
    55267 SS fraction | 0.3 
    55268 Gap open (HH/SS/other) | 18/18/6 
    55269 Gap extend | 1 
    55270 SS matrix |  |  | H | S | O 
    55271 ---|---|---|--- 
    55272 H | 6 | -9 | -6 
    55273 S |  | 6 | -6 
    55274 O |  |  | 4 
    55275 Iteration cutoff | 2 
    55276  
    55277 Matchmaker 3j0c.pdb1, chain D (#1.18) with AF3 E1 422-461.pdb, chain A (#388),
    55278 sequence alignment score = 626.9 
    55279 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    55280 2.916) 
    55281  
    55282 
    55283 > hide sel cartoons
    55284 
    55285 > select #1.18/E
    55286 
    55287 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    55288 
    55289 > show sel cartoons
    55290 
    55291 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    55292 
    55293 Chain information for AF3 E2 1-352.pdb #389 
    55294 --- 
    55295 Chain | Description 
    55296 B | No description available 
    55297  
    55298 
    55299 > matchmaker #389 to #1.18 & sel
    55300 
    55301 Parameters 
    55302 --- 
    55303 Chain pairing | bb 
    55304 Alignment algorithm | Needleman-Wunsch 
    55305 Similarity matrix | BLOSUM-62 
    55306 SS fraction | 0.3 
    55307 Gap open (HH/SS/other) | 18/18/6 
    55308 Gap extend | 1 
    55309 SS matrix |  |  | H | S | O 
    55310 ---|---|---|--- 
    55311 H | 6 | -9 | -6 
    55312 S |  | 6 | -6 
    55313 O |  |  | 4 
    55314 Iteration cutoff | 2 
    55315  
    55316 Matchmaker 3j0c.pdb1, chain E (#1.18) with AF3 E2 1-352.pdb, chain B (#389),
    55317 sequence alignment score = 594.5 
    55318 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    55319 6.147) 
    55320  
    55321 
    55322 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    55323 
    55324 Chain information for AF3 E2 353-438.pdb #390 
    55325 --- 
    55326 Chain | Description 
    55327 B | No description available 
    55328  
    55329 
    55330 > matchmaker #390 to #1.18 & sel
    55331 
    55332 Parameters 
    55333 --- 
    55334 Chain pairing | bb 
    55335 Alignment algorithm | Needleman-Wunsch 
    55336 Similarity matrix | BLOSUM-62 
    55337 SS fraction | 0.3 
    55338 Gap open (HH/SS/other) | 18/18/6 
    55339 Gap extend | 1 
    55340 SS matrix |  |  | H | S | O 
    55341 ---|---|---|--- 
    55342 H | 6 | -9 | -6 
    55343 S |  | 6 | -6 
    55344 O |  |  | 4 
    55345 Iteration cutoff | 2 
    55346  
    55347 Matchmaker 3j0c.pdb1, chain E (#1.18) with AF3 E2 353-438.pdb, chain B (#390),
    55348 sequence alignment score = 340.2 
    55349 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    55350 8.673) 
    55351  
    55352 
    55353 > hide sel cartoons
    55354 
    55355 > select #1.18/F
    55356 
    55357 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    55358 
    55359 > show sel cartoons
    55360 
    55361 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    55362 
    55363 Chain information for AF3 CA.pdb #391 
    55364 --- 
    55365 Chain | Description 
    55366 A | No description available 
    55367  
    55368 
    55369 > matchmaker #391 to #1.18 & sel
    55370 
    55371 Parameters 
    55372 --- 
    55373 Chain pairing | bb 
    55374 Alignment algorithm | Needleman-Wunsch 
    55375 Similarity matrix | BLOSUM-62 
    55376 SS fraction | 0.3 
    55377 Gap open (HH/SS/other) | 18/18/6 
    55378 Gap extend | 1 
    55379 SS matrix |  |  | H | S | O 
    55380 ---|---|---|--- 
    55381 H | 6 | -9 | -6 
    55382 S |  | 6 | -6 
    55383 O |  |  | 4 
    55384 Iteration cutoff | 2 
    55385  
    55386 Matchmaker 3j0c.pdb1, chain F (#1.18) with AF3 CA.pdb, chain A (#391),
    55387 sequence alignment score = 335.3 
    55388 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    55389 2.550) 
    55390  
    55391 
    55392 > hide sel cartoons
    55393 
    55394 > color #387 dodgerblue
    55395 
    55396 > color #388 dodgerblue
    55397 
    55398 > color #389 #00b305ff
    55399 
    55400 > color #390 #00b305ff
    55401 
    55402 > color #391 #f15839ff
    55403 
    55404 > select #1.19/D
    55405 
    55406 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    55407 
    55408 > show sel cartoons
    55409 
    55410 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    55411 
    55412 Chain information for AF3 E1 1-421.pdb #392 
    55413 --- 
    55414 Chain | Description 
    55415 A | No description available 
    55416  
    55417 
    55418 > matchmaker #391 to #1.19 & sel
    55419 
    55420 Parameters 
    55421 --- 
    55422 Chain pairing | bb 
    55423 Alignment algorithm | Needleman-Wunsch 
    55424 Similarity matrix | BLOSUM-62 
    55425 SS fraction | 0.3 
    55426 Gap open (HH/SS/other) | 18/18/6 
    55427 Gap extend | 1 
    55428 SS matrix |  |  | H | S | O 
    55429 ---|---|---|--- 
    55430 H | 6 | -9 | -6 
    55431 S |  | 6 | -6 
    55432 O |  |  | 4 
    55433 Iteration cutoff | 2 
    55434  
    55435 Matchmaker 3j0c.pdb1, chain D (#1.19) with AF3 CA.pdb, chain A (#391),
    55436 sequence alignment score = 32.6 
    55437 RMSD between 11 pruned atom pairs is 1.228 angstroms; (across all 110 pairs:
    55438 22.710) 
    55439  
    55440 
    55441 > select #1.18/F
    55442 
    55443 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    55444 
    55445 > show sel cartoons
    55446 
    55447 > matchmaker #391 to #1.18 & sel
    55448 
    55449 Parameters 
    55450 --- 
    55451 Chain pairing | bb 
    55452 Alignment algorithm | Needleman-Wunsch 
    55453 Similarity matrix | BLOSUM-62 
    55454 SS fraction | 0.3 
    55455 Gap open (HH/SS/other) | 18/18/6 
    55456 Gap extend | 1 
    55457 SS matrix |  |  | H | S | O 
    55458 ---|---|---|--- 
    55459 H | 6 | -9 | -6 
    55460 S |  | 6 | -6 
    55461 O |  |  | 4 
    55462 Iteration cutoff | 2 
    55463  
    55464 Matchmaker 3j0c.pdb1, chain F (#1.18) with AF3 CA.pdb, chain A (#391),
    55465 sequence alignment score = 335.3 
    55466 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    55467 2.550) 
    55468  
    55469 
    55470 > hide sel cartoons
    55471 
    55472 > select #1.19/D
    55473 
    55474 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    55475 
    55476 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    55477 
    55478 Chain information for AF3 E1 1-421.pdb #393 
    55479 --- 
    55480 Chain | Description 
    55481 A | No description available 
    55482  
    55483 
    55484 The cached device pixel ratio value was stale on window expose. Please file a
    55485 QTBUG which explains how to reproduce. 
    55486 
    55487 > close #393
    55488 
    55489 > matchmaker #392 to #1.19 & sel
    55490 
    55491 Parameters 
    55492 --- 
    55493 Chain pairing | bb 
    55494 Alignment algorithm | Needleman-Wunsch 
    55495 Similarity matrix | BLOSUM-62 
    55496 SS fraction | 0.3 
    55497 Gap open (HH/SS/other) | 18/18/6 
    55498 Gap extend | 1 
    55499 SS matrix |  |  | H | S | O 
    55500 ---|---|---|--- 
    55501 H | 6 | -9 | -6 
    55502 S |  | 6 | -6 
    55503 O |  |  | 4 
    55504 Iteration cutoff | 2 
    55505  
    55506 Matchmaker 3j0c.pdb1, chain D (#1.19) with AF3 E1 1-421.pdb, chain A (#392),
    55507 sequence alignment score = 1060.7 
    55508 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    55509 3.032) 
    55510  
    55511 
    55512 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    55513 
    55514 Chain information for AF3 E1 422-461.pdb #393 
    55515 --- 
    55516 Chain | Description 
    55517 A | No description available 
    55518  
    55519 
    55520 > matchmaker #393 to #1.19 & sel
    55521 
    55522 Parameters 
    55523 --- 
    55524 Chain pairing | bb 
    55525 Alignment algorithm | Needleman-Wunsch 
    55526 Similarity matrix | BLOSUM-62 
    55527 SS fraction | 0.3 
    55528 Gap open (HH/SS/other) | 18/18/6 
    55529 Gap extend | 1 
    55530 SS matrix |  |  | H | S | O 
    55531 ---|---|---|--- 
    55532 H | 6 | -9 | -6 
    55533 S |  | 6 | -6 
    55534 O |  |  | 4 
    55535 Iteration cutoff | 2 
    55536  
    55537 Matchmaker 3j0c.pdb1, chain D (#1.19) with AF3 E1 422-461.pdb, chain A (#393),
    55538 sequence alignment score = 626.9 
    55539 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    55540 2.916) 
    55541  
    55542 
    55543 > hide sel cartoons
    55544 
    55545 > select #1.19/E
    55546 
    55547 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    55548 
    55549 > show sel cartoons
    55550 
    55551 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    55552 
    55553 Chain information for AF3 E2 1-352.pdb #394 
    55554 --- 
    55555 Chain | Description 
    55556 B | No description available 
    55557  
    55558 
    55559 > matchmaker #394 to #1.19 & sel
    55560 
    55561 Parameters 
    55562 --- 
    55563 Chain pairing | bb 
    55564 Alignment algorithm | Needleman-Wunsch 
    55565 Similarity matrix | BLOSUM-62 
    55566 SS fraction | 0.3 
    55567 Gap open (HH/SS/other) | 18/18/6 
    55568 Gap extend | 1 
    55569 SS matrix |  |  | H | S | O 
    55570 ---|---|---|--- 
    55571 H | 6 | -9 | -6 
    55572 S |  | 6 | -6 
    55573 O |  |  | 4 
    55574 Iteration cutoff | 2 
    55575  
    55576 Matchmaker 3j0c.pdb1, chain E (#1.19) with AF3 E2 1-352.pdb, chain B (#394),
    55577 sequence alignment score = 594.5 
    55578 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    55579 6.147) 
    55580  
    55581 
    55582 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    55583 
    55584 Chain information for AF3 E2 353-438.pdb #395 
    55585 --- 
    55586 Chain | Description 
    55587 B | No description available 
    55588  
    55589 
    55590 > matchmaker #395 to #1.19 & sel
    55591 
    55592 Parameters 
    55593 --- 
    55594 Chain pairing | bb 
    55595 Alignment algorithm | Needleman-Wunsch 
    55596 Similarity matrix | BLOSUM-62 
    55597 SS fraction | 0.3 
    55598 Gap open (HH/SS/other) | 18/18/6 
    55599 Gap extend | 1 
    55600 SS matrix |  |  | H | S | O 
    55601 ---|---|---|--- 
    55602 H | 6 | -9 | -6 
    55603 S |  | 6 | -6 
    55604 O |  |  | 4 
    55605 Iteration cutoff | 2 
    55606  
    55607 Matchmaker 3j0c.pdb1, chain E (#1.19) with AF3 E2 353-438.pdb, chain B (#395),
    55608 sequence alignment score = 340.2 
    55609 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    55610 8.673) 
    55611  
    55612 
    55613 > hide sel cartoons
    55614 
    55615 > select #1.19/F
    55616 
    55617 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    55618 
    55619 > show sel cartoons
    55620 
    55621 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    55622 
    55623 Chain information for AF3 CA.pdb #396 
    55624 --- 
    55625 Chain | Description 
    55626 A | No description available 
    55627  
    55628 
    55629 > matchmaker #396 to #1.19 & sel
    55630 
    55631 Parameters 
    55632 --- 
    55633 Chain pairing | bb 
    55634 Alignment algorithm | Needleman-Wunsch 
    55635 Similarity matrix | BLOSUM-62 
    55636 SS fraction | 0.3 
    55637 Gap open (HH/SS/other) | 18/18/6 
    55638 Gap extend | 1 
    55639 SS matrix |  |  | H | S | O 
    55640 ---|---|---|--- 
    55641 H | 6 | -9 | -6 
    55642 S |  | 6 | -6 
    55643 O |  |  | 4 
    55644 Iteration cutoff | 2 
    55645  
    55646 Matchmaker 3j0c.pdb1, chain F (#1.19) with AF3 CA.pdb, chain A (#396),
    55647 sequence alignment score = 335.3 
    55648 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    55649 2.550) 
    55650  
    55651 
    55652 > hide sel cartoons
    55653 
    55654 > color #392 dodgerblue
    55655 
    55656 > color #393 dodgerblue
    55657 
    55658 > color #394 #00b305ff
    55659 
    55660 > color #395 #00b305ff
    55661 
    55662 > color #396 #f15839ff
    55663 
    55664 > select #1.20/D
    55665 
    55666 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    55667 
    55668 > show sel cartoons
    55669 
    55670 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    55671 
    55672 Chain information for AF3 E1 1-421.pdb #397 
    55673 --- 
    55674 Chain | Description 
    55675 A | No description available 
    55676  
    55677 
    55678 > matchmaker #397 to #1.20 & sel
    55679 
    55680 Parameters 
    55681 --- 
    55682 Chain pairing | bb 
    55683 Alignment algorithm | Needleman-Wunsch 
    55684 Similarity matrix | BLOSUM-62 
    55685 SS fraction | 0.3 
    55686 Gap open (HH/SS/other) | 18/18/6 
    55687 Gap extend | 1 
    55688 SS matrix |  |  | H | S | O 
    55689 ---|---|---|--- 
    55690 H | 6 | -9 | -6 
    55691 S |  | 6 | -6 
    55692 O |  |  | 4 
    55693 Iteration cutoff | 2 
    55694  
    55695 Matchmaker 3j0c.pdb1, chain D (#1.20) with AF3 E1 1-421.pdb, chain A (#397),
    55696 sequence alignment score = 1060.7 
    55697 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    55698 3.032) 
    55699  
    55700 
    55701 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    55702 
    55703 Chain information for AF3 E1 422-461.pdb #398 
    55704 --- 
    55705 Chain | Description 
    55706 A | No description available 
    55707  
    55708 
    55709 > matchmaker #398 to #1.20 & sel
    55710 
    55711 Parameters 
    55712 --- 
    55713 Chain pairing | bb 
    55714 Alignment algorithm | Needleman-Wunsch 
    55715 Similarity matrix | BLOSUM-62 
    55716 SS fraction | 0.3 
    55717 Gap open (HH/SS/other) | 18/18/6 
    55718 Gap extend | 1 
    55719 SS matrix |  |  | H | S | O 
    55720 ---|---|---|--- 
    55721 H | 6 | -9 | -6 
    55722 S |  | 6 | -6 
    55723 O |  |  | 4 
    55724 Iteration cutoff | 2 
    55725  
    55726 Matchmaker 3j0c.pdb1, chain D (#1.20) with AF3 E1 422-461.pdb, chain A (#398),
    55727 sequence alignment score = 626.9 
    55728 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    55729 2.916) 
    55730  
    55731 
    55732 > hide sel cartoons
    55733 
    55734 > select #1.20/E
    55735 
    55736 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    55737 
    55738 > show sel cartoons
    55739 
    55740 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    55741 
    55742 Chain information for AF3 E2 1-352.pdb #399 
    55743 --- 
    55744 Chain | Description 
    55745 B | No description available 
    55746  
    55747 
    55748 > matchmaker #399 to #1.20 & sel
    55749 
    55750 Parameters 
    55751 --- 
    55752 Chain pairing | bb 
    55753 Alignment algorithm | Needleman-Wunsch 
    55754 Similarity matrix | BLOSUM-62 
    55755 SS fraction | 0.3 
    55756 Gap open (HH/SS/other) | 18/18/6 
    55757 Gap extend | 1 
    55758 SS matrix |  |  | H | S | O 
    55759 ---|---|---|--- 
    55760 H | 6 | -9 | -6 
    55761 S |  | 6 | -6 
    55762 O |  |  | 4 
    55763 Iteration cutoff | 2 
    55764  
    55765 Matchmaker 3j0c.pdb1, chain E (#1.20) with AF3 E2 1-352.pdb, chain B (#399),
    55766 sequence alignment score = 594.5 
    55767 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    55768 6.147) 
    55769  
    55770 
    55771 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    55772 
    55773 Chain information for AF3 E2 353-438.pdb #400 
    55774 --- 
    55775 Chain | Description 
    55776 B | No description available 
    55777  
    55778 
    55779 > matchmaker #400 to #1.20 & sel
    55780 
    55781 Parameters 
    55782 --- 
    55783 Chain pairing | bb 
    55784 Alignment algorithm | Needleman-Wunsch 
    55785 Similarity matrix | BLOSUM-62 
    55786 SS fraction | 0.3 
    55787 Gap open (HH/SS/other) | 18/18/6 
    55788 Gap extend | 1 
    55789 SS matrix |  |  | H | S | O 
    55790 ---|---|---|--- 
    55791 H | 6 | -9 | -6 
    55792 S |  | 6 | -6 
    55793 O |  |  | 4 
    55794 Iteration cutoff | 2 
    55795  
    55796 Matchmaker 3j0c.pdb1, chain E (#1.20) with AF3 E2 353-438.pdb, chain B (#400),
    55797 sequence alignment score = 340.2 
    55798 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    55799 8.673) 
    55800  
    55801 
    55802 > hide sel cartoons
    55803 
    55804 > select #1.20/F
    55805 
    55806 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    55807 
    55808 > show sel cartoons
    55809 
    55810 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    55811 
    55812 Chain information for AF3 CA.pdb #401 
    55813 --- 
    55814 Chain | Description 
    55815 A | No description available 
    55816  
    55817 
    55818 > matchmaker #401 to #1.20 & sel
    55819 
    55820 Parameters 
    55821 --- 
    55822 Chain pairing | bb 
    55823 Alignment algorithm | Needleman-Wunsch 
    55824 Similarity matrix | BLOSUM-62 
    55825 SS fraction | 0.3 
    55826 Gap open (HH/SS/other) | 18/18/6 
    55827 Gap extend | 1 
    55828 SS matrix |  |  | H | S | O 
    55829 ---|---|---|--- 
    55830 H | 6 | -9 | -6 
    55831 S |  | 6 | -6 
    55832 O |  |  | 4 
    55833 Iteration cutoff | 2 
    55834  
    55835 Matchmaker 3j0c.pdb1, chain F (#1.20) with AF3 CA.pdb, chain A (#401),
    55836 sequence alignment score = 335.3 
    55837 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    55838 2.550) 
    55839  
    55840 
    55841 > hide sel cartoons
    55842 
    55843 > color #397 dodgerblue
    55844 
    55845 > color #398 dodgerblue
    55846 
    55847 > color #399 #00b305ff
    55848 
    55849 > color #400 #00b305ff
    55850 
    55851 > color #401 #f15839ff
    55852 
    55853 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    55854 
    55855 > select add #347
    55856 
    55857 4419 atoms, 4528 bonds, 583 residues, 2 models selected 
    55858 
    55859 > select subtract #347
    55860 
    55861 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    55862 
    55863 > select add #347
    55864 
    55865 4419 atoms, 4528 bonds, 583 residues, 2 models selected 
    55866 
    55867 > select subtract #347
    55868 
    55869 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    55870 
    55871 > hide #347-396 models
    55872 
    55873 > select #1.21/D
    55874 
    55875 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    55876 
    55877 > show sel cartoons
    55878 
    55879 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    55880 
    55881 Chain information for AF3 E1 1-421.pdb #402 
    55882 --- 
    55883 Chain | Description 
    55884 A | No description available 
    55885  
    55886 
    55887 > matchmaker #402 to #1.21 & sel
    55888 
    55889 Parameters 
    55890 --- 
    55891 Chain pairing | bb 
    55892 Alignment algorithm | Needleman-Wunsch 
    55893 Similarity matrix | BLOSUM-62 
    55894 SS fraction | 0.3 
    55895 Gap open (HH/SS/other) | 18/18/6 
    55896 Gap extend | 1 
    55897 SS matrix |  |  | H | S | O 
    55898 ---|---|---|--- 
    55899 H | 6 | -9 | -6 
    55900 S |  | 6 | -6 
    55901 O |  |  | 4 
    55902 Iteration cutoff | 2 
    55903  
    55904 Matchmaker 3j0c.pdb1, chain D (#1.21) with AF3 E1 1-421.pdb, chain A (#402),
    55905 sequence alignment score = 1060.7 
    55906 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    55907 3.032) 
    55908  
    55909 
    55910 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    55911 
    55912 Chain information for AF3 E1 422-461.pdb #403 
    55913 --- 
    55914 Chain | Description 
    55915 A | No description available 
    55916  
    55917 
    55918 > matchmaker #403 to #1.21 & sel
    55919 
    55920 Parameters 
    55921 --- 
    55922 Chain pairing | bb 
    55923 Alignment algorithm | Needleman-Wunsch 
    55924 Similarity matrix | BLOSUM-62 
    55925 SS fraction | 0.3 
    55926 Gap open (HH/SS/other) | 18/18/6 
    55927 Gap extend | 1 
    55928 SS matrix |  |  | H | S | O 
    55929 ---|---|---|--- 
    55930 H | 6 | -9 | -6 
    55931 S |  | 6 | -6 
    55932 O |  |  | 4 
    55933 Iteration cutoff | 2 
    55934  
    55935 Matchmaker 3j0c.pdb1, chain D (#1.21) with AF3 E1 422-461.pdb, chain A (#403),
    55936 sequence alignment score = 626.9 
    55937 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    55938 2.916) 
    55939  
    55940 
    55941 > hide sel cartoons
    55942 
    55943 > select #1.21/E
    55944 
    55945 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    55946 
    55947 > show sel cartoons
    55948 
    55949 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    55950 
    55951 Chain information for AF3 E2 1-352.pdb #404 
    55952 --- 
    55953 Chain | Description 
    55954 B | No description available 
    55955  
    55956 
    55957 > matchmaker #404 to #1.21 & sel
    55958 
    55959 Parameters 
    55960 --- 
    55961 Chain pairing | bb 
    55962 Alignment algorithm | Needleman-Wunsch 
    55963 Similarity matrix | BLOSUM-62 
    55964 SS fraction | 0.3 
    55965 Gap open (HH/SS/other) | 18/18/6 
    55966 Gap extend | 1 
    55967 SS matrix |  |  | H | S | O 
    55968 ---|---|---|--- 
    55969 H | 6 | -9 | -6 
    55970 S |  | 6 | -6 
    55971 O |  |  | 4 
    55972 Iteration cutoff | 2 
    55973  
    55974 Matchmaker 3j0c.pdb1, chain E (#1.21) with AF3 E2 1-352.pdb, chain B (#404),
    55975 sequence alignment score = 594.5 
    55976 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    55977 6.147) 
    55978  
    55979 
    55980 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    55981 
    55982 Chain information for AF3 E2 353-438.pdb #405 
    55983 --- 
    55984 Chain | Description 
    55985 B | No description available 
    55986  
    55987 
    55988 > matchmaker #405 to #1.21 & sel
    55989 
    55990 Parameters 
    55991 --- 
    55992 Chain pairing | bb 
    55993 Alignment algorithm | Needleman-Wunsch 
    55994 Similarity matrix | BLOSUM-62 
    55995 SS fraction | 0.3 
    55996 Gap open (HH/SS/other) | 18/18/6 
    55997 Gap extend | 1 
    55998 SS matrix |  |  | H | S | O 
    55999 ---|---|---|--- 
    56000 H | 6 | -9 | -6 
    56001 S |  | 6 | -6 
    56002 O |  |  | 4 
    56003 Iteration cutoff | 2 
    56004  
    56005 Matchmaker 3j0c.pdb1, chain E (#1.21) with AF3 E2 353-438.pdb, chain B (#405),
    56006 sequence alignment score = 340.2 
    56007 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    56008 8.673) 
    56009  
    56010 
    56011 > hide sel cartoons
    56012 
    56013 > select #1.21/F
    56014 
    56015 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    56016 
    56017 > show sel cartoons
    56018 
    56019 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    56020 
    56021 Chain information for AF3 CA.pdb #406 
    56022 --- 
    56023 Chain | Description 
    56024 A | No description available 
    56025  
    56026 
    56027 > matchmaker #406 to #1.21 & sel
    56028 
    56029 Parameters 
    56030 --- 
    56031 Chain pairing | bb 
    56032 Alignment algorithm | Needleman-Wunsch 
    56033 Similarity matrix | BLOSUM-62 
    56034 SS fraction | 0.3 
    56035 Gap open (HH/SS/other) | 18/18/6 
    56036 Gap extend | 1 
    56037 SS matrix |  |  | H | S | O 
    56038 ---|---|---|--- 
    56039 H | 6 | -9 | -6 
    56040 S |  | 6 | -6 
    56041 O |  |  | 4 
    56042 Iteration cutoff | 2 
    56043  
    56044 Matchmaker 3j0c.pdb1, chain F (#1.21) with AF3 CA.pdb, chain A (#406),
    56045 sequence alignment score = 335.3 
    56046 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    56047 2.550) 
    56048  
    56049 
    56050 > hide sel cartoons
    56051 
    56052 > color #402 dodgerblue
    56053 
    56054 > color #403 dodgerblue
    56055 
    56056 > color #404 #00b305ff
    56057 
    56058 > color #405 #00b305ff
    56059 
    56060 > color #406 #f15839ff
    56061 
    56062 > select #1.22/D
    56063 
    56064 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    56065 
    56066 > show sel cartoons
    56067 
    56068 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    56069 
    56070 Chain information for AF3 E1 1-421.pdb #407 
    56071 --- 
    56072 Chain | Description 
    56073 A | No description available 
    56074  
    56075 
    56076 > matchmaker #407 to #1.22 & sel
    56077 
    56078 Parameters 
    56079 --- 
    56080 Chain pairing | bb 
    56081 Alignment algorithm | Needleman-Wunsch 
    56082 Similarity matrix | BLOSUM-62 
    56083 SS fraction | 0.3 
    56084 Gap open (HH/SS/other) | 18/18/6 
    56085 Gap extend | 1 
    56086 SS matrix |  |  | H | S | O 
    56087 ---|---|---|--- 
    56088 H | 6 | -9 | -6 
    56089 S |  | 6 | -6 
    56090 O |  |  | 4 
    56091 Iteration cutoff | 2 
    56092  
    56093 Matchmaker 3j0c.pdb1, chain D (#1.22) with AF3 E1 1-421.pdb, chain A (#407),
    56094 sequence alignment score = 1060.7 
    56095 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    56096 3.032) 
    56097  
    56098 
    56099 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    56100 
    56101 Chain information for AF3 E1 422-461.pdb #408 
    56102 --- 
    56103 Chain | Description 
    56104 A | No description available 
    56105  
    56106 
    56107 > matchmaker #408 to #1.22 & sel
    56108 
    56109 Parameters 
    56110 --- 
    56111 Chain pairing | bb 
    56112 Alignment algorithm | Needleman-Wunsch 
    56113 Similarity matrix | BLOSUM-62 
    56114 SS fraction | 0.3 
    56115 Gap open (HH/SS/other) | 18/18/6 
    56116 Gap extend | 1 
    56117 SS matrix |  |  | H | S | O 
    56118 ---|---|---|--- 
    56119 H | 6 | -9 | -6 
    56120 S |  | 6 | -6 
    56121 O |  |  | 4 
    56122 Iteration cutoff | 2 
    56123  
    56124 Matchmaker 3j0c.pdb1, chain D (#1.22) with AF3 E1 422-461.pdb, chain A (#408),
    56125 sequence alignment score = 626.9 
    56126 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    56127 2.916) 
    56128  
    56129 
    56130 > hide sel cartoons
    56131 
    56132 > select #1.22/E
    56133 
    56134 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    56135 
    56136 > show sel cartoons
    56137 
    56138 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    56139 
    56140 Chain information for AF3 E2 1-352.pdb #409 
    56141 --- 
    56142 Chain | Description 
    56143 B | No description available 
    56144  
    56145 
    56146 > matchmaker #409 to #1.22 & sel
    56147 
    56148 Parameters 
    56149 --- 
    56150 Chain pairing | bb 
    56151 Alignment algorithm | Needleman-Wunsch 
    56152 Similarity matrix | BLOSUM-62 
    56153 SS fraction | 0.3 
    56154 Gap open (HH/SS/other) | 18/18/6 
    56155 Gap extend | 1 
    56156 SS matrix |  |  | H | S | O 
    56157 ---|---|---|--- 
    56158 H | 6 | -9 | -6 
    56159 S |  | 6 | -6 
    56160 O |  |  | 4 
    56161 Iteration cutoff | 2 
    56162  
    56163 Matchmaker 3j0c.pdb1, chain E (#1.22) with AF3 E2 1-352.pdb, chain B (#409),
    56164 sequence alignment score = 594.5 
    56165 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    56166 6.147) 
    56167  
    56168 
    56169 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    56170 
    56171 Chain information for AF3 E2 353-438.pdb #410 
    56172 --- 
    56173 Chain | Description 
    56174 B | No description available 
    56175  
    56176 
    56177 > matchmaker #410 to #1.22 & sel
    56178 
    56179 Parameters 
    56180 --- 
    56181 Chain pairing | bb 
    56182 Alignment algorithm | Needleman-Wunsch 
    56183 Similarity matrix | BLOSUM-62 
    56184 SS fraction | 0.3 
    56185 Gap open (HH/SS/other) | 18/18/6 
    56186 Gap extend | 1 
    56187 SS matrix |  |  | H | S | O 
    56188 ---|---|---|--- 
    56189 H | 6 | -9 | -6 
    56190 S |  | 6 | -6 
    56191 O |  |  | 4 
    56192 Iteration cutoff | 2 
    56193  
    56194 Matchmaker 3j0c.pdb1, chain E (#1.22) with AF3 E2 353-438.pdb, chain B (#410),
    56195 sequence alignment score = 340.2 
    56196 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    56197 8.673) 
    56198  
    56199 
    56200 > select #1.22/F
    56201 
    56202 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    56203 
    56204 > show sel cartoons
    56205 
    56206 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    56207 
    56208 Chain information for AF3 CA.pdb #411 
    56209 --- 
    56210 Chain | Description 
    56211 A | No description available 
    56212  
    56213 
    56214 > matchmaker #411 to #1.22 & sel
    56215 
    56216 Parameters 
    56217 --- 
    56218 Chain pairing | bb 
    56219 Alignment algorithm | Needleman-Wunsch 
    56220 Similarity matrix | BLOSUM-62 
    56221 SS fraction | 0.3 
    56222 Gap open (HH/SS/other) | 18/18/6 
    56223 Gap extend | 1 
    56224 SS matrix |  |  | H | S | O 
    56225 ---|---|---|--- 
    56226 H | 6 | -9 | -6 
    56227 S |  | 6 | -6 
    56228 O |  |  | 4 
    56229 Iteration cutoff | 2 
    56230  
    56231 Matchmaker 3j0c.pdb1, chain F (#1.22) with AF3 CA.pdb, chain A (#411),
    56232 sequence alignment score = 335.3 
    56233 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    56234 2.550) 
    56235  
    56236 
    56237 > hide sel cartoons
    56238 
    56239 > color #407 dodgerblue
    56240 
    56241 > color #408 dodgerblue
    56242 
    56243 > color #409 #00b305ff
    56244 
    56245 > color #410 #00b305ff
    56246 
    56247 > color #411 #f15839ff
    56248 
    56249 > select #1.22/E
    56250 
    56251 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    56252 
    56253 > hide sel cartoons
    56254 
    56255 > select #1.23/D
    56256 
    56257 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    56258 
    56259 > show sel cartoons
    56260 
    56261 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    56262 
    56263 Chain information for AF3 E1 1-421.pdb #412 
    56264 --- 
    56265 Chain | Description 
    56266 A | No description available 
    56267  
    56268 
    56269 > matchmaker #412 to #1.23 & sel
    56270 
    56271 Parameters 
    56272 --- 
    56273 Chain pairing | bb 
    56274 Alignment algorithm | Needleman-Wunsch 
    56275 Similarity matrix | BLOSUM-62 
    56276 SS fraction | 0.3 
    56277 Gap open (HH/SS/other) | 18/18/6 
    56278 Gap extend | 1 
    56279 SS matrix |  |  | H | S | O 
    56280 ---|---|---|--- 
    56281 H | 6 | -9 | -6 
    56282 S |  | 6 | -6 
    56283 O |  |  | 4 
    56284 Iteration cutoff | 2 
    56285  
    56286 Matchmaker 3j0c.pdb1, chain D (#1.23) with AF3 E1 1-421.pdb, chain A (#412),
    56287 sequence alignment score = 1060.7 
    56288 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    56289 3.032) 
    56290  
    56291 
    56292 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    56293 
    56294 Chain information for AF3 E1 422-461.pdb #413 
    56295 --- 
    56296 Chain | Description 
    56297 A | No description available 
    56298  
    56299 
    56300 > matchmaker #413 to #1.23 & sel
    56301 
    56302 Parameters 
    56303 --- 
    56304 Chain pairing | bb 
    56305 Alignment algorithm | Needleman-Wunsch 
    56306 Similarity matrix | BLOSUM-62 
    56307 SS fraction | 0.3 
    56308 Gap open (HH/SS/other) | 18/18/6 
    56309 Gap extend | 1 
    56310 SS matrix |  |  | H | S | O 
    56311 ---|---|---|--- 
    56312 H | 6 | -9 | -6 
    56313 S |  | 6 | -6 
    56314 O |  |  | 4 
    56315 Iteration cutoff | 2 
    56316  
    56317 Matchmaker 3j0c.pdb1, chain D (#1.23) with AF3 E1 422-461.pdb, chain A (#413),
    56318 sequence alignment score = 626.9 
    56319 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    56320 2.916) 
    56321  
    56322 
    56323 > hide sel cartoons
    56324 
    56325 > select #1.23/F
    56326 
    56327 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    56328 
    56329 > show sel cartoons
    56330 
    56331 > hide sel cartoons
    56332 
    56333 > select #1.23/E
    56334 
    56335 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    56336 
    56337 > show sel cartoons
    56338 
    56339 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    56340 
    56341 Chain information for AF3 E2 1-352.pdb #414 
    56342 --- 
    56343 Chain | Description 
    56344 B | No description available 
    56345  
    56346 
    56347 > matchmaker #414 to #1.23 & sel
    56348 
    56349 Parameters 
    56350 --- 
    56351 Chain pairing | bb 
    56352 Alignment algorithm | Needleman-Wunsch 
    56353 Similarity matrix | BLOSUM-62 
    56354 SS fraction | 0.3 
    56355 Gap open (HH/SS/other) | 18/18/6 
    56356 Gap extend | 1 
    56357 SS matrix |  |  | H | S | O 
    56358 ---|---|---|--- 
    56359 H | 6 | -9 | -6 
    56360 S |  | 6 | -6 
    56361 O |  |  | 4 
    56362 Iteration cutoff | 2 
    56363  
    56364 Matchmaker 3j0c.pdb1, chain E (#1.23) with AF3 E2 1-352.pdb, chain B (#414),
    56365 sequence alignment score = 594.5 
    56366 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    56367 6.147) 
    56368  
    56369 
    56370 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    56371 
    56372 Chain information for AF3 E2 353-438.pdb #415 
    56373 --- 
    56374 Chain | Description 
    56375 B | No description available 
    56376  
    56377 
    56378 > matchmaker #415 to #1.23 & sel
    56379 
    56380 Parameters 
    56381 --- 
    56382 Chain pairing | bb 
    56383 Alignment algorithm | Needleman-Wunsch 
    56384 Similarity matrix | BLOSUM-62 
    56385 SS fraction | 0.3 
    56386 Gap open (HH/SS/other) | 18/18/6 
    56387 Gap extend | 1 
    56388 SS matrix |  |  | H | S | O 
    56389 ---|---|---|--- 
    56390 H | 6 | -9 | -6 
    56391 S |  | 6 | -6 
    56392 O |  |  | 4 
    56393 Iteration cutoff | 2 
    56394  
    56395 Matchmaker 3j0c.pdb1, chain E (#1.23) with AF3 E2 353-438.pdb, chain B (#415),
    56396 sequence alignment score = 340.2 
    56397 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    56398 8.673) 
    56399  
    56400 
    56401 > hide sel cartoons
    56402 
    56403 > select #1.23/F
    56404 
    56405 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    56406 
    56407 > show sel cartoons
    56408 
    56409 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    56410 
    56411 Chain information for AF3 CA.pdb #416 
    56412 --- 
    56413 Chain | Description 
    56414 A | No description available 
    56415  
    56416 
    56417 > matchmaker #416 to #1.23 & sel
    56418 
    56419 Parameters 
    56420 --- 
    56421 Chain pairing | bb 
    56422 Alignment algorithm | Needleman-Wunsch 
    56423 Similarity matrix | BLOSUM-62 
    56424 SS fraction | 0.3 
    56425 Gap open (HH/SS/other) | 18/18/6 
    56426 Gap extend | 1 
    56427 SS matrix |  |  | H | S | O 
    56428 ---|---|---|--- 
    56429 H | 6 | -9 | -6 
    56430 S |  | 6 | -6 
    56431 O |  |  | 4 
    56432 Iteration cutoff | 2 
    56433  
    56434 Matchmaker 3j0c.pdb1, chain F (#1.23) with AF3 CA.pdb, chain A (#416),
    56435 sequence alignment score = 335.3 
    56436 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    56437 2.550) 
    56438  
    56439 
    56440 > hide sel cartoons
    56441 
    56442 > color #412 dodgerblue
    56443 
    56444 > color #413 dodgerblue
    56445 
    56446 > color #414 #00b305ff
    56447 
    56448 > color #415 #00b305ff
    56449 
    56450 > color #416 #f15839ff
    56451 
    56452 > select #1.24/D
    56453 
    56454 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    56455 
    56456 > show sel cartoons
    56457 
    56458 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    56459 
    56460 Chain information for AF3 E1 1-421.pdb #417 
    56461 --- 
    56462 Chain | Description 
    56463 A | No description available 
    56464  
    56465 
    56466 > matchmaker #417 to #1.24 & sel
    56467 
    56468 Parameters 
    56469 --- 
    56470 Chain pairing | bb 
    56471 Alignment algorithm | Needleman-Wunsch 
    56472 Similarity matrix | BLOSUM-62 
    56473 SS fraction | 0.3 
    56474 Gap open (HH/SS/other) | 18/18/6 
    56475 Gap extend | 1 
    56476 SS matrix |  |  | H | S | O 
    56477 ---|---|---|--- 
    56478 H | 6 | -9 | -6 
    56479 S |  | 6 | -6 
    56480 O |  |  | 4 
    56481 Iteration cutoff | 2 
    56482  
    56483 Matchmaker 3j0c.pdb1, chain D (#1.24) with AF3 E1 1-421.pdb, chain A (#417),
    56484 sequence alignment score = 1060.7 
    56485 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    56486 3.032) 
    56487  
    56488 
    56489 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    56490 
    56491 Chain information for AF3 E1 422-461.pdb #418 
    56492 --- 
    56493 Chain | Description 
    56494 A | No description available 
    56495  
    56496 
    56497 > matchmaker #418 to #1.24 & sel
    56498 
    56499 Parameters 
    56500 --- 
    56501 Chain pairing | bb 
    56502 Alignment algorithm | Needleman-Wunsch 
    56503 Similarity matrix | BLOSUM-62 
    56504 SS fraction | 0.3 
    56505 Gap open (HH/SS/other) | 18/18/6 
    56506 Gap extend | 1 
    56507 SS matrix |  |  | H | S | O 
    56508 ---|---|---|--- 
    56509 H | 6 | -9 | -6 
    56510 S |  | 6 | -6 
    56511 O |  |  | 4 
    56512 Iteration cutoff | 2 
    56513  
    56514 Matchmaker 3j0c.pdb1, chain D (#1.24) with AF3 E1 422-461.pdb, chain A (#418),
    56515 sequence alignment score = 626.9 
    56516 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    56517 2.916) 
    56518  
    56519 
    56520 > hide sel cartoons
    56521 
    56522 > select #1.24/E
    56523 
    56524 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    56525 
    56526 > show sel cartoons
    56527 
    56528 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    56529 
    56530 Chain information for AF3 E2 1-352.pdb #419 
    56531 --- 
    56532 Chain | Description 
    56533 B | No description available 
    56534  
    56535 
    56536 > matchmaker #419 to #1.24 & sel
    56537 
    56538 Parameters 
    56539 --- 
    56540 Chain pairing | bb 
    56541 Alignment algorithm | Needleman-Wunsch 
    56542 Similarity matrix | BLOSUM-62 
    56543 SS fraction | 0.3 
    56544 Gap open (HH/SS/other) | 18/18/6 
    56545 Gap extend | 1 
    56546 SS matrix |  |  | H | S | O 
    56547 ---|---|---|--- 
    56548 H | 6 | -9 | -6 
    56549 S |  | 6 | -6 
    56550 O |  |  | 4 
    56551 Iteration cutoff | 2 
    56552  
    56553 Matchmaker 3j0c.pdb1, chain E (#1.24) with AF3 E2 1-352.pdb, chain B (#419),
    56554 sequence alignment score = 594.5 
    56555 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    56556 6.147) 
    56557  
    56558 
    56559 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    56560 
    56561 Chain information for AF3 E2 353-438.pdb #420 
    56562 --- 
    56563 Chain | Description 
    56564 B | No description available 
    56565  
    56566 
    56567 > matchmaker #420 to #1.24 & sel
    56568 
    56569 Parameters 
    56570 --- 
    56571 Chain pairing | bb 
    56572 Alignment algorithm | Needleman-Wunsch 
    56573 Similarity matrix | BLOSUM-62 
    56574 SS fraction | 0.3 
    56575 Gap open (HH/SS/other) | 18/18/6 
    56576 Gap extend | 1 
    56577 SS matrix |  |  | H | S | O 
    56578 ---|---|---|--- 
    56579 H | 6 | -9 | -6 
    56580 S |  | 6 | -6 
    56581 O |  |  | 4 
    56582 Iteration cutoff | 2 
    56583  
    56584 Matchmaker 3j0c.pdb1, chain E (#1.24) with AF3 E2 353-438.pdb, chain B (#420),
    56585 sequence alignment score = 340.2 
    56586 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    56587 8.673) 
    56588  
    56589 
    56590 > hide sel cartoons
    56591 
    56592 > select #1.24/F
    56593 
    56594 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    56595 
    56596 > show sel cartoons
    56597 
    56598 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    56599 
    56600 Chain information for AF3 CA.pdb #421 
    56601 --- 
    56602 Chain | Description 
    56603 A | No description available 
    56604  
    56605 
    56606 > matchmaker #421 to #1.24 & sel
    56607 
    56608 Parameters 
    56609 --- 
    56610 Chain pairing | bb 
    56611 Alignment algorithm | Needleman-Wunsch 
    56612 Similarity matrix | BLOSUM-62 
    56613 SS fraction | 0.3 
    56614 Gap open (HH/SS/other) | 18/18/6 
    56615 Gap extend | 1 
    56616 SS matrix |  |  | H | S | O 
    56617 ---|---|---|--- 
    56618 H | 6 | -9 | -6 
    56619 S |  | 6 | -6 
    56620 O |  |  | 4 
    56621 Iteration cutoff | 2 
    56622  
    56623 Matchmaker 3j0c.pdb1, chain F (#1.24) with AF3 CA.pdb, chain A (#421),
    56624 sequence alignment score = 335.3 
    56625 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    56626 2.550) 
    56627  
    56628 
    56629 > hide sel cartoons
    56630 
    56631 > color #417 dodgerblue
    56632 
    56633 > color #418 dodgerblue
    56634 
    56635 > color #419 #00b305ff
    56636 
    56637 > color #420 #00b305ff
    56638 
    56639 > color #421 #f15839ff
    56640 
    56641 > select #1.25/D
    56642 
    56643 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    56644 
    56645 > show sel cartoons
    56646 
    56647 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    56648 
    56649 Chain information for AF3 E1 1-421.pdb #422 
    56650 --- 
    56651 Chain | Description 
    56652 A | No description available 
    56653  
    56654 
    56655 > matchmaker #422 to #1.25 & sel
    56656 
    56657 Parameters 
    56658 --- 
    56659 Chain pairing | bb 
    56660 Alignment algorithm | Needleman-Wunsch 
    56661 Similarity matrix | BLOSUM-62 
    56662 SS fraction | 0.3 
    56663 Gap open (HH/SS/other) | 18/18/6 
    56664 Gap extend | 1 
    56665 SS matrix |  |  | H | S | O 
    56666 ---|---|---|--- 
    56667 H | 6 | -9 | -6 
    56668 S |  | 6 | -6 
    56669 O |  |  | 4 
    56670 Iteration cutoff | 2 
    56671  
    56672 Matchmaker 3j0c.pdb1, chain D (#1.25) with AF3 E1 1-421.pdb, chain A (#422),
    56673 sequence alignment score = 1060.7 
    56674 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    56675 3.032) 
    56676  
    56677 
    56678 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    56679 
    56680 Chain information for AF3 E1 422-461.pdb #423 
    56681 --- 
    56682 Chain | Description 
    56683 A | No description available 
    56684  
    56685 
    56686 > matchmaker #423 to #1.25 & sel
    56687 
    56688 Parameters 
    56689 --- 
    56690 Chain pairing | bb 
    56691 Alignment algorithm | Needleman-Wunsch 
    56692 Similarity matrix | BLOSUM-62 
    56693 SS fraction | 0.3 
    56694 Gap open (HH/SS/other) | 18/18/6 
    56695 Gap extend | 1 
    56696 SS matrix |  |  | H | S | O 
    56697 ---|---|---|--- 
    56698 H | 6 | -9 | -6 
    56699 S |  | 6 | -6 
    56700 O |  |  | 4 
    56701 Iteration cutoff | 2 
    56702  
    56703 Matchmaker 3j0c.pdb1, chain D (#1.25) with AF3 E1 422-461.pdb, chain A (#423),
    56704 sequence alignment score = 626.9 
    56705 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    56706 2.916) 
    56707  
    56708 
    56709 > hide sel cartoons
    56710 
    56711 > select #1.25/E
    56712 
    56713 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    56714 
    56715 > show sel cartoons
    56716 
    56717 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    56718 
    56719 Chain information for AF3 E2 1-352.pdb #424 
    56720 --- 
    56721 Chain | Description 
    56722 B | No description available 
    56723  
    56724 
    56725 > matchmaker #424 to #1.25 & sel
    56726 
    56727 Parameters 
    56728 --- 
    56729 Chain pairing | bb 
    56730 Alignment algorithm | Needleman-Wunsch 
    56731 Similarity matrix | BLOSUM-62 
    56732 SS fraction | 0.3 
    56733 Gap open (HH/SS/other) | 18/18/6 
    56734 Gap extend | 1 
    56735 SS matrix |  |  | H | S | O 
    56736 ---|---|---|--- 
    56737 H | 6 | -9 | -6 
    56738 S |  | 6 | -6 
    56739 O |  |  | 4 
    56740 Iteration cutoff | 2 
    56741  
    56742 Matchmaker 3j0c.pdb1, chain E (#1.25) with AF3 E2 1-352.pdb, chain B (#424),
    56743 sequence alignment score = 594.5 
    56744 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    56745 6.147) 
    56746  
    56747 
    56748 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    56749 
    56750 Chain information for AF3 E2 353-438.pdb #425 
    56751 --- 
    56752 Chain | Description 
    56753 B | No description available 
    56754  
    56755 
    56756 > matchmaker #425 to #1.25 & sel
    56757 
    56758 Parameters 
    56759 --- 
    56760 Chain pairing | bb 
    56761 Alignment algorithm | Needleman-Wunsch 
    56762 Similarity matrix | BLOSUM-62 
    56763 SS fraction | 0.3 
    56764 Gap open (HH/SS/other) | 18/18/6 
    56765 Gap extend | 1 
    56766 SS matrix |  |  | H | S | O 
    56767 ---|---|---|--- 
    56768 H | 6 | -9 | -6 
    56769 S |  | 6 | -6 
    56770 O |  |  | 4 
    56771 Iteration cutoff | 2 
    56772  
    56773 Matchmaker 3j0c.pdb1, chain E (#1.25) with AF3 E2 353-438.pdb, chain B (#425),
    56774 sequence alignment score = 340.2 
    56775 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    56776 8.673) 
    56777  
    56778 
    56779 > hide sel cartoons
    56780 
    56781 > select #1.25/F
    56782 
    56783 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    56784 
    56785 > show sel cartoons
    56786 
    56787 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    56788 
    56789 Chain information for AF3 CA.pdb #426 
    56790 --- 
    56791 Chain | Description 
    56792 A | No description available 
    56793  
    56794 
    56795 > matchmaker #426 to #1.25 & sel
    56796 
    56797 Parameters 
    56798 --- 
    56799 Chain pairing | bb 
    56800 Alignment algorithm | Needleman-Wunsch 
    56801 Similarity matrix | BLOSUM-62 
    56802 SS fraction | 0.3 
    56803 Gap open (HH/SS/other) | 18/18/6 
    56804 Gap extend | 1 
    56805 SS matrix |  |  | H | S | O 
    56806 ---|---|---|--- 
    56807 H | 6 | -9 | -6 
    56808 S |  | 6 | -6 
    56809 O |  |  | 4 
    56810 Iteration cutoff | 2 
    56811  
    56812 Matchmaker 3j0c.pdb1, chain F (#1.25) with AF3 CA.pdb, chain A (#426),
    56813 sequence alignment score = 335.3 
    56814 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    56815 2.550) 
    56816  
    56817 
    56818 > hide sel cartoons
    56819 
    56820 > color #422 dodgerblue
    56821 
    56822 > color #423 dodgerblue
    56823 
    56824 > color #424 #00b305ff
    56825 
    56826 > color #425 #00b305ff
    56827 
    56828 > color #426 #f15839ff
    56829 
    56830 > select #1.26/D
    56831 
    56832 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    56833 
    56834 > show sel cartoons
    56835 
    56836 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    56837 
    56838 Chain information for AF3 E1 1-421.pdb #427 
    56839 --- 
    56840 Chain | Description 
    56841 A | No description available 
    56842  
    56843 
    56844 > matchmaker #427 to #1.26 & sel
    56845 
    56846 Parameters 
    56847 --- 
    56848 Chain pairing | bb 
    56849 Alignment algorithm | Needleman-Wunsch 
    56850 Similarity matrix | BLOSUM-62 
    56851 SS fraction | 0.3 
    56852 Gap open (HH/SS/other) | 18/18/6 
    56853 Gap extend | 1 
    56854 SS matrix |  |  | H | S | O 
    56855 ---|---|---|--- 
    56856 H | 6 | -9 | -6 
    56857 S |  | 6 | -6 
    56858 O |  |  | 4 
    56859 Iteration cutoff | 2 
    56860  
    56861 Matchmaker 3j0c.pdb1, chain D (#1.26) with AF3 E1 1-421.pdb, chain A (#427),
    56862 sequence alignment score = 1060.7 
    56863 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    56864 3.032) 
    56865  
    56866 
    56867 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    56868 
    56869 Chain information for AF3 E1 422-461.pdb #428 
    56870 --- 
    56871 Chain | Description 
    56872 A | No description available 
    56873  
    56874 
    56875 > matchmaker #428 to #1.26 & sel
    56876 
    56877 Parameters 
    56878 --- 
    56879 Chain pairing | bb 
    56880 Alignment algorithm | Needleman-Wunsch 
    56881 Similarity matrix | BLOSUM-62 
    56882 SS fraction | 0.3 
    56883 Gap open (HH/SS/other) | 18/18/6 
    56884 Gap extend | 1 
    56885 SS matrix |  |  | H | S | O 
    56886 ---|---|---|--- 
    56887 H | 6 | -9 | -6 
    56888 S |  | 6 | -6 
    56889 O |  |  | 4 
    56890 Iteration cutoff | 2 
    56891  
    56892 Matchmaker 3j0c.pdb1, chain D (#1.26) with AF3 E1 422-461.pdb, chain A (#428),
    56893 sequence alignment score = 626.9 
    56894 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    56895 2.916) 
    56896  
    56897 
    56898 > hide sel cartoons
    56899 
    56900 > select #1.26/E
    56901 
    56902 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    56903 
    56904 > show sel cartoons
    56905 
    56906 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    56907 
    56908 Chain information for AF3 E2 1-352.pdb #429 
    56909 --- 
    56910 Chain | Description 
    56911 B | No description available 
    56912  
    56913 
    56914 > matchmaker #429 to #1.26 & sel
    56915 
    56916 Parameters 
    56917 --- 
    56918 Chain pairing | bb 
    56919 Alignment algorithm | Needleman-Wunsch 
    56920 Similarity matrix | BLOSUM-62 
    56921 SS fraction | 0.3 
    56922 Gap open (HH/SS/other) | 18/18/6 
    56923 Gap extend | 1 
    56924 SS matrix |  |  | H | S | O 
    56925 ---|---|---|--- 
    56926 H | 6 | -9 | -6 
    56927 S |  | 6 | -6 
    56928 O |  |  | 4 
    56929 Iteration cutoff | 2 
    56930  
    56931 Matchmaker 3j0c.pdb1, chain E (#1.26) with AF3 E2 1-352.pdb, chain B (#429),
    56932 sequence alignment score = 594.5 
    56933 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    56934 6.147) 
    56935  
    56936 
    56937 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    56938 
    56939 Chain information for AF3 E2 353-438.pdb #430 
    56940 --- 
    56941 Chain | Description 
    56942 B | No description available 
    56943  
    56944 
    56945 > matchmaker #430 to #1.26 & sel
    56946 
    56947 Parameters 
    56948 --- 
    56949 Chain pairing | bb 
    56950 Alignment algorithm | Needleman-Wunsch 
    56951 Similarity matrix | BLOSUM-62 
    56952 SS fraction | 0.3 
    56953 Gap open (HH/SS/other) | 18/18/6 
    56954 Gap extend | 1 
    56955 SS matrix |  |  | H | S | O 
    56956 ---|---|---|--- 
    56957 H | 6 | -9 | -6 
    56958 S |  | 6 | -6 
    56959 O |  |  | 4 
    56960 Iteration cutoff | 2 
    56961  
    56962 Matchmaker 3j0c.pdb1, chain E (#1.26) with AF3 E2 353-438.pdb, chain B (#430),
    56963 sequence alignment score = 340.2 
    56964 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    56965 8.673) 
    56966  
    56967 
    56968 > hide sel cartoons
    56969 
    56970 > select #1.26/F
    56971 
    56972 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    56973 
    56974 > show sel cartoons
    56975 
    56976 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    56977 
    56978 Chain information for AF3 CA.pdb #431 
    56979 --- 
    56980 Chain | Description 
    56981 A | No description available 
    56982  
    56983 
    56984 > matchmaker #431 to #1.26 & sel
    56985 
    56986 Parameters 
    56987 --- 
    56988 Chain pairing | bb 
    56989 Alignment algorithm | Needleman-Wunsch 
    56990 Similarity matrix | BLOSUM-62 
    56991 SS fraction | 0.3 
    56992 Gap open (HH/SS/other) | 18/18/6 
    56993 Gap extend | 1 
    56994 SS matrix |  |  | H | S | O 
    56995 ---|---|---|--- 
    56996 H | 6 | -9 | -6 
    56997 S |  | 6 | -6 
    56998 O |  |  | 4 
    56999 Iteration cutoff | 2 
    57000  
    57001 Matchmaker 3j0c.pdb1, chain F (#1.26) with AF3 CA.pdb, chain A (#431),
    57002 sequence alignment score = 335.3 
    57003 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    57004 2.550) 
    57005  
    57006 
    57007 > hide sel cartoons
    57008 
    57009 > color #427 dodgerblue
    57010 
    57011 > color #428 dodgerblue
    57012 
    57013 > color #429 #00b305ff
    57014 
    57015 > color #430 #00b305ff
    57016 
    57017 > color #431 #f15839ff
    57018 
    57019 > select #1.27/D
    57020 
    57021 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    57022 
    57023 > show sel cartoons
    57024 
    57025 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    57026 
    57027 Chain information for AF3 E1 1-421.pdb #432 
    57028 --- 
    57029 Chain | Description 
    57030 A | No description available 
    57031  
    57032 
    57033 > matchmaker #432 to #1.27 & sel
    57034 
    57035 Parameters 
    57036 --- 
    57037 Chain pairing | bb 
    57038 Alignment algorithm | Needleman-Wunsch 
    57039 Similarity matrix | BLOSUM-62 
    57040 SS fraction | 0.3 
    57041 Gap open (HH/SS/other) | 18/18/6 
    57042 Gap extend | 1 
    57043 SS matrix |  |  | H | S | O 
    57044 ---|---|---|--- 
    57045 H | 6 | -9 | -6 
    57046 S |  | 6 | -6 
    57047 O |  |  | 4 
    57048 Iteration cutoff | 2 
    57049  
    57050 Matchmaker 3j0c.pdb1, chain D (#1.27) with AF3 E1 1-421.pdb, chain A (#432),
    57051 sequence alignment score = 1060.7 
    57052 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    57053 3.032) 
    57054  
    57055 
    57056 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    57057 
    57058 Chain information for AF3 E1 422-461.pdb #433 
    57059 --- 
    57060 Chain | Description 
    57061 A | No description available 
    57062  
    57063 
    57064 > matchmaker #433 to #1.27 & sel
    57065 
    57066 Parameters 
    57067 --- 
    57068 Chain pairing | bb 
    57069 Alignment algorithm | Needleman-Wunsch 
    57070 Similarity matrix | BLOSUM-62 
    57071 SS fraction | 0.3 
    57072 Gap open (HH/SS/other) | 18/18/6 
    57073 Gap extend | 1 
    57074 SS matrix |  |  | H | S | O 
    57075 ---|---|---|--- 
    57076 H | 6 | -9 | -6 
    57077 S |  | 6 | -6 
    57078 O |  |  | 4 
    57079 Iteration cutoff | 2 
    57080  
    57081 Matchmaker 3j0c.pdb1, chain D (#1.27) with AF3 E1 422-461.pdb, chain A (#433),
    57082 sequence alignment score = 626.9 
    57083 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    57084 2.916) 
    57085  
    57086 
    57087 > hide sel cartoons
    57088 
    57089 > select #1.27/E
    57090 
    57091 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    57092 
    57093 > show sel cartoons
    57094 
    57095 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    57096 
    57097 Chain information for AF3 E2 1-352.pdb #434 
    57098 --- 
    57099 Chain | Description 
    57100 B | No description available 
    57101  
    57102 
    57103 > matchmaker #434 to #1.27 & sel
    57104 
    57105 Parameters 
    57106 --- 
    57107 Chain pairing | bb 
    57108 Alignment algorithm | Needleman-Wunsch 
    57109 Similarity matrix | BLOSUM-62 
    57110 SS fraction | 0.3 
    57111 Gap open (HH/SS/other) | 18/18/6 
    57112 Gap extend | 1 
    57113 SS matrix |  |  | H | S | O 
    57114 ---|---|---|--- 
    57115 H | 6 | -9 | -6 
    57116 S |  | 6 | -6 
    57117 O |  |  | 4 
    57118 Iteration cutoff | 2 
    57119  
    57120 Matchmaker 3j0c.pdb1, chain E (#1.27) with AF3 E2 1-352.pdb, chain B (#434),
    57121 sequence alignment score = 594.5 
    57122 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    57123 6.147) 
    57124  
    57125 
    57126 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    57127 
    57128 Chain information for AF3 E2 353-438.pdb #435 
    57129 --- 
    57130 Chain | Description 
    57131 B | No description available 
    57132  
    57133 
    57134 > matchmaker #435 to #1.27 & sel
    57135 
    57136 Parameters 
    57137 --- 
    57138 Chain pairing | bb 
    57139 Alignment algorithm | Needleman-Wunsch 
    57140 Similarity matrix | BLOSUM-62 
    57141 SS fraction | 0.3 
    57142 Gap open (HH/SS/other) | 18/18/6 
    57143 Gap extend | 1 
    57144 SS matrix |  |  | H | S | O 
    57145 ---|---|---|--- 
    57146 H | 6 | -9 | -6 
    57147 S |  | 6 | -6 
    57148 O |  |  | 4 
    57149 Iteration cutoff | 2 
    57150  
    57151 Matchmaker 3j0c.pdb1, chain E (#1.27) with AF3 E2 353-438.pdb, chain B (#435),
    57152 sequence alignment score = 340.2 
    57153 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    57154 8.673) 
    57155  
    57156 
    57157 > hide sel cartoons
    57158 
    57159 > select #1.27/F
    57160 
    57161 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    57162 
    57163 > show sel cartoons
    57164 
    57165 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    57166 
    57167 Chain information for AF3 CA.pdb #436 
    57168 --- 
    57169 Chain | Description 
    57170 A | No description available 
    57171  
    57172 
    57173 > matchmaker #436 to #1.27 & sel
    57174 
    57175 Parameters 
    57176 --- 
    57177 Chain pairing | bb 
    57178 Alignment algorithm | Needleman-Wunsch 
    57179 Similarity matrix | BLOSUM-62 
    57180 SS fraction | 0.3 
    57181 Gap open (HH/SS/other) | 18/18/6 
    57182 Gap extend | 1 
    57183 SS matrix |  |  | H | S | O 
    57184 ---|---|---|--- 
    57185 H | 6 | -9 | -6 
    57186 S |  | 6 | -6 
    57187 O |  |  | 4 
    57188 Iteration cutoff | 2 
    57189  
    57190 Matchmaker 3j0c.pdb1, chain F (#1.27) with AF3 CA.pdb, chain A (#436),
    57191 sequence alignment score = 335.3 
    57192 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    57193 2.550) 
    57194  
    57195 
    57196 > hide sel cartoons
    57197 
    57198 > color #432 dodgerblue
    57199 
    57200 > color #433 dodgerblue
    57201 
    57202 > color #434 #00b305ff
    57203 
    57204 > color #435 #00b305ff
    57205 
    57206 > color #436 #f15839ff
    57207 
    57208 > select #1.28/D
    57209 
    57210 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    57211 
    57212 > show sel cartoons
    57213 
    57214 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    57215 
    57216 Chain information for AF3 E1 1-421.pdb #437 
    57217 --- 
    57218 Chain | Description 
    57219 A | No description available 
    57220  
    57221 
    57222 > matchmaker #437 to #1.28 & sel
    57223 
    57224 Parameters 
    57225 --- 
    57226 Chain pairing | bb 
    57227 Alignment algorithm | Needleman-Wunsch 
    57228 Similarity matrix | BLOSUM-62 
    57229 SS fraction | 0.3 
    57230 Gap open (HH/SS/other) | 18/18/6 
    57231 Gap extend | 1 
    57232 SS matrix |  |  | H | S | O 
    57233 ---|---|---|--- 
    57234 H | 6 | -9 | -6 
    57235 S |  | 6 | -6 
    57236 O |  |  | 4 
    57237 Iteration cutoff | 2 
    57238  
    57239 Matchmaker 3j0c.pdb1, chain D (#1.28) with AF3 E1 1-421.pdb, chain A (#437),
    57240 sequence alignment score = 1060.7 
    57241 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    57242 3.032) 
    57243  
    57244 
    57245 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    57246 
    57247 Chain information for AF3 E1 422-461.pdb #438 
    57248 --- 
    57249 Chain | Description 
    57250 A | No description available 
    57251  
    57252 
    57253 > matchmaker #438 to #1.28 & sel
    57254 
    57255 Parameters 
    57256 --- 
    57257 Chain pairing | bb 
    57258 Alignment algorithm | Needleman-Wunsch 
    57259 Similarity matrix | BLOSUM-62 
    57260 SS fraction | 0.3 
    57261 Gap open (HH/SS/other) | 18/18/6 
    57262 Gap extend | 1 
    57263 SS matrix |  |  | H | S | O 
    57264 ---|---|---|--- 
    57265 H | 6 | -9 | -6 
    57266 S |  | 6 | -6 
    57267 O |  |  | 4 
    57268 Iteration cutoff | 2 
    57269  
    57270 Matchmaker 3j0c.pdb1, chain D (#1.28) with AF3 E1 422-461.pdb, chain A (#438),
    57271 sequence alignment score = 626.9 
    57272 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    57273 2.916) 
    57274  
    57275 
    57276 > hide sel cartoons
    57277 
    57278 > select #1.28/E
    57279 
    57280 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    57281 
    57282 > show sel cartoons
    57283 
    57284 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    57285 
    57286 Chain information for AF3 E2 1-352.pdb #439 
    57287 --- 
    57288 Chain | Description 
    57289 B | No description available 
    57290  
    57291 
    57292 > matchmaker #439 to #1.28 & sel
    57293 
    57294 Parameters 
    57295 --- 
    57296 Chain pairing | bb 
    57297 Alignment algorithm | Needleman-Wunsch 
    57298 Similarity matrix | BLOSUM-62 
    57299 SS fraction | 0.3 
    57300 Gap open (HH/SS/other) | 18/18/6 
    57301 Gap extend | 1 
    57302 SS matrix |  |  | H | S | O 
    57303 ---|---|---|--- 
    57304 H | 6 | -9 | -6 
    57305 S |  | 6 | -6 
    57306 O |  |  | 4 
    57307 Iteration cutoff | 2 
    57308  
    57309 Matchmaker 3j0c.pdb1, chain E (#1.28) with AF3 E2 1-352.pdb, chain B (#439),
    57310 sequence alignment score = 594.5 
    57311 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    57312 6.147) 
    57313  
    57314 
    57315 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    57316 
    57317 Chain information for AF3 E2 353-438.pdb #440 
    57318 --- 
    57319 Chain | Description 
    57320 B | No description available 
    57321  
    57322 
    57323 > matchmaker #440 to #1.28 & sel
    57324 
    57325 Parameters 
    57326 --- 
    57327 Chain pairing | bb 
    57328 Alignment algorithm | Needleman-Wunsch 
    57329 Similarity matrix | BLOSUM-62 
    57330 SS fraction | 0.3 
    57331 Gap open (HH/SS/other) | 18/18/6 
    57332 Gap extend | 1 
    57333 SS matrix |  |  | H | S | O 
    57334 ---|---|---|--- 
    57335 H | 6 | -9 | -6 
    57336 S |  | 6 | -6 
    57337 O |  |  | 4 
    57338 Iteration cutoff | 2 
    57339  
    57340 Matchmaker 3j0c.pdb1, chain E (#1.28) with AF3 E2 353-438.pdb, chain B (#440),
    57341 sequence alignment score = 340.2 
    57342 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    57343 8.673) 
    57344  
    57345 
    57346 > hide sel cartoons
    57347 
    57348 > select #1.28/F
    57349 
    57350 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    57351 
    57352 > show sel cartoons
    57353 
    57354 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    57355 
    57356 Chain information for AF3 CA.pdb #441 
    57357 --- 
    57358 Chain | Description 
    57359 A | No description available 
    57360  
    57361 
    57362 > matchmaker #441 to #1.28 & sel
    57363 
    57364 Parameters 
    57365 --- 
    57366 Chain pairing | bb 
    57367 Alignment algorithm | Needleman-Wunsch 
    57368 Similarity matrix | BLOSUM-62 
    57369 SS fraction | 0.3 
    57370 Gap open (HH/SS/other) | 18/18/6 
    57371 Gap extend | 1 
    57372 SS matrix |  |  | H | S | O 
    57373 ---|---|---|--- 
    57374 H | 6 | -9 | -6 
    57375 S |  | 6 | -6 
    57376 O |  |  | 4 
    57377 Iteration cutoff | 2 
    57378  
    57379 Matchmaker 3j0c.pdb1, chain F (#1.28) with AF3 CA.pdb, chain A (#441),
    57380 sequence alignment score = 335.3 
    57381 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    57382 2.550) 
    57383  
    57384 
    57385 > hide sel cartoons
    57386 
    57387 > color #437 dodgerblue
    57388 
    57389 > color #438 dodgerblue
    57390 
    57391 > color #439 #00b305ff
    57392 
    57393 > color #440 #00b305ff
    57394 
    57395 > color #441 #f15839ff
    57396 
    57397 > select #1.29/D
    57398 
    57399 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    57400 
    57401 > show sel cartoons
    57402 
    57403 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    57404 
    57405 Chain information for AF3 E1 1-421.pdb #442 
    57406 --- 
    57407 Chain | Description 
    57408 A | No description available 
    57409  
    57410 
    57411 > matchmaker #442 to #1.29 & sel
    57412 
    57413 Parameters 
    57414 --- 
    57415 Chain pairing | bb 
    57416 Alignment algorithm | Needleman-Wunsch 
    57417 Similarity matrix | BLOSUM-62 
    57418 SS fraction | 0.3 
    57419 Gap open (HH/SS/other) | 18/18/6 
    57420 Gap extend | 1 
    57421 SS matrix |  |  | H | S | O 
    57422 ---|---|---|--- 
    57423 H | 6 | -9 | -6 
    57424 S |  | 6 | -6 
    57425 O |  |  | 4 
    57426 Iteration cutoff | 2 
    57427  
    57428 Matchmaker 3j0c.pdb1, chain D (#1.29) with AF3 E1 1-421.pdb, chain A (#442),
    57429 sequence alignment score = 1060.7 
    57430 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    57431 3.032) 
    57432  
    57433 
    57434 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    57435 
    57436 Chain information for AF3 E1 422-461.pdb #443 
    57437 --- 
    57438 Chain | Description 
    57439 A | No description available 
    57440  
    57441 
    57442 > matchmaker #443 to #1.29 & sel
    57443 
    57444 Parameters 
    57445 --- 
    57446 Chain pairing | bb 
    57447 Alignment algorithm | Needleman-Wunsch 
    57448 Similarity matrix | BLOSUM-62 
    57449 SS fraction | 0.3 
    57450 Gap open (HH/SS/other) | 18/18/6 
    57451 Gap extend | 1 
    57452 SS matrix |  |  | H | S | O 
    57453 ---|---|---|--- 
    57454 H | 6 | -9 | -6 
    57455 S |  | 6 | -6 
    57456 O |  |  | 4 
    57457 Iteration cutoff | 2 
    57458  
    57459 Matchmaker 3j0c.pdb1, chain D (#1.29) with AF3 E1 422-461.pdb, chain A (#443),
    57460 sequence alignment score = 626.9 
    57461 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    57462 2.916) 
    57463  
    57464 
    57465 > hide sel cartoons
    57466 
    57467 > select #1.29/E
    57468 
    57469 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    57470 
    57471 > show sel cartoons
    57472 
    57473 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    57474 
    57475 Chain information for AF3 E2 1-352.pdb #444 
    57476 --- 
    57477 Chain | Description 
    57478 B | No description available 
    57479  
    57480 
    57481 > matchmaker #444 to #1.29 & sel
    57482 
    57483 Parameters 
    57484 --- 
    57485 Chain pairing | bb 
    57486 Alignment algorithm | Needleman-Wunsch 
    57487 Similarity matrix | BLOSUM-62 
    57488 SS fraction | 0.3 
    57489 Gap open (HH/SS/other) | 18/18/6 
    57490 Gap extend | 1 
    57491 SS matrix |  |  | H | S | O 
    57492 ---|---|---|--- 
    57493 H | 6 | -9 | -6 
    57494 S |  | 6 | -6 
    57495 O |  |  | 4 
    57496 Iteration cutoff | 2 
    57497  
    57498 Matchmaker 3j0c.pdb1, chain E (#1.29) with AF3 E2 1-352.pdb, chain B (#444),
    57499 sequence alignment score = 594.5 
    57500 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    57501 6.147) 
    57502  
    57503 
    57504 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    57505 
    57506 Chain information for AF3 E2 353-438.pdb #445 
    57507 --- 
    57508 Chain | Description 
    57509 B | No description available 
    57510  
    57511 
    57512 > matchmaker #445 to #1.29 & sel
    57513 
    57514 Parameters 
    57515 --- 
    57516 Chain pairing | bb 
    57517 Alignment algorithm | Needleman-Wunsch 
    57518 Similarity matrix | BLOSUM-62 
    57519 SS fraction | 0.3 
    57520 Gap open (HH/SS/other) | 18/18/6 
    57521 Gap extend | 1 
    57522 SS matrix |  |  | H | S | O 
    57523 ---|---|---|--- 
    57524 H | 6 | -9 | -6 
    57525 S |  | 6 | -6 
    57526 O |  |  | 4 
    57527 Iteration cutoff | 2 
    57528  
    57529 Matchmaker 3j0c.pdb1, chain E (#1.29) with AF3 E2 353-438.pdb, chain B (#445),
    57530 sequence alignment score = 340.2 
    57531 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    57532 8.673) 
    57533  
    57534 
    57535 > hide sel cartoons
    57536 
    57537 > select #1.29/F
    57538 
    57539 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    57540 
    57541 > show sel cartoons
    57542 
    57543 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    57544 
    57545 Chain information for AF3 CA.pdb #446 
    57546 --- 
    57547 Chain | Description 
    57548 A | No description available 
    57549  
    57550 
    57551 > matchmaker #446 to #1.29 & sel
    57552 
    57553 Parameters 
    57554 --- 
    57555 Chain pairing | bb 
    57556 Alignment algorithm | Needleman-Wunsch 
    57557 Similarity matrix | BLOSUM-62 
    57558 SS fraction | 0.3 
    57559 Gap open (HH/SS/other) | 18/18/6 
    57560 Gap extend | 1 
    57561 SS matrix |  |  | H | S | O 
    57562 ---|---|---|--- 
    57563 H | 6 | -9 | -6 
    57564 S |  | 6 | -6 
    57565 O |  |  | 4 
    57566 Iteration cutoff | 2 
    57567  
    57568 Matchmaker 3j0c.pdb1, chain F (#1.29) with AF3 CA.pdb, chain A (#446),
    57569 sequence alignment score = 335.3 
    57570 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    57571 2.550) 
    57572  
    57573 
    57574 > hide sel cartoons
    57575 
    57576 > color #442 dodgerblue
    57577 
    57578 > color #443 dodgerblue
    57579 
    57580 > color #444 #00b305ff
    57581 
    57582 > color #445 #00b305ff
    57583 
    57584 > color #446 #f15839ff
    57585 
    57586 > select #1.30/D
    57587 
    57588 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    57589 
    57590 > show sel cartoons
    57591 
    57592 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    57593 
    57594 Chain information for AF3 E1 1-421.pdb #447 
    57595 --- 
    57596 Chain | Description 
    57597 A | No description available 
    57598  
    57599 
    57600 > matchmaker #447 to #1.30 & sel
    57601 
    57602 Parameters 
    57603 --- 
    57604 Chain pairing | bb 
    57605 Alignment algorithm | Needleman-Wunsch 
    57606 Similarity matrix | BLOSUM-62 
    57607 SS fraction | 0.3 
    57608 Gap open (HH/SS/other) | 18/18/6 
    57609 Gap extend | 1 
    57610 SS matrix |  |  | H | S | O 
    57611 ---|---|---|--- 
    57612 H | 6 | -9 | -6 
    57613 S |  | 6 | -6 
    57614 O |  |  | 4 
    57615 Iteration cutoff | 2 
    57616  
    57617 Matchmaker 3j0c.pdb1, chain D (#1.30) with AF3 E1 1-421.pdb, chain A (#447),
    57618 sequence alignment score = 1060.7 
    57619 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    57620 3.032) 
    57621  
    57622 
    57623 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    57624 
    57625 Chain information for AF3 E1 422-461.pdb #448 
    57626 --- 
    57627 Chain | Description 
    57628 A | No description available 
    57629  
    57630 
    57631 > matchmaker #448 to #1.30 & sel
    57632 
    57633 Parameters 
    57634 --- 
    57635 Chain pairing | bb 
    57636 Alignment algorithm | Needleman-Wunsch 
    57637 Similarity matrix | BLOSUM-62 
    57638 SS fraction | 0.3 
    57639 Gap open (HH/SS/other) | 18/18/6 
    57640 Gap extend | 1 
    57641 SS matrix |  |  | H | S | O 
    57642 ---|---|---|--- 
    57643 H | 6 | -9 | -6 
    57644 S |  | 6 | -6 
    57645 O |  |  | 4 
    57646 Iteration cutoff | 2 
    57647  
    57648 Matchmaker 3j0c.pdb1, chain D (#1.30) with AF3 E1 422-461.pdb, chain A (#448),
    57649 sequence alignment score = 626.9 
    57650 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    57651 2.916) 
    57652  
    57653 
    57654 > hide sel cartoons
    57655 
    57656 > select #1.30/E
    57657 
    57658 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    57659 
    57660 > show sel cartoons
    57661 
    57662 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    57663 
    57664 Chain information for AF3 E2 1-352.pdb #449 
    57665 --- 
    57666 Chain | Description 
    57667 B | No description available 
    57668  
    57669 
    57670 > matchmaker #449 to #1.30 & sel
    57671 
    57672 Parameters 
    57673 --- 
    57674 Chain pairing | bb 
    57675 Alignment algorithm | Needleman-Wunsch 
    57676 Similarity matrix | BLOSUM-62 
    57677 SS fraction | 0.3 
    57678 Gap open (HH/SS/other) | 18/18/6 
    57679 Gap extend | 1 
    57680 SS matrix |  |  | H | S | O 
    57681 ---|---|---|--- 
    57682 H | 6 | -9 | -6 
    57683 S |  | 6 | -6 
    57684 O |  |  | 4 
    57685 Iteration cutoff | 2 
    57686  
    57687 Matchmaker 3j0c.pdb1, chain E (#1.30) with AF3 E2 1-352.pdb, chain B (#449),
    57688 sequence alignment score = 594.5 
    57689 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    57690 6.147) 
    57691  
    57692 
    57693 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    57694 
    57695 Chain information for AF3 E2 353-438.pdb #450 
    57696 --- 
    57697 Chain | Description 
    57698 B | No description available 
    57699  
    57700 
    57701 > matchmaker #450 to #1.30 & sel
    57702 
    57703 Parameters 
    57704 --- 
    57705 Chain pairing | bb 
    57706 Alignment algorithm | Needleman-Wunsch 
    57707 Similarity matrix | BLOSUM-62 
    57708 SS fraction | 0.3 
    57709 Gap open (HH/SS/other) | 18/18/6 
    57710 Gap extend | 1 
    57711 SS matrix |  |  | H | S | O 
    57712 ---|---|---|--- 
    57713 H | 6 | -9 | -6 
    57714 S |  | 6 | -6 
    57715 O |  |  | 4 
    57716 Iteration cutoff | 2 
    57717  
    57718 Matchmaker 3j0c.pdb1, chain E (#1.30) with AF3 E2 353-438.pdb, chain B (#450),
    57719 sequence alignment score = 340.2 
    57720 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    57721 8.673) 
    57722  
    57723 
    57724 > hide sel cartoons
    57725 
    57726 > select #1.30/F
    57727 
    57728 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    57729 
    57730 > show sel cartoons
    57731 
    57732 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    57733 
    57734 Chain information for AF3 CA.pdb #451 
    57735 --- 
    57736 Chain | Description 
    57737 A | No description available 
    57738  
    57739 
    57740 > matchmaker #451 to #1.30 & sel
    57741 
    57742 Parameters 
    57743 --- 
    57744 Chain pairing | bb 
    57745 Alignment algorithm | Needleman-Wunsch 
    57746 Similarity matrix | BLOSUM-62 
    57747 SS fraction | 0.3 
    57748 Gap open (HH/SS/other) | 18/18/6 
    57749 Gap extend | 1 
    57750 SS matrix |  |  | H | S | O 
    57751 ---|---|---|--- 
    57752 H | 6 | -9 | -6 
    57753 S |  | 6 | -6 
    57754 O |  |  | 4 
    57755 Iteration cutoff | 2 
    57756  
    57757 Matchmaker 3j0c.pdb1, chain F (#1.30) with AF3 CA.pdb, chain A (#451),
    57758 sequence alignment score = 335.3 
    57759 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    57760 2.550) 
    57761  
    57762 
    57763 > hide sel cartoons
    57764 
    57765 > color #447 dodgerblue
    57766 
    57767 > color #448 dodgerblue
    57768 
    57769 > color #449 #00b305ff
    57770 
    57771 > color #450 #00b305ff
    57772 
    57773 > color #451 #f15839ff
    57774 
    57775 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    57776 
    57777 > hide #397-451 models
    57778 
    57779 > select #1.31/D
    57780 
    57781 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    57782 
    57783 > show sel cartoons
    57784 
    57785 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    57786 
    57787 Chain information for AF3 E1 1-421.pdb #452 
    57788 --- 
    57789 Chain | Description 
    57790 A | No description available 
    57791  
    57792 
    57793 > matchmaker #452 to #1.31 & sel
    57794 
    57795 Parameters 
    57796 --- 
    57797 Chain pairing | bb 
    57798 Alignment algorithm | Needleman-Wunsch 
    57799 Similarity matrix | BLOSUM-62 
    57800 SS fraction | 0.3 
    57801 Gap open (HH/SS/other) | 18/18/6 
    57802 Gap extend | 1 
    57803 SS matrix |  |  | H | S | O 
    57804 ---|---|---|--- 
    57805 H | 6 | -9 | -6 
    57806 S |  | 6 | -6 
    57807 O |  |  | 4 
    57808 Iteration cutoff | 2 
    57809  
    57810 Matchmaker 3j0c.pdb1, chain D (#1.31) with AF3 E1 1-421.pdb, chain A (#452),
    57811 sequence alignment score = 1060.7 
    57812 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    57813 3.032) 
    57814  
    57815 
    57816 > view sel
    57817 
    57818 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    57819 
    57820 Chain information for AF3 E1 422-461.pdb #453 
    57821 --- 
    57822 Chain | Description 
    57823 A | No description available 
    57824  
    57825 
    57826 > matchmaker #453 to #1.31 & sel
    57827 
    57828 Parameters 
    57829 --- 
    57830 Chain pairing | bb 
    57831 Alignment algorithm | Needleman-Wunsch 
    57832 Similarity matrix | BLOSUM-62 
    57833 SS fraction | 0.3 
    57834 Gap open (HH/SS/other) | 18/18/6 
    57835 Gap extend | 1 
    57836 SS matrix |  |  | H | S | O 
    57837 ---|---|---|--- 
    57838 H | 6 | -9 | -6 
    57839 S |  | 6 | -6 
    57840 O |  |  | 4 
    57841 Iteration cutoff | 2 
    57842  
    57843 Matchmaker 3j0c.pdb1, chain D (#1.31) with AF3 E1 422-461.pdb, chain A (#453),
    57844 sequence alignment score = 626.9 
    57845 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    57846 2.916) 
    57847  
    57848 
    57849 > view
    57850 
    57851 > hide sel cartoons
    57852 
    57853 > select #1.31/E
    57854 
    57855 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    57856 
    57857 > show sel cartoons
    57858 
    57859 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    57860 
    57861 Chain information for AF3 E2 1-352.pdb #454 
    57862 --- 
    57863 Chain | Description 
    57864 B | No description available 
    57865  
    57866 
    57867 > matchmaker #454 to #1.31 & sel
    57868 
    57869 Parameters 
    57870 --- 
    57871 Chain pairing | bb 
    57872 Alignment algorithm | Needleman-Wunsch 
    57873 Similarity matrix | BLOSUM-62 
    57874 SS fraction | 0.3 
    57875 Gap open (HH/SS/other) | 18/18/6 
    57876 Gap extend | 1 
    57877 SS matrix |  |  | H | S | O 
    57878 ---|---|---|--- 
    57879 H | 6 | -9 | -6 
    57880 S |  | 6 | -6 
    57881 O |  |  | 4 
    57882 Iteration cutoff | 2 
    57883  
    57884 Matchmaker 3j0c.pdb1, chain E (#1.31) with AF3 E2 1-352.pdb, chain B (#454),
    57885 sequence alignment score = 594.5 
    57886 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    57887 6.147) 
    57888  
    57889 
    57890 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    57891 
    57892 Chain information for AF3 E2 353-438.pdb #455 
    57893 --- 
    57894 Chain | Description 
    57895 B | No description available 
    57896  
    57897 
    57898 > matchmaker #455 to #1.31 & sel
    57899 
    57900 Parameters 
    57901 --- 
    57902 Chain pairing | bb 
    57903 Alignment algorithm | Needleman-Wunsch 
    57904 Similarity matrix | BLOSUM-62 
    57905 SS fraction | 0.3 
    57906 Gap open (HH/SS/other) | 18/18/6 
    57907 Gap extend | 1 
    57908 SS matrix |  |  | H | S | O 
    57909 ---|---|---|--- 
    57910 H | 6 | -9 | -6 
    57911 S |  | 6 | -6 
    57912 O |  |  | 4 
    57913 Iteration cutoff | 2 
    57914  
    57915 Matchmaker 3j0c.pdb1, chain E (#1.31) with AF3 E2 353-438.pdb, chain B (#455),
    57916 sequence alignment score = 340.2 
    57917 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    57918 8.673) 
    57919  
    57920 
    57921 > hide sel cartoons
    57922 
    57923 > select #1.31/F
    57924 
    57925 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    57926 
    57927 > show sel cartoons
    57928 
    57929 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    57930 
    57931 Chain information for AF3 CA.pdb #456 
    57932 --- 
    57933 Chain | Description 
    57934 A | No description available 
    57935  
    57936 
    57937 > matchmaker #456 to #1.31 & sel
    57938 
    57939 Parameters 
    57940 --- 
    57941 Chain pairing | bb 
    57942 Alignment algorithm | Needleman-Wunsch 
    57943 Similarity matrix | BLOSUM-62 
    57944 SS fraction | 0.3 
    57945 Gap open (HH/SS/other) | 18/18/6 
    57946 Gap extend | 1 
    57947 SS matrix |  |  | H | S | O 
    57948 ---|---|---|--- 
    57949 H | 6 | -9 | -6 
    57950 S |  | 6 | -6 
    57951 O |  |  | 4 
    57952 Iteration cutoff | 2 
    57953  
    57954 Matchmaker 3j0c.pdb1, chain F (#1.31) with AF3 CA.pdb, chain A (#456),
    57955 sequence alignment score = 335.3 
    57956 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    57957 2.550) 
    57958  
    57959 
    57960 > hide sel cartoons
    57961 
    57962 > color #452 dodgerblue
    57963 
    57964 > color #453 dodgerblue
    57965 
    57966 > color #454 #00b305ff
    57967 
    57968 > color #455 #00b305ff
    57969 
    57970 > color #456 #f15839ff
    57971 
    57972 > select #1.32/D
    57973 
    57974 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    57975 
    57976 > show sel cartoons
    57977 
    57978 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    57979 
    57980 Chain information for AF3 E1 1-421.pdb #457 
    57981 --- 
    57982 Chain | Description 
    57983 A | No description available 
    57984  
    57985 
    57986 > matchmaker #457 to #1.32 & sel
    57987 
    57988 Parameters 
    57989 --- 
    57990 Chain pairing | bb 
    57991 Alignment algorithm | Needleman-Wunsch 
    57992 Similarity matrix | BLOSUM-62 
    57993 SS fraction | 0.3 
    57994 Gap open (HH/SS/other) | 18/18/6 
    57995 Gap extend | 1 
    57996 SS matrix |  |  | H | S | O 
    57997 ---|---|---|--- 
    57998 H | 6 | -9 | -6 
    57999 S |  | 6 | -6 
    58000 O |  |  | 4 
    58001 Iteration cutoff | 2 
    58002  
    58003 Matchmaker 3j0c.pdb1, chain D (#1.32) with AF3 E1 1-421.pdb, chain A (#457),
    58004 sequence alignment score = 1060.7 
    58005 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    58006 3.032) 
    58007  
    58008 
    58009 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    58010 
    58011 Chain information for AF3 E1 422-461.pdb #458 
    58012 --- 
    58013 Chain | Description 
    58014 A | No description available 
    58015  
    58016 
    58017 > matchmaker #458 to #1.32 & sel
    58018 
    58019 Parameters 
    58020 --- 
    58021 Chain pairing | bb 
    58022 Alignment algorithm | Needleman-Wunsch 
    58023 Similarity matrix | BLOSUM-62 
    58024 SS fraction | 0.3 
    58025 Gap open (HH/SS/other) | 18/18/6 
    58026 Gap extend | 1 
    58027 SS matrix |  |  | H | S | O 
    58028 ---|---|---|--- 
    58029 H | 6 | -9 | -6 
    58030 S |  | 6 | -6 
    58031 O |  |  | 4 
    58032 Iteration cutoff | 2 
    58033  
    58034 Matchmaker 3j0c.pdb1, chain D (#1.32) with AF3 E1 422-461.pdb, chain A (#458),
    58035 sequence alignment score = 626.9 
    58036 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    58037 2.916) 
    58038  
    58039 
    58040 > hide sel cartoons
    58041 
    58042 > select #1.31/E
    58043 
    58044 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    58045 
    58046 > show sel cartoons
    58047 
    58048 > hide sel cartoons
    58049 
    58050 > select #1.32/E
    58051 
    58052 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    58053 
    58054 > show sel cartoons
    58055 
    58056 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    58057 
    58058 Chain information for AF3 E2 1-352.pdb #459 
    58059 --- 
    58060 Chain | Description 
    58061 B | No description available 
    58062  
    58063 
    58064 > matchmaker #459 to #1.32 & sel
    58065 
    58066 Parameters 
    58067 --- 
    58068 Chain pairing | bb 
    58069 Alignment algorithm | Needleman-Wunsch 
    58070 Similarity matrix | BLOSUM-62 
    58071 SS fraction | 0.3 
    58072 Gap open (HH/SS/other) | 18/18/6 
    58073 Gap extend | 1 
    58074 SS matrix |  |  | H | S | O 
    58075 ---|---|---|--- 
    58076 H | 6 | -9 | -6 
    58077 S |  | 6 | -6 
    58078 O |  |  | 4 
    58079 Iteration cutoff | 2 
    58080  
    58081 Matchmaker 3j0c.pdb1, chain E (#1.32) with AF3 E2 1-352.pdb, chain B (#459),
    58082 sequence alignment score = 594.5 
    58083 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    58084 6.147) 
    58085  
    58086 
    58087 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    58088 
    58089 Chain information for AF3 E2 353-438.pdb #460 
    58090 --- 
    58091 Chain | Description 
    58092 B | No description available 
    58093  
    58094 
    58095 > matchmaker #460 to #1.32 & sel
    58096 
    58097 Parameters 
    58098 --- 
    58099 Chain pairing | bb 
    58100 Alignment algorithm | Needleman-Wunsch 
    58101 Similarity matrix | BLOSUM-62 
    58102 SS fraction | 0.3 
    58103 Gap open (HH/SS/other) | 18/18/6 
    58104 Gap extend | 1 
    58105 SS matrix |  |  | H | S | O 
    58106 ---|---|---|--- 
    58107 H | 6 | -9 | -6 
    58108 S |  | 6 | -6 
    58109 O |  |  | 4 
    58110 Iteration cutoff | 2 
    58111  
    58112 Matchmaker 3j0c.pdb1, chain E (#1.32) with AF3 E2 353-438.pdb, chain B (#460),
    58113 sequence alignment score = 340.2 
    58114 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    58115 8.673) 
    58116  
    58117 
    58118 > hide sel cartoons
    58119 
    58120 > select #1.32/F
    58121 
    58122 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    58123 
    58124 > show sel cartoons
    58125 
    58126 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    58127 
    58128 Chain information for AF3 CA.pdb #461 
    58129 --- 
    58130 Chain | Description 
    58131 A | No description available 
    58132  
    58133 
    58134 > matchmaker #461 to #1.32 & sel
    58135 
    58136 Parameters 
    58137 --- 
    58138 Chain pairing | bb 
    58139 Alignment algorithm | Needleman-Wunsch 
    58140 Similarity matrix | BLOSUM-62 
    58141 SS fraction | 0.3 
    58142 Gap open (HH/SS/other) | 18/18/6 
    58143 Gap extend | 1 
    58144 SS matrix |  |  | H | S | O 
    58145 ---|---|---|--- 
    58146 H | 6 | -9 | -6 
    58147 S |  | 6 | -6 
    58148 O |  |  | 4 
    58149 Iteration cutoff | 2 
    58150  
    58151 Matchmaker 3j0c.pdb1, chain F (#1.32) with AF3 CA.pdb, chain A (#461),
    58152 sequence alignment score = 335.3 
    58153 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    58154 2.550) 
    58155  
    58156 
    58157 > hide sel cartoons
    58158 
    58159 > color #457 dodgerblue
    58160 
    58161 > color #458 dodgerblue
    58162 
    58163 > color #459 #00b305ff
    58164 
    58165 > color #460 #00b305ff
    58166 
    58167 > color #461 #f15839ff
    58168 
    58169 > select #1.33/D
    58170 
    58171 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    58172 
    58173 > show sel cartoons
    58174 
    58175 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    58176 
    58177 Chain information for AF3 E1 1-421.pdb #462 
    58178 --- 
    58179 Chain | Description 
    58180 A | No description available 
    58181  
    58182 
    58183 > matchmaker #462 to #1.33 & sel
    58184 
    58185 Parameters 
    58186 --- 
    58187 Chain pairing | bb 
    58188 Alignment algorithm | Needleman-Wunsch 
    58189 Similarity matrix | BLOSUM-62 
    58190 SS fraction | 0.3 
    58191 Gap open (HH/SS/other) | 18/18/6 
    58192 Gap extend | 1 
    58193 SS matrix |  |  | H | S | O 
    58194 ---|---|---|--- 
    58195 H | 6 | -9 | -6 
    58196 S |  | 6 | -6 
    58197 O |  |  | 4 
    58198 Iteration cutoff | 2 
    58199  
    58200 Matchmaker 3j0c.pdb1, chain D (#1.33) with AF3 E1 1-421.pdb, chain A (#462),
    58201 sequence alignment score = 1060.7 
    58202 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    58203 3.032) 
    58204  
    58205 
    58206 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    58207 
    58208 Chain information for AF3 E1 422-461.pdb #463 
    58209 --- 
    58210 Chain | Description 
    58211 A | No description available 
    58212  
    58213 
    58214 > matchmaker #463 to #1.33 & sel
    58215 
    58216 Parameters 
    58217 --- 
    58218 Chain pairing | bb 
    58219 Alignment algorithm | Needleman-Wunsch 
    58220 Similarity matrix | BLOSUM-62 
    58221 SS fraction | 0.3 
    58222 Gap open (HH/SS/other) | 18/18/6 
    58223 Gap extend | 1 
    58224 SS matrix |  |  | H | S | O 
    58225 ---|---|---|--- 
    58226 H | 6 | -9 | -6 
    58227 S |  | 6 | -6 
    58228 O |  |  | 4 
    58229 Iteration cutoff | 2 
    58230  
    58231 Matchmaker 3j0c.pdb1, chain D (#1.33) with AF3 E1 422-461.pdb, chain A (#463),
    58232 sequence alignment score = 626.9 
    58233 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    58234 2.916) 
    58235  
    58236 
    58237 > hide sel cartoons
    58238 
    58239 > select #1.33/E
    58240 
    58241 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    58242 
    58243 > show sel cartoons
    58244 
    58245 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    58246 
    58247 Chain information for AF3 E2 1-352.pdb #464 
    58248 --- 
    58249 Chain | Description 
    58250 B | No description available 
    58251  
    58252 
    58253 > matchmaker #464 to #1.33 & sel
    58254 
    58255 Parameters 
    58256 --- 
    58257 Chain pairing | bb 
    58258 Alignment algorithm | Needleman-Wunsch 
    58259 Similarity matrix | BLOSUM-62 
    58260 SS fraction | 0.3 
    58261 Gap open (HH/SS/other) | 18/18/6 
    58262 Gap extend | 1 
    58263 SS matrix |  |  | H | S | O 
    58264 ---|---|---|--- 
    58265 H | 6 | -9 | -6 
    58266 S |  | 6 | -6 
    58267 O |  |  | 4 
    58268 Iteration cutoff | 2 
    58269  
    58270 Matchmaker 3j0c.pdb1, chain E (#1.33) with AF3 E2 1-352.pdb, chain B (#464),
    58271 sequence alignment score = 594.5 
    58272 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    58273 6.147) 
    58274  
    58275 
    58276 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    58277 
    58278 Chain information for AF3 E2 353-438.pdb #465 
    58279 --- 
    58280 Chain | Description 
    58281 B | No description available 
    58282  
    58283 
    58284 > matchmaker #465 to #1.33 & sel
    58285 
    58286 Parameters 
    58287 --- 
    58288 Chain pairing | bb 
    58289 Alignment algorithm | Needleman-Wunsch 
    58290 Similarity matrix | BLOSUM-62 
    58291 SS fraction | 0.3 
    58292 Gap open (HH/SS/other) | 18/18/6 
    58293 Gap extend | 1 
    58294 SS matrix |  |  | H | S | O 
    58295 ---|---|---|--- 
    58296 H | 6 | -9 | -6 
    58297 S |  | 6 | -6 
    58298 O |  |  | 4 
    58299 Iteration cutoff | 2 
    58300  
    58301 Matchmaker 3j0c.pdb1, chain E (#1.33) with AF3 E2 353-438.pdb, chain B (#465),
    58302 sequence alignment score = 340.2 
    58303 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    58304 8.673) 
    58305  
    58306 
    58307 > hide sel cartoons
    58308 
    58309 > select #1.33/F
    58310 
    58311 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    58312 
    58313 > show sel cartoons
    58314 
    58315 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    58316 
    58317 Chain information for AF3 CA.pdb #466 
    58318 --- 
    58319 Chain | Description 
    58320 A | No description available 
    58321  
    58322 
    58323 > matchmaker #466 to #1.33 & sel
    58324 
    58325 Parameters 
    58326 --- 
    58327 Chain pairing | bb 
    58328 Alignment algorithm | Needleman-Wunsch 
    58329 Similarity matrix | BLOSUM-62 
    58330 SS fraction | 0.3 
    58331 Gap open (HH/SS/other) | 18/18/6 
    58332 Gap extend | 1 
    58333 SS matrix |  |  | H | S | O 
    58334 ---|---|---|--- 
    58335 H | 6 | -9 | -6 
    58336 S |  | 6 | -6 
    58337 O |  |  | 4 
    58338 Iteration cutoff | 2 
    58339  
    58340 Matchmaker 3j0c.pdb1, chain F (#1.33) with AF3 CA.pdb, chain A (#466),
    58341 sequence alignment score = 335.3 
    58342 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    58343 2.550) 
    58344  
    58345 
    58346 > hide sel cartoons
    58347 
    58348 > color #462 dodgerblue
    58349 
    58350 > color #463 dodgerblue
    58351 
    58352 > color #464 #00b305ff
    58353 
    58354 > color #465 #00b305ff
    58355 
    58356 > color #466 #f15839ff
    58357 
    58358 > select #1.34/D
    58359 
    58360 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    58361 
    58362 > show sel cartoons
    58363 
    58364 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    58365 
    58366 Chain information for AF3 E1 1-421.pdb #467 
    58367 --- 
    58368 Chain | Description 
    58369 A | No description available 
    58370  
    58371 
    58372 > view
    58373 
    58374 > matchmaker #467 to #1.34 & sel
    58375 
    58376 Parameters 
    58377 --- 
    58378 Chain pairing | bb 
    58379 Alignment algorithm | Needleman-Wunsch 
    58380 Similarity matrix | BLOSUM-62 
    58381 SS fraction | 0.3 
    58382 Gap open (HH/SS/other) | 18/18/6 
    58383 Gap extend | 1 
    58384 SS matrix |  |  | H | S | O 
    58385 ---|---|---|--- 
    58386 H | 6 | -9 | -6 
    58387 S |  | 6 | -6 
    58388 O |  |  | 4 
    58389 Iteration cutoff | 2 
    58390  
    58391 Matchmaker 3j0c.pdb1, chain D (#1.34) with AF3 E1 1-421.pdb, chain A (#467),
    58392 sequence alignment score = 1060.7 
    58393 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    58394 3.032) 
    58395  
    58396 
    58397 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    58398 
    58399 Chain information for AF3 E1 422-461.pdb #468 
    58400 --- 
    58401 Chain | Description 
    58402 A | No description available 
    58403  
    58404 
    58405 > matchmaker #468 to #1.34 & sel
    58406 
    58407 Parameters 
    58408 --- 
    58409 Chain pairing | bb 
    58410 Alignment algorithm | Needleman-Wunsch 
    58411 Similarity matrix | BLOSUM-62 
    58412 SS fraction | 0.3 
    58413 Gap open (HH/SS/other) | 18/18/6 
    58414 Gap extend | 1 
    58415 SS matrix |  |  | H | S | O 
    58416 ---|---|---|--- 
    58417 H | 6 | -9 | -6 
    58418 S |  | 6 | -6 
    58419 O |  |  | 4 
    58420 Iteration cutoff | 2 
    58421  
    58422 Matchmaker 3j0c.pdb1, chain D (#1.34) with AF3 E1 422-461.pdb, chain A (#468),
    58423 sequence alignment score = 626.9 
    58424 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    58425 2.916) 
    58426  
    58427 
    58428 > hide sel cartoons
    58429 
    58430 > select #1.34/E
    58431 
    58432 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    58433 
    58434 > show sel cartoons
    58435 
    58436 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    58437 
    58438 Chain information for AF3 E2 1-352.pdb #469 
    58439 --- 
    58440 Chain | Description 
    58441 B | No description available 
    58442  
    58443 
    58444 > matchmaker #469 to #1.34 & sel
    58445 
    58446 Parameters 
    58447 --- 
    58448 Chain pairing | bb 
    58449 Alignment algorithm | Needleman-Wunsch 
    58450 Similarity matrix | BLOSUM-62 
    58451 SS fraction | 0.3 
    58452 Gap open (HH/SS/other) | 18/18/6 
    58453 Gap extend | 1 
    58454 SS matrix |  |  | H | S | O 
    58455 ---|---|---|--- 
    58456 H | 6 | -9 | -6 
    58457 S |  | 6 | -6 
    58458 O |  |  | 4 
    58459 Iteration cutoff | 2 
    58460  
    58461 Matchmaker 3j0c.pdb1, chain E (#1.34) with AF3 E2 1-352.pdb, chain B (#469),
    58462 sequence alignment score = 594.5 
    58463 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    58464 6.147) 
    58465  
    58466 
    58467 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    58468 
    58469 Chain information for AF3 E2 353-438.pdb #470 
    58470 --- 
    58471 Chain | Description 
    58472 B | No description available 
    58473  
    58474 
    58475 > matchmaker #470 to #1.34 & sel
    58476 
    58477 Parameters 
    58478 --- 
    58479 Chain pairing | bb 
    58480 Alignment algorithm | Needleman-Wunsch 
    58481 Similarity matrix | BLOSUM-62 
    58482 SS fraction | 0.3 
    58483 Gap open (HH/SS/other) | 18/18/6 
    58484 Gap extend | 1 
    58485 SS matrix |  |  | H | S | O 
    58486 ---|---|---|--- 
    58487 H | 6 | -9 | -6 
    58488 S |  | 6 | -6 
    58489 O |  |  | 4 
    58490 Iteration cutoff | 2 
    58491  
    58492 Matchmaker 3j0c.pdb1, chain E (#1.34) with AF3 E2 353-438.pdb, chain B (#470),
    58493 sequence alignment score = 340.2 
    58494 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    58495 8.673) 
    58496  
    58497 
    58498 > hide sel cartoons
    58499 
    58500 > select #1.34/F
    58501 
    58502 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    58503 
    58504 > show sel cartoons
    58505 
    58506 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    58507 
    58508 Chain information for AF3 CA.pdb #471 
    58509 --- 
    58510 Chain | Description 
    58511 A | No description available 
    58512  
    58513 
    58514 > matchmaker #471 to #1.34 & sel
    58515 
    58516 Parameters 
    58517 --- 
    58518 Chain pairing | bb 
    58519 Alignment algorithm | Needleman-Wunsch 
    58520 Similarity matrix | BLOSUM-62 
    58521 SS fraction | 0.3 
    58522 Gap open (HH/SS/other) | 18/18/6 
    58523 Gap extend | 1 
    58524 SS matrix |  |  | H | S | O 
    58525 ---|---|---|--- 
    58526 H | 6 | -9 | -6 
    58527 S |  | 6 | -6 
    58528 O |  |  | 4 
    58529 Iteration cutoff | 2 
    58530  
    58531 Matchmaker 3j0c.pdb1, chain F (#1.34) with AF3 CA.pdb, chain A (#471),
    58532 sequence alignment score = 335.3 
    58533 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    58534 2.550) 
    58535  
    58536 
    58537 > hide sel cartoons
    58538 
    58539 > color #467 dodgerblue
    58540 
    58541 > color #468 dodgerblue
    58542 
    58543 > color #469 #00b305ff
    58544 
    58545 > color #470 #00b305ff
    58546 
    58547 > color #471 #f15839ff
    58548 
    58549 > select #1.35/D
    58550 
    58551 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    58552 
    58553 > show sel cartoons
    58554 
    58555 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    58556 
    58557 Chain information for AF3 E1 1-421.pdb #472 
    58558 --- 
    58559 Chain | Description 
    58560 A | No description available 
    58561  
    58562 
    58563 > matchmaker #472 to #1.35 & sel
    58564 
    58565 Parameters 
    58566 --- 
    58567 Chain pairing | bb 
    58568 Alignment algorithm | Needleman-Wunsch 
    58569 Similarity matrix | BLOSUM-62 
    58570 SS fraction | 0.3 
    58571 Gap open (HH/SS/other) | 18/18/6 
    58572 Gap extend | 1 
    58573 SS matrix |  |  | H | S | O 
    58574 ---|---|---|--- 
    58575 H | 6 | -9 | -6 
    58576 S |  | 6 | -6 
    58577 O |  |  | 4 
    58578 Iteration cutoff | 2 
    58579  
    58580 Matchmaker 3j0c.pdb1, chain D (#1.35) with AF3 E1 1-421.pdb, chain A (#472),
    58581 sequence alignment score = 1060.7 
    58582 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    58583 3.032) 
    58584  
    58585 
    58586 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    58587 
    58588 Chain information for AF3 E1 422-461.pdb #473 
    58589 --- 
    58590 Chain | Description 
    58591 A | No description available 
    58592  
    58593 
    58594 > matchmaker #473 to #1.35 & sel
    58595 
    58596 Parameters 
    58597 --- 
    58598 Chain pairing | bb 
    58599 Alignment algorithm | Needleman-Wunsch 
    58600 Similarity matrix | BLOSUM-62 
    58601 SS fraction | 0.3 
    58602 Gap open (HH/SS/other) | 18/18/6 
    58603 Gap extend | 1 
    58604 SS matrix |  |  | H | S | O 
    58605 ---|---|---|--- 
    58606 H | 6 | -9 | -6 
    58607 S |  | 6 | -6 
    58608 O |  |  | 4 
    58609 Iteration cutoff | 2 
    58610  
    58611 Matchmaker 3j0c.pdb1, chain D (#1.35) with AF3 E1 422-461.pdb, chain A (#473),
    58612 sequence alignment score = 626.9 
    58613 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    58614 2.916) 
    58615  
    58616 
    58617 > hide sel cartoons
    58618 
    58619 > select #1.35/E
    58620 
    58621 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    58622 
    58623 > show sel cartoons
    58624 
    58625 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    58626 
    58627 Chain information for AF3 E2 1-352.pdb #474 
    58628 --- 
    58629 Chain | Description 
    58630 B | No description available 
    58631  
    58632 
    58633 > matchmaker #474 to #1.35 & sel
    58634 
    58635 Parameters 
    58636 --- 
    58637 Chain pairing | bb 
    58638 Alignment algorithm | Needleman-Wunsch 
    58639 Similarity matrix | BLOSUM-62 
    58640 SS fraction | 0.3 
    58641 Gap open (HH/SS/other) | 18/18/6 
    58642 Gap extend | 1 
    58643 SS matrix |  |  | H | S | O 
    58644 ---|---|---|--- 
    58645 H | 6 | -9 | -6 
    58646 S |  | 6 | -6 
    58647 O |  |  | 4 
    58648 Iteration cutoff | 2 
    58649  
    58650 Matchmaker 3j0c.pdb1, chain E (#1.35) with AF3 E2 1-352.pdb, chain B (#474),
    58651 sequence alignment score = 594.5 
    58652 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    58653 6.147) 
    58654  
    58655 
    58656 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    58657 
    58658 Chain information for AF3 E2 353-438.pdb #475 
    58659 --- 
    58660 Chain | Description 
    58661 B | No description available 
    58662  
    58663 
    58664 > matchmaker #475 to #1.35 & sel
    58665 
    58666 Parameters 
    58667 --- 
    58668 Chain pairing | bb 
    58669 Alignment algorithm | Needleman-Wunsch 
    58670 Similarity matrix | BLOSUM-62 
    58671 SS fraction | 0.3 
    58672 Gap open (HH/SS/other) | 18/18/6 
    58673 Gap extend | 1 
    58674 SS matrix |  |  | H | S | O 
    58675 ---|---|---|--- 
    58676 H | 6 | -9 | -6 
    58677 S |  | 6 | -6 
    58678 O |  |  | 4 
    58679 Iteration cutoff | 2 
    58680  
    58681 Matchmaker 3j0c.pdb1, chain E (#1.35) with AF3 E2 353-438.pdb, chain B (#475),
    58682 sequence alignment score = 340.2 
    58683 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    58684 8.673) 
    58685  
    58686 
    58687 > hide sel cartoons
    58688 
    58689 > select #1.35/F
    58690 
    58691 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    58692 
    58693 > show sel cartoons
    58694 
    58695 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    58696 
    58697 Chain information for AF3 CA.pdb #476 
    58698 --- 
    58699 Chain | Description 
    58700 A | No description available 
    58701  
    58702 
    58703 > matchmaker #476 to #1.35 & sel
    58704 
    58705 Parameters 
    58706 --- 
    58707 Chain pairing | bb 
    58708 Alignment algorithm | Needleman-Wunsch 
    58709 Similarity matrix | BLOSUM-62 
    58710 SS fraction | 0.3 
    58711 Gap open (HH/SS/other) | 18/18/6 
    58712 Gap extend | 1 
    58713 SS matrix |  |  | H | S | O 
    58714 ---|---|---|--- 
    58715 H | 6 | -9 | -6 
    58716 S |  | 6 | -6 
    58717 O |  |  | 4 
    58718 Iteration cutoff | 2 
    58719  
    58720 Matchmaker 3j0c.pdb1, chain F (#1.35) with AF3 CA.pdb, chain A (#476),
    58721 sequence alignment score = 335.3 
    58722 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    58723 2.550) 
    58724  
    58725 
    58726 > hide sel cartoons
    58727 
    58728 > color #472 dodgerblue
    58729 
    58730 > color #473 dodgerblue
    58731 
    58732 > color #474 #00b305ff
    58733 
    58734 > color #475 #00b305ff
    58735 
    58736 > color #476 #f15839ff
    58737 
    58738 > select #1.36/D
    58739 
    58740 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    58741 
    58742 > show sel cartoons
    58743 
    58744 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    58745 
    58746 Chain information for AF3 E1 1-421.pdb #477 
    58747 --- 
    58748 Chain | Description 
    58749 A | No description available 
    58750  
    58751 
    58752 > matchmaker #477 to #1.36 & sel
    58753 
    58754 Parameters 
    58755 --- 
    58756 Chain pairing | bb 
    58757 Alignment algorithm | Needleman-Wunsch 
    58758 Similarity matrix | BLOSUM-62 
    58759 SS fraction | 0.3 
    58760 Gap open (HH/SS/other) | 18/18/6 
    58761 Gap extend | 1 
    58762 SS matrix |  |  | H | S | O 
    58763 ---|---|---|--- 
    58764 H | 6 | -9 | -6 
    58765 S |  | 6 | -6 
    58766 O |  |  | 4 
    58767 Iteration cutoff | 2 
    58768  
    58769 Matchmaker 3j0c.pdb1, chain D (#1.36) with AF3 E1 1-421.pdb, chain A (#477),
    58770 sequence alignment score = 1060.7 
    58771 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    58772 3.032) 
    58773  
    58774 
    58775 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    58776 
    58777 Chain information for AF3 E1 422-461.pdb #478 
    58778 --- 
    58779 Chain | Description 
    58780 A | No description available 
    58781  
    58782 
    58783 > matchmaker #478 to #1.36 & sel
    58784 
    58785 Parameters 
    58786 --- 
    58787 Chain pairing | bb 
    58788 Alignment algorithm | Needleman-Wunsch 
    58789 Similarity matrix | BLOSUM-62 
    58790 SS fraction | 0.3 
    58791 Gap open (HH/SS/other) | 18/18/6 
    58792 Gap extend | 1 
    58793 SS matrix |  |  | H | S | O 
    58794 ---|---|---|--- 
    58795 H | 6 | -9 | -6 
    58796 S |  | 6 | -6 
    58797 O |  |  | 4 
    58798 Iteration cutoff | 2 
    58799  
    58800 Matchmaker 3j0c.pdb1, chain D (#1.36) with AF3 E1 422-461.pdb, chain A (#478),
    58801 sequence alignment score = 626.9 
    58802 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    58803 2.916) 
    58804  
    58805 
    58806 > hide sel cartoons
    58807 
    58808 > select #1.36/E
    58809 
    58810 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    58811 
    58812 > show sel cartoons
    58813 
    58814 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    58815 
    58816 Chain information for AF3 E2 1-352.pdb #479 
    58817 --- 
    58818 Chain | Description 
    58819 B | No description available 
    58820  
    58821 
    58822 > matchmaker #479 to #1.36 & sel
    58823 
    58824 Parameters 
    58825 --- 
    58826 Chain pairing | bb 
    58827 Alignment algorithm | Needleman-Wunsch 
    58828 Similarity matrix | BLOSUM-62 
    58829 SS fraction | 0.3 
    58830 Gap open (HH/SS/other) | 18/18/6 
    58831 Gap extend | 1 
    58832 SS matrix |  |  | H | S | O 
    58833 ---|---|---|--- 
    58834 H | 6 | -9 | -6 
    58835 S |  | 6 | -6 
    58836 O |  |  | 4 
    58837 Iteration cutoff | 2 
    58838  
    58839 Matchmaker 3j0c.pdb1, chain E (#1.36) with AF3 E2 1-352.pdb, chain B (#479),
    58840 sequence alignment score = 594.5 
    58841 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    58842 6.147) 
    58843  
    58844 
    58845 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    58846 
    58847 Chain information for AF3 E2 353-438.pdb #480 
    58848 --- 
    58849 Chain | Description 
    58850 B | No description available 
    58851  
    58852 
    58853 > matchmaker #480 to #1.36 & sel
    58854 
    58855 Parameters 
    58856 --- 
    58857 Chain pairing | bb 
    58858 Alignment algorithm | Needleman-Wunsch 
    58859 Similarity matrix | BLOSUM-62 
    58860 SS fraction | 0.3 
    58861 Gap open (HH/SS/other) | 18/18/6 
    58862 Gap extend | 1 
    58863 SS matrix |  |  | H | S | O 
    58864 ---|---|---|--- 
    58865 H | 6 | -9 | -6 
    58866 S |  | 6 | -6 
    58867 O |  |  | 4 
    58868 Iteration cutoff | 2 
    58869  
    58870 Matchmaker 3j0c.pdb1, chain E (#1.36) with AF3 E2 353-438.pdb, chain B (#480),
    58871 sequence alignment score = 340.2 
    58872 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    58873 8.673) 
    58874  
    58875 
    58876 > hide sel cartoons
    58877 
    58878 > select #1.36/F
    58879 
    58880 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    58881 
    58882 > show sel cartoons
    58883 
    58884 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    58885 
    58886 Chain information for AF3 CA.pdb #481 
    58887 --- 
    58888 Chain | Description 
    58889 A | No description available 
    58890  
    58891 
    58892 > matchmaker #481 to #1.36 & sel
    58893 
    58894 Parameters 
    58895 --- 
    58896 Chain pairing | bb 
    58897 Alignment algorithm | Needleman-Wunsch 
    58898 Similarity matrix | BLOSUM-62 
    58899 SS fraction | 0.3 
    58900 Gap open (HH/SS/other) | 18/18/6 
    58901 Gap extend | 1 
    58902 SS matrix |  |  | H | S | O 
    58903 ---|---|---|--- 
    58904 H | 6 | -9 | -6 
    58905 S |  | 6 | -6 
    58906 O |  |  | 4 
    58907 Iteration cutoff | 2 
    58908  
    58909 Matchmaker 3j0c.pdb1, chain F (#1.36) with AF3 CA.pdb, chain A (#481),
    58910 sequence alignment score = 335.3 
    58911 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    58912 2.550) 
    58913  
    58914 
    58915 > hide sel cartoons
    58916 
    58917 > color #477 dodgerblue
    58918 
    58919 > color #478 dodgerblue
    58920 
    58921 > color #479 #00b305ff
    58922 
    58923 > color #480 #00b305ff
    58924 
    58925 > color #481 #f15839ff
    58926 
    58927 > select #1.37/D
    58928 
    58929 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    58930 
    58931 > show sel cartoons
    58932 
    58933 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    58934 
    58935 Chain information for AF3 E1 1-421.pdb #482 
    58936 --- 
    58937 Chain | Description 
    58938 A | No description available 
    58939  
    58940 
    58941 > matchmaker #482 to #1.37 & sel
    58942 
    58943 Parameters 
    58944 --- 
    58945 Chain pairing | bb 
    58946 Alignment algorithm | Needleman-Wunsch 
    58947 Similarity matrix | BLOSUM-62 
    58948 SS fraction | 0.3 
    58949 Gap open (HH/SS/other) | 18/18/6 
    58950 Gap extend | 1 
    58951 SS matrix |  |  | H | S | O 
    58952 ---|---|---|--- 
    58953 H | 6 | -9 | -6 
    58954 S |  | 6 | -6 
    58955 O |  |  | 4 
    58956 Iteration cutoff | 2 
    58957  
    58958 Matchmaker 3j0c.pdb1, chain D (#1.37) with AF3 E1 1-421.pdb, chain A (#482),
    58959 sequence alignment score = 1060.7 
    58960 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    58961 3.032) 
    58962  
    58963 
    58964 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    58965 
    58966 Chain information for AF3 E1 422-461.pdb #483 
    58967 --- 
    58968 Chain | Description 
    58969 A | No description available 
    58970  
    58971 
    58972 > matchmaker #483 to #1.37 & sel
    58973 
    58974 Parameters 
    58975 --- 
    58976 Chain pairing | bb 
    58977 Alignment algorithm | Needleman-Wunsch 
    58978 Similarity matrix | BLOSUM-62 
    58979 SS fraction | 0.3 
    58980 Gap open (HH/SS/other) | 18/18/6 
    58981 Gap extend | 1 
    58982 SS matrix |  |  | H | S | O 
    58983 ---|---|---|--- 
    58984 H | 6 | -9 | -6 
    58985 S |  | 6 | -6 
    58986 O |  |  | 4 
    58987 Iteration cutoff | 2 
    58988  
    58989 Matchmaker 3j0c.pdb1, chain D (#1.37) with AF3 E1 422-461.pdb, chain A (#483),
    58990 sequence alignment score = 626.9 
    58991 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    58992 2.916) 
    58993  
    58994 
    58995 > hide sel cartoons
    58996 
    58997 > select #1.37/E
    58998 
    58999 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    59000 
    59001 > show sel cartoons
    59002 
    59003 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    59004 
    59005 Chain information for AF3 E2 1-352.pdb #484 
    59006 --- 
    59007 Chain | Description 
    59008 B | No description available 
    59009  
    59010 
    59011 > matchmaker #484 to #1.37 & sel
    59012 
    59013 Parameters 
    59014 --- 
    59015 Chain pairing | bb 
    59016 Alignment algorithm | Needleman-Wunsch 
    59017 Similarity matrix | BLOSUM-62 
    59018 SS fraction | 0.3 
    59019 Gap open (HH/SS/other) | 18/18/6 
    59020 Gap extend | 1 
    59021 SS matrix |  |  | H | S | O 
    59022 ---|---|---|--- 
    59023 H | 6 | -9 | -6 
    59024 S |  | 6 | -6 
    59025 O |  |  | 4 
    59026 Iteration cutoff | 2 
    59027  
    59028 Matchmaker 3j0c.pdb1, chain E (#1.37) with AF3 E2 1-352.pdb, chain B (#484),
    59029 sequence alignment score = 594.5 
    59030 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    59031 6.147) 
    59032  
    59033 
    59034 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    59035 
    59036 Chain information for AF3 E2 353-438.pdb #485 
    59037 --- 
    59038 Chain | Description 
    59039 B | No description available 
    59040  
    59041 
    59042 > matchmaker #485 to #1.37 & sel
    59043 
    59044 Parameters 
    59045 --- 
    59046 Chain pairing | bb 
    59047 Alignment algorithm | Needleman-Wunsch 
    59048 Similarity matrix | BLOSUM-62 
    59049 SS fraction | 0.3 
    59050 Gap open (HH/SS/other) | 18/18/6 
    59051 Gap extend | 1 
    59052 SS matrix |  |  | H | S | O 
    59053 ---|---|---|--- 
    59054 H | 6 | -9 | -6 
    59055 S |  | 6 | -6 
    59056 O |  |  | 4 
    59057 Iteration cutoff | 2 
    59058  
    59059 Matchmaker 3j0c.pdb1, chain E (#1.37) with AF3 E2 353-438.pdb, chain B (#485),
    59060 sequence alignment score = 340.2 
    59061 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    59062 8.673) 
    59063  
    59064 
    59065 > hide sel cartoons
    59066 
    59067 [Repeated 1 time(s)]
    59068 
    59069 > select #1.37/F
    59070 
    59071 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    59072 
    59073 > show sel cartoons
    59074 
    59075 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    59076 
    59077 Chain information for AF3 CA.pdb #486 
    59078 --- 
    59079 Chain | Description 
    59080 A | No description available 
    59081  
    59082 
    59083 > matchmaker #486 to #1.37 & sel
    59084 
    59085 Parameters 
    59086 --- 
    59087 Chain pairing | bb 
    59088 Alignment algorithm | Needleman-Wunsch 
    59089 Similarity matrix | BLOSUM-62 
    59090 SS fraction | 0.3 
    59091 Gap open (HH/SS/other) | 18/18/6 
    59092 Gap extend | 1 
    59093 SS matrix |  |  | H | S | O 
    59094 ---|---|---|--- 
    59095 H | 6 | -9 | -6 
    59096 S |  | 6 | -6 
    59097 O |  |  | 4 
    59098 Iteration cutoff | 2 
    59099  
    59100 Matchmaker 3j0c.pdb1, chain F (#1.37) with AF3 CA.pdb, chain A (#486),
    59101 sequence alignment score = 335.3 
    59102 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    59103 2.550) 
    59104  
    59105 
    59106 > hide sel cartoons
    59107 
    59108 [Repeated 1 time(s)]
    59109 
    59110 > color #482 dodgerblue
    59111 
    59112 > color #483 dodgerblue
    59113 
    59114 > color #484 #00b305ff
    59115 
    59116 > color #485 #00b305ff
    59117 
    59118 > color #486 #f15839ff
    59119 
    59120 > select #1.38/D
    59121 
    59122 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    59123 
    59124 > show sel cartoons
    59125 
    59126 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    59127 
    59128 Chain information for AF3 E1 1-421.pdb #487 
    59129 --- 
    59130 Chain | Description 
    59131 A | No description available 
    59132  
    59133 
    59134 > matchmaker #487 to #1.38 & sel
    59135 
    59136 Parameters 
    59137 --- 
    59138 Chain pairing | bb 
    59139 Alignment algorithm | Needleman-Wunsch 
    59140 Similarity matrix | BLOSUM-62 
    59141 SS fraction | 0.3 
    59142 Gap open (HH/SS/other) | 18/18/6 
    59143 Gap extend | 1 
    59144 SS matrix |  |  | H | S | O 
    59145 ---|---|---|--- 
    59146 H | 6 | -9 | -6 
    59147 S |  | 6 | -6 
    59148 O |  |  | 4 
    59149 Iteration cutoff | 2 
    59150  
    59151 Matchmaker 3j0c.pdb1, chain D (#1.38) with AF3 E1 1-421.pdb, chain A (#487),
    59152 sequence alignment score = 1060.7 
    59153 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    59154 3.032) 
    59155  
    59156 
    59157 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    59158 
    59159 Chain information for AF3 E1 422-461.pdb #488 
    59160 --- 
    59161 Chain | Description 
    59162 A | No description available 
    59163  
    59164 
    59165 > matchmaker #488 to #1.38 & sel
    59166 
    59167 Parameters 
    59168 --- 
    59169 Chain pairing | bb 
    59170 Alignment algorithm | Needleman-Wunsch 
    59171 Similarity matrix | BLOSUM-62 
    59172 SS fraction | 0.3 
    59173 Gap open (HH/SS/other) | 18/18/6 
    59174 Gap extend | 1 
    59175 SS matrix |  |  | H | S | O 
    59176 ---|---|---|--- 
    59177 H | 6 | -9 | -6 
    59178 S |  | 6 | -6 
    59179 O |  |  | 4 
    59180 Iteration cutoff | 2 
    59181  
    59182 Matchmaker 3j0c.pdb1, chain D (#1.38) with AF3 E1 422-461.pdb, chain A (#488),
    59183 sequence alignment score = 626.9 
    59184 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    59185 2.916) 
    59186  
    59187 
    59188 > hide sel cartoons
    59189 
    59190 > select #1.38/E
    59191 
    59192 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    59193 
    59194 > show sel cartoons
    59195 
    59196 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    59197 
    59198 Chain information for AF3 E2 1-352.pdb #489 
    59199 --- 
    59200 Chain | Description 
    59201 B | No description available 
    59202  
    59203 
    59204 > matchmaker #489 to #1.38 & sel
    59205 
    59206 Parameters 
    59207 --- 
    59208 Chain pairing | bb 
    59209 Alignment algorithm | Needleman-Wunsch 
    59210 Similarity matrix | BLOSUM-62 
    59211 SS fraction | 0.3 
    59212 Gap open (HH/SS/other) | 18/18/6 
    59213 Gap extend | 1 
    59214 SS matrix |  |  | H | S | O 
    59215 ---|---|---|--- 
    59216 H | 6 | -9 | -6 
    59217 S |  | 6 | -6 
    59218 O |  |  | 4 
    59219 Iteration cutoff | 2 
    59220  
    59221 Matchmaker 3j0c.pdb1, chain E (#1.38) with AF3 E2 1-352.pdb, chain B (#489),
    59222 sequence alignment score = 594.5 
    59223 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    59224 6.147) 
    59225  
    59226 
    59227 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    59228 
    59229 Chain information for AF3 E2 353-438.pdb #490 
    59230 --- 
    59231 Chain | Description 
    59232 B | No description available 
    59233  
    59234 
    59235 > matchmaker #490 to #1.38 & sel
    59236 
    59237 Parameters 
    59238 --- 
    59239 Chain pairing | bb 
    59240 Alignment algorithm | Needleman-Wunsch 
    59241 Similarity matrix | BLOSUM-62 
    59242 SS fraction | 0.3 
    59243 Gap open (HH/SS/other) | 18/18/6 
    59244 Gap extend | 1 
    59245 SS matrix |  |  | H | S | O 
    59246 ---|---|---|--- 
    59247 H | 6 | -9 | -6 
    59248 S |  | 6 | -6 
    59249 O |  |  | 4 
    59250 Iteration cutoff | 2 
    59251  
    59252 Matchmaker 3j0c.pdb1, chain E (#1.38) with AF3 E2 353-438.pdb, chain B (#490),
    59253 sequence alignment score = 340.2 
    59254 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    59255 8.673) 
    59256  
    59257 
    59258 > hide sel cartoons
    59259 
    59260 > select #1.38/F
    59261 
    59262 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    59263 
    59264 > show sel cartoons
    59265 
    59266 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    59267 
    59268 Chain information for AF3 CA.pdb #491 
    59269 --- 
    59270 Chain | Description 
    59271 A | No description available 
    59272  
    59273 
    59274 > matchmaker #491 to #1.38 & sel
    59275 
    59276 Parameters 
    59277 --- 
    59278 Chain pairing | bb 
    59279 Alignment algorithm | Needleman-Wunsch 
    59280 Similarity matrix | BLOSUM-62 
    59281 SS fraction | 0.3 
    59282 Gap open (HH/SS/other) | 18/18/6 
    59283 Gap extend | 1 
    59284 SS matrix |  |  | H | S | O 
    59285 ---|---|---|--- 
    59286 H | 6 | -9 | -6 
    59287 S |  | 6 | -6 
    59288 O |  |  | 4 
    59289 Iteration cutoff | 2 
    59290  
    59291 Matchmaker 3j0c.pdb1, chain F (#1.38) with AF3 CA.pdb, chain A (#491),
    59292 sequence alignment score = 335.3 
    59293 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    59294 2.550) 
    59295  
    59296 
    59297 > hide sel cartoons
    59298 
    59299 [Repeated 1 time(s)]
    59300 
    59301 > color #487 dodgerblue
    59302 
    59303 > color #488 dodgerblue
    59304 
    59305 > color #489 #00b305ff
    59306 
    59307 > color #490 #00b305ff
    59308 
    59309 > color #491 #f15839ff
    59310 
    59311 > select #1.39/D
    59312 
    59313 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    59314 
    59315 > show sel cartoons
    59316 
    59317 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    59318 
    59319 Chain information for AF3 E1 1-421.pdb #492 
    59320 --- 
    59321 Chain | Description 
    59322 A | No description available 
    59323  
    59324 
    59325 > matchmaker #492 to #1.39 & sel
    59326 
    59327 Parameters 
    59328 --- 
    59329 Chain pairing | bb 
    59330 Alignment algorithm | Needleman-Wunsch 
    59331 Similarity matrix | BLOSUM-62 
    59332 SS fraction | 0.3 
    59333 Gap open (HH/SS/other) | 18/18/6 
    59334 Gap extend | 1 
    59335 SS matrix |  |  | H | S | O 
    59336 ---|---|---|--- 
    59337 H | 6 | -9 | -6 
    59338 S |  | 6 | -6 
    59339 O |  |  | 4 
    59340 Iteration cutoff | 2 
    59341  
    59342 Matchmaker 3j0c.pdb1, chain D (#1.39) with AF3 E1 1-421.pdb, chain A (#492),
    59343 sequence alignment score = 1060.7 
    59344 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    59345 3.032) 
    59346  
    59347 
    59348 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    59349 
    59350 Chain information for AF3 E1 422-461.pdb #493 
    59351 --- 
    59352 Chain | Description 
    59353 A | No description available 
    59354  
    59355 
    59356 > matchmaker #493 to #1.39 & sel
    59357 
    59358 Parameters 
    59359 --- 
    59360 Chain pairing | bb 
    59361 Alignment algorithm | Needleman-Wunsch 
    59362 Similarity matrix | BLOSUM-62 
    59363 SS fraction | 0.3 
    59364 Gap open (HH/SS/other) | 18/18/6 
    59365 Gap extend | 1 
    59366 SS matrix |  |  | H | S | O 
    59367 ---|---|---|--- 
    59368 H | 6 | -9 | -6 
    59369 S |  | 6 | -6 
    59370 O |  |  | 4 
    59371 Iteration cutoff | 2 
    59372  
    59373 Matchmaker 3j0c.pdb1, chain D (#1.39) with AF3 E1 422-461.pdb, chain A (#493),
    59374 sequence alignment score = 626.9 
    59375 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    59376 2.916) 
    59377  
    59378 
    59379 > hide sel cartoons
    59380 
    59381 > select #1.39/E
    59382 
    59383 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    59384 
    59385 > show sel cartoons
    59386 
    59387 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    59388 
    59389 Chain information for AF3 E2 1-352.pdb #494 
    59390 --- 
    59391 Chain | Description 
    59392 B | No description available 
    59393  
    59394 
    59395 > matchmaker #494 to #1.39 & sel
    59396 
    59397 Parameters 
    59398 --- 
    59399 Chain pairing | bb 
    59400 Alignment algorithm | Needleman-Wunsch 
    59401 Similarity matrix | BLOSUM-62 
    59402 SS fraction | 0.3 
    59403 Gap open (HH/SS/other) | 18/18/6 
    59404 Gap extend | 1 
    59405 SS matrix |  |  | H | S | O 
    59406 ---|---|---|--- 
    59407 H | 6 | -9 | -6 
    59408 S |  | 6 | -6 
    59409 O |  |  | 4 
    59410 Iteration cutoff | 2 
    59411  
    59412 Matchmaker 3j0c.pdb1, chain E (#1.39) with AF3 E2 1-352.pdb, chain B (#494),
    59413 sequence alignment score = 594.5 
    59414 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    59415 6.147) 
    59416  
    59417 
    59418 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    59419 
    59420 Chain information for AF3 E2 353-438.pdb #495 
    59421 --- 
    59422 Chain | Description 
    59423 B | No description available 
    59424  
    59425 
    59426 > matchmaker #495 to #1.39 & sel
    59427 
    59428 Parameters 
    59429 --- 
    59430 Chain pairing | bb 
    59431 Alignment algorithm | Needleman-Wunsch 
    59432 Similarity matrix | BLOSUM-62 
    59433 SS fraction | 0.3 
    59434 Gap open (HH/SS/other) | 18/18/6 
    59435 Gap extend | 1 
    59436 SS matrix |  |  | H | S | O 
    59437 ---|---|---|--- 
    59438 H | 6 | -9 | -6 
    59439 S |  | 6 | -6 
    59440 O |  |  | 4 
    59441 Iteration cutoff | 2 
    59442  
    59443 Matchmaker 3j0c.pdb1, chain E (#1.39) with AF3 E2 353-438.pdb, chain B (#495),
    59444 sequence alignment score = 340.2 
    59445 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    59446 8.673) 
    59447  
    59448 
    59449 > hide sel cartoons
    59450 
    59451 > select #1.39/F
    59452 
    59453 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    59454 
    59455 > show sel cartoons
    59456 
    59457 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    59458 
    59459 Chain information for AF3 CA.pdb #496 
    59460 --- 
    59461 Chain | Description 
    59462 A | No description available 
    59463  
    59464 
    59465 > matchmaker #496 to #1.39 & sel
    59466 
    59467 Parameters 
    59468 --- 
    59469 Chain pairing | bb 
    59470 Alignment algorithm | Needleman-Wunsch 
    59471 Similarity matrix | BLOSUM-62 
    59472 SS fraction | 0.3 
    59473 Gap open (HH/SS/other) | 18/18/6 
    59474 Gap extend | 1 
    59475 SS matrix |  |  | H | S | O 
    59476 ---|---|---|--- 
    59477 H | 6 | -9 | -6 
    59478 S |  | 6 | -6 
    59479 O |  |  | 4 
    59480 Iteration cutoff | 2 
    59481  
    59482 Matchmaker 3j0c.pdb1, chain F (#1.39) with AF3 CA.pdb, chain A (#496),
    59483 sequence alignment score = 335.3 
    59484 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    59485 2.550) 
    59486  
    59487 
    59488 > hide sel cartoons
    59489 
    59490 > color #492 dodgerblue
    59491 
    59492 > color #493 dodgerblue
    59493 
    59494 > color #494 #00b305ff
    59495 
    59496 > color #495 #00b305ff
    59497 
    59498 > color #496 #f15839ff
    59499 
    59500 > select #1.40/D
    59501 
    59502 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    59503 
    59504 > show sel cartoons
    59505 
    59506 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    59507 
    59508 Chain information for AF3 E1 1-421.pdb #497 
    59509 --- 
    59510 Chain | Description 
    59511 A | No description available 
    59512  
    59513 
    59514 > matchmaker #497 to #1.40 & sel
    59515 
    59516 Parameters 
    59517 --- 
    59518 Chain pairing | bb 
    59519 Alignment algorithm | Needleman-Wunsch 
    59520 Similarity matrix | BLOSUM-62 
    59521 SS fraction | 0.3 
    59522 Gap open (HH/SS/other) | 18/18/6 
    59523 Gap extend | 1 
    59524 SS matrix |  |  | H | S | O 
    59525 ---|---|---|--- 
    59526 H | 6 | -9 | -6 
    59527 S |  | 6 | -6 
    59528 O |  |  | 4 
    59529 Iteration cutoff | 2 
    59530  
    59531 Matchmaker 3j0c.pdb1, chain D (#1.40) with AF3 E1 1-421.pdb, chain A (#497),
    59532 sequence alignment score = 1060.7 
    59533 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    59534 3.032) 
    59535  
    59536 
    59537 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    59538 
    59539 Chain information for AF3 E1 422-461.pdb #498 
    59540 --- 
    59541 Chain | Description 
    59542 A | No description available 
    59543  
    59544 
    59545 > matchmaker #498 to #1.40 & sel
    59546 
    59547 Parameters 
    59548 --- 
    59549 Chain pairing | bb 
    59550 Alignment algorithm | Needleman-Wunsch 
    59551 Similarity matrix | BLOSUM-62 
    59552 SS fraction | 0.3 
    59553 Gap open (HH/SS/other) | 18/18/6 
    59554 Gap extend | 1 
    59555 SS matrix |  |  | H | S | O 
    59556 ---|---|---|--- 
    59557 H | 6 | -9 | -6 
    59558 S |  | 6 | -6 
    59559 O |  |  | 4 
    59560 Iteration cutoff | 2 
    59561  
    59562 Matchmaker 3j0c.pdb1, chain D (#1.40) with AF3 E1 422-461.pdb, chain A (#498),
    59563 sequence alignment score = 626.9 
    59564 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    59565 2.916) 
    59566  
    59567 
    59568 > hide sel cartoons
    59569 
    59570 > select #1.40/E
    59571 
    59572 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    59573 
    59574 > show sel cartoons
    59575 
    59576 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    59577 
    59578 Chain information for AF3 E2 1-352.pdb #499 
    59579 --- 
    59580 Chain | Description 
    59581 B | No description available 
    59582  
    59583 
    59584 > matchmaker #499 to #1.40 & sel
    59585 
    59586 Parameters 
    59587 --- 
    59588 Chain pairing | bb 
    59589 Alignment algorithm | Needleman-Wunsch 
    59590 Similarity matrix | BLOSUM-62 
    59591 SS fraction | 0.3 
    59592 Gap open (HH/SS/other) | 18/18/6 
    59593 Gap extend | 1 
    59594 SS matrix |  |  | H | S | O 
    59595 ---|---|---|--- 
    59596 H | 6 | -9 | -6 
    59597 S |  | 6 | -6 
    59598 O |  |  | 4 
    59599 Iteration cutoff | 2 
    59600  
    59601 Matchmaker 3j0c.pdb1, chain E (#1.40) with AF3 E2 1-352.pdb, chain B (#499),
    59602 sequence alignment score = 594.5 
    59603 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    59604 6.147) 
    59605  
    59606 
    59607 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    59608 
    59609 Chain information for AF3 E2 353-438.pdb #500 
    59610 --- 
    59611 Chain | Description 
    59612 B | No description available 
    59613  
    59614 
    59615 > matchmaker #500 to #1.40 & sel
    59616 
    59617 Parameters 
    59618 --- 
    59619 Chain pairing | bb 
    59620 Alignment algorithm | Needleman-Wunsch 
    59621 Similarity matrix | BLOSUM-62 
    59622 SS fraction | 0.3 
    59623 Gap open (HH/SS/other) | 18/18/6 
    59624 Gap extend | 1 
    59625 SS matrix |  |  | H | S | O 
    59626 ---|---|---|--- 
    59627 H | 6 | -9 | -6 
    59628 S |  | 6 | -6 
    59629 O |  |  | 4 
    59630 Iteration cutoff | 2 
    59631  
    59632 Matchmaker 3j0c.pdb1, chain E (#1.40) with AF3 E2 353-438.pdb, chain B (#500),
    59633 sequence alignment score = 340.2 
    59634 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    59635 8.673) 
    59636  
    59637 
    59638 > select #1.40/F
    59639 
    59640 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    59641 
    59642 > show sel cartoons
    59643 
    59644 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    59645 
    59646 Chain information for AF3 CA.pdb #501 
    59647 --- 
    59648 Chain | Description 
    59649 A | No description available 
    59650  
    59651 
    59652 > matchmaker #501 to #1.40 & sel
    59653 
    59654 Parameters 
    59655 --- 
    59656 Chain pairing | bb 
    59657 Alignment algorithm | Needleman-Wunsch 
    59658 Similarity matrix | BLOSUM-62 
    59659 SS fraction | 0.3 
    59660 Gap open (HH/SS/other) | 18/18/6 
    59661 Gap extend | 1 
    59662 SS matrix |  |  | H | S | O 
    59663 ---|---|---|--- 
    59664 H | 6 | -9 | -6 
    59665 S |  | 6 | -6 
    59666 O |  |  | 4 
    59667 Iteration cutoff | 2 
    59668  
    59669 Matchmaker 3j0c.pdb1, chain F (#1.40) with AF3 CA.pdb, chain A (#501),
    59670 sequence alignment score = 335.3 
    59671 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    59672 2.550) 
    59673  
    59674 
    59675 > hide sel cartoons
    59676 
    59677 > select #1.40/E
    59678 
    59679 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    59680 
    59681 > hide sel cartoons
    59682 
    59683 > color #497 dodgerblue
    59684 
    59685 > color #498 dodgerblue
    59686 
    59687 > color #499 #00b305ff
    59688 
    59689 > color #500 #00b305ff
    59690 
    59691 > color #501 #f15839ff
    59692 
    59693 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    59694 
    59695 > hide #452-501 models
    59696 
    59697 > select #1.41/D
    59698 
    59699 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    59700 
    59701 > show sel cartoons
    59702 
    59703 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    59704 
    59705 Chain information for AF3 E1 1-421.pdb #502 
    59706 --- 
    59707 Chain | Description 
    59708 A | No description available 
    59709  
    59710 
    59711 > matchmaker #502 to #1.41 & sel
    59712 
    59713 Parameters 
    59714 --- 
    59715 Chain pairing | bb 
    59716 Alignment algorithm | Needleman-Wunsch 
    59717 Similarity matrix | BLOSUM-62 
    59718 SS fraction | 0.3 
    59719 Gap open (HH/SS/other) | 18/18/6 
    59720 Gap extend | 1 
    59721 SS matrix |  |  | H | S | O 
    59722 ---|---|---|--- 
    59723 H | 6 | -9 | -6 
    59724 S |  | 6 | -6 
    59725 O |  |  | 4 
    59726 Iteration cutoff | 2 
    59727  
    59728 Matchmaker 3j0c.pdb1, chain D (#1.41) with AF3 E1 1-421.pdb, chain A (#502),
    59729 sequence alignment score = 1060.7 
    59730 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    59731 3.032) 
    59732  
    59733 
    59734 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    59735 
    59736 Chain information for AF3 E1 422-461.pdb #503 
    59737 --- 
    59738 Chain | Description 
    59739 A | No description available 
    59740  
    59741 
    59742 > matchmaker #503 to #1.41 & sel
    59743 
    59744 Parameters 
    59745 --- 
    59746 Chain pairing | bb 
    59747 Alignment algorithm | Needleman-Wunsch 
    59748 Similarity matrix | BLOSUM-62 
    59749 SS fraction | 0.3 
    59750 Gap open (HH/SS/other) | 18/18/6 
    59751 Gap extend | 1 
    59752 SS matrix |  |  | H | S | O 
    59753 ---|---|---|--- 
    59754 H | 6 | -9 | -6 
    59755 S |  | 6 | -6 
    59756 O |  |  | 4 
    59757 Iteration cutoff | 2 
    59758  
    59759 Matchmaker 3j0c.pdb1, chain D (#1.41) with AF3 E1 422-461.pdb, chain A (#503),
    59760 sequence alignment score = 626.9 
    59761 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    59762 2.916) 
    59763  
    59764 
    59765 > hide sel cartoons
    59766 
    59767 > select #1.41/E
    59768 
    59769 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    59770 
    59771 > show sel cartoons
    59772 
    59773 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    59774 
    59775 Chain information for AF3 E2 1-352.pdb #504 
    59776 --- 
    59777 Chain | Description 
    59778 B | No description available 
    59779  
    59780 
    59781 > matchmaker #504 to #1.41 & sel
    59782 
    59783 Parameters 
    59784 --- 
    59785 Chain pairing | bb 
    59786 Alignment algorithm | Needleman-Wunsch 
    59787 Similarity matrix | BLOSUM-62 
    59788 SS fraction | 0.3 
    59789 Gap open (HH/SS/other) | 18/18/6 
    59790 Gap extend | 1 
    59791 SS matrix |  |  | H | S | O 
    59792 ---|---|---|--- 
    59793 H | 6 | -9 | -6 
    59794 S |  | 6 | -6 
    59795 O |  |  | 4 
    59796 Iteration cutoff | 2 
    59797  
    59798 Matchmaker 3j0c.pdb1, chain E (#1.41) with AF3 E2 1-352.pdb, chain B (#504),
    59799 sequence alignment score = 594.5 
    59800 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    59801 6.147) 
    59802  
    59803 
    59804 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    59805 
    59806 Chain information for AF3 E2 353-438.pdb #505 
    59807 --- 
    59808 Chain | Description 
    59809 B | No description available 
    59810  
    59811 
    59812 > matchmaker #505 to #1.41 & sel
    59813 
    59814 Parameters 
    59815 --- 
    59816 Chain pairing | bb 
    59817 Alignment algorithm | Needleman-Wunsch 
    59818 Similarity matrix | BLOSUM-62 
    59819 SS fraction | 0.3 
    59820 Gap open (HH/SS/other) | 18/18/6 
    59821 Gap extend | 1 
    59822 SS matrix |  |  | H | S | O 
    59823 ---|---|---|--- 
    59824 H | 6 | -9 | -6 
    59825 S |  | 6 | -6 
    59826 O |  |  | 4 
    59827 Iteration cutoff | 2 
    59828  
    59829 Matchmaker 3j0c.pdb1, chain E (#1.41) with AF3 E2 353-438.pdb, chain B (#505),
    59830 sequence alignment score = 340.2 
    59831 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    59832 8.673) 
    59833  
    59834 
    59835 > hide sel cartoons
    59836 
    59837 > select #1.41/F
    59838 
    59839 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    59840 
    59841 > show sel cartoons
    59842 
    59843 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    59844 
    59845 Chain information for AF3 CA.pdb #506 
    59846 --- 
    59847 Chain | Description 
    59848 A | No description available 
    59849  
    59850 
    59851 > matchmaker #506 to #1.41 & sel
    59852 
    59853 Parameters 
    59854 --- 
    59855 Chain pairing | bb 
    59856 Alignment algorithm | Needleman-Wunsch 
    59857 Similarity matrix | BLOSUM-62 
    59858 SS fraction | 0.3 
    59859 Gap open (HH/SS/other) | 18/18/6 
    59860 Gap extend | 1 
    59861 SS matrix |  |  | H | S | O 
    59862 ---|---|---|--- 
    59863 H | 6 | -9 | -6 
    59864 S |  | 6 | -6 
    59865 O |  |  | 4 
    59866 Iteration cutoff | 2 
    59867  
    59868 Matchmaker 3j0c.pdb1, chain F (#1.41) with AF3 CA.pdb, chain A (#506),
    59869 sequence alignment score = 335.3 
    59870 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    59871 2.550) 
    59872  
    59873 
    59874 > hide sel cartoons
    59875 
    59876 [Repeated 1 time(s)]
    59877 
    59878 > color #502 dodgerblue
    59879 
    59880 > color #503 dodgerblue
    59881 
    59882 > color #504 #00b305ff
    59883 
    59884 > color #505 #00b305ff
    59885 
    59886 > color #506 #f15839ff
    59887 
    59888 > select #1.42/D
    59889 
    59890 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    59891 
    59892 > show sel cartoons
    59893 
    59894 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    59895 
    59896 Chain information for AF3 E1 1-421.pdb #507 
    59897 --- 
    59898 Chain | Description 
    59899 A | No description available 
    59900  
    59901 
    59902 > matchmaker #507 to #1.42 & sel
    59903 
    59904 Parameters 
    59905 --- 
    59906 Chain pairing | bb 
    59907 Alignment algorithm | Needleman-Wunsch 
    59908 Similarity matrix | BLOSUM-62 
    59909 SS fraction | 0.3 
    59910 Gap open (HH/SS/other) | 18/18/6 
    59911 Gap extend | 1 
    59912 SS matrix |  |  | H | S | O 
    59913 ---|---|---|--- 
    59914 H | 6 | -9 | -6 
    59915 S |  | 6 | -6 
    59916 O |  |  | 4 
    59917 Iteration cutoff | 2 
    59918  
    59919 Matchmaker 3j0c.pdb1, chain D (#1.42) with AF3 E1 1-421.pdb, chain A (#507),
    59920 sequence alignment score = 1060.7 
    59921 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    59922 3.032) 
    59923  
    59924 
    59925 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    59926 
    59927 Chain information for AF3 E1 422-461.pdb #508 
    59928 --- 
    59929 Chain | Description 
    59930 A | No description available 
    59931  
    59932 
    59933 > matchmaker #508 to #1.42 & sel
    59934 
    59935 Parameters 
    59936 --- 
    59937 Chain pairing | bb 
    59938 Alignment algorithm | Needleman-Wunsch 
    59939 Similarity matrix | BLOSUM-62 
    59940 SS fraction | 0.3 
    59941 Gap open (HH/SS/other) | 18/18/6 
    59942 Gap extend | 1 
    59943 SS matrix |  |  | H | S | O 
    59944 ---|---|---|--- 
    59945 H | 6 | -9 | -6 
    59946 S |  | 6 | -6 
    59947 O |  |  | 4 
    59948 Iteration cutoff | 2 
    59949  
    59950 Matchmaker 3j0c.pdb1, chain D (#1.42) with AF3 E1 422-461.pdb, chain A (#508),
    59951 sequence alignment score = 626.9 
    59952 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    59953 2.916) 
    59954  
    59955 
    59956 > hide sel cartoons
    59957 
    59958 > select #1.42/E
    59959 
    59960 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    59961 
    59962 > show sel cartoons
    59963 
    59964 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    59965 
    59966 Chain information for AF3 E2 1-352.pdb #509 
    59967 --- 
    59968 Chain | Description 
    59969 B | No description available 
    59970  
    59971 
    59972 > matchmaker #509 to #1.42 & sel
    59973 
    59974 Parameters 
    59975 --- 
    59976 Chain pairing | bb 
    59977 Alignment algorithm | Needleman-Wunsch 
    59978 Similarity matrix | BLOSUM-62 
    59979 SS fraction | 0.3 
    59980 Gap open (HH/SS/other) | 18/18/6 
    59981 Gap extend | 1 
    59982 SS matrix |  |  | H | S | O 
    59983 ---|---|---|--- 
    59984 H | 6 | -9 | -6 
    59985 S |  | 6 | -6 
    59986 O |  |  | 4 
    59987 Iteration cutoff | 2 
    59988  
    59989 Matchmaker 3j0c.pdb1, chain E (#1.42) with AF3 E2 1-352.pdb, chain B (#509),
    59990 sequence alignment score = 594.5 
    59991 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    59992 6.147) 
    59993  
    59994 
    59995 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    59996 
    59997 Chain information for AF3 E2 353-438.pdb #510 
    59998 --- 
    59999 Chain | Description 
    60000 B | No description available 
    60001  
    60002 
    60003 > matchmaker #510 to #1.42 & sel
    60004 
    60005 Parameters 
    60006 --- 
    60007 Chain pairing | bb 
    60008 Alignment algorithm | Needleman-Wunsch 
    60009 Similarity matrix | BLOSUM-62 
    60010 SS fraction | 0.3 
    60011 Gap open (HH/SS/other) | 18/18/6 
    60012 Gap extend | 1 
    60013 SS matrix |  |  | H | S | O 
    60014 ---|---|---|--- 
    60015 H | 6 | -9 | -6 
    60016 S |  | 6 | -6 
    60017 O |  |  | 4 
    60018 Iteration cutoff | 2 
    60019  
    60020 Matchmaker 3j0c.pdb1, chain E (#1.42) with AF3 E2 353-438.pdb, chain B (#510),
    60021 sequence alignment score = 340.2 
    60022 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    60023 8.673) 
    60024  
    60025 
    60026 > hide sel cartoons
    60027 
    60028 > select #1.42/F
    60029 
    60030 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    60031 
    60032 > show sel cartoons
    60033 
    60034 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    60035 
    60036 Chain information for AF3 CA.pdb #511 
    60037 --- 
    60038 Chain | Description 
    60039 A | No description available 
    60040  
    60041 
    60042 > matchmaker #511 to #1.42 & sel
    60043 
    60044 Parameters 
    60045 --- 
    60046 Chain pairing | bb 
    60047 Alignment algorithm | Needleman-Wunsch 
    60048 Similarity matrix | BLOSUM-62 
    60049 SS fraction | 0.3 
    60050 Gap open (HH/SS/other) | 18/18/6 
    60051 Gap extend | 1 
    60052 SS matrix |  |  | H | S | O 
    60053 ---|---|---|--- 
    60054 H | 6 | -9 | -6 
    60055 S |  | 6 | -6 
    60056 O |  |  | 4 
    60057 Iteration cutoff | 2 
    60058  
    60059 Matchmaker 3j0c.pdb1, chain F (#1.42) with AF3 CA.pdb, chain A (#511),
    60060 sequence alignment score = 335.3 
    60061 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    60062 2.550) 
    60063  
    60064 
    60065 > hide sel cartoons
    60066 
    60067 > color #507 dodgerblue
    60068 
    60069 > color #508 dodgerblue
    60070 
    60071 > color #509 #00b305ff
    60072 
    60073 > color #510 #00b305ff
    60074 
    60075 > color #511 #f15839ff
    60076 
    60077 > select #1.43/D
    60078 
    60079 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    60080 
    60081 > show sel cartoons
    60082 
    60083 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    60084 
    60085 Chain information for AF3 E1 1-421.pdb #512 
    60086 --- 
    60087 Chain | Description 
    60088 A | No description available 
    60089  
    60090 
    60091 > matchmaker #512 to #1.43 & sel
    60092 
    60093 Parameters 
    60094 --- 
    60095 Chain pairing | bb 
    60096 Alignment algorithm | Needleman-Wunsch 
    60097 Similarity matrix | BLOSUM-62 
    60098 SS fraction | 0.3 
    60099 Gap open (HH/SS/other) | 18/18/6 
    60100 Gap extend | 1 
    60101 SS matrix |  |  | H | S | O 
    60102 ---|---|---|--- 
    60103 H | 6 | -9 | -6 
    60104 S |  | 6 | -6 
    60105 O |  |  | 4 
    60106 Iteration cutoff | 2 
    60107  
    60108 Matchmaker 3j0c.pdb1, chain D (#1.43) with AF3 E1 1-421.pdb, chain A (#512),
    60109 sequence alignment score = 1060.7 
    60110 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    60111 3.032) 
    60112  
    60113 
    60114 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    60115 
    60116 Chain information for AF3 E1 422-461.pdb #513 
    60117 --- 
    60118 Chain | Description 
    60119 A | No description available 
    60120  
    60121 
    60122 > matchmaker #513 to #1.43 & sel
    60123 
    60124 Parameters 
    60125 --- 
    60126 Chain pairing | bb 
    60127 Alignment algorithm | Needleman-Wunsch 
    60128 Similarity matrix | BLOSUM-62 
    60129 SS fraction | 0.3 
    60130 Gap open (HH/SS/other) | 18/18/6 
    60131 Gap extend | 1 
    60132 SS matrix |  |  | H | S | O 
    60133 ---|---|---|--- 
    60134 H | 6 | -9 | -6 
    60135 S |  | 6 | -6 
    60136 O |  |  | 4 
    60137 Iteration cutoff | 2 
    60138  
    60139 Matchmaker 3j0c.pdb1, chain D (#1.43) with AF3 E1 422-461.pdb, chain A (#513),
    60140 sequence alignment score = 626.9 
    60141 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    60142 2.916) 
    60143  
    60144 
    60145 > hide sel cartoons
    60146 
    60147 > select #1.43/E
    60148 
    60149 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    60150 
    60151 > show sel cartoons
    60152 
    60153 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    60154 
    60155 Chain information for AF3 E2 1-352.pdb #514 
    60156 --- 
    60157 Chain | Description 
    60158 B | No description available 
    60159  
    60160 
    60161 > matchmaker #514 to #1.43 & sel
    60162 
    60163 Parameters 
    60164 --- 
    60165 Chain pairing | bb 
    60166 Alignment algorithm | Needleman-Wunsch 
    60167 Similarity matrix | BLOSUM-62 
    60168 SS fraction | 0.3 
    60169 Gap open (HH/SS/other) | 18/18/6 
    60170 Gap extend | 1 
    60171 SS matrix |  |  | H | S | O 
    60172 ---|---|---|--- 
    60173 H | 6 | -9 | -6 
    60174 S |  | 6 | -6 
    60175 O |  |  | 4 
    60176 Iteration cutoff | 2 
    60177  
    60178 Matchmaker 3j0c.pdb1, chain E (#1.43) with AF3 E2 1-352.pdb, chain B (#514),
    60179 sequence alignment score = 594.5 
    60180 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    60181 6.147) 
    60182  
    60183 
    60184 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    60185 
    60186 Chain information for AF3 E2 353-438.pdb #515 
    60187 --- 
    60188 Chain | Description 
    60189 B | No description available 
    60190  
    60191 
    60192 > matchmaker #515 to #1.43 & sel
    60193 
    60194 Parameters 
    60195 --- 
    60196 Chain pairing | bb 
    60197 Alignment algorithm | Needleman-Wunsch 
    60198 Similarity matrix | BLOSUM-62 
    60199 SS fraction | 0.3 
    60200 Gap open (HH/SS/other) | 18/18/6 
    60201 Gap extend | 1 
    60202 SS matrix |  |  | H | S | O 
    60203 ---|---|---|--- 
    60204 H | 6 | -9 | -6 
    60205 S |  | 6 | -6 
    60206 O |  |  | 4 
    60207 Iteration cutoff | 2 
    60208  
    60209 Matchmaker 3j0c.pdb1, chain E (#1.43) with AF3 E2 353-438.pdb, chain B (#515),
    60210 sequence alignment score = 340.2 
    60211 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    60212 8.673) 
    60213  
    60214 
    60215 > hide sel cartoons
    60216 
    60217 > select #1.43/F
    60218 
    60219 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    60220 
    60221 > show sel cartoons
    60222 
    60223 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    60224 
    60225 Chain information for AF3 CA.pdb #516 
    60226 --- 
    60227 Chain | Description 
    60228 A | No description available 
    60229  
    60230 
    60231 > matchmaker #516 to #1.43 & sel
    60232 
    60233 Parameters 
    60234 --- 
    60235 Chain pairing | bb 
    60236 Alignment algorithm | Needleman-Wunsch 
    60237 Similarity matrix | BLOSUM-62 
    60238 SS fraction | 0.3 
    60239 Gap open (HH/SS/other) | 18/18/6 
    60240 Gap extend | 1 
    60241 SS matrix |  |  | H | S | O 
    60242 ---|---|---|--- 
    60243 H | 6 | -9 | -6 
    60244 S |  | 6 | -6 
    60245 O |  |  | 4 
    60246 Iteration cutoff | 2 
    60247  
    60248 Matchmaker 3j0c.pdb1, chain F (#1.43) with AF3 CA.pdb, chain A (#516),
    60249 sequence alignment score = 335.3 
    60250 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    60251 2.550) 
    60252  
    60253 
    60254 > hide sel cartoons
    60255 
    60256 > color #512 dodgerblue
    60257 
    60258 > color #513 dodgerblue
    60259 
    60260 > color #515 #00b305ff
    60261 
    60262 > color #516 #f15839ff
    60263 
    60264 > select #1.44/D
    60265 
    60266 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    60267 
    60268 > show sel cartoons
    60269 
    60270 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    60271 
    60272 Chain information for AF3 E1 1-421.pdb #517 
    60273 --- 
    60274 Chain | Description 
    60275 A | No description available 
    60276  
    60277 
    60278 > matchmaker #517 to #1.44 & sel
    60279 
    60280 Parameters 
    60281 --- 
    60282 Chain pairing | bb 
    60283 Alignment algorithm | Needleman-Wunsch 
    60284 Similarity matrix | BLOSUM-62 
    60285 SS fraction | 0.3 
    60286 Gap open (HH/SS/other) | 18/18/6 
    60287 Gap extend | 1 
    60288 SS matrix |  |  | H | S | O 
    60289 ---|---|---|--- 
    60290 H | 6 | -9 | -6 
    60291 S |  | 6 | -6 
    60292 O |  |  | 4 
    60293 Iteration cutoff | 2 
    60294  
    60295 Matchmaker 3j0c.pdb1, chain D (#1.44) with AF3 E1 1-421.pdb, chain A (#517),
    60296 sequence alignment score = 1060.7 
    60297 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    60298 3.032) 
    60299  
    60300 
    60301 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    60302 
    60303 Chain information for AF3 E1 422-461.pdb #518 
    60304 --- 
    60305 Chain | Description 
    60306 A | No description available 
    60307  
    60308 
    60309 > matchmaker #518 to #1.44 & sel
    60310 
    60311 Parameters 
    60312 --- 
    60313 Chain pairing | bb 
    60314 Alignment algorithm | Needleman-Wunsch 
    60315 Similarity matrix | BLOSUM-62 
    60316 SS fraction | 0.3 
    60317 Gap open (HH/SS/other) | 18/18/6 
    60318 Gap extend | 1 
    60319 SS matrix |  |  | H | S | O 
    60320 ---|---|---|--- 
    60321 H | 6 | -9 | -6 
    60322 S |  | 6 | -6 
    60323 O |  |  | 4 
    60324 Iteration cutoff | 2 
    60325  
    60326 Matchmaker 3j0c.pdb1, chain D (#1.44) with AF3 E1 422-461.pdb, chain A (#518),
    60327 sequence alignment score = 626.9 
    60328 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    60329 2.916) 
    60330  
    60331 
    60332 > hide sel cartoons
    60333 
    60334 > select #1.44/E
    60335 
    60336 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    60337 
    60338 > show sel cartoons
    60339 
    60340 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    60341 
    60342 Chain information for AF3 E2 1-352.pdb #519 
    60343 --- 
    60344 Chain | Description 
    60345 B | No description available 
    60346  
    60347 
    60348 > matchmaker #519 to #1.44 & sel
    60349 
    60350 Parameters 
    60351 --- 
    60352 Chain pairing | bb 
    60353 Alignment algorithm | Needleman-Wunsch 
    60354 Similarity matrix | BLOSUM-62 
    60355 SS fraction | 0.3 
    60356 Gap open (HH/SS/other) | 18/18/6 
    60357 Gap extend | 1 
    60358 SS matrix |  |  | H | S | O 
    60359 ---|---|---|--- 
    60360 H | 6 | -9 | -6 
    60361 S |  | 6 | -6 
    60362 O |  |  | 4 
    60363 Iteration cutoff | 2 
    60364  
    60365 Matchmaker 3j0c.pdb1, chain E (#1.44) with AF3 E2 1-352.pdb, chain B (#519),
    60366 sequence alignment score = 594.5 
    60367 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    60368 6.147) 
    60369  
    60370 
    60371 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    60372 
    60373 Chain information for AF3 E2 353-438.pdb #520 
    60374 --- 
    60375 Chain | Description 
    60376 B | No description available 
    60377  
    60378 
    60379 > matchmaker #520 to #1.44 & sel
    60380 
    60381 Parameters 
    60382 --- 
    60383 Chain pairing | bb 
    60384 Alignment algorithm | Needleman-Wunsch 
    60385 Similarity matrix | BLOSUM-62 
    60386 SS fraction | 0.3 
    60387 Gap open (HH/SS/other) | 18/18/6 
    60388 Gap extend | 1 
    60389 SS matrix |  |  | H | S | O 
    60390 ---|---|---|--- 
    60391 H | 6 | -9 | -6 
    60392 S |  | 6 | -6 
    60393 O |  |  | 4 
    60394 Iteration cutoff | 2 
    60395  
    60396 Matchmaker 3j0c.pdb1, chain E (#1.44) with AF3 E2 353-438.pdb, chain B (#520),
    60397 sequence alignment score = 340.2 
    60398 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    60399 8.673) 
    60400  
    60401 
    60402 > hide sel cartoons
    60403 
    60404 > select #1.44/F
    60405 
    60406 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    60407 
    60408 > show sel cartoons
    60409 
    60410 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    60411 
    60412 Chain information for AF3 CA.pdb #521 
    60413 --- 
    60414 Chain | Description 
    60415 A | No description available 
    60416  
    60417 
    60418 > matchmaker #521 to #1.44 & sel
    60419 
    60420 Parameters 
    60421 --- 
    60422 Chain pairing | bb 
    60423 Alignment algorithm | Needleman-Wunsch 
    60424 Similarity matrix | BLOSUM-62 
    60425 SS fraction | 0.3 
    60426 Gap open (HH/SS/other) | 18/18/6 
    60427 Gap extend | 1 
    60428 SS matrix |  |  | H | S | O 
    60429 ---|---|---|--- 
    60430 H | 6 | -9 | -6 
    60431 S |  | 6 | -6 
    60432 O |  |  | 4 
    60433 Iteration cutoff | 2 
    60434  
    60435 Matchmaker 3j0c.pdb1, chain F (#1.44) with AF3 CA.pdb, chain A (#521),
    60436 sequence alignment score = 335.3 
    60437 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    60438 2.550) 
    60439  
    60440 
    60441 > hide sel cartoons
    60442 
    60443 > color #517 dodgerblue
    60444 
    60445 > color #518 dodgerblue
    60446 
    60447 > color #519 #00b305ff
    60448 
    60449 > color #520 #00b305ff
    60450 
    60451 > color #521 #f15839ff
    60452 
    60453 > select #1.45/D
    60454 
    60455 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    60456 
    60457 > show sel cartoons
    60458 
    60459 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    60460 
    60461 Chain information for AF3 E1 1-421.pdb #522 
    60462 --- 
    60463 Chain | Description 
    60464 A | No description available 
    60465  
    60466 
    60467 > matchmaker #522 to #1.45 & sel
    60468 
    60469 Parameters 
    60470 --- 
    60471 Chain pairing | bb 
    60472 Alignment algorithm | Needleman-Wunsch 
    60473 Similarity matrix | BLOSUM-62 
    60474 SS fraction | 0.3 
    60475 Gap open (HH/SS/other) | 18/18/6 
    60476 Gap extend | 1 
    60477 SS matrix |  |  | H | S | O 
    60478 ---|---|---|--- 
    60479 H | 6 | -9 | -6 
    60480 S |  | 6 | -6 
    60481 O |  |  | 4 
    60482 Iteration cutoff | 2 
    60483  
    60484 Matchmaker 3j0c.pdb1, chain D (#1.45) with AF3 E1 1-421.pdb, chain A (#522),
    60485 sequence alignment score = 1060.7 
    60486 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    60487 3.032) 
    60488  
    60489 
    60490 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    60491 
    60492 Chain information for AF3 E1 422-461.pdb #523 
    60493 --- 
    60494 Chain | Description 
    60495 A | No description available 
    60496  
    60497 
    60498 > matchmaker #523 to #1.45 & sel
    60499 
    60500 Parameters 
    60501 --- 
    60502 Chain pairing | bb 
    60503 Alignment algorithm | Needleman-Wunsch 
    60504 Similarity matrix | BLOSUM-62 
    60505 SS fraction | 0.3 
    60506 Gap open (HH/SS/other) | 18/18/6 
    60507 Gap extend | 1 
    60508 SS matrix |  |  | H | S | O 
    60509 ---|---|---|--- 
    60510 H | 6 | -9 | -6 
    60511 S |  | 6 | -6 
    60512 O |  |  | 4 
    60513 Iteration cutoff | 2 
    60514  
    60515 Matchmaker 3j0c.pdb1, chain D (#1.45) with AF3 E1 422-461.pdb, chain A (#523),
    60516 sequence alignment score = 626.9 
    60517 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    60518 2.916) 
    60519  
    60520 
    60521 > hide sel cartoons
    60522 
    60523 > select #1.45/E
    60524 
    60525 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    60526 
    60527 > show sel cartoons
    60528 
    60529 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    60530 
    60531 Chain information for AF3 E2 1-352.pdb #524 
    60532 --- 
    60533 Chain | Description 
    60534 B | No description available 
    60535  
    60536 
    60537 > matchmaker #524 to #1.45 & sel
    60538 
    60539 Parameters 
    60540 --- 
    60541 Chain pairing | bb 
    60542 Alignment algorithm | Needleman-Wunsch 
    60543 Similarity matrix | BLOSUM-62 
    60544 SS fraction | 0.3 
    60545 Gap open (HH/SS/other) | 18/18/6 
    60546 Gap extend | 1 
    60547 SS matrix |  |  | H | S | O 
    60548 ---|---|---|--- 
    60549 H | 6 | -9 | -6 
    60550 S |  | 6 | -6 
    60551 O |  |  | 4 
    60552 Iteration cutoff | 2 
    60553  
    60554 Matchmaker 3j0c.pdb1, chain E (#1.45) with AF3 E2 1-352.pdb, chain B (#524),
    60555 sequence alignment score = 594.5 
    60556 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    60557 6.147) 
    60558  
    60559 
    60560 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    60561 
    60562 Chain information for AF3 E2 353-438.pdb #525 
    60563 --- 
    60564 Chain | Description 
    60565 B | No description available 
    60566  
    60567 
    60568 > matchmaker #525 to #1.45 & sel
    60569 
    60570 Parameters 
    60571 --- 
    60572 Chain pairing | bb 
    60573 Alignment algorithm | Needleman-Wunsch 
    60574 Similarity matrix | BLOSUM-62 
    60575 SS fraction | 0.3 
    60576 Gap open (HH/SS/other) | 18/18/6 
    60577 Gap extend | 1 
    60578 SS matrix |  |  | H | S | O 
    60579 ---|---|---|--- 
    60580 H | 6 | -9 | -6 
    60581 S |  | 6 | -6 
    60582 O |  |  | 4 
    60583 Iteration cutoff | 2 
    60584  
    60585 Matchmaker 3j0c.pdb1, chain E (#1.45) with AF3 E2 353-438.pdb, chain B (#525),
    60586 sequence alignment score = 340.2 
    60587 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    60588 8.673) 
    60589  
    60590 
    60591 > hide sel cartoons
    60592 
    60593 > select #1.45/F
    60594 
    60595 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    60596 
    60597 > show sel cartoons
    60598 
    60599 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    60600 
    60601 Chain information for AF3 CA.pdb #526 
    60602 --- 
    60603 Chain | Description 
    60604 A | No description available 
    60605  
    60606 
    60607 > matchmaker #526 to #1.45 & sel
    60608 
    60609 Parameters 
    60610 --- 
    60611 Chain pairing | bb 
    60612 Alignment algorithm | Needleman-Wunsch 
    60613 Similarity matrix | BLOSUM-62 
    60614 SS fraction | 0.3 
    60615 Gap open (HH/SS/other) | 18/18/6 
    60616 Gap extend | 1 
    60617 SS matrix |  |  | H | S | O 
    60618 ---|---|---|--- 
    60619 H | 6 | -9 | -6 
    60620 S |  | 6 | -6 
    60621 O |  |  | 4 
    60622 Iteration cutoff | 2 
    60623  
    60624 Matchmaker 3j0c.pdb1, chain F (#1.45) with AF3 CA.pdb, chain A (#526),
    60625 sequence alignment score = 335.3 
    60626 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    60627 2.550) 
    60628  
    60629 
    60630 > hide sel cartoons
    60631 
    60632 > color #522 dodgerblue
    60633 
    60634 > color #523 dodgerblue
    60635 
    60636 > color #524 #00b305ff
    60637 
    60638 > color #525 #00b305ff
    60639 
    60640 > color #526 #f15839ff
    60641 
    60642 > select #1.46/D
    60643 
    60644 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    60645 
    60646 > show sel cartoons
    60647 
    60648 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    60649 
    60650 Chain information for AF3 E1 1-421.pdb #527 
    60651 --- 
    60652 Chain | Description 
    60653 A | No description available 
    60654  
    60655 
    60656 > matchmaker #527 to #1.46 & sel
    60657 
    60658 Parameters 
    60659 --- 
    60660 Chain pairing | bb 
    60661 Alignment algorithm | Needleman-Wunsch 
    60662 Similarity matrix | BLOSUM-62 
    60663 SS fraction | 0.3 
    60664 Gap open (HH/SS/other) | 18/18/6 
    60665 Gap extend | 1 
    60666 SS matrix |  |  | H | S | O 
    60667 ---|---|---|--- 
    60668 H | 6 | -9 | -6 
    60669 S |  | 6 | -6 
    60670 O |  |  | 4 
    60671 Iteration cutoff | 2 
    60672  
    60673 Matchmaker 3j0c.pdb1, chain D (#1.46) with AF3 E1 1-421.pdb, chain A (#527),
    60674 sequence alignment score = 1060.7 
    60675 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    60676 3.032) 
    60677  
    60678 
    60679 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    60680 
    60681 Chain information for AF3 E1 422-461.pdb #528 
    60682 --- 
    60683 Chain | Description 
    60684 A | No description available 
    60685  
    60686 
    60687 > matchmaker #528 to #1.46 & sel
    60688 
    60689 Parameters 
    60690 --- 
    60691 Chain pairing | bb 
    60692 Alignment algorithm | Needleman-Wunsch 
    60693 Similarity matrix | BLOSUM-62 
    60694 SS fraction | 0.3 
    60695 Gap open (HH/SS/other) | 18/18/6 
    60696 Gap extend | 1 
    60697 SS matrix |  |  | H | S | O 
    60698 ---|---|---|--- 
    60699 H | 6 | -9 | -6 
    60700 S |  | 6 | -6 
    60701 O |  |  | 4 
    60702 Iteration cutoff | 2 
    60703  
    60704 Matchmaker 3j0c.pdb1, chain D (#1.46) with AF3 E1 422-461.pdb, chain A (#528),
    60705 sequence alignment score = 626.9 
    60706 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    60707 2.916) 
    60708  
    60709 
    60710 > hide sel cartoons
    60711 
    60712 > select #1.46/E
    60713 
    60714 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    60715 
    60716 > show sel cartoons
    60717 
    60718 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    60719 
    60720 Chain information for AF3 E2 1-352.pdb #529 
    60721 --- 
    60722 Chain | Description 
    60723 B | No description available 
    60724  
    60725 
    60726 > matchmaker #529 to #1.46 & sel
    60727 
    60728 Parameters 
    60729 --- 
    60730 Chain pairing | bb 
    60731 Alignment algorithm | Needleman-Wunsch 
    60732 Similarity matrix | BLOSUM-62 
    60733 SS fraction | 0.3 
    60734 Gap open (HH/SS/other) | 18/18/6 
    60735 Gap extend | 1 
    60736 SS matrix |  |  | H | S | O 
    60737 ---|---|---|--- 
    60738 H | 6 | -9 | -6 
    60739 S |  | 6 | -6 
    60740 O |  |  | 4 
    60741 Iteration cutoff | 2 
    60742  
    60743 Matchmaker 3j0c.pdb1, chain E (#1.46) with AF3 E2 1-352.pdb, chain B (#529),
    60744 sequence alignment score = 594.5 
    60745 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    60746 6.147) 
    60747  
    60748 
    60749 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    60750 
    60751 Chain information for AF3 E2 353-438.pdb #530 
    60752 --- 
    60753 Chain | Description 
    60754 B | No description available 
    60755  
    60756 
    60757 > matchmaker #530 to #1.46 & sel
    60758 
    60759 Parameters 
    60760 --- 
    60761 Chain pairing | bb 
    60762 Alignment algorithm | Needleman-Wunsch 
    60763 Similarity matrix | BLOSUM-62 
    60764 SS fraction | 0.3 
    60765 Gap open (HH/SS/other) | 18/18/6 
    60766 Gap extend | 1 
    60767 SS matrix |  |  | H | S | O 
    60768 ---|---|---|--- 
    60769 H | 6 | -9 | -6 
    60770 S |  | 6 | -6 
    60771 O |  |  | 4 
    60772 Iteration cutoff | 2 
    60773  
    60774 Matchmaker 3j0c.pdb1, chain E (#1.46) with AF3 E2 353-438.pdb, chain B (#530),
    60775 sequence alignment score = 340.2 
    60776 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    60777 8.673) 
    60778  
    60779 
    60780 > hide sel cartoons
    60781 
    60782 > select #1.46/F
    60783 
    60784 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    60785 
    60786 > show sel cartoons
    60787 
    60788 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    60789 
    60790 Chain information for AF3 CA.pdb #531 
    60791 --- 
    60792 Chain | Description 
    60793 A | No description available 
    60794  
    60795 
    60796 > matchmaker #531 to #1.46 & sel
    60797 
    60798 Parameters 
    60799 --- 
    60800 Chain pairing | bb 
    60801 Alignment algorithm | Needleman-Wunsch 
    60802 Similarity matrix | BLOSUM-62 
    60803 SS fraction | 0.3 
    60804 Gap open (HH/SS/other) | 18/18/6 
    60805 Gap extend | 1 
    60806 SS matrix |  |  | H | S | O 
    60807 ---|---|---|--- 
    60808 H | 6 | -9 | -6 
    60809 S |  | 6 | -6 
    60810 O |  |  | 4 
    60811 Iteration cutoff | 2 
    60812  
    60813 Matchmaker 3j0c.pdb1, chain F (#1.46) with AF3 CA.pdb, chain A (#531),
    60814 sequence alignment score = 335.3 
    60815 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    60816 2.550) 
    60817  
    60818 
    60819 > hide sel cartoons
    60820 
    60821 > color #527 dodgerblue
    60822 
    60823 > color #528 dodgerblue
    60824 
    60825 > color #529 #00b305ff
    60826 
    60827 > color #530 #00b305ff
    60828 
    60829 > color #531 #f15839ff
    60830 
    60831 > select #1.47/D
    60832 
    60833 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    60834 
    60835 > show sel cartoons
    60836 
    60837 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    60838 
    60839 Chain information for AF3 E1 1-421.pdb #532 
    60840 --- 
    60841 Chain | Description 
    60842 A | No description available 
    60843  
    60844 
    60845 > matchmaker #532 to #1.47 & sel
    60846 
    60847 Parameters 
    60848 --- 
    60849 Chain pairing | bb 
    60850 Alignment algorithm | Needleman-Wunsch 
    60851 Similarity matrix | BLOSUM-62 
    60852 SS fraction | 0.3 
    60853 Gap open (HH/SS/other) | 18/18/6 
    60854 Gap extend | 1 
    60855 SS matrix |  |  | H | S | O 
    60856 ---|---|---|--- 
    60857 H | 6 | -9 | -6 
    60858 S |  | 6 | -6 
    60859 O |  |  | 4 
    60860 Iteration cutoff | 2 
    60861  
    60862 Matchmaker 3j0c.pdb1, chain D (#1.47) with AF3 E1 1-421.pdb, chain A (#532),
    60863 sequence alignment score = 1060.7 
    60864 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    60865 3.032) 
    60866  
    60867 
    60868 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    60869 
    60870 Chain information for AF3 E1 422-461.pdb #533 
    60871 --- 
    60872 Chain | Description 
    60873 A | No description available 
    60874  
    60875 
    60876 > matchmaker #533 to #1.47 & sel
    60877 
    60878 Parameters 
    60879 --- 
    60880 Chain pairing | bb 
    60881 Alignment algorithm | Needleman-Wunsch 
    60882 Similarity matrix | BLOSUM-62 
    60883 SS fraction | 0.3 
    60884 Gap open (HH/SS/other) | 18/18/6 
    60885 Gap extend | 1 
    60886 SS matrix |  |  | H | S | O 
    60887 ---|---|---|--- 
    60888 H | 6 | -9 | -6 
    60889 S |  | 6 | -6 
    60890 O |  |  | 4 
    60891 Iteration cutoff | 2 
    60892  
    60893 Matchmaker 3j0c.pdb1, chain D (#1.47) with AF3 E1 422-461.pdb, chain A (#533),
    60894 sequence alignment score = 626.9 
    60895 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    60896 2.916) 
    60897  
    60898 
    60899 > hide sel cartoons
    60900 
    60901 > select #1.47/E
    60902 
    60903 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    60904 
    60905 > show sel cartoons
    60906 
    60907 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    60908 
    60909 Chain information for AF3 E2 1-352.pdb #534 
    60910 --- 
    60911 Chain | Description 
    60912 B | No description available 
    60913  
    60914 
    60915 > matchmaker #534 to #1.47 & sel
    60916 
    60917 Parameters 
    60918 --- 
    60919 Chain pairing | bb 
    60920 Alignment algorithm | Needleman-Wunsch 
    60921 Similarity matrix | BLOSUM-62 
    60922 SS fraction | 0.3 
    60923 Gap open (HH/SS/other) | 18/18/6 
    60924 Gap extend | 1 
    60925 SS matrix |  |  | H | S | O 
    60926 ---|---|---|--- 
    60927 H | 6 | -9 | -6 
    60928 S |  | 6 | -6 
    60929 O |  |  | 4 
    60930 Iteration cutoff | 2 
    60931  
    60932 Matchmaker 3j0c.pdb1, chain E (#1.47) with AF3 E2 1-352.pdb, chain B (#534),
    60933 sequence alignment score = 594.5 
    60934 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    60935 6.147) 
    60936  
    60937 
    60938 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    60939 
    60940 Chain information for AF3 E2 353-438.pdb #535 
    60941 --- 
    60942 Chain | Description 
    60943 B | No description available 
    60944  
    60945 
    60946 > matchmaker #535 to #1.47 & sel
    60947 
    60948 Parameters 
    60949 --- 
    60950 Chain pairing | bb 
    60951 Alignment algorithm | Needleman-Wunsch 
    60952 Similarity matrix | BLOSUM-62 
    60953 SS fraction | 0.3 
    60954 Gap open (HH/SS/other) | 18/18/6 
    60955 Gap extend | 1 
    60956 SS matrix |  |  | H | S | O 
    60957 ---|---|---|--- 
    60958 H | 6 | -9 | -6 
    60959 S |  | 6 | -6 
    60960 O |  |  | 4 
    60961 Iteration cutoff | 2 
    60962  
    60963 Matchmaker 3j0c.pdb1, chain E (#1.47) with AF3 E2 353-438.pdb, chain B (#535),
    60964 sequence alignment score = 340.2 
    60965 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    60966 8.673) 
    60967  
    60968 
    60969 > hide sel cartoons
    60970 
    60971 > select #1.47/F
    60972 
    60973 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    60974 
    60975 > show sel cartoons
    60976 
    60977 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    60978 
    60979 Chain information for AF3 CA.pdb #536 
    60980 --- 
    60981 Chain | Description 
    60982 A | No description available 
    60983  
    60984 
    60985 > matchmaker #536 to #1.47 & sel
    60986 
    60987 Parameters 
    60988 --- 
    60989 Chain pairing | bb 
    60990 Alignment algorithm | Needleman-Wunsch 
    60991 Similarity matrix | BLOSUM-62 
    60992 SS fraction | 0.3 
    60993 Gap open (HH/SS/other) | 18/18/6 
    60994 Gap extend | 1 
    60995 SS matrix |  |  | H | S | O 
    60996 ---|---|---|--- 
    60997 H | 6 | -9 | -6 
    60998 S |  | 6 | -6 
    60999 O |  |  | 4 
    61000 Iteration cutoff | 2 
    61001  
    61002 Matchmaker 3j0c.pdb1, chain F (#1.47) with AF3 CA.pdb, chain A (#536),
    61003 sequence alignment score = 335.3 
    61004 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    61005 2.550) 
    61006  
    61007 
    61008 > hide sel cartoons
    61009 
    61010 > color #532 dodgerblue
    61011 
    61012 > color #533 dodgerblue
    61013 
    61014 > color #534 #00b305ff
    61015 
    61016 > color #535 #00b305ff
    61017 
    61018 > color #536 #f15839ff
    61019 
    61020 > select #1.48/D
    61021 
    61022 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    61023 
    61024 > show sel cartoons
    61025 
    61026 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    61027 
    61028 Chain information for AF3 E1 1-421.pdb #537 
    61029 --- 
    61030 Chain | Description 
    61031 A | No description available 
    61032  
    61033 
    61034 > matchmaker #537 to #1.48 & sel
    61035 
    61036 Parameters 
    61037 --- 
    61038 Chain pairing | bb 
    61039 Alignment algorithm | Needleman-Wunsch 
    61040 Similarity matrix | BLOSUM-62 
    61041 SS fraction | 0.3 
    61042 Gap open (HH/SS/other) | 18/18/6 
    61043 Gap extend | 1 
    61044 SS matrix |  |  | H | S | O 
    61045 ---|---|---|--- 
    61046 H | 6 | -9 | -6 
    61047 S |  | 6 | -6 
    61048 O |  |  | 4 
    61049 Iteration cutoff | 2 
    61050  
    61051 Matchmaker 3j0c.pdb1, chain D (#1.48) with AF3 E1 1-421.pdb, chain A (#537),
    61052 sequence alignment score = 1060.7 
    61053 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    61054 3.032) 
    61055  
    61056 
    61057 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    61058 
    61059 Chain information for AF3 E1 422-461.pdb #538 
    61060 --- 
    61061 Chain | Description 
    61062 A | No description available 
    61063  
    61064 
    61065 > matchmaker #538 to #1.48 & sel
    61066 
    61067 Parameters 
    61068 --- 
    61069 Chain pairing | bb 
    61070 Alignment algorithm | Needleman-Wunsch 
    61071 Similarity matrix | BLOSUM-62 
    61072 SS fraction | 0.3 
    61073 Gap open (HH/SS/other) | 18/18/6 
    61074 Gap extend | 1 
    61075 SS matrix |  |  | H | S | O 
    61076 ---|---|---|--- 
    61077 H | 6 | -9 | -6 
    61078 S |  | 6 | -6 
    61079 O |  |  | 4 
    61080 Iteration cutoff | 2 
    61081  
    61082 Matchmaker 3j0c.pdb1, chain D (#1.48) with AF3 E1 422-461.pdb, chain A (#538),
    61083 sequence alignment score = 626.9 
    61084 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    61085 2.916) 
    61086  
    61087 
    61088 > hide sel cartoons
    61089 
    61090 > select #1.48/E
    61091 
    61092 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    61093 
    61094 > show sel cartoons
    61095 
    61096 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    61097 
    61098 Chain information for AF3 E2 1-352.pdb #539 
    61099 --- 
    61100 Chain | Description 
    61101 B | No description available 
    61102  
    61103 
    61104 > matchmaker #539 to #1.48 & sel
    61105 
    61106 Parameters 
    61107 --- 
    61108 Chain pairing | bb 
    61109 Alignment algorithm | Needleman-Wunsch 
    61110 Similarity matrix | BLOSUM-62 
    61111 SS fraction | 0.3 
    61112 Gap open (HH/SS/other) | 18/18/6 
    61113 Gap extend | 1 
    61114 SS matrix |  |  | H | S | O 
    61115 ---|---|---|--- 
    61116 H | 6 | -9 | -6 
    61117 S |  | 6 | -6 
    61118 O |  |  | 4 
    61119 Iteration cutoff | 2 
    61120  
    61121 Matchmaker 3j0c.pdb1, chain E (#1.48) with AF3 E2 1-352.pdb, chain B (#539),
    61122 sequence alignment score = 594.5 
    61123 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    61124 6.147) 
    61125  
    61126 
    61127 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    61128 
    61129 Chain information for AF3 E2 353-438.pdb #540 
    61130 --- 
    61131 Chain | Description 
    61132 B | No description available 
    61133  
    61134 
    61135 > matchmaker #540 to #1.48 & sel
    61136 
    61137 Parameters 
    61138 --- 
    61139 Chain pairing | bb 
    61140 Alignment algorithm | Needleman-Wunsch 
    61141 Similarity matrix | BLOSUM-62 
    61142 SS fraction | 0.3 
    61143 Gap open (HH/SS/other) | 18/18/6 
    61144 Gap extend | 1 
    61145 SS matrix |  |  | H | S | O 
    61146 ---|---|---|--- 
    61147 H | 6 | -9 | -6 
    61148 S |  | 6 | -6 
    61149 O |  |  | 4 
    61150 Iteration cutoff | 2 
    61151  
    61152 Matchmaker 3j0c.pdb1, chain E (#1.48) with AF3 E2 353-438.pdb, chain B (#540),
    61153 sequence alignment score = 340.2 
    61154 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    61155 8.673) 
    61156  
    61157 
    61158 > hide sel cartoons
    61159 
    61160 > select #1.48/F
    61161 
    61162 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    61163 
    61164 > show sel cartoons
    61165 
    61166 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    61167 
    61168 Chain information for AF3 CA.pdb #541 
    61169 --- 
    61170 Chain | Description 
    61171 A | No description available 
    61172  
    61173 
    61174 > matchmaker #541 to #1.48 & sel
    61175 
    61176 Parameters 
    61177 --- 
    61178 Chain pairing | bb 
    61179 Alignment algorithm | Needleman-Wunsch 
    61180 Similarity matrix | BLOSUM-62 
    61181 SS fraction | 0.3 
    61182 Gap open (HH/SS/other) | 18/18/6 
    61183 Gap extend | 1 
    61184 SS matrix |  |  | H | S | O 
    61185 ---|---|---|--- 
    61186 H | 6 | -9 | -6 
    61187 S |  | 6 | -6 
    61188 O |  |  | 4 
    61189 Iteration cutoff | 2 
    61190  
    61191 Matchmaker 3j0c.pdb1, chain F (#1.48) with AF3 CA.pdb, chain A (#541),
    61192 sequence alignment score = 335.3 
    61193 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    61194 2.550) 
    61195  
    61196 
    61197 > hide sel cartoons
    61198 
    61199 > color #537 dodgerblue
    61200 
    61201 > color #538 dodgerblue
    61202 
    61203 > color #539 #00b305ff
    61204 
    61205 > color #540 #00b305ff
    61206 
    61207 > color #541 #f15839ff
    61208 
    61209 > select #1.49/D
    61210 
    61211 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    61212 
    61213 > show sel cartoons
    61214 
    61215 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    61216 
    61217 Chain information for AF3 E1 1-421.pdb #542 
    61218 --- 
    61219 Chain | Description 
    61220 A | No description available 
    61221  
    61222 
    61223 > matchmaker #542 to #1.49 & sel
    61224 
    61225 Parameters 
    61226 --- 
    61227 Chain pairing | bb 
    61228 Alignment algorithm | Needleman-Wunsch 
    61229 Similarity matrix | BLOSUM-62 
    61230 SS fraction | 0.3 
    61231 Gap open (HH/SS/other) | 18/18/6 
    61232 Gap extend | 1 
    61233 SS matrix |  |  | H | S | O 
    61234 ---|---|---|--- 
    61235 H | 6 | -9 | -6 
    61236 S |  | 6 | -6 
    61237 O |  |  | 4 
    61238 Iteration cutoff | 2 
    61239  
    61240 Matchmaker 3j0c.pdb1, chain D (#1.49) with AF3 E1 1-421.pdb, chain A (#542),
    61241 sequence alignment score = 1060.7 
    61242 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    61243 3.032) 
    61244  
    61245 
    61246 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    61247 
    61248 Chain information for AF3 E1 422-461.pdb #543 
    61249 --- 
    61250 Chain | Description 
    61251 A | No description available 
    61252  
    61253 
    61254 > matchmaker #543 to #1.49 & sel
    61255 
    61256 Parameters 
    61257 --- 
    61258 Chain pairing | bb 
    61259 Alignment algorithm | Needleman-Wunsch 
    61260 Similarity matrix | BLOSUM-62 
    61261 SS fraction | 0.3 
    61262 Gap open (HH/SS/other) | 18/18/6 
    61263 Gap extend | 1 
    61264 SS matrix |  |  | H | S | O 
    61265 ---|---|---|--- 
    61266 H | 6 | -9 | -6 
    61267 S |  | 6 | -6 
    61268 O |  |  | 4 
    61269 Iteration cutoff | 2 
    61270  
    61271 Matchmaker 3j0c.pdb1, chain D (#1.49) with AF3 E1 422-461.pdb, chain A (#543),
    61272 sequence alignment score = 626.9 
    61273 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    61274 2.916) 
    61275  
    61276 
    61277 > hide sel cartoons
    61278 
    61279 > select #1.49/E
    61280 
    61281 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    61282 
    61283 > show sel cartoons
    61284 
    61285 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    61286 
    61287 Chain information for AF3 E2 1-352.pdb #544 
    61288 --- 
    61289 Chain | Description 
    61290 B | No description available 
    61291  
    61292 
    61293 > matchmaker #544 to #1.49 & sel
    61294 
    61295 Parameters 
    61296 --- 
    61297 Chain pairing | bb 
    61298 Alignment algorithm | Needleman-Wunsch 
    61299 Similarity matrix | BLOSUM-62 
    61300 SS fraction | 0.3 
    61301 Gap open (HH/SS/other) | 18/18/6 
    61302 Gap extend | 1 
    61303 SS matrix |  |  | H | S | O 
    61304 ---|---|---|--- 
    61305 H | 6 | -9 | -6 
    61306 S |  | 6 | -6 
    61307 O |  |  | 4 
    61308 Iteration cutoff | 2 
    61309  
    61310 Matchmaker 3j0c.pdb1, chain E (#1.49) with AF3 E2 1-352.pdb, chain B (#544),
    61311 sequence alignment score = 594.5 
    61312 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    61313 6.147) 
    61314  
    61315 
    61316 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    61317 
    61318 Chain information for AF3 E2 353-438.pdb #545 
    61319 --- 
    61320 Chain | Description 
    61321 B | No description available 
    61322  
    61323 
    61324 > matchmaker #545 to #1.49 & sel
    61325 
    61326 Parameters 
    61327 --- 
    61328 Chain pairing | bb 
    61329 Alignment algorithm | Needleman-Wunsch 
    61330 Similarity matrix | BLOSUM-62 
    61331 SS fraction | 0.3 
    61332 Gap open (HH/SS/other) | 18/18/6 
    61333 Gap extend | 1 
    61334 SS matrix |  |  | H | S | O 
    61335 ---|---|---|--- 
    61336 H | 6 | -9 | -6 
    61337 S |  | 6 | -6 
    61338 O |  |  | 4 
    61339 Iteration cutoff | 2 
    61340  
    61341 Matchmaker 3j0c.pdb1, chain E (#1.49) with AF3 E2 353-438.pdb, chain B (#545),
    61342 sequence alignment score = 340.2 
    61343 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    61344 8.673) 
    61345  
    61346 
    61347 > hide sel cartoons
    61348 
    61349 > select #1.49/F
    61350 
    61351 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    61352 
    61353 > show sel cartoons
    61354 
    61355 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    61356 
    61357 Chain information for AF3 CA.pdb #546 
    61358 --- 
    61359 Chain | Description 
    61360 A | No description available 
    61361  
    61362 
    61363 > matchmaker #546 to #1.49 & sel
    61364 
    61365 Parameters 
    61366 --- 
    61367 Chain pairing | bb 
    61368 Alignment algorithm | Needleman-Wunsch 
    61369 Similarity matrix | BLOSUM-62 
    61370 SS fraction | 0.3 
    61371 Gap open (HH/SS/other) | 18/18/6 
    61372 Gap extend | 1 
    61373 SS matrix |  |  | H | S | O 
    61374 ---|---|---|--- 
    61375 H | 6 | -9 | -6 
    61376 S |  | 6 | -6 
    61377 O |  |  | 4 
    61378 Iteration cutoff | 2 
    61379  
    61380 Matchmaker 3j0c.pdb1, chain F (#1.49) with AF3 CA.pdb, chain A (#546),
    61381 sequence alignment score = 335.3 
    61382 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    61383 2.550) 
    61384  
    61385 
    61386 > hide sel cartoons
    61387 
    61388 > color #542 dodgerblue
    61389 
    61390 > color #543 dodgerblue
    61391 
    61392 > color #544 #00b305ff
    61393 
    61394 > color #545 #00b305ff
    61395 
    61396 > color #546 #f15839ff
    61397 
    61398 > select #1.50/D
    61399 
    61400 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    61401 
    61402 > show sel cartoons
    61403 
    61404 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    61405 
    61406 Chain information for AF3 E1 1-421.pdb #547 
    61407 --- 
    61408 Chain | Description 
    61409 A | No description available 
    61410  
    61411 
    61412 > matchmaker #547 to #1.50 & sel
    61413 
    61414 Parameters 
    61415 --- 
    61416 Chain pairing | bb 
    61417 Alignment algorithm | Needleman-Wunsch 
    61418 Similarity matrix | BLOSUM-62 
    61419 SS fraction | 0.3 
    61420 Gap open (HH/SS/other) | 18/18/6 
    61421 Gap extend | 1 
    61422 SS matrix |  |  | H | S | O 
    61423 ---|---|---|--- 
    61424 H | 6 | -9 | -6 
    61425 S |  | 6 | -6 
    61426 O |  |  | 4 
    61427 Iteration cutoff | 2 
    61428  
    61429 Matchmaker 3j0c.pdb1, chain D (#1.50) with AF3 E1 1-421.pdb, chain A (#547),
    61430 sequence alignment score = 1060.7 
    61431 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    61432 3.032) 
    61433  
    61434 
    61435 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    61436 
    61437 Chain information for AF3 E1 422-461.pdb #548 
    61438 --- 
    61439 Chain | Description 
    61440 A | No description available 
    61441  
    61442 
    61443 > matchmaker #548 to #1.50 & sel
    61444 
    61445 Parameters 
    61446 --- 
    61447 Chain pairing | bb 
    61448 Alignment algorithm | Needleman-Wunsch 
    61449 Similarity matrix | BLOSUM-62 
    61450 SS fraction | 0.3 
    61451 Gap open (HH/SS/other) | 18/18/6 
    61452 Gap extend | 1 
    61453 SS matrix |  |  | H | S | O 
    61454 ---|---|---|--- 
    61455 H | 6 | -9 | -6 
    61456 S |  | 6 | -6 
    61457 O |  |  | 4 
    61458 Iteration cutoff | 2 
    61459  
    61460 Matchmaker 3j0c.pdb1, chain D (#1.50) with AF3 E1 422-461.pdb, chain A (#548),
    61461 sequence alignment score = 626.9 
    61462 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    61463 2.916) 
    61464  
    61465 
    61466 > hide sel cartoons
    61467 
    61468 > select #1.50/E
    61469 
    61470 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    61471 
    61472 > show sel cartoons
    61473 
    61474 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    61475 
    61476 Chain information for AF3 E2 1-352.pdb #549 
    61477 --- 
    61478 Chain | Description 
    61479 B | No description available 
    61480  
    61481 
    61482 > matchmaker #549 to #1.50 & sel
    61483 
    61484 Parameters 
    61485 --- 
    61486 Chain pairing | bb 
    61487 Alignment algorithm | Needleman-Wunsch 
    61488 Similarity matrix | BLOSUM-62 
    61489 SS fraction | 0.3 
    61490 Gap open (HH/SS/other) | 18/18/6 
    61491 Gap extend | 1 
    61492 SS matrix |  |  | H | S | O 
    61493 ---|---|---|--- 
    61494 H | 6 | -9 | -6 
    61495 S |  | 6 | -6 
    61496 O |  |  | 4 
    61497 Iteration cutoff | 2 
    61498  
    61499 Matchmaker 3j0c.pdb1, chain E (#1.50) with AF3 E2 1-352.pdb, chain B (#549),
    61500 sequence alignment score = 594.5 
    61501 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    61502 6.147) 
    61503  
    61504 
    61505 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    61506 
    61507 Chain information for AF3 E2 353-438.pdb #550 
    61508 --- 
    61509 Chain | Description 
    61510 B | No description available 
    61511  
    61512 
    61513 > matchmaker #550 to #1.50 & sel
    61514 
    61515 Parameters 
    61516 --- 
    61517 Chain pairing | bb 
    61518 Alignment algorithm | Needleman-Wunsch 
    61519 Similarity matrix | BLOSUM-62 
    61520 SS fraction | 0.3 
    61521 Gap open (HH/SS/other) | 18/18/6 
    61522 Gap extend | 1 
    61523 SS matrix |  |  | H | S | O 
    61524 ---|---|---|--- 
    61525 H | 6 | -9 | -6 
    61526 S |  | 6 | -6 
    61527 O |  |  | 4 
    61528 Iteration cutoff | 2 
    61529  
    61530 Matchmaker 3j0c.pdb1, chain E (#1.50) with AF3 E2 353-438.pdb, chain B (#550),
    61531 sequence alignment score = 340.2 
    61532 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    61533 8.673) 
    61534  
    61535 
    61536 > hide sel cartoons
    61537 
    61538 > select #1.50/F
    61539 
    61540 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    61541 
    61542 > show sel cartoons
    61543 
    61544 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    61545 
    61546 Chain information for AF3 CA.pdb #551 
    61547 --- 
    61548 Chain | Description 
    61549 A | No description available 
    61550  
    61551 
    61552 > matchmaker #551 to #1.50 & sel
    61553 
    61554 Parameters 
    61555 --- 
    61556 Chain pairing | bb 
    61557 Alignment algorithm | Needleman-Wunsch 
    61558 Similarity matrix | BLOSUM-62 
    61559 SS fraction | 0.3 
    61560 Gap open (HH/SS/other) | 18/18/6 
    61561 Gap extend | 1 
    61562 SS matrix |  |  | H | S | O 
    61563 ---|---|---|--- 
    61564 H | 6 | -9 | -6 
    61565 S |  | 6 | -6 
    61566 O |  |  | 4 
    61567 Iteration cutoff | 2 
    61568  
    61569 Matchmaker 3j0c.pdb1, chain F (#1.50) with AF3 CA.pdb, chain A (#551),
    61570 sequence alignment score = 335.3 
    61571 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    61572 2.550) 
    61573  
    61574 
    61575 > hide sel cartoons
    61576 
    61577 > color #547 dodgerblue
    61578 
    61579 > color #548 dodgerblue
    61580 
    61581 > color #549 #00b305ff
    61582 
    61583 > color #550 #00b305ff
    61584 
    61585 > color #551 #f15839ff
    61586 
    61587 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    61588 
    61589 > hide #502-551 models
    61590 
    61591 > show #547 models
    61592 
    61593 > show #548 models
    61594 
    61595 > select #1.50/D
    61596 
    61597 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    61598 
    61599 > show sel cartoons
    61600 
    61601 > hide sel cartoons
    61602 
    61603 [Repeated 1 time(s)]
    61604 
    61605 > hide #547 models
    61606 
    61607 > hide #548 models
    61608 
    61609 > select #1.51/D
    61610 
    61611 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    61612 
    61613 > show sel cartoons
    61614 
    61615 > view
    61616 
    61617 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    61618 
    61619 Chain information for AF3 E1 1-421.pdb #552 
    61620 --- 
    61621 Chain | Description 
    61622 A | No description available 
    61623  
    61624 
    61625 > matchmaker #552 to #1.51 & sel
    61626 
    61627 Parameters 
    61628 --- 
    61629 Chain pairing | bb 
    61630 Alignment algorithm | Needleman-Wunsch 
    61631 Similarity matrix | BLOSUM-62 
    61632 SS fraction | 0.3 
    61633 Gap open (HH/SS/other) | 18/18/6 
    61634 Gap extend | 1 
    61635 SS matrix |  |  | H | S | O 
    61636 ---|---|---|--- 
    61637 H | 6 | -9 | -6 
    61638 S |  | 6 | -6 
    61639 O |  |  | 4 
    61640 Iteration cutoff | 2 
    61641  
    61642 Matchmaker 3j0c.pdb1, chain D (#1.51) with AF3 E1 1-421.pdb, chain A (#552),
    61643 sequence alignment score = 1060.7 
    61644 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    61645 3.032) 
    61646  
    61647 
    61648 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    61649 
    61650 Chain information for AF3 E1 422-461.pdb #553 
    61651 --- 
    61652 Chain | Description 
    61653 A | No description available 
    61654  
    61655 
    61656 > matchmaker #553 to #1.51 & sel
    61657 
    61658 Parameters 
    61659 --- 
    61660 Chain pairing | bb 
    61661 Alignment algorithm | Needleman-Wunsch 
    61662 Similarity matrix | BLOSUM-62 
    61663 SS fraction | 0.3 
    61664 Gap open (HH/SS/other) | 18/18/6 
    61665 Gap extend | 1 
    61666 SS matrix |  |  | H | S | O 
    61667 ---|---|---|--- 
    61668 H | 6 | -9 | -6 
    61669 S |  | 6 | -6 
    61670 O |  |  | 4 
    61671 Iteration cutoff | 2 
    61672  
    61673 Matchmaker 3j0c.pdb1, chain D (#1.51) with AF3 E1 422-461.pdb, chain A (#553),
    61674 sequence alignment score = 626.9 
    61675 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    61676 2.916) 
    61677  
    61678 
    61679 > hide sel cartoons
    61680 
    61681 > select #1.51/E
    61682 
    61683 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    61684 
    61685 > show sel cartoons
    61686 
    61687 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    61688 
    61689 Chain information for AF3 E2 1-352.pdb #554 
    61690 --- 
    61691 Chain | Description 
    61692 B | No description available 
    61693  
    61694 
    61695 > matchmaker #554 to #1.51 & sel
    61696 
    61697 Parameters 
    61698 --- 
    61699 Chain pairing | bb 
    61700 Alignment algorithm | Needleman-Wunsch 
    61701 Similarity matrix | BLOSUM-62 
    61702 SS fraction | 0.3 
    61703 Gap open (HH/SS/other) | 18/18/6 
    61704 Gap extend | 1 
    61705 SS matrix |  |  | H | S | O 
    61706 ---|---|---|--- 
    61707 H | 6 | -9 | -6 
    61708 S |  | 6 | -6 
    61709 O |  |  | 4 
    61710 Iteration cutoff | 2 
    61711  
    61712 Matchmaker 3j0c.pdb1, chain E (#1.51) with AF3 E2 1-352.pdb, chain B (#554),
    61713 sequence alignment score = 594.5 
    61714 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    61715 6.147) 
    61716  
    61717 
    61718 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    61719 
    61720 Chain information for AF3 E2 353-438.pdb #555 
    61721 --- 
    61722 Chain | Description 
    61723 B | No description available 
    61724  
    61725 
    61726 > matchmaker #555 to #1.51 & sel
    61727 
    61728 Parameters 
    61729 --- 
    61730 Chain pairing | bb 
    61731 Alignment algorithm | Needleman-Wunsch 
    61732 Similarity matrix | BLOSUM-62 
    61733 SS fraction | 0.3 
    61734 Gap open (HH/SS/other) | 18/18/6 
    61735 Gap extend | 1 
    61736 SS matrix |  |  | H | S | O 
    61737 ---|---|---|--- 
    61738 H | 6 | -9 | -6 
    61739 S |  | 6 | -6 
    61740 O |  |  | 4 
    61741 Iteration cutoff | 2 
    61742  
    61743 Matchmaker 3j0c.pdb1, chain E (#1.51) with AF3 E2 353-438.pdb, chain B (#555),
    61744 sequence alignment score = 340.2 
    61745 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    61746 8.673) 
    61747  
    61748 
    61749 > hide sel cartoons
    61750 
    61751 > select #1.51/F
    61752 
    61753 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    61754 
    61755 > show sel cartoons
    61756 
    61757 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    61758 
    61759 Chain information for AF3 CA.pdb #556 
    61760 --- 
    61761 Chain | Description 
    61762 A | No description available 
    61763  
    61764 
    61765 > matchmaker #556 to #1.51 & sel
    61766 
    61767 Parameters 
    61768 --- 
    61769 Chain pairing | bb 
    61770 Alignment algorithm | Needleman-Wunsch 
    61771 Similarity matrix | BLOSUM-62 
    61772 SS fraction | 0.3 
    61773 Gap open (HH/SS/other) | 18/18/6 
    61774 Gap extend | 1 
    61775 SS matrix |  |  | H | S | O 
    61776 ---|---|---|--- 
    61777 H | 6 | -9 | -6 
    61778 S |  | 6 | -6 
    61779 O |  |  | 4 
    61780 Iteration cutoff | 2 
    61781  
    61782 Matchmaker 3j0c.pdb1, chain F (#1.51) with AF3 CA.pdb, chain A (#556),
    61783 sequence alignment score = 335.3 
    61784 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    61785 2.550) 
    61786  
    61787 
    61788 > hide sel cartoons
    61789 
    61790 > color #552 dodgerblue
    61791 
    61792 > color #553 dodgerblue
    61793 
    61794 > color #554 #00b305ff
    61795 
    61796 > color #555 #00b305ff
    61797 
    61798 > color #556 #f15839ff
    61799 
    61800 > select #1.52/D
    61801 
    61802 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    61803 
    61804 > show sel cartoons
    61805 
    61806 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    61807 
    61808 Chain information for AF3 E1 1-421.pdb #557 
    61809 --- 
    61810 Chain | Description 
    61811 A | No description available 
    61812  
    61813 
    61814 > matchmaker #557 to #1.52 & sel
    61815 
    61816 Parameters 
    61817 --- 
    61818 Chain pairing | bb 
    61819 Alignment algorithm | Needleman-Wunsch 
    61820 Similarity matrix | BLOSUM-62 
    61821 SS fraction | 0.3 
    61822 Gap open (HH/SS/other) | 18/18/6 
    61823 Gap extend | 1 
    61824 SS matrix |  |  | H | S | O 
    61825 ---|---|---|--- 
    61826 H | 6 | -9 | -6 
    61827 S |  | 6 | -6 
    61828 O |  |  | 4 
    61829 Iteration cutoff | 2 
    61830  
    61831 Matchmaker 3j0c.pdb1, chain D (#1.52) with AF3 E1 1-421.pdb, chain A (#557),
    61832 sequence alignment score = 1060.7 
    61833 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    61834 3.032) 
    61835  
    61836 
    61837 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    61838 
    61839 Chain information for AF3 E1 422-461.pdb #558 
    61840 --- 
    61841 Chain | Description 
    61842 A | No description available 
    61843  
    61844 
    61845 > matchmaker #558 to #1.52 & sel
    61846 
    61847 Parameters 
    61848 --- 
    61849 Chain pairing | bb 
    61850 Alignment algorithm | Needleman-Wunsch 
    61851 Similarity matrix | BLOSUM-62 
    61852 SS fraction | 0.3 
    61853 Gap open (HH/SS/other) | 18/18/6 
    61854 Gap extend | 1 
    61855 SS matrix |  |  | H | S | O 
    61856 ---|---|---|--- 
    61857 H | 6 | -9 | -6 
    61858 S |  | 6 | -6 
    61859 O |  |  | 4 
    61860 Iteration cutoff | 2 
    61861  
    61862 Matchmaker 3j0c.pdb1, chain D (#1.52) with AF3 E1 422-461.pdb, chain A (#558),
    61863 sequence alignment score = 626.9 
    61864 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    61865 2.916) 
    61866  
    61867 
    61868 > hide sel cartoons
    61869 
    61870 > select #1.52/E
    61871 
    61872 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    61873 
    61874 > show sel cartoons
    61875 
    61876 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    61877 
    61878 Chain information for AF3 E2 1-352.pdb #559 
    61879 --- 
    61880 Chain | Description 
    61881 B | No description available 
    61882  
    61883 
    61884 > matchmaker #559 to #1.52 & sel
    61885 
    61886 Parameters 
    61887 --- 
    61888 Chain pairing | bb 
    61889 Alignment algorithm | Needleman-Wunsch 
    61890 Similarity matrix | BLOSUM-62 
    61891 SS fraction | 0.3 
    61892 Gap open (HH/SS/other) | 18/18/6 
    61893 Gap extend | 1 
    61894 SS matrix |  |  | H | S | O 
    61895 ---|---|---|--- 
    61896 H | 6 | -9 | -6 
    61897 S |  | 6 | -6 
    61898 O |  |  | 4 
    61899 Iteration cutoff | 2 
    61900  
    61901 Matchmaker 3j0c.pdb1, chain E (#1.52) with AF3 E2 1-352.pdb, chain B (#559),
    61902 sequence alignment score = 594.5 
    61903 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    61904 6.147) 
    61905  
    61906 
    61907 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    61908 
    61909 Chain information for AF3 E2 353-438.pdb #560 
    61910 --- 
    61911 Chain | Description 
    61912 B | No description available 
    61913  
    61914 
    61915 > matchmaker #560 to #1.52 & sel
    61916 
    61917 Parameters 
    61918 --- 
    61919 Chain pairing | bb 
    61920 Alignment algorithm | Needleman-Wunsch 
    61921 Similarity matrix | BLOSUM-62 
    61922 SS fraction | 0.3 
    61923 Gap open (HH/SS/other) | 18/18/6 
    61924 Gap extend | 1 
    61925 SS matrix |  |  | H | S | O 
    61926 ---|---|---|--- 
    61927 H | 6 | -9 | -6 
    61928 S |  | 6 | -6 
    61929 O |  |  | 4 
    61930 Iteration cutoff | 2 
    61931  
    61932 Matchmaker 3j0c.pdb1, chain E (#1.52) with AF3 E2 353-438.pdb, chain B (#560),
    61933 sequence alignment score = 340.2 
    61934 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    61935 8.673) 
    61936  
    61937 
    61938 > hide sel cartoons
    61939 
    61940 > select #1.52/F
    61941 
    61942 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    61943 
    61944 > show sel cartoons
    61945 
    61946 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    61947 
    61948 Chain information for AF3 CA.pdb #561 
    61949 --- 
    61950 Chain | Description 
    61951 A | No description available 
    61952  
    61953 
    61954 > matchmaker #561 to #1.52 & sel
    61955 
    61956 Parameters 
    61957 --- 
    61958 Chain pairing | bb 
    61959 Alignment algorithm | Needleman-Wunsch 
    61960 Similarity matrix | BLOSUM-62 
    61961 SS fraction | 0.3 
    61962 Gap open (HH/SS/other) | 18/18/6 
    61963 Gap extend | 1 
    61964 SS matrix |  |  | H | S | O 
    61965 ---|---|---|--- 
    61966 H | 6 | -9 | -6 
    61967 S |  | 6 | -6 
    61968 O |  |  | 4 
    61969 Iteration cutoff | 2 
    61970  
    61971 Matchmaker 3j0c.pdb1, chain F (#1.52) with AF3 CA.pdb, chain A (#561),
    61972 sequence alignment score = 335.3 
    61973 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    61974 2.550) 
    61975  
    61976 
    61977 > hide sel cartoons
    61978 
    61979 > color #557 dodgerblue
    61980 
    61981 > color #558 dodgerblue
    61982 
    61983 > color #559 #00b305ff
    61984 
    61985 > color #560 #00b305ff
    61986 
    61987 > color #561 #f15839ff
    61988 
    61989 > select #1.53/D
    61990 
    61991 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    61992 
    61993 > select #1.53/D
    61994 
    61995 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    61996 
    61997 > show sel cartoons
    61998 
    61999 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    62000 
    62001 Chain information for AF3 E1 1-421.pdb #562 
    62002 --- 
    62003 Chain | Description 
    62004 A | No description available 
    62005  
    62006 
    62007 > matchmaker #562 to #1.53 & sel
    62008 
    62009 Parameters 
    62010 --- 
    62011 Chain pairing | bb 
    62012 Alignment algorithm | Needleman-Wunsch 
    62013 Similarity matrix | BLOSUM-62 
    62014 SS fraction | 0.3 
    62015 Gap open (HH/SS/other) | 18/18/6 
    62016 Gap extend | 1 
    62017 SS matrix |  |  | H | S | O 
    62018 ---|---|---|--- 
    62019 H | 6 | -9 | -6 
    62020 S |  | 6 | -6 
    62021 O |  |  | 4 
    62022 Iteration cutoff | 2 
    62023  
    62024 Matchmaker 3j0c.pdb1, chain D (#1.53) with AF3 E1 1-421.pdb, chain A (#562),
    62025 sequence alignment score = 1060.7 
    62026 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    62027 3.032) 
    62028  
    62029 
    62030 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    62031 
    62032 Chain information for AF3 E1 422-461.pdb #563 
    62033 --- 
    62034 Chain | Description 
    62035 A | No description available 
    62036  
    62037 
    62038 > matchmaker #563 to #1.53 & sel
    62039 
    62040 Parameters 
    62041 --- 
    62042 Chain pairing | bb 
    62043 Alignment algorithm | Needleman-Wunsch 
    62044 Similarity matrix | BLOSUM-62 
    62045 SS fraction | 0.3 
    62046 Gap open (HH/SS/other) | 18/18/6 
    62047 Gap extend | 1 
    62048 SS matrix |  |  | H | S | O 
    62049 ---|---|---|--- 
    62050 H | 6 | -9 | -6 
    62051 S |  | 6 | -6 
    62052 O |  |  | 4 
    62053 Iteration cutoff | 2 
    62054  
    62055 Matchmaker 3j0c.pdb1, chain D (#1.53) with AF3 E1 422-461.pdb, chain A (#563),
    62056 sequence alignment score = 626.9 
    62057 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    62058 2.916) 
    62059  
    62060 
    62061 > hide sel cartoons
    62062 
    62063 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    62064 
    62065 Chain information for AF3 E2 1-352.pdb #564 
    62066 --- 
    62067 Chain | Description 
    62068 B | No description available 
    62069  
    62070 
    62071 > select #1.53/E
    62072 
    62073 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    62074 
    62075 > show sel cartoons
    62076 
    62077 > matchmaker #564 to #1.53 & sel
    62078 
    62079 Parameters 
    62080 --- 
    62081 Chain pairing | bb 
    62082 Alignment algorithm | Needleman-Wunsch 
    62083 Similarity matrix | BLOSUM-62 
    62084 SS fraction | 0.3 
    62085 Gap open (HH/SS/other) | 18/18/6 
    62086 Gap extend | 1 
    62087 SS matrix |  |  | H | S | O 
    62088 ---|---|---|--- 
    62089 H | 6 | -9 | -6 
    62090 S |  | 6 | -6 
    62091 O |  |  | 4 
    62092 Iteration cutoff | 2 
    62093  
    62094 Matchmaker 3j0c.pdb1, chain E (#1.53) with AF3 E2 1-352.pdb, chain B (#564),
    62095 sequence alignment score = 594.5 
    62096 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    62097 6.147) 
    62098  
    62099 
    62100 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    62101 
    62102 Chain information for AF3 E2 353-438.pdb #565 
    62103 --- 
    62104 Chain | Description 
    62105 B | No description available 
    62106  
    62107 
    62108 > matchmaker #565 to #1.53 & sel
    62109 
    62110 Parameters 
    62111 --- 
    62112 Chain pairing | bb 
    62113 Alignment algorithm | Needleman-Wunsch 
    62114 Similarity matrix | BLOSUM-62 
    62115 SS fraction | 0.3 
    62116 Gap open (HH/SS/other) | 18/18/6 
    62117 Gap extend | 1 
    62118 SS matrix |  |  | H | S | O 
    62119 ---|---|---|--- 
    62120 H | 6 | -9 | -6 
    62121 S |  | 6 | -6 
    62122 O |  |  | 4 
    62123 Iteration cutoff | 2 
    62124  
    62125 Matchmaker 3j0c.pdb1, chain E (#1.53) with AF3 E2 353-438.pdb, chain B (#565),
    62126 sequence alignment score = 340.2 
    62127 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    62128 8.673) 
    62129  
    62130 
    62131 > hide sel cartoons
    62132 
    62133 > select #1.53/F
    62134 
    62135 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    62136 
    62137 > show sel cartoons
    62138 
    62139 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    62140 
    62141 Chain information for AF3 CA.pdb #566 
    62142 --- 
    62143 Chain | Description 
    62144 A | No description available 
    62145  
    62146 
    62147 > matchmaker #566 to #1.53 & sel
    62148 
    62149 Parameters 
    62150 --- 
    62151 Chain pairing | bb 
    62152 Alignment algorithm | Needleman-Wunsch 
    62153 Similarity matrix | BLOSUM-62 
    62154 SS fraction | 0.3 
    62155 Gap open (HH/SS/other) | 18/18/6 
    62156 Gap extend | 1 
    62157 SS matrix |  |  | H | S | O 
    62158 ---|---|---|--- 
    62159 H | 6 | -9 | -6 
    62160 S |  | 6 | -6 
    62161 O |  |  | 4 
    62162 Iteration cutoff | 2 
    62163  
    62164 Matchmaker 3j0c.pdb1, chain F (#1.53) with AF3 CA.pdb, chain A (#566),
    62165 sequence alignment score = 335.3 
    62166 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    62167 2.550) 
    62168  
    62169 
    62170 > hide sel cartoons
    62171 
    62172 > color #562 dodgerblue
    62173 
    62174 > color #563 dodgerblue
    62175 
    62176 > color #564 #00b305ff
    62177 
    62178 > color #565 #00b305ff
    62179 
    62180 > color #566 #f15839ff
    62181 
    62182 > select #1.54/D
    62183 
    62184 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    62185 
    62186 > show sel cartoons
    62187 
    62188 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    62189 
    62190 Chain information for AF3 E1 1-421.pdb #567 
    62191 --- 
    62192 Chain | Description 
    62193 A | No description available 
    62194  
    62195 
    62196 > matchmaker #567 to #1.53 & sel
    62197 
    62198 No 'to' model specified 
    62199 
    62200 > matchmaker #567 to #1.54 & sel
    62201 
    62202 Parameters 
    62203 --- 
    62204 Chain pairing | bb 
    62205 Alignment algorithm | Needleman-Wunsch 
    62206 Similarity matrix | BLOSUM-62 
    62207 SS fraction | 0.3 
    62208 Gap open (HH/SS/other) | 18/18/6 
    62209 Gap extend | 1 
    62210 SS matrix |  |  | H | S | O 
    62211 ---|---|---|--- 
    62212 H | 6 | -9 | -6 
    62213 S |  | 6 | -6 
    62214 O |  |  | 4 
    62215 Iteration cutoff | 2 
    62216  
    62217 Matchmaker 3j0c.pdb1, chain D (#1.54) with AF3 E1 1-421.pdb, chain A (#567),
    62218 sequence alignment score = 1060.7 
    62219 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    62220 3.032) 
    62221  
    62222 
    62223 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    62224 
    62225 Chain information for AF3 E1 422-461.pdb #568 
    62226 --- 
    62227 Chain | Description 
    62228 A | No description available 
    62229  
    62230 
    62231 > matchmaker #568 to #1.54 & sel
    62232 
    62233 Parameters 
    62234 --- 
    62235 Chain pairing | bb 
    62236 Alignment algorithm | Needleman-Wunsch 
    62237 Similarity matrix | BLOSUM-62 
    62238 SS fraction | 0.3 
    62239 Gap open (HH/SS/other) | 18/18/6 
    62240 Gap extend | 1 
    62241 SS matrix |  |  | H | S | O 
    62242 ---|---|---|--- 
    62243 H | 6 | -9 | -6 
    62244 S |  | 6 | -6 
    62245 O |  |  | 4 
    62246 Iteration cutoff | 2 
    62247  
    62248 Matchmaker 3j0c.pdb1, chain D (#1.54) with AF3 E1 422-461.pdb, chain A (#568),
    62249 sequence alignment score = 626.9 
    62250 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    62251 2.916) 
    62252  
    62253 
    62254 > hide sel cartoons
    62255 
    62256 > select #1.54/E
    62257 
    62258 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    62259 
    62260 > show sel cartoons
    62261 
    62262 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    62263 
    62264 Chain information for AF3 E2 1-352.pdb #569 
    62265 --- 
    62266 Chain | Description 
    62267 B | No description available 
    62268  
    62269 
    62270 > matchmaker #569 to #1.54 & sel
    62271 
    62272 Parameters 
    62273 --- 
    62274 Chain pairing | bb 
    62275 Alignment algorithm | Needleman-Wunsch 
    62276 Similarity matrix | BLOSUM-62 
    62277 SS fraction | 0.3 
    62278 Gap open (HH/SS/other) | 18/18/6 
    62279 Gap extend | 1 
    62280 SS matrix |  |  | H | S | O 
    62281 ---|---|---|--- 
    62282 H | 6 | -9 | -6 
    62283 S |  | 6 | -6 
    62284 O |  |  | 4 
    62285 Iteration cutoff | 2 
    62286  
    62287 Matchmaker 3j0c.pdb1, chain E (#1.54) with AF3 E2 1-352.pdb, chain B (#569),
    62288 sequence alignment score = 594.5 
    62289 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    62290 6.147) 
    62291  
    62292 
    62293 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    62294 
    62295 Chain information for AF3 E2 353-438.pdb #570 
    62296 --- 
    62297 Chain | Description 
    62298 B | No description available 
    62299  
    62300 
    62301 > matchmaker #570 to #1.54 & sel
    62302 
    62303 Parameters 
    62304 --- 
    62305 Chain pairing | bb 
    62306 Alignment algorithm | Needleman-Wunsch 
    62307 Similarity matrix | BLOSUM-62 
    62308 SS fraction | 0.3 
    62309 Gap open (HH/SS/other) | 18/18/6 
    62310 Gap extend | 1 
    62311 SS matrix |  |  | H | S | O 
    62312 ---|---|---|--- 
    62313 H | 6 | -9 | -6 
    62314 S |  | 6 | -6 
    62315 O |  |  | 4 
    62316 Iteration cutoff | 2 
    62317  
    62318 Matchmaker 3j0c.pdb1, chain E (#1.54) with AF3 E2 353-438.pdb, chain B (#570),
    62319 sequence alignment score = 340.2 
    62320 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    62321 8.673) 
    62322  
    62323 
    62324 > hide sel cartoons
    62325 
    62326 > select #1.54/F
    62327 
    62328 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    62329 
    62330 > show sel cartoons
    62331 
    62332 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    62333 
    62334 Chain information for AF3 CA.pdb #571 
    62335 --- 
    62336 Chain | Description 
    62337 A | No description available 
    62338  
    62339 
    62340 > matchmaker #571 to #1.54 & sel
    62341 
    62342 Parameters 
    62343 --- 
    62344 Chain pairing | bb 
    62345 Alignment algorithm | Needleman-Wunsch 
    62346 Similarity matrix | BLOSUM-62 
    62347 SS fraction | 0.3 
    62348 Gap open (HH/SS/other) | 18/18/6 
    62349 Gap extend | 1 
    62350 SS matrix |  |  | H | S | O 
    62351 ---|---|---|--- 
    62352 H | 6 | -9 | -6 
    62353 S |  | 6 | -6 
    62354 O |  |  | 4 
    62355 Iteration cutoff | 2 
    62356  
    62357 Matchmaker 3j0c.pdb1, chain F (#1.54) with AF3 CA.pdb, chain A (#571),
    62358 sequence alignment score = 335.3 
    62359 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    62360 2.550) 
    62361  
    62362 
    62363 > hide sel cartoons
    62364 
    62365 > color #567 dodgerblue
    62366 
    62367 > color #568 dodgerblue
    62368 
    62369 > color #569 #00b305ff
    62370 
    62371 > color #570 #00b305ff
    62372 
    62373 > color #571 #f15839ff
    62374 
    62375 > select #1.55/D
    62376 
    62377 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    62378 
    62379 > show sel cartoons
    62380 
    62381 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    62382 
    62383 Chain information for AF3 E1 1-421.pdb #572 
    62384 --- 
    62385 Chain | Description 
    62386 A | No description available 
    62387  
    62388 
    62389 > matchmaker #572 to #1.55 & sel
    62390 
    62391 Parameters 
    62392 --- 
    62393 Chain pairing | bb 
    62394 Alignment algorithm | Needleman-Wunsch 
    62395 Similarity matrix | BLOSUM-62 
    62396 SS fraction | 0.3 
    62397 Gap open (HH/SS/other) | 18/18/6 
    62398 Gap extend | 1 
    62399 SS matrix |  |  | H | S | O 
    62400 ---|---|---|--- 
    62401 H | 6 | -9 | -6 
    62402 S |  | 6 | -6 
    62403 O |  |  | 4 
    62404 Iteration cutoff | 2 
    62405  
    62406 Matchmaker 3j0c.pdb1, chain D (#1.55) with AF3 E1 1-421.pdb, chain A (#572),
    62407 sequence alignment score = 1060.7 
    62408 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    62409 3.032) 
    62410  
    62411 
    62412 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    62413 
    62414 Chain information for AF3 E1 422-461.pdb #573 
    62415 --- 
    62416 Chain | Description 
    62417 A | No description available 
    62418  
    62419 
    62420 > matchmaker #573 to #1.55 & sel
    62421 
    62422 Parameters 
    62423 --- 
    62424 Chain pairing | bb 
    62425 Alignment algorithm | Needleman-Wunsch 
    62426 Similarity matrix | BLOSUM-62 
    62427 SS fraction | 0.3 
    62428 Gap open (HH/SS/other) | 18/18/6 
    62429 Gap extend | 1 
    62430 SS matrix |  |  | H | S | O 
    62431 ---|---|---|--- 
    62432 H | 6 | -9 | -6 
    62433 S |  | 6 | -6 
    62434 O |  |  | 4 
    62435 Iteration cutoff | 2 
    62436  
    62437 Matchmaker 3j0c.pdb1, chain D (#1.55) with AF3 E1 422-461.pdb, chain A (#573),
    62438 sequence alignment score = 626.9 
    62439 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    62440 2.916) 
    62441  
    62442 
    62443 > hide sel cartoons
    62444 
    62445 > select #1.55/E
    62446 
    62447 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    62448 
    62449 > show sel cartoons
    62450 
    62451 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    62452 
    62453 Chain information for AF3 E2 1-352.pdb #574 
    62454 --- 
    62455 Chain | Description 
    62456 B | No description available 
    62457  
    62458 
    62459 > matchmaker #574 to #1.55 & sel
    62460 
    62461 Parameters 
    62462 --- 
    62463 Chain pairing | bb 
    62464 Alignment algorithm | Needleman-Wunsch 
    62465 Similarity matrix | BLOSUM-62 
    62466 SS fraction | 0.3 
    62467 Gap open (HH/SS/other) | 18/18/6 
    62468 Gap extend | 1 
    62469 SS matrix |  |  | H | S | O 
    62470 ---|---|---|--- 
    62471 H | 6 | -9 | -6 
    62472 S |  | 6 | -6 
    62473 O |  |  | 4 
    62474 Iteration cutoff | 2 
    62475  
    62476 Matchmaker 3j0c.pdb1, chain E (#1.55) with AF3 E2 1-352.pdb, chain B (#574),
    62477 sequence alignment score = 594.5 
    62478 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    62479 6.147) 
    62480  
    62481 
    62482 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    62483 
    62484 Chain information for AF3 E2 353-438.pdb #575 
    62485 --- 
    62486 Chain | Description 
    62487 B | No description available 
    62488  
    62489 
    62490 > matchmaker #575 to #1.55 & sel
    62491 
    62492 Parameters 
    62493 --- 
    62494 Chain pairing | bb 
    62495 Alignment algorithm | Needleman-Wunsch 
    62496 Similarity matrix | BLOSUM-62 
    62497 SS fraction | 0.3 
    62498 Gap open (HH/SS/other) | 18/18/6 
    62499 Gap extend | 1 
    62500 SS matrix |  |  | H | S | O 
    62501 ---|---|---|--- 
    62502 H | 6 | -9 | -6 
    62503 S |  | 6 | -6 
    62504 O |  |  | 4 
    62505 Iteration cutoff | 2 
    62506  
    62507 Matchmaker 3j0c.pdb1, chain E (#1.55) with AF3 E2 353-438.pdb, chain B (#575),
    62508 sequence alignment score = 340.2 
    62509 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    62510 8.673) 
    62511  
    62512 
    62513 > hide sel cartoons
    62514 
    62515 The cached device pixel ratio value was stale on window expose. Please file a
    62516 QTBUG which explains how to reproduce. 
    62517 
    62518 > select #1.55/F
    62519 
    62520 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    62521 
    62522 > show sel cartoons
    62523 
    62524 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    62525 
    62526 Chain information for AF3 CA.pdb #576 
    62527 --- 
    62528 Chain | Description 
    62529 A | No description available 
    62530  
    62531 
    62532 > matchmaker #576 to #1.55 & sel
    62533 
    62534 Parameters 
    62535 --- 
    62536 Chain pairing | bb 
    62537 Alignment algorithm | Needleman-Wunsch 
    62538 Similarity matrix | BLOSUM-62 
    62539 SS fraction | 0.3 
    62540 Gap open (HH/SS/other) | 18/18/6 
    62541 Gap extend | 1 
    62542 SS matrix |  |  | H | S | O 
    62543 ---|---|---|--- 
    62544 H | 6 | -9 | -6 
    62545 S |  | 6 | -6 
    62546 O |  |  | 4 
    62547 Iteration cutoff | 2 
    62548  
    62549 Matchmaker 3j0c.pdb1, chain F (#1.55) with AF3 CA.pdb, chain A (#576),
    62550 sequence alignment score = 335.3 
    62551 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    62552 2.550) 
    62553  
    62554 
    62555 > hide sel cartoons
    62556 
    62557 > color #572 dodgerblue
    62558 
    62559 > color #573 dodgerblue
    62560 
    62561 > color #574 #00b305ff
    62562 
    62563 > color #575 #00b305ff
    62564 
    62565 > color #576 #f15839ff
    62566 
    62567 > select #1.56/D
    62568 
    62569 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    62570 
    62571 > show sel cartoons
    62572 
    62573 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    62574 
    62575 Chain information for AF3 E1 1-421.pdb #577 
    62576 --- 
    62577 Chain | Description 
    62578 A | No description available 
    62579  
    62580 
    62581 > matchmaker #577 to #1.56 & sel
    62582 
    62583 Parameters 
    62584 --- 
    62585 Chain pairing | bb 
    62586 Alignment algorithm | Needleman-Wunsch 
    62587 Similarity matrix | BLOSUM-62 
    62588 SS fraction | 0.3 
    62589 Gap open (HH/SS/other) | 18/18/6 
    62590 Gap extend | 1 
    62591 SS matrix |  |  | H | S | O 
    62592 ---|---|---|--- 
    62593 H | 6 | -9 | -6 
    62594 S |  | 6 | -6 
    62595 O |  |  | 4 
    62596 Iteration cutoff | 2 
    62597  
    62598 Matchmaker 3j0c.pdb1, chain D (#1.56) with AF3 E1 1-421.pdb, chain A (#577),
    62599 sequence alignment score = 1060.7 
    62600 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    62601 3.032) 
    62602  
    62603 
    62604 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    62605 
    62606 Chain information for AF3 E1 422-461.pdb #578 
    62607 --- 
    62608 Chain | Description 
    62609 A | No description available 
    62610  
    62611 
    62612 > matchmaker #578 to #1.56 & sel
    62613 
    62614 Parameters 
    62615 --- 
    62616 Chain pairing | bb 
    62617 Alignment algorithm | Needleman-Wunsch 
    62618 Similarity matrix | BLOSUM-62 
    62619 SS fraction | 0.3 
    62620 Gap open (HH/SS/other) | 18/18/6 
    62621 Gap extend | 1 
    62622 SS matrix |  |  | H | S | O 
    62623 ---|---|---|--- 
    62624 H | 6 | -9 | -6 
    62625 S |  | 6 | -6 
    62626 O |  |  | 4 
    62627 Iteration cutoff | 2 
    62628  
    62629 Matchmaker 3j0c.pdb1, chain D (#1.56) with AF3 E1 422-461.pdb, chain A (#578),
    62630 sequence alignment score = 626.9 
    62631 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    62632 2.916) 
    62633  
    62634 
    62635 > hide sel cartoons
    62636 
    62637 > select #1.56/E
    62638 
    62639 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    62640 
    62641 > show sel cartoons
    62642 
    62643 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    62644 
    62645 Chain information for AF3 E2 1-352.pdb #579 
    62646 --- 
    62647 Chain | Description 
    62648 B | No description available 
    62649  
    62650 
    62651 > matchmaker #579 to #1.56 & sel
    62652 
    62653 Parameters 
    62654 --- 
    62655 Chain pairing | bb 
    62656 Alignment algorithm | Needleman-Wunsch 
    62657 Similarity matrix | BLOSUM-62 
    62658 SS fraction | 0.3 
    62659 Gap open (HH/SS/other) | 18/18/6 
    62660 Gap extend | 1 
    62661 SS matrix |  |  | H | S | O 
    62662 ---|---|---|--- 
    62663 H | 6 | -9 | -6 
    62664 S |  | 6 | -6 
    62665 O |  |  | 4 
    62666 Iteration cutoff | 2 
    62667  
    62668 Matchmaker 3j0c.pdb1, chain E (#1.56) with AF3 E2 1-352.pdb, chain B (#579),
    62669 sequence alignment score = 594.5 
    62670 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    62671 6.147) 
    62672  
    62673 
    62674 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    62675 
    62676 Chain information for AF3 E2 353-438.pdb #580 
    62677 --- 
    62678 Chain | Description 
    62679 B | No description available 
    62680  
    62681 
    62682 > matchmaker #580 to #1.56 & sel
    62683 
    62684 Parameters 
    62685 --- 
    62686 Chain pairing | bb 
    62687 Alignment algorithm | Needleman-Wunsch 
    62688 Similarity matrix | BLOSUM-62 
    62689 SS fraction | 0.3 
    62690 Gap open (HH/SS/other) | 18/18/6 
    62691 Gap extend | 1 
    62692 SS matrix |  |  | H | S | O 
    62693 ---|---|---|--- 
    62694 H | 6 | -9 | -6 
    62695 S |  | 6 | -6 
    62696 O |  |  | 4 
    62697 Iteration cutoff | 2 
    62698  
    62699 Matchmaker 3j0c.pdb1, chain E (#1.56) with AF3 E2 353-438.pdb, chain B (#580),
    62700 sequence alignment score = 340.2 
    62701 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    62702 8.673) 
    62703  
    62704 
    62705 > hide sel cartoons
    62706 
    62707 > select #1.56/F
    62708 
    62709 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    62710 
    62711 > show sel cartoons
    62712 
    62713 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    62714 
    62715 Chain information for AF3 CA.pdb #581 
    62716 --- 
    62717 Chain | Description 
    62718 A | No description available 
    62719  
    62720 
    62721 > matchmaker #581 to #1.56 & sel
    62722 
    62723 Parameters 
    62724 --- 
    62725 Chain pairing | bb 
    62726 Alignment algorithm | Needleman-Wunsch 
    62727 Similarity matrix | BLOSUM-62 
    62728 SS fraction | 0.3 
    62729 Gap open (HH/SS/other) | 18/18/6 
    62730 Gap extend | 1 
    62731 SS matrix |  |  | H | S | O 
    62732 ---|---|---|--- 
    62733 H | 6 | -9 | -6 
    62734 S |  | 6 | -6 
    62735 O |  |  | 4 
    62736 Iteration cutoff | 2 
    62737  
    62738 Matchmaker 3j0c.pdb1, chain F (#1.56) with AF3 CA.pdb, chain A (#581),
    62739 sequence alignment score = 335.3 
    62740 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    62741 2.550) 
    62742  
    62743 
    62744 > hide sel cartoons
    62745 
    62746 > color #577 dodgerblue
    62747 
    62748 > color #578 dodgerblue
    62749 
    62750 > color #579 #00b305ff
    62751 
    62752 > color #580 #00b305ff
    62753 
    62754 > color #581 #f15839ff
    62755 
    62756 > select #1.57/D
    62757 
    62758 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    62759 
    62760 > show sel cartoons
    62761 
    62762 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    62763 
    62764 Chain information for AF3 E1 1-421.pdb #582 
    62765 --- 
    62766 Chain | Description 
    62767 A | No description available 
    62768  
    62769 
    62770 > matchmaker #582 to #1.57 & sel
    62771 
    62772 Parameters 
    62773 --- 
    62774 Chain pairing | bb 
    62775 Alignment algorithm | Needleman-Wunsch 
    62776 Similarity matrix | BLOSUM-62 
    62777 SS fraction | 0.3 
    62778 Gap open (HH/SS/other) | 18/18/6 
    62779 Gap extend | 1 
    62780 SS matrix |  |  | H | S | O 
    62781 ---|---|---|--- 
    62782 H | 6 | -9 | -6 
    62783 S |  | 6 | -6 
    62784 O |  |  | 4 
    62785 Iteration cutoff | 2 
    62786  
    62787 Matchmaker 3j0c.pdb1, chain D (#1.57) with AF3 E1 1-421.pdb, chain A (#582),
    62788 sequence alignment score = 1060.7 
    62789 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    62790 3.032) 
    62791  
    62792 
    62793 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    62794 
    62795 Chain information for AF3 E1 422-461.pdb #583 
    62796 --- 
    62797 Chain | Description 
    62798 A | No description available 
    62799  
    62800 
    62801 > matchmaker #583 to #1.57 & sel
    62802 
    62803 Parameters 
    62804 --- 
    62805 Chain pairing | bb 
    62806 Alignment algorithm | Needleman-Wunsch 
    62807 Similarity matrix | BLOSUM-62 
    62808 SS fraction | 0.3 
    62809 Gap open (HH/SS/other) | 18/18/6 
    62810 Gap extend | 1 
    62811 SS matrix |  |  | H | S | O 
    62812 ---|---|---|--- 
    62813 H | 6 | -9 | -6 
    62814 S |  | 6 | -6 
    62815 O |  |  | 4 
    62816 Iteration cutoff | 2 
    62817  
    62818 Matchmaker 3j0c.pdb1, chain D (#1.57) with AF3 E1 422-461.pdb, chain A (#583),
    62819 sequence alignment score = 626.9 
    62820 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    62821 2.916) 
    62822  
    62823 
    62824 > hide sel cartoons
    62825 
    62826 > select #1.57/E
    62827 
    62828 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    62829 
    62830 > show sel cartoons
    62831 
    62832 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    62833 
    62834 Chain information for AF3 E2 1-352.pdb #584 
    62835 --- 
    62836 Chain | Description 
    62837 B | No description available 
    62838  
    62839 
    62840 > matchmaker #584 to #1.57 & sel
    62841 
    62842 Parameters 
    62843 --- 
    62844 Chain pairing | bb 
    62845 Alignment algorithm | Needleman-Wunsch 
    62846 Similarity matrix | BLOSUM-62 
    62847 SS fraction | 0.3 
    62848 Gap open (HH/SS/other) | 18/18/6 
    62849 Gap extend | 1 
    62850 SS matrix |  |  | H | S | O 
    62851 ---|---|---|--- 
    62852 H | 6 | -9 | -6 
    62853 S |  | 6 | -6 
    62854 O |  |  | 4 
    62855 Iteration cutoff | 2 
    62856  
    62857 Matchmaker 3j0c.pdb1, chain E (#1.57) with AF3 E2 1-352.pdb, chain B (#584),
    62858 sequence alignment score = 594.5 
    62859 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    62860 6.147) 
    62861  
    62862 
    62863 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    62864 
    62865 Chain information for AF3 E2 353-438.pdb #585 
    62866 --- 
    62867 Chain | Description 
    62868 B | No description available 
    62869  
    62870 
    62871 > matchmaker #585 to #1.57 & sel
    62872 
    62873 Parameters 
    62874 --- 
    62875 Chain pairing | bb 
    62876 Alignment algorithm | Needleman-Wunsch 
    62877 Similarity matrix | BLOSUM-62 
    62878 SS fraction | 0.3 
    62879 Gap open (HH/SS/other) | 18/18/6 
    62880 Gap extend | 1 
    62881 SS matrix |  |  | H | S | O 
    62882 ---|---|---|--- 
    62883 H | 6 | -9 | -6 
    62884 S |  | 6 | -6 
    62885 O |  |  | 4 
    62886 Iteration cutoff | 2 
    62887  
    62888 Matchmaker 3j0c.pdb1, chain E (#1.57) with AF3 E2 353-438.pdb, chain B (#585),
    62889 sequence alignment score = 340.2 
    62890 RMSD between 38 pruned atom pairs is 0.819 angstroms; (across all 84 pairs:
    62891 8.673) 
    62892  
    62893 
    62894 > hide sel cartoons
    62895 
    62896 > select #1.57/F
    62897 
    62898 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    62899 
    62900 > show sel cartoons
    62901 
    62902 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    62903 
    62904 Chain information for AF3 CA.pdb #586 
    62905 --- 
    62906 Chain | Description 
    62907 A | No description available 
    62908  
    62909 
    62910 > matchmaker #586 to #1.57 & sel
    62911 
    62912 Parameters 
    62913 --- 
    62914 Chain pairing | bb 
    62915 Alignment algorithm | Needleman-Wunsch 
    62916 Similarity matrix | BLOSUM-62 
    62917 SS fraction | 0.3 
    62918 Gap open (HH/SS/other) | 18/18/6 
    62919 Gap extend | 1 
    62920 SS matrix |  |  | H | S | O 
    62921 ---|---|---|--- 
    62922 H | 6 | -9 | -6 
    62923 S |  | 6 | -6 
    62924 O |  |  | 4 
    62925 Iteration cutoff | 2 
    62926  
    62927 Matchmaker 3j0c.pdb1, chain F (#1.57) with AF3 CA.pdb, chain A (#586),
    62928 sequence alignment score = 335.3 
    62929 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    62930 2.550) 
    62931  
    62932 
    62933 > hide sel cartoons
    62934 
    62935 > color #582 dodgerblue
    62936 
    62937 > color #583 dodgerblue
    62938 
    62939 > color #584 #00b305ff
    62940 
    62941 > color #585 #00b305ff
    62942 
    62943 > color #586 #f15839ff
    62944 
    62945 > select #1.58/D
    62946 
    62947 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    62948 
    62949 > show sel cartoons
    62950 
    62951 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    62952 
    62953 Chain information for AF3 E1 1-421.pdb #587 
    62954 --- 
    62955 Chain | Description 
    62956 A | No description available 
    62957  
    62958 
    62959 > matchmaker #587 to #1.58 & sel
    62960 
    62961 Parameters 
    62962 --- 
    62963 Chain pairing | bb 
    62964 Alignment algorithm | Needleman-Wunsch 
    62965 Similarity matrix | BLOSUM-62 
    62966 SS fraction | 0.3 
    62967 Gap open (HH/SS/other) | 18/18/6 
    62968 Gap extend | 1 
    62969 SS matrix |  |  | H | S | O 
    62970 ---|---|---|--- 
    62971 H | 6 | -9 | -6 
    62972 S |  | 6 | -6 
    62973 O |  |  | 4 
    62974 Iteration cutoff | 2 
    62975  
    62976 Matchmaker 3j0c.pdb1, chain D (#1.58) with AF3 E1 1-421.pdb, chain A (#587),
    62977 sequence alignment score = 1060.7 
    62978 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    62979 3.032) 
    62980  
    62981 
    62982 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    62983 
    62984 Chain information for AF3 E1 422-461.pdb #588 
    62985 --- 
    62986 Chain | Description 
    62987 A | No description available 
    62988  
    62989 
    62990 > matchmaker #588 to #1.58 & sel
    62991 
    62992 Parameters 
    62993 --- 
    62994 Chain pairing | bb 
    62995 Alignment algorithm | Needleman-Wunsch 
    62996 Similarity matrix | BLOSUM-62 
    62997 SS fraction | 0.3 
    62998 Gap open (HH/SS/other) | 18/18/6 
    62999 Gap extend | 1 
    63000 SS matrix |  |  | H | S | O 
    63001 ---|---|---|--- 
    63002 H | 6 | -9 | -6 
    63003 S |  | 6 | -6 
    63004 O |  |  | 4 
    63005 Iteration cutoff | 2 
    63006  
    63007 Matchmaker 3j0c.pdb1, chain D (#1.58) with AF3 E1 422-461.pdb, chain A (#588),
    63008 sequence alignment score = 626.9 
    63009 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    63010 2.916) 
    63011  
    63012 
    63013 > hide sel atoms
    63014 
    63015 > hide sel cartoons
    63016 
    63017 > select #1.58/E
    63018 
    63019 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    63020 
    63021 > show sel cartoons
    63022 
    63023 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    63024 
    63025 Chain information for AF3 E2 1-352.pdb #589 
    63026 --- 
    63027 Chain | Description 
    63028 B | No description available 
    63029  
    63030 
    63031 > matchmaker #589 to #1.58 & sel
    63032 
    63033 Parameters 
    63034 --- 
    63035 Chain pairing | bb 
    63036 Alignment algorithm | Needleman-Wunsch 
    63037 Similarity matrix | BLOSUM-62 
    63038 SS fraction | 0.3 
    63039 Gap open (HH/SS/other) | 18/18/6 
    63040 Gap extend | 1 
    63041 SS matrix |  |  | H | S | O 
    63042 ---|---|---|--- 
    63043 H | 6 | -9 | -6 
    63044 S |  | 6 | -6 
    63045 O |  |  | 4 
    63046 Iteration cutoff | 2 
    63047  
    63048 Matchmaker 3j0c.pdb1, chain E (#1.58) with AF3 E2 1-352.pdb, chain B (#589),
    63049 sequence alignment score = 594.5 
    63050 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    63051 6.147) 
    63052  
    63053 
    63054 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    63055 
    63056 Chain information for AF3 E2 353-438.pdb #590 
    63057 --- 
    63058 Chain | Description 
    63059 B | No description available 
    63060  
    63061 
    63062 > matchmaker #590 to #1.58 & sel
    63063 
    63064 Parameters 
    63065 --- 
    63066 Chain pairing | bb 
    63067 Alignment algorithm | Needleman-Wunsch 
    63068 Similarity matrix | BLOSUM-62 
    63069 SS fraction | 0.3 
    63070 Gap open (HH/SS/other) | 18/18/6 
    63071 Gap extend | 1 
    63072 SS matrix |  |  | H | S | O 
    63073 ---|---|---|--- 
    63074 H | 6 | -9 | -6 
    63075 S |  | 6 | -6 
    63076 O |  |  | 4 
    63077 Iteration cutoff | 2 
    63078  
    63079 Matchmaker 3j0c.pdb1, chain E (#1.58) with AF3 E2 353-438.pdb, chain B (#590),
    63080 sequence alignment score = 340.2 
    63081 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    63082 8.673) 
    63083  
    63084 
    63085 > hide sel cartoons
    63086 
    63087 > select #1.58/F
    63088 
    63089 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    63090 
    63091 > show sel cartoons
    63092 
    63093 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    63094 
    63095 Chain information for AF3 CA.pdb #591 
    63096 --- 
    63097 Chain | Description 
    63098 A | No description available 
    63099  
    63100 
    63101 > matchmaker #591 to #1.58 & sel
    63102 
    63103 Parameters 
    63104 --- 
    63105 Chain pairing | bb 
    63106 Alignment algorithm | Needleman-Wunsch 
    63107 Similarity matrix | BLOSUM-62 
    63108 SS fraction | 0.3 
    63109 Gap open (HH/SS/other) | 18/18/6 
    63110 Gap extend | 1 
    63111 SS matrix |  |  | H | S | O 
    63112 ---|---|---|--- 
    63113 H | 6 | -9 | -6 
    63114 S |  | 6 | -6 
    63115 O |  |  | 4 
    63116 Iteration cutoff | 2 
    63117  
    63118 Matchmaker 3j0c.pdb1, chain F (#1.58) with AF3 CA.pdb, chain A (#591),
    63119 sequence alignment score = 335.3 
    63120 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    63121 2.550) 
    63122  
    63123 
    63124 > hide sel cartoons
    63125 
    63126 > color #587 dodgerblue
    63127 
    63128 > color #588 dodgerblue
    63129 
    63130 > color #589 #00b305ff
    63131 
    63132 > color #590 #00b305ff
    63133 
    63134 > color #591 #f15839ff
    63135 
    63136 > select #1.59/D
    63137 
    63138 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    63139 
    63140 > show sel cartoons
    63141 
    63142 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    63143 
    63144 Chain information for AF3 E1 1-421.pdb #592 
    63145 --- 
    63146 Chain | Description 
    63147 A | No description available 
    63148  
    63149 
    63150 > matchmaker #592 to #1.59 & sel
    63151 
    63152 Parameters 
    63153 --- 
    63154 Chain pairing | bb 
    63155 Alignment algorithm | Needleman-Wunsch 
    63156 Similarity matrix | BLOSUM-62 
    63157 SS fraction | 0.3 
    63158 Gap open (HH/SS/other) | 18/18/6 
    63159 Gap extend | 1 
    63160 SS matrix |  |  | H | S | O 
    63161 ---|---|---|--- 
    63162 H | 6 | -9 | -6 
    63163 S |  | 6 | -6 
    63164 O |  |  | 4 
    63165 Iteration cutoff | 2 
    63166  
    63167 Matchmaker 3j0c.pdb1, chain D (#1.59) with AF3 E1 1-421.pdb, chain A (#592),
    63168 sequence alignment score = 1060.7 
    63169 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    63170 3.032) 
    63171  
    63172 
    63173 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    63174 
    63175 Chain information for AF3 E1 422-461.pdb #593 
    63176 --- 
    63177 Chain | Description 
    63178 A | No description available 
    63179  
    63180 
    63181 > matchmaker #593 to #1.59 & sel
    63182 
    63183 Parameters 
    63184 --- 
    63185 Chain pairing | bb 
    63186 Alignment algorithm | Needleman-Wunsch 
    63187 Similarity matrix | BLOSUM-62 
    63188 SS fraction | 0.3 
    63189 Gap open (HH/SS/other) | 18/18/6 
    63190 Gap extend | 1 
    63191 SS matrix |  |  | H | S | O 
    63192 ---|---|---|--- 
    63193 H | 6 | -9 | -6 
    63194 S |  | 6 | -6 
    63195 O |  |  | 4 
    63196 Iteration cutoff | 2 
    63197  
    63198 Matchmaker 3j0c.pdb1, chain D (#1.59) with AF3 E1 422-461.pdb, chain A (#593),
    63199 sequence alignment score = 626.9 
    63200 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    63201 2.916) 
    63202  
    63203 
    63204 > hide sel cartoons
    63205 
    63206 > select #1.59/E
    63207 
    63208 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    63209 
    63210 > show sel cartoons
    63211 
    63212 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    63213 
    63214 Chain information for AF3 E2 1-352.pdb #594 
    63215 --- 
    63216 Chain | Description 
    63217 B | No description available 
    63218  
    63219 
    63220 > matchmaker #594 to #1.59 & sel
    63221 
    63222 Parameters 
    63223 --- 
    63224 Chain pairing | bb 
    63225 Alignment algorithm | Needleman-Wunsch 
    63226 Similarity matrix | BLOSUM-62 
    63227 SS fraction | 0.3 
    63228 Gap open (HH/SS/other) | 18/18/6 
    63229 Gap extend | 1 
    63230 SS matrix |  |  | H | S | O 
    63231 ---|---|---|--- 
    63232 H | 6 | -9 | -6 
    63233 S |  | 6 | -6 
    63234 O |  |  | 4 
    63235 Iteration cutoff | 2 
    63236  
    63237 Matchmaker 3j0c.pdb1, chain E (#1.59) with AF3 E2 1-352.pdb, chain B (#594),
    63238 sequence alignment score = 594.5 
    63239 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    63240 6.147) 
    63241  
    63242 
    63243 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    63244 
    63245 Chain information for AF3 E2 353-438.pdb #595 
    63246 --- 
    63247 Chain | Description 
    63248 B | No description available 
    63249  
    63250 
    63251 > matchmaker #595 to #1.59 & sel
    63252 
    63253 Parameters 
    63254 --- 
    63255 Chain pairing | bb 
    63256 Alignment algorithm | Needleman-Wunsch 
    63257 Similarity matrix | BLOSUM-62 
    63258 SS fraction | 0.3 
    63259 Gap open (HH/SS/other) | 18/18/6 
    63260 Gap extend | 1 
    63261 SS matrix |  |  | H | S | O 
    63262 ---|---|---|--- 
    63263 H | 6 | -9 | -6 
    63264 S |  | 6 | -6 
    63265 O |  |  | 4 
    63266 Iteration cutoff | 2 
    63267  
    63268 Matchmaker 3j0c.pdb1, chain E (#1.59) with AF3 E2 353-438.pdb, chain B (#595),
    63269 sequence alignment score = 340.2 
    63270 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    63271 8.673) 
    63272  
    63273 
    63274 > hide sel cartoons
    63275 
    63276 > select #1.59/F
    63277 
    63278 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    63279 
    63280 > show sel cartoons
    63281 
    63282 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    63283 
    63284 Chain information for AF3 CA.pdb #596 
    63285 --- 
    63286 Chain | Description 
    63287 A | No description available 
    63288  
    63289 
    63290 > matchmaker #596 to #1.59 & sel
    63291 
    63292 Parameters 
    63293 --- 
    63294 Chain pairing | bb 
    63295 Alignment algorithm | Needleman-Wunsch 
    63296 Similarity matrix | BLOSUM-62 
    63297 SS fraction | 0.3 
    63298 Gap open (HH/SS/other) | 18/18/6 
    63299 Gap extend | 1 
    63300 SS matrix |  |  | H | S | O 
    63301 ---|---|---|--- 
    63302 H | 6 | -9 | -6 
    63303 S |  | 6 | -6 
    63304 O |  |  | 4 
    63305 Iteration cutoff | 2 
    63306  
    63307 Matchmaker 3j0c.pdb1, chain F (#1.59) with AF3 CA.pdb, chain A (#596),
    63308 sequence alignment score = 335.3 
    63309 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    63310 2.550) 
    63311  
    63312 
    63313 > hide sel atoms
    63314 
    63315 > hide sel cartoons
    63316 
    63317 > color #592 dodgerblue
    63318 
    63319 > color #593 dodgerblue
    63320 
    63321 > color #594 #00b305ff
    63322 
    63323 > color #595 #00b305ff
    63324 
    63325 > color #596 #f15839ff
    63326 
    63327 > select #1.60/D
    63328 
    63329 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    63330 
    63331 > show sel cartoons
    63332 
    63333 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    63334 
    63335 Chain information for AF3 E1 1-421.pdb #597 
    63336 --- 
    63337 Chain | Description 
    63338 A | No description available 
    63339  
    63340 
    63341 > matchmaker #597 to #1.60 & sel
    63342 
    63343 Parameters 
    63344 --- 
    63345 Chain pairing | bb 
    63346 Alignment algorithm | Needleman-Wunsch 
    63347 Similarity matrix | BLOSUM-62 
    63348 SS fraction | 0.3 
    63349 Gap open (HH/SS/other) | 18/18/6 
    63350 Gap extend | 1 
    63351 SS matrix |  |  | H | S | O 
    63352 ---|---|---|--- 
    63353 H | 6 | -9 | -6 
    63354 S |  | 6 | -6 
    63355 O |  |  | 4 
    63356 Iteration cutoff | 2 
    63357  
    63358 Matchmaker 3j0c.pdb1, chain D (#1.60) with AF3 E1 1-421.pdb, chain A (#597),
    63359 sequence alignment score = 1060.7 
    63360 RMSD between 248 pruned atom pairs is 1.180 angstroms; (across all 403 pairs:
    63361 3.032) 
    63362  
    63363 
    63364 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    63365 
    63366 Chain information for AF3 E1 422-461.pdb #598 
    63367 --- 
    63368 Chain | Description 
    63369 A | No description available 
    63370  
    63371 
    63372 > matchmaker #598 to #1.60 & sel
    63373 
    63374 Parameters 
    63375 --- 
    63376 Chain pairing | bb 
    63377 Alignment algorithm | Needleman-Wunsch 
    63378 Similarity matrix | BLOSUM-62 
    63379 SS fraction | 0.3 
    63380 Gap open (HH/SS/other) | 18/18/6 
    63381 Gap extend | 1 
    63382 SS matrix |  |  | H | S | O 
    63383 ---|---|---|--- 
    63384 H | 6 | -9 | -6 
    63385 S |  | 6 | -6 
    63386 O |  |  | 4 
    63387 Iteration cutoff | 2 
    63388  
    63389 Matchmaker 3j0c.pdb1, chain D (#1.60) with AF3 E1 422-461.pdb, chain A (#598),
    63390 sequence alignment score = 626.9 
    63391 RMSD between 28 pruned atom pairs is 0.543 angstroms; (across all 38 pairs:
    63392 2.916) 
    63393  
    63394 
    63395 > hide sel cartoons
    63396 
    63397 > select #1.60/E
    63398 
    63399 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    63400 
    63401 > show sel cartoons
    63402 
    63403 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    63404 
    63405 Chain information for AF3 E2 1-352.pdb #599 
    63406 --- 
    63407 Chain | Description 
    63408 B | No description available 
    63409  
    63410 
    63411 > matchmaker #599 to #1.60 & sel
    63412 
    63413 Parameters 
    63414 --- 
    63415 Chain pairing | bb 
    63416 Alignment algorithm | Needleman-Wunsch 
    63417 Similarity matrix | BLOSUM-62 
    63418 SS fraction | 0.3 
    63419 Gap open (HH/SS/other) | 18/18/6 
    63420 Gap extend | 1 
    63421 SS matrix |  |  | H | S | O 
    63422 ---|---|---|--- 
    63423 H | 6 | -9 | -6 
    63424 S |  | 6 | -6 
    63425 O |  |  | 4 
    63426 Iteration cutoff | 2 
    63427  
    63428 Matchmaker 3j0c.pdb1, chain E (#1.60) with AF3 E2 1-352.pdb, chain B (#599),
    63429 sequence alignment score = 594.5 
    63430 RMSD between 109 pruned atom pairs is 0.994 angstroms; (across all 333 pairs:
    63431 6.147) 
    63432  
    63433 
    63434 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    63435 
    63436 Chain information for AF3 E2 353-438.pdb #600 
    63437 --- 
    63438 Chain | Description 
    63439 B | No description available 
    63440  
    63441 
    63442 > matchmaker #600 to #1.60 & sel
    63443 
    63444 Parameters 
    63445 --- 
    63446 Chain pairing | bb 
    63447 Alignment algorithm | Needleman-Wunsch 
    63448 Similarity matrix | BLOSUM-62 
    63449 SS fraction | 0.3 
    63450 Gap open (HH/SS/other) | 18/18/6 
    63451 Gap extend | 1 
    63452 SS matrix |  |  | H | S | O 
    63453 ---|---|---|--- 
    63454 H | 6 | -9 | -6 
    63455 S |  | 6 | -6 
    63456 O |  |  | 4 
    63457 Iteration cutoff | 2 
    63458  
    63459 Matchmaker 3j0c.pdb1, chain E (#1.60) with AF3 E2 353-438.pdb, chain B (#600),
    63460 sequence alignment score = 340.2 
    63461 RMSD between 38 pruned atom pairs is 0.818 angstroms; (across all 84 pairs:
    63462 8.673) 
    63463  
    63464 
    63465 > hide sel cartoons
    63466 
    63467 > select #1.60/F
    63468 
    63469 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    63470 
    63471 > show sel cartoons
    63472 
    63473 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    63474 
    63475 Chain information for AF3 CA.pdb #601 
    63476 --- 
    63477 Chain | Description 
    63478 A | No description available 
    63479  
    63480 
    63481 > matchmaker #601 to #1.60 & sel
    63482 
    63483 Parameters 
    63484 --- 
    63485 Chain pairing | bb 
    63486 Alignment algorithm | Needleman-Wunsch 
    63487 Similarity matrix | BLOSUM-62 
    63488 SS fraction | 0.3 
    63489 Gap open (HH/SS/other) | 18/18/6 
    63490 Gap extend | 1 
    63491 SS matrix |  |  | H | S | O 
    63492 ---|---|---|--- 
    63493 H | 6 | -9 | -6 
    63494 S |  | 6 | -6 
    63495 O |  |  | 4 
    63496 Iteration cutoff | 2 
    63497  
    63498 Matchmaker 3j0c.pdb1, chain F (#1.60) with AF3 CA.pdb, chain A (#601),
    63499 sequence alignment score = 335.3 
    63500 RMSD between 117 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    63501 2.550) 
    63502  
    63503 
    63504 > hide sel cartoons
    63505 
    63506 > color #597 dodgerblue
    63507 
    63508 > color #598 dodgerblue
    63509 
    63510 > color #599 #00b305ff
    63511 
    63512 > color #600 #00b305ff
    63513 
    63514 > color #601 #f15839ff
    63515 
    63516 > view sel
    63517 
    63518 No displayed objects specified. 
    63519 
    63520 > view
    63521 
    63522 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    63523 
    63524 > show #2-601 models
    63525 
    63526 > view
    63527 
    63528 > hide sel cartoons
    63529 
    63530 > save /Users/Jean/Desktop/image1.png supersample 3
    63531 
    63532 > hide #300 models
    63533 
    63534 > show #300 models
    63535 
    63536 > hide #299 models
    63537 
    63538 > show #299 models
    63539 
    63540 > hide #299 models
    63541 
    63542 > show #299 models
    63543 
    63544 > select
    63545 
    63546 2871120 atoms, 2944244 bonds, 373800 residues, 661 models selected 
    63547 
    63548 > show sel cartoons
    63549 
    63550 > hide #!1 models
    63551 
    63552 > select subtract #1
    63553 
    63554 962880 atoms, 985560 bonds, 127320 residues, 600 models selected 
    63555 
    63556 > select clear
    63557 
    63558 > view
    63559 
    63560 > hide #2-601 cartoons
    63561 
    63562 > show #2-601 atoms
    63563 
    63564 > style #2-601 sphere
    63565 
    63566 Changed 962880 atom styles 
    63567 
    63568 > save /Users/Jean/Desktop/image1.png supersample 3
    63569 
    63570 > view
    63571 
    63572 > color #514 #00b305ff
    63573 
    63574 > view
    63575 
    63576 > hide #2-601 atoms
    63577 
    63578 > show #2-601 cartoons
    63579 
    63580 > save /Users/Jean/Desktop/image2.png supersample 3
    63581 
    63582 > hide #2-601 cartoons
    63583 
    63584 > select #1.1/G
    63585 
    63586 3370 atoms, 3467 bonds, 442 residues, 1 model selected 
    63587 
    63588 > show #2-601 cartoons
    63589 
    63590 > select clear
    63591 
    63592 > hide #2-601 cartoons
    63593 
    63594 > select clear
    63595 
    63596 > select #1.1/G
    63597 
    63598 3370 atoms, 3467 bonds, 442 residues, 1 model selected 
    63599 
    63600 > show #2-601 cartoons
    63601 
    63602 > hide #2-601 models
    63603 
    63604 > select #1.1/G
    63605 
    63606 3370 atoms, 3467 bonds, 442 residues, 1 model selected 
    63607 
    63608 > view sel
    63609 
    63610 No displayed objects specified. 
    63611 
    63612 > show #!1 models
    63613 
    63614 > select ~sel & ##selected
    63615 
    63616 28434 atoms, 29221 bonds, 3666 residues, 1 model selected 
    63617 
    63618 > select ~sel
    63619 
    63620 2842686 atoms, 2915023 bonds, 370134 residues, 661 models selected 
    63621 
    63622 > hide sel & #1.1-60 cartoons
    63623 
    63624 > select #1.1/G
    63625 
    63626 3370 atoms, 3467 bonds, 442 residues, 1 model selected 
    63627 
    63628 > show sel cartoons
    63629 
    63630 > ui mousemode right select
    63631 
    63632 > select clear
    63633 
    63634 > select #1.1/B:287
    63635 
    63636 8 atoms, 7 bonds, 1 residue, 1 model selected 
    63637 
    63638 > select #1.1/G
    63639 
    63640 3370 atoms, 3467 bonds, 442 residues, 1 model selected 
    63641 
    63642 > hide #1.1 models
    63643 
    63644 > show #1.1 models
    63645 
    63646 > hide #1.1 models
    63647 
    63648 > show #1.1 models
    63649 
    63650 > select add #1.1
    63651 
    63652 31804 atoms, 32688 bonds, 4108 residues, 1 model selected 
    63653 
    63654 > select subtract #1.1
    63655 
    63656 Nothing selected 
    63657 
    63658 > select #1.1/G
    63659 
    63660 3370 atoms, 3467 bonds, 442 residues, 1 model selected 
    63661 
    63662 > select ~sel & ##selected
    63663 
    63664 28434 atoms, 29221 bonds, 3666 residues, 1 model selected 
    63665 
    63666 > hide sel cartoons
    63667 
    63668 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    63669 
    63670 Chain information for AF3 E1 1-421.pdb #602 
    63671 --- 
    63672 Chain | Description 
    63673 A | No description available 
    63674  
    63675 
    63676 > view sel
    63677 
    63678 No displayed objects specified. 
    63679 
    63680 > view
    63681 
    63682 > matchmaker #602 to #1.1 & sel
    63683 
    63684 Parameters 
    63685 --- 
    63686 Chain pairing | bb 
    63687 Alignment algorithm | Needleman-Wunsch 
    63688 Similarity matrix | BLOSUM-62 
    63689 SS fraction | 0.3 
    63690 Gap open (HH/SS/other) | 18/18/6 
    63691 Gap extend | 1 
    63692 SS matrix |  |  | H | S | O 
    63693 ---|---|---|--- 
    63694 H | 6 | -9 | -6 
    63695 S |  | 6 | -6 
    63696 O |  |  | 4 
    63697 Iteration cutoff | 2 
    63698  
    63699 Matchmaker 3j0c.pdb1, chain A (#1.1) with AF3 E1 1-421.pdb, chain A (#602),
    63700 sequence alignment score = 1060.7 
    63701 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    63702 3.020) 
    63703  
    63704 
    63705 > select #1.1/G
    63706 
    63707 3370 atoms, 3467 bonds, 442 residues, 1 model selected 
    63708 
    63709 > matchmaker #602 to #1.1 & sel
    63710 
    63711 Parameters 
    63712 --- 
    63713 Chain pairing | bb 
    63714 Alignment algorithm | Needleman-Wunsch 
    63715 Similarity matrix | BLOSUM-62 
    63716 SS fraction | 0.3 
    63717 Gap open (HH/SS/other) | 18/18/6 
    63718 Gap extend | 1 
    63719 SS matrix |  |  | H | S | O 
    63720 ---|---|---|--- 
    63721 H | 6 | -9 | -6 
    63722 S |  | 6 | -6 
    63723 O |  |  | 4 
    63724 Iteration cutoff | 2 
    63725  
    63726 Matchmaker 3j0c.pdb1, chain G (#1.1) with AF3 E1 1-421.pdb, chain A (#602),
    63727 sequence alignment score = 1060.7 
    63728 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    63729 2.985) 
    63730  
    63731 
    63732 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    63733 
    63734 Chain information for AF3 E1 422-461.pdb #603 
    63735 --- 
    63736 Chain | Description 
    63737 A | No description available 
    63738  
    63739 
    63740 > matchmaker #603 to #1.1 & sel
    63741 
    63742 Parameters 
    63743 --- 
    63744 Chain pairing | bb 
    63745 Alignment algorithm | Needleman-Wunsch 
    63746 Similarity matrix | BLOSUM-62 
    63747 SS fraction | 0.3 
    63748 Gap open (HH/SS/other) | 18/18/6 
    63749 Gap extend | 1 
    63750 SS matrix |  |  | H | S | O 
    63751 ---|---|---|--- 
    63752 H | 6 | -9 | -6 
    63753 S |  | 6 | -6 
    63754 O |  |  | 4 
    63755 Iteration cutoff | 2 
    63756  
    63757 Matchmaker 3j0c.pdb1, chain G (#1.1) with AF3 E1 422-461.pdb, chain A (#603),
    63758 sequence alignment score = 626.9 
    63759 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    63760 2.997) 
    63761  
    63762 
    63763 > hide sel cartoons
    63764 
    63765 > select #1.1/H
    63766 
    63767 3304 atoms, 3400 bonds, 423 residues, 1 model selected 
    63768 
    63769 > show sel cartoons
    63770 
    63771 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    63772 
    63773 Chain information for AF3 E2 1-352.pdb #604 
    63774 --- 
    63775 Chain | Description 
    63776 B | No description available 
    63777  
    63778 
    63779 > matchmaker #603 to #1.1 & sel
    63780 
    63781 Parameters 
    63782 --- 
    63783 Chain pairing | bb 
    63784 Alignment algorithm | Needleman-Wunsch 
    63785 Similarity matrix | BLOSUM-62 
    63786 SS fraction | 0.3 
    63787 Gap open (HH/SS/other) | 18/18/6 
    63788 Gap extend | 1 
    63789 SS matrix |  |  | H | S | O 
    63790 ---|---|---|--- 
    63791 H | 6 | -9 | -6 
    63792 S |  | 6 | -6 
    63793 O |  |  | 4 
    63794 Iteration cutoff | 2 
    63795  
    63796 Matchmaker 3j0c.pdb1, chain H (#1.1) with AF3 E1 422-461.pdb, chain A (#603),
    63797 sequence alignment score = 9.2 
    63798 RMSD between 6 pruned atom pairs is 0.871 angstroms; (across all 11 pairs:
    63799 3.614) 
    63800  
    63801 
    63802 > select #1.1/G
    63803 
    63804 3370 atoms, 3467 bonds, 442 residues, 1 model selected 
    63805 
    63806 > show sel cartoons
    63807 
    63808 > matchmaker #603 to #1.1 & sel
    63809 
    63810 Parameters 
    63811 --- 
    63812 Chain pairing | bb 
    63813 Alignment algorithm | Needleman-Wunsch 
    63814 Similarity matrix | BLOSUM-62 
    63815 SS fraction | 0.3 
    63816 Gap open (HH/SS/other) | 18/18/6 
    63817 Gap extend | 1 
    63818 SS matrix |  |  | H | S | O 
    63819 ---|---|---|--- 
    63820 H | 6 | -9 | -6 
    63821 S |  | 6 | -6 
    63822 O |  |  | 4 
    63823 Iteration cutoff | 2 
    63824  
    63825 Matchmaker 3j0c.pdb1, chain G (#1.1) with AF3 E1 422-461.pdb, chain A (#603),
    63826 sequence alignment score = 626.9 
    63827 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    63828 2.997) 
    63829  
    63830 
    63831 > matchmaker #604 to #1.2 & sel
    63832 
    63833 No 'to' model specified 
    63834 
    63835 > matchmaker #604 to #1.1 & sel
    63836 
    63837 Parameters 
    63838 --- 
    63839 Chain pairing | bb 
    63840 Alignment algorithm | Needleman-Wunsch 
    63841 Similarity matrix | BLOSUM-62 
    63842 SS fraction | 0.3 
    63843 Gap open (HH/SS/other) | 18/18/6 
    63844 Gap extend | 1 
    63845 SS matrix |  |  | H | S | O 
    63846 ---|---|---|--- 
    63847 H | 6 | -9 | -6 
    63848 S |  | 6 | -6 
    63849 O |  |  | 4 
    63850 Iteration cutoff | 2 
    63851  
    63852 Matchmaker 3j0c.pdb1, chain G (#1.1) with AF3 E2 1-352.pdb, chain B (#604),
    63853 sequence alignment score = 71.8 
    63854 RMSD between 4 pruned atom pairs is 1.398 angstroms; (across all 265 pairs:
    63855 48.114) 
    63856  
    63857 
    63858 > select #1.1/H
    63859 
    63860 3304 atoms, 3400 bonds, 423 residues, 1 model selected 
    63861 
    63862 > matchmaker #604 to #1.1 & sel
    63863 
    63864 Parameters 
    63865 --- 
    63866 Chain pairing | bb 
    63867 Alignment algorithm | Needleman-Wunsch 
    63868 Similarity matrix | BLOSUM-62 
    63869 SS fraction | 0.3 
    63870 Gap open (HH/SS/other) | 18/18/6 
    63871 Gap extend | 1 
    63872 SS matrix |  |  | H | S | O 
    63873 ---|---|---|--- 
    63874 H | 6 | -9 | -6 
    63875 S |  | 6 | -6 
    63876 O |  |  | 4 
    63877 Iteration cutoff | 2 
    63878  
    63879 Matchmaker 3j0c.pdb1, chain H (#1.1) with AF3 E2 1-352.pdb, chain B (#604),
    63880 sequence alignment score = 590.9 
    63881 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    63882 6.107) 
    63883  
    63884 
    63885 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    63886 
    63887 Chain information for AF3 E2 353-438.pdb #605 
    63888 --- 
    63889 Chain | Description 
    63890 B | No description available 
    63891  
    63892 
    63893 > matchmaker #605 to #1.1 & sel
    63894 
    63895 Parameters 
    63896 --- 
    63897 Chain pairing | bb 
    63898 Alignment algorithm | Needleman-Wunsch 
    63899 Similarity matrix | BLOSUM-62 
    63900 SS fraction | 0.3 
    63901 Gap open (HH/SS/other) | 18/18/6 
    63902 Gap extend | 1 
    63903 SS matrix |  |  | H | S | O 
    63904 ---|---|---|--- 
    63905 H | 6 | -9 | -6 
    63906 S |  | 6 | -6 
    63907 O |  |  | 4 
    63908 Iteration cutoff | 2 
    63909  
    63910 Matchmaker 3j0c.pdb1, chain H (#1.1) with AF3 E2 353-438.pdb, chain B (#605),
    63911 sequence alignment score = 329.4 
    63912 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    63913 8.150) 
    63914  
    63915 
    63916 > select #1.1/H
    63917 
    63918 3304 atoms, 3400 bonds, 423 residues, 1 model selected 
    63919 
    63920 > show sel cartoons
    63921 
    63922 [Repeated 1 time(s)]
    63923 
    63924 > select #1.1/H
    63925 
    63926 3304 atoms, 3400 bonds, 423 residues, 1 model selected 
    63927 
    63928 > select #1.1/H
    63929 
    63930 3304 atoms, 3400 bonds, 423 residues, 1 model selected 
    63931 
    63932 > show sel cartoons
    63933 
    63934 > show sel atoms
    63935 
    63936 > hide sel cartoons
    63937 
    63938 > hide sel atoms
    63939 
    63940 > select #1.1/G
    63941 
    63942 3370 atoms, 3467 bonds, 442 residues, 1 model selected 
    63943 
    63944 > hide sel cartoons
    63945 
    63946 > select #1.1/I
    63947 
    63948 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    63949 
    63950 > show sel cartoons
    63951 
    63952 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    63953 
    63954 Chain information for AF3 CA.pdb #606 
    63955 --- 
    63956 Chain | Description 
    63957 A | No description available 
    63958  
    63959 
    63960 > matchmaker #606 to #1.1 & sel
    63961 
    63962 Parameters 
    63963 --- 
    63964 Chain pairing | bb 
    63965 Alignment algorithm | Needleman-Wunsch 
    63966 Similarity matrix | BLOSUM-62 
    63967 SS fraction | 0.3 
    63968 Gap open (HH/SS/other) | 18/18/6 
    63969 Gap extend | 1 
    63970 SS matrix |  |  | H | S | O 
    63971 ---|---|---|--- 
    63972 H | 6 | -9 | -6 
    63973 S |  | 6 | -6 
    63974 O |  |  | 4 
    63975 Iteration cutoff | 2 
    63976  
    63977 Matchmaker 3j0c.pdb1, chain I (#1.1) with AF3 CA.pdb, chain A (#606), sequence
    63978 alignment score = 306.5 
    63979 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    63980 2.689) 
    63981  
    63982 
    63983 > hide sel cartoons
    63984 
    63985 > color #602 dodgerblue
    63986 
    63987 > color #603 dodgerblue
    63988 
    63989 > color #604 #00b305ff
    63990 
    63991 > color #605 #00b305ff
    63992 
    63993 > color #606 #f15839ff
    63994 
    63995 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    63996 
    63997 ——— End of log from Tue Jul 16 18:02:55 2024 ———
    63998 
    63999 opened ChimeraX session 
    64000 
    64001 > ui tool show Matchmaker
    64002 
    64003 The cached device pixel ratio value was stale on window expose. Please file a
    64004 QTBUG which explains how to reproduce. 
    64005 
    64006 > select #1.2/G
    64007 
    64008 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    64009 
    64010 > show sel cartoons
    64011 
    64012 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    64013 
    64014 Chain information for AF3 E1 1-421.pdb #607 
    64015 --- 
    64016 Chain | Description 
    64017 A | No description available 
    64018  
    64019 
    64020 > matchmaker #607 to #1.2 & sel
    64021 
    64022 Parameters 
    64023 --- 
    64024 Chain pairing | bb 
    64025 Alignment algorithm | Needleman-Wunsch 
    64026 Similarity matrix | BLOSUM-62 
    64027 SS fraction | 0.3 
    64028 Gap open (HH/SS/other) | 18/18/6 
    64029 Gap extend | 1 
    64030 SS matrix |  |  | H | S | O 
    64031 ---|---|---|--- 
    64032 H | 6 | -9 | -6 
    64033 S |  | 6 | -6 
    64034 O |  |  | 4 
    64035 Iteration cutoff | 2 
    64036  
    64037 Matchmaker 3j0c.pdb1, chain G (#1.2) with AF3 E1 1-421.pdb, chain A (#607),
    64038 sequence alignment score = 1060.7 
    64039 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    64040 2.985) 
    64041  
    64042 
    64043 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    64044 
    64045 Chain information for AF3 E1 422-461.pdb #608 
    64046 --- 
    64047 Chain | Description 
    64048 A | No description available 
    64049  
    64050 
    64051 > matchmaker #608 to #1.2 & sel
    64052 
    64053 Parameters 
    64054 --- 
    64055 Chain pairing | bb 
    64056 Alignment algorithm | Needleman-Wunsch 
    64057 Similarity matrix | BLOSUM-62 
    64058 SS fraction | 0.3 
    64059 Gap open (HH/SS/other) | 18/18/6 
    64060 Gap extend | 1 
    64061 SS matrix |  |  | H | S | O 
    64062 ---|---|---|--- 
    64063 H | 6 | -9 | -6 
    64064 S |  | 6 | -6 
    64065 O |  |  | 4 
    64066 Iteration cutoff | 2 
    64067  
    64068 Matchmaker 3j0c.pdb1, chain G (#1.2) with AF3 E1 422-461.pdb, chain A (#608),
    64069 sequence alignment score = 626.9 
    64070 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    64071 2.997) 
    64072  
    64073 
    64074 > select #1.2/H
    64075 
    64076 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    64077 
    64078 > show sel cartoons
    64079 
    64080 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    64081 
    64082 Chain information for AF3 E2 1-352.pdb #609 
    64083 --- 
    64084 Chain | Description 
    64085 B | No description available 
    64086  
    64087 
    64088 > matchmaker #609 to #1.2 & sel
    64089 
    64090 Parameters 
    64091 --- 
    64092 Chain pairing | bb 
    64093 Alignment algorithm | Needleman-Wunsch 
    64094 Similarity matrix | BLOSUM-62 
    64095 SS fraction | 0.3 
    64096 Gap open (HH/SS/other) | 18/18/6 
    64097 Gap extend | 1 
    64098 SS matrix |  |  | H | S | O 
    64099 ---|---|---|--- 
    64100 H | 6 | -9 | -6 
    64101 S |  | 6 | -6 
    64102 O |  |  | 4 
    64103 Iteration cutoff | 2 
    64104  
    64105 Matchmaker 3j0c.pdb1, chain H (#1.2) with AF3 E2 1-352.pdb, chain B (#609),
    64106 sequence alignment score = 590.9 
    64107 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    64108 6.107) 
    64109  
    64110 
    64111 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    64112 
    64113 Chain information for AF3 E2 353-438.pdb #610 
    64114 --- 
    64115 Chain | Description 
    64116 B | No description available 
    64117  
    64118 
    64119 > matchmaker #610 to #1.2 & sel
    64120 
    64121 Parameters 
    64122 --- 
    64123 Chain pairing | bb 
    64124 Alignment algorithm | Needleman-Wunsch 
    64125 Similarity matrix | BLOSUM-62 
    64126 SS fraction | 0.3 
    64127 Gap open (HH/SS/other) | 18/18/6 
    64128 Gap extend | 1 
    64129 SS matrix |  |  | H | S | O 
    64130 ---|---|---|--- 
    64131 H | 6 | -9 | -6 
    64132 S |  | 6 | -6 
    64133 O |  |  | 4 
    64134 Iteration cutoff | 2 
    64135  
    64136 Matchmaker 3j0c.pdb1, chain H (#1.2) with AF3 E2 353-438.pdb, chain B (#610),
    64137 sequence alignment score = 329.4 
    64138 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    64139 8.150) 
    64140  
    64141 
    64142 > hide sel cartoons
    64143 
    64144 > select #1.2/I
    64145 
    64146 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    64147 
    64148 > show sel cartoons
    64149 
    64150 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    64151 
    64152 Chain information for AF3 CA.pdb #611 
    64153 --- 
    64154 Chain | Description 
    64155 A | No description available 
    64156  
    64157 
    64158 > matchmaker #611 to #1.2 & sel
    64159 
    64160 Parameters 
    64161 --- 
    64162 Chain pairing | bb 
    64163 Alignment algorithm | Needleman-Wunsch 
    64164 Similarity matrix | BLOSUM-62 
    64165 SS fraction | 0.3 
    64166 Gap open (HH/SS/other) | 18/18/6 
    64167 Gap extend | 1 
    64168 SS matrix |  |  | H | S | O 
    64169 ---|---|---|--- 
    64170 H | 6 | -9 | -6 
    64171 S |  | 6 | -6 
    64172 O |  |  | 4 
    64173 Iteration cutoff | 2 
    64174  
    64175 Matchmaker 3j0c.pdb1, chain I (#1.2) with AF3 CA.pdb, chain A (#611), sequence
    64176 alignment score = 306.5 
    64177 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    64178 2.689) 
    64179  
    64180 
    64181 > hide sel cartoons
    64182 
    64183 > color #607 dodgerblue
    64184 
    64185 > color #608 dodgerblue
    64186 
    64187 > color #609 #00b305ff
    64188 
    64189 > color #610 #00b305ff
    64190 
    64191 > color #611 #f15839ff
    64192 
    64193 > select #1.2/G
    64194 
    64195 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    64196 
    64197 > hide sel cartoons
    64198 
    64199 > select #1.3/G
    64200 
    64201 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    64202 
    64203 > show sel cartoons
    64204 
    64205 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    64206 
    64207 Chain information for AF3 E1 1-421.pdb #612 
    64208 --- 
    64209 Chain | Description 
    64210 A | No description available 
    64211  
    64212 
    64213 > matchmaker #612 to #1.2 & sel
    64214 
    64215 No 'to' model specified 
    64216 
    64217 > matchmaker #612 to #1.3 & sel
    64218 
    64219 Parameters 
    64220 --- 
    64221 Chain pairing | bb 
    64222 Alignment algorithm | Needleman-Wunsch 
    64223 Similarity matrix | BLOSUM-62 
    64224 SS fraction | 0.3 
    64225 Gap open (HH/SS/other) | 18/18/6 
    64226 Gap extend | 1 
    64227 SS matrix |  |  | H | S | O 
    64228 ---|---|---|--- 
    64229 H | 6 | -9 | -6 
    64230 S |  | 6 | -6 
    64231 O |  |  | 4 
    64232 Iteration cutoff | 2 
    64233  
    64234 Matchmaker 3j0c.pdb1, chain G (#1.3) with AF3 E1 1-421.pdb, chain A (#612),
    64235 sequence alignment score = 1060.7 
    64236 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    64237 2.985) 
    64238  
    64239 
    64240 > matchmaker #612 to #1.3 & sel
    64241 
    64242 Parameters 
    64243 --- 
    64244 Chain pairing | bb 
    64245 Alignment algorithm | Needleman-Wunsch 
    64246 Similarity matrix | BLOSUM-62 
    64247 SS fraction | 0.3 
    64248 Gap open (HH/SS/other) | 18/18/6 
    64249 Gap extend | 1 
    64250 SS matrix |  |  | H | S | O 
    64251 ---|---|---|--- 
    64252 H | 6 | -9 | -6 
    64253 S |  | 6 | -6 
    64254 O |  |  | 4 
    64255 Iteration cutoff | 2 
    64256  
    64257 Matchmaker 3j0c.pdb1, chain G (#1.3) with AF3 E1 1-421.pdb, chain A (#612),
    64258 sequence alignment score = 1060.7 
    64259 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    64260 2.985) 
    64261  
    64262 
    64263 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    64264 
    64265 Chain information for AF3 E1 422-461.pdb #613 
    64266 --- 
    64267 Chain | Description 
    64268 A | No description available 
    64269  
    64270 
    64271 > matchmaker #613 to #1.3 & sel
    64272 
    64273 Parameters 
    64274 --- 
    64275 Chain pairing | bb 
    64276 Alignment algorithm | Needleman-Wunsch 
    64277 Similarity matrix | BLOSUM-62 
    64278 SS fraction | 0.3 
    64279 Gap open (HH/SS/other) | 18/18/6 
    64280 Gap extend | 1 
    64281 SS matrix |  |  | H | S | O 
    64282 ---|---|---|--- 
    64283 H | 6 | -9 | -6 
    64284 S |  | 6 | -6 
    64285 O |  |  | 4 
    64286 Iteration cutoff | 2 
    64287  
    64288 Matchmaker 3j0c.pdb1, chain G (#1.3) with AF3 E1 422-461.pdb, chain A (#613),
    64289 sequence alignment score = 626.9 
    64290 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    64291 2.997) 
    64292  
    64293 
    64294 > hide sel cartoons
    64295 
    64296 > select #1.3/H
    64297 
    64298 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    64299 
    64300 > show sel cartoons
    64301 
    64302 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    64303 
    64304 Chain information for AF3 E2 1-352.pdb #614 
    64305 --- 
    64306 Chain | Description 
    64307 B | No description available 
    64308  
    64309 
    64310 > matchmaker #614 to #1.3 & sel
    64311 
    64312 Parameters 
    64313 --- 
    64314 Chain pairing | bb 
    64315 Alignment algorithm | Needleman-Wunsch 
    64316 Similarity matrix | BLOSUM-62 
    64317 SS fraction | 0.3 
    64318 Gap open (HH/SS/other) | 18/18/6 
    64319 Gap extend | 1 
    64320 SS matrix |  |  | H | S | O 
    64321 ---|---|---|--- 
    64322 H | 6 | -9 | -6 
    64323 S |  | 6 | -6 
    64324 O |  |  | 4 
    64325 Iteration cutoff | 2 
    64326  
    64327 Matchmaker 3j0c.pdb1, chain H (#1.3) with AF3 E2 1-352.pdb, chain B (#614),
    64328 sequence alignment score = 590.9 
    64329 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    64330 6.107) 
    64331  
    64332 
    64333 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    64334 
    64335 Chain information for AF3 E2 353-438.pdb #615 
    64336 --- 
    64337 Chain | Description 
    64338 B | No description available 
    64339  
    64340 
    64341 > matchmaker #615 to #1.3 & sel
    64342 
    64343 Parameters 
    64344 --- 
    64345 Chain pairing | bb 
    64346 Alignment algorithm | Needleman-Wunsch 
    64347 Similarity matrix | BLOSUM-62 
    64348 SS fraction | 0.3 
    64349 Gap open (HH/SS/other) | 18/18/6 
    64350 Gap extend | 1 
    64351 SS matrix |  |  | H | S | O 
    64352 ---|---|---|--- 
    64353 H | 6 | -9 | -6 
    64354 S |  | 6 | -6 
    64355 O |  |  | 4 
    64356 Iteration cutoff | 2 
    64357  
    64358 Matchmaker 3j0c.pdb1, chain H (#1.3) with AF3 E2 353-438.pdb, chain B (#615),
    64359 sequence alignment score = 329.4 
    64360 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    64361 8.150) 
    64362  
    64363 
    64364 > hide sel cartoons
    64365 
    64366 > select #1.3/I
    64367 
    64368 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    64369 
    64370 > show sel cartoons
    64371 
    64372 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    64373 
    64374 Chain information for AF3 CA.pdb #616 
    64375 --- 
    64376 Chain | Description 
    64377 A | No description available 
    64378  
    64379 
    64380 > matchmaker #616 to #1.3 & sel
    64381 
    64382 Parameters 
    64383 --- 
    64384 Chain pairing | bb 
    64385 Alignment algorithm | Needleman-Wunsch 
    64386 Similarity matrix | BLOSUM-62 
    64387 SS fraction | 0.3 
    64388 Gap open (HH/SS/other) | 18/18/6 
    64389 Gap extend | 1 
    64390 SS matrix |  |  | H | S | O 
    64391 ---|---|---|--- 
    64392 H | 6 | -9 | -6 
    64393 S |  | 6 | -6 
    64394 O |  |  | 4 
    64395 Iteration cutoff | 2 
    64396  
    64397 Matchmaker 3j0c.pdb1, chain I (#1.3) with AF3 CA.pdb, chain A (#616), sequence
    64398 alignment score = 306.5 
    64399 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    64400 2.689) 
    64401  
    64402 
    64403 > hide sel cartoons
    64404 
    64405 > color #612 dodgerblue
    64406 
    64407 > color #613 dodgerblue
    64408 
    64409 > color #614 #00b305ff
    64410 
    64411 > color #615 #00b305ff
    64412 
    64413 > color #616 #f15839ff
    64414 
    64415 > select #1.4/G
    64416 
    64417 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    64418 
    64419 > show sel cartoons
    64420 
    64421 > hide sel cartoons
    64422 
    64423 > select #1.3/H
    64424 
    64425 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    64426 
    64427 > show sel cartoons
    64428 
    64429 > hide sel cartoons
    64430 
    64431 > select #1.4/G
    64432 
    64433 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    64434 
    64435 > show sel cartoons
    64436 
    64437 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    64438 
    64439 Chain information for AF3 E1 1-421.pdb #617 
    64440 --- 
    64441 Chain | Description 
    64442 A | No description available 
    64443  
    64444 
    64445 > matchmaker #617 to #1.4 & sel
    64446 
    64447 Parameters 
    64448 --- 
    64449 Chain pairing | bb 
    64450 Alignment algorithm | Needleman-Wunsch 
    64451 Similarity matrix | BLOSUM-62 
    64452 SS fraction | 0.3 
    64453 Gap open (HH/SS/other) | 18/18/6 
    64454 Gap extend | 1 
    64455 SS matrix |  |  | H | S | O 
    64456 ---|---|---|--- 
    64457 H | 6 | -9 | -6 
    64458 S |  | 6 | -6 
    64459 O |  |  | 4 
    64460 Iteration cutoff | 2 
    64461  
    64462 Matchmaker 3j0c.pdb1, chain G (#1.4) with AF3 E1 1-421.pdb, chain A (#617),
    64463 sequence alignment score = 1060.7 
    64464 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    64465 2.985) 
    64466  
    64467 
    64468 > hide sel cartoons
    64469 
    64470 > show sel cartoons
    64471 
    64472 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    64473 
    64474 Chain information for AF3 E1 422-461.pdb #618 
    64475 --- 
    64476 Chain | Description 
    64477 A | No description available 
    64478  
    64479 
    64480 > matchmaker #618 to #1.4 & sel
    64481 
    64482 Parameters 
    64483 --- 
    64484 Chain pairing | bb 
    64485 Alignment algorithm | Needleman-Wunsch 
    64486 Similarity matrix | BLOSUM-62 
    64487 SS fraction | 0.3 
    64488 Gap open (HH/SS/other) | 18/18/6 
    64489 Gap extend | 1 
    64490 SS matrix |  |  | H | S | O 
    64491 ---|---|---|--- 
    64492 H | 6 | -9 | -6 
    64493 S |  | 6 | -6 
    64494 O |  |  | 4 
    64495 Iteration cutoff | 2 
    64496  
    64497 Matchmaker 3j0c.pdb1, chain G (#1.4) with AF3 E1 422-461.pdb, chain A (#618),
    64498 sequence alignment score = 626.9 
    64499 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    64500 2.997) 
    64501  
    64502 
    64503 > hide sel cartoons
    64504 
    64505 > select #1.4/H
    64506 
    64507 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    64508 
    64509 > show sel cartoons
    64510 
    64511 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    64512 
    64513 Chain information for AF3 E2 1-352.pdb #619 
    64514 --- 
    64515 Chain | Description 
    64516 B | No description available 
    64517  
    64518 
    64519 > matchmaker #619 to #1.4 & sel
    64520 
    64521 Parameters 
    64522 --- 
    64523 Chain pairing | bb 
    64524 Alignment algorithm | Needleman-Wunsch 
    64525 Similarity matrix | BLOSUM-62 
    64526 SS fraction | 0.3 
    64527 Gap open (HH/SS/other) | 18/18/6 
    64528 Gap extend | 1 
    64529 SS matrix |  |  | H | S | O 
    64530 ---|---|---|--- 
    64531 H | 6 | -9 | -6 
    64532 S |  | 6 | -6 
    64533 O |  |  | 4 
    64534 Iteration cutoff | 2 
    64535  
    64536 Matchmaker 3j0c.pdb1, chain H (#1.4) with AF3 E2 1-352.pdb, chain B (#619),
    64537 sequence alignment score = 590.9 
    64538 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    64539 6.107) 
    64540  
    64541 
    64542 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    64543 
    64544 Chain information for AF3 E2 353-438.pdb #620 
    64545 --- 
    64546 Chain | Description 
    64547 B | No description available 
    64548  
    64549 
    64550 > matchmaker #620 to #1.4 & sel
    64551 
    64552 Parameters 
    64553 --- 
    64554 Chain pairing | bb 
    64555 Alignment algorithm | Needleman-Wunsch 
    64556 Similarity matrix | BLOSUM-62 
    64557 SS fraction | 0.3 
    64558 Gap open (HH/SS/other) | 18/18/6 
    64559 Gap extend | 1 
    64560 SS matrix |  |  | H | S | O 
    64561 ---|---|---|--- 
    64562 H | 6 | -9 | -6 
    64563 S |  | 6 | -6 
    64564 O |  |  | 4 
    64565 Iteration cutoff | 2 
    64566  
    64567 Matchmaker 3j0c.pdb1, chain H (#1.4) with AF3 E2 353-438.pdb, chain B (#620),
    64568 sequence alignment score = 329.4 
    64569 RMSD between 40 pruned atom pairs is 0.937 angstroms; (across all 84 pairs:
    64570 8.150) 
    64571  
    64572 
    64573 > hide sel cartoons
    64574 
    64575 > select #1.4/I
    64576 
    64577 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    64578 
    64579 > show sel cartoons
    64580 
    64581 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    64582 
    64583 Chain information for AF3 CA.pdb #621 
    64584 --- 
    64585 Chain | Description 
    64586 A | No description available 
    64587  
    64588 
    64589 > matchmaker #621 to #1.4 & sel
    64590 
    64591 Parameters 
    64592 --- 
    64593 Chain pairing | bb 
    64594 Alignment algorithm | Needleman-Wunsch 
    64595 Similarity matrix | BLOSUM-62 
    64596 SS fraction | 0.3 
    64597 Gap open (HH/SS/other) | 18/18/6 
    64598 Gap extend | 1 
    64599 SS matrix |  |  | H | S | O 
    64600 ---|---|---|--- 
    64601 H | 6 | -9 | -6 
    64602 S |  | 6 | -6 
    64603 O |  |  | 4 
    64604 Iteration cutoff | 2 
    64605  
    64606 Matchmaker 3j0c.pdb1, chain I (#1.4) with AF3 CA.pdb, chain A (#621), sequence
    64607 alignment score = 306.5 
    64608 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    64609 2.689) 
    64610  
    64611 
    64612 > hide sel cartoons
    64613 
    64614 > color #617 dodgerblue
    64615 
    64616 > color #618 dodgerblue
    64617 
    64618 > color #619 #00b305ff
    64619 
    64620 > color #620 #00b305ff
    64621 
    64622 > color #621 #f15839ff
    64623 
    64624 > select #1.5/G
    64625 
    64626 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    64627 
    64628 > show sel cartoons
    64629 
    64630 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    64631 
    64632 Chain information for AF3 E1 1-421.pdb #622 
    64633 --- 
    64634 Chain | Description 
    64635 A | No description available 
    64636  
    64637 
    64638 > matchmaker #622 to #1.4 & sel
    64639 
    64640 No 'to' model specified 
    64641 
    64642 > matchmaker #622 to #1.5 & sel
    64643 
    64644 Parameters 
    64645 --- 
    64646 Chain pairing | bb 
    64647 Alignment algorithm | Needleman-Wunsch 
    64648 Similarity matrix | BLOSUM-62 
    64649 SS fraction | 0.3 
    64650 Gap open (HH/SS/other) | 18/18/6 
    64651 Gap extend | 1 
    64652 SS matrix |  |  | H | S | O 
    64653 ---|---|---|--- 
    64654 H | 6 | -9 | -6 
    64655 S |  | 6 | -6 
    64656 O |  |  | 4 
    64657 Iteration cutoff | 2 
    64658  
    64659 Matchmaker 3j0c.pdb1, chain G (#1.5) with AF3 E1 1-421.pdb, chain A (#622),
    64660 sequence alignment score = 1060.7 
    64661 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    64662 2.985) 
    64663  
    64664 
    64665 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    64666 
    64667 Chain information for AF3 E1 422-461.pdb #623 
    64668 --- 
    64669 Chain | Description 
    64670 A | No description available 
    64671  
    64672 
    64673 > matchmaker #623 to #1.5 & sel
    64674 
    64675 Parameters 
    64676 --- 
    64677 Chain pairing | bb 
    64678 Alignment algorithm | Needleman-Wunsch 
    64679 Similarity matrix | BLOSUM-62 
    64680 SS fraction | 0.3 
    64681 Gap open (HH/SS/other) | 18/18/6 
    64682 Gap extend | 1 
    64683 SS matrix |  |  | H | S | O 
    64684 ---|---|---|--- 
    64685 H | 6 | -9 | -6 
    64686 S |  | 6 | -6 
    64687 O |  |  | 4 
    64688 Iteration cutoff | 2 
    64689  
    64690 Matchmaker 3j0c.pdb1, chain G (#1.5) with AF3 E1 422-461.pdb, chain A (#623),
    64691 sequence alignment score = 626.9 
    64692 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    64693 2.997) 
    64694  
    64695 
    64696 > hide sel cartoons
    64697 
    64698 > select #1.5/H
    64699 
    64700 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    64701 
    64702 > show sel cartoons
    64703 
    64704 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    64705 
    64706 Chain information for AF3 E2 1-352.pdb #624 
    64707 --- 
    64708 Chain | Description 
    64709 B | No description available 
    64710  
    64711 
    64712 > matchmaker #624 to #1.5 & sel
    64713 
    64714 Parameters 
    64715 --- 
    64716 Chain pairing | bb 
    64717 Alignment algorithm | Needleman-Wunsch 
    64718 Similarity matrix | BLOSUM-62 
    64719 SS fraction | 0.3 
    64720 Gap open (HH/SS/other) | 18/18/6 
    64721 Gap extend | 1 
    64722 SS matrix |  |  | H | S | O 
    64723 ---|---|---|--- 
    64724 H | 6 | -9 | -6 
    64725 S |  | 6 | -6 
    64726 O |  |  | 4 
    64727 Iteration cutoff | 2 
    64728  
    64729 Matchmaker 3j0c.pdb1, chain H (#1.5) with AF3 E2 1-352.pdb, chain B (#624),
    64730 sequence alignment score = 590.9 
    64731 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    64732 6.107) 
    64733  
    64734 
    64735 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    64736 
    64737 Chain information for AF3 E2 353-438.pdb #625 
    64738 --- 
    64739 Chain | Description 
    64740 B | No description available 
    64741  
    64742 
    64743 > hide sel cartoons
    64744 
    64745 > show sel cartoons
    64746 
    64747 > matchmaker #625 to #1.5 & sel
    64748 
    64749 Parameters 
    64750 --- 
    64751 Chain pairing | bb 
    64752 Alignment algorithm | Needleman-Wunsch 
    64753 Similarity matrix | BLOSUM-62 
    64754 SS fraction | 0.3 
    64755 Gap open (HH/SS/other) | 18/18/6 
    64756 Gap extend | 1 
    64757 SS matrix |  |  | H | S | O 
    64758 ---|---|---|--- 
    64759 H | 6 | -9 | -6 
    64760 S |  | 6 | -6 
    64761 O |  |  | 4 
    64762 Iteration cutoff | 2 
    64763  
    64764 Matchmaker 3j0c.pdb1, chain H (#1.5) with AF3 E2 353-438.pdb, chain B (#625),
    64765 sequence alignment score = 329.4 
    64766 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    64767 8.150) 
    64768  
    64769 
    64770 > select #1.5/I
    64771 
    64772 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    64773 
    64774 > show sel cartoons
    64775 
    64776 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    64777 
    64778 Chain information for AF3 CA.pdb #626 
    64779 --- 
    64780 Chain | Description 
    64781 A | No description available 
    64782  
    64783 
    64784 > matchmaker #626 to #1.5 & sel
    64785 
    64786 Parameters 
    64787 --- 
    64788 Chain pairing | bb 
    64789 Alignment algorithm | Needleman-Wunsch 
    64790 Similarity matrix | BLOSUM-62 
    64791 SS fraction | 0.3 
    64792 Gap open (HH/SS/other) | 18/18/6 
    64793 Gap extend | 1 
    64794 SS matrix |  |  | H | S | O 
    64795 ---|---|---|--- 
    64796 H | 6 | -9 | -6 
    64797 S |  | 6 | -6 
    64798 O |  |  | 4 
    64799 Iteration cutoff | 2 
    64800  
    64801 Matchmaker 3j0c.pdb1, chain I (#1.5) with AF3 CA.pdb, chain A (#626), sequence
    64802 alignment score = 306.5 
    64803 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    64804 2.689) 
    64805  
    64806 
    64807 > hide sel cartoons
    64808 
    64809 > color #622 dodgerblue
    64810 
    64811 > color #623 dodgerblue
    64812 
    64813 > color #624 #00b305ff
    64814 
    64815 > color #625 #00b305ff
    64816 
    64817 > color #626 #f15839ff
    64818 
    64819 > select #1.5/H
    64820 
    64821 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    64822 
    64823 > hide sel cartoons
    64824 
    64825 > select #1.6/G
    64826 
    64827 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    64828 
    64829 > show sel cartoons
    64830 
    64831 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    64832 
    64833 Chain information for AF3 E1 1-421.pdb #627 
    64834 --- 
    64835 Chain | Description 
    64836 A | No description available 
    64837  
    64838 
    64839 > matchmaker #627 to #1.6 & sel
    64840 
    64841 Parameters 
    64842 --- 
    64843 Chain pairing | bb 
    64844 Alignment algorithm | Needleman-Wunsch 
    64845 Similarity matrix | BLOSUM-62 
    64846 SS fraction | 0.3 
    64847 Gap open (HH/SS/other) | 18/18/6 
    64848 Gap extend | 1 
    64849 SS matrix |  |  | H | S | O 
    64850 ---|---|---|--- 
    64851 H | 6 | -9 | -6 
    64852 S |  | 6 | -6 
    64853 O |  |  | 4 
    64854 Iteration cutoff | 2 
    64855  
    64856 Matchmaker 3j0c.pdb1, chain G (#1.6) with AF3 E1 1-421.pdb, chain A (#627),
    64857 sequence alignment score = 1060.7 
    64858 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    64859 2.985) 
    64860  
    64861 
    64862 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    64863 
    64864 Chain information for AF3 E1 422-461.pdb #628 
    64865 --- 
    64866 Chain | Description 
    64867 A | No description available 
    64868  
    64869 
    64870 > matchmaker #628 to #1.6 & sel
    64871 
    64872 Parameters 
    64873 --- 
    64874 Chain pairing | bb 
    64875 Alignment algorithm | Needleman-Wunsch 
    64876 Similarity matrix | BLOSUM-62 
    64877 SS fraction | 0.3 
    64878 Gap open (HH/SS/other) | 18/18/6 
    64879 Gap extend | 1 
    64880 SS matrix |  |  | H | S | O 
    64881 ---|---|---|--- 
    64882 H | 6 | -9 | -6 
    64883 S |  | 6 | -6 
    64884 O |  |  | 4 
    64885 Iteration cutoff | 2 
    64886  
    64887 Matchmaker 3j0c.pdb1, chain G (#1.6) with AF3 E1 422-461.pdb, chain A (#628),
    64888 sequence alignment score = 626.9 
    64889 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    64890 2.997) 
    64891  
    64892 
    64893 > hide sel cartoons
    64894 
    64895 > select #1.6/H
    64896 
    64897 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    64898 
    64899 > show sel cartoons
    64900 
    64901 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    64902 
    64903 Chain information for AF3 E2 1-352.pdb #629 
    64904 --- 
    64905 Chain | Description 
    64906 B | No description available 
    64907  
    64908 
    64909 > matchmaker #629 to #1.6 & sel
    64910 
    64911 Parameters 
    64912 --- 
    64913 Chain pairing | bb 
    64914 Alignment algorithm | Needleman-Wunsch 
    64915 Similarity matrix | BLOSUM-62 
    64916 SS fraction | 0.3 
    64917 Gap open (HH/SS/other) | 18/18/6 
    64918 Gap extend | 1 
    64919 SS matrix |  |  | H | S | O 
    64920 ---|---|---|--- 
    64921 H | 6 | -9 | -6 
    64922 S |  | 6 | -6 
    64923 O |  |  | 4 
    64924 Iteration cutoff | 2 
    64925  
    64926 Matchmaker 3j0c.pdb1, chain H (#1.6) with AF3 E2 1-352.pdb, chain B (#629),
    64927 sequence alignment score = 590.9 
    64928 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    64929 6.107) 
    64930  
    64931 
    64932 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    64933 
    64934 Chain information for AF3 E2 353-438.pdb #630 
    64935 --- 
    64936 Chain | Description 
    64937 B | No description available 
    64938  
    64939 
    64940 > matchmaker #630 to #1.6 & sel
    64941 
    64942 Parameters 
    64943 --- 
    64944 Chain pairing | bb 
    64945 Alignment algorithm | Needleman-Wunsch 
    64946 Similarity matrix | BLOSUM-62 
    64947 SS fraction | 0.3 
    64948 Gap open (HH/SS/other) | 18/18/6 
    64949 Gap extend | 1 
    64950 SS matrix |  |  | H | S | O 
    64951 ---|---|---|--- 
    64952 H | 6 | -9 | -6 
    64953 S |  | 6 | -6 
    64954 O |  |  | 4 
    64955 Iteration cutoff | 2 
    64956  
    64957 Matchmaker 3j0c.pdb1, chain H (#1.6) with AF3 E2 353-438.pdb, chain B (#630),
    64958 sequence alignment score = 329.4 
    64959 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    64960 8.150) 
    64961  
    64962 
    64963 > hide sel cartoons
    64964 
    64965 > select #1.6/I
    64966 
    64967 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    64968 
    64969 > show sel cartoons
    64970 
    64971 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    64972 
    64973 Chain information for AF3 CA.pdb #631 
    64974 --- 
    64975 Chain | Description 
    64976 A | No description available 
    64977  
    64978 
    64979 > matchmaker #631 to #1.6 & sel
    64980 
    64981 Parameters 
    64982 --- 
    64983 Chain pairing | bb 
    64984 Alignment algorithm | Needleman-Wunsch 
    64985 Similarity matrix | BLOSUM-62 
    64986 SS fraction | 0.3 
    64987 Gap open (HH/SS/other) | 18/18/6 
    64988 Gap extend | 1 
    64989 SS matrix |  |  | H | S | O 
    64990 ---|---|---|--- 
    64991 H | 6 | -9 | -6 
    64992 S |  | 6 | -6 
    64993 O |  |  | 4 
    64994 Iteration cutoff | 2 
    64995  
    64996 Matchmaker 3j0c.pdb1, chain I (#1.6) with AF3 CA.pdb, chain A (#631), sequence
    64997 alignment score = 306.5 
    64998 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    64999 2.689) 
    65000  
    65001 
    65002 > hide sel cartoons
    65003 
    65004 > color #627 dodgerblue
    65005 
    65006 > color #628 dodgerblue
    65007 
    65008 > color #629 #00b305ff
    65009 
    65010 > color #630 #00b305ff
    65011 
    65012 > color #631 #f15839ff
    65013 
    65014 > select #1.7/G
    65015 
    65016 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    65017 
    65018 > show sel cartoons
    65019 
    65020 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    65021 
    65022 Chain information for AF3 E1 1-421.pdb #632 
    65023 --- 
    65024 Chain | Description 
    65025 A | No description available 
    65026  
    65027 
    65028 > matchmaker #632 to #1.7 & sel
    65029 
    65030 Parameters 
    65031 --- 
    65032 Chain pairing | bb 
    65033 Alignment algorithm | Needleman-Wunsch 
    65034 Similarity matrix | BLOSUM-62 
    65035 SS fraction | 0.3 
    65036 Gap open (HH/SS/other) | 18/18/6 
    65037 Gap extend | 1 
    65038 SS matrix |  |  | H | S | O 
    65039 ---|---|---|--- 
    65040 H | 6 | -9 | -6 
    65041 S |  | 6 | -6 
    65042 O |  |  | 4 
    65043 Iteration cutoff | 2 
    65044  
    65045 Matchmaker 3j0c.pdb1, chain G (#1.7) with AF3 E1 1-421.pdb, chain A (#632),
    65046 sequence alignment score = 1060.7 
    65047 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    65048 2.985) 
    65049  
    65050 
    65051 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    65052 
    65053 Chain information for AF3 E1 422-461.pdb #633 
    65054 --- 
    65055 Chain | Description 
    65056 A | No description available 
    65057  
    65058 
    65059 > matchmaker #633 to #1.7 & sel
    65060 
    65061 Parameters 
    65062 --- 
    65063 Chain pairing | bb 
    65064 Alignment algorithm | Needleman-Wunsch 
    65065 Similarity matrix | BLOSUM-62 
    65066 SS fraction | 0.3 
    65067 Gap open (HH/SS/other) | 18/18/6 
    65068 Gap extend | 1 
    65069 SS matrix |  |  | H | S | O 
    65070 ---|---|---|--- 
    65071 H | 6 | -9 | -6 
    65072 S |  | 6 | -6 
    65073 O |  |  | 4 
    65074 Iteration cutoff | 2 
    65075  
    65076 Matchmaker 3j0c.pdb1, chain G (#1.7) with AF3 E1 422-461.pdb, chain A (#633),
    65077 sequence alignment score = 626.9 
    65078 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    65079 2.997) 
    65080  
    65081 
    65082 > hide sel cartoons
    65083 
    65084 > select #1.7/H
    65085 
    65086 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    65087 
    65088 > show sel cartoons
    65089 
    65090 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    65091 
    65092 Chain information for AF3 E2 1-352.pdb #634 
    65093 --- 
    65094 Chain | Description 
    65095 B | No description available 
    65096  
    65097 
    65098 > matchmaker #634 to #1.7 & sel
    65099 
    65100 Parameters 
    65101 --- 
    65102 Chain pairing | bb 
    65103 Alignment algorithm | Needleman-Wunsch 
    65104 Similarity matrix | BLOSUM-62 
    65105 SS fraction | 0.3 
    65106 Gap open (HH/SS/other) | 18/18/6 
    65107 Gap extend | 1 
    65108 SS matrix |  |  | H | S | O 
    65109 ---|---|---|--- 
    65110 H | 6 | -9 | -6 
    65111 S |  | 6 | -6 
    65112 O |  |  | 4 
    65113 Iteration cutoff | 2 
    65114  
    65115 Matchmaker 3j0c.pdb1, chain H (#1.7) with AF3 E2 1-352.pdb, chain B (#634),
    65116 sequence alignment score = 590.9 
    65117 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    65118 6.107) 
    65119  
    65120 
    65121 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    65122 
    65123 Chain information for AF3 E2 353-438.pdb #635 
    65124 --- 
    65125 Chain | Description 
    65126 B | No description available 
    65127  
    65128 
    65129 > matchmaker #635 to #1.7 & sel
    65130 
    65131 Parameters 
    65132 --- 
    65133 Chain pairing | bb 
    65134 Alignment algorithm | Needleman-Wunsch 
    65135 Similarity matrix | BLOSUM-62 
    65136 SS fraction | 0.3 
    65137 Gap open (HH/SS/other) | 18/18/6 
    65138 Gap extend | 1 
    65139 SS matrix |  |  | H | S | O 
    65140 ---|---|---|--- 
    65141 H | 6 | -9 | -6 
    65142 S |  | 6 | -6 
    65143 O |  |  | 4 
    65144 Iteration cutoff | 2 
    65145  
    65146 Matchmaker 3j0c.pdb1, chain H (#1.7) with AF3 E2 353-438.pdb, chain B (#635),
    65147 sequence alignment score = 329.4 
    65148 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    65149 8.150) 
    65150  
    65151 
    65152 > hide sel cartoons
    65153 
    65154 > select #1.7/I
    65155 
    65156 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    65157 
    65158 > show sel cartoons
    65159 
    65160 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    65161 
    65162 Chain information for AF3 CA.pdb #636 
    65163 --- 
    65164 Chain | Description 
    65165 A | No description available 
    65166  
    65167 
    65168 > matchmaker #636 to #1.7 & sel
    65169 
    65170 Parameters 
    65171 --- 
    65172 Chain pairing | bb 
    65173 Alignment algorithm | Needleman-Wunsch 
    65174 Similarity matrix | BLOSUM-62 
    65175 SS fraction | 0.3 
    65176 Gap open (HH/SS/other) | 18/18/6 
    65177 Gap extend | 1 
    65178 SS matrix |  |  | H | S | O 
    65179 ---|---|---|--- 
    65180 H | 6 | -9 | -6 
    65181 S |  | 6 | -6 
    65182 O |  |  | 4 
    65183 Iteration cutoff | 2 
    65184  
    65185 Matchmaker 3j0c.pdb1, chain I (#1.7) with AF3 CA.pdb, chain A (#636), sequence
    65186 alignment score = 306.5 
    65187 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    65188 2.689) 
    65189  
    65190 
    65191 > hide sel cartoons
    65192 
    65193 > color #632 dodgerblue
    65194 
    65195 > color #633 dodgerblue
    65196 
    65197 > color #634 #00b305ff
    65198 
    65199 > color #635 #00b305ff
    65200 
    65201 > color #636 #f15839ff
    65202 
    65203 > select #1.8/G
    65204 
    65205 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    65206 
    65207 > show sel cartoons
    65208 
    65209 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    65210 
    65211 Chain information for AF3 E1 1-421.pdb #637 
    65212 --- 
    65213 Chain | Description 
    65214 A | No description available 
    65215  
    65216 
    65217 > matchmaker #637 to #1.7 & sel
    65218 
    65219 No 'to' model specified 
    65220 
    65221 > matchmaker #637 to #1.8 & sel
    65222 
    65223 Parameters 
    65224 --- 
    65225 Chain pairing | bb 
    65226 Alignment algorithm | Needleman-Wunsch 
    65227 Similarity matrix | BLOSUM-62 
    65228 SS fraction | 0.3 
    65229 Gap open (HH/SS/other) | 18/18/6 
    65230 Gap extend | 1 
    65231 SS matrix |  |  | H | S | O 
    65232 ---|---|---|--- 
    65233 H | 6 | -9 | -6 
    65234 S |  | 6 | -6 
    65235 O |  |  | 4 
    65236 Iteration cutoff | 2 
    65237  
    65238 Matchmaker 3j0c.pdb1, chain G (#1.8) with AF3 E1 1-421.pdb, chain A (#637),
    65239 sequence alignment score = 1060.7 
    65240 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    65241 2.985) 
    65242  
    65243 
    65244 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    65245 
    65246 Chain information for AF3 E1 422-461.pdb #638 
    65247 --- 
    65248 Chain | Description 
    65249 A | No description available 
    65250  
    65251 
    65252 > matchmaker #638 to #1.8 & sel
    65253 
    65254 Parameters 
    65255 --- 
    65256 Chain pairing | bb 
    65257 Alignment algorithm | Needleman-Wunsch 
    65258 Similarity matrix | BLOSUM-62 
    65259 SS fraction | 0.3 
    65260 Gap open (HH/SS/other) | 18/18/6 
    65261 Gap extend | 1 
    65262 SS matrix |  |  | H | S | O 
    65263 ---|---|---|--- 
    65264 H | 6 | -9 | -6 
    65265 S |  | 6 | -6 
    65266 O |  |  | 4 
    65267 Iteration cutoff | 2 
    65268  
    65269 Matchmaker 3j0c.pdb1, chain G (#1.8) with AF3 E1 422-461.pdb, chain A (#638),
    65270 sequence alignment score = 626.9 
    65271 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    65272 2.997) 
    65273  
    65274 
    65275 > hide sel cartoons
    65276 
    65277 > select #1.8/H
    65278 
    65279 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    65280 
    65281 > show sel cartoons
    65282 
    65283 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    65284 
    65285 Chain information for AF3 E2 1-352.pdb #639 
    65286 --- 
    65287 Chain | Description 
    65288 B | No description available 
    65289  
    65290 
    65291 > matchmaker #639 to #1.8 & sel
    65292 
    65293 Parameters 
    65294 --- 
    65295 Chain pairing | bb 
    65296 Alignment algorithm | Needleman-Wunsch 
    65297 Similarity matrix | BLOSUM-62 
    65298 SS fraction | 0.3 
    65299 Gap open (HH/SS/other) | 18/18/6 
    65300 Gap extend | 1 
    65301 SS matrix |  |  | H | S | O 
    65302 ---|---|---|--- 
    65303 H | 6 | -9 | -6 
    65304 S |  | 6 | -6 
    65305 O |  |  | 4 
    65306 Iteration cutoff | 2 
    65307  
    65308 Matchmaker 3j0c.pdb1, chain H (#1.8) with AF3 E2 1-352.pdb, chain B (#639),
    65309 sequence alignment score = 590.9 
    65310 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    65311 6.107) 
    65312  
    65313 
    65314 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    65315 
    65316 Chain information for AF3 E2 353-438.pdb #640 
    65317 --- 
    65318 Chain | Description 
    65319 B | No description available 
    65320  
    65321 
    65322 > matchmaker #640 to #1.8 & sel
    65323 
    65324 Parameters 
    65325 --- 
    65326 Chain pairing | bb 
    65327 Alignment algorithm | Needleman-Wunsch 
    65328 Similarity matrix | BLOSUM-62 
    65329 SS fraction | 0.3 
    65330 Gap open (HH/SS/other) | 18/18/6 
    65331 Gap extend | 1 
    65332 SS matrix |  |  | H | S | O 
    65333 ---|---|---|--- 
    65334 H | 6 | -9 | -6 
    65335 S |  | 6 | -6 
    65336 O |  |  | 4 
    65337 Iteration cutoff | 2 
    65338  
    65339 Matchmaker 3j0c.pdb1, chain H (#1.8) with AF3 E2 353-438.pdb, chain B (#640),
    65340 sequence alignment score = 329.4 
    65341 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    65342 8.150) 
    65343  
    65344 
    65345 > hide sel cartoons
    65346 
    65347 > select #1.8/I
    65348 
    65349 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    65350 
    65351 > show sel cartoons
    65352 
    65353 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    65354 
    65355 Chain information for AF3 CA.pdb #641 
    65356 --- 
    65357 Chain | Description 
    65358 A | No description available 
    65359  
    65360 
    65361 > matchmaker #641 to #1.8 & sel
    65362 
    65363 Parameters 
    65364 --- 
    65365 Chain pairing | bb 
    65366 Alignment algorithm | Needleman-Wunsch 
    65367 Similarity matrix | BLOSUM-62 
    65368 SS fraction | 0.3 
    65369 Gap open (HH/SS/other) | 18/18/6 
    65370 Gap extend | 1 
    65371 SS matrix |  |  | H | S | O 
    65372 ---|---|---|--- 
    65373 H | 6 | -9 | -6 
    65374 S |  | 6 | -6 
    65375 O |  |  | 4 
    65376 Iteration cutoff | 2 
    65377  
    65378 Matchmaker 3j0c.pdb1, chain I (#1.8) with AF3 CA.pdb, chain A (#641), sequence
    65379 alignment score = 306.5 
    65380 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    65381 2.689) 
    65382  
    65383 
    65384 > hide sel cartoons
    65385 
    65386 > color #637 dodgerblue
    65387 
    65388 > color #638 dodgerblue
    65389 
    65390 > color #639 #00b305ff
    65391 
    65392 > color #640 #00b305ff
    65393 
    65394 > color #641 #f15839ff
    65395 
    65396 > select #1.9/G
    65397 
    65398 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    65399 
    65400 > show sel cartoons
    65401 
    65402 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    65403 
    65404 Chain information for AF3 E1 1-421.pdb #642 
    65405 --- 
    65406 Chain | Description 
    65407 A | No description available 
    65408  
    65409 
    65410 > matchmaker #642 to #1.8 & sel
    65411 
    65412 No 'to' model specified 
    65413 
    65414 > matchmaker #642 to #1.9 & sel
    65415 
    65416 Parameters 
    65417 --- 
    65418 Chain pairing | bb 
    65419 Alignment algorithm | Needleman-Wunsch 
    65420 Similarity matrix | BLOSUM-62 
    65421 SS fraction | 0.3 
    65422 Gap open (HH/SS/other) | 18/18/6 
    65423 Gap extend | 1 
    65424 SS matrix |  |  | H | S | O 
    65425 ---|---|---|--- 
    65426 H | 6 | -9 | -6 
    65427 S |  | 6 | -6 
    65428 O |  |  | 4 
    65429 Iteration cutoff | 2 
    65430  
    65431 Matchmaker 3j0c.pdb1, chain G (#1.9) with AF3 E1 1-421.pdb, chain A (#642),
    65432 sequence alignment score = 1060.7 
    65433 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    65434 2.985) 
    65435  
    65436 
    65437 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    65438 
    65439 Chain information for AF3 E1 422-461.pdb #643 
    65440 --- 
    65441 Chain | Description 
    65442 A | No description available 
    65443  
    65444 
    65445 > matchmaker #643 to #1.9 & sel
    65446 
    65447 Parameters 
    65448 --- 
    65449 Chain pairing | bb 
    65450 Alignment algorithm | Needleman-Wunsch 
    65451 Similarity matrix | BLOSUM-62 
    65452 SS fraction | 0.3 
    65453 Gap open (HH/SS/other) | 18/18/6 
    65454 Gap extend | 1 
    65455 SS matrix |  |  | H | S | O 
    65456 ---|---|---|--- 
    65457 H | 6 | -9 | -6 
    65458 S |  | 6 | -6 
    65459 O |  |  | 4 
    65460 Iteration cutoff | 2 
    65461  
    65462 Matchmaker 3j0c.pdb1, chain G (#1.9) with AF3 E1 422-461.pdb, chain A (#643),
    65463 sequence alignment score = 626.9 
    65464 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    65465 2.997) 
    65466  
    65467 
    65468 > hide sel cartoons
    65469 
    65470 > select #1.9/H
    65471 
    65472 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    65473 
    65474 > show sel cartoons
    65475 
    65476 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    65477 
    65478 Chain information for AF3 E2 1-352.pdb #644 
    65479 --- 
    65480 Chain | Description 
    65481 B | No description available 
    65482  
    65483 
    65484 > matchmaker #644 to #1.9 & sel
    65485 
    65486 Parameters 
    65487 --- 
    65488 Chain pairing | bb 
    65489 Alignment algorithm | Needleman-Wunsch 
    65490 Similarity matrix | BLOSUM-62 
    65491 SS fraction | 0.3 
    65492 Gap open (HH/SS/other) | 18/18/6 
    65493 Gap extend | 1 
    65494 SS matrix |  |  | H | S | O 
    65495 ---|---|---|--- 
    65496 H | 6 | -9 | -6 
    65497 S |  | 6 | -6 
    65498 O |  |  | 4 
    65499 Iteration cutoff | 2 
    65500  
    65501 Matchmaker 3j0c.pdb1, chain H (#1.9) with AF3 E2 1-352.pdb, chain B (#644),
    65502 sequence alignment score = 590.9 
    65503 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    65504 6.107) 
    65505  
    65506 
    65507 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    65508 
    65509 Chain information for AF3 E2 353-438.pdb #645 
    65510 --- 
    65511 Chain | Description 
    65512 B | No description available 
    65513  
    65514 
    65515 > matchmaker #645 to #1.9 & sel
    65516 
    65517 Parameters 
    65518 --- 
    65519 Chain pairing | bb 
    65520 Alignment algorithm | Needleman-Wunsch 
    65521 Similarity matrix | BLOSUM-62 
    65522 SS fraction | 0.3 
    65523 Gap open (HH/SS/other) | 18/18/6 
    65524 Gap extend | 1 
    65525 SS matrix |  |  | H | S | O 
    65526 ---|---|---|--- 
    65527 H | 6 | -9 | -6 
    65528 S |  | 6 | -6 
    65529 O |  |  | 4 
    65530 Iteration cutoff | 2 
    65531  
    65532 Matchmaker 3j0c.pdb1, chain H (#1.9) with AF3 E2 353-438.pdb, chain B (#645),
    65533 sequence alignment score = 329.4 
    65534 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    65535 8.150) 
    65536  
    65537 
    65538 > hide sel cartoons
    65539 
    65540 > select #1.9/I
    65541 
    65542 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    65543 
    65544 > show sel cartoons
    65545 
    65546 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    65547 
    65548 Chain information for AF3 CA.pdb #646 
    65549 --- 
    65550 Chain | Description 
    65551 A | No description available 
    65552  
    65553 
    65554 > matchmaker #646 to #1.9 & sel
    65555 
    65556 Parameters 
    65557 --- 
    65558 Chain pairing | bb 
    65559 Alignment algorithm | Needleman-Wunsch 
    65560 Similarity matrix | BLOSUM-62 
    65561 SS fraction | 0.3 
    65562 Gap open (HH/SS/other) | 18/18/6 
    65563 Gap extend | 1 
    65564 SS matrix |  |  | H | S | O 
    65565 ---|---|---|--- 
    65566 H | 6 | -9 | -6 
    65567 S |  | 6 | -6 
    65568 O |  |  | 4 
    65569 Iteration cutoff | 2 
    65570  
    65571 Matchmaker 3j0c.pdb1, chain I (#1.9) with AF3 CA.pdb, chain A (#646), sequence
    65572 alignment score = 306.5 
    65573 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    65574 2.689) 
    65575  
    65576 
    65577 > hide sel cartoons
    65578 
    65579 > color #642 dodgerblue
    65580 
    65581 > color #643 dodgerblue
    65582 
    65583 > color #644 #00b305ff
    65584 
    65585 > color #645 #00b305ff
    65586 
    65587 > color #646 #f15839ff
    65588 
    65589 > select #1.10/G
    65590 
    65591 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    65592 
    65593 > show sel cartoons
    65594 
    65595 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    65596 
    65597 Chain information for AF3 E1 1-421.pdb #647 
    65598 --- 
    65599 Chain | Description 
    65600 A | No description available 
    65601  
    65602 
    65603 > matchmaker #647 to #1.10 & sel
    65604 
    65605 Parameters 
    65606 --- 
    65607 Chain pairing | bb 
    65608 Alignment algorithm | Needleman-Wunsch 
    65609 Similarity matrix | BLOSUM-62 
    65610 SS fraction | 0.3 
    65611 Gap open (HH/SS/other) | 18/18/6 
    65612 Gap extend | 1 
    65613 SS matrix |  |  | H | S | O 
    65614 ---|---|---|--- 
    65615 H | 6 | -9 | -6 
    65616 S |  | 6 | -6 
    65617 O |  |  | 4 
    65618 Iteration cutoff | 2 
    65619  
    65620 Matchmaker 3j0c.pdb1, chain G (#1.10) with AF3 E1 1-421.pdb, chain A (#647),
    65621 sequence alignment score = 1060.7 
    65622 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    65623 2.985) 
    65624  
    65625 
    65626 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    65627 
    65628 Chain information for AF3 E1 422-461.pdb #648 
    65629 --- 
    65630 Chain | Description 
    65631 A | No description available 
    65632  
    65633 
    65634 > matchmaker #648 to #1.10 & sel
    65635 
    65636 Parameters 
    65637 --- 
    65638 Chain pairing | bb 
    65639 Alignment algorithm | Needleman-Wunsch 
    65640 Similarity matrix | BLOSUM-62 
    65641 SS fraction | 0.3 
    65642 Gap open (HH/SS/other) | 18/18/6 
    65643 Gap extend | 1 
    65644 SS matrix |  |  | H | S | O 
    65645 ---|---|---|--- 
    65646 H | 6 | -9 | -6 
    65647 S |  | 6 | -6 
    65648 O |  |  | 4 
    65649 Iteration cutoff | 2 
    65650  
    65651 Matchmaker 3j0c.pdb1, chain G (#1.10) with AF3 E1 422-461.pdb, chain A (#648),
    65652 sequence alignment score = 626.9 
    65653 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    65654 2.996) 
    65655  
    65656 
    65657 > hide sel cartoons
    65658 
    65659 > select #1.10/H
    65660 
    65661 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    65662 
    65663 > show sel cartoons
    65664 
    65665 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    65666 
    65667 Chain information for AF3 E2 1-352.pdb #649 
    65668 --- 
    65669 Chain | Description 
    65670 B | No description available 
    65671  
    65672 
    65673 > matchmaker #649 to #1.10 & sel
    65674 
    65675 Parameters 
    65676 --- 
    65677 Chain pairing | bb 
    65678 Alignment algorithm | Needleman-Wunsch 
    65679 Similarity matrix | BLOSUM-62 
    65680 SS fraction | 0.3 
    65681 Gap open (HH/SS/other) | 18/18/6 
    65682 Gap extend | 1 
    65683 SS matrix |  |  | H | S | O 
    65684 ---|---|---|--- 
    65685 H | 6 | -9 | -6 
    65686 S |  | 6 | -6 
    65687 O |  |  | 4 
    65688 Iteration cutoff | 2 
    65689  
    65690 Matchmaker 3j0c.pdb1, chain H (#1.10) with AF3 E2 1-352.pdb, chain B (#649),
    65691 sequence alignment score = 590.9 
    65692 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    65693 6.107) 
    65694  
    65695 
    65696 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    65697 
    65698 Chain information for AF3 E2 353-438.pdb #650 
    65699 --- 
    65700 Chain | Description 
    65701 B | No description available 
    65702  
    65703 
    65704 > matchmaker #650 to #1.10 & sel
    65705 
    65706 Parameters 
    65707 --- 
    65708 Chain pairing | bb 
    65709 Alignment algorithm | Needleman-Wunsch 
    65710 Similarity matrix | BLOSUM-62 
    65711 SS fraction | 0.3 
    65712 Gap open (HH/SS/other) | 18/18/6 
    65713 Gap extend | 1 
    65714 SS matrix |  |  | H | S | O 
    65715 ---|---|---|--- 
    65716 H | 6 | -9 | -6 
    65717 S |  | 6 | -6 
    65718 O |  |  | 4 
    65719 Iteration cutoff | 2 
    65720  
    65721 Matchmaker 3j0c.pdb1, chain H (#1.10) with AF3 E2 353-438.pdb, chain B (#650),
    65722 sequence alignment score = 329.4 
    65723 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    65724 8.151) 
    65725  
    65726 
    65727 > hide sel cartoons
    65728 
    65729 > select #1.10/I
    65730 
    65731 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    65732 
    65733 > show sel cartoons
    65734 
    65735 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    65736 
    65737 Chain information for AF3 CA.pdb #651 
    65738 --- 
    65739 Chain | Description 
    65740 A | No description available 
    65741  
    65742 
    65743 > matchmaker #651 to #1.10 & sel
    65744 
    65745 Parameters 
    65746 --- 
    65747 Chain pairing | bb 
    65748 Alignment algorithm | Needleman-Wunsch 
    65749 Similarity matrix | BLOSUM-62 
    65750 SS fraction | 0.3 
    65751 Gap open (HH/SS/other) | 18/18/6 
    65752 Gap extend | 1 
    65753 SS matrix |  |  | H | S | O 
    65754 ---|---|---|--- 
    65755 H | 6 | -9 | -6 
    65756 S |  | 6 | -6 
    65757 O |  |  | 4 
    65758 Iteration cutoff | 2 
    65759  
    65760 Matchmaker 3j0c.pdb1, chain I (#1.10) with AF3 CA.pdb, chain A (#651),
    65761 sequence alignment score = 306.5 
    65762 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    65763 2.689) 
    65764  
    65765 
    65766 > hide sel cartoons
    65767 
    65768 > color #647 dodgerblue
    65769 
    65770 > color #648 dodgerblue
    65771 
    65772 > color #649 #00b305ff
    65773 
    65774 > color #650 #00b305ff
    65775 
    65776 > color #651 #f15839ff
    65777 
    65778 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    65779 
    65780 > hide #602 models
    65781 
    65782 > hide #603 models
    65783 
    65784 > hide #604 models
    65785 
    65786 > hide #605 models
    65787 
    65788 > hide #606 models
    65789 
    65790 > hide #607 models
    65791 
    65792 > hide #608 models
    65793 
    65794 > hide #609 models
    65795 
    65796 > hide #610 models
    65797 
    65798 > hide #611 models
    65799 
    65800 > hide #612 models
    65801 
    65802 > hide #613 models
    65803 
    65804 > hide #614 models
    65805 
    65806 > hide #615 models
    65807 
    65808 > hide #616 models
    65809 
    65810 > hide #617 models
    65811 
    65812 > hide #618 models
    65813 
    65814 > hide #619 models
    65815 
    65816 > hide #620 models
    65817 
    65818 > hide #621 models
    65819 
    65820 > hide #622 models
    65821 
    65822 > hide #623 models
    65823 
    65824 > hide #624 models
    65825 
    65826 > hide #625 models
    65827 
    65828 > hide #626 models
    65829 
    65830 > hide #627 models
    65831 
    65832 > hide #628 models
    65833 
    65834 > hide #629 models
    65835 
    65836 > hide #630 models
    65837 
    65838 > hide #631 models
    65839 
    65840 > hide #632 models
    65841 
    65842 > hide #633 models
    65843 
    65844 > hide #634 models
    65845 
    65846 > hide #635 models
    65847 
    65848 > hide #636 models
    65849 
    65850 > hide #637 models
    65851 
    65852 > hide #638 models
    65853 
    65854 > hide #639 models
    65855 
    65856 > hide #640 models
    65857 
    65858 > hide #641 models
    65859 
    65860 > hide #642 models
    65861 
    65862 > hide #643 models
    65863 
    65864 > hide #644 models
    65865 
    65866 > hide #645 models
    65867 
    65868 > hide #646 models
    65869 
    65870 > hide #647 models
    65871 
    65872 > hide #648 models
    65873 
    65874 > hide #649 models
    65875 
    65876 > hide #650 models
    65877 
    65878 > hide #651 models
    65879 
    65880 > select #1.11/G
    65881 
    65882 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    65883 
    65884 > show sel cartoons
    65885 
    65886 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    65887 
    65888 Chain information for AF3 E1 1-421.pdb #652 
    65889 --- 
    65890 Chain | Description 
    65891 A | No description available 
    65892  
    65893 
    65894 > matchmaker #652 to #1.11 & sel
    65895 
    65896 Parameters 
    65897 --- 
    65898 Chain pairing | bb 
    65899 Alignment algorithm | Needleman-Wunsch 
    65900 Similarity matrix | BLOSUM-62 
    65901 SS fraction | 0.3 
    65902 Gap open (HH/SS/other) | 18/18/6 
    65903 Gap extend | 1 
    65904 SS matrix |  |  | H | S | O 
    65905 ---|---|---|--- 
    65906 H | 6 | -9 | -6 
    65907 S |  | 6 | -6 
    65908 O |  |  | 4 
    65909 Iteration cutoff | 2 
    65910  
    65911 Matchmaker 3j0c.pdb1, chain G (#1.11) with AF3 E1 1-421.pdb, chain A (#652),
    65912 sequence alignment score = 1060.7 
    65913 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    65914 2.985) 
    65915  
    65916 
    65917 > view
    65918 
    65919 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    65920 
    65921 Chain information for AF3 E1 422-461.pdb #653 
    65922 --- 
    65923 Chain | Description 
    65924 A | No description available 
    65925  
    65926 
    65927 > matchmaker #653 to #1.11 & sel
    65928 
    65929 Parameters 
    65930 --- 
    65931 Chain pairing | bb 
    65932 Alignment algorithm | Needleman-Wunsch 
    65933 Similarity matrix | BLOSUM-62 
    65934 SS fraction | 0.3 
    65935 Gap open (HH/SS/other) | 18/18/6 
    65936 Gap extend | 1 
    65937 SS matrix |  |  | H | S | O 
    65938 ---|---|---|--- 
    65939 H | 6 | -9 | -6 
    65940 S |  | 6 | -6 
    65941 O |  |  | 4 
    65942 Iteration cutoff | 2 
    65943  
    65944 Matchmaker 3j0c.pdb1, chain G (#1.11) with AF3 E1 422-461.pdb, chain A (#653),
    65945 sequence alignment score = 626.9 
    65946 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    65947 2.997) 
    65948  
    65949 
    65950 > hide sel cartoons
    65951 
    65952 > select #1.11/H
    65953 
    65954 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    65955 
    65956 > show sel cartoons
    65957 
    65958 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    65959 
    65960 Chain information for AF3 E2 1-352.pdb #654 
    65961 --- 
    65962 Chain | Description 
    65963 B | No description available 
    65964  
    65965 
    65966 > matchmaker #654 to #1.11 & sel
    65967 
    65968 Parameters 
    65969 --- 
    65970 Chain pairing | bb 
    65971 Alignment algorithm | Needleman-Wunsch 
    65972 Similarity matrix | BLOSUM-62 
    65973 SS fraction | 0.3 
    65974 Gap open (HH/SS/other) | 18/18/6 
    65975 Gap extend | 1 
    65976 SS matrix |  |  | H | S | O 
    65977 ---|---|---|--- 
    65978 H | 6 | -9 | -6 
    65979 S |  | 6 | -6 
    65980 O |  |  | 4 
    65981 Iteration cutoff | 2 
    65982  
    65983 Matchmaker 3j0c.pdb1, chain H (#1.11) with AF3 E2 1-352.pdb, chain B (#654),
    65984 sequence alignment score = 590.9 
    65985 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    65986 6.107) 
    65987  
    65988 
    65989 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    65990 
    65991 Chain information for AF3 E2 353-438.pdb #655 
    65992 --- 
    65993 Chain | Description 
    65994 B | No description available 
    65995  
    65996 
    65997 > matchmaker #655 to #1.11 & sel
    65998 
    65999 Parameters 
    66000 --- 
    66001 Chain pairing | bb 
    66002 Alignment algorithm | Needleman-Wunsch 
    66003 Similarity matrix | BLOSUM-62 
    66004 SS fraction | 0.3 
    66005 Gap open (HH/SS/other) | 18/18/6 
    66006 Gap extend | 1 
    66007 SS matrix |  |  | H | S | O 
    66008 ---|---|---|--- 
    66009 H | 6 | -9 | -6 
    66010 S |  | 6 | -6 
    66011 O |  |  | 4 
    66012 Iteration cutoff | 2 
    66013  
    66014 Matchmaker 3j0c.pdb1, chain H (#1.11) with AF3 E2 353-438.pdb, chain B (#655),
    66015 sequence alignment score = 329.4 
    66016 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    66017 8.151) 
    66018  
    66019 
    66020 > hide sel cartoons
    66021 
    66022 > select #1.11/I
    66023 
    66024 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    66025 
    66026 > show sel cartoons
    66027 
    66028 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    66029 
    66030 Chain information for AF3 CA.pdb #656 
    66031 --- 
    66032 Chain | Description 
    66033 A | No description available 
    66034  
    66035 
    66036 > matchmaker #656 to #1.11 & sel
    66037 
    66038 Parameters 
    66039 --- 
    66040 Chain pairing | bb 
    66041 Alignment algorithm | Needleman-Wunsch 
    66042 Similarity matrix | BLOSUM-62 
    66043 SS fraction | 0.3 
    66044 Gap open (HH/SS/other) | 18/18/6 
    66045 Gap extend | 1 
    66046 SS matrix |  |  | H | S | O 
    66047 ---|---|---|--- 
    66048 H | 6 | -9 | -6 
    66049 S |  | 6 | -6 
    66050 O |  |  | 4 
    66051 Iteration cutoff | 2 
    66052  
    66053 Matchmaker 3j0c.pdb1, chain I (#1.11) with AF3 CA.pdb, chain A (#656),
    66054 sequence alignment score = 306.5 
    66055 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    66056 2.689) 
    66057  
    66058 
    66059 > hide sel cartoons
    66060 
    66061 > color #652 dodgerblue
    66062 
    66063 > color #653 dodgerblue
    66064 
    66065 > color #654 #00b305ff
    66066 
    66067 > color #655 #00b305ff
    66068 
    66069 > color #656 #f15839ff
    66070 
    66071 > select #1.12/G
    66072 
    66073 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    66074 
    66075 > show sel cartoons
    66076 
    66077 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    66078 
    66079 Chain information for AF3 E1 1-421.pdb #657 
    66080 --- 
    66081 Chain | Description 
    66082 A | No description available 
    66083  
    66084 
    66085 > matchmaker #657 to #1.12 & sel
    66086 
    66087 Parameters 
    66088 --- 
    66089 Chain pairing | bb 
    66090 Alignment algorithm | Needleman-Wunsch 
    66091 Similarity matrix | BLOSUM-62 
    66092 SS fraction | 0.3 
    66093 Gap open (HH/SS/other) | 18/18/6 
    66094 Gap extend | 1 
    66095 SS matrix |  |  | H | S | O 
    66096 ---|---|---|--- 
    66097 H | 6 | -9 | -6 
    66098 S |  | 6 | -6 
    66099 O |  |  | 4 
    66100 Iteration cutoff | 2 
    66101  
    66102 Matchmaker 3j0c.pdb1, chain G (#1.12) with AF3 E1 1-421.pdb, chain A (#657),
    66103 sequence alignment score = 1060.7 
    66104 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    66105 2.985) 
    66106  
    66107 
    66108 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    66109 
    66110 Chain information for AF3 E1 422-461.pdb #658 
    66111 --- 
    66112 Chain | Description 
    66113 A | No description available 
    66114  
    66115 
    66116 > matchmaker #658 to #1.12 & sel
    66117 
    66118 Parameters 
    66119 --- 
    66120 Chain pairing | bb 
    66121 Alignment algorithm | Needleman-Wunsch 
    66122 Similarity matrix | BLOSUM-62 
    66123 SS fraction | 0.3 
    66124 Gap open (HH/SS/other) | 18/18/6 
    66125 Gap extend | 1 
    66126 SS matrix |  |  | H | S | O 
    66127 ---|---|---|--- 
    66128 H | 6 | -9 | -6 
    66129 S |  | 6 | -6 
    66130 O |  |  | 4 
    66131 Iteration cutoff | 2 
    66132  
    66133 Matchmaker 3j0c.pdb1, chain G (#1.12) with AF3 E1 422-461.pdb, chain A (#658),
    66134 sequence alignment score = 626.9 
    66135 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    66136 2.997) 
    66137  
    66138 
    66139 > hide sel cartoons
    66140 
    66141 > select #1.12/H
    66142 
    66143 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    66144 
    66145 > show sel cartoons
    66146 
    66147 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    66148 
    66149 Chain information for AF3 E2 1-352.pdb #659 
    66150 --- 
    66151 Chain | Description 
    66152 B | No description available 
    66153  
    66154 
    66155 > matchmaker #659 to #1.12 & sel
    66156 
    66157 Parameters 
    66158 --- 
    66159 Chain pairing | bb 
    66160 Alignment algorithm | Needleman-Wunsch 
    66161 Similarity matrix | BLOSUM-62 
    66162 SS fraction | 0.3 
    66163 Gap open (HH/SS/other) | 18/18/6 
    66164 Gap extend | 1 
    66165 SS matrix |  |  | H | S | O 
    66166 ---|---|---|--- 
    66167 H | 6 | -9 | -6 
    66168 S |  | 6 | -6 
    66169 O |  |  | 4 
    66170 Iteration cutoff | 2 
    66171  
    66172 Matchmaker 3j0c.pdb1, chain H (#1.12) with AF3 E2 1-352.pdb, chain B (#659),
    66173 sequence alignment score = 590.9 
    66174 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    66175 6.107) 
    66176  
    66177 
    66178 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    66179 
    66180 Chain information for AF3 E2 353-438.pdb #660 
    66181 --- 
    66182 Chain | Description 
    66183 B | No description available 
    66184  
    66185 
    66186 > matchmaker #660 to #1.12 & sel
    66187 
    66188 Parameters 
    66189 --- 
    66190 Chain pairing | bb 
    66191 Alignment algorithm | Needleman-Wunsch 
    66192 Similarity matrix | BLOSUM-62 
    66193 SS fraction | 0.3 
    66194 Gap open (HH/SS/other) | 18/18/6 
    66195 Gap extend | 1 
    66196 SS matrix |  |  | H | S | O 
    66197 ---|---|---|--- 
    66198 H | 6 | -9 | -6 
    66199 S |  | 6 | -6 
    66200 O |  |  | 4 
    66201 Iteration cutoff | 2 
    66202  
    66203 Matchmaker 3j0c.pdb1, chain H (#1.12) with AF3 E2 353-438.pdb, chain B (#660),
    66204 sequence alignment score = 329.4 
    66205 RMSD between 40 pruned atom pairs is 0.937 angstroms; (across all 84 pairs:
    66206 8.150) 
    66207  
    66208 
    66209 > hide sel cartoons
    66210 
    66211 > select #1.12/I
    66212 
    66213 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    66214 
    66215 > show sel cartoons
    66216 
    66217 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    66218 
    66219 Chain information for AF3 CA.pdb #661 
    66220 --- 
    66221 Chain | Description 
    66222 A | No description available 
    66223  
    66224 
    66225 > matchmaker #661 to #1.12 & sel
    66226 
    66227 Parameters 
    66228 --- 
    66229 Chain pairing | bb 
    66230 Alignment algorithm | Needleman-Wunsch 
    66231 Similarity matrix | BLOSUM-62 
    66232 SS fraction | 0.3 
    66233 Gap open (HH/SS/other) | 18/18/6 
    66234 Gap extend | 1 
    66235 SS matrix |  |  | H | S | O 
    66236 ---|---|---|--- 
    66237 H | 6 | -9 | -6 
    66238 S |  | 6 | -6 
    66239 O |  |  | 4 
    66240 Iteration cutoff | 2 
    66241  
    66242 Matchmaker 3j0c.pdb1, chain I (#1.12) with AF3 CA.pdb, chain A (#661),
    66243 sequence alignment score = 306.5 
    66244 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    66245 2.689) 
    66246  
    66247 
    66248 > hide sel cartoons
    66249 
    66250 > color #657 dodgerblue
    66251 
    66252 > color #658 dodgerblue
    66253 
    66254 > color #659 #00b305ff
    66255 
    66256 > color #660 #00b305ff
    66257 
    66258 > color #661 #f15839ff
    66259 
    66260 > select #1.13/G
    66261 
    66262 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    66263 
    66264 > show sel cartoons
    66265 
    66266 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    66267 
    66268 Chain information for AF3 E1 1-421.pdb #662 
    66269 --- 
    66270 Chain | Description 
    66271 A | No description available 
    66272  
    66273 
    66274 > matchmaker #662 to #1.13 & sel
    66275 
    66276 Parameters 
    66277 --- 
    66278 Chain pairing | bb 
    66279 Alignment algorithm | Needleman-Wunsch 
    66280 Similarity matrix | BLOSUM-62 
    66281 SS fraction | 0.3 
    66282 Gap open (HH/SS/other) | 18/18/6 
    66283 Gap extend | 1 
    66284 SS matrix |  |  | H | S | O 
    66285 ---|---|---|--- 
    66286 H | 6 | -9 | -6 
    66287 S |  | 6 | -6 
    66288 O |  |  | 4 
    66289 Iteration cutoff | 2 
    66290  
    66291 Matchmaker 3j0c.pdb1, chain G (#1.13) with AF3 E1 1-421.pdb, chain A (#662),
    66292 sequence alignment score = 1060.7 
    66293 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    66294 2.985) 
    66295  
    66296 
    66297 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    66298 
    66299 Chain information for AF3 E1 422-461.pdb #663 
    66300 --- 
    66301 Chain | Description 
    66302 A | No description available 
    66303  
    66304 
    66305 > matchmaker #663 to #1.13 & sel
    66306 
    66307 Parameters 
    66308 --- 
    66309 Chain pairing | bb 
    66310 Alignment algorithm | Needleman-Wunsch 
    66311 Similarity matrix | BLOSUM-62 
    66312 SS fraction | 0.3 
    66313 Gap open (HH/SS/other) | 18/18/6 
    66314 Gap extend | 1 
    66315 SS matrix |  |  | H | S | O 
    66316 ---|---|---|--- 
    66317 H | 6 | -9 | -6 
    66318 S |  | 6 | -6 
    66319 O |  |  | 4 
    66320 Iteration cutoff | 2 
    66321  
    66322 Matchmaker 3j0c.pdb1, chain G (#1.13) with AF3 E1 422-461.pdb, chain A (#663),
    66323 sequence alignment score = 626.9 
    66324 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    66325 2.997) 
    66326  
    66327 
    66328 > hide sel cartoons
    66329 
    66330 > select #1.13/I
    66331 
    66332 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    66333 
    66334 > show sel cartoons
    66335 
    66336 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    66337 
    66338 Chain information for AF3 CA.pdb #664 
    66339 --- 
    66340 Chain | Description 
    66341 A | No description available 
    66342  
    66343 
    66344 > matchmaker #664 to #1.13 & sel
    66345 
    66346 Parameters 
    66347 --- 
    66348 Chain pairing | bb 
    66349 Alignment algorithm | Needleman-Wunsch 
    66350 Similarity matrix | BLOSUM-62 
    66351 SS fraction | 0.3 
    66352 Gap open (HH/SS/other) | 18/18/6 
    66353 Gap extend | 1 
    66354 SS matrix |  |  | H | S | O 
    66355 ---|---|---|--- 
    66356 H | 6 | -9 | -6 
    66357 S |  | 6 | -6 
    66358 O |  |  | 4 
    66359 Iteration cutoff | 2 
    66360  
    66361 Matchmaker 3j0c.pdb1, chain I (#1.13) with AF3 CA.pdb, chain A (#664),
    66362 sequence alignment score = 306.5 
    66363 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    66364 2.689) 
    66365  
    66366 
    66367 > hide sel cartoons
    66368 
    66369 > select #1.13/H
    66370 
    66371 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    66372 
    66373 > show sel cartoons
    66374 
    66375 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    66376 
    66377 Chain information for AF3 E2 1-352.pdb #665 
    66378 --- 
    66379 Chain | Description 
    66380 B | No description available 
    66381  
    66382 
    66383 > matchmaker #665 to #1.13 & sel
    66384 
    66385 Parameters 
    66386 --- 
    66387 Chain pairing | bb 
    66388 Alignment algorithm | Needleman-Wunsch 
    66389 Similarity matrix | BLOSUM-62 
    66390 SS fraction | 0.3 
    66391 Gap open (HH/SS/other) | 18/18/6 
    66392 Gap extend | 1 
    66393 SS matrix |  |  | H | S | O 
    66394 ---|---|---|--- 
    66395 H | 6 | -9 | -6 
    66396 S |  | 6 | -6 
    66397 O |  |  | 4 
    66398 Iteration cutoff | 2 
    66399  
    66400 Matchmaker 3j0c.pdb1, chain H (#1.13) with AF3 E2 1-352.pdb, chain B (#665),
    66401 sequence alignment score = 590.9 
    66402 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    66403 6.107) 
    66404  
    66405 
    66406 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    66407 
    66408 Chain information for AF3 E2 353-438.pdb #666 
    66409 --- 
    66410 Chain | Description 
    66411 B | No description available 
    66412  
    66413 
    66414 > matchmaker #666 to #1.13 & sel
    66415 
    66416 Parameters 
    66417 --- 
    66418 Chain pairing | bb 
    66419 Alignment algorithm | Needleman-Wunsch 
    66420 Similarity matrix | BLOSUM-62 
    66421 SS fraction | 0.3 
    66422 Gap open (HH/SS/other) | 18/18/6 
    66423 Gap extend | 1 
    66424 SS matrix |  |  | H | S | O 
    66425 ---|---|---|--- 
    66426 H | 6 | -9 | -6 
    66427 S |  | 6 | -6 
    66428 O |  |  | 4 
    66429 Iteration cutoff | 2 
    66430  
    66431 Matchmaker 3j0c.pdb1, chain H (#1.13) with AF3 E2 353-438.pdb, chain B (#666),
    66432 sequence alignment score = 329.4 
    66433 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    66434 8.150) 
    66435  
    66436 
    66437 > hide sel cartoons
    66438 
    66439 > close #664
    66440 
    66441 > select #1.13/I
    66442 
    66443 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    66444 
    66445 > show sel cartoons
    66446 
    66447 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    66448 
    66449 Chain information for AF3 CA.pdb #664 
    66450 --- 
    66451 Chain | Description 
    66452 A | No description available 
    66453  
    66454 
    66455 > close #666
    66456 
    66457 > close #665
    66458 
    66459 > close #664
    66460 
    66461 > hide sel cartoons
    66462 
    66463 > select #1.13/H
    66464 
    66465 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    66466 
    66467 > show sel cartoons
    66468 
    66469 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    66470 
    66471 Chain information for AF3 E2 1-352.pdb #664 
    66472 --- 
    66473 Chain | Description 
    66474 B | No description available 
    66475  
    66476 
    66477 > matchmaker #664 to #1.13 & sel
    66478 
    66479 Parameters 
    66480 --- 
    66481 Chain pairing | bb 
    66482 Alignment algorithm | Needleman-Wunsch 
    66483 Similarity matrix | BLOSUM-62 
    66484 SS fraction | 0.3 
    66485 Gap open (HH/SS/other) | 18/18/6 
    66486 Gap extend | 1 
    66487 SS matrix |  |  | H | S | O 
    66488 ---|---|---|--- 
    66489 H | 6 | -9 | -6 
    66490 S |  | 6 | -6 
    66491 O |  |  | 4 
    66492 Iteration cutoff | 2 
    66493  
    66494 Matchmaker 3j0c.pdb1, chain H (#1.13) with AF3 E2 1-352.pdb, chain B (#664),
    66495 sequence alignment score = 590.9 
    66496 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    66497 6.107) 
    66498  
    66499 
    66500 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    66501 
    66502 Chain information for AF3 E2 353-438.pdb #665 
    66503 --- 
    66504 Chain | Description 
    66505 B | No description available 
    66506  
    66507 
    66508 > matchmaker #665 to #1.13 & sel
    66509 
    66510 Parameters 
    66511 --- 
    66512 Chain pairing | bb 
    66513 Alignment algorithm | Needleman-Wunsch 
    66514 Similarity matrix | BLOSUM-62 
    66515 SS fraction | 0.3 
    66516 Gap open (HH/SS/other) | 18/18/6 
    66517 Gap extend | 1 
    66518 SS matrix |  |  | H | S | O 
    66519 ---|---|---|--- 
    66520 H | 6 | -9 | -6 
    66521 S |  | 6 | -6 
    66522 O |  |  | 4 
    66523 Iteration cutoff | 2 
    66524  
    66525 Matchmaker 3j0c.pdb1, chain H (#1.13) with AF3 E2 353-438.pdb, chain B (#665),
    66526 sequence alignment score = 329.4 
    66527 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    66528 8.150) 
    66529  
    66530 
    66531 > hide sel cartoons
    66532 
    66533 > select #1.13/I
    66534 
    66535 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    66536 
    66537 > show sel cartoons
    66538 
    66539 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    66540 
    66541 Chain information for AF3 CA.pdb #666 
    66542 --- 
    66543 Chain | Description 
    66544 A | No description available 
    66545  
    66546 
    66547 > matchmaker #666 to #1.13 & sel
    66548 
    66549 Parameters 
    66550 --- 
    66551 Chain pairing | bb 
    66552 Alignment algorithm | Needleman-Wunsch 
    66553 Similarity matrix | BLOSUM-62 
    66554 SS fraction | 0.3 
    66555 Gap open (HH/SS/other) | 18/18/6 
    66556 Gap extend | 1 
    66557 SS matrix |  |  | H | S | O 
    66558 ---|---|---|--- 
    66559 H | 6 | -9 | -6 
    66560 S |  | 6 | -6 
    66561 O |  |  | 4 
    66562 Iteration cutoff | 2 
    66563  
    66564 Matchmaker 3j0c.pdb1, chain I (#1.13) with AF3 CA.pdb, chain A (#666),
    66565 sequence alignment score = 306.5 
    66566 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    66567 2.689) 
    66568  
    66569 
    66570 > hide sel cartoons
    66571 
    66572 > color #662 dodgerblue
    66573 
    66574 > color #663 dodgerblue
    66575 
    66576 > color #664 #00b305ff
    66577 
    66578 > color #665 #00b305ff
    66579 
    66580 > color #666 #f15839ff
    66581 
    66582 > select #1.14/G
    66583 
    66584 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    66585 
    66586 > show sel cartoons
    66587 
    66588 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    66589 
    66590 Chain information for AF3 E1 1-421.pdb #667 
    66591 --- 
    66592 Chain | Description 
    66593 A | No description available 
    66594  
    66595 
    66596 > matchmaker #667 to #1.13 & sel
    66597 
    66598 No 'to' model specified 
    66599 
    66600 > matchmaker #667 to #1.14 & sel
    66601 
    66602 Parameters 
    66603 --- 
    66604 Chain pairing | bb 
    66605 Alignment algorithm | Needleman-Wunsch 
    66606 Similarity matrix | BLOSUM-62 
    66607 SS fraction | 0.3 
    66608 Gap open (HH/SS/other) | 18/18/6 
    66609 Gap extend | 1 
    66610 SS matrix |  |  | H | S | O 
    66611 ---|---|---|--- 
    66612 H | 6 | -9 | -6 
    66613 S |  | 6 | -6 
    66614 O |  |  | 4 
    66615 Iteration cutoff | 2 
    66616  
    66617 Matchmaker 3j0c.pdb1, chain G (#1.14) with AF3 E1 1-421.pdb, chain A (#667),
    66618 sequence alignment score = 1060.7 
    66619 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    66620 2.985) 
    66621  
    66622 
    66623 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    66624 
    66625 Chain information for AF3 E1 422-461.pdb #668 
    66626 --- 
    66627 Chain | Description 
    66628 A | No description available 
    66629  
    66630 
    66631 > matchmaker #668 to #1.14 & sel
    66632 
    66633 Parameters 
    66634 --- 
    66635 Chain pairing | bb 
    66636 Alignment algorithm | Needleman-Wunsch 
    66637 Similarity matrix | BLOSUM-62 
    66638 SS fraction | 0.3 
    66639 Gap open (HH/SS/other) | 18/18/6 
    66640 Gap extend | 1 
    66641 SS matrix |  |  | H | S | O 
    66642 ---|---|---|--- 
    66643 H | 6 | -9 | -6 
    66644 S |  | 6 | -6 
    66645 O |  |  | 4 
    66646 Iteration cutoff | 2 
    66647  
    66648 Matchmaker 3j0c.pdb1, chain G (#1.14) with AF3 E1 422-461.pdb, chain A (#668),
    66649 sequence alignment score = 626.9 
    66650 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    66651 2.997) 
    66652  
    66653 
    66654 > hide sel cartoons
    66655 
    66656 > select #1.13/H
    66657 
    66658 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    66659 
    66660 > show sel cartoons
    66661 
    66662 > select #1.14/H
    66663 
    66664 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    66665 
    66666 > show sel cartoons
    66667 
    66668 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    66669 
    66670 Chain information for AF3 E2 1-352.pdb #669 
    66671 --- 
    66672 Chain | Description 
    66673 B | No description available 
    66674  
    66675 
    66676 > matchmaker #669 to #1.14 & sel
    66677 
    66678 Parameters 
    66679 --- 
    66680 Chain pairing | bb 
    66681 Alignment algorithm | Needleman-Wunsch 
    66682 Similarity matrix | BLOSUM-62 
    66683 SS fraction | 0.3 
    66684 Gap open (HH/SS/other) | 18/18/6 
    66685 Gap extend | 1 
    66686 SS matrix |  |  | H | S | O 
    66687 ---|---|---|--- 
    66688 H | 6 | -9 | -6 
    66689 S |  | 6 | -6 
    66690 O |  |  | 4 
    66691 Iteration cutoff | 2 
    66692  
    66693 Matchmaker 3j0c.pdb1, chain H (#1.14) with AF3 E2 1-352.pdb, chain B (#669),
    66694 sequence alignment score = 590.9 
    66695 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    66696 6.107) 
    66697  
    66698 
    66699 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    66700 
    66701 Chain information for AF3 E2 353-438.pdb #670 
    66702 --- 
    66703 Chain | Description 
    66704 B | No description available 
    66705  
    66706 
    66707 > matchmaker #670 to #1.14 & sel
    66708 
    66709 Parameters 
    66710 --- 
    66711 Chain pairing | bb 
    66712 Alignment algorithm | Needleman-Wunsch 
    66713 Similarity matrix | BLOSUM-62 
    66714 SS fraction | 0.3 
    66715 Gap open (HH/SS/other) | 18/18/6 
    66716 Gap extend | 1 
    66717 SS matrix |  |  | H | S | O 
    66718 ---|---|---|--- 
    66719 H | 6 | -9 | -6 
    66720 S |  | 6 | -6 
    66721 O |  |  | 4 
    66722 Iteration cutoff | 2 
    66723  
    66724 Matchmaker 3j0c.pdb1, chain H (#1.14) with AF3 E2 353-438.pdb, chain B (#670),
    66725 sequence alignment score = 329.4 
    66726 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    66727 8.150) 
    66728  
    66729 
    66730 > hide sel cartoons
    66731 
    66732 > select #1.14/I
    66733 
    66734 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    66735 
    66736 > show sel cartoons
    66737 
    66738 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    66739 
    66740 Chain information for AF3 CA.pdb #671 
    66741 --- 
    66742 Chain | Description 
    66743 A | No description available 
    66744  
    66745 
    66746 > matchmaker #671 to #1.14 & sel
    66747 
    66748 Parameters 
    66749 --- 
    66750 Chain pairing | bb 
    66751 Alignment algorithm | Needleman-Wunsch 
    66752 Similarity matrix | BLOSUM-62 
    66753 SS fraction | 0.3 
    66754 Gap open (HH/SS/other) | 18/18/6 
    66755 Gap extend | 1 
    66756 SS matrix |  |  | H | S | O 
    66757 ---|---|---|--- 
    66758 H | 6 | -9 | -6 
    66759 S |  | 6 | -6 
    66760 O |  |  | 4 
    66761 Iteration cutoff | 2 
    66762  
    66763 Matchmaker 3j0c.pdb1, chain I (#1.14) with AF3 CA.pdb, chain A (#671),
    66764 sequence alignment score = 306.5 
    66765 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    66766 2.689) 
    66767  
    66768 
    66769 > hide sel cartoons
    66770 
    66771 > color #667 dodgerblue
    66772 
    66773 > color #668 dodgerblue
    66774 
    66775 > color #669 #00b305ff
    66776 
    66777 > color #670 #00b305ff
    66778 
    66779 > color #671 #f15839ff
    66780 
    66781 > select #1.13/H
    66782 
    66783 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    66784 
    66785 > hide sel cartoons
    66786 
    66787 > select #1.14/G
    66788 
    66789 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    66790 
    66791 > show sel cartoons
    66792 
    66793 > hide sel cartoons
    66794 
    66795 > select #1.15/G
    66796 
    66797 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    66798 
    66799 > show sel cartoons
    66800 
    66801 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    66802 
    66803 Chain information for AF3 E1 1-421.pdb #672 
    66804 --- 
    66805 Chain | Description 
    66806 A | No description available 
    66807  
    66808 
    66809 > matchmaker #672 to #1.15 & sel
    66810 
    66811 Parameters 
    66812 --- 
    66813 Chain pairing | bb 
    66814 Alignment algorithm | Needleman-Wunsch 
    66815 Similarity matrix | BLOSUM-62 
    66816 SS fraction | 0.3 
    66817 Gap open (HH/SS/other) | 18/18/6 
    66818 Gap extend | 1 
    66819 SS matrix |  |  | H | S | O 
    66820 ---|---|---|--- 
    66821 H | 6 | -9 | -6 
    66822 S |  | 6 | -6 
    66823 O |  |  | 4 
    66824 Iteration cutoff | 2 
    66825  
    66826 Matchmaker 3j0c.pdb1, chain G (#1.15) with AF3 E1 1-421.pdb, chain A (#672),
    66827 sequence alignment score = 1060.7 
    66828 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    66829 2.985) 
    66830  
    66831 
    66832 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    66833 
    66834 Chain information for AF3 E1 422-461.pdb #673 
    66835 --- 
    66836 Chain | Description 
    66837 A | No description available 
    66838  
    66839 
    66840 > matchmaker #673 to #1.15 & sel
    66841 
    66842 Parameters 
    66843 --- 
    66844 Chain pairing | bb 
    66845 Alignment algorithm | Needleman-Wunsch 
    66846 Similarity matrix | BLOSUM-62 
    66847 SS fraction | 0.3 
    66848 Gap open (HH/SS/other) | 18/18/6 
    66849 Gap extend | 1 
    66850 SS matrix |  |  | H | S | O 
    66851 ---|---|---|--- 
    66852 H | 6 | -9 | -6 
    66853 S |  | 6 | -6 
    66854 O |  |  | 4 
    66855 Iteration cutoff | 2 
    66856  
    66857 Matchmaker 3j0c.pdb1, chain G (#1.15) with AF3 E1 422-461.pdb, chain A (#673),
    66858 sequence alignment score = 626.9 
    66859 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    66860 2.997) 
    66861  
    66862 
    66863 > hide sel cartoons
    66864 
    66865 > select #1.15/H
    66866 
    66867 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    66868 
    66869 > show sel cartoons
    66870 
    66871 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    66872 
    66873 Chain information for AF3 E2 1-352.pdb #674 
    66874 --- 
    66875 Chain | Description 
    66876 B | No description available 
    66877  
    66878 
    66879 > matchmaker #674 to #1.15 & sel
    66880 
    66881 Parameters 
    66882 --- 
    66883 Chain pairing | bb 
    66884 Alignment algorithm | Needleman-Wunsch 
    66885 Similarity matrix | BLOSUM-62 
    66886 SS fraction | 0.3 
    66887 Gap open (HH/SS/other) | 18/18/6 
    66888 Gap extend | 1 
    66889 SS matrix |  |  | H | S | O 
    66890 ---|---|---|--- 
    66891 H | 6 | -9 | -6 
    66892 S |  | 6 | -6 
    66893 O |  |  | 4 
    66894 Iteration cutoff | 2 
    66895  
    66896 Matchmaker 3j0c.pdb1, chain H (#1.15) with AF3 E2 1-352.pdb, chain B (#674),
    66897 sequence alignment score = 590.9 
    66898 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    66899 6.107) 
    66900  
    66901 
    66902 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    66903 
    66904 Chain information for AF3 E2 353-438.pdb #675 
    66905 --- 
    66906 Chain | Description 
    66907 B | No description available 
    66908  
    66909 
    66910 > matchmaker #675 to #1.15 & sel
    66911 
    66912 Parameters 
    66913 --- 
    66914 Chain pairing | bb 
    66915 Alignment algorithm | Needleman-Wunsch 
    66916 Similarity matrix | BLOSUM-62 
    66917 SS fraction | 0.3 
    66918 Gap open (HH/SS/other) | 18/18/6 
    66919 Gap extend | 1 
    66920 SS matrix |  |  | H | S | O 
    66921 ---|---|---|--- 
    66922 H | 6 | -9 | -6 
    66923 S |  | 6 | -6 
    66924 O |  |  | 4 
    66925 Iteration cutoff | 2 
    66926  
    66927 Matchmaker 3j0c.pdb1, chain H (#1.15) with AF3 E2 353-438.pdb, chain B (#675),
    66928 sequence alignment score = 329.4 
    66929 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    66930 8.150) 
    66931  
    66932 
    66933 > hide sel cartoons
    66934 
    66935 > select #1.15/I
    66936 
    66937 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    66938 
    66939 > show sel cartoons
    66940 
    66941 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    66942 
    66943 Chain information for AF3 CA.pdb #676 
    66944 --- 
    66945 Chain | Description 
    66946 A | No description available 
    66947  
    66948 
    66949 > matchmaker #676 to #1.15 & sel
    66950 
    66951 Parameters 
    66952 --- 
    66953 Chain pairing | bb 
    66954 Alignment algorithm | Needleman-Wunsch 
    66955 Similarity matrix | BLOSUM-62 
    66956 SS fraction | 0.3 
    66957 Gap open (HH/SS/other) | 18/18/6 
    66958 Gap extend | 1 
    66959 SS matrix |  |  | H | S | O 
    66960 ---|---|---|--- 
    66961 H | 6 | -9 | -6 
    66962 S |  | 6 | -6 
    66963 O |  |  | 4 
    66964 Iteration cutoff | 2 
    66965  
    66966 Matchmaker 3j0c.pdb1, chain I (#1.15) with AF3 CA.pdb, chain A (#676),
    66967 sequence alignment score = 306.5 
    66968 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    66969 2.689) 
    66970  
    66971 
    66972 > hide sel cartoons
    66973 
    66974 > color #672 dodgerblue
    66975 
    66976 > color #673 dodgerblue
    66977 
    66978 > color #674 #00b305ff
    66979 
    66980 > color #675 #00b305ff
    66981 
    66982 > color #676 #f15839ff
    66983 
    66984 > select #1.16/G
    66985 
    66986 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    66987 
    66988 > show sel cartoons
    66989 
    66990 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    66991 
    66992 Chain information for AF3 E1 1-421.pdb #677 
    66993 --- 
    66994 Chain | Description 
    66995 A | No description available 
    66996  
    66997 
    66998 > matchmaker #677 to #1.15 & sel
    66999 
    67000 No 'to' model specified 
    67001 
    67002 > matchmaker #677 to #1.16 & sel
    67003 
    67004 Parameters 
    67005 --- 
    67006 Chain pairing | bb 
    67007 Alignment algorithm | Needleman-Wunsch 
    67008 Similarity matrix | BLOSUM-62 
    67009 SS fraction | 0.3 
    67010 Gap open (HH/SS/other) | 18/18/6 
    67011 Gap extend | 1 
    67012 SS matrix |  |  | H | S | O 
    67013 ---|---|---|--- 
    67014 H | 6 | -9 | -6 
    67015 S |  | 6 | -6 
    67016 O |  |  | 4 
    67017 Iteration cutoff | 2 
    67018  
    67019 Matchmaker 3j0c.pdb1, chain G (#1.16) with AF3 E1 1-421.pdb, chain A (#677),
    67020 sequence alignment score = 1060.7 
    67021 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    67022 2.985) 
    67023  
    67024 
    67025 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    67026 
    67027 Chain information for AF3 E1 422-461.pdb #678 
    67028 --- 
    67029 Chain | Description 
    67030 A | No description available 
    67031  
    67032 
    67033 > matchmaker #678 to #1.16 & sel
    67034 
    67035 Parameters 
    67036 --- 
    67037 Chain pairing | bb 
    67038 Alignment algorithm | Needleman-Wunsch 
    67039 Similarity matrix | BLOSUM-62 
    67040 SS fraction | 0.3 
    67041 Gap open (HH/SS/other) | 18/18/6 
    67042 Gap extend | 1 
    67043 SS matrix |  |  | H | S | O 
    67044 ---|---|---|--- 
    67045 H | 6 | -9 | -6 
    67046 S |  | 6 | -6 
    67047 O |  |  | 4 
    67048 Iteration cutoff | 2 
    67049  
    67050 Matchmaker 3j0c.pdb1, chain G (#1.16) with AF3 E1 422-461.pdb, chain A (#678),
    67051 sequence alignment score = 626.9 
    67052 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    67053 2.997) 
    67054  
    67055 
    67056 > hide sel cartoons
    67057 
    67058 > select #1.16/H
    67059 
    67060 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    67061 
    67062 > show sel cartoons
    67063 
    67064 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    67065 
    67066 Chain information for AF3 E2 1-352.pdb #679 
    67067 --- 
    67068 Chain | Description 
    67069 B | No description available 
    67070  
    67071 
    67072 > matchmaker #679 to #1.16 & sel
    67073 
    67074 Parameters 
    67075 --- 
    67076 Chain pairing | bb 
    67077 Alignment algorithm | Needleman-Wunsch 
    67078 Similarity matrix | BLOSUM-62 
    67079 SS fraction | 0.3 
    67080 Gap open (HH/SS/other) | 18/18/6 
    67081 Gap extend | 1 
    67082 SS matrix |  |  | H | S | O 
    67083 ---|---|---|--- 
    67084 H | 6 | -9 | -6 
    67085 S |  | 6 | -6 
    67086 O |  |  | 4 
    67087 Iteration cutoff | 2 
    67088  
    67089 Matchmaker 3j0c.pdb1, chain H (#1.16) with AF3 E2 1-352.pdb, chain B (#679),
    67090 sequence alignment score = 590.9 
    67091 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    67092 6.107) 
    67093  
    67094 
    67095 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    67096 
    67097 Chain information for AF3 E2 353-438.pdb #680 
    67098 --- 
    67099 Chain | Description 
    67100 B | No description available 
    67101  
    67102 
    67103 > matchmaker #680 to #1.16 & sel
    67104 
    67105 Parameters 
    67106 --- 
    67107 Chain pairing | bb 
    67108 Alignment algorithm | Needleman-Wunsch 
    67109 Similarity matrix | BLOSUM-62 
    67110 SS fraction | 0.3 
    67111 Gap open (HH/SS/other) | 18/18/6 
    67112 Gap extend | 1 
    67113 SS matrix |  |  | H | S | O 
    67114 ---|---|---|--- 
    67115 H | 6 | -9 | -6 
    67116 S |  | 6 | -6 
    67117 O |  |  | 4 
    67118 Iteration cutoff | 2 
    67119  
    67120 Matchmaker 3j0c.pdb1, chain H (#1.16) with AF3 E2 353-438.pdb, chain B (#680),
    67121 sequence alignment score = 329.4 
    67122 RMSD between 40 pruned atom pairs is 0.937 angstroms; (across all 84 pairs:
    67123 8.150) 
    67124  
    67125 
    67126 > hide sel cartoons
    67127 
    67128 > select #1.16/I
    67129 
    67130 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    67131 
    67132 > show sel cartoons
    67133 
    67134 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    67135 
    67136 Chain information for AF3 CA.pdb #681 
    67137 --- 
    67138 Chain | Description 
    67139 A | No description available 
    67140  
    67141 
    67142 > matchmaker #681 to #1.16 & sel
    67143 
    67144 Parameters 
    67145 --- 
    67146 Chain pairing | bb 
    67147 Alignment algorithm | Needleman-Wunsch 
    67148 Similarity matrix | BLOSUM-62 
    67149 SS fraction | 0.3 
    67150 Gap open (HH/SS/other) | 18/18/6 
    67151 Gap extend | 1 
    67152 SS matrix |  |  | H | S | O 
    67153 ---|---|---|--- 
    67154 H | 6 | -9 | -6 
    67155 S |  | 6 | -6 
    67156 O |  |  | 4 
    67157 Iteration cutoff | 2 
    67158  
    67159 Matchmaker 3j0c.pdb1, chain I (#1.16) with AF3 CA.pdb, chain A (#681),
    67160 sequence alignment score = 306.5 
    67161 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    67162 2.689) 
    67163  
    67164 
    67165 > hide sel cartoons
    67166 
    67167 > color #677 dodgerblue
    67168 
    67169 > color #678 dodgerblue
    67170 
    67171 > color #679 #00b305ff
    67172 
    67173 > color #680 dodgerblue
    67174 
    67175 > color #680 #00b305ff
    67176 
    67177 > color #681 #f15839ff
    67178 
    67179 > select #1.17/G
    67180 
    67181 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    67182 
    67183 > show sel cartoons
    67184 
    67185 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    67186 
    67187 Chain information for AF3 E1 1-421.pdb #682 
    67188 --- 
    67189 Chain | Description 
    67190 A | No description available 
    67191  
    67192 
    67193 > matchmaker #682 to #1.16 & sel
    67194 
    67195 No 'to' model specified 
    67196 
    67197 > matchmaker #682 to #1.17 & sel
    67198 
    67199 Parameters 
    67200 --- 
    67201 Chain pairing | bb 
    67202 Alignment algorithm | Needleman-Wunsch 
    67203 Similarity matrix | BLOSUM-62 
    67204 SS fraction | 0.3 
    67205 Gap open (HH/SS/other) | 18/18/6 
    67206 Gap extend | 1 
    67207 SS matrix |  |  | H | S | O 
    67208 ---|---|---|--- 
    67209 H | 6 | -9 | -6 
    67210 S |  | 6 | -6 
    67211 O |  |  | 4 
    67212 Iteration cutoff | 2 
    67213  
    67214 Matchmaker 3j0c.pdb1, chain G (#1.17) with AF3 E1 1-421.pdb, chain A (#682),
    67215 sequence alignment score = 1060.7 
    67216 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    67217 2.985) 
    67218  
    67219 
    67220 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    67221 
    67222 Chain information for AF3 E1 422-461.pdb #683 
    67223 --- 
    67224 Chain | Description 
    67225 A | No description available 
    67226  
    67227 
    67228 > matchmaker #683 to #1.17 & sel
    67229 
    67230 Parameters 
    67231 --- 
    67232 Chain pairing | bb 
    67233 Alignment algorithm | Needleman-Wunsch 
    67234 Similarity matrix | BLOSUM-62 
    67235 SS fraction | 0.3 
    67236 Gap open (HH/SS/other) | 18/18/6 
    67237 Gap extend | 1 
    67238 SS matrix |  |  | H | S | O 
    67239 ---|---|---|--- 
    67240 H | 6 | -9 | -6 
    67241 S |  | 6 | -6 
    67242 O |  |  | 4 
    67243 Iteration cutoff | 2 
    67244  
    67245 Matchmaker 3j0c.pdb1, chain G (#1.17) with AF3 E1 422-461.pdb, chain A (#683),
    67246 sequence alignment score = 626.9 
    67247 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    67248 2.997) 
    67249  
    67250 
    67251 > hide sel cartoons
    67252 
    67253 > select #1.17/H
    67254 
    67255 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    67256 
    67257 > show sel cartoons
    67258 
    67259 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    67260 
    67261 Chain information for AF3 E2 1-352.pdb #684 
    67262 --- 
    67263 Chain | Description 
    67264 B | No description available 
    67265  
    67266 
    67267 > matchmaker #684 to #1.17 & sel
    67268 
    67269 Parameters 
    67270 --- 
    67271 Chain pairing | bb 
    67272 Alignment algorithm | Needleman-Wunsch 
    67273 Similarity matrix | BLOSUM-62 
    67274 SS fraction | 0.3 
    67275 Gap open (HH/SS/other) | 18/18/6 
    67276 Gap extend | 1 
    67277 SS matrix |  |  | H | S | O 
    67278 ---|---|---|--- 
    67279 H | 6 | -9 | -6 
    67280 S |  | 6 | -6 
    67281 O |  |  | 4 
    67282 Iteration cutoff | 2 
    67283  
    67284 Matchmaker 3j0c.pdb1, chain H (#1.17) with AF3 E2 1-352.pdb, chain B (#684),
    67285 sequence alignment score = 590.9 
    67286 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    67287 6.107) 
    67288  
    67289 
    67290 > hide sel cartoons
    67291 
    67292 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    67293 
    67294 Chain information for AF3 E2 353-438.pdb #685 
    67295 --- 
    67296 Chain | Description 
    67297 B | No description available 
    67298  
    67299 
    67300 > matchmaker #685 to #1.17 & sel
    67301 
    67302 Parameters 
    67303 --- 
    67304 Chain pairing | bb 
    67305 Alignment algorithm | Needleman-Wunsch 
    67306 Similarity matrix | BLOSUM-62 
    67307 SS fraction | 0.3 
    67308 Gap open (HH/SS/other) | 18/18/6 
    67309 Gap extend | 1 
    67310 SS matrix |  |  | H | S | O 
    67311 ---|---|---|--- 
    67312 H | 6 | -9 | -6 
    67313 S |  | 6 | -6 
    67314 O |  |  | 4 
    67315 Iteration cutoff | 2 
    67316  
    67317 Matchmaker 3j0c.pdb1, chain H (#1.17) with AF3 E2 353-438.pdb, chain B (#685),
    67318 sequence alignment score = 329.4 
    67319 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    67320 8.150) 
    67321  
    67322 
    67323 > select #1.17/I
    67324 
    67325 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    67326 
    67327 > show sel cartoons
    67328 
    67329 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    67330 
    67331 Chain information for AF3 CA.pdb #686 
    67332 --- 
    67333 Chain | Description 
    67334 A | No description available 
    67335  
    67336 
    67337 > matchmaker #686 to #1.17 & sel
    67338 
    67339 Parameters 
    67340 --- 
    67341 Chain pairing | bb 
    67342 Alignment algorithm | Needleman-Wunsch 
    67343 Similarity matrix | BLOSUM-62 
    67344 SS fraction | 0.3 
    67345 Gap open (HH/SS/other) | 18/18/6 
    67346 Gap extend | 1 
    67347 SS matrix |  |  | H | S | O 
    67348 ---|---|---|--- 
    67349 H | 6 | -9 | -6 
    67350 S |  | 6 | -6 
    67351 O |  |  | 4 
    67352 Iteration cutoff | 2 
    67353  
    67354 Matchmaker 3j0c.pdb1, chain I (#1.17) with AF3 CA.pdb, chain A (#686),
    67355 sequence alignment score = 306.5 
    67356 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    67357 2.689) 
    67358  
    67359 
    67360 > hide sel cartoons
    67361 
    67362 > color #682 dodgerblue
    67363 
    67364 > color #683 dodgerblue
    67365 
    67366 > color #684 #00b305ff
    67367 
    67368 > color #685 #00b305ff
    67369 
    67370 > color #686 #f15839ff
    67371 
    67372 > select #1.18/G
    67373 
    67374 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    67375 
    67376 > show sel cartoons
    67377 
    67378 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    67379 
    67380 Chain information for AF3 E1 1-421.pdb #687 
    67381 --- 
    67382 Chain | Description 
    67383 A | No description available 
    67384  
    67385 
    67386 > matchmaker #687 to #1.18 & sel
    67387 
    67388 Parameters 
    67389 --- 
    67390 Chain pairing | bb 
    67391 Alignment algorithm | Needleman-Wunsch 
    67392 Similarity matrix | BLOSUM-62 
    67393 SS fraction | 0.3 
    67394 Gap open (HH/SS/other) | 18/18/6 
    67395 Gap extend | 1 
    67396 SS matrix |  |  | H | S | O 
    67397 ---|---|---|--- 
    67398 H | 6 | -9 | -6 
    67399 S |  | 6 | -6 
    67400 O |  |  | 4 
    67401 Iteration cutoff | 2 
    67402  
    67403 Matchmaker 3j0c.pdb1, chain G (#1.18) with AF3 E1 1-421.pdb, chain A (#687),
    67404 sequence alignment score = 1060.7 
    67405 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    67406 2.985) 
    67407  
    67408 
    67409 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    67410 
    67411 Chain information for AF3 E1 422-461.pdb #688 
    67412 --- 
    67413 Chain | Description 
    67414 A | No description available 
    67415  
    67416 
    67417 > matchmaker #688 to #1.18 & sel
    67418 
    67419 Parameters 
    67420 --- 
    67421 Chain pairing | bb 
    67422 Alignment algorithm | Needleman-Wunsch 
    67423 Similarity matrix | BLOSUM-62 
    67424 SS fraction | 0.3 
    67425 Gap open (HH/SS/other) | 18/18/6 
    67426 Gap extend | 1 
    67427 SS matrix |  |  | H | S | O 
    67428 ---|---|---|--- 
    67429 H | 6 | -9 | -6 
    67430 S |  | 6 | -6 
    67431 O |  |  | 4 
    67432 Iteration cutoff | 2 
    67433  
    67434 Matchmaker 3j0c.pdb1, chain G (#1.18) with AF3 E1 422-461.pdb, chain A (#688),
    67435 sequence alignment score = 626.9 
    67436 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    67437 2.997) 
    67438  
    67439 
    67440 > hide sel cartoons
    67441 
    67442 > select #1.18/H
    67443 
    67444 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    67445 
    67446 > show sel cartoons
    67447 
    67448 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    67449 
    67450 Chain information for AF3 E2 1-352.pdb #689 
    67451 --- 
    67452 Chain | Description 
    67453 B | No description available 
    67454  
    67455 
    67456 > matchmaker #689 to #1.18 & sel
    67457 
    67458 Parameters 
    67459 --- 
    67460 Chain pairing | bb 
    67461 Alignment algorithm | Needleman-Wunsch 
    67462 Similarity matrix | BLOSUM-62 
    67463 SS fraction | 0.3 
    67464 Gap open (HH/SS/other) | 18/18/6 
    67465 Gap extend | 1 
    67466 SS matrix |  |  | H | S | O 
    67467 ---|---|---|--- 
    67468 H | 6 | -9 | -6 
    67469 S |  | 6 | -6 
    67470 O |  |  | 4 
    67471 Iteration cutoff | 2 
    67472  
    67473 Matchmaker 3j0c.pdb1, chain H (#1.18) with AF3 E2 1-352.pdb, chain B (#689),
    67474 sequence alignment score = 590.9 
    67475 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    67476 6.107) 
    67477  
    67478 
    67479 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    67480 
    67481 Chain information for AF3 E2 353-438.pdb #690 
    67482 --- 
    67483 Chain | Description 
    67484 B | No description available 
    67485  
    67486 
    67487 > matchmaker #690 to #1.18 & sel
    67488 
    67489 Parameters 
    67490 --- 
    67491 Chain pairing | bb 
    67492 Alignment algorithm | Needleman-Wunsch 
    67493 Similarity matrix | BLOSUM-62 
    67494 SS fraction | 0.3 
    67495 Gap open (HH/SS/other) | 18/18/6 
    67496 Gap extend | 1 
    67497 SS matrix |  |  | H | S | O 
    67498 ---|---|---|--- 
    67499 H | 6 | -9 | -6 
    67500 S |  | 6 | -6 
    67501 O |  |  | 4 
    67502 Iteration cutoff | 2 
    67503  
    67504 Matchmaker 3j0c.pdb1, chain H (#1.18) with AF3 E2 353-438.pdb, chain B (#690),
    67505 sequence alignment score = 329.4 
    67506 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    67507 8.150) 
    67508  
    67509 
    67510 > hide sel cartoons
    67511 
    67512 > select #1.18/I
    67513 
    67514 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    67515 
    67516 > show sel cartoons
    67517 
    67518 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    67519 
    67520 Chain information for AF3 CA.pdb #691 
    67521 --- 
    67522 Chain | Description 
    67523 A | No description available 
    67524  
    67525 
    67526 > matchmaker #691 to #1.18 & sel
    67527 
    67528 Parameters 
    67529 --- 
    67530 Chain pairing | bb 
    67531 Alignment algorithm | Needleman-Wunsch 
    67532 Similarity matrix | BLOSUM-62 
    67533 SS fraction | 0.3 
    67534 Gap open (HH/SS/other) | 18/18/6 
    67535 Gap extend | 1 
    67536 SS matrix |  |  | H | S | O 
    67537 ---|---|---|--- 
    67538 H | 6 | -9 | -6 
    67539 S |  | 6 | -6 
    67540 O |  |  | 4 
    67541 Iteration cutoff | 2 
    67542  
    67543 Matchmaker 3j0c.pdb1, chain I (#1.18) with AF3 CA.pdb, chain A (#691),
    67544 sequence alignment score = 306.5 
    67545 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    67546 2.689) 
    67547  
    67548 
    67549 > hide sel cartoons
    67550 
    67551 > color #687 dodgerblue
    67552 
    67553 > color #688 dodgerblue
    67554 
    67555 > color #689 #00b305ff
    67556 
    67557 > color #690 #00b305ff
    67558 
    67559 > color #691 #f15839ff
    67560 
    67561 > select #1.19/G
    67562 
    67563 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    67564 
    67565 > show sel cartoons
    67566 
    67567 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    67568 
    67569 Chain information for AF3 E1 1-421.pdb #692 
    67570 --- 
    67571 Chain | Description 
    67572 A | No description available 
    67573  
    67574 
    67575 > matchmaker #692 to #1.18 & sel
    67576 
    67577 No 'to' model specified 
    67578 
    67579 > matchmaker #692 to #1.19 & sel
    67580 
    67581 Parameters 
    67582 --- 
    67583 Chain pairing | bb 
    67584 Alignment algorithm | Needleman-Wunsch 
    67585 Similarity matrix | BLOSUM-62 
    67586 SS fraction | 0.3 
    67587 Gap open (HH/SS/other) | 18/18/6 
    67588 Gap extend | 1 
    67589 SS matrix |  |  | H | S | O 
    67590 ---|---|---|--- 
    67591 H | 6 | -9 | -6 
    67592 S |  | 6 | -6 
    67593 O |  |  | 4 
    67594 Iteration cutoff | 2 
    67595  
    67596 Matchmaker 3j0c.pdb1, chain G (#1.19) with AF3 E1 1-421.pdb, chain A (#692),
    67597 sequence alignment score = 1060.7 
    67598 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    67599 2.985) 
    67600  
    67601 
    67602 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    67603 
    67604 Chain information for AF3 E1 422-461.pdb #693 
    67605 --- 
    67606 Chain | Description 
    67607 A | No description available 
    67608  
    67609 
    67610 > matchmaker #693 to #1.19 & sel
    67611 
    67612 Parameters 
    67613 --- 
    67614 Chain pairing | bb 
    67615 Alignment algorithm | Needleman-Wunsch 
    67616 Similarity matrix | BLOSUM-62 
    67617 SS fraction | 0.3 
    67618 Gap open (HH/SS/other) | 18/18/6 
    67619 Gap extend | 1 
    67620 SS matrix |  |  | H | S | O 
    67621 ---|---|---|--- 
    67622 H | 6 | -9 | -6 
    67623 S |  | 6 | -6 
    67624 O |  |  | 4 
    67625 Iteration cutoff | 2 
    67626  
    67627 Matchmaker 3j0c.pdb1, chain G (#1.19) with AF3 E1 422-461.pdb, chain A (#693),
    67628 sequence alignment score = 626.9 
    67629 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    67630 2.997) 
    67631  
    67632 
    67633 > hide sel cartoons
    67634 
    67635 > select #1.19/H
    67636 
    67637 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    67638 
    67639 > show sel cartoons
    67640 
    67641 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    67642 
    67643 Chain information for AF3 E2 1-352.pdb #694 
    67644 --- 
    67645 Chain | Description 
    67646 B | No description available 
    67647  
    67648 
    67649 > matchmaker #694 to #1.19 & sel
    67650 
    67651 Parameters 
    67652 --- 
    67653 Chain pairing | bb 
    67654 Alignment algorithm | Needleman-Wunsch 
    67655 Similarity matrix | BLOSUM-62 
    67656 SS fraction | 0.3 
    67657 Gap open (HH/SS/other) | 18/18/6 
    67658 Gap extend | 1 
    67659 SS matrix |  |  | H | S | O 
    67660 ---|---|---|--- 
    67661 H | 6 | -9 | -6 
    67662 S |  | 6 | -6 
    67663 O |  |  | 4 
    67664 Iteration cutoff | 2 
    67665  
    67666 Matchmaker 3j0c.pdb1, chain H (#1.19) with AF3 E2 1-352.pdb, chain B (#694),
    67667 sequence alignment score = 590.9 
    67668 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    67669 6.107) 
    67670  
    67671 
    67672 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    67673 
    67674 Chain information for AF3 E2 353-438.pdb #695 
    67675 --- 
    67676 Chain | Description 
    67677 B | No description available 
    67678  
    67679 
    67680 > matchmaker #695 to #1.19 & sel
    67681 
    67682 Parameters 
    67683 --- 
    67684 Chain pairing | bb 
    67685 Alignment algorithm | Needleman-Wunsch 
    67686 Similarity matrix | BLOSUM-62 
    67687 SS fraction | 0.3 
    67688 Gap open (HH/SS/other) | 18/18/6 
    67689 Gap extend | 1 
    67690 SS matrix |  |  | H | S | O 
    67691 ---|---|---|--- 
    67692 H | 6 | -9 | -6 
    67693 S |  | 6 | -6 
    67694 O |  |  | 4 
    67695 Iteration cutoff | 2 
    67696  
    67697 Matchmaker 3j0c.pdb1, chain H (#1.19) with AF3 E2 353-438.pdb, chain B (#695),
    67698 sequence alignment score = 329.4 
    67699 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    67700 8.150) 
    67701  
    67702 
    67703 > hide sel cartoons
    67704 
    67705 > select #1.19/I
    67706 
    67707 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    67708 
    67709 > show sel cartoons
    67710 
    67711 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    67712 
    67713 Chain information for AF3 CA.pdb #696 
    67714 --- 
    67715 Chain | Description 
    67716 A | No description available 
    67717  
    67718 
    67719 > matchmaker #696 to #1.19 & sel
    67720 
    67721 Parameters 
    67722 --- 
    67723 Chain pairing | bb 
    67724 Alignment algorithm | Needleman-Wunsch 
    67725 Similarity matrix | BLOSUM-62 
    67726 SS fraction | 0.3 
    67727 Gap open (HH/SS/other) | 18/18/6 
    67728 Gap extend | 1 
    67729 SS matrix |  |  | H | S | O 
    67730 ---|---|---|--- 
    67731 H | 6 | -9 | -6 
    67732 S |  | 6 | -6 
    67733 O |  |  | 4 
    67734 Iteration cutoff | 2 
    67735  
    67736 Matchmaker 3j0c.pdb1, chain I (#1.19) with AF3 CA.pdb, chain A (#696),
    67737 sequence alignment score = 306.5 
    67738 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    67739 2.689) 
    67740  
    67741 
    67742 > hide sel cartoons
    67743 
    67744 > color #692 dodgerblue
    67745 
    67746 > color #693 dodgerblue
    67747 
    67748 > color #694 #00b305ff
    67749 
    67750 > color #695 #00b305ff
    67751 
    67752 > color #696 #f15839ff
    67753 
    67754 > select #1.20/G
    67755 
    67756 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    67757 
    67758 > show sel cartoons
    67759 
    67760 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    67761 
    67762 Chain information for AF3 E1 1-421.pdb #697 
    67763 --- 
    67764 Chain | Description 
    67765 A | No description available 
    67766  
    67767 
    67768 > matchmaker #697 to #1.20 & sel
    67769 
    67770 Parameters 
    67771 --- 
    67772 Chain pairing | bb 
    67773 Alignment algorithm | Needleman-Wunsch 
    67774 Similarity matrix | BLOSUM-62 
    67775 SS fraction | 0.3 
    67776 Gap open (HH/SS/other) | 18/18/6 
    67777 Gap extend | 1 
    67778 SS matrix |  |  | H | S | O 
    67779 ---|---|---|--- 
    67780 H | 6 | -9 | -6 
    67781 S |  | 6 | -6 
    67782 O |  |  | 4 
    67783 Iteration cutoff | 2 
    67784  
    67785 Matchmaker 3j0c.pdb1, chain G (#1.20) with AF3 E1 1-421.pdb, chain A (#697),
    67786 sequence alignment score = 1060.7 
    67787 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    67788 2.985) 
    67789  
    67790 
    67791 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    67792 
    67793 Chain information for AF3 E1 422-461.pdb #698 
    67794 --- 
    67795 Chain | Description 
    67796 A | No description available 
    67797  
    67798 
    67799 > matchmaker #698 to #1.20 & sel
    67800 
    67801 Parameters 
    67802 --- 
    67803 Chain pairing | bb 
    67804 Alignment algorithm | Needleman-Wunsch 
    67805 Similarity matrix | BLOSUM-62 
    67806 SS fraction | 0.3 
    67807 Gap open (HH/SS/other) | 18/18/6 
    67808 Gap extend | 1 
    67809 SS matrix |  |  | H | S | O 
    67810 ---|---|---|--- 
    67811 H | 6 | -9 | -6 
    67812 S |  | 6 | -6 
    67813 O |  |  | 4 
    67814 Iteration cutoff | 2 
    67815  
    67816 Matchmaker 3j0c.pdb1, chain G (#1.20) with AF3 E1 422-461.pdb, chain A (#698),
    67817 sequence alignment score = 626.9 
    67818 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    67819 2.997) 
    67820  
    67821 
    67822 > hide sel cartoons
    67823 
    67824 > select #1.20/H
    67825 
    67826 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    67827 
    67828 > show sel cartoons
    67829 
    67830 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    67831 
    67832 Chain information for AF3 E2 1-352.pdb #699 
    67833 --- 
    67834 Chain | Description 
    67835 B | No description available 
    67836  
    67837 
    67838 > matchmaker #699 to #1.20 & sel
    67839 
    67840 Parameters 
    67841 --- 
    67842 Chain pairing | bb 
    67843 Alignment algorithm | Needleman-Wunsch 
    67844 Similarity matrix | BLOSUM-62 
    67845 SS fraction | 0.3 
    67846 Gap open (HH/SS/other) | 18/18/6 
    67847 Gap extend | 1 
    67848 SS matrix |  |  | H | S | O 
    67849 ---|---|---|--- 
    67850 H | 6 | -9 | -6 
    67851 S |  | 6 | -6 
    67852 O |  |  | 4 
    67853 Iteration cutoff | 2 
    67854  
    67855 Matchmaker 3j0c.pdb1, chain H (#1.20) with AF3 E2 1-352.pdb, chain B (#699),
    67856 sequence alignment score = 590.9 
    67857 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    67858 6.107) 
    67859  
    67860 
    67861 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    67862 
    67863 Chain information for AF3 E2 353-438.pdb #700 
    67864 --- 
    67865 Chain | Description 
    67866 B | No description available 
    67867  
    67868 
    67869 > matchmaker #700 to #1.20 & sel
    67870 
    67871 Parameters 
    67872 --- 
    67873 Chain pairing | bb 
    67874 Alignment algorithm | Needleman-Wunsch 
    67875 Similarity matrix | BLOSUM-62 
    67876 SS fraction | 0.3 
    67877 Gap open (HH/SS/other) | 18/18/6 
    67878 Gap extend | 1 
    67879 SS matrix |  |  | H | S | O 
    67880 ---|---|---|--- 
    67881 H | 6 | -9 | -6 
    67882 S |  | 6 | -6 
    67883 O |  |  | 4 
    67884 Iteration cutoff | 2 
    67885  
    67886 Matchmaker 3j0c.pdb1, chain H (#1.20) with AF3 E2 353-438.pdb, chain B (#700),
    67887 sequence alignment score = 329.4 
    67888 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    67889 8.150) 
    67890  
    67891 
    67892 > hide sel cartoons
    67893 
    67894 > select #1.20/I
    67895 
    67896 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    67897 
    67898 > show sel cartoons
    67899 
    67900 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    67901 
    67902 Chain information for AF3 CA.pdb #701 
    67903 --- 
    67904 Chain | Description 
    67905 A | No description available 
    67906  
    67907 
    67908 > matchmaker #701 to #1.20 & sel
    67909 
    67910 Parameters 
    67911 --- 
    67912 Chain pairing | bb 
    67913 Alignment algorithm | Needleman-Wunsch 
    67914 Similarity matrix | BLOSUM-62 
    67915 SS fraction | 0.3 
    67916 Gap open (HH/SS/other) | 18/18/6 
    67917 Gap extend | 1 
    67918 SS matrix |  |  | H | S | O 
    67919 ---|---|---|--- 
    67920 H | 6 | -9 | -6 
    67921 S |  | 6 | -6 
    67922 O |  |  | 4 
    67923 Iteration cutoff | 2 
    67924  
    67925 Matchmaker 3j0c.pdb1, chain I (#1.20) with AF3 CA.pdb, chain A (#701),
    67926 sequence alignment score = 306.5 
    67927 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    67928 2.689) 
    67929  
    67930 
    67931 > hide sel cartoons
    67932 
    67933 > color #697 dodgerblue
    67934 
    67935 > color #698 dodgerblue
    67936 
    67937 > color #699 #00b305ff
    67938 
    67939 > color #700 #00b305ff
    67940 
    67941 > color #701 #f15839ff
    67942 
    67943 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    67944 
    67945 > hide #652 models
    67946 
    67947 > hide #653 models
    67948 
    67949 > hide #654 models
    67950 
    67951 > hide #655 models
    67952 
    67953 > hide #656 models
    67954 
    67955 > hide #657 models
    67956 
    67957 > hide #658 models
    67958 
    67959 > hide #660 models
    67960 
    67961 > hide #661 models
    67962 
    67963 > hide #659 models
    67964 
    67965 > hide #662 models
    67966 
    67967 > hide #663 models
    67968 
    67969 > hide #664 models
    67970 
    67971 > hide #665 models
    67972 
    67973 > hide #666 models
    67974 
    67975 > hide #667 models
    67976 
    67977 > hide #668 models
    67978 
    67979 > hide #669 models
    67980 
    67981 > hide #670 models
    67982 
    67983 > hide #671 models
    67984 
    67985 > hide #672 models
    67986 
    67987 > hide #673 models
    67988 
    67989 > hide #674 models
    67990 
    67991 > hide #675 models
    67992 
    67993 > hide #676 models
    67994 
    67995 > hide #677 models
    67996 
    67997 > hide #678 models
    67998 
    67999 > hide #679 models
    68000 
    68001 > hide #680 models
    68002 
    68003 > hide #681 models
    68004 
    68005 > hide #682 models
    68006 
    68007 > hide #683 models
    68008 
    68009 > hide #684 models
    68010 
    68011 > hide #685 models
    68012 
    68013 > hide #686 models
    68014 
    68015 > hide #687 models
    68016 
    68017 > hide #688 models
    68018 
    68019 > hide #689 models
    68020 
    68021 > hide #690 models
    68022 
    68023 > hide #691 models
    68024 
    68025 > hide #692 models
    68026 
    68027 > hide #693 models
    68028 
    68029 > hide #694 models
    68030 
    68031 > hide #695 models
    68032 
    68033 > hide #696 models
    68034 
    68035 > hide #697 models
    68036 
    68037 > hide #698 models
    68038 
    68039 > hide #699 models
    68040 
    68041 > hide #700 models
    68042 
    68043 > hide #701 models
    68044 
    68045 > select #1.21/G
    68046 
    68047 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    68048 
    68049 > show sel cartoons
    68050 
    68051 > view
    68052 
    68053 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    68054 
    68055 Chain information for AF3 E1 1-421.pdb #702 
    68056 --- 
    68057 Chain | Description 
    68058 A | No description available 
    68059  
    68060 
    68061 > matchmaker #702 to #1.21 & sel
    68062 
    68063 Parameters 
    68064 --- 
    68065 Chain pairing | bb 
    68066 Alignment algorithm | Needleman-Wunsch 
    68067 Similarity matrix | BLOSUM-62 
    68068 SS fraction | 0.3 
    68069 Gap open (HH/SS/other) | 18/18/6 
    68070 Gap extend | 1 
    68071 SS matrix |  |  | H | S | O 
    68072 ---|---|---|--- 
    68073 H | 6 | -9 | -6 
    68074 S |  | 6 | -6 
    68075 O |  |  | 4 
    68076 Iteration cutoff | 2 
    68077  
    68078 Matchmaker 3j0c.pdb1, chain G (#1.21) with AF3 E1 1-421.pdb, chain A (#702),
    68079 sequence alignment score = 1060.7 
    68080 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    68081 2.985) 
    68082  
    68083 
    68084 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    68085 
    68086 Chain information for AF3 E1 422-461.pdb #703 
    68087 --- 
    68088 Chain | Description 
    68089 A | No description available 
    68090  
    68091 
    68092 > matchmaker #703 to #1.21 & sel
    68093 
    68094 Parameters 
    68095 --- 
    68096 Chain pairing | bb 
    68097 Alignment algorithm | Needleman-Wunsch 
    68098 Similarity matrix | BLOSUM-62 
    68099 SS fraction | 0.3 
    68100 Gap open (HH/SS/other) | 18/18/6 
    68101 Gap extend | 1 
    68102 SS matrix |  |  | H | S | O 
    68103 ---|---|---|--- 
    68104 H | 6 | -9 | -6 
    68105 S |  | 6 | -6 
    68106 O |  |  | 4 
    68107 Iteration cutoff | 2 
    68108  
    68109 Matchmaker 3j0c.pdb1, chain G (#1.21) with AF3 E1 422-461.pdb, chain A (#703),
    68110 sequence alignment score = 626.9 
    68111 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    68112 2.997) 
    68113  
    68114 
    68115 > select #1.21/H
    68116 
    68117 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    68118 
    68119 > show sel cartoons
    68120 
    68121 [Repeated 1 time(s)]
    68122 
    68123 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    68124 
    68125 Chain information for AF3 E2 1-352.pdb #704 
    68126 --- 
    68127 Chain | Description 
    68128 B | No description available 
    68129  
    68130 
    68131 > matchmaker #704 to #1.21 & sel
    68132 
    68133 Parameters 
    68134 --- 
    68135 Chain pairing | bb 
    68136 Alignment algorithm | Needleman-Wunsch 
    68137 Similarity matrix | BLOSUM-62 
    68138 SS fraction | 0.3 
    68139 Gap open (HH/SS/other) | 18/18/6 
    68140 Gap extend | 1 
    68141 SS matrix |  |  | H | S | O 
    68142 ---|---|---|--- 
    68143 H | 6 | -9 | -6 
    68144 S |  | 6 | -6 
    68145 O |  |  | 4 
    68146 Iteration cutoff | 2 
    68147  
    68148 Matchmaker 3j0c.pdb1, chain H (#1.21) with AF3 E2 1-352.pdb, chain B (#704),
    68149 sequence alignment score = 590.9 
    68150 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    68151 6.107) 
    68152  
    68153 
    68154 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    68155 
    68156 Chain information for AF3 E2 353-438.pdb #705 
    68157 --- 
    68158 Chain | Description 
    68159 B | No description available 
    68160  
    68161 
    68162 > matchmaker #705 to #1.21 & sel
    68163 
    68164 Parameters 
    68165 --- 
    68166 Chain pairing | bb 
    68167 Alignment algorithm | Needleman-Wunsch 
    68168 Similarity matrix | BLOSUM-62 
    68169 SS fraction | 0.3 
    68170 Gap open (HH/SS/other) | 18/18/6 
    68171 Gap extend | 1 
    68172 SS matrix |  |  | H | S | O 
    68173 ---|---|---|--- 
    68174 H | 6 | -9 | -6 
    68175 S |  | 6 | -6 
    68176 O |  |  | 4 
    68177 Iteration cutoff | 2 
    68178  
    68179 Matchmaker 3j0c.pdb1, chain H (#1.21) with AF3 E2 353-438.pdb, chain B (#705),
    68180 sequence alignment score = 329.4 
    68181 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    68182 8.150) 
    68183  
    68184 
    68185 > hide sel cartoons
    68186 
    68187 > select #1.21/G
    68188 
    68189 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    68190 
    68191 > hide sel cartoons
    68192 
    68193 > select #1.21/I
    68194 
    68195 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    68196 
    68197 > show sel cartoons
    68198 
    68199 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    68200 
    68201 Chain information for AF3 CA.pdb #706 
    68202 --- 
    68203 Chain | Description 
    68204 A | No description available 
    68205  
    68206 
    68207 > matchmaker #706 to #1.21 & sel
    68208 
    68209 Parameters 
    68210 --- 
    68211 Chain pairing | bb 
    68212 Alignment algorithm | Needleman-Wunsch 
    68213 Similarity matrix | BLOSUM-62 
    68214 SS fraction | 0.3 
    68215 Gap open (HH/SS/other) | 18/18/6 
    68216 Gap extend | 1 
    68217 SS matrix |  |  | H | S | O 
    68218 ---|---|---|--- 
    68219 H | 6 | -9 | -6 
    68220 S |  | 6 | -6 
    68221 O |  |  | 4 
    68222 Iteration cutoff | 2 
    68223  
    68224 Matchmaker 3j0c.pdb1, chain I (#1.21) with AF3 CA.pdb, chain A (#706),
    68225 sequence alignment score = 306.5 
    68226 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    68227 2.689) 
    68228  
    68229 
    68230 > hide sel cartoons
    68231 
    68232 > color #702 dodgerblue
    68233 
    68234 > color #703 dodgerblue
    68235 
    68236 > color #704 #00b305ff
    68237 
    68238 > color #705 #00b305ff
    68239 
    68240 > color #706 #f15839ff
    68241 
    68242 > select #1.22/G
    68243 
    68244 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    68245 
    68246 > show sel cartoons
    68247 
    68248 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    68249 
    68250 Chain information for AF3 E1 1-421.pdb #707 
    68251 --- 
    68252 Chain | Description 
    68253 A | No description available 
    68254  
    68255 
    68256 > matchmaker #707 to #1.22 & sel
    68257 
    68258 Parameters 
    68259 --- 
    68260 Chain pairing | bb 
    68261 Alignment algorithm | Needleman-Wunsch 
    68262 Similarity matrix | BLOSUM-62 
    68263 SS fraction | 0.3 
    68264 Gap open (HH/SS/other) | 18/18/6 
    68265 Gap extend | 1 
    68266 SS matrix |  |  | H | S | O 
    68267 ---|---|---|--- 
    68268 H | 6 | -9 | -6 
    68269 S |  | 6 | -6 
    68270 O |  |  | 4 
    68271 Iteration cutoff | 2 
    68272  
    68273 Matchmaker 3j0c.pdb1, chain G (#1.22) with AF3 E1 1-421.pdb, chain A (#707),
    68274 sequence alignment score = 1060.7 
    68275 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    68276 2.985) 
    68277  
    68278 
    68279 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    68280 
    68281 Chain information for AF3 E1 422-461.pdb #708 
    68282 --- 
    68283 Chain | Description 
    68284 A | No description available 
    68285  
    68286 
    68287 > matchmaker #708 to #1.22 & sel
    68288 
    68289 Parameters 
    68290 --- 
    68291 Chain pairing | bb 
    68292 Alignment algorithm | Needleman-Wunsch 
    68293 Similarity matrix | BLOSUM-62 
    68294 SS fraction | 0.3 
    68295 Gap open (HH/SS/other) | 18/18/6 
    68296 Gap extend | 1 
    68297 SS matrix |  |  | H | S | O 
    68298 ---|---|---|--- 
    68299 H | 6 | -9 | -6 
    68300 S |  | 6 | -6 
    68301 O |  |  | 4 
    68302 Iteration cutoff | 2 
    68303  
    68304 Matchmaker 3j0c.pdb1, chain G (#1.22) with AF3 E1 422-461.pdb, chain A (#708),
    68305 sequence alignment score = 626.9 
    68306 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    68307 2.996) 
    68308  
    68309 
    68310 > hide sel cartoons
    68311 
    68312 > select #1.21/H
    68313 
    68314 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    68315 
    68316 > show sel cartoons
    68317 
    68318 > hide sel cartoons
    68319 
    68320 > select #1.22/H
    68321 
    68322 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    68323 
    68324 > show sel cartoons
    68325 
    68326 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    68327 
    68328 Chain information for AF3 E2 1-352.pdb #709 
    68329 --- 
    68330 Chain | Description 
    68331 B | No description available 
    68332  
    68333 
    68334 > matchmaker #709 to #1.22 & sel
    68335 
    68336 Parameters 
    68337 --- 
    68338 Chain pairing | bb 
    68339 Alignment algorithm | Needleman-Wunsch 
    68340 Similarity matrix | BLOSUM-62 
    68341 SS fraction | 0.3 
    68342 Gap open (HH/SS/other) | 18/18/6 
    68343 Gap extend | 1 
    68344 SS matrix |  |  | H | S | O 
    68345 ---|---|---|--- 
    68346 H | 6 | -9 | -6 
    68347 S |  | 6 | -6 
    68348 O |  |  | 4 
    68349 Iteration cutoff | 2 
    68350  
    68351 Matchmaker 3j0c.pdb1, chain H (#1.22) with AF3 E2 1-352.pdb, chain B (#709),
    68352 sequence alignment score = 590.9 
    68353 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    68354 6.107) 
    68355  
    68356 
    68357 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    68358 
    68359 Chain information for AF3 E2 353-438.pdb #710 
    68360 --- 
    68361 Chain | Description 
    68362 B | No description available 
    68363  
    68364 
    68365 > matchmaker #710 to #1.22 & sel
    68366 
    68367 Parameters 
    68368 --- 
    68369 Chain pairing | bb 
    68370 Alignment algorithm | Needleman-Wunsch 
    68371 Similarity matrix | BLOSUM-62 
    68372 SS fraction | 0.3 
    68373 Gap open (HH/SS/other) | 18/18/6 
    68374 Gap extend | 1 
    68375 SS matrix |  |  | H | S | O 
    68376 ---|---|---|--- 
    68377 H | 6 | -9 | -6 
    68378 S |  | 6 | -6 
    68379 O |  |  | 4 
    68380 Iteration cutoff | 2 
    68381  
    68382 Matchmaker 3j0c.pdb1, chain H (#1.22) with AF3 E2 353-438.pdb, chain B (#710),
    68383 sequence alignment score = 329.4 
    68384 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    68385 8.151) 
    68386  
    68387 
    68388 > hide sel cartoons
    68389 
    68390 > select #1.22/I
    68391 
    68392 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    68393 
    68394 > show sel cartoons
    68395 
    68396 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    68397 
    68398 Chain information for AF3 CA.pdb #711 
    68399 --- 
    68400 Chain | Description 
    68401 A | No description available 
    68402  
    68403 
    68404 > matchmaker #711 to #1.22 & sel
    68405 
    68406 Parameters 
    68407 --- 
    68408 Chain pairing | bb 
    68409 Alignment algorithm | Needleman-Wunsch 
    68410 Similarity matrix | BLOSUM-62 
    68411 SS fraction | 0.3 
    68412 Gap open (HH/SS/other) | 18/18/6 
    68413 Gap extend | 1 
    68414 SS matrix |  |  | H | S | O 
    68415 ---|---|---|--- 
    68416 H | 6 | -9 | -6 
    68417 S |  | 6 | -6 
    68418 O |  |  | 4 
    68419 Iteration cutoff | 2 
    68420  
    68421 Matchmaker 3j0c.pdb1, chain I (#1.22) with AF3 CA.pdb, chain A (#711),
    68422 sequence alignment score = 306.5 
    68423 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    68424 2.689) 
    68425  
    68426 
    68427 > hide sel cartoons
    68428 
    68429 > color #707 dodgerblue
    68430 
    68431 > color #708 dodgerblue
    68432 
    68433 > color #709 #00b305ff
    68434 
    68435 > color #710 #00b305ff
    68436 
    68437 > color #711 #f15839ff
    68438 
    68439 > select #1.23/G
    68440 
    68441 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    68442 
    68443 > show sel cartoons
    68444 
    68445 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    68446 
    68447 Chain information for AF3 E1 1-421.pdb #712 
    68448 --- 
    68449 Chain | Description 
    68450 A | No description available 
    68451  
    68452 
    68453 > matchmaker #712 to #1.23 & sel
    68454 
    68455 Parameters 
    68456 --- 
    68457 Chain pairing | bb 
    68458 Alignment algorithm | Needleman-Wunsch 
    68459 Similarity matrix | BLOSUM-62 
    68460 SS fraction | 0.3 
    68461 Gap open (HH/SS/other) | 18/18/6 
    68462 Gap extend | 1 
    68463 SS matrix |  |  | H | S | O 
    68464 ---|---|---|--- 
    68465 H | 6 | -9 | -6 
    68466 S |  | 6 | -6 
    68467 O |  |  | 4 
    68468 Iteration cutoff | 2 
    68469  
    68470 Matchmaker 3j0c.pdb1, chain G (#1.23) with AF3 E1 1-421.pdb, chain A (#712),
    68471 sequence alignment score = 1060.7 
    68472 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    68473 2.985) 
    68474  
    68475 
    68476 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    68477 
    68478 Chain information for AF3 E1 422-461.pdb #713 
    68479 --- 
    68480 Chain | Description 
    68481 A | No description available 
    68482  
    68483 
    68484 > matchmaker #713 to #1.23 & sel
    68485 
    68486 Parameters 
    68487 --- 
    68488 Chain pairing | bb 
    68489 Alignment algorithm | Needleman-Wunsch 
    68490 Similarity matrix | BLOSUM-62 
    68491 SS fraction | 0.3 
    68492 Gap open (HH/SS/other) | 18/18/6 
    68493 Gap extend | 1 
    68494 SS matrix |  |  | H | S | O 
    68495 ---|---|---|--- 
    68496 H | 6 | -9 | -6 
    68497 S |  | 6 | -6 
    68498 O |  |  | 4 
    68499 Iteration cutoff | 2 
    68500  
    68501 Matchmaker 3j0c.pdb1, chain G (#1.23) with AF3 E1 422-461.pdb, chain A (#713),
    68502 sequence alignment score = 626.9 
    68503 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    68504 2.997) 
    68505  
    68506 
    68507 > hide sel cartoons
    68508 
    68509 > select #1.23/H
    68510 
    68511 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    68512 
    68513 > show sel cartoons
    68514 
    68515 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    68516 
    68517 Chain information for AF3 E2 1-352.pdb #714 
    68518 --- 
    68519 Chain | Description 
    68520 B | No description available 
    68521  
    68522 
    68523 > matchmaker #714 to #1.23 & sel
    68524 
    68525 Parameters 
    68526 --- 
    68527 Chain pairing | bb 
    68528 Alignment algorithm | Needleman-Wunsch 
    68529 Similarity matrix | BLOSUM-62 
    68530 SS fraction | 0.3 
    68531 Gap open (HH/SS/other) | 18/18/6 
    68532 Gap extend | 1 
    68533 SS matrix |  |  | H | S | O 
    68534 ---|---|---|--- 
    68535 H | 6 | -9 | -6 
    68536 S |  | 6 | -6 
    68537 O |  |  | 4 
    68538 Iteration cutoff | 2 
    68539  
    68540 Matchmaker 3j0c.pdb1, chain H (#1.23) with AF3 E2 1-352.pdb, chain B (#714),
    68541 sequence alignment score = 590.9 
    68542 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    68543 6.107) 
    68544  
    68545 
    68546 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    68547 
    68548 Chain information for AF3 E2 353-438.pdb #715 
    68549 --- 
    68550 Chain | Description 
    68551 B | No description available 
    68552  
    68553 
    68554 > matchmaker #715 to #1.23 & sel
    68555 
    68556 Parameters 
    68557 --- 
    68558 Chain pairing | bb 
    68559 Alignment algorithm | Needleman-Wunsch 
    68560 Similarity matrix | BLOSUM-62 
    68561 SS fraction | 0.3 
    68562 Gap open (HH/SS/other) | 18/18/6 
    68563 Gap extend | 1 
    68564 SS matrix |  |  | H | S | O 
    68565 ---|---|---|--- 
    68566 H | 6 | -9 | -6 
    68567 S |  | 6 | -6 
    68568 O |  |  | 4 
    68569 Iteration cutoff | 2 
    68570  
    68571 Matchmaker 3j0c.pdb1, chain H (#1.23) with AF3 E2 353-438.pdb, chain B (#715),
    68572 sequence alignment score = 329.4 
    68573 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    68574 8.150) 
    68575  
    68576 
    68577 > hide sel cartoons
    68578 
    68579 > select #1.23/I
    68580 
    68581 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    68582 
    68583 > show sel cartoons
    68584 
    68585 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    68586 
    68587 Chain information for AF3 CA.pdb #716 
    68588 --- 
    68589 Chain | Description 
    68590 A | No description available 
    68591  
    68592 
    68593 > matchmaker #716 to #1.23 & sel
    68594 
    68595 Parameters 
    68596 --- 
    68597 Chain pairing | bb 
    68598 Alignment algorithm | Needleman-Wunsch 
    68599 Similarity matrix | BLOSUM-62 
    68600 SS fraction | 0.3 
    68601 Gap open (HH/SS/other) | 18/18/6 
    68602 Gap extend | 1 
    68603 SS matrix |  |  | H | S | O 
    68604 ---|---|---|--- 
    68605 H | 6 | -9 | -6 
    68606 S |  | 6 | -6 
    68607 O |  |  | 4 
    68608 Iteration cutoff | 2 
    68609  
    68610 Matchmaker 3j0c.pdb1, chain I (#1.23) with AF3 CA.pdb, chain A (#716),
    68611 sequence alignment score = 306.5 
    68612 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    68613 2.689) 
    68614  
    68615 
    68616 > hide sel cartoons
    68617 
    68618 > color #712 dodgerblue
    68619 
    68620 > color #713 dodgerblue
    68621 
    68622 > color #714 #00b305ff
    68623 
    68624 > color #715 #00b305ff
    68625 
    68626 > color #716 #f15839ff
    68627 
    68628 > select #1.24/G
    68629 
    68630 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    68631 
    68632 > show sel cartoons
    68633 
    68634 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    68635 
    68636 Chain information for AF3 E1 1-421.pdb #717 
    68637 --- 
    68638 Chain | Description 
    68639 A | No description available 
    68640  
    68641 
    68642 > matchmaker #717 to #1.23 & sel
    68643 
    68644 No 'to' model specified 
    68645 
    68646 > matchmaker #717 to #1.24 & sel
    68647 
    68648 Parameters 
    68649 --- 
    68650 Chain pairing | bb 
    68651 Alignment algorithm | Needleman-Wunsch 
    68652 Similarity matrix | BLOSUM-62 
    68653 SS fraction | 0.3 
    68654 Gap open (HH/SS/other) | 18/18/6 
    68655 Gap extend | 1 
    68656 SS matrix |  |  | H | S | O 
    68657 ---|---|---|--- 
    68658 H | 6 | -9 | -6 
    68659 S |  | 6 | -6 
    68660 O |  |  | 4 
    68661 Iteration cutoff | 2 
    68662  
    68663 Matchmaker 3j0c.pdb1, chain G (#1.24) with AF3 E1 1-421.pdb, chain A (#717),
    68664 sequence alignment score = 1060.7 
    68665 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    68666 2.985) 
    68667  
    68668 
    68669 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    68670 
    68671 Chain information for AF3 E1 422-461.pdb #718 
    68672 --- 
    68673 Chain | Description 
    68674 A | No description available 
    68675  
    68676 
    68677 > matchmaker #718 to #1.24 & sel
    68678 
    68679 Parameters 
    68680 --- 
    68681 Chain pairing | bb 
    68682 Alignment algorithm | Needleman-Wunsch 
    68683 Similarity matrix | BLOSUM-62 
    68684 SS fraction | 0.3 
    68685 Gap open (HH/SS/other) | 18/18/6 
    68686 Gap extend | 1 
    68687 SS matrix |  |  | H | S | O 
    68688 ---|---|---|--- 
    68689 H | 6 | -9 | -6 
    68690 S |  | 6 | -6 
    68691 O |  |  | 4 
    68692 Iteration cutoff | 2 
    68693  
    68694 Matchmaker 3j0c.pdb1, chain G (#1.24) with AF3 E1 422-461.pdb, chain A (#718),
    68695 sequence alignment score = 626.9 
    68696 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    68697 2.997) 
    68698  
    68699 
    68700 > hide sel cartoons
    68701 
    68702 > select #1.24/H
    68703 
    68704 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    68705 
    68706 > show sel cartoons
    68707 
    68708 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    68709 
    68710 Chain information for AF3 E2 1-352.pdb #719 
    68711 --- 
    68712 Chain | Description 
    68713 B | No description available 
    68714  
    68715 
    68716 > matchmaker #719 to #1.24 & sel
    68717 
    68718 Parameters 
    68719 --- 
    68720 Chain pairing | bb 
    68721 Alignment algorithm | Needleman-Wunsch 
    68722 Similarity matrix | BLOSUM-62 
    68723 SS fraction | 0.3 
    68724 Gap open (HH/SS/other) | 18/18/6 
    68725 Gap extend | 1 
    68726 SS matrix |  |  | H | S | O 
    68727 ---|---|---|--- 
    68728 H | 6 | -9 | -6 
    68729 S |  | 6 | -6 
    68730 O |  |  | 4 
    68731 Iteration cutoff | 2 
    68732  
    68733 Matchmaker 3j0c.pdb1, chain H (#1.24) with AF3 E2 1-352.pdb, chain B (#719),
    68734 sequence alignment score = 590.9 
    68735 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    68736 6.107) 
    68737  
    68738 
    68739 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    68740 
    68741 Chain information for AF3 E2 353-438.pdb #720 
    68742 --- 
    68743 Chain | Description 
    68744 B | No description available 
    68745  
    68746 
    68747 > matchmaker #720 to #1.24 & sel
    68748 
    68749 Parameters 
    68750 --- 
    68751 Chain pairing | bb 
    68752 Alignment algorithm | Needleman-Wunsch 
    68753 Similarity matrix | BLOSUM-62 
    68754 SS fraction | 0.3 
    68755 Gap open (HH/SS/other) | 18/18/6 
    68756 Gap extend | 1 
    68757 SS matrix |  |  | H | S | O 
    68758 ---|---|---|--- 
    68759 H | 6 | -9 | -6 
    68760 S |  | 6 | -6 
    68761 O |  |  | 4 
    68762 Iteration cutoff | 2 
    68763  
    68764 Matchmaker 3j0c.pdb1, chain H (#1.24) with AF3 E2 353-438.pdb, chain B (#720),
    68765 sequence alignment score = 329.4 
    68766 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    68767 8.150) 
    68768  
    68769 
    68770 > hide sel cartoons
    68771 
    68772 > select #1.24/I
    68773 
    68774 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    68775 
    68776 > show sel cartoons
    68777 
    68778 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    68779 
    68780 Chain information for AF3 CA.pdb #721 
    68781 --- 
    68782 Chain | Description 
    68783 A | No description available 
    68784  
    68785 
    68786 > matchmaker #721 to #1.24 & sel
    68787 
    68788 Parameters 
    68789 --- 
    68790 Chain pairing | bb 
    68791 Alignment algorithm | Needleman-Wunsch 
    68792 Similarity matrix | BLOSUM-62 
    68793 SS fraction | 0.3 
    68794 Gap open (HH/SS/other) | 18/18/6 
    68795 Gap extend | 1 
    68796 SS matrix |  |  | H | S | O 
    68797 ---|---|---|--- 
    68798 H | 6 | -9 | -6 
    68799 S |  | 6 | -6 
    68800 O |  |  | 4 
    68801 Iteration cutoff | 2 
    68802  
    68803 Matchmaker 3j0c.pdb1, chain I (#1.24) with AF3 CA.pdb, chain A (#721),
    68804 sequence alignment score = 306.5 
    68805 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    68806 2.689) 
    68807  
    68808 
    68809 > hide sel cartoons
    68810 
    68811 > color #717 dodgerblue
    68812 
    68813 > color #718 dodgerblue
    68814 
    68815 > color #719 #00b305ff
    68816 
    68817 > color #720 #00b305ff
    68818 
    68819 > color #721 #f15839ff
    68820 
    68821 > select #1.25/G
    68822 
    68823 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    68824 
    68825 > show sel cartoons
    68826 
    68827 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    68828 
    68829 Chain information for AF3 E1 1-421.pdb #722 
    68830 --- 
    68831 Chain | Description 
    68832 A | No description available 
    68833  
    68834 
    68835 > matchmaker #722 to #1.25 & sel
    68836 
    68837 Parameters 
    68838 --- 
    68839 Chain pairing | bb 
    68840 Alignment algorithm | Needleman-Wunsch 
    68841 Similarity matrix | BLOSUM-62 
    68842 SS fraction | 0.3 
    68843 Gap open (HH/SS/other) | 18/18/6 
    68844 Gap extend | 1 
    68845 SS matrix |  |  | H | S | O 
    68846 ---|---|---|--- 
    68847 H | 6 | -9 | -6 
    68848 S |  | 6 | -6 
    68849 O |  |  | 4 
    68850 Iteration cutoff | 2 
    68851  
    68852 Matchmaker 3j0c.pdb1, chain G (#1.25) with AF3 E1 1-421.pdb, chain A (#722),
    68853 sequence alignment score = 1060.7 
    68854 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    68855 2.985) 
    68856  
    68857 
    68858 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    68859 
    68860 Chain information for AF3 E1 422-461.pdb #723 
    68861 --- 
    68862 Chain | Description 
    68863 A | No description available 
    68864  
    68865 
    68866 > matchmaker #723 to #1.25 & sel
    68867 
    68868 Parameters 
    68869 --- 
    68870 Chain pairing | bb 
    68871 Alignment algorithm | Needleman-Wunsch 
    68872 Similarity matrix | BLOSUM-62 
    68873 SS fraction | 0.3 
    68874 Gap open (HH/SS/other) | 18/18/6 
    68875 Gap extend | 1 
    68876 SS matrix |  |  | H | S | O 
    68877 ---|---|---|--- 
    68878 H | 6 | -9 | -6 
    68879 S |  | 6 | -6 
    68880 O |  |  | 4 
    68881 Iteration cutoff | 2 
    68882  
    68883 Matchmaker 3j0c.pdb1, chain G (#1.25) with AF3 E1 422-461.pdb, chain A (#723),
    68884 sequence alignment score = 626.9 
    68885 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    68886 2.997) 
    68887  
    68888 
    68889 > hide sel cartoons
    68890 
    68891 > select #1.25/H
    68892 
    68893 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    68894 
    68895 > show sel cartoons
    68896 
    68897 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    68898 
    68899 Chain information for AF3 E2 1-352.pdb #724 
    68900 --- 
    68901 Chain | Description 
    68902 B | No description available 
    68903  
    68904 
    68905 > matchmaker #724 to #1.25 & sel
    68906 
    68907 Parameters 
    68908 --- 
    68909 Chain pairing | bb 
    68910 Alignment algorithm | Needleman-Wunsch 
    68911 Similarity matrix | BLOSUM-62 
    68912 SS fraction | 0.3 
    68913 Gap open (HH/SS/other) | 18/18/6 
    68914 Gap extend | 1 
    68915 SS matrix |  |  | H | S | O 
    68916 ---|---|---|--- 
    68917 H | 6 | -9 | -6 
    68918 S |  | 6 | -6 
    68919 O |  |  | 4 
    68920 Iteration cutoff | 2 
    68921  
    68922 Matchmaker 3j0c.pdb1, chain H (#1.25) with AF3 E2 1-352.pdb, chain B (#724),
    68923 sequence alignment score = 590.9 
    68924 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    68925 6.107) 
    68926  
    68927 
    68928 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    68929 
    68930 Chain information for AF3 E2 353-438.pdb #725 
    68931 --- 
    68932 Chain | Description 
    68933 B | No description available 
    68934  
    68935 
    68936 > matchmaker #725 to #1.25 & sel
    68937 
    68938 Parameters 
    68939 --- 
    68940 Chain pairing | bb 
    68941 Alignment algorithm | Needleman-Wunsch 
    68942 Similarity matrix | BLOSUM-62 
    68943 SS fraction | 0.3 
    68944 Gap open (HH/SS/other) | 18/18/6 
    68945 Gap extend | 1 
    68946 SS matrix |  |  | H | S | O 
    68947 ---|---|---|--- 
    68948 H | 6 | -9 | -6 
    68949 S |  | 6 | -6 
    68950 O |  |  | 4 
    68951 Iteration cutoff | 2 
    68952  
    68953 Matchmaker 3j0c.pdb1, chain H (#1.25) with AF3 E2 353-438.pdb, chain B (#725),
    68954 sequence alignment score = 329.4 
    68955 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    68956 8.150) 
    68957  
    68958 
    68959 > hide sel cartoons
    68960 
    68961 > select #1.25/I
    68962 
    68963 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    68964 
    68965 > show sel cartoons
    68966 
    68967 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    68968 
    68969 Chain information for AF3 CA.pdb #726 
    68970 --- 
    68971 Chain | Description 
    68972 A | No description available 
    68973  
    68974 
    68975 > matchmaker #726 to #1.25 & sel
    68976 
    68977 Parameters 
    68978 --- 
    68979 Chain pairing | bb 
    68980 Alignment algorithm | Needleman-Wunsch 
    68981 Similarity matrix | BLOSUM-62 
    68982 SS fraction | 0.3 
    68983 Gap open (HH/SS/other) | 18/18/6 
    68984 Gap extend | 1 
    68985 SS matrix |  |  | H | S | O 
    68986 ---|---|---|--- 
    68987 H | 6 | -9 | -6 
    68988 S |  | 6 | -6 
    68989 O |  |  | 4 
    68990 Iteration cutoff | 2 
    68991  
    68992 Matchmaker 3j0c.pdb1, chain I (#1.25) with AF3 CA.pdb, chain A (#726),
    68993 sequence alignment score = 306.5 
    68994 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    68995 2.689) 
    68996  
    68997 
    68998 > hide sel cartoons
    68999 
    69000 > color #722 dodgerblue
    69001 
    69002 > color #723 dodgerblue
    69003 
    69004 > color #724 #00b305ff
    69005 
    69006 > color #725 #00b305ff
    69007 
    69008 > color #726 #f15839ff
    69009 
    69010 > select #1.26/G
    69011 
    69012 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    69013 
    69014 > show sel cartoons
    69015 
    69016 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    69017 
    69018 Chain information for AF3 E1 1-421.pdb #727 
    69019 --- 
    69020 Chain | Description 
    69021 A | No description available 
    69022  
    69023 
    69024 > matchmaker #727 to #1.25 & sel
    69025 
    69026 No 'to' model specified 
    69027 
    69028 > matchmaker #727 to #1.26 & sel
    69029 
    69030 Parameters 
    69031 --- 
    69032 Chain pairing | bb 
    69033 Alignment algorithm | Needleman-Wunsch 
    69034 Similarity matrix | BLOSUM-62 
    69035 SS fraction | 0.3 
    69036 Gap open (HH/SS/other) | 18/18/6 
    69037 Gap extend | 1 
    69038 SS matrix |  |  | H | S | O 
    69039 ---|---|---|--- 
    69040 H | 6 | -9 | -6 
    69041 S |  | 6 | -6 
    69042 O |  |  | 4 
    69043 Iteration cutoff | 2 
    69044  
    69045 Matchmaker 3j0c.pdb1, chain G (#1.26) with AF3 E1 1-421.pdb, chain A (#727),
    69046 sequence alignment score = 1060.7 
    69047 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    69048 2.985) 
    69049  
    69050 
    69051 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    69052 
    69053 Chain information for AF3 E1 422-461.pdb #728 
    69054 --- 
    69055 Chain | Description 
    69056 A | No description available 
    69057  
    69058 
    69059 > matchmaker #728 to #1.26 & sel
    69060 
    69061 Parameters 
    69062 --- 
    69063 Chain pairing | bb 
    69064 Alignment algorithm | Needleman-Wunsch 
    69065 Similarity matrix | BLOSUM-62 
    69066 SS fraction | 0.3 
    69067 Gap open (HH/SS/other) | 18/18/6 
    69068 Gap extend | 1 
    69069 SS matrix |  |  | H | S | O 
    69070 ---|---|---|--- 
    69071 H | 6 | -9 | -6 
    69072 S |  | 6 | -6 
    69073 O |  |  | 4 
    69074 Iteration cutoff | 2 
    69075  
    69076 Matchmaker 3j0c.pdb1, chain G (#1.26) with AF3 E1 422-461.pdb, chain A (#728),
    69077 sequence alignment score = 626.9 
    69078 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    69079 2.997) 
    69080  
    69081 
    69082 > hide sel cartoons
    69083 
    69084 > select #1.26/H
    69085 
    69086 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    69087 
    69088 > show sel cartoons
    69089 
    69090 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    69091 
    69092 Chain information for AF3 E2 1-352.pdb #729 
    69093 --- 
    69094 Chain | Description 
    69095 B | No description available 
    69096  
    69097 
    69098 > matchmaker #729 to #1.26 & sel
    69099 
    69100 Parameters 
    69101 --- 
    69102 Chain pairing | bb 
    69103 Alignment algorithm | Needleman-Wunsch 
    69104 Similarity matrix | BLOSUM-62 
    69105 SS fraction | 0.3 
    69106 Gap open (HH/SS/other) | 18/18/6 
    69107 Gap extend | 1 
    69108 SS matrix |  |  | H | S | O 
    69109 ---|---|---|--- 
    69110 H | 6 | -9 | -6 
    69111 S |  | 6 | -6 
    69112 O |  |  | 4 
    69113 Iteration cutoff | 2 
    69114  
    69115 Matchmaker 3j0c.pdb1, chain H (#1.26) with AF3 E2 1-352.pdb, chain B (#729),
    69116 sequence alignment score = 590.9 
    69117 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    69118 6.107) 
    69119  
    69120 
    69121 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    69122 
    69123 Chain information for AF3 E2 353-438.pdb #730 
    69124 --- 
    69125 Chain | Description 
    69126 B | No description available 
    69127  
    69128 
    69129 > matchmaker #730 to #1.26 & sel
    69130 
    69131 Parameters 
    69132 --- 
    69133 Chain pairing | bb 
    69134 Alignment algorithm | Needleman-Wunsch 
    69135 Similarity matrix | BLOSUM-62 
    69136 SS fraction | 0.3 
    69137 Gap open (HH/SS/other) | 18/18/6 
    69138 Gap extend | 1 
    69139 SS matrix |  |  | H | S | O 
    69140 ---|---|---|--- 
    69141 H | 6 | -9 | -6 
    69142 S |  | 6 | -6 
    69143 O |  |  | 4 
    69144 Iteration cutoff | 2 
    69145  
    69146 Matchmaker 3j0c.pdb1, chain H (#1.26) with AF3 E2 353-438.pdb, chain B (#730),
    69147 sequence alignment score = 329.4 
    69148 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    69149 8.150) 
    69150  
    69151 
    69152 > hide sel cartoons
    69153 
    69154 > select #1.27/I
    69155 
    69156 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    69157 
    69158 > show sel cartoons
    69159 
    69160 > hide sel cartoons
    69161 
    69162 > select #1.26/F
    69163 
    69164 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    69165 
    69166 > show sel cartoons
    69167 
    69168 > hide sel cartoons
    69169 
    69170 > select #1.25/H
    69171 
    69172 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    69173 
    69174 > show sel cartoons
    69175 
    69176 > hide sel cartoons
    69177 
    69178 > select #1.25/I
    69179 
    69180 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    69181 
    69182 > select #1.26/I
    69183 
    69184 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    69185 
    69186 > show sel cartoons
    69187 
    69188 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    69189 
    69190 Chain information for AF3 CA.pdb #731 
    69191 --- 
    69192 Chain | Description 
    69193 A | No description available 
    69194  
    69195 
    69196 > matchmaker #731 to #1.26 & sel
    69197 
    69198 Parameters 
    69199 --- 
    69200 Chain pairing | bb 
    69201 Alignment algorithm | Needleman-Wunsch 
    69202 Similarity matrix | BLOSUM-62 
    69203 SS fraction | 0.3 
    69204 Gap open (HH/SS/other) | 18/18/6 
    69205 Gap extend | 1 
    69206 SS matrix |  |  | H | S | O 
    69207 ---|---|---|--- 
    69208 H | 6 | -9 | -6 
    69209 S |  | 6 | -6 
    69210 O |  |  | 4 
    69211 Iteration cutoff | 2 
    69212  
    69213 Matchmaker 3j0c.pdb1, chain I (#1.26) with AF3 CA.pdb, chain A (#731),
    69214 sequence alignment score = 306.5 
    69215 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    69216 2.689) 
    69217  
    69218 
    69219 > hide sel cartoons
    69220 
    69221 > color #727 dodgerblue
    69222 
    69223 > color #728 dodgerblue
    69224 
    69225 > color #729 #00b305ff
    69226 
    69227 > color #730 #00b305ff
    69228 
    69229 > color #731 #f15839ff
    69230 
    69231 > select #1.27/G
    69232 
    69233 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    69234 
    69235 > show sel cartoons
    69236 
    69237 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    69238 
    69239 Chain information for AF3 E1 1-421.pdb #732 
    69240 --- 
    69241 Chain | Description 
    69242 A | No description available 
    69243  
    69244 
    69245 > matchmaker #732 to #1.27 & sel
    69246 
    69247 Parameters 
    69248 --- 
    69249 Chain pairing | bb 
    69250 Alignment algorithm | Needleman-Wunsch 
    69251 Similarity matrix | BLOSUM-62 
    69252 SS fraction | 0.3 
    69253 Gap open (HH/SS/other) | 18/18/6 
    69254 Gap extend | 1 
    69255 SS matrix |  |  | H | S | O 
    69256 ---|---|---|--- 
    69257 H | 6 | -9 | -6 
    69258 S |  | 6 | -6 
    69259 O |  |  | 4 
    69260 Iteration cutoff | 2 
    69261  
    69262 Matchmaker 3j0c.pdb1, chain G (#1.27) with AF3 E1 1-421.pdb, chain A (#732),
    69263 sequence alignment score = 1060.7 
    69264 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    69265 2.985) 
    69266  
    69267 
    69268 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    69269 
    69270 Chain information for AF3 E1 422-461.pdb #733 
    69271 --- 
    69272 Chain | Description 
    69273 A | No description available 
    69274  
    69275 
    69276 > matchmaker #733 to #1.27 & sel
    69277 
    69278 Parameters 
    69279 --- 
    69280 Chain pairing | bb 
    69281 Alignment algorithm | Needleman-Wunsch 
    69282 Similarity matrix | BLOSUM-62 
    69283 SS fraction | 0.3 
    69284 Gap open (HH/SS/other) | 18/18/6 
    69285 Gap extend | 1 
    69286 SS matrix |  |  | H | S | O 
    69287 ---|---|---|--- 
    69288 H | 6 | -9 | -6 
    69289 S |  | 6 | -6 
    69290 O |  |  | 4 
    69291 Iteration cutoff | 2 
    69292  
    69293 Matchmaker 3j0c.pdb1, chain G (#1.27) with AF3 E1 422-461.pdb, chain A (#733),
    69294 sequence alignment score = 626.9 
    69295 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    69296 2.997) 
    69297  
    69298 
    69299 > hide sel cartoons
    69300 
    69301 > select #1.27/H
    69302 
    69303 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    69304 
    69305 > show sel cartoons
    69306 
    69307 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    69308 
    69309 Chain information for AF3 E2 1-352.pdb #734 
    69310 --- 
    69311 Chain | Description 
    69312 B | No description available 
    69313  
    69314 
    69315 > matchmaker #734 to #1.27 & sel
    69316 
    69317 Parameters 
    69318 --- 
    69319 Chain pairing | bb 
    69320 Alignment algorithm | Needleman-Wunsch 
    69321 Similarity matrix | BLOSUM-62 
    69322 SS fraction | 0.3 
    69323 Gap open (HH/SS/other) | 18/18/6 
    69324 Gap extend | 1 
    69325 SS matrix |  |  | H | S | O 
    69326 ---|---|---|--- 
    69327 H | 6 | -9 | -6 
    69328 S |  | 6 | -6 
    69329 O |  |  | 4 
    69330 Iteration cutoff | 2 
    69331  
    69332 Matchmaker 3j0c.pdb1, chain H (#1.27) with AF3 E2 1-352.pdb, chain B (#734),
    69333 sequence alignment score = 590.9 
    69334 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    69335 6.107) 
    69336  
    69337 
    69338 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    69339 
    69340 Chain information for AF3 E2 353-438.pdb #735 
    69341 --- 
    69342 Chain | Description 
    69343 B | No description available 
    69344  
    69345 
    69346 > matchmaker #735 to #1.27 & sel
    69347 
    69348 Parameters 
    69349 --- 
    69350 Chain pairing | bb 
    69351 Alignment algorithm | Needleman-Wunsch 
    69352 Similarity matrix | BLOSUM-62 
    69353 SS fraction | 0.3 
    69354 Gap open (HH/SS/other) | 18/18/6 
    69355 Gap extend | 1 
    69356 SS matrix |  |  | H | S | O 
    69357 ---|---|---|--- 
    69358 H | 6 | -9 | -6 
    69359 S |  | 6 | -6 
    69360 O |  |  | 4 
    69361 Iteration cutoff | 2 
    69362  
    69363 Matchmaker 3j0c.pdb1, chain H (#1.27) with AF3 E2 353-438.pdb, chain B (#735),
    69364 sequence alignment score = 329.4 
    69365 RMSD between 40 pruned atom pairs is 0.937 angstroms; (across all 84 pairs:
    69366 8.151) 
    69367  
    69368 
    69369 > hide sel cartoons
    69370 
    69371 > select #1.27/I
    69372 
    69373 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    69374 
    69375 > show sel cartoons
    69376 
    69377 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    69378 
    69379 Chain information for AF3 CA.pdb #736 
    69380 --- 
    69381 Chain | Description 
    69382 A | No description available 
    69383  
    69384 
    69385 > matchmaker #736 to #1.27 & sel
    69386 
    69387 Parameters 
    69388 --- 
    69389 Chain pairing | bb 
    69390 Alignment algorithm | Needleman-Wunsch 
    69391 Similarity matrix | BLOSUM-62 
    69392 SS fraction | 0.3 
    69393 Gap open (HH/SS/other) | 18/18/6 
    69394 Gap extend | 1 
    69395 SS matrix |  |  | H | S | O 
    69396 ---|---|---|--- 
    69397 H | 6 | -9 | -6 
    69398 S |  | 6 | -6 
    69399 O |  |  | 4 
    69400 Iteration cutoff | 2 
    69401  
    69402 Matchmaker 3j0c.pdb1, chain I (#1.27) with AF3 CA.pdb, chain A (#736),
    69403 sequence alignment score = 306.5 
    69404 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    69405 2.689) 
    69406  
    69407 
    69408 > hide sel cartoons
    69409 
    69410 > color #732 dodgerblue
    69411 
    69412 > color #733 dodgerblue
    69413 
    69414 > color #734 #00b305ff
    69415 
    69416 > color #735 #00b305ff
    69417 
    69418 > color #736 #f15839ff
    69419 
    69420 > select #1.28/G
    69421 
    69422 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    69423 
    69424 > show sel cartoons
    69425 
    69426 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    69427 
    69428 Chain information for AF3 E1 1-421.pdb #737 
    69429 --- 
    69430 Chain | Description 
    69431 A | No description available 
    69432  
    69433 
    69434 > matchmaker #737 to #1.28 & sel
    69435 
    69436 Parameters 
    69437 --- 
    69438 Chain pairing | bb 
    69439 Alignment algorithm | Needleman-Wunsch 
    69440 Similarity matrix | BLOSUM-62 
    69441 SS fraction | 0.3 
    69442 Gap open (HH/SS/other) | 18/18/6 
    69443 Gap extend | 1 
    69444 SS matrix |  |  | H | S | O 
    69445 ---|---|---|--- 
    69446 H | 6 | -9 | -6 
    69447 S |  | 6 | -6 
    69448 O |  |  | 4 
    69449 Iteration cutoff | 2 
    69450  
    69451 Matchmaker 3j0c.pdb1, chain G (#1.28) with AF3 E1 1-421.pdb, chain A (#737),
    69452 sequence alignment score = 1060.7 
    69453 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    69454 2.985) 
    69455  
    69456 
    69457 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    69458 
    69459 Chain information for AF3 E1 422-461.pdb #738 
    69460 --- 
    69461 Chain | Description 
    69462 A | No description available 
    69463  
    69464 
    69465 > matchmaker #738 to #1.28 & sel
    69466 
    69467 Parameters 
    69468 --- 
    69469 Chain pairing | bb 
    69470 Alignment algorithm | Needleman-Wunsch 
    69471 Similarity matrix | BLOSUM-62 
    69472 SS fraction | 0.3 
    69473 Gap open (HH/SS/other) | 18/18/6 
    69474 Gap extend | 1 
    69475 SS matrix |  |  | H | S | O 
    69476 ---|---|---|--- 
    69477 H | 6 | -9 | -6 
    69478 S |  | 6 | -6 
    69479 O |  |  | 4 
    69480 Iteration cutoff | 2 
    69481  
    69482 Matchmaker 3j0c.pdb1, chain G (#1.28) with AF3 E1 422-461.pdb, chain A (#738),
    69483 sequence alignment score = 626.9 
    69484 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    69485 2.997) 
    69486  
    69487 
    69488 > hide sel cartoons
    69489 
    69490 > select #1.28/H
    69491 
    69492 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    69493 
    69494 > show sel cartoons
    69495 
    69496 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    69497 
    69498 Chain information for AF3 E2 1-352.pdb #739 
    69499 --- 
    69500 Chain | Description 
    69501 B | No description available 
    69502  
    69503 
    69504 > matchmaker #739 to #1.28 & sel
    69505 
    69506 Parameters 
    69507 --- 
    69508 Chain pairing | bb 
    69509 Alignment algorithm | Needleman-Wunsch 
    69510 Similarity matrix | BLOSUM-62 
    69511 SS fraction | 0.3 
    69512 Gap open (HH/SS/other) | 18/18/6 
    69513 Gap extend | 1 
    69514 SS matrix |  |  | H | S | O 
    69515 ---|---|---|--- 
    69516 H | 6 | -9 | -6 
    69517 S |  | 6 | -6 
    69518 O |  |  | 4 
    69519 Iteration cutoff | 2 
    69520  
    69521 Matchmaker 3j0c.pdb1, chain H (#1.28) with AF3 E2 1-352.pdb, chain B (#739),
    69522 sequence alignment score = 590.9 
    69523 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    69524 6.107) 
    69525  
    69526 
    69527 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    69528 
    69529 Chain information for AF3 E2 353-438.pdb #740 
    69530 --- 
    69531 Chain | Description 
    69532 B | No description available 
    69533  
    69534 
    69535 > matchmaker #740 to #1.28 & sel
    69536 
    69537 Parameters 
    69538 --- 
    69539 Chain pairing | bb 
    69540 Alignment algorithm | Needleman-Wunsch 
    69541 Similarity matrix | BLOSUM-62 
    69542 SS fraction | 0.3 
    69543 Gap open (HH/SS/other) | 18/18/6 
    69544 Gap extend | 1 
    69545 SS matrix |  |  | H | S | O 
    69546 ---|---|---|--- 
    69547 H | 6 | -9 | -6 
    69548 S |  | 6 | -6 
    69549 O |  |  | 4 
    69550 Iteration cutoff | 2 
    69551  
    69552 Matchmaker 3j0c.pdb1, chain H (#1.28) with AF3 E2 353-438.pdb, chain B (#740),
    69553 sequence alignment score = 329.4 
    69554 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    69555 8.150) 
    69556  
    69557 
    69558 > hide sel cartoons
    69559 
    69560 > select #1.28/I
    69561 
    69562 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    69563 
    69564 > show sel cartoons
    69565 
    69566 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    69567 
    69568 Chain information for AF3 CA.pdb #741 
    69569 --- 
    69570 Chain | Description 
    69571 A | No description available 
    69572  
    69573 
    69574 > matchmaker #741 to #1.28 & sel
    69575 
    69576 Parameters 
    69577 --- 
    69578 Chain pairing | bb 
    69579 Alignment algorithm | Needleman-Wunsch 
    69580 Similarity matrix | BLOSUM-62 
    69581 SS fraction | 0.3 
    69582 Gap open (HH/SS/other) | 18/18/6 
    69583 Gap extend | 1 
    69584 SS matrix |  |  | H | S | O 
    69585 ---|---|---|--- 
    69586 H | 6 | -9 | -6 
    69587 S |  | 6 | -6 
    69588 O |  |  | 4 
    69589 Iteration cutoff | 2 
    69590  
    69591 Matchmaker 3j0c.pdb1, chain I (#1.28) with AF3 CA.pdb, chain A (#741),
    69592 sequence alignment score = 306.5 
    69593 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    69594 2.689) 
    69595  
    69596 
    69597 > hide sel cartoons
    69598 
    69599 > color #737 dodgerblue
    69600 
    69601 > color #738 dodgerblue
    69602 
    69603 > color #739 #00b305ff
    69604 
    69605 > color #740 #00b305ff
    69606 
    69607 > color #741 #f15839ff
    69608 
    69609 > select #1.29/G
    69610 
    69611 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    69612 
    69613 > show sel cartoons
    69614 
    69615 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    69616 
    69617 Chain information for AF3 E1 1-421.pdb #742 
    69618 --- 
    69619 Chain | Description 
    69620 A | No description available 
    69621  
    69622 
    69623 > matchmaker #742 to #1.29 & sel
    69624 
    69625 Parameters 
    69626 --- 
    69627 Chain pairing | bb 
    69628 Alignment algorithm | Needleman-Wunsch 
    69629 Similarity matrix | BLOSUM-62 
    69630 SS fraction | 0.3 
    69631 Gap open (HH/SS/other) | 18/18/6 
    69632 Gap extend | 1 
    69633 SS matrix |  |  | H | S | O 
    69634 ---|---|---|--- 
    69635 H | 6 | -9 | -6 
    69636 S |  | 6 | -6 
    69637 O |  |  | 4 
    69638 Iteration cutoff | 2 
    69639  
    69640 Matchmaker 3j0c.pdb1, chain G (#1.29) with AF3 E1 1-421.pdb, chain A (#742),
    69641 sequence alignment score = 1060.7 
    69642 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    69643 2.985) 
    69644  
    69645 
    69646 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    69647 
    69648 Chain information for AF3 E1 422-461.pdb #743 
    69649 --- 
    69650 Chain | Description 
    69651 A | No description available 
    69652  
    69653 
    69654 > matchmaker #743 to #1.29 & sel
    69655 
    69656 Parameters 
    69657 --- 
    69658 Chain pairing | bb 
    69659 Alignment algorithm | Needleman-Wunsch 
    69660 Similarity matrix | BLOSUM-62 
    69661 SS fraction | 0.3 
    69662 Gap open (HH/SS/other) | 18/18/6 
    69663 Gap extend | 1 
    69664 SS matrix |  |  | H | S | O 
    69665 ---|---|---|--- 
    69666 H | 6 | -9 | -6 
    69667 S |  | 6 | -6 
    69668 O |  |  | 4 
    69669 Iteration cutoff | 2 
    69670  
    69671 Matchmaker 3j0c.pdb1, chain G (#1.29) with AF3 E1 422-461.pdb, chain A (#743),
    69672 sequence alignment score = 626.9 
    69673 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    69674 2.997) 
    69675  
    69676 
    69677 > hide sel cartoons
    69678 
    69679 > select #1.29/H
    69680 
    69681 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    69682 
    69683 > show sel cartoons
    69684 
    69685 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    69686 
    69687 Chain information for AF3 E2 1-352.pdb #744 
    69688 --- 
    69689 Chain | Description 
    69690 B | No description available 
    69691  
    69692 
    69693 > matchmaker #744 to #1.29 & sel
    69694 
    69695 Parameters 
    69696 --- 
    69697 Chain pairing | bb 
    69698 Alignment algorithm | Needleman-Wunsch 
    69699 Similarity matrix | BLOSUM-62 
    69700 SS fraction | 0.3 
    69701 Gap open (HH/SS/other) | 18/18/6 
    69702 Gap extend | 1 
    69703 SS matrix |  |  | H | S | O 
    69704 ---|---|---|--- 
    69705 H | 6 | -9 | -6 
    69706 S |  | 6 | -6 
    69707 O |  |  | 4 
    69708 Iteration cutoff | 2 
    69709  
    69710 Matchmaker 3j0c.pdb1, chain H (#1.29) with AF3 E2 1-352.pdb, chain B (#744),
    69711 sequence alignment score = 590.9 
    69712 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    69713 6.107) 
    69714  
    69715 
    69716 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    69717 
    69718 Chain information for AF3 E2 353-438.pdb #745 
    69719 --- 
    69720 Chain | Description 
    69721 B | No description available 
    69722  
    69723 
    69724 > matchmaker #745 to #1.29 & sel
    69725 
    69726 Parameters 
    69727 --- 
    69728 Chain pairing | bb 
    69729 Alignment algorithm | Needleman-Wunsch 
    69730 Similarity matrix | BLOSUM-62 
    69731 SS fraction | 0.3 
    69732 Gap open (HH/SS/other) | 18/18/6 
    69733 Gap extend | 1 
    69734 SS matrix |  |  | H | S | O 
    69735 ---|---|---|--- 
    69736 H | 6 | -9 | -6 
    69737 S |  | 6 | -6 
    69738 O |  |  | 4 
    69739 Iteration cutoff | 2 
    69740  
    69741 Matchmaker 3j0c.pdb1, chain H (#1.29) with AF3 E2 353-438.pdb, chain B (#745),
    69742 sequence alignment score = 329.4 
    69743 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    69744 8.150) 
    69745  
    69746 
    69747 > hide sel cartoons
    69748 
    69749 > select #1.29/I
    69750 
    69751 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    69752 
    69753 > show sel cartoons
    69754 
    69755 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    69756 
    69757 Chain information for AF3 CA.pdb #746 
    69758 --- 
    69759 Chain | Description 
    69760 A | No description available 
    69761  
    69762 
    69763 > matchmaker #746 to #1.29 & sel
    69764 
    69765 Parameters 
    69766 --- 
    69767 Chain pairing | bb 
    69768 Alignment algorithm | Needleman-Wunsch 
    69769 Similarity matrix | BLOSUM-62 
    69770 SS fraction | 0.3 
    69771 Gap open (HH/SS/other) | 18/18/6 
    69772 Gap extend | 1 
    69773 SS matrix |  |  | H | S | O 
    69774 ---|---|---|--- 
    69775 H | 6 | -9 | -6 
    69776 S |  | 6 | -6 
    69777 O |  |  | 4 
    69778 Iteration cutoff | 2 
    69779  
    69780 Matchmaker 3j0c.pdb1, chain I (#1.29) with AF3 CA.pdb, chain A (#746),
    69781 sequence alignment score = 306.5 
    69782 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    69783 2.689) 
    69784  
    69785 
    69786 > hide sel cartoons
    69787 
    69788 > color #742 dodgerblue
    69789 
    69790 > color #743 dodgerblue
    69791 
    69792 > color #744 #00b305ff
    69793 
    69794 > color #745 #00b305ff
    69795 
    69796 > color #746 #f15839ff
    69797 
    69798 > select #1.30/G
    69799 
    69800 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    69801 
    69802 > show sel cartoons
    69803 
    69804 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    69805 
    69806 Chain information for AF3 E1 1-421.pdb #747 
    69807 --- 
    69808 Chain | Description 
    69809 A | No description available 
    69810  
    69811 
    69812 > matchmaker #747 to #1.30 & sel
    69813 
    69814 Parameters 
    69815 --- 
    69816 Chain pairing | bb 
    69817 Alignment algorithm | Needleman-Wunsch 
    69818 Similarity matrix | BLOSUM-62 
    69819 SS fraction | 0.3 
    69820 Gap open (HH/SS/other) | 18/18/6 
    69821 Gap extend | 1 
    69822 SS matrix |  |  | H | S | O 
    69823 ---|---|---|--- 
    69824 H | 6 | -9 | -6 
    69825 S |  | 6 | -6 
    69826 O |  |  | 4 
    69827 Iteration cutoff | 2 
    69828  
    69829 Matchmaker 3j0c.pdb1, chain G (#1.30) with AF3 E1 1-421.pdb, chain A (#747),
    69830 sequence alignment score = 1060.7 
    69831 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    69832 2.985) 
    69833  
    69834 
    69835 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    69836 
    69837 Chain information for AF3 E1 422-461.pdb #748 
    69838 --- 
    69839 Chain | Description 
    69840 A | No description available 
    69841  
    69842 
    69843 > matchmaker #748 to #1.30 & sel
    69844 
    69845 Parameters 
    69846 --- 
    69847 Chain pairing | bb 
    69848 Alignment algorithm | Needleman-Wunsch 
    69849 Similarity matrix | BLOSUM-62 
    69850 SS fraction | 0.3 
    69851 Gap open (HH/SS/other) | 18/18/6 
    69852 Gap extend | 1 
    69853 SS matrix |  |  | H | S | O 
    69854 ---|---|---|--- 
    69855 H | 6 | -9 | -6 
    69856 S |  | 6 | -6 
    69857 O |  |  | 4 
    69858 Iteration cutoff | 2 
    69859  
    69860 Matchmaker 3j0c.pdb1, chain G (#1.30) with AF3 E1 422-461.pdb, chain A (#748),
    69861 sequence alignment score = 626.9 
    69862 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    69863 2.997) 
    69864  
    69865 
    69866 > hide sel cartoons
    69867 
    69868 > select #1.30/H
    69869 
    69870 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    69871 
    69872 > show sel cartoons
    69873 
    69874 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    69875 
    69876 Chain information for AF3 E2 1-352.pdb #749 
    69877 --- 
    69878 Chain | Description 
    69879 B | No description available 
    69880  
    69881 
    69882 > matchmaker #749 to #1.30 & sel
    69883 
    69884 Parameters 
    69885 --- 
    69886 Chain pairing | bb 
    69887 Alignment algorithm | Needleman-Wunsch 
    69888 Similarity matrix | BLOSUM-62 
    69889 SS fraction | 0.3 
    69890 Gap open (HH/SS/other) | 18/18/6 
    69891 Gap extend | 1 
    69892 SS matrix |  |  | H | S | O 
    69893 ---|---|---|--- 
    69894 H | 6 | -9 | -6 
    69895 S |  | 6 | -6 
    69896 O |  |  | 4 
    69897 Iteration cutoff | 2 
    69898  
    69899 Matchmaker 3j0c.pdb1, chain H (#1.30) with AF3 E2 1-352.pdb, chain B (#749),
    69900 sequence alignment score = 590.9 
    69901 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    69902 6.107) 
    69903  
    69904 
    69905 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    69906 
    69907 Chain information for AF3 E2 353-438.pdb #750 
    69908 --- 
    69909 Chain | Description 
    69910 B | No description available 
    69911  
    69912 
    69913 > matchmaker #750 to #1.30 & sel
    69914 
    69915 Parameters 
    69916 --- 
    69917 Chain pairing | bb 
    69918 Alignment algorithm | Needleman-Wunsch 
    69919 Similarity matrix | BLOSUM-62 
    69920 SS fraction | 0.3 
    69921 Gap open (HH/SS/other) | 18/18/6 
    69922 Gap extend | 1 
    69923 SS matrix |  |  | H | S | O 
    69924 ---|---|---|--- 
    69925 H | 6 | -9 | -6 
    69926 S |  | 6 | -6 
    69927 O |  |  | 4 
    69928 Iteration cutoff | 2 
    69929  
    69930 Matchmaker 3j0c.pdb1, chain H (#1.30) with AF3 E2 353-438.pdb, chain B (#750),
    69931 sequence alignment score = 329.4 
    69932 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    69933 8.150) 
    69934  
    69935 
    69936 > hide sel cartoons
    69937 
    69938 > select #1.30/H
    69939 
    69940 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    69941 
    69942 > show sel cartoons
    69943 
    69944 > hide sel cartoons
    69945 
    69946 > select #1.30/I
    69947 
    69948 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    69949 
    69950 > show sel cartoons
    69951 
    69952 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    69953 
    69954 Chain information for AF3 CA.pdb #751 
    69955 --- 
    69956 Chain | Description 
    69957 A | No description available 
    69958  
    69959 
    69960 > matchmaker #751 to #1.30 & sel
    69961 
    69962 Parameters 
    69963 --- 
    69964 Chain pairing | bb 
    69965 Alignment algorithm | Needleman-Wunsch 
    69966 Similarity matrix | BLOSUM-62 
    69967 SS fraction | 0.3 
    69968 Gap open (HH/SS/other) | 18/18/6 
    69969 Gap extend | 1 
    69970 SS matrix |  |  | H | S | O 
    69971 ---|---|---|--- 
    69972 H | 6 | -9 | -6 
    69973 S |  | 6 | -6 
    69974 O |  |  | 4 
    69975 Iteration cutoff | 2 
    69976  
    69977 Matchmaker 3j0c.pdb1, chain I (#1.30) with AF3 CA.pdb, chain A (#751),
    69978 sequence alignment score = 306.5 
    69979 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    69980 2.689) 
    69981  
    69982 
    69983 > hide sel cartoons
    69984 
    69985 > color #747 dodgerblue
    69986 
    69987 > color #748 dodgerblue
    69988 
    69989 > color #749 #00b305ff
    69990 
    69991 > color #750 #00b305ff
    69992 
    69993 > color #751 #f15839ff
    69994 
    69995 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    69996 
    69997 ——— End of log from Wed Jul 17 13:58:06 2024 ———
    69998 
    69999 opened ChimeraX session 
    70000 
    70001 > ui tool show Matchmaker
    70002 
    70003 The cached device pixel ratio value was stale on window expose. Please file a
    70004 QTBUG which explains how to reproduce. 
    70005 
    70006 > hide #702 models
    70007 
    70008 > hide #703 models
    70009 
    70010 > hide #704 models
    70011 
    70012 > hide #705 models
    70013 
    70014 > hide #706 models
    70015 
    70016 > hide #707 models
    70017 
    70018 > hide #708 models
    70019 
    70020 > hide #709 models
    70021 
    70022 > hide #710 models
    70023 
    70024 > hide #711 models
    70025 
    70026 > hide #712 models
    70027 
    70028 > hide #713 models
    70029 
    70030 > hide #714 models
    70031 
    70032 > hide #715 models
    70033 
    70034 > hide #716 models
    70035 
    70036 > hide #717 models
    70037 
    70038 > hide #718 models
    70039 
    70040 > hide #719 models
    70041 
    70042 > hide #720 models
    70043 
    70044 > hide #721 models
    70045 
    70046 > hide #722 models
    70047 
    70048 > hide #723 models
    70049 
    70050 > hide #724 models
    70051 
    70052 > hide #725 models
    70053 
    70054 > hide #726 models
    70055 
    70056 > hide #727 models
    70057 
    70058 > hide #728 models
    70059 
    70060 > hide #729 models
    70061 
    70062 > hide #730 models
    70063 
    70064 > hide #731 models
    70065 
    70066 > hide #732 models
    70067 
    70068 > hide #733 models
    70069 
    70070 > hide #734 models
    70071 
    70072 > hide #735 models
    70073 
    70074 > hide #736 models
    70075 
    70076 > hide #737 models
    70077 
    70078 > hide #738 models
    70079 
    70080 > hide #739 models
    70081 
    70082 > hide #740 models
    70083 
    70084 > hide #741 models
    70085 
    70086 > hide #742 models
    70087 
    70088 > hide #743 models
    70089 
    70090 > hide #744 models
    70091 
    70092 > hide #745 models
    70093 
    70094 > hide #746 models
    70095 
    70096 > hide #747 models
    70097 
    70098 > hide #748 models
    70099 
    70100 > hide #749 models
    70101 
    70102 > hide #750 models
    70103 
    70104 > hide #751 models
    70105 
    70106 > select #1.31/G
    70107 
    70108 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    70109 
    70110 > show sel cartoons
    70111 
    70112 > view
    70113 
    70114 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    70115 
    70116 Chain information for AF3 E1 1-421.pdb #752 
    70117 --- 
    70118 Chain | Description 
    70119 A | No description available 
    70120  
    70121 
    70122 > matchmaker #752 to #1.1
    70123 
    70124 Parameters 
    70125 --- 
    70126 Chain pairing | bb 
    70127 Alignment algorithm | Needleman-Wunsch 
    70128 Similarity matrix | BLOSUM-62 
    70129 SS fraction | 0.3 
    70130 Gap open (HH/SS/other) | 18/18/6 
    70131 Gap extend | 1 
    70132 SS matrix |  |  | H | S | O 
    70133 ---|---|---|--- 
    70134 H | 6 | -9 | -6 
    70135 S |  | 6 | -6 
    70136 O |  |  | 4 
    70137 Iteration cutoff | 2 
    70138  
    70139 Matchmaker 3j0c.pdb1, chain A (#1.1) with AF3 E1 1-421.pdb, chain A (#752),
    70140 sequence alignment score = 1060.7 
    70141 RMSD between 248 pruned atom pairs is 1.169 angstroms; (across all 403 pairs:
    70142 3.020) 
    70143  
    70144 
    70145 > matchmaker #752 to #1.1 & sel
    70146 
    70147 No 'to' model specified 
    70148 
    70149 > matchmaker #752 to #1.1 & sel
    70150 
    70151 No 'to' model specified 
    70152 
    70153 > close #752
    70154 
    70155 > hide sel cartoons
    70156 
    70157 > select #1.31/G
    70158 
    70159 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    70160 
    70161 > show sel cartoons
    70162 
    70163 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    70164 
    70165 Chain information for AF3 E1 1-421.pdb #752 
    70166 --- 
    70167 Chain | Description 
    70168 A | No description available 
    70169  
    70170 
    70171 > matchmaker #752 to #1.1 & sel
    70172 
    70173 No 'to' model specified 
    70174 
    70175 > matchmaker #752 & sel to #1.1 & sel
    70176 
    70177 No 'to' model specified 
    70178 
    70179 > select #1.1/H
    70180 
    70181 3304 atoms, 3400 bonds, 423 residues, 1 model selected 
    70182 
    70183 > show sel cartoons
    70184 
    70185 > hide sel cartoons
    70186 
    70187 > select #1.31/G
    70188 
    70189 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    70190 
    70191 > show sel cartoons
    70192 
    70193 > matchmaker #752 to #1.1 & sel
    70194 
    70195 No 'to' model specified 
    70196 
    70197 > show #751 models
    70198 
    70199 > show #750 models
    70200 
    70201 > show #749 models
    70202 
    70203 > show #748 models
    70204 
    70205 > show #747 models
    70206 
    70207 > select #1.30/H
    70208 
    70209 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    70210 
    70211 > hide sel cartoons
    70212 
    70213 > show sel cartoons
    70214 
    70215 > hide sel cartoons
    70216 
    70217 > select #1.30/G
    70218 
    70219 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    70220 
    70221 > show sel cartoons
    70222 
    70223 > hide sel cartoons
    70224 
    70225 > matchmaker #752 to #1.31 & sel
    70226 
    70227 No 'to' model specified 
    70228 
    70229 > select #1.31/G
    70230 
    70231 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    70232 
    70233 > show sel cartoons
    70234 
    70235 > matchmaker #752 to #1.31 & sel
    70236 
    70237 Parameters 
    70238 --- 
    70239 Chain pairing | bb 
    70240 Alignment algorithm | Needleman-Wunsch 
    70241 Similarity matrix | BLOSUM-62 
    70242 SS fraction | 0.3 
    70243 Gap open (HH/SS/other) | 18/18/6 
    70244 Gap extend | 1 
    70245 SS matrix |  |  | H | S | O 
    70246 ---|---|---|--- 
    70247 H | 6 | -9 | -6 
    70248 S |  | 6 | -6 
    70249 O |  |  | 4 
    70250 Iteration cutoff | 2 
    70251  
    70252 Matchmaker 3j0c.pdb1, chain G (#1.31) with AF3 E1 1-421.pdb, chain A (#752),
    70253 sequence alignment score = 1060.7 
    70254 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    70255 2.985) 
    70256  
    70257 
    70258 > view
    70259 
    70260 > hide sel cartoons
    70261 
    70262 > show sel cartoons
    70263 
    70264 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    70265 
    70266 Chain information for AF3 E1 422-461.pdb #753 
    70267 --- 
    70268 Chain | Description 
    70269 A | No description available 
    70270  
    70271 
    70272 > matchmaker #753 to #1.31 & sel
    70273 
    70274 Parameters 
    70275 --- 
    70276 Chain pairing | bb 
    70277 Alignment algorithm | Needleman-Wunsch 
    70278 Similarity matrix | BLOSUM-62 
    70279 SS fraction | 0.3 
    70280 Gap open (HH/SS/other) | 18/18/6 
    70281 Gap extend | 1 
    70282 SS matrix |  |  | H | S | O 
    70283 ---|---|---|--- 
    70284 H | 6 | -9 | -6 
    70285 S |  | 6 | -6 
    70286 O |  |  | 4 
    70287 Iteration cutoff | 2 
    70288  
    70289 Matchmaker 3j0c.pdb1, chain G (#1.31) with AF3 E1 422-461.pdb, chain A (#753),
    70290 sequence alignment score = 626.9 
    70291 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    70292 2.997) 
    70293  
    70294 
    70295 > hide sel cartoons
    70296 
    70297 > select #1.31/H
    70298 
    70299 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    70300 
    70301 > show sel cartoons
    70302 
    70303 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    70304 
    70305 Chain information for AF3 E2 1-352.pdb #754 
    70306 --- 
    70307 Chain | Description 
    70308 B | No description available 
    70309  
    70310 
    70311 > matchmaker #754 to #1.31 & sel
    70312 
    70313 Parameters 
    70314 --- 
    70315 Chain pairing | bb 
    70316 Alignment algorithm | Needleman-Wunsch 
    70317 Similarity matrix | BLOSUM-62 
    70318 SS fraction | 0.3 
    70319 Gap open (HH/SS/other) | 18/18/6 
    70320 Gap extend | 1 
    70321 SS matrix |  |  | H | S | O 
    70322 ---|---|---|--- 
    70323 H | 6 | -9 | -6 
    70324 S |  | 6 | -6 
    70325 O |  |  | 4 
    70326 Iteration cutoff | 2 
    70327  
    70328 Matchmaker 3j0c.pdb1, chain H (#1.31) with AF3 E2 1-352.pdb, chain B (#754),
    70329 sequence alignment score = 590.9 
    70330 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    70331 6.107) 
    70332  
    70333 
    70334 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    70335 
    70336 Chain information for AF3 E2 353-438.pdb #755 
    70337 --- 
    70338 Chain | Description 
    70339 B | No description available 
    70340  
    70341 
    70342 > matchmaker #755 to #1.31 & sel
    70343 
    70344 Parameters 
    70345 --- 
    70346 Chain pairing | bb 
    70347 Alignment algorithm | Needleman-Wunsch 
    70348 Similarity matrix | BLOSUM-62 
    70349 SS fraction | 0.3 
    70350 Gap open (HH/SS/other) | 18/18/6 
    70351 Gap extend | 1 
    70352 SS matrix |  |  | H | S | O 
    70353 ---|---|---|--- 
    70354 H | 6 | -9 | -6 
    70355 S |  | 6 | -6 
    70356 O |  |  | 4 
    70357 Iteration cutoff | 2 
    70358  
    70359 Matchmaker 3j0c.pdb1, chain H (#1.31) with AF3 E2 353-438.pdb, chain B (#755),
    70360 sequence alignment score = 329.4 
    70361 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    70362 8.150) 
    70363  
    70364 
    70365 > hide sel cartoons
    70366 
    70367 > select #1.31/I
    70368 
    70369 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    70370 
    70371 > show sel cartoons
    70372 
    70373 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    70374 
    70375 Chain information for AF3 CA.pdb #756 
    70376 --- 
    70377 Chain | Description 
    70378 A | No description available 
    70379  
    70380 
    70381 > matchmaker #756 to #1.31 & sel
    70382 
    70383 Parameters 
    70384 --- 
    70385 Chain pairing | bb 
    70386 Alignment algorithm | Needleman-Wunsch 
    70387 Similarity matrix | BLOSUM-62 
    70388 SS fraction | 0.3 
    70389 Gap open (HH/SS/other) | 18/18/6 
    70390 Gap extend | 1 
    70391 SS matrix |  |  | H | S | O 
    70392 ---|---|---|--- 
    70393 H | 6 | -9 | -6 
    70394 S |  | 6 | -6 
    70395 O |  |  | 4 
    70396 Iteration cutoff | 2 
    70397  
    70398 Matchmaker 3j0c.pdb1, chain I (#1.31) with AF3 CA.pdb, chain A (#756),
    70399 sequence alignment score = 306.5 
    70400 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    70401 2.689) 
    70402  
    70403 
    70404 > hide sel cartoons
    70405 
    70406 > hide #747 models
    70407 
    70408 > hide #748 models
    70409 
    70410 > hide #749 models
    70411 
    70412 > hide #750 models
    70413 
    70414 > hide #751 models
    70415 
    70416 > color #752 dodgerblue
    70417 
    70418 > color #753 dodgerblue
    70419 
    70420 > color #754 #00b305ff
    70421 
    70422 > color #755 #00b305ff
    70423 
    70424 > color #756 #f15839ff
    70425 
    70426 > select #1.32/G
    70427 
    70428 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    70429 
    70430 > show sel cartoons
    70431 
    70432 [Repeated 1 time(s)]
    70433 
    70434 > view
    70435 
    70436 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    70437 
    70438 Chain information for AF3 E1 1-421.pdb #757 
    70439 --- 
    70440 Chain | Description 
    70441 A | No description available 
    70442  
    70443 
    70444 > matchmaker #757 to #1.32 & sel
    70445 
    70446 Parameters 
    70447 --- 
    70448 Chain pairing | bb 
    70449 Alignment algorithm | Needleman-Wunsch 
    70450 Similarity matrix | BLOSUM-62 
    70451 SS fraction | 0.3 
    70452 Gap open (HH/SS/other) | 18/18/6 
    70453 Gap extend | 1 
    70454 SS matrix |  |  | H | S | O 
    70455 ---|---|---|--- 
    70456 H | 6 | -9 | -6 
    70457 S |  | 6 | -6 
    70458 O |  |  | 4 
    70459 Iteration cutoff | 2 
    70460  
    70461 Matchmaker 3j0c.pdb1, chain G (#1.32) with AF3 E1 1-421.pdb, chain A (#757),
    70462 sequence alignment score = 1060.7 
    70463 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    70464 2.985) 
    70465  
    70466 
    70467 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    70468 
    70469 Chain information for AF3 E1 422-461.pdb #758 
    70470 --- 
    70471 Chain | Description 
    70472 A | No description available 
    70473  
    70474 
    70475 > matchmaker #758 to #1.32 & sel
    70476 
    70477 Parameters 
    70478 --- 
    70479 Chain pairing | bb 
    70480 Alignment algorithm | Needleman-Wunsch 
    70481 Similarity matrix | BLOSUM-62 
    70482 SS fraction | 0.3 
    70483 Gap open (HH/SS/other) | 18/18/6 
    70484 Gap extend | 1 
    70485 SS matrix |  |  | H | S | O 
    70486 ---|---|---|--- 
    70487 H | 6 | -9 | -6 
    70488 S |  | 6 | -6 
    70489 O |  |  | 4 
    70490 Iteration cutoff | 2 
    70491  
    70492 Matchmaker 3j0c.pdb1, chain G (#1.32) with AF3 E1 422-461.pdb, chain A (#758),
    70493 sequence alignment score = 626.9 
    70494 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    70495 2.997) 
    70496  
    70497 
    70498 > hide sel cartoons
    70499 
    70500 > select #1.32/H
    70501 
    70502 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    70503 
    70504 > show sel cartoons
    70505 
    70506 [Repeated 1 time(s)]
    70507 
    70508 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    70509 
    70510 Chain information for AF3 E2 1-352.pdb #759 
    70511 --- 
    70512 Chain | Description 
    70513 B | No description available 
    70514  
    70515 
    70516 > matchmaker #759 to #1.32 & sel
    70517 
    70518 Parameters 
    70519 --- 
    70520 Chain pairing | bb 
    70521 Alignment algorithm | Needleman-Wunsch 
    70522 Similarity matrix | BLOSUM-62 
    70523 SS fraction | 0.3 
    70524 Gap open (HH/SS/other) | 18/18/6 
    70525 Gap extend | 1 
    70526 SS matrix |  |  | H | S | O 
    70527 ---|---|---|--- 
    70528 H | 6 | -9 | -6 
    70529 S |  | 6 | -6 
    70530 O |  |  | 4 
    70531 Iteration cutoff | 2 
    70532  
    70533 Matchmaker 3j0c.pdb1, chain H (#1.32) with AF3 E2 1-352.pdb, chain B (#759),
    70534 sequence alignment score = 590.9 
    70535 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    70536 6.107) 
    70537  
    70538 
    70539 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    70540 
    70541 Chain information for AF3 E2 353-438.pdb #760 
    70542 --- 
    70543 Chain | Description 
    70544 B | No description available 
    70545  
    70546 
    70547 > matchmaker #760 to #1.32 & sel
    70548 
    70549 Parameters 
    70550 --- 
    70551 Chain pairing | bb 
    70552 Alignment algorithm | Needleman-Wunsch 
    70553 Similarity matrix | BLOSUM-62 
    70554 SS fraction | 0.3 
    70555 Gap open (HH/SS/other) | 18/18/6 
    70556 Gap extend | 1 
    70557 SS matrix |  |  | H | S | O 
    70558 ---|---|---|--- 
    70559 H | 6 | -9 | -6 
    70560 S |  | 6 | -6 
    70561 O |  |  | 4 
    70562 Iteration cutoff | 2 
    70563  
    70564 Matchmaker 3j0c.pdb1, chain H (#1.32) with AF3 E2 353-438.pdb, chain B (#760),
    70565 sequence alignment score = 329.4 
    70566 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    70567 8.150) 
    70568  
    70569 
    70570 > hide sel cartoons
    70571 
    70572 > select #1.32/I
    70573 
    70574 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    70575 
    70576 > show sel cartoons
    70577 
    70578 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    70579 
    70580 Chain information for AF3 CA.pdb #761 
    70581 --- 
    70582 Chain | Description 
    70583 A | No description available 
    70584  
    70585 
    70586 > matchmaker #761 to #1.32 & sel
    70587 
    70588 Parameters 
    70589 --- 
    70590 Chain pairing | bb 
    70591 Alignment algorithm | Needleman-Wunsch 
    70592 Similarity matrix | BLOSUM-62 
    70593 SS fraction | 0.3 
    70594 Gap open (HH/SS/other) | 18/18/6 
    70595 Gap extend | 1 
    70596 SS matrix |  |  | H | S | O 
    70597 ---|---|---|--- 
    70598 H | 6 | -9 | -6 
    70599 S |  | 6 | -6 
    70600 O |  |  | 4 
    70601 Iteration cutoff | 2 
    70602  
    70603 Matchmaker 3j0c.pdb1, chain I (#1.32) with AF3 CA.pdb, chain A (#761),
    70604 sequence alignment score = 306.5 
    70605 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    70606 2.689) 
    70607  
    70608 
    70609 > hide sel cartoons
    70610 
    70611 > color #757 dodgerblue
    70612 
    70613 > color #758 dodgerblue
    70614 
    70615 > color #759 #00b305ff
    70616 
    70617 > color #760 #00b305ff
    70618 
    70619 > color #761 #f15839ff
    70620 
    70621 > select #1.33/G
    70622 
    70623 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    70624 
    70625 > show sel cartoons
    70626 
    70627 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    70628 
    70629 Chain information for AF3 E1 1-421.pdb #762 
    70630 --- 
    70631 Chain | Description 
    70632 A | No description available 
    70633  
    70634 
    70635 > matchmaker #762 to #1.33 & sel
    70636 
    70637 Parameters 
    70638 --- 
    70639 Chain pairing | bb 
    70640 Alignment algorithm | Needleman-Wunsch 
    70641 Similarity matrix | BLOSUM-62 
    70642 SS fraction | 0.3 
    70643 Gap open (HH/SS/other) | 18/18/6 
    70644 Gap extend | 1 
    70645 SS matrix |  |  | H | S | O 
    70646 ---|---|---|--- 
    70647 H | 6 | -9 | -6 
    70648 S |  | 6 | -6 
    70649 O |  |  | 4 
    70650 Iteration cutoff | 2 
    70651  
    70652 Matchmaker 3j0c.pdb1, chain G (#1.33) with AF3 E1 1-421.pdb, chain A (#762),
    70653 sequence alignment score = 1060.7 
    70654 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    70655 2.985) 
    70656  
    70657 
    70658 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    70659 
    70660 Chain information for AF3 E1 422-461.pdb #763 
    70661 --- 
    70662 Chain | Description 
    70663 A | No description available 
    70664  
    70665 
    70666 > matchmaker #763 to #1.33 & sel
    70667 
    70668 Parameters 
    70669 --- 
    70670 Chain pairing | bb 
    70671 Alignment algorithm | Needleman-Wunsch 
    70672 Similarity matrix | BLOSUM-62 
    70673 SS fraction | 0.3 
    70674 Gap open (HH/SS/other) | 18/18/6 
    70675 Gap extend | 1 
    70676 SS matrix |  |  | H | S | O 
    70677 ---|---|---|--- 
    70678 H | 6 | -9 | -6 
    70679 S |  | 6 | -6 
    70680 O |  |  | 4 
    70681 Iteration cutoff | 2 
    70682  
    70683 Matchmaker 3j0c.pdb1, chain G (#1.33) with AF3 E1 422-461.pdb, chain A (#763),
    70684 sequence alignment score = 626.9 
    70685 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    70686 2.997) 
    70687  
    70688 
    70689 > select #1.32/H
    70690 
    70691 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    70692 
    70693 > show sel cartoons
    70694 
    70695 > hide sel cartoons
    70696 
    70697 > select #1.33/H
    70698 
    70699 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    70700 
    70701 > show sel cartoons
    70702 
    70703 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    70704 
    70705 Chain information for AF3 E2 1-352.pdb #764 
    70706 --- 
    70707 Chain | Description 
    70708 B | No description available 
    70709  
    70710 
    70711 > matchmaker #764 to #1.33 & sel
    70712 
    70713 Parameters 
    70714 --- 
    70715 Chain pairing | bb 
    70716 Alignment algorithm | Needleman-Wunsch 
    70717 Similarity matrix | BLOSUM-62 
    70718 SS fraction | 0.3 
    70719 Gap open (HH/SS/other) | 18/18/6 
    70720 Gap extend | 1 
    70721 SS matrix |  |  | H | S | O 
    70722 ---|---|---|--- 
    70723 H | 6 | -9 | -6 
    70724 S |  | 6 | -6 
    70725 O |  |  | 4 
    70726 Iteration cutoff | 2 
    70727  
    70728 Matchmaker 3j0c.pdb1, chain H (#1.33) with AF3 E2 1-352.pdb, chain B (#764),
    70729 sequence alignment score = 590.9 
    70730 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    70731 6.107) 
    70732  
    70733 
    70734 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    70735 
    70736 Chain information for AF3 E2 353-438.pdb #765 
    70737 --- 
    70738 Chain | Description 
    70739 B | No description available 
    70740  
    70741 
    70742 > matchmaker #765 to #1.33 & sel
    70743 
    70744 Parameters 
    70745 --- 
    70746 Chain pairing | bb 
    70747 Alignment algorithm | Needleman-Wunsch 
    70748 Similarity matrix | BLOSUM-62 
    70749 SS fraction | 0.3 
    70750 Gap open (HH/SS/other) | 18/18/6 
    70751 Gap extend | 1 
    70752 SS matrix |  |  | H | S | O 
    70753 ---|---|---|--- 
    70754 H | 6 | -9 | -6 
    70755 S |  | 6 | -6 
    70756 O |  |  | 4 
    70757 Iteration cutoff | 2 
    70758  
    70759 Matchmaker 3j0c.pdb1, chain H (#1.33) with AF3 E2 353-438.pdb, chain B (#765),
    70760 sequence alignment score = 329.4 
    70761 RMSD between 40 pruned atom pairs is 0.937 angstroms; (across all 84 pairs:
    70762 8.151) 
    70763  
    70764 
    70765 > hide sel cartoons
    70766 
    70767 > select #1.33/I
    70768 
    70769 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    70770 
    70771 > show sel cartoons
    70772 
    70773 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    70774 
    70775 Chain information for AF3 CA.pdb #766 
    70776 --- 
    70777 Chain | Description 
    70778 A | No description available 
    70779  
    70780 
    70781 > matchmaker #766 to #1.33 & sel
    70782 
    70783 Parameters 
    70784 --- 
    70785 Chain pairing | bb 
    70786 Alignment algorithm | Needleman-Wunsch 
    70787 Similarity matrix | BLOSUM-62 
    70788 SS fraction | 0.3 
    70789 Gap open (HH/SS/other) | 18/18/6 
    70790 Gap extend | 1 
    70791 SS matrix |  |  | H | S | O 
    70792 ---|---|---|--- 
    70793 H | 6 | -9 | -6 
    70794 S |  | 6 | -6 
    70795 O |  |  | 4 
    70796 Iteration cutoff | 2 
    70797  
    70798 Matchmaker 3j0c.pdb1, chain I (#1.33) with AF3 CA.pdb, chain A (#766),
    70799 sequence alignment score = 306.5 
    70800 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    70801 2.689) 
    70802  
    70803 
    70804 > hide sel cartoons
    70805 
    70806 > color #762 dodgerblue
    70807 
    70808 > color #763 dodgerblue
    70809 
    70810 > color #764 #00b305ff
    70811 
    70812 > color #765 #00b305ff
    70813 
    70814 > color #766 #f15839ff
    70815 
    70816 > select #1.33/G
    70817 
    70818 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    70819 
    70820 > hide sel cartoons
    70821 
    70822 > select #1.34/G
    70823 
    70824 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    70825 
    70826 > show sel cartoons
    70827 
    70828 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    70829 
    70830 Chain information for AF3 E1 1-421.pdb #767 
    70831 --- 
    70832 Chain | Description 
    70833 A | No description available 
    70834  
    70835 
    70836 > matchmaker #767 to #1.34 & sel
    70837 
    70838 Parameters 
    70839 --- 
    70840 Chain pairing | bb 
    70841 Alignment algorithm | Needleman-Wunsch 
    70842 Similarity matrix | BLOSUM-62 
    70843 SS fraction | 0.3 
    70844 Gap open (HH/SS/other) | 18/18/6 
    70845 Gap extend | 1 
    70846 SS matrix |  |  | H | S | O 
    70847 ---|---|---|--- 
    70848 H | 6 | -9 | -6 
    70849 S |  | 6 | -6 
    70850 O |  |  | 4 
    70851 Iteration cutoff | 2 
    70852  
    70853 Matchmaker 3j0c.pdb1, chain G (#1.34) with AF3 E1 1-421.pdb, chain A (#767),
    70854 sequence alignment score = 1060.7 
    70855 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    70856 2.985) 
    70857  
    70858 
    70859 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    70860 
    70861 Chain information for AF3 E1 422-461.pdb #768 
    70862 --- 
    70863 Chain | Description 
    70864 A | No description available 
    70865  
    70866 
    70867 > matchmaker #768 to #1.34 & sel
    70868 
    70869 Parameters 
    70870 --- 
    70871 Chain pairing | bb 
    70872 Alignment algorithm | Needleman-Wunsch 
    70873 Similarity matrix | BLOSUM-62 
    70874 SS fraction | 0.3 
    70875 Gap open (HH/SS/other) | 18/18/6 
    70876 Gap extend | 1 
    70877 SS matrix |  |  | H | S | O 
    70878 ---|---|---|--- 
    70879 H | 6 | -9 | -6 
    70880 S |  | 6 | -6 
    70881 O |  |  | 4 
    70882 Iteration cutoff | 2 
    70883  
    70884 Matchmaker 3j0c.pdb1, chain G (#1.34) with AF3 E1 422-461.pdb, chain A (#768),
    70885 sequence alignment score = 626.9 
    70886 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    70887 2.997) 
    70888  
    70889 
    70890 > hide sel cartoons
    70891 
    70892 > select #1.34/H
    70893 
    70894 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    70895 
    70896 > show sel cartoons
    70897 
    70898 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    70899 
    70900 Chain information for AF3 E2 1-352.pdb #769 
    70901 --- 
    70902 Chain | Description 
    70903 B | No description available 
    70904  
    70905 
    70906 > matchmaker #769 to #1.34 & sel
    70907 
    70908 Parameters 
    70909 --- 
    70910 Chain pairing | bb 
    70911 Alignment algorithm | Needleman-Wunsch 
    70912 Similarity matrix | BLOSUM-62 
    70913 SS fraction | 0.3 
    70914 Gap open (HH/SS/other) | 18/18/6 
    70915 Gap extend | 1 
    70916 SS matrix |  |  | H | S | O 
    70917 ---|---|---|--- 
    70918 H | 6 | -9 | -6 
    70919 S |  | 6 | -6 
    70920 O |  |  | 4 
    70921 Iteration cutoff | 2 
    70922  
    70923 Matchmaker 3j0c.pdb1, chain H (#1.34) with AF3 E2 1-352.pdb, chain B (#769),
    70924 sequence alignment score = 590.9 
    70925 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    70926 6.107) 
    70927  
    70928 
    70929 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    70930 
    70931 Chain information for AF3 E2 353-438.pdb #770 
    70932 --- 
    70933 Chain | Description 
    70934 B | No description available 
    70935  
    70936 
    70937 > matchmaker #770 to #1.34 & sel
    70938 
    70939 Parameters 
    70940 --- 
    70941 Chain pairing | bb 
    70942 Alignment algorithm | Needleman-Wunsch 
    70943 Similarity matrix | BLOSUM-62 
    70944 SS fraction | 0.3 
    70945 Gap open (HH/SS/other) | 18/18/6 
    70946 Gap extend | 1 
    70947 SS matrix |  |  | H | S | O 
    70948 ---|---|---|--- 
    70949 H | 6 | -9 | -6 
    70950 S |  | 6 | -6 
    70951 O |  |  | 4 
    70952 Iteration cutoff | 2 
    70953  
    70954 Matchmaker 3j0c.pdb1, chain H (#1.34) with AF3 E2 353-438.pdb, chain B (#770),
    70955 sequence alignment score = 329.4 
    70956 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    70957 8.150) 
    70958  
    70959 
    70960 > hide sel cartoons
    70961 
    70962 > select #1.34/I
    70963 
    70964 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    70965 
    70966 > show sel cartoons
    70967 
    70968 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    70969 
    70970 Chain information for AF3 CA.pdb #771 
    70971 --- 
    70972 Chain | Description 
    70973 A | No description available 
    70974  
    70975 
    70976 > matchmaker #771 to #1.34 & sel
    70977 
    70978 Parameters 
    70979 --- 
    70980 Chain pairing | bb 
    70981 Alignment algorithm | Needleman-Wunsch 
    70982 Similarity matrix | BLOSUM-62 
    70983 SS fraction | 0.3 
    70984 Gap open (HH/SS/other) | 18/18/6 
    70985 Gap extend | 1 
    70986 SS matrix |  |  | H | S | O 
    70987 ---|---|---|--- 
    70988 H | 6 | -9 | -6 
    70989 S |  | 6 | -6 
    70990 O |  |  | 4 
    70991 Iteration cutoff | 2 
    70992  
    70993 Matchmaker 3j0c.pdb1, chain I (#1.34) with AF3 CA.pdb, chain A (#771),
    70994 sequence alignment score = 306.5 
    70995 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    70996 2.689) 
    70997  
    70998 
    70999 > hide sel cartoons
    71000 
    71001 > color #767 dodgerblue
    71002 
    71003 > color #768 dodgerblue
    71004 
    71005 > color #769 #00b305ff
    71006 
    71007 > color #770 #00b305ff
    71008 
    71009 > color #771 #f15839ff
    71010 
    71011 > select #1.35/G
    71012 
    71013 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    71014 
    71015 > show sel cartoons
    71016 
    71017 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    71018 
    71019 Chain information for AF3 E1 1-421.pdb #772 
    71020 --- 
    71021 Chain | Description 
    71022 A | No description available 
    71023  
    71024 
    71025 > matchmaker #772 to #1.34 & sel
    71026 
    71027 No 'to' model specified 
    71028 
    71029 > matchmaker #772 to #1.35 & sel
    71030 
    71031 Parameters 
    71032 --- 
    71033 Chain pairing | bb 
    71034 Alignment algorithm | Needleman-Wunsch 
    71035 Similarity matrix | BLOSUM-62 
    71036 SS fraction | 0.3 
    71037 Gap open (HH/SS/other) | 18/18/6 
    71038 Gap extend | 1 
    71039 SS matrix |  |  | H | S | O 
    71040 ---|---|---|--- 
    71041 H | 6 | -9 | -6 
    71042 S |  | 6 | -6 
    71043 O |  |  | 4 
    71044 Iteration cutoff | 2 
    71045  
    71046 Matchmaker 3j0c.pdb1, chain G (#1.35) with AF3 E1 1-421.pdb, chain A (#772),
    71047 sequence alignment score = 1060.7 
    71048 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    71049 2.985) 
    71050  
    71051 
    71052 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    71053 
    71054 Chain information for AF3 E1 422-461.pdb #773 
    71055 --- 
    71056 Chain | Description 
    71057 A | No description available 
    71058  
    71059 
    71060 > matchmaker #773 to #1.35 & sel
    71061 
    71062 Parameters 
    71063 --- 
    71064 Chain pairing | bb 
    71065 Alignment algorithm | Needleman-Wunsch 
    71066 Similarity matrix | BLOSUM-62 
    71067 SS fraction | 0.3 
    71068 Gap open (HH/SS/other) | 18/18/6 
    71069 Gap extend | 1 
    71070 SS matrix |  |  | H | S | O 
    71071 ---|---|---|--- 
    71072 H | 6 | -9 | -6 
    71073 S |  | 6 | -6 
    71074 O |  |  | 4 
    71075 Iteration cutoff | 2 
    71076  
    71077 Matchmaker 3j0c.pdb1, chain G (#1.35) with AF3 E1 422-461.pdb, chain A (#773),
    71078 sequence alignment score = 626.9 
    71079 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    71080 2.997) 
    71081  
    71082 
    71083 > hide sel cartoons
    71084 
    71085 > select #1.35/H
    71086 
    71087 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    71088 
    71089 > show sel cartoons
    71090 
    71091 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    71092 
    71093 Chain information for AF3 E2 1-352.pdb #774 
    71094 --- 
    71095 Chain | Description 
    71096 B | No description available 
    71097  
    71098 
    71099 > matchmaker #774 to #1.35 & sel
    71100 
    71101 Parameters 
    71102 --- 
    71103 Chain pairing | bb 
    71104 Alignment algorithm | Needleman-Wunsch 
    71105 Similarity matrix | BLOSUM-62 
    71106 SS fraction | 0.3 
    71107 Gap open (HH/SS/other) | 18/18/6 
    71108 Gap extend | 1 
    71109 SS matrix |  |  | H | S | O 
    71110 ---|---|---|--- 
    71111 H | 6 | -9 | -6 
    71112 S |  | 6 | -6 
    71113 O |  |  | 4 
    71114 Iteration cutoff | 2 
    71115  
    71116 Matchmaker 3j0c.pdb1, chain H (#1.35) with AF3 E2 1-352.pdb, chain B (#774),
    71117 sequence alignment score = 590.9 
    71118 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    71119 6.107) 
    71120  
    71121 
    71122 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    71123 
    71124 Chain information for AF3 E2 353-438.pdb #775 
    71125 --- 
    71126 Chain | Description 
    71127 B | No description available 
    71128  
    71129 
    71130 > matchmaker #775 to #1.35 & sel
    71131 
    71132 Parameters 
    71133 --- 
    71134 Chain pairing | bb 
    71135 Alignment algorithm | Needleman-Wunsch 
    71136 Similarity matrix | BLOSUM-62 
    71137 SS fraction | 0.3 
    71138 Gap open (HH/SS/other) | 18/18/6 
    71139 Gap extend | 1 
    71140 SS matrix |  |  | H | S | O 
    71141 ---|---|---|--- 
    71142 H | 6 | -9 | -6 
    71143 S |  | 6 | -6 
    71144 O |  |  | 4 
    71145 Iteration cutoff | 2 
    71146  
    71147 Matchmaker 3j0c.pdb1, chain H (#1.35) with AF3 E2 353-438.pdb, chain B (#775),
    71148 sequence alignment score = 329.4 
    71149 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    71150 8.150) 
    71151  
    71152 
    71153 > hide sel cartoons
    71154 
    71155 > select #1.35/I
    71156 
    71157 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    71158 
    71159 > show sel cartoons
    71160 
    71161 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    71162 
    71163 Chain information for AF3 CA.pdb #776 
    71164 --- 
    71165 Chain | Description 
    71166 A | No description available 
    71167  
    71168 
    71169 > matchmaker #776 to #1.35 & sel
    71170 
    71171 Parameters 
    71172 --- 
    71173 Chain pairing | bb 
    71174 Alignment algorithm | Needleman-Wunsch 
    71175 Similarity matrix | BLOSUM-62 
    71176 SS fraction | 0.3 
    71177 Gap open (HH/SS/other) | 18/18/6 
    71178 Gap extend | 1 
    71179 SS matrix |  |  | H | S | O 
    71180 ---|---|---|--- 
    71181 H | 6 | -9 | -6 
    71182 S |  | 6 | -6 
    71183 O |  |  | 4 
    71184 Iteration cutoff | 2 
    71185  
    71186 Matchmaker 3j0c.pdb1, chain I (#1.35) with AF3 CA.pdb, chain A (#776),
    71187 sequence alignment score = 306.5 
    71188 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    71189 2.689) 
    71190  
    71191 
    71192 > hide sel cartoons
    71193 
    71194 > color #772 dodgerblue
    71195 
    71196 > color #773 dodgerblue
    71197 
    71198 > color #774 #00b305ff
    71199 
    71200 > color #775 #00b305ff
    71201 
    71202 > color #776 #f15839ff
    71203 
    71204 > select #1.36/G
    71205 
    71206 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    71207 
    71208 > show sel cartoons
    71209 
    71210 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    71211 
    71212 Chain information for AF3 E1 1-421.pdb #777 
    71213 --- 
    71214 Chain | Description 
    71215 A | No description available 
    71216  
    71217 
    71218 > matchmaker #777 to #1.36 & sel
    71219 
    71220 Parameters 
    71221 --- 
    71222 Chain pairing | bb 
    71223 Alignment algorithm | Needleman-Wunsch 
    71224 Similarity matrix | BLOSUM-62 
    71225 SS fraction | 0.3 
    71226 Gap open (HH/SS/other) | 18/18/6 
    71227 Gap extend | 1 
    71228 SS matrix |  |  | H | S | O 
    71229 ---|---|---|--- 
    71230 H | 6 | -9 | -6 
    71231 S |  | 6 | -6 
    71232 O |  |  | 4 
    71233 Iteration cutoff | 2 
    71234  
    71235 Matchmaker 3j0c.pdb1, chain G (#1.36) with AF3 E1 1-421.pdb, chain A (#777),
    71236 sequence alignment score = 1060.7 
    71237 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    71238 2.985) 
    71239  
    71240 
    71241 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    71242 
    71243 Chain information for AF3 E1 422-461.pdb #778 
    71244 --- 
    71245 Chain | Description 
    71246 A | No description available 
    71247  
    71248 
    71249 > matchmaker #778 to #1.36 & sel
    71250 
    71251 Parameters 
    71252 --- 
    71253 Chain pairing | bb 
    71254 Alignment algorithm | Needleman-Wunsch 
    71255 Similarity matrix | BLOSUM-62 
    71256 SS fraction | 0.3 
    71257 Gap open (HH/SS/other) | 18/18/6 
    71258 Gap extend | 1 
    71259 SS matrix |  |  | H | S | O 
    71260 ---|---|---|--- 
    71261 H | 6 | -9 | -6 
    71262 S |  | 6 | -6 
    71263 O |  |  | 4 
    71264 Iteration cutoff | 2 
    71265  
    71266 Matchmaker 3j0c.pdb1, chain G (#1.36) with AF3 E1 422-461.pdb, chain A (#778),
    71267 sequence alignment score = 626.9 
    71268 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    71269 2.997) 
    71270  
    71271 
    71272 > hide sel cartoons
    71273 
    71274 > select #1.36/H
    71275 
    71276 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    71277 
    71278 > show sel cartoons
    71279 
    71280 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    71281 
    71282 Chain information for AF3 E2 1-352.pdb #779 
    71283 --- 
    71284 Chain | Description 
    71285 B | No description available 
    71286  
    71287 
    71288 > matchmaker #779 to #1.36 & sel
    71289 
    71290 Parameters 
    71291 --- 
    71292 Chain pairing | bb 
    71293 Alignment algorithm | Needleman-Wunsch 
    71294 Similarity matrix | BLOSUM-62 
    71295 SS fraction | 0.3 
    71296 Gap open (HH/SS/other) | 18/18/6 
    71297 Gap extend | 1 
    71298 SS matrix |  |  | H | S | O 
    71299 ---|---|---|--- 
    71300 H | 6 | -9 | -6 
    71301 S |  | 6 | -6 
    71302 O |  |  | 4 
    71303 Iteration cutoff | 2 
    71304  
    71305 Matchmaker 3j0c.pdb1, chain H (#1.36) with AF3 E2 1-352.pdb, chain B (#779),
    71306 sequence alignment score = 590.9 
    71307 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    71308 6.107) 
    71309  
    71310 
    71311 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    71312 
    71313 Chain information for AF3 E2 353-438.pdb #780 
    71314 --- 
    71315 Chain | Description 
    71316 B | No description available 
    71317  
    71318 
    71319 > matchmaker #780 to #1.36 & sel
    71320 
    71321 Parameters 
    71322 --- 
    71323 Chain pairing | bb 
    71324 Alignment algorithm | Needleman-Wunsch 
    71325 Similarity matrix | BLOSUM-62 
    71326 SS fraction | 0.3 
    71327 Gap open (HH/SS/other) | 18/18/6 
    71328 Gap extend | 1 
    71329 SS matrix |  |  | H | S | O 
    71330 ---|---|---|--- 
    71331 H | 6 | -9 | -6 
    71332 S |  | 6 | -6 
    71333 O |  |  | 4 
    71334 Iteration cutoff | 2 
    71335  
    71336 Matchmaker 3j0c.pdb1, chain H (#1.36) with AF3 E2 353-438.pdb, chain B (#780),
    71337 sequence alignment score = 329.4 
    71338 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    71339 8.151) 
    71340  
    71341 
    71342 > hide sel cartoons
    71343 
    71344 > select #1.36/I
    71345 
    71346 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    71347 
    71348 > show sel cartoons
    71349 
    71350 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    71351 
    71352 Chain information for AF3 CA.pdb #781 
    71353 --- 
    71354 Chain | Description 
    71355 A | No description available 
    71356  
    71357 
    71358 > matchmaker #781 to #1.36 & sel
    71359 
    71360 Parameters 
    71361 --- 
    71362 Chain pairing | bb 
    71363 Alignment algorithm | Needleman-Wunsch 
    71364 Similarity matrix | BLOSUM-62 
    71365 SS fraction | 0.3 
    71366 Gap open (HH/SS/other) | 18/18/6 
    71367 Gap extend | 1 
    71368 SS matrix |  |  | H | S | O 
    71369 ---|---|---|--- 
    71370 H | 6 | -9 | -6 
    71371 S |  | 6 | -6 
    71372 O |  |  | 4 
    71373 Iteration cutoff | 2 
    71374  
    71375 Matchmaker 3j0c.pdb1, chain I (#1.36) with AF3 CA.pdb, chain A (#781),
    71376 sequence alignment score = 306.5 
    71377 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    71378 2.689) 
    71379  
    71380 
    71381 > hide sel cartoons
    71382 
    71383 > color #777 dodgerblue
    71384 
    71385 > color #778 dodgerblue
    71386 
    71387 > color #779 #00b305ff
    71388 
    71389 > color #780 #00b305ff
    71390 
    71391 > color #781 #f15839ff
    71392 
    71393 > select #1.38/G
    71394 
    71395 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    71396 
    71397 > show sel cartoons
    71398 
    71399 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    71400 
    71401 Chain information for AF3 E1 1-421.pdb #782 
    71402 --- 
    71403 Chain | Description 
    71404 A | No description available 
    71405  
    71406 
    71407 > matchmaker #782 to #1.36 & sel
    71408 
    71409 No 'to' model specified 
    71410 
    71411 > matchmaker #782 to #1.37 & sel
    71412 
    71413 No 'to' model specified 
    71414 
    71415 > matchmaker #782 to #1.37 & sel
    71416 
    71417 No 'to' model specified 
    71418 
    71419 > hide sel cartoons
    71420 
    71421 > select #1.38/G
    71422 
    71423 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    71424 
    71425 > show sel cartoons
    71426 
    71427 > matchmaker #782 to #1.38 & sel
    71428 
    71429 Parameters 
    71430 --- 
    71431 Chain pairing | bb 
    71432 Alignment algorithm | Needleman-Wunsch 
    71433 Similarity matrix | BLOSUM-62 
    71434 SS fraction | 0.3 
    71435 Gap open (HH/SS/other) | 18/18/6 
    71436 Gap extend | 1 
    71437 SS matrix |  |  | H | S | O 
    71438 ---|---|---|--- 
    71439 H | 6 | -9 | -6 
    71440 S |  | 6 | -6 
    71441 O |  |  | 4 
    71442 Iteration cutoff | 2 
    71443  
    71444 Matchmaker 3j0c.pdb1, chain G (#1.38) with AF3 E1 1-421.pdb, chain A (#782),
    71445 sequence alignment score = 1060.7 
    71446 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    71447 2.985) 
    71448  
    71449 
    71450 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    71451 
    71452 Chain information for AF3 E1 422-461.pdb #783 
    71453 --- 
    71454 Chain | Description 
    71455 A | No description available 
    71456  
    71457 
    71458 > matchmaker #783 to #1.38 & sel
    71459 
    71460 Parameters 
    71461 --- 
    71462 Chain pairing | bb 
    71463 Alignment algorithm | Needleman-Wunsch 
    71464 Similarity matrix | BLOSUM-62 
    71465 SS fraction | 0.3 
    71466 Gap open (HH/SS/other) | 18/18/6 
    71467 Gap extend | 1 
    71468 SS matrix |  |  | H | S | O 
    71469 ---|---|---|--- 
    71470 H | 6 | -9 | -6 
    71471 S |  | 6 | -6 
    71472 O |  |  | 4 
    71473 Iteration cutoff | 2 
    71474  
    71475 Matchmaker 3j0c.pdb1, chain G (#1.38) with AF3 E1 422-461.pdb, chain A (#783),
    71476 sequence alignment score = 626.9 
    71477 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    71478 2.997) 
    71479  
    71480 
    71481 > hide sel cartoons
    71482 
    71483 > select #1.38/H
    71484 
    71485 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    71486 
    71487 > show sel cartoons
    71488 
    71489 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    71490 
    71491 Chain information for AF3 E2 1-352.pdb #784 
    71492 --- 
    71493 Chain | Description 
    71494 B | No description available 
    71495  
    71496 
    71497 > matchmaker #784 to #1.38 & sel
    71498 
    71499 Parameters 
    71500 --- 
    71501 Chain pairing | bb 
    71502 Alignment algorithm | Needleman-Wunsch 
    71503 Similarity matrix | BLOSUM-62 
    71504 SS fraction | 0.3 
    71505 Gap open (HH/SS/other) | 18/18/6 
    71506 Gap extend | 1 
    71507 SS matrix |  |  | H | S | O 
    71508 ---|---|---|--- 
    71509 H | 6 | -9 | -6 
    71510 S |  | 6 | -6 
    71511 O |  |  | 4 
    71512 Iteration cutoff | 2 
    71513  
    71514 Matchmaker 3j0c.pdb1, chain H (#1.38) with AF3 E2 1-352.pdb, chain B (#784),
    71515 sequence alignment score = 590.9 
    71516 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    71517 6.107) 
    71518  
    71519 
    71520 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    71521 
    71522 Chain information for AF3 E2 353-438.pdb #785 
    71523 --- 
    71524 Chain | Description 
    71525 B | No description available 
    71526  
    71527 
    71528 > matchmaker #785 to #1.38 & sel
    71529 
    71530 Parameters 
    71531 --- 
    71532 Chain pairing | bb 
    71533 Alignment algorithm | Needleman-Wunsch 
    71534 Similarity matrix | BLOSUM-62 
    71535 SS fraction | 0.3 
    71536 Gap open (HH/SS/other) | 18/18/6 
    71537 Gap extend | 1 
    71538 SS matrix |  |  | H | S | O 
    71539 ---|---|---|--- 
    71540 H | 6 | -9 | -6 
    71541 S |  | 6 | -6 
    71542 O |  |  | 4 
    71543 Iteration cutoff | 2 
    71544  
    71545 Matchmaker 3j0c.pdb1, chain H (#1.38) with AF3 E2 353-438.pdb, chain B (#785),
    71546 sequence alignment score = 329.4 
    71547 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    71548 8.150) 
    71549  
    71550 
    71551 > hide sel cartoons
    71552 
    71553 > select #1.38/I
    71554 
    71555 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    71556 
    71557 > show sel cartoons
    71558 
    71559 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    71560 
    71561 Chain information for AF3 CA.pdb #786 
    71562 --- 
    71563 Chain | Description 
    71564 A | No description available 
    71565  
    71566 
    71567 > matchmaker #786 to #1.38 & sel
    71568 
    71569 Parameters 
    71570 --- 
    71571 Chain pairing | bb 
    71572 Alignment algorithm | Needleman-Wunsch 
    71573 Similarity matrix | BLOSUM-62 
    71574 SS fraction | 0.3 
    71575 Gap open (HH/SS/other) | 18/18/6 
    71576 Gap extend | 1 
    71577 SS matrix |  |  | H | S | O 
    71578 ---|---|---|--- 
    71579 H | 6 | -9 | -6 
    71580 S |  | 6 | -6 
    71581 O |  |  | 4 
    71582 Iteration cutoff | 2 
    71583  
    71584 Matchmaker 3j0c.pdb1, chain I (#1.38) with AF3 CA.pdb, chain A (#786),
    71585 sequence alignment score = 306.5 
    71586 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    71587 2.689) 
    71588  
    71589 
    71590 > hide sel cartoons
    71591 
    71592 > color #782 dodgerblue
    71593 
    71594 > color #783 dodgerblue
    71595 
    71596 > color #784 #00b305ff
    71597 
    71598 > color #785 #00b305ff
    71599 
    71600 > color #786 #f15839ff
    71601 
    71602 > select #1.39/G
    71603 
    71604 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    71605 
    71606 > show sel cartoons
    71607 
    71608 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    71609 
    71610 Chain information for AF3 E1 1-421.pdb #787 
    71611 --- 
    71612 Chain | Description 
    71613 A | No description available 
    71614  
    71615 
    71616 > matchmaker #787 to #1.38 & sel
    71617 
    71618 No 'to' model specified 
    71619 
    71620 > matchmaker #787 to #1.39 & sel
    71621 
    71622 Parameters 
    71623 --- 
    71624 Chain pairing | bb 
    71625 Alignment algorithm | Needleman-Wunsch 
    71626 Similarity matrix | BLOSUM-62 
    71627 SS fraction | 0.3 
    71628 Gap open (HH/SS/other) | 18/18/6 
    71629 Gap extend | 1 
    71630 SS matrix |  |  | H | S | O 
    71631 ---|---|---|--- 
    71632 H | 6 | -9 | -6 
    71633 S |  | 6 | -6 
    71634 O |  |  | 4 
    71635 Iteration cutoff | 2 
    71636  
    71637 Matchmaker 3j0c.pdb1, chain G (#1.39) with AF3 E1 1-421.pdb, chain A (#787),
    71638 sequence alignment score = 1060.7 
    71639 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    71640 2.985) 
    71641  
    71642 
    71643 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    71644 
    71645 Chain information for AF3 E1 422-461.pdb #788 
    71646 --- 
    71647 Chain | Description 
    71648 A | No description available 
    71649  
    71650 
    71651 > matchmaker #788 to #1.39 & sel
    71652 
    71653 Parameters 
    71654 --- 
    71655 Chain pairing | bb 
    71656 Alignment algorithm | Needleman-Wunsch 
    71657 Similarity matrix | BLOSUM-62 
    71658 SS fraction | 0.3 
    71659 Gap open (HH/SS/other) | 18/18/6 
    71660 Gap extend | 1 
    71661 SS matrix |  |  | H | S | O 
    71662 ---|---|---|--- 
    71663 H | 6 | -9 | -6 
    71664 S |  | 6 | -6 
    71665 O |  |  | 4 
    71666 Iteration cutoff | 2 
    71667  
    71668 Matchmaker 3j0c.pdb1, chain G (#1.39) with AF3 E1 422-461.pdb, chain A (#788),
    71669 sequence alignment score = 626.9 
    71670 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    71671 2.997) 
    71672  
    71673 
    71674 > hide sel cartoons
    71675 
    71676 > select #1.39/H
    71677 
    71678 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    71679 
    71680 > show sel cartoons
    71681 
    71682 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    71683 
    71684 Chain information for AF3 E2 1-352.pdb #789 
    71685 --- 
    71686 Chain | Description 
    71687 B | No description available 
    71688  
    71689 
    71690 > matchmaker #789 to #1.39 & sel
    71691 
    71692 Parameters 
    71693 --- 
    71694 Chain pairing | bb 
    71695 Alignment algorithm | Needleman-Wunsch 
    71696 Similarity matrix | BLOSUM-62 
    71697 SS fraction | 0.3 
    71698 Gap open (HH/SS/other) | 18/18/6 
    71699 Gap extend | 1 
    71700 SS matrix |  |  | H | S | O 
    71701 ---|---|---|--- 
    71702 H | 6 | -9 | -6 
    71703 S |  | 6 | -6 
    71704 O |  |  | 4 
    71705 Iteration cutoff | 2 
    71706  
    71707 Matchmaker 3j0c.pdb1, chain H (#1.39) with AF3 E2 1-352.pdb, chain B (#789),
    71708 sequence alignment score = 590.9 
    71709 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    71710 6.107) 
    71711  
    71712 
    71713 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    71714 
    71715 Chain information for AF3 E2 353-438.pdb #790 
    71716 --- 
    71717 Chain | Description 
    71718 B | No description available 
    71719  
    71720 
    71721 > matchmaker #790 to #1.39 & sel
    71722 
    71723 Parameters 
    71724 --- 
    71725 Chain pairing | bb 
    71726 Alignment algorithm | Needleman-Wunsch 
    71727 Similarity matrix | BLOSUM-62 
    71728 SS fraction | 0.3 
    71729 Gap open (HH/SS/other) | 18/18/6 
    71730 Gap extend | 1 
    71731 SS matrix |  |  | H | S | O 
    71732 ---|---|---|--- 
    71733 H | 6 | -9 | -6 
    71734 S |  | 6 | -6 
    71735 O |  |  | 4 
    71736 Iteration cutoff | 2 
    71737  
    71738 Matchmaker 3j0c.pdb1, chain H (#1.39) with AF3 E2 353-438.pdb, chain B (#790),
    71739 sequence alignment score = 329.4 
    71740 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    71741 8.151) 
    71742  
    71743 
    71744 > hide sel cartoons
    71745 
    71746 > select #1.39/I
    71747 
    71748 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    71749 
    71750 > show sel cartoons
    71751 
    71752 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    71753 
    71754 Chain information for AF3 CA.pdb #791 
    71755 --- 
    71756 Chain | Description 
    71757 A | No description available 
    71758  
    71759 
    71760 > matchmaker #791 to #1.39 & sel
    71761 
    71762 Parameters 
    71763 --- 
    71764 Chain pairing | bb 
    71765 Alignment algorithm | Needleman-Wunsch 
    71766 Similarity matrix | BLOSUM-62 
    71767 SS fraction | 0.3 
    71768 Gap open (HH/SS/other) | 18/18/6 
    71769 Gap extend | 1 
    71770 SS matrix |  |  | H | S | O 
    71771 ---|---|---|--- 
    71772 H | 6 | -9 | -6 
    71773 S |  | 6 | -6 
    71774 O |  |  | 4 
    71775 Iteration cutoff | 2 
    71776  
    71777 Matchmaker 3j0c.pdb1, chain I (#1.39) with AF3 CA.pdb, chain A (#791),
    71778 sequence alignment score = 306.5 
    71779 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    71780 2.689) 
    71781  
    71782 
    71783 > hide sel cartoons
    71784 
    71785 > color #787 dodgerblue
    71786 
    71787 > color #788 dodgerblue
    71788 
    71789 > color #789 #00b305ff
    71790 
    71791 > color #790 #00b305ff
    71792 
    71793 > color #791 #f15839ff
    71794 
    71795 > select #1.40/G
    71796 
    71797 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    71798 
    71799 > show sel cartoons
    71800 
    71801 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    71802 
    71803 Chain information for AF3 E1 1-421.pdb #792 
    71804 --- 
    71805 Chain | Description 
    71806 A | No description available 
    71807  
    71808 
    71809 > matchmaker #792 to #1.39 & sel
    71810 
    71811 No 'to' model specified 
    71812 
    71813 > matchmaker #792 to #1.40 & sel
    71814 
    71815 Parameters 
    71816 --- 
    71817 Chain pairing | bb 
    71818 Alignment algorithm | Needleman-Wunsch 
    71819 Similarity matrix | BLOSUM-62 
    71820 SS fraction | 0.3 
    71821 Gap open (HH/SS/other) | 18/18/6 
    71822 Gap extend | 1 
    71823 SS matrix |  |  | H | S | O 
    71824 ---|---|---|--- 
    71825 H | 6 | -9 | -6 
    71826 S |  | 6 | -6 
    71827 O |  |  | 4 
    71828 Iteration cutoff | 2 
    71829  
    71830 Matchmaker 3j0c.pdb1, chain G (#1.40) with AF3 E1 1-421.pdb, chain A (#792),
    71831 sequence alignment score = 1060.7 
    71832 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    71833 2.985) 
    71834  
    71835 
    71836 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    71837 
    71838 Chain information for AF3 E1 422-461.pdb #793 
    71839 --- 
    71840 Chain | Description 
    71841 A | No description available 
    71842  
    71843 
    71844 > matchmaker #793 to #1.40 & sel
    71845 
    71846 Parameters 
    71847 --- 
    71848 Chain pairing | bb 
    71849 Alignment algorithm | Needleman-Wunsch 
    71850 Similarity matrix | BLOSUM-62 
    71851 SS fraction | 0.3 
    71852 Gap open (HH/SS/other) | 18/18/6 
    71853 Gap extend | 1 
    71854 SS matrix |  |  | H | S | O 
    71855 ---|---|---|--- 
    71856 H | 6 | -9 | -6 
    71857 S |  | 6 | -6 
    71858 O |  |  | 4 
    71859 Iteration cutoff | 2 
    71860  
    71861 Matchmaker 3j0c.pdb1, chain G (#1.40) with AF3 E1 422-461.pdb, chain A (#793),
    71862 sequence alignment score = 626.9 
    71863 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    71864 2.997) 
    71865  
    71866 
    71867 > hide sel cartoons
    71868 
    71869 > select #1.40/H
    71870 
    71871 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    71872 
    71873 > show sel cartoons
    71874 
    71875 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    71876 
    71877 Chain information for AF3 E2 1-352.pdb #794 
    71878 --- 
    71879 Chain | Description 
    71880 B | No description available 
    71881  
    71882 
    71883 > matchmaker #794 to #1.40 & sel
    71884 
    71885 Parameters 
    71886 --- 
    71887 Chain pairing | bb 
    71888 Alignment algorithm | Needleman-Wunsch 
    71889 Similarity matrix | BLOSUM-62 
    71890 SS fraction | 0.3 
    71891 Gap open (HH/SS/other) | 18/18/6 
    71892 Gap extend | 1 
    71893 SS matrix |  |  | H | S | O 
    71894 ---|---|---|--- 
    71895 H | 6 | -9 | -6 
    71896 S |  | 6 | -6 
    71897 O |  |  | 4 
    71898 Iteration cutoff | 2 
    71899  
    71900 Matchmaker 3j0c.pdb1, chain H (#1.40) with AF3 E2 1-352.pdb, chain B (#794),
    71901 sequence alignment score = 590.9 
    71902 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    71903 6.107) 
    71904  
    71905 
    71906 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    71907 
    71908 Chain information for AF3 E2 353-438.pdb #795 
    71909 --- 
    71910 Chain | Description 
    71911 B | No description available 
    71912  
    71913 
    71914 > matchmaker #795 to #1.40 & sel
    71915 
    71916 Parameters 
    71917 --- 
    71918 Chain pairing | bb 
    71919 Alignment algorithm | Needleman-Wunsch 
    71920 Similarity matrix | BLOSUM-62 
    71921 SS fraction | 0.3 
    71922 Gap open (HH/SS/other) | 18/18/6 
    71923 Gap extend | 1 
    71924 SS matrix |  |  | H | S | O 
    71925 ---|---|---|--- 
    71926 H | 6 | -9 | -6 
    71927 S |  | 6 | -6 
    71928 O |  |  | 4 
    71929 Iteration cutoff | 2 
    71930  
    71931 Matchmaker 3j0c.pdb1, chain H (#1.40) with AF3 E2 353-438.pdb, chain B (#795),
    71932 sequence alignment score = 329.4 
    71933 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    71934 8.150) 
    71935  
    71936 
    71937 > hide sel cartoons
    71938 
    71939 > select #1.40/I
    71940 
    71941 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    71942 
    71943 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    71944 
    71945 Chain information for AF3 CA.pdb #796 
    71946 --- 
    71947 Chain | Description 
    71948 A | No description available 
    71949  
    71950 
    71951 > matchmaker #796 to #1.40 & sel
    71952 
    71953 Parameters 
    71954 --- 
    71955 Chain pairing | bb 
    71956 Alignment algorithm | Needleman-Wunsch 
    71957 Similarity matrix | BLOSUM-62 
    71958 SS fraction | 0.3 
    71959 Gap open (HH/SS/other) | 18/18/6 
    71960 Gap extend | 1 
    71961 SS matrix |  |  | H | S | O 
    71962 ---|---|---|--- 
    71963 H | 6 | -9 | -6 
    71964 S |  | 6 | -6 
    71965 O |  |  | 4 
    71966 Iteration cutoff | 2 
    71967  
    71968 Matchmaker 3j0c.pdb1, chain I (#1.40) with AF3 CA.pdb, chain A (#796),
    71969 sequence alignment score = 306.5 
    71970 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    71971 2.689) 
    71972  
    71973 
    71974 > color #792 dodgerblue
    71975 
    71976 > color #793 dodgerblue
    71977 
    71978 > color #794 #00b305ff
    71979 
    71980 > color #795 #00b305ff
    71981 
    71982 > color #796 #f15839ff
    71983 
    71984 > show #751 models
    71985 
    71986 > show #750 models
    71987 
    71988 > show #749 models
    71989 
    71990 > show #748 models
    71991 
    71992 > show #747 models
    71993 
    71994 > hide #747 models
    71995 
    71996 > hide #748 models
    71997 
    71998 > hide #749 models
    71999 
    72000 > hide #750 models
    72001 
    72002 > hide #751 models
    72003 
    72004 > select #1.37/G
    72005 
    72006 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    72007 
    72008 > show sel cartoons
    72009 
    72010 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    72011 
    72012 Chain information for AF3 E1 1-421.pdb #797 
    72013 --- 
    72014 Chain | Description 
    72015 A | No description available 
    72016  
    72017 
    72018 > matchmaker #796 to #1.37 & sel
    72019 
    72020 Parameters 
    72021 --- 
    72022 Chain pairing | bb 
    72023 Alignment algorithm | Needleman-Wunsch 
    72024 Similarity matrix | BLOSUM-62 
    72025 SS fraction | 0.3 
    72026 Gap open (HH/SS/other) | 18/18/6 
    72027 Gap extend | 1 
    72028 SS matrix |  |  | H | S | O 
    72029 ---|---|---|--- 
    72030 H | 6 | -9 | -6 
    72031 S |  | 6 | -6 
    72032 O |  |  | 4 
    72033 Iteration cutoff | 2 
    72034  
    72035 Matchmaker 3j0c.pdb1, chain G (#1.37) with AF3 CA.pdb, chain A (#796),
    72036 sequence alignment score = 32.6 
    72037 RMSD between 10 pruned atom pairs is 1.151 angstroms; (across all 110 pairs:
    72038 22.900) 
    72039  
    72040 
    72041 > matchmaker #796 to #1.40 & sel
    72042 
    72043 No 'to' model specified 
    72044 
    72045 > select #1.40/I
    72046 
    72047 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    72048 
    72049 > show sel cartoons
    72050 
    72051 > matchmaker #796 to #1.40 & sel
    72052 
    72053 Parameters 
    72054 --- 
    72055 Chain pairing | bb 
    72056 Alignment algorithm | Needleman-Wunsch 
    72057 Similarity matrix | BLOSUM-62 
    72058 SS fraction | 0.3 
    72059 Gap open (HH/SS/other) | 18/18/6 
    72060 Gap extend | 1 
    72061 SS matrix |  |  | H | S | O 
    72062 ---|---|---|--- 
    72063 H | 6 | -9 | -6 
    72064 S |  | 6 | -6 
    72065 O |  |  | 4 
    72066 Iteration cutoff | 2 
    72067  
    72068 Matchmaker 3j0c.pdb1, chain I (#1.40) with AF3 CA.pdb, chain A (#796),
    72069 sequence alignment score = 306.5 
    72070 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    72071 2.689) 
    72072  
    72073 
    72074 > hide sel cartoons
    72075 
    72076 > select #1.37/G
    72077 
    72078 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    72079 
    72080 > matchmaker #797 to #1.37 & sel
    72081 
    72082 Parameters 
    72083 --- 
    72084 Chain pairing | bb 
    72085 Alignment algorithm | Needleman-Wunsch 
    72086 Similarity matrix | BLOSUM-62 
    72087 SS fraction | 0.3 
    72088 Gap open (HH/SS/other) | 18/18/6 
    72089 Gap extend | 1 
    72090 SS matrix |  |  | H | S | O 
    72091 ---|---|---|--- 
    72092 H | 6 | -9 | -6 
    72093 S |  | 6 | -6 
    72094 O |  |  | 4 
    72095 Iteration cutoff | 2 
    72096  
    72097 Matchmaker 3j0c.pdb1, chain G (#1.37) with AF3 E1 1-421.pdb, chain A (#797),
    72098 sequence alignment score = 1060.7 
    72099 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    72100 2.985) 
    72101  
    72102 
    72103 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    72104 
    72105 Chain information for AF3 E1 422-461.pdb #798 
    72106 --- 
    72107 Chain | Description 
    72108 A | No description available 
    72109  
    72110 
    72111 > matchmaker #798 to #1.37 & sel
    72112 
    72113 Parameters 
    72114 --- 
    72115 Chain pairing | bb 
    72116 Alignment algorithm | Needleman-Wunsch 
    72117 Similarity matrix | BLOSUM-62 
    72118 SS fraction | 0.3 
    72119 Gap open (HH/SS/other) | 18/18/6 
    72120 Gap extend | 1 
    72121 SS matrix |  |  | H | S | O 
    72122 ---|---|---|--- 
    72123 H | 6 | -9 | -6 
    72124 S |  | 6 | -6 
    72125 O |  |  | 4 
    72126 Iteration cutoff | 2 
    72127  
    72128 Matchmaker 3j0c.pdb1, chain G (#1.37) with AF3 E1 422-461.pdb, chain A (#798),
    72129 sequence alignment score = 626.9 
    72130 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    72131 2.997) 
    72132  
    72133 
    72134 > hide sel cartoons
    72135 
    72136 > select #1.37/H
    72137 
    72138 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    72139 
    72140 > show sel cartoons
    72141 
    72142 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    72143 
    72144 Chain information for AF3 E2 1-352.pdb #799 
    72145 --- 
    72146 Chain | Description 
    72147 B | No description available 
    72148  
    72149 
    72150 > matchmaker #799 to #1.37 & sel
    72151 
    72152 Parameters 
    72153 --- 
    72154 Chain pairing | bb 
    72155 Alignment algorithm | Needleman-Wunsch 
    72156 Similarity matrix | BLOSUM-62 
    72157 SS fraction | 0.3 
    72158 Gap open (HH/SS/other) | 18/18/6 
    72159 Gap extend | 1 
    72160 SS matrix |  |  | H | S | O 
    72161 ---|---|---|--- 
    72162 H | 6 | -9 | -6 
    72163 S |  | 6 | -6 
    72164 O |  |  | 4 
    72165 Iteration cutoff | 2 
    72166  
    72167 Matchmaker 3j0c.pdb1, chain H (#1.37) with AF3 E2 1-352.pdb, chain B (#799),
    72168 sequence alignment score = 590.9 
    72169 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    72170 6.107) 
    72171  
    72172 
    72173 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    72174 
    72175 Chain information for AF3 E2 353-438.pdb #800 
    72176 --- 
    72177 Chain | Description 
    72178 B | No description available 
    72179  
    72180 
    72181 > matchmaker #800 to #1.37 & sel
    72182 
    72183 Parameters 
    72184 --- 
    72185 Chain pairing | bb 
    72186 Alignment algorithm | Needleman-Wunsch 
    72187 Similarity matrix | BLOSUM-62 
    72188 SS fraction | 0.3 
    72189 Gap open (HH/SS/other) | 18/18/6 
    72190 Gap extend | 1 
    72191 SS matrix |  |  | H | S | O 
    72192 ---|---|---|--- 
    72193 H | 6 | -9 | -6 
    72194 S |  | 6 | -6 
    72195 O |  |  | 4 
    72196 Iteration cutoff | 2 
    72197  
    72198 Matchmaker 3j0c.pdb1, chain H (#1.37) with AF3 E2 353-438.pdb, chain B (#800),
    72199 sequence alignment score = 329.4 
    72200 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    72201 8.150) 
    72202  
    72203 
    72204 > hide sel cartoons
    72205 
    72206 > select #1.37/I
    72207 
    72208 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    72209 
    72210 > show sel cartoons
    72211 
    72212 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    72213 
    72214 Chain information for AF3 CA.pdb #801 
    72215 --- 
    72216 Chain | Description 
    72217 A | No description available 
    72218  
    72219 
    72220 > matchmaker #801 to #1.37 & sel
    72221 
    72222 Parameters 
    72223 --- 
    72224 Chain pairing | bb 
    72225 Alignment algorithm | Needleman-Wunsch 
    72226 Similarity matrix | BLOSUM-62 
    72227 SS fraction | 0.3 
    72228 Gap open (HH/SS/other) | 18/18/6 
    72229 Gap extend | 1 
    72230 SS matrix |  |  | H | S | O 
    72231 ---|---|---|--- 
    72232 H | 6 | -9 | -6 
    72233 S |  | 6 | -6 
    72234 O |  |  | 4 
    72235 Iteration cutoff | 2 
    72236  
    72237 Matchmaker 3j0c.pdb1, chain I (#1.37) with AF3 CA.pdb, chain A (#801),
    72238 sequence alignment score = 306.5 
    72239 RMSD between 119 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    72240 2.689) 
    72241  
    72242 
    72243 > hide sel cartoons
    72244 
    72245 > color #797 dodgerblue
    72246 
    72247 > color #798 dodgerblue
    72248 
    72249 > color #799 #00b305ff
    72250 
    72251 > color #800 #00b305ff
    72252 
    72253 > color #801 #f15839ff
    72254 
    72255 > save "/Users/Jean/Desktop/SAV2 virion 2 VEEV 3j0c.cxs" includeMaps true
    72256 
    72257 > hide #752 models
    72258 
    72259 > hide #753 models
    72260 
    72261 > hide #754 models
    72262 
    72263 > hide #755 models
    72264 
    72265 > hide #756 models
    72266 
    72267 > hide #757 models
    72268 
    72269 > hide #758 models
    72270 
    72271 > hide #759 models
    72272 
    72273 > hide #760 models
    72274 
    72275 > hide #761 models
    72276 
    72277 > hide #762 models
    72278 
    72279 > hide #763 models
    72280 
    72281 > hide #764 models
    72282 
    72283 > hide #765 models
    72284 
    72285 > hide #766 models
    72286 
    72287 > hide #767 models
    72288 
    72289 > hide #768 models
    72290 
    72291 > hide #769 models
    72292 
    72293 > hide #770 models
    72294 
    72295 > hide #771 models
    72296 
    72297 > hide #772 models
    72298 
    72299 > hide #773 models
    72300 
    72301 > hide #774 models
    72302 
    72303 > hide #776 models
    72304 
    72305 > hide #775 models
    72306 
    72307 > hide #777 models
    72308 
    72309 > hide #778 models
    72310 
    72311 > hide #779 models
    72312 
    72313 > hide #780 models
    72314 
    72315 > hide #781 models
    72316 
    72317 > hide #782 models
    72318 
    72319 > hide #783 models
    72320 
    72321 > hide #784 models
    72322 
    72323 > hide #785 models
    72324 
    72325 > hide #786 models
    72326 
    72327 > hide #787 models
    72328 
    72329 > hide #788 models
    72330 
    72331 > hide #789 models
    72332 
    72333 > hide #790 models
    72334 
    72335 > hide #791 models
    72336 
    72337 > hide #792 models
    72338 
    72339 > hide #793 models
    72340 
    72341 > hide #794 models
    72342 
    72343 > hide #795 models
    72344 
    72345 > hide #796 models
    72346 
    72347 > hide #797 models
    72348 
    72349 > hide #798 models
    72350 
    72351 > hide #799 models
    72352 
    72353 > hide #800 models
    72354 
    72355 > hide #801 models
    72356 
    72357 > select #1.38/G
    72358 
    72359 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    72360 
    72361 > show sel cartoons
    72362 
    72363 > hide sel cartoons
    72364 
    72365 > select #1.41/G
    72366 
    72367 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    72368 
    72369 > show sel cartoons
    72370 
    72371 > view
    72372 
    72373 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    72374 
    72375 Chain information for AF3 E1 1-421.pdb #802 
    72376 --- 
    72377 Chain | Description 
    72378 A | No description available 
    72379  
    72380 
    72381 > matchmaker #802 to #1.41 & sel
    72382 
    72383 Parameters 
    72384 --- 
    72385 Chain pairing | bb 
    72386 Alignment algorithm | Needleman-Wunsch 
    72387 Similarity matrix | BLOSUM-62 
    72388 SS fraction | 0.3 
    72389 Gap open (HH/SS/other) | 18/18/6 
    72390 Gap extend | 1 
    72391 SS matrix |  |  | H | S | O 
    72392 ---|---|---|--- 
    72393 H | 6 | -9 | -6 
    72394 S |  | 6 | -6 
    72395 O |  |  | 4 
    72396 Iteration cutoff | 2 
    72397  
    72398 Matchmaker 3j0c.pdb1, chain G (#1.41) with AF3 E1 1-421.pdb, chain A (#802),
    72399 sequence alignment score = 1060.7 
    72400 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    72401 2.985) 
    72402  
    72403 
    72404 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    72405 
    72406 Chain information for AF3 E1 422-461.pdb #803 
    72407 --- 
    72408 Chain | Description 
    72409 A | No description available 
    72410  
    72411 
    72412 > matchmaker #803 to #1.41 & sel
    72413 
    72414 Parameters 
    72415 --- 
    72416 Chain pairing | bb 
    72417 Alignment algorithm | Needleman-Wunsch 
    72418 Similarity matrix | BLOSUM-62 
    72419 SS fraction | 0.3 
    72420 Gap open (HH/SS/other) | 18/18/6 
    72421 Gap extend | 1 
    72422 SS matrix |  |  | H | S | O 
    72423 ---|---|---|--- 
    72424 H | 6 | -9 | -6 
    72425 S |  | 6 | -6 
    72426 O |  |  | 4 
    72427 Iteration cutoff | 2 
    72428  
    72429 Matchmaker 3j0c.pdb1, chain G (#1.41) with AF3 E1 422-461.pdb, chain A (#803),
    72430 sequence alignment score = 626.9 
    72431 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    72432 2.997) 
    72433  
    72434 
    72435 > hide sel cartoons
    72436 
    72437 > select #1.41/H
    72438 
    72439 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    72440 
    72441 > show sel cartoons
    72442 
    72443 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    72444 
    72445 Chain information for AF3 E2 1-352.pdb #804 
    72446 --- 
    72447 Chain | Description 
    72448 B | No description available 
    72449  
    72450 
    72451 > matchmaker #804 to #1.41 & sel
    72452 
    72453 Parameters 
    72454 --- 
    72455 Chain pairing | bb 
    72456 Alignment algorithm | Needleman-Wunsch 
    72457 Similarity matrix | BLOSUM-62 
    72458 SS fraction | 0.3 
    72459 Gap open (HH/SS/other) | 18/18/6 
    72460 Gap extend | 1 
    72461 SS matrix |  |  | H | S | O 
    72462 ---|---|---|--- 
    72463 H | 6 | -9 | -6 
    72464 S |  | 6 | -6 
    72465 O |  |  | 4 
    72466 Iteration cutoff | 2 
    72467  
    72468 Matchmaker 3j0c.pdb1, chain H (#1.41) with AF3 E2 1-352.pdb, chain B (#804),
    72469 sequence alignment score = 590.9 
    72470 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    72471 6.107) 
    72472  
    72473 
    72474 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    72475 
    72476 Chain information for AF3 E2 353-438.pdb #805 
    72477 --- 
    72478 Chain | Description 
    72479 B | No description available 
    72480  
    72481 
    72482 > matchmaker #805 to #1.41 & sel
    72483 
    72484 Parameters 
    72485 --- 
    72486 Chain pairing | bb 
    72487 Alignment algorithm | Needleman-Wunsch 
    72488 Similarity matrix | BLOSUM-62 
    72489 SS fraction | 0.3 
    72490 Gap open (HH/SS/other) | 18/18/6 
    72491 Gap extend | 1 
    72492 SS matrix |  |  | H | S | O 
    72493 ---|---|---|--- 
    72494 H | 6 | -9 | -6 
    72495 S |  | 6 | -6 
    72496 O |  |  | 4 
    72497 Iteration cutoff | 2 
    72498  
    72499 Matchmaker 3j0c.pdb1, chain H (#1.41) with AF3 E2 353-438.pdb, chain B (#805),
    72500 sequence alignment score = 329.4 
    72501 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    72502 8.150) 
    72503  
    72504 
    72505 > hide sel cartoons
    72506 
    72507 > select #1.41/I
    72508 
    72509 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    72510 
    72511 > show sel cartoons
    72512 
    72513 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    72514 
    72515 Chain information for AF3 CA.pdb #806 
    72516 --- 
    72517 Chain | Description 
    72518 A | No description available 
    72519  
    72520 
    72521 > matchmaker #806 to #1.41 & sel
    72522 
    72523 Parameters 
    72524 --- 
    72525 Chain pairing | bb 
    72526 Alignment algorithm | Needleman-Wunsch 
    72527 Similarity matrix | BLOSUM-62 
    72528 SS fraction | 0.3 
    72529 Gap open (HH/SS/other) | 18/18/6 
    72530 Gap extend | 1 
    72531 SS matrix |  |  | H | S | O 
    72532 ---|---|---|--- 
    72533 H | 6 | -9 | -6 
    72534 S |  | 6 | -6 
    72535 O |  |  | 4 
    72536 Iteration cutoff | 2 
    72537  
    72538 Matchmaker 3j0c.pdb1, chain I (#1.41) with AF3 CA.pdb, chain A (#806),
    72539 sequence alignment score = 306.5 
    72540 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    72541 2.689) 
    72542  
    72543 
    72544 > hide sel cartoons
    72545 
    72546 > color #802 dodgerblue
    72547 
    72548 > color #803 dodgerblue
    72549 
    72550 > color #804 #00b305ff
    72551 
    72552 > color #805 #00b305ff
    72553 
    72554 > color #806 #f15839ff
    72555 
    72556 > select #1.42/G
    72557 
    72558 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    72559 
    72560 > show sel cartoons
    72561 
    72562 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    72563 
    72564 Chain information for AF3 E1 1-421.pdb #807 
    72565 --- 
    72566 Chain | Description 
    72567 A | No description available 
    72568  
    72569 
    72570 > matchmaker #807 to #1.42 & sel
    72571 
    72572 Parameters 
    72573 --- 
    72574 Chain pairing | bb 
    72575 Alignment algorithm | Needleman-Wunsch 
    72576 Similarity matrix | BLOSUM-62 
    72577 SS fraction | 0.3 
    72578 Gap open (HH/SS/other) | 18/18/6 
    72579 Gap extend | 1 
    72580 SS matrix |  |  | H | S | O 
    72581 ---|---|---|--- 
    72582 H | 6 | -9 | -6 
    72583 S |  | 6 | -6 
    72584 O |  |  | 4 
    72585 Iteration cutoff | 2 
    72586  
    72587 Matchmaker 3j0c.pdb1, chain G (#1.42) with AF3 E1 1-421.pdb, chain A (#807),
    72588 sequence alignment score = 1060.7 
    72589 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    72590 2.985) 
    72591  
    72592 
    72593 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    72594 
    72595 Chain information for AF3 E1 422-461.pdb #808 
    72596 --- 
    72597 Chain | Description 
    72598 A | No description available 
    72599  
    72600 
    72601 > matchmaker #808 to #1.42 & sel
    72602 
    72603 Parameters 
    72604 --- 
    72605 Chain pairing | bb 
    72606 Alignment algorithm | Needleman-Wunsch 
    72607 Similarity matrix | BLOSUM-62 
    72608 SS fraction | 0.3 
    72609 Gap open (HH/SS/other) | 18/18/6 
    72610 Gap extend | 1 
    72611 SS matrix |  |  | H | S | O 
    72612 ---|---|---|--- 
    72613 H | 6 | -9 | -6 
    72614 S |  | 6 | -6 
    72615 O |  |  | 4 
    72616 Iteration cutoff | 2 
    72617  
    72618 Matchmaker 3j0c.pdb1, chain G (#1.42) with AF3 E1 422-461.pdb, chain A (#808),
    72619 sequence alignment score = 626.9 
    72620 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    72621 2.997) 
    72622  
    72623 
    72624 > hide sel cartoons
    72625 
    72626 > select #1.42/H
    72627 
    72628 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    72629 
    72630 > show sel cartoons
    72631 
    72632 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    72633 
    72634 Chain information for AF3 E2 1-352.pdb #809 
    72635 --- 
    72636 Chain | Description 
    72637 B | No description available 
    72638  
    72639 
    72640 > matchmaker #809 to #1.42 & sel
    72641 
    72642 Parameters 
    72643 --- 
    72644 Chain pairing | bb 
    72645 Alignment algorithm | Needleman-Wunsch 
    72646 Similarity matrix | BLOSUM-62 
    72647 SS fraction | 0.3 
    72648 Gap open (HH/SS/other) | 18/18/6 
    72649 Gap extend | 1 
    72650 SS matrix |  |  | H | S | O 
    72651 ---|---|---|--- 
    72652 H | 6 | -9 | -6 
    72653 S |  | 6 | -6 
    72654 O |  |  | 4 
    72655 Iteration cutoff | 2 
    72656  
    72657 Matchmaker 3j0c.pdb1, chain H (#1.42) with AF3 E2 1-352.pdb, chain B (#809),
    72658 sequence alignment score = 590.9 
    72659 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    72660 6.107) 
    72661  
    72662 
    72663 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    72664 
    72665 Chain information for AF3 E2 353-438.pdb #810 
    72666 --- 
    72667 Chain | Description 
    72668 B | No description available 
    72669  
    72670 
    72671 > matchmaker #810 to #1.42 & sel
    72672 
    72673 Parameters 
    72674 --- 
    72675 Chain pairing | bb 
    72676 Alignment algorithm | Needleman-Wunsch 
    72677 Similarity matrix | BLOSUM-62 
    72678 SS fraction | 0.3 
    72679 Gap open (HH/SS/other) | 18/18/6 
    72680 Gap extend | 1 
    72681 SS matrix |  |  | H | S | O 
    72682 ---|---|---|--- 
    72683 H | 6 | -9 | -6 
    72684 S |  | 6 | -6 
    72685 O |  |  | 4 
    72686 Iteration cutoff | 2 
    72687  
    72688 Matchmaker 3j0c.pdb1, chain H (#1.42) with AF3 E2 353-438.pdb, chain B (#810),
    72689 sequence alignment score = 329.4 
    72690 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    72691 8.151) 
    72692  
    72693 
    72694 > hide sel cartoons
    72695 
    72696 > select #1.42/I
    72697 
    72698 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    72699 
    72700 > show sel cartoons
    72701 
    72702 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    72703 
    72704 Chain information for AF3 CA.pdb #811 
    72705 --- 
    72706 Chain | Description 
    72707 A | No description available 
    72708  
    72709 
    72710 > matchmaker #811 to #1.42 & sel
    72711 
    72712 Parameters 
    72713 --- 
    72714 Chain pairing | bb 
    72715 Alignment algorithm | Needleman-Wunsch 
    72716 Similarity matrix | BLOSUM-62 
    72717 SS fraction | 0.3 
    72718 Gap open (HH/SS/other) | 18/18/6 
    72719 Gap extend | 1 
    72720 SS matrix |  |  | H | S | O 
    72721 ---|---|---|--- 
    72722 H | 6 | -9 | -6 
    72723 S |  | 6 | -6 
    72724 O |  |  | 4 
    72725 Iteration cutoff | 2 
    72726  
    72727 Matchmaker 3j0c.pdb1, chain I (#1.42) with AF3 CA.pdb, chain A (#811),
    72728 sequence alignment score = 306.5 
    72729 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    72730 2.689) 
    72731  
    72732 
    72733 > hide sel cartoons
    72734 
    72735 > color #807 dodgerblue
    72736 
    72737 > color #808 dodgerblue
    72738 
    72739 > color #809 #00b305ff
    72740 
    72741 > color #810 #00b305ff
    72742 
    72743 > color #811 #f15839ff
    72744 
    72745 > select #1.43/G
    72746 
    72747 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    72748 
    72749 > show sel cartoons
    72750 
    72751 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    72752 
    72753 Chain information for AF3 E1 1-421.pdb #812 
    72754 --- 
    72755 Chain | Description 
    72756 A | No description available 
    72757  
    72758 
    72759 > matchmaker #812 to #1.42 & sel
    72760 
    72761 No 'to' model specified 
    72762 
    72763 > matchmaker #812 to #1.43 & sel
    72764 
    72765 Parameters 
    72766 --- 
    72767 Chain pairing | bb 
    72768 Alignment algorithm | Needleman-Wunsch 
    72769 Similarity matrix | BLOSUM-62 
    72770 SS fraction | 0.3 
    72771 Gap open (HH/SS/other) | 18/18/6 
    72772 Gap extend | 1 
    72773 SS matrix |  |  | H | S | O 
    72774 ---|---|---|--- 
    72775 H | 6 | -9 | -6 
    72776 S |  | 6 | -6 
    72777 O |  |  | 4 
    72778 Iteration cutoff | 2 
    72779  
    72780 Matchmaker 3j0c.pdb1, chain G (#1.43) with AF3 E1 1-421.pdb, chain A (#812),
    72781 sequence alignment score = 1060.7 
    72782 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    72783 2.985) 
    72784  
    72785 
    72786 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    72787 
    72788 Chain information for AF3 E1 422-461.pdb #813 
    72789 --- 
    72790 Chain | Description 
    72791 A | No description available 
    72792  
    72793 
    72794 > matchmaker #813 to #1.43 & sel
    72795 
    72796 Parameters 
    72797 --- 
    72798 Chain pairing | bb 
    72799 Alignment algorithm | Needleman-Wunsch 
    72800 Similarity matrix | BLOSUM-62 
    72801 SS fraction | 0.3 
    72802 Gap open (HH/SS/other) | 18/18/6 
    72803 Gap extend | 1 
    72804 SS matrix |  |  | H | S | O 
    72805 ---|---|---|--- 
    72806 H | 6 | -9 | -6 
    72807 S |  | 6 | -6 
    72808 O |  |  | 4 
    72809 Iteration cutoff | 2 
    72810  
    72811 Matchmaker 3j0c.pdb1, chain G (#1.43) with AF3 E1 422-461.pdb, chain A (#813),
    72812 sequence alignment score = 626.9 
    72813 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    72814 2.997) 
    72815  
    72816 
    72817 > hide sel cartoons
    72818 
    72819 > select #1.43/H
    72820 
    72821 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    72822 
    72823 > show sel cartoons
    72824 
    72825 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    72826 
    72827 Chain information for AF3 E2 1-352.pdb #814 
    72828 --- 
    72829 Chain | Description 
    72830 B | No description available 
    72831  
    72832 
    72833 > matchmaker #814 to #1.43 & sel
    72834 
    72835 Parameters 
    72836 --- 
    72837 Chain pairing | bb 
    72838 Alignment algorithm | Needleman-Wunsch 
    72839 Similarity matrix | BLOSUM-62 
    72840 SS fraction | 0.3 
    72841 Gap open (HH/SS/other) | 18/18/6 
    72842 Gap extend | 1 
    72843 SS matrix |  |  | H | S | O 
    72844 ---|---|---|--- 
    72845 H | 6 | -9 | -6 
    72846 S |  | 6 | -6 
    72847 O |  |  | 4 
    72848 Iteration cutoff | 2 
    72849  
    72850 Matchmaker 3j0c.pdb1, chain H (#1.43) with AF3 E2 1-352.pdb, chain B (#814),
    72851 sequence alignment score = 590.9 
    72852 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    72853 6.107) 
    72854  
    72855 
    72856 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    72857 
    72858 Chain information for AF3 E2 353-438.pdb #815 
    72859 --- 
    72860 Chain | Description 
    72861 B | No description available 
    72862  
    72863 
    72864 > matchmaker #815 to #1.43 & sel
    72865 
    72866 Parameters 
    72867 --- 
    72868 Chain pairing | bb 
    72869 Alignment algorithm | Needleman-Wunsch 
    72870 Similarity matrix | BLOSUM-62 
    72871 SS fraction | 0.3 
    72872 Gap open (HH/SS/other) | 18/18/6 
    72873 Gap extend | 1 
    72874 SS matrix |  |  | H | S | O 
    72875 ---|---|---|--- 
    72876 H | 6 | -9 | -6 
    72877 S |  | 6 | -6 
    72878 O |  |  | 4 
    72879 Iteration cutoff | 2 
    72880  
    72881 Matchmaker 3j0c.pdb1, chain H (#1.43) with AF3 E2 353-438.pdb, chain B (#815),
    72882 sequence alignment score = 329.4 
    72883 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    72884 8.150) 
    72885  
    72886 
    72887 > hide sel cartoons
    72888 
    72889 > select #1.43/I
    72890 
    72891 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    72892 
    72893 > show sel cartoons
    72894 
    72895 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    72896 
    72897 Chain information for AF3 CA.pdb #816 
    72898 --- 
    72899 Chain | Description 
    72900 A | No description available 
    72901  
    72902 
    72903 > matchmaker #816 to #1.43 & sel
    72904 
    72905 Parameters 
    72906 --- 
    72907 Chain pairing | bb 
    72908 Alignment algorithm | Needleman-Wunsch 
    72909 Similarity matrix | BLOSUM-62 
    72910 SS fraction | 0.3 
    72911 Gap open (HH/SS/other) | 18/18/6 
    72912 Gap extend | 1 
    72913 SS matrix |  |  | H | S | O 
    72914 ---|---|---|--- 
    72915 H | 6 | -9 | -6 
    72916 S |  | 6 | -6 
    72917 O |  |  | 4 
    72918 Iteration cutoff | 2 
    72919  
    72920 Matchmaker 3j0c.pdb1, chain I (#1.43) with AF3 CA.pdb, chain A (#816),
    72921 sequence alignment score = 306.5 
    72922 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    72923 2.689) 
    72924  
    72925 
    72926 > hide sel cartoons
    72927 
    72928 > color #812 dodgerblue
    72929 
    72930 > color #813 dodgerblue
    72931 
    72932 > color #814 #00b305ff
    72933 
    72934 > color #815 #00b305ff
    72935 
    72936 > color #816 #f15839ff
    72937 
    72938 > select #1.43/G
    72939 
    72940 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    72941 
    72942 > show sel cartoons
    72943 
    72944 > hide sel cartoons
    72945 
    72946 > select #1.44/G
    72947 
    72948 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    72949 
    72950 > show sel cartoons
    72951 
    72952 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    72953 
    72954 Chain information for AF3 E1 1-421.pdb #817 
    72955 --- 
    72956 Chain | Description 
    72957 A | No description available 
    72958  
    72959 
    72960 > matchmaker #817 to #1.44 & sel
    72961 
    72962 Parameters 
    72963 --- 
    72964 Chain pairing | bb 
    72965 Alignment algorithm | Needleman-Wunsch 
    72966 Similarity matrix | BLOSUM-62 
    72967 SS fraction | 0.3 
    72968 Gap open (HH/SS/other) | 18/18/6 
    72969 Gap extend | 1 
    72970 SS matrix |  |  | H | S | O 
    72971 ---|---|---|--- 
    72972 H | 6 | -9 | -6 
    72973 S |  | 6 | -6 
    72974 O |  |  | 4 
    72975 Iteration cutoff | 2 
    72976  
    72977 Matchmaker 3j0c.pdb1, chain G (#1.44) with AF3 E1 1-421.pdb, chain A (#817),
    72978 sequence alignment score = 1060.7 
    72979 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    72980 2.985) 
    72981  
    72982 
    72983 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    72984 
    72985 Chain information for AF3 E1 422-461.pdb #818 
    72986 --- 
    72987 Chain | Description 
    72988 A | No description available 
    72989  
    72990 
    72991 > matchmaker #818 to #1.44 & sel
    72992 
    72993 Parameters 
    72994 --- 
    72995 Chain pairing | bb 
    72996 Alignment algorithm | Needleman-Wunsch 
    72997 Similarity matrix | BLOSUM-62 
    72998 SS fraction | 0.3 
    72999 Gap open (HH/SS/other) | 18/18/6 
    73000 Gap extend | 1 
    73001 SS matrix |  |  | H | S | O 
    73002 ---|---|---|--- 
    73003 H | 6 | -9 | -6 
    73004 S |  | 6 | -6 
    73005 O |  |  | 4 
    73006 Iteration cutoff | 2 
    73007  
    73008 Matchmaker 3j0c.pdb1, chain G (#1.44) with AF3 E1 422-461.pdb, chain A (#818),
    73009 sequence alignment score = 626.9 
    73010 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    73011 2.997) 
    73012  
    73013 
    73014 > hide sel cartoons
    73015 
    73016 > select #1.44/H
    73017 
    73018 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    73019 
    73020 > show sel cartoons
    73021 
    73022 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    73023 
    73024 Chain information for AF3 E2 1-352.pdb #819 
    73025 --- 
    73026 Chain | Description 
    73027 B | No description available 
    73028  
    73029 
    73030 > matchmaker #819 to #1.44 & sel
    73031 
    73032 Parameters 
    73033 --- 
    73034 Chain pairing | bb 
    73035 Alignment algorithm | Needleman-Wunsch 
    73036 Similarity matrix | BLOSUM-62 
    73037 SS fraction | 0.3 
    73038 Gap open (HH/SS/other) | 18/18/6 
    73039 Gap extend | 1 
    73040 SS matrix |  |  | H | S | O 
    73041 ---|---|---|--- 
    73042 H | 6 | -9 | -6 
    73043 S |  | 6 | -6 
    73044 O |  |  | 4 
    73045 Iteration cutoff | 2 
    73046  
    73047 Matchmaker 3j0c.pdb1, chain H (#1.44) with AF3 E2 1-352.pdb, chain B (#819),
    73048 sequence alignment score = 590.9 
    73049 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    73050 6.107) 
    73051  
    73052 
    73053 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    73054 
    73055 Chain information for AF3 E2 353-438.pdb #820 
    73056 --- 
    73057 Chain | Description 
    73058 B | No description available 
    73059  
    73060 
    73061 > matchmaker #820 to #1.44 & sel
    73062 
    73063 Parameters 
    73064 --- 
    73065 Chain pairing | bb 
    73066 Alignment algorithm | Needleman-Wunsch 
    73067 Similarity matrix | BLOSUM-62 
    73068 SS fraction | 0.3 
    73069 Gap open (HH/SS/other) | 18/18/6 
    73070 Gap extend | 1 
    73071 SS matrix |  |  | H | S | O 
    73072 ---|---|---|--- 
    73073 H | 6 | -9 | -6 
    73074 S |  | 6 | -6 
    73075 O |  |  | 4 
    73076 Iteration cutoff | 2 
    73077  
    73078 Matchmaker 3j0c.pdb1, chain H (#1.44) with AF3 E2 353-438.pdb, chain B (#820),
    73079 sequence alignment score = 329.4 
    73080 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    73081 8.151) 
    73082  
    73083 
    73084 > show sel cartoons
    73085 
    73086 > hide sel cartoons
    73087 
    73088 > select #1.44/I
    73089 
    73090 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    73091 
    73092 > show sel cartoons
    73093 
    73094 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    73095 
    73096 Chain information for AF3 CA.pdb #821 
    73097 --- 
    73098 Chain | Description 
    73099 A | No description available 
    73100  
    73101 
    73102 > matchmaker #821 to #1.44 & sel
    73103 
    73104 Parameters 
    73105 --- 
    73106 Chain pairing | bb 
    73107 Alignment algorithm | Needleman-Wunsch 
    73108 Similarity matrix | BLOSUM-62 
    73109 SS fraction | 0.3 
    73110 Gap open (HH/SS/other) | 18/18/6 
    73111 Gap extend | 1 
    73112 SS matrix |  |  | H | S | O 
    73113 ---|---|---|--- 
    73114 H | 6 | -9 | -6 
    73115 S |  | 6 | -6 
    73116 O |  |  | 4 
    73117 Iteration cutoff | 2 
    73118  
    73119 Matchmaker 3j0c.pdb1, chain I (#1.44) with AF3 CA.pdb, chain A (#821),
    73120 sequence alignment score = 306.5 
    73121 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    73122 2.689) 
    73123  
    73124 
    73125 > hide sel cartoons
    73126 
    73127 > color #817 dodgerblue
    73128 
    73129 > color #818 dodgerblue
    73130 
    73131 > color #819 #00b305ff
    73132 
    73133 > color #820 #00b305ff
    73134 
    73135 > color #821 #f15839ff
    73136 
    73137 > select #1.45/G
    73138 
    73139 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    73140 
    73141 > show sel cartoons
    73142 
    73143 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    73144 
    73145 Chain information for AF3 E1 1-421.pdb #822 
    73146 --- 
    73147 Chain | Description 
    73148 A | No description available 
    73149  
    73150 
    73151 > matchmaker #822 to #1.45 & sel
    73152 
    73153 Parameters 
    73154 --- 
    73155 Chain pairing | bb 
    73156 Alignment algorithm | Needleman-Wunsch 
    73157 Similarity matrix | BLOSUM-62 
    73158 SS fraction | 0.3 
    73159 Gap open (HH/SS/other) | 18/18/6 
    73160 Gap extend | 1 
    73161 SS matrix |  |  | H | S | O 
    73162 ---|---|---|--- 
    73163 H | 6 | -9 | -6 
    73164 S |  | 6 | -6 
    73165 O |  |  | 4 
    73166 Iteration cutoff | 2 
    73167  
    73168 Matchmaker 3j0c.pdb1, chain G (#1.45) with AF3 E1 1-421.pdb, chain A (#822),
    73169 sequence alignment score = 1060.7 
    73170 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    73171 2.985) 
    73172  
    73173 
    73174 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    73175 
    73176 Chain information for AF3 E1 422-461.pdb #823 
    73177 --- 
    73178 Chain | Description 
    73179 A | No description available 
    73180  
    73181 
    73182 > matchmaker #823 to #1.45 & sel
    73183 
    73184 Parameters 
    73185 --- 
    73186 Chain pairing | bb 
    73187 Alignment algorithm | Needleman-Wunsch 
    73188 Similarity matrix | BLOSUM-62 
    73189 SS fraction | 0.3 
    73190 Gap open (HH/SS/other) | 18/18/6 
    73191 Gap extend | 1 
    73192 SS matrix |  |  | H | S | O 
    73193 ---|---|---|--- 
    73194 H | 6 | -9 | -6 
    73195 S |  | 6 | -6 
    73196 O |  |  | 4 
    73197 Iteration cutoff | 2 
    73198  
    73199 Matchmaker 3j0c.pdb1, chain G (#1.45) with AF3 E1 422-461.pdb, chain A (#823),
    73200 sequence alignment score = 626.9 
    73201 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    73202 2.997) 
    73203  
    73204 
    73205 > hide sel cartoons
    73206 
    73207 > select #1.45/H
    73208 
    73209 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    73210 
    73211 > show sel cartoons
    73212 
    73213 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    73214 
    73215 Chain information for AF3 E2 1-352.pdb #824 
    73216 --- 
    73217 Chain | Description 
    73218 B | No description available 
    73219  
    73220 
    73221 > matchmaker #824 to #1.45 & sel
    73222 
    73223 Parameters 
    73224 --- 
    73225 Chain pairing | bb 
    73226 Alignment algorithm | Needleman-Wunsch 
    73227 Similarity matrix | BLOSUM-62 
    73228 SS fraction | 0.3 
    73229 Gap open (HH/SS/other) | 18/18/6 
    73230 Gap extend | 1 
    73231 SS matrix |  |  | H | S | O 
    73232 ---|---|---|--- 
    73233 H | 6 | -9 | -6 
    73234 S |  | 6 | -6 
    73235 O |  |  | 4 
    73236 Iteration cutoff | 2 
    73237  
    73238 Matchmaker 3j0c.pdb1, chain H (#1.45) with AF3 E2 1-352.pdb, chain B (#824),
    73239 sequence alignment score = 590.9 
    73240 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    73241 6.107) 
    73242  
    73243 
    73244 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    73245 
    73246 Chain information for AF3 E2 353-438.pdb #825 
    73247 --- 
    73248 Chain | Description 
    73249 B | No description available 
    73250  
    73251 
    73252 > matchmaker #825 to #1.45 & sel
    73253 
    73254 Parameters 
    73255 --- 
    73256 Chain pairing | bb 
    73257 Alignment algorithm | Needleman-Wunsch 
    73258 Similarity matrix | BLOSUM-62 
    73259 SS fraction | 0.3 
    73260 Gap open (HH/SS/other) | 18/18/6 
    73261 Gap extend | 1 
    73262 SS matrix |  |  | H | S | O 
    73263 ---|---|---|--- 
    73264 H | 6 | -9 | -6 
    73265 S |  | 6 | -6 
    73266 O |  |  | 4 
    73267 Iteration cutoff | 2 
    73268  
    73269 Matchmaker 3j0c.pdb1, chain H (#1.45) with AF3 E2 353-438.pdb, chain B (#825),
    73270 sequence alignment score = 329.4 
    73271 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    73272 8.150) 
    73273  
    73274 
    73275 > hide sel cartoons
    73276 
    73277 > select #1.45/I
    73278 
    73279 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    73280 
    73281 > show sel cartoons
    73282 
    73283 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    73284 
    73285 Chain information for AF3 CA.pdb #826 
    73286 --- 
    73287 Chain | Description 
    73288 A | No description available 
    73289  
    73290 
    73291 > matchmaker #826 to #1.45 & sel
    73292 
    73293 Parameters 
    73294 --- 
    73295 Chain pairing | bb 
    73296 Alignment algorithm | Needleman-Wunsch 
    73297 Similarity matrix | BLOSUM-62 
    73298 SS fraction | 0.3 
    73299 Gap open (HH/SS/other) | 18/18/6 
    73300 Gap extend | 1 
    73301 SS matrix |  |  | H | S | O 
    73302 ---|---|---|--- 
    73303 H | 6 | -9 | -6 
    73304 S |  | 6 | -6 
    73305 O |  |  | 4 
    73306 Iteration cutoff | 2 
    73307  
    73308 Matchmaker 3j0c.pdb1, chain I (#1.45) with AF3 CA.pdb, chain A (#826),
    73309 sequence alignment score = 306.5 
    73310 RMSD between 119 pruned atom pairs is 1.149 angstroms; (across all 161 pairs:
    73311 2.689) 
    73312  
    73313 
    73314 > hide sel cartoons
    73315 
    73316 > color #822 dodgerblue
    73317 
    73318 > color #823 dodgerblue
    73319 
    73320 > color #824 #00b305ff
    73321 
    73322 > color #825 #00b305ff
    73323 
    73324 > color #826 #f15839ff
    73325 
    73326 > select #1.46/G
    73327 
    73328 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    73329 
    73330 > show sel cartoons
    73331 
    73332 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    73333 
    73334 Chain information for AF3 E1 1-421.pdb #827 
    73335 --- 
    73336 Chain | Description 
    73337 A | No description available 
    73338  
    73339 
    73340 > matchmaker #827 to #1.46 & sel
    73341 
    73342 Parameters 
    73343 --- 
    73344 Chain pairing | bb 
    73345 Alignment algorithm | Needleman-Wunsch 
    73346 Similarity matrix | BLOSUM-62 
    73347 SS fraction | 0.3 
    73348 Gap open (HH/SS/other) | 18/18/6 
    73349 Gap extend | 1 
    73350 SS matrix |  |  | H | S | O 
    73351 ---|---|---|--- 
    73352 H | 6 | -9 | -6 
    73353 S |  | 6 | -6 
    73354 O |  |  | 4 
    73355 Iteration cutoff | 2 
    73356  
    73357 Matchmaker 3j0c.pdb1, chain G (#1.46) with AF3 E1 1-421.pdb, chain A (#827),
    73358 sequence alignment score = 1060.7 
    73359 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    73360 2.985) 
    73361  
    73362 
    73363 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    73364 
    73365 Chain information for AF3 E1 422-461.pdb #828 
    73366 --- 
    73367 Chain | Description 
    73368 A | No description available 
    73369  
    73370 
    73371 > matchmaker #828 to #1.46 & sel
    73372 
    73373 Parameters 
    73374 --- 
    73375 Chain pairing | bb 
    73376 Alignment algorithm | Needleman-Wunsch 
    73377 Similarity matrix | BLOSUM-62 
    73378 SS fraction | 0.3 
    73379 Gap open (HH/SS/other) | 18/18/6 
    73380 Gap extend | 1 
    73381 SS matrix |  |  | H | S | O 
    73382 ---|---|---|--- 
    73383 H | 6 | -9 | -6 
    73384 S |  | 6 | -6 
    73385 O |  |  | 4 
    73386 Iteration cutoff | 2 
    73387  
    73388 Matchmaker 3j0c.pdb1, chain G (#1.46) with AF3 E1 422-461.pdb, chain A (#828),
    73389 sequence alignment score = 626.9 
    73390 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    73391 2.997) 
    73392  
    73393 
    73394 > hide sel cartoons
    73395 
    73396 > select #1.46/H
    73397 
    73398 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    73399 
    73400 > show sel cartoons
    73401 
    73402 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    73403 
    73404 Chain information for AF3 E2 1-352.pdb #829 
    73405 --- 
    73406 Chain | Description 
    73407 B | No description available 
    73408  
    73409 
    73410 > matchmaker #829 to #1.46 & sel
    73411 
    73412 Parameters 
    73413 --- 
    73414 Chain pairing | bb 
    73415 Alignment algorithm | Needleman-Wunsch 
    73416 Similarity matrix | BLOSUM-62 
    73417 SS fraction | 0.3 
    73418 Gap open (HH/SS/other) | 18/18/6 
    73419 Gap extend | 1 
    73420 SS matrix |  |  | H | S | O 
    73421 ---|---|---|--- 
    73422 H | 6 | -9 | -6 
    73423 S |  | 6 | -6 
    73424 O |  |  | 4 
    73425 Iteration cutoff | 2 
    73426  
    73427 Matchmaker 3j0c.pdb1, chain H (#1.46) with AF3 E2 1-352.pdb, chain B (#829),
    73428 sequence alignment score = 590.9 
    73429 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    73430 6.107) 
    73431  
    73432 
    73433 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    73434 
    73435 Chain information for AF3 E2 353-438.pdb #830 
    73436 --- 
    73437 Chain | Description 
    73438 B | No description available 
    73439  
    73440 
    73441 > matchmaker #830 to #1.46 & sel
    73442 
    73443 Parameters 
    73444 --- 
    73445 Chain pairing | bb 
    73446 Alignment algorithm | Needleman-Wunsch 
    73447 Similarity matrix | BLOSUM-62 
    73448 SS fraction | 0.3 
    73449 Gap open (HH/SS/other) | 18/18/6 
    73450 Gap extend | 1 
    73451 SS matrix |  |  | H | S | O 
    73452 ---|---|---|--- 
    73453 H | 6 | -9 | -6 
    73454 S |  | 6 | -6 
    73455 O |  |  | 4 
    73456 Iteration cutoff | 2 
    73457  
    73458 Matchmaker 3j0c.pdb1, chain H (#1.46) with AF3 E2 353-438.pdb, chain B (#830),
    73459 sequence alignment score = 329.4 
    73460 RMSD between 40 pruned atom pairs is 0.937 angstroms; (across all 84 pairs:
    73461 8.150) 
    73462  
    73463 
    73464 > hide sel cartoons
    73465 
    73466 > select #1.46/I
    73467 
    73468 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    73469 
    73470 > show sel cartoons
    73471 
    73472 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    73473 
    73474 Chain information for AF3 CA.pdb #831 
    73475 --- 
    73476 Chain | Description 
    73477 A | No description available 
    73478  
    73479 
    73480 > matchmaker #831 to #1.46 & sel
    73481 
    73482 Parameters 
    73483 --- 
    73484 Chain pairing | bb 
    73485 Alignment algorithm | Needleman-Wunsch 
    73486 Similarity matrix | BLOSUM-62 
    73487 SS fraction | 0.3 
    73488 Gap open (HH/SS/other) | 18/18/6 
    73489 Gap extend | 1 
    73490 SS matrix |  |  | H | S | O 
    73491 ---|---|---|--- 
    73492 H | 6 | -9 | -6 
    73493 S |  | 6 | -6 
    73494 O |  |  | 4 
    73495 Iteration cutoff | 2 
    73496  
    73497 Matchmaker 3j0c.pdb1, chain I (#1.46) with AF3 CA.pdb, chain A (#831),
    73498 sequence alignment score = 306.5 
    73499 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    73500 2.689) 
    73501  
    73502 
    73503 > hide sel cartoons
    73504 
    73505 > color #827 dodgerblue
    73506 
    73507 > color #828 dodgerblue
    73508 
    73509 > color #829 #00b305ff
    73510 
    73511 > color #830 #00b305ff
    73512 
    73513 > color #831 #f15839ff
    73514 
    73515 > select #1.47/G
    73516 
    73517 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    73518 
    73519 > show sel cartoons
    73520 
    73521 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    73522 
    73523 Chain information for AF3 E1 1-421.pdb #832 
    73524 --- 
    73525 Chain | Description 
    73526 A | No description available 
    73527  
    73528 
    73529 > matchmaker #832 to #1.47 & sel
    73530 
    73531 Parameters 
    73532 --- 
    73533 Chain pairing | bb 
    73534 Alignment algorithm | Needleman-Wunsch 
    73535 Similarity matrix | BLOSUM-62 
    73536 SS fraction | 0.3 
    73537 Gap open (HH/SS/other) | 18/18/6 
    73538 Gap extend | 1 
    73539 SS matrix |  |  | H | S | O 
    73540 ---|---|---|--- 
    73541 H | 6 | -9 | -6 
    73542 S |  | 6 | -6 
    73543 O |  |  | 4 
    73544 Iteration cutoff | 2 
    73545  
    73546 Matchmaker 3j0c.pdb1, chain G (#1.47) with AF3 E1 1-421.pdb, chain A (#832),
    73547 sequence alignment score = 1060.7 
    73548 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    73549 2.985) 
    73550  
    73551 
    73552 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    73553 
    73554 Chain information for AF3 E1 422-461.pdb #833 
    73555 --- 
    73556 Chain | Description 
    73557 A | No description available 
    73558  
    73559 
    73560 > matchmaker #833 to #1.47 & sel
    73561 
    73562 Parameters 
    73563 --- 
    73564 Chain pairing | bb 
    73565 Alignment algorithm | Needleman-Wunsch 
    73566 Similarity matrix | BLOSUM-62 
    73567 SS fraction | 0.3 
    73568 Gap open (HH/SS/other) | 18/18/6 
    73569 Gap extend | 1 
    73570 SS matrix |  |  | H | S | O 
    73571 ---|---|---|--- 
    73572 H | 6 | -9 | -6 
    73573 S |  | 6 | -6 
    73574 O |  |  | 4 
    73575 Iteration cutoff | 2 
    73576  
    73577 Matchmaker 3j0c.pdb1, chain G (#1.47) with AF3 E1 422-461.pdb, chain A (#833),
    73578 sequence alignment score = 626.9 
    73579 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    73580 2.997) 
    73581  
    73582 
    73583 > hide sel cartoons
    73584 
    73585 > select #1.47/H
    73586 
    73587 3304 atoms, 3395 bonds, 423 residues, 1 model selected 
    73588 
    73589 > show sel cartoons
    73590 
    73591 > open "/Users/Jean/Desktop/AF3 E2 1-352.pdb"
    73592 
    73593 Chain information for AF3 E2 1-352.pdb #834 
    73594 --- 
    73595 Chain | Description 
    73596 B | No description available 
    73597  
    73598 
    73599 > matchmaker #834 to #1.47 & sel
    73600 
    73601 Parameters 
    73602 --- 
    73603 Chain pairing | bb 
    73604 Alignment algorithm | Needleman-Wunsch 
    73605 Similarity matrix | BLOSUM-62 
    73606 SS fraction | 0.3 
    73607 Gap open (HH/SS/other) | 18/18/6 
    73608 Gap extend | 1 
    73609 SS matrix |  |  | H | S | O 
    73610 ---|---|---|--- 
    73611 H | 6 | -9 | -6 
    73612 S |  | 6 | -6 
    73613 O |  |  | 4 
    73614 Iteration cutoff | 2 
    73615  
    73616 Matchmaker 3j0c.pdb1, chain H (#1.47) with AF3 E2 1-352.pdb, chain B (#834),
    73617 sequence alignment score = 590.9 
    73618 RMSD between 103 pruned atom pairs is 1.024 angstroms; (across all 333 pairs:
    73619 6.107) 
    73620  
    73621 
    73622 > open "/Users/Jean/Desktop/AF3 E2 353-438.pdb"
    73623 
    73624 Chain information for AF3 E2 353-438.pdb #835 
    73625 --- 
    73626 Chain | Description 
    73627 B | No description available 
    73628  
    73629 
    73630 > matchmaker #835 to #1.47 & sel
    73631 
    73632 Parameters 
    73633 --- 
    73634 Chain pairing | bb 
    73635 Alignment algorithm | Needleman-Wunsch 
    73636 Similarity matrix | BLOSUM-62 
    73637 SS fraction | 0.3 
    73638 Gap open (HH/SS/other) | 18/18/6 
    73639 Gap extend | 1 
    73640 SS matrix |  |  | H | S | O 
    73641 ---|---|---|--- 
    73642 H | 6 | -9 | -6 
    73643 S |  | 6 | -6 
    73644 O |  |  | 4 
    73645 Iteration cutoff | 2 
    73646  
    73647 Matchmaker 3j0c.pdb1, chain H (#1.47) with AF3 E2 353-438.pdb, chain B (#835),
    73648 sequence alignment score = 329.4 
    73649 RMSD between 40 pruned atom pairs is 0.938 angstroms; (across all 84 pairs:
    73650 8.150) 
    73651  
    73652 
    73653 > hide sel cartoons
    73654 
    73655 > select #1.47/I
    73656 
    73657 1277 atoms, 1305 bonds, 162 residues, 1 model selected 
    73658 
    73659 > show sel cartoons
    73660 
    73661 > open "/Users/Jean/Desktop/AF3 CA.pdb"
    73662 
    73663 Chain information for AF3 CA.pdb #836 
    73664 --- 
    73665 Chain | Description 
    73666 A | No description available 
    73667  
    73668 
    73669 > matchmaker #836 to #1.47 & sel
    73670 
    73671 Parameters 
    73672 --- 
    73673 Chain pairing | bb 
    73674 Alignment algorithm | Needleman-Wunsch 
    73675 Similarity matrix | BLOSUM-62 
    73676 SS fraction | 0.3 
    73677 Gap open (HH/SS/other) | 18/18/6 
    73678 Gap extend | 1 
    73679 SS matrix |  |  | H | S | O 
    73680 ---|---|---|--- 
    73681 H | 6 | -9 | -6 
    73682 S |  | 6 | -6 
    73683 O |  |  | 4 
    73684 Iteration cutoff | 2 
    73685  
    73686 Matchmaker 3j0c.pdb1, chain I (#1.47) with AF3 CA.pdb, chain A (#836),
    73687 sequence alignment score = 306.5 
    73688 RMSD between 119 pruned atom pairs is 1.150 angstroms; (across all 161 pairs:
    73689 2.689) 
    73690  
    73691 
    73692 > hide sel cartoons
    73693 
    73694 > color #832 dodgerblue
    73695 
    73696 > color #833 dodgerblue
    73697 
    73698 > color #834 #00b305ff
    73699 
    73700 > color #835 #00b305ff
    73701 
    73702 > color #836 #f15839ff
    73703 
    73704 > select #1.48/G
    73705 
    73706 3370 atoms, 3461 bonds, 442 residues, 1 model selected 
    73707 
    73708 > show sel cartoons
    73709 
    73710 > open "/Users/Jean/Desktop/AF3 E1 1-421.pdb"
    73711 
    73712 Chain information for AF3 E1 1-421.pdb #837 
    73713 --- 
    73714 Chain | Description 
    73715 A | No description available 
    73716  
    73717 
    73718 > matchmaker #837 to #1.48 & sel
    73719 
    73720 Parameters 
    73721 --- 
    73722 Chain pairing | bb 
    73723 Alignment algorithm | Needleman-Wunsch 
    73724 Similarity matrix | BLOSUM-62 
    73725 SS fraction | 0.3 
    73726 Gap open (HH/SS/other) | 18/18/6 
    73727 Gap extend | 1 
    73728 SS matrix |  |  | H | S | O 
    73729 ---|---|---|--- 
    73730 H | 6 | -9 | -6 
    73731 S |  | 6 | -6 
    73732 O |  |  | 4 
    73733 Iteration cutoff | 2 
    73734  
    73735 Matchmaker 3j0c.pdb1, chain G (#1.48) with AF3 E1 1-421.pdb, chain A (#837),
    73736 sequence alignment score = 1060.7 
    73737 RMSD between 273 pruned atom pairs is 1.168 angstroms; (across all 403 pairs:
    73738 2.985) 
    73739  
    73740 
    73741 > open "/Users/Jean/Desktop/AF3 E1 422-461.pdb"
    73742 
    73743 Chain information for AF3 E1 422-461.pdb #838 
    73744 --- 
    73745 Chain | Description 
    73746 A | No description available 
    73747  
    73748 
    73749 > matchmaker #838 to #1.48 & sel
    73750 
    73751 Parameters 
    73752 --- 
    73753 Chain pairing | bb 
    73754 Alignment algorithm | Needleman-Wunsch 
    73755 Similarity matrix | BLOSUM-62 
    73756 SS fraction | 0.3 
    73757 Gap open (HH/SS/other) | 18/18/6 
    73758 Gap extend | 1 
    73759 SS matrix |  |  | H | S | O 
    73760 ---|---|---|--- 
    73761 H | 6 | -9 | -6 
    73762 S |  | 6 | -6 
    73763 O |  |  | 4 
    73764 Iteration cutoff | 2 
    73765  
    73766 Matchmaker 3j0c.pdb1, chain G (#1.48) with AF3 E1 422-461.pdb, chain A (#838),
    73767 sequence alignment score = 626.9 
    73768 RMSD between 27 pruned atom pairs is 0.513 angstroms; (across all 38 pairs:
    73769 2.997) 
    73770  
    73771 
     1485[deleted to fit within ticket size limits]
    737721486> hide sel cartoons
    737731487