Changes between Initial Version and Version 1 of Ticket #20136


Ignore:
Timestamp:
Apr 6, 2026, 1:23:30 PM (2 days ago)
Author:
Eric Pettersen
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #20136

    • Property Component Unassigned → Window Toolkit
    • Property Owner set to Eric Pettersen
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → accepted
    • Property Summary ChimeraX bug report submission → Crash on Mac waking from sleep

  • Ticket #20136 – Description

    initial v1  
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    1499    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/graphics\/_graphics.cpython-311-darwin.so",
    1500    "name" : "_graphics.cpython-311-darwin.so"
    1501  },
    1502  {
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    1507    "uuid" : "1e310bc7-5f96-396b-816d-5b40a3dde12c",
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    1509    "name" : "_pdbio.cpython-311-darwin.so"
    1510  },
    1511  {
    1512    "source" : "P",
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    1517    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/_imagingmath.cpython-311-darwin.so",
    1518    "name" : "_imagingmath.cpython-311-darwin.so"
    1519  },
    1520  {
    1521    "source" : "P",
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    1525    "uuid" : "644b1794-90c5-3838-9ffa-b772683aeb37",
    1526    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/alignment_algs\/_sw.cpython-311-darwin.so",
    1527    "name" : "_sw.cpython-311-darwin.so"
    1528  },
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    1535    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/alignment_algs\/libalign_algs.dylib",
    1536    "name" : "libalign_algs.dylib"
    1537  },
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    1543    "uuid" : "4e700338-6839-3c7c-9f41-a201e7f185e5",
    1544    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/dssp\/_dssp.cpython-311-darwin.so",
    1545    "name" : "_dssp.cpython-311-darwin.so"
    1546  },
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    1552    "uuid" : "93fd54d8-5d5e-319d-94c5-2702d533d751",
    1553    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/alignment_algs\/_nw.cpython-311-darwin.so",
    1554    "name" : "_nw.cpython-311-darwin.so"
    1555  },
    1556  {
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    1558    "arch" : "arm64",
    1559    "base" : 13896777728,
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    1561    "uuid" : "cc06500d-d418-3365-b197-36b1304a819e",
    1562    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtOpenGL.abi3.so",
    1563    "name" : "QtOpenGL.abi3.so"
    1564  },
    1565  {
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    1570    "uuid" : "b32a8c32-a5e0-3a8b-9a0d-00a26b160215",
    1571    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtOpenGLWidgets.abi3.so",
    1572    "name" : "QtOpenGLWidgets.abi3.so"
    1573  },
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    1581    "name" : "QtOpenGLWidgets"
    1582  },
    1583  {
    1584    "source" : "P",
    1585    "arch" : "arm64",
    1586    "base" : 5433196544,
    1587    "size" : 81920,
    1588    "uuid" : "d7bd530c-3353-37a6-b81f-ee3179d65811",
    1589    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lz4\/_version.cpython-311-darwin.so",
    1590    "name" : "_version.cpython-311-darwin.so"
    1591  },
    1592  {
    1593    "source" : "P",
    1594    "arch" : "arm64",
    1595    "base" : 5438783488,
    1596    "size" : 180224,
    1597    "uuid" : "87eed069-25fc-30f6-aa30-1e54859d92e2",
    1598    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lz4\/frame\/_frame.cpython-311-darwin.so",
    1599    "name" : "_frame.cpython-311-darwin.so"
    1600  },
    1601  {
    1602    "source" : "P",
    1603    "arch" : "arm64",
    1604    "base" : 5439062016,
    1605    "size" : 131072,
    1606    "uuid" : "c1a3c2d3-b21b-3231-839d-fcbc83ca2028",
    1607    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/core\/_serialize.cpython-311-darwin.so",
    1608    "name" : "_serialize.cpython-311-darwin.so"
    1609  },
    1610  {
    1611    "source" : "P",
    1612    "arch" : "arm64",
    1613    "base" : 5439291392,
    1614    "size" : 131072,
    1615    "uuid" : "650aead6-ce16-39bb-9ba1-4bf9986b96d6",
    1616    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/msgpack\/_cmsgpack.cpython-311-darwin.so",
    1617    "name" : "_cmsgpack.cpython-311-darwin.so"
    1618  },
    1619  {
    1620    "source" : "P",
    1621    "arch" : "arm64",
    1622    "base" : 13093060608,
    1623    "size" : 49152,
    1624    "uuid" : "f4191524-316f-3e56-8aa1-9a441a05fd70",
    1625    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atom_search\/ast.cpython-311-darwin.so",
    1626    "name" : "ast.cpython-311-darwin.so"
    1627  },
    1628  {
    1629    "source" : "P",
    1630    "arch" : "arm64e",
    1631    "base" : 6485135360,
    1632    "size" : 243284,
    1633    "uuid" : "6e4a96ad-04b8-3e8a-b91d-087e62306246",
    1634    "path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
    1635    "name" : "libsystem_kernel.dylib"
    1636  },
    1637  {
    1638    "source" : "P",
    1639    "arch" : "arm64e",
    1640    "base" : 6485381120,
    1641    "size" : 51784,
    1642    "uuid" : "d6494ba9-171e-39fc-b1aa-28ecf87975d1",
    1643    "path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
    1644    "name" : "libsystem_pthread.dylib"
    1645  },
    1646  {
    1647    "source" : "P",
    1648    "arch" : "arm64e",
    1649    "base" : 6483902464,
    1650    "size" : 528964,
    1651    "uuid" : "dfea8794-80ce-37c3-8f6a-108aa1d0b1b0",
    1652    "path" : "\/usr\/lib\/system\/libsystem_c.dylib",
    1653    "name" : "libsystem_c.dylib"
    1654  },
    1655  {
    1656    "source" : "P",
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    1658    "base" : 6485630976,
    1659    "size" : 32268,
    1660    "uuid" : "fd19a599-8750-31f9-924f-c2810c938371",
    1661    "path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
    1662    "name" : "libsystem_platform.dylib"
    1663  },
    1664  {
    1665    "source" : "P",
    1666    "arch" : "arm64e",
    1667    "base" : 6552334336,
    1668    "CFBundleShortVersionString" : "6.9",
    1669    "CFBundleIdentifier" : "com.apple.AppKit",
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    1671    "uuid" : "860c164c-d04c-30ff-8c6f-e672b74caf11",
    1672    "path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
    1673    "name" : "AppKit",
    1674    "CFBundleVersion" : "2575.70.52"
    1675  },
    1676  {
    1677    "source" : "P",
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    1680    "CFBundleShortVersionString" : "1.600.0",
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    1684    "path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
    1685    "name" : "SkyLight"
    1686  },
    1687  {
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    1692    "uuid" : "24ce0d89-4114-30c2-a81a-3db1f5931cff",
    1693    "path" : "\/usr\/lib\/system\/libdispatch.dylib",
    1694    "name" : "libdispatch.dylib"
    1695  },
    1696  {
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    1717    "name" : "HIToolbox"
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     155[deleted to fit within ticket limits]
     156
    1746157],
    1747158 "sharedCache" : {
    … …  
    30811492> ui tool show Matchmaker
    30821493
    3083 > matchmaker #5 to #6 & sel
    3084 
    3085 Computing secondary structure 
    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 fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
    3102 fold_hqba_yhbp_co_model_1.cif, chain A (#5), sequence alignment score = 870.8 
    3103 RMSD between 167 pruned atom pairs is 0.433 angstroms; (across all 167 pairs:
    3104 0.433) 
    3105 
    3106 
    3107 > hide #9 models
    3108 
    3109 > show #4 models
    3110 
    3111 > open /Users/taic/Library/CloudStorage/OneDrive-
    3112 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq_co/fold_hqba_yhbq_co_model_0.cif
    3113 
    3114 Chain information for fold_hqba_yhbq_co_model_0.cif #7 
    3115 --- 
    3116 Chain | Description 
    3117 A | . 
    3118 B | . 
    3119 
    3120 
    3121 > open /Users/taic/Library/CloudStorage/OneDrive-
    3122 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq_co/fold_hqba_yhbq_co_model_1.cif
    3123 
    3124 Chain information for fold_hqba_yhbq_co_model_1.cif #8 
    3125 --- 
    3126 Chain | Description 
    3127 A | . 
    3128 B | . 
    3129 
    3130 
    3131 > open /Users/taic/Library/CloudStorage/OneDrive-
    3132 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq_co/fold_hqba_yhbq_co_model_2.cif
    3133 
    3134 Chain information for fold_hqba_yhbq_co_model_2.cif #10 
    3135 --- 
    3136 Chain | Description 
    3137 A | . 
    3138 B | . 
    3139 
    3140 
    3141 > open /Users/taic/Library/CloudStorage/OneDrive-
    3142 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq_co/fold_hqba_yhbq_co_model_3.cif
    3143 
    3144 Chain information for fold_hqba_yhbq_co_model_3.cif #11 
    3145 --- 
    3146 Chain | Description 
    3147 A | . 
    3148 B | . 
    3149 
    3150 
    3151 > open /Users/taic/Library/CloudStorage/OneDrive-
    3152 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq_co/fold_hqba_yhbq_co_model_4.cif
    3153 
    3154 Chain information for fold_hqba_yhbq_co_model_4.cif #12 
    3155 --- 
    3156 Chain | Description 
    3157 A | . 
    3158 B | . 
    3159 
    3160 Computing secondary structure 
    3161 
    3162 > select #6/A
    3163 
    3164 1311 atoms, 1341 bonds, 167 residues, 1 model selected 
    3165 
    3166 > ui tool show Matchmaker
    3167 
    3168 > matchmaker #4-5,7-12 to #6 & sel
    3169 
    3170 Computing secondary structure 
    3171 Parameters 
    3172 --- 
    3173 Chain pairing | bb 
    3174 Alignment algorithm | Needleman-Wunsch 
    3175 Similarity matrix | BLOSUM-62 
    3176 SS fraction | 0.3 
    3177 Gap open (HH/SS/other) | 18/18/6 
    3178 Gap extend | 1 
    3179 SS matrix |  |  | H | S | O 
    3180 ---|---|---|--- 
    3181 H | 6 | -9 | -6 
    3182 S |  | 6 | -6 
    3183 O |  |  | 4 
    3184 Iteration cutoff | 2 
    3185 
    3186 Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
    3187 fold_hqba_yhbp_co_model_0.cif, chain A (#4), sequence alignment score = 852.8 
    3188 RMSD between 167 pruned atom pairs is 0.391 angstroms; (across all 167 pairs:
    3189 0.391) 
    3190 
    3191 Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
    3192 fold_hqba_yhbp_co_model_1.cif, chain A (#5), sequence alignment score = 870.8 
    3193 RMSD between 167 pruned atom pairs is 0.433 angstroms; (across all 167 pairs:
    3194 0.433) 
    3195 
    3196 Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
    3197 fold_hqba_yhbq_co_model_0.cif, chain A (#7), sequence alignment score = 867.8 
    3198 RMSD between 167 pruned atom pairs is 0.202 angstroms; (across all 167 pairs:
    3199 0.202) 
    3200 
    3201 Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
    3202 fold_hqba_yhbq_co_model_1.cif, chain A (#8), sequence alignment score = 867.8 
    3203 RMSD between 167 pruned atom pairs is 0.376 angstroms; (across all 167 pairs:
    3204 0.376) 
    3205 
    3206 Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
    3207 fold_hqba_yhbp_co_model_4.cif, chain A (#9), sequence alignment score = 873.8 
    3208 RMSD between 167 pruned atom pairs is 0.297 angstroms; (across all 167 pairs:
    3209 0.297) 
    3210 
    3211 Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
    3212 fold_hqba_yhbq_co_model_2.cif, chain A (#10), sequence alignment score = 870.8 
    3213 RMSD between 167 pruned atom pairs is 0.280 angstroms; (across all 167 pairs:
    3214 0.280) 
    3215 
    3216 Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
    3217 fold_hqba_yhbq_co_model_3.cif, chain A (#11), sequence alignment score = 867.8 
    3218 RMSD between 167 pruned atom pairs is 0.317 angstroms; (across all 167 pairs:
    3219 0.317) 
    3220 
    3221 Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
    3222 fold_hqba_yhbq_co_model_4.cif, chain A (#12), sequence alignment score = 867.8 
    3223 RMSD between 167 pruned atom pairs is 0.293 angstroms; (across all 167 pairs:
    3224 0.293) 
    3225 
    3226 
    3227 > hide #4 models
    3228 
    3229 > hide #5 models
    3230 
    3231 > hide #8 models
    3232 
    3233 > hide #10 models
    3234 
    3235 > hide #11 models
    3236 
    3237 > hide #12 models
    3238 
    3239 > show #8 models
    3240 
    3241 > hide #7 models
    3242 
    3243 > show #10 models
    3244 
    3245 > hide #8 models
    3246 
    3247 > show #11 models
    3248 
    3249 > hide #10 models
    3250 
    3251 > show #12 models
    3252 
    3253 > hide #11 models
    3254 
    3255 > show #4 models
    3256 
    3257 > hide #4 models
    3258 
    3259 > show #!6 models
    3260 
    3261 > hide #!6 models
    3262 
    3263 > show #!6 models
    3264 
    3265 > hide #!6 models
    3266 
    3267 > show #!6 models
    3268 
    3269 > show #!3 models
    3270 
    3271 > hide #12 models
    3272 
    3273 > show #12 models
    3274 
    3275 > hide #!3 models
    3276 
    3277 > show #!3 models
    3278 
    3279 > hide #!6 models
    3280 
    3281 > show #!6 models
    3282 
    3283 > hide #12 models
    3284 
    3285 > select clear
    3286 
    3287 > show #7 models
    3288 
    3289 > hide #7 models
    3290 
    3291 > show #4 models
    3292 
    3293 > hide #!6 models
    3294 
    3295 > hide #4 models
    3296 
    3297 > show #!6 models
    3298 
    3299 > hide #!6 models
    3300 
    3301 > show #4 models
    3302 
    3303 > show #5 models
    3304 
    3305 > hide #5 models
    3306 
    3307 > show #5 models
    3308 
    3309 > hide #4 models
    3310 
    3311 > hide #5 models
    3312 
    3313 > show #9 models
    3314 
    3315 > hide #9 models
    3316 
    3317 > show #9 models
    3318 
    3319 > hide #9 models
    3320 
    3321 > show #7 models
    3322 
    3323 > color #7#!3 bychain
    3324 
    3325 > hide #7 models
    3326 
    3327 > color #3 lime
    3328 
    3329 > show #7 models
    3330 
    3331 > show #8 models
    3332 
    3333 > hide #7 models
    3334 
    3335 > show #7 models
    3336 
    3337 > hide #8 models
    3338 
    3339 > show #9 models
    3340 
    3341 > hide #9 models
    3342 
    3343 > show #10 models
    3344 
    3345 > hide #10 models
    3346 
    3347 > show #11 models
    3348 
    3349 > hide #11 models
    3350 
    3351 > show #12 models
    3352 
    3353 > hide #12 models
    3354 
    3355 > show #9 models
    3356 
    3357 > hide #!3 models
    3358 
    3359 > hide #7 models
    3360 
    3361 > show #5 models
    3362 
    3363 > hide #9 models
    3364 
    3365 > show #9 models
    3366 
    3367 > hide #5 models
    3368 
    3369 > delete atoms #9
    3370 
    3371 > delete bonds #9
    3372 
    3373 > show #7 models
    3374 
    3375 > show #!3 models
    3376 
    3377 > show #8 models
    3378 
    3379 > hide #7 models
    3380 
    3381 > show #7 models
    3382 
    3383 > hide #8 models
    3384 
    3385 > show #!6 models
    3386 
    3387 > hide #!6 models
    3388 
    3389 > show #!6 models
    3390 
    3391 > hide #!6 models
    3392 
    3393 > show #8 models
    3394 
    3395 > show #10 models
    3396 
    3397 > show #11 models
    3398 
    3399 > show #12 models
    3400 
    3401 > hide #7 models
    3402 
    3403 > hide #!3 models
    3404 
    3405 > show #4 models
    3406 
    3407 > hide #8 models
    3408 
    3409 > hide #10 models
    3410 
    3411 > hide #12 models
    3412 
    3413 > hide #11 models
    3414 
    3415 > show #!6 models
    3416 
    3417 > show #5 models
    3418 
    3419 > hide #4 models
    3420 
    3421 > hide #!6 models
    3422 
    3423 > open /Users/taic/Library/CloudStorage/OneDrive-
    3424 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu/fold_hqba_ubiu_model_0.cif
    3425 
    3426 Chain information for fold_hqba_ubiu_model_0.cif #9 
    3427 --- 
    3428 Chain | Description 
    3429 A | . 
    3430 B | . 
    3431 
    3432 
    3433 > open /Users/taic/Library/CloudStorage/OneDrive-
    3434 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu/fold_hqba_ubiu_model_1.cif
    3435 
    3436 Chain information for fold_hqba_ubiu_model_1.cif #13 
    3437 --- 
    3438 Chain | Description 
    3439 A | . 
    3440 B | . 
    3441 
    3442 
    3443 > open /Users/taic/Library/CloudStorage/OneDrive-
    3444 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu/fold_hqba_ubiu_model_2.cif
    3445 
    3446 Chain information for fold_hqba_ubiu_model_2.cif #14 
    3447 --- 
    3448 Chain | Description 
    3449 A | . 
    3450 B | . 
    3451 
    3452 
    3453 > open /Users/taic/Library/CloudStorage/OneDrive-
    3454 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu/fold_hqba_ubiu_model_3.cif
    3455 
    3456 Chain information for fold_hqba_ubiu_model_3.cif #15 
    3457 --- 
    3458 Chain | Description 
    3459 A | . 
    3460 B | . 
    3461 
    3462 
    3463 > open /Users/taic/Library/CloudStorage/OneDrive-
    3464 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu/fold_hqba_ubiu_model_4.cif
    3465 
    3466 Chain information for fold_hqba_ubiu_model_4.cif #16 
    3467 --- 
    3468 Chain | Description 
    3469 A | . 
    3470 B | . 
    3471 
    3472 Computing secondary structure 
    3473 
    3474 > show #!6 models
    3475 
    3476 > hide #5 models
    3477 
    3478 > hide #9 models
    3479 
    3480 > ui tool show Matchmaker
    3481 
    3482 > select #6/A
    3483 
    3484 1311 atoms, 1341 bonds, 167 residues, 1 model selected 
    3485 
    3486 > ui tool show Matchmaker
    3487 
    3488 > matchmaker #9-16 to #6 & sel
    3489 
    3490 Computing secondary structure 
    3491 Parameters 
    3492 --- 
    3493 Chain pairing | bb 
    3494 Alignment algorithm | Needleman-Wunsch 
    3495 Similarity matrix | BLOSUM-62 
    3496 SS fraction | 0.3 
    3497 Gap open (HH/SS/other) | 18/18/6 
    3498 Gap extend | 1 
    3499 SS matrix |  |  | H | S | O 
    3500 ---|---|---|--- 
    3501 H | 6 | -9 | -6 
    3502 S |  | 6 | -6 
    3503 O |  |  | 4 
    3504 Iteration cutoff | 2 
    3505 
    3506 Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
    3507 fold_hqba_ubiu_model_0.cif, chain A (#9), sequence alignment score = 870.8 
    3508 RMSD between 167 pruned atom pairs is 0.273 angstroms; (across all 167 pairs:
    3509 0.273) 
    3510 
    3511 Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
    3512 fold_hqba_yhbq_co_model_2.cif, chain A (#10), sequence alignment score = 870.8 
    3513 RMSD between 167 pruned atom pairs is 0.280 angstroms; (across all 167 pairs:
    3514 0.280) 
    3515 
    3516 Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
    3517 fold_hqba_yhbq_co_model_3.cif, chain A (#11), sequence alignment score = 867.8 
    3518 RMSD between 167 pruned atom pairs is 0.317 angstroms; (across all 167 pairs:
    3519 0.317) 
    3520 
    3521 Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
    3522 fold_hqba_yhbq_co_model_4.cif, chain A (#12), sequence alignment score = 867.8 
    3523 RMSD between 167 pruned atom pairs is 0.293 angstroms; (across all 167 pairs:
    3524 0.293) 
    3525 
    3526 Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
    3527 fold_hqba_ubiu_model_1.cif, chain A (#13), sequence alignment score = 870.8 
    3528 RMSD between 167 pruned atom pairs is 0.260 angstroms; (across all 167 pairs:
    3529 0.260) 
    3530 
    3531 Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
    3532 fold_hqba_ubiu_model_2.cif, chain A (#14), sequence alignment score = 867.8 
    3533 RMSD between 167 pruned atom pairs is 0.235 angstroms; (across all 167 pairs:
    3534 0.235) 
    3535 
    3536 Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
    3537 fold_hqba_ubiu_model_3.cif, chain A (#15), sequence alignment score = 870.8 
    3538 RMSD between 167 pruned atom pairs is 0.229 angstroms; (across all 167 pairs:
    3539 0.229) 
    3540 
    3541 Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
    3542 fold_hqba_ubiu_model_4.cif, chain A (#16), sequence alignment score = 867.8 
    3543 RMSD between 167 pruned atom pairs is 0.219 angstroms; (across all 167 pairs:
    3544 0.219) 
    3545 
    3546 
    3547 > show #9 models
    3548 
    3549 > hide #!6 models
    3550 
    3551 > show #!6 models
    3552 
    3553 > hide #9 models
    3554 
    3555 > select #6/A
    3556 
    3557 1311 atoms, 1341 bonds, 167 residues, 1 model selected 
    3558 
    3559 > hide #13 models
    3560 
    3561 > hide #14 models
    3562 
    3563 > hide #15 models
    3564 
    3565 > hide #16 models
    3566 
    3567 > show #9 models
    3568 
    3569 > hide #!6 models
    3570 
    3571 > ui tool show Matchmaker
    3572 
    3573 > select #6/A
    3574 
    3575 1311 atoms, 1341 bonds, 167 residues, 1 model selected 
    3576 
    3577 > matchmaker #9-16 to #6 & sel
    3578 
    3579 Computing secondary structure 
    3580 Parameters 
    3581 --- 
    3582 Chain pairing | bb 
    3583 Alignment algorithm | Needleman-Wunsch 
    3584 Similarity matrix | BLOSUM-62 
    3585 SS fraction | 0.3 
    3586 Gap open (HH/SS/other) | 18/18/6 
    3587 Gap extend | 1 
    3588 SS matrix |  |  | H | S | O 
    3589 ---|---|---|--- 
    3590 H | 6 | -9 | -6 
    3591 S |  | 6 | -6 
    3592 O |  |  | 4 
    3593 Iteration cutoff | 2 
    3594 
    3595 Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
    3596 fold_hqba_ubiu_model_0.cif, chain A (#9), sequence alignment score = 870.8 
    3597 RMSD between 167 pruned atom pairs is 0.273 angstroms; (across all 167 pairs:
    3598 0.273) 
    3599 
    3600 Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
    3601 fold_hqba_yhbq_co_model_2.cif, chain A (#10), sequence alignment score = 870.8 
    3602 RMSD between 167 pruned atom pairs is 0.280 angstroms; (across all 167 pairs:
    3603 0.280) 
    3604 
    3605 Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
    3606 fold_hqba_yhbq_co_model_3.cif, chain A (#11), sequence alignment score = 867.8 
    3607 RMSD between 167 pruned atom pairs is 0.317 angstroms; (across all 167 pairs:
    3608 0.317) 
    3609 
    3610 Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
    3611 fold_hqba_yhbq_co_model_4.cif, chain A (#12), sequence alignment score = 867.8 
    3612 RMSD between 167 pruned atom pairs is 0.293 angstroms; (across all 167 pairs:
    3613 0.293) 
    3614 
    3615 Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
    3616 fold_hqba_ubiu_model_1.cif, chain A (#13), sequence alignment score = 870.8 
    3617 RMSD between 167 pruned atom pairs is 0.260 angstroms; (across all 167 pairs:
    3618 0.260) 
    3619 
    3620 Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
    3621 fold_hqba_ubiu_model_2.cif, chain A (#14), sequence alignment score = 867.8 
    3622 RMSD between 167 pruned atom pairs is 0.235 angstroms; (across all 167 pairs:
    3623 0.235) 
    3624 
    3625 Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
    3626 fold_hqba_ubiu_model_3.cif, chain A (#15), sequence alignment score = 870.8 
    3627 RMSD between 167 pruned atom pairs is 0.229 angstroms; (across all 167 pairs:
    3628 0.229) 
    3629 
    3630 Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
    3631 fold_hqba_ubiu_model_4.cif, chain A (#16), sequence alignment score = 867.8 
    3632 RMSD between 167 pruned atom pairs is 0.219 angstroms; (across all 167 pairs:
    3633 0.219) 
    3634 
    3635 
    3636 > show #!6 models
    3637 
    3638 > hide #!6 models
    3639 
    3640 > show #13 models
    3641 
    3642 > show #14 models
    3643 
    3644 > show #15 models
    3645 
    3646 > show #16 models
    3647 
    3648 > hide #9 models
    3649 
    3650 > delete atoms #13-16
    3651 
    3652 > delete bonds #13-16
    3653 
    3654 > show #9 models
    3655 
    3656 > color #9 bychain
    3657 
    3658 > show #!6 models
    3659 
    3660 > show #!3 models
    3661 
    3662 > hide #!6 models
    3663 
    3664 > show #!6 models
    3665 
    3666 > hide #9 models
    3667 
    3668 > select clear
    3669 
    3670 > select #6/A:164
    3671 
    3672 11 atoms, 11 bonds, 1 residue, 1 model selected 
    3673 
    3674 > select #6/A:23,24,27
    3675 
    3676 24 atoms, 22 bonds, 3 residues, 1 model selected 
    3677 
    3678 > select #6/A:23,24,27,167
    3679 
    3680 36 atoms, 34 bonds, 4 residues, 1 model selected 
    3681 
    3682 > color (#!6 & sel) cyan
    3683 
    3684 > select clear
    3685 
    3686 > show #9 models
    3687 
    3688 > hide #!6 models
    3689 
    3690 > show #7 models
    3691 
    3692 > hide #9 models
    3693 
    3694 > show #!6 models
    3695 
    3696 > hide #!6 models
    3697 
    3698 > show #8 models
    3699 
    3700 > show #10 models
    3701 
    3702 > show #11 models
    3703 
    3704 > show #12 models
    3705 
    3706 > hide #8 models
    3707 
    3708 > hide #10 models
    3709 
    3710 > hide #11 models
    3711 
    3712 > hide #12 models
    3713 
    3714 > show #!6 models
    3715 
    3716 > hide #7 models
    3717 
    3718 > show #4 models
    3719 
    3720 > show #5 models
    3721 
    3722 > hide #!6 models
    3723 
    3724 > hide #5 models
    3725 
    3726 > show #5 models
    3727 
    3728 > hide #4 models
    3729 
    3730 > show #!6 models
    3731 
    3732 > hide #5 models
    3733 
    3734 > open /Users/taic/Library/CloudStorage/OneDrive-
    3735 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq/fold_hqba_yhbq_model_0.cif
    3736 
    3737 Chain information for fold_hqba_yhbq_model_0.cif #13 
    3738 --- 
    3739 Chain | Description 
    3740 A | . 
    3741 B | . 
    3742 
    3743 
    3744 > open /Users/taic/Library/CloudStorage/OneDrive-
    3745 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq/fold_hqba_yhbq_model_1.cif
    3746 
    3747 Chain information for fold_hqba_yhbq_model_1.cif #14 
    3748 --- 
    3749 Chain | Description 
    3750 A | . 
    3751 B | . 
    3752 
    3753 
    3754 > open /Users/taic/Library/CloudStorage/OneDrive-
    3755 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq/fold_hqba_yhbq_model_2.cif
    3756 
    3757 Chain information for fold_hqba_yhbq_model_2.cif #15 
    3758 --- 
    3759 Chain | Description 
    3760 A | . 
    3761 B | . 
    3762 
    3763 
    3764 > open /Users/taic/Library/CloudStorage/OneDrive-
    3765 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq/fold_hqba_yhbq_model_3.cif
    3766 
    3767 Chain information for fold_hqba_yhbq_model_3.cif #16 
    3768 --- 
    3769 Chain | Description 
    3770 A | . 
    3771 B | . 
    3772 
    3773 
    3774 > open /Users/taic/Library/CloudStorage/OneDrive-
    3775 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq/fold_hqba_yhbq_model_4.cif
    3776 
    3777 Chain information for fold_hqba_yhbq_model_4.cif #17 
    3778 --- 
    3779 Chain | Description 
    3780 A | . 
    3781 B | . 
    3782 
    3783 Computing secondary structure 
    3784 
    3785 > select #6/A
    3786 
    3787 1311 atoms, 1341 bonds, 167 residues, 1 model selected 
    3788 
    3789 > ui tool show Matchmaker
    3790 
    3791 > matchmaker #13-17 to #6 & sel
    3792 
    3793 Computing secondary structure 
    3794 Parameters 
    3795 --- 
    3796 Chain pairing | bb 
    3797 Alignment algorithm | Needleman-Wunsch 
    3798 Similarity matrix | BLOSUM-62 
    3799 SS fraction | 0.3 
    3800 Gap open (HH/SS/other) | 18/18/6 
    3801 Gap extend | 1 
    3802 SS matrix |  |  | H | S | O 
    3803 ---|---|---|--- 
    3804 H | 6 | -9 | -6 
    3805 S |  | 6 | -6 
    3806 O |  |  | 4 
    3807 Iteration cutoff | 2 
    3808 
    3809 Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
    3810 fold_hqba_yhbq_model_0.cif, chain A (#13), sequence alignment score = 870.8 
    3811 RMSD between 167 pruned atom pairs is 0.328 angstroms; (across all 167 pairs:
    3812 0.328) 
    3813 
    3814 Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
    3815 fold_hqba_yhbq_model_1.cif, chain A (#14), sequence alignment score = 867.8 
    3816 RMSD between 167 pruned atom pairs is 0.165 angstroms; (across all 167 pairs:
    3817 0.165) 
    3818 
    3819 Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
    3820 fold_hqba_yhbq_model_2.cif, chain A (#15), sequence alignment score = 867.8 
    3821 RMSD between 167 pruned atom pairs is 0.359 angstroms; (across all 167 pairs:
    3822 0.359) 
    3823 
    3824 Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
    3825 fold_hqba_yhbq_model_3.cif, chain A (#16), sequence alignment score = 870.8 
    3826 RMSD between 167 pruned atom pairs is 0.208 angstroms; (across all 167 pairs:
    3827 0.208) 
    3828 
    3829 Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
    3830 fold_hqba_yhbq_model_4.cif, chain A (#17), sequence alignment score = 873.8 
    3831 RMSD between 167 pruned atom pairs is 0.288 angstroms; (across all 167 pairs:
    3832 0.288) 
    3833 
    3834 
    3835 > matchmaker #13-17 to #6 & sel
    3836 
    3837 Computing secondary structure 
    3838 Parameters 
    3839 --- 
    3840 Chain pairing | bb 
    3841 Alignment algorithm | Needleman-Wunsch 
    3842 Similarity matrix | BLOSUM-62 
    3843 SS fraction | 0.3 
    3844 Gap open (HH/SS/other) | 18/18/6 
    3845 Gap extend | 1 
    3846 SS matrix |  |  | H | S | O 
    3847 ---|---|---|--- 
    3848 H | 6 | -9 | -6 
    3849 S |  | 6 | -6 
    3850 O |  |  | 4 
    3851 Iteration cutoff | 2 
    3852 
    3853 Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
    3854 fold_hqba_yhbq_model_0.cif, chain A (#13), sequence alignment score = 870.8 
    3855 RMSD between 167 pruned atom pairs is 0.328 angstroms; (across all 167 pairs:
    3856 0.328) 
    3857 
    3858 Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
    3859 fold_hqba_yhbq_model_1.cif, chain A (#14), sequence alignment score = 867.8 
    3860 RMSD between 167 pruned atom pairs is 0.165 angstroms; (across all 167 pairs:
    3861 0.165) 
    3862 
    3863 Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
    3864 fold_hqba_yhbq_model_2.cif, chain A (#15), sequence alignment score = 867.8 
    3865 RMSD between 167 pruned atom pairs is 0.359 angstroms; (across all 167 pairs:
    3866 0.359) 
    3867 
    3868 Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
    3869 fold_hqba_yhbq_model_3.cif, chain A (#16), sequence alignment score = 870.8 
    3870 RMSD between 167 pruned atom pairs is 0.208 angstroms; (across all 167 pairs:
    3871 0.208) 
    3872 
    3873 Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
    3874 fold_hqba_yhbq_model_4.cif, chain A (#17), sequence alignment score = 873.8 
    3875 RMSD between 167 pruned atom pairs is 0.288 angstroms; (across all 167 pairs:
    3876 0.288) 
    3877 
    3878 
    3879 > hide #!6 models
    3880 
    3881 > show #7 models
    3882 
    3883 > show #8 models
    3884 
    3885 > hide #8 models
    3886 
    3887 > show #8 models
    3888 
    3889 > show #10 models
    3890 
    3891 > show #11 models
    3892 
    3893 > hide #11 models
    3894 
    3895 > show #11 models
    3896 
    3897 > show #12 models
    3898 
    3899 > hide #!3 models
    3900 
    3901 > hide #7 models
    3902 
    3903 > hide #13 models
    3904 
    3905 > delete atoms #8,10-12,14-17
    3906 
    3907 > delete bonds #8,10-12,14-17
    3908 
    3909 > show #4 models
    3910 
    3911 > show #5 models
    3912 
    3913 > hide #5 models
    3914 
    3915 > show #7 models
    3916 
    3917 > show #9 models
    3918 
    3919 > hide #7 models
    3920 
    3921 > hide #4 models
    3922 
    3923 > show #13 models
    3924 
    3925 > show #!6 models
    3926 
    3927 > hide #!6 models
    3928 
    3929 > show #4 models
    3930 
    3931 > hide #9 models
    3932 
    3933 > show #5 models
    3934 
    3935 > hide #5 models
    3936 
    3937 > hide #4 models
    3938 
    3939 > show #!6 models
    3940 
    3941 > show #4 models
    3942 
    3943 > hide #4 models
    3944 
    3945 > show #4 models
    3946 
    3947 > hide #4 models
    3948 
    3949 > show #7 models
    3950 
    3951 > hide #!6 models
    3952 
    3953 > show #9 models
    3954 
    3955 > hide #13 models
    3956 
    3957 > hide #9 models
    3958 
    3959 > open /Users/taic/Library/CloudStorage/OneDrive-
    3960 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu_fe/fold_hqba_ubiu_fe_model_0.cif
    3961 
    3962 Chain information for fold_hqba_ubiu_fe_model_0.cif #8 
    3963 --- 
    3964 Chain | Description 
    3965 A | . 
    3966 B | . 
    3967 
    3968 
    3969 > open /Users/taic/Library/CloudStorage/OneDrive-
    3970 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu_fe/fold_hqba_ubiu_fe_model_1.cif
    3971 
    3972 Chain information for fold_hqba_ubiu_fe_model_1.cif #10 
    3973 --- 
    3974 Chain | Description 
    3975 A | . 
    3976 B | . 
    3977 
    3978 
    3979 > open /Users/taic/Library/CloudStorage/OneDrive-
    3980 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu_fe/fold_hqba_ubiu_fe_model_2.cif
    3981 
    3982 Chain information for fold_hqba_ubiu_fe_model_2.cif #11 
    3983 --- 
    3984 Chain | Description 
    3985 A | . 
    3986 B | . 
    3987 
    3988 
    3989 > open /Users/taic/Library/CloudStorage/OneDrive-
    3990 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu_fe/fold_hqba_ubiu_fe_model_3.cif
    3991 
    3992 Chain information for fold_hqba_ubiu_fe_model_3.cif #12 
    3993 --- 
    3994 Chain | Description 
    3995 A | . 
    3996 B | . 
    3997 
    3998 
    3999 > open /Users/taic/Library/CloudStorage/OneDrive-
    4000 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu_fe/fold_hqba_ubiu_fe_model_4.cif
    4001 
    4002 Chain information for fold_hqba_ubiu_fe_model_4.cif #14 
    4003 --- 
    4004 Chain | Description 
    4005 A | . 
    4006 B | . 
    4007 
    4008 Computing secondary structure 
    4009 
    4010 > select #6/A
    4011 
    4012 1311 atoms, 1341 bonds, 167 residues, 1 model selected 
    4013 
    4014 > ui tool show Matchmaker
    4015 
    4016 > matchmaker #8-14 to #6 & sel
    4017 
    4018 Computing secondary structure 
    4019 Parameters 
    4020 --- 
    4021 Chain pairing | bb 
    4022 Alignment algorithm | Needleman-Wunsch 
    4023 Similarity matrix | BLOSUM-62 
    4024 SS fraction | 0.3 
    4025 Gap open (HH/SS/other) | 18/18/6 
    4026 Gap extend | 1 
    4027 SS matrix |  |  | H | S | O 
    4028 ---|---|---|--- 
    4029 H | 6 | -9 | -6 
    4030 S |  | 6 | -6 
    4031 O |  |  | 4 
    4032 Iteration cutoff | 2 
    4033 
    4034 Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
    4035 fold_hqba_ubiu_fe_model_0.cif, chain A (#8), sequence alignment score = 870.8 
    4036 RMSD between 167 pruned atom pairs is 0.214 angstroms; (across all 167 pairs:
    4037 0.214) 
    4038 
    4039 Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
    4040 fold_hqba_ubiu_model_0.cif, chain A (#9), sequence alignment score = 870.8 
    4041 RMSD between 167 pruned atom pairs is 0.273 angstroms; (across all 167 pairs:
    4042 0.273) 
    4043 
    4044 Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
    4045 fold_hqba_ubiu_fe_model_1.cif, chain A (#10), sequence alignment score = 870.8 
    4046 RMSD between 167 pruned atom pairs is 0.234 angstroms; (across all 167 pairs:
    4047 0.234) 
    4048 
    4049 Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
    4050 fold_hqba_ubiu_fe_model_2.cif, chain A (#11), sequence alignment score = 870.8 
    4051 RMSD between 167 pruned atom pairs is 0.284 angstroms; (across all 167 pairs:
    4052 0.284) 
    4053 
    4054 Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
    4055 fold_hqba_ubiu_fe_model_3.cif, chain A (#12), sequence alignment score = 870.8 
    4056 RMSD between 167 pruned atom pairs is 0.300 angstroms; (across all 167 pairs:
    4057 0.300) 
    4058 
    4059 Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
    4060 fold_hqba_yhbq_model_0.cif, chain A (#13), sequence alignment score = 870.8 
    4061 RMSD between 167 pruned atom pairs is 0.328 angstroms; (across all 167 pairs:
    4062 0.328) 
    4063 
    4064 Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
    4065 fold_hqba_ubiu_fe_model_4.cif, chain A (#14), sequence alignment score = 870.8 
    4066 RMSD between 167 pruned atom pairs is 0.275 angstroms; (across all 167 pairs:
    4067 0.275) 
    4068 
    4069 
    4070 > hide #8 models
    4071 
    4072 > hide #7 models
    4073 
    4074 > hide #10 models
    4075 
    4076 > hide #11 models
    4077 
    4078 > hide #12 models
    4079 
    4080 > hide #14 models
    4081 
    4082 > show #!6 models
    4083 
    4084 > show #8 models
    4085 
    4086 > hide #!6 models
    4087 
    4088 > show #10 models
    4089 
    4090 > hide #8 models
    4091 
    4092 > show #12 models
    4093 
    4094 > show #11 models
    4095 
    4096 > hide #10 models
    4097 
    4098 > hide #12 models
    4099 
    4100 > show #8 models
    4101 
    4102 > show #10 models
    4103 
    4104 > show #12 models
    4105 
    4106 > show #13 models
    4107 
    4108 > show #14 models
    4109 
    4110 > color #8,10-14 bychain
    4111 
    4112 > hide #13 models
    4113 
    4114 > hide #8 models
    4115 
    4116 > hide #11 models
    4117 
    4118 > hide #12 models
    4119 
    4120 > hide #14 models
    4121 
    4122 > show #11 models
    4123 
    4124 > hide #10 models
    4125 
    4126 > show #9 models
    4127 
    4128 > hide #11 models
    4129 
    4130 > show #8 models
    4131 
    4132 > hide #9 models
    4133 
    4134 > show #10 models
    4135 
    4136 > hide #8 models
    4137 
    4138 > show #11 models
    4139 
    4140 > hide #10 models
    4141 
    4142 > select #11/B:176
    4143 
    4144 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4145 
    4146 > select #11/B:193
    4147 
    4148 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4149 
    4150 > select add #11/B:176
    4151 
    4152 12 atoms, 10 bonds, 2 residues, 1 model selected 
    4153 
    4154 > select add #11/B:232
    4155 
    4156 18 atoms, 15 bonds, 3 residues, 1 model selected 
    4157 
    4158 > select add #11/B:169
    4159 
    4160 24 atoms, 20 bonds, 4 residues, 1 model selected 
    4161 
    4162 > color sel yellow
    4163 
    4164 > select clear
    4165 
    4166 > show #12 models
    4167 
    4168 > hide #11 models
    4169 
    4170 > select add #12/B:172
    4171 
    4172 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4173 
    4174 > select add #12/B:176
    4175 
    4176 12 atoms, 10 bonds, 2 residues, 1 model selected 
    4177 
    4178 > select clear
    4179 
    4180 > show #14 models
    4181 
    4182 > hide #12 models
    4183 
    4184 > show #8 models
    4185 
    4186 > show #9 models
    4187 
    4188 > hide #14 models
    4189 
    4190 > show #10 models
    4191 
    4192 > hide #9 models
    4193 
    4194 > select #10/B
    4195 
    4196 2361 atoms, 2413 bonds, 300 residues, 1 model selected 
    4197 
    4198 > select #8/B
    4199 
    4200 2361 atoms, 2413 bonds, 300 residues, 1 model selected 
    4201 
    4202 > hide #10 models
    4203 
    4204 > show #9 models
    4205 
    4206 > rainbow sel
    4207 
    4208 > select clear
    4209 
    4210 > hide #8 models
    4211 
    4212 > show #10 models
    4213 
    4214 > show #8 models
    4215 
    4216 > hide #9 models
    4217 
    4218 > hide #10 models
    4219 
    4220 > show #9 models
    4221 
    4222 > hide #9 models
    4223 
    4224 > show #9 models
    4225 
    4226 > show #10 models
    4227 
    4228 > show #11 models
    4229 
    4230 > show #12 models
    4231 
    4232 > show #14 models
    4233 
    4234 > select #9/B#10/B#11/B#12/B#14/B
    4235 
    4236 11805 atoms, 12065 bonds, 1500 residues, 5 models selected 
    4237 
    4238 > rainbow sel
    4239 
    4240 > select clear
    4241 
    4242 > hide #9 models
    4243 
    4244 > hide #8 models
    4245 
    4246 > hide #10 models
    4247 
    4248 > hide #11 models
    4249 
    4250 > hide #12 models
    4251 
    4252 > hide #14 models
    4253 
    4254 > show #9 models
    4255 
    4256 > select #9/B:1-131
    4257 
    4258 1030 atoms, 1053 bonds, 131 residues, 1 model selected 
    4259 
    4260 > show #8 models
    4261 
    4262 > hide #8 models
    4263 
    4264 > show #8 models
    4265 
    4266 > hide #9 models
    4267 
    4268 > show #7 models
    4269 
    4270 > show #9 models
    4271 
    4272 > hide #7 models
    4273 
    4274 > hide #8 models
    4275 
    4276 > show #8 models
    4277 
    4278 > hide #9 models
    4279 
    4280 > show #10 models
    4281 
    4282 > hide #8 models
    4283 
    4284 > show #11 models
    4285 
    4286 > hide #10 models
    4287 
    4288 > show #12 models
    4289 
    4290 > hide #11 models
    4291 
    4292 > show #14 models
    4293 
    4294 > hide #12 models
    4295 
    4296 > show #9 models
    4297 
    4298 > show #8 models
    4299 
    4300 > show #10 models
    4301 
    4302 > show #11 models
    4303 
    4304 > show #13 models
    4305 
    4306 > hide #13 models
    4307 
    4308 > show #12 models
    4309 
    4310 > hide #14 models
    4311 
    4312 > hide #12 models
    4313 
    4314 > hide #11 models
    4315 
    4316 > hide #10 models
    4317 
    4318 > show #10 models
    4319 
    4320 > show #11 models
    4321 
    4322 > show #12 models
    4323 
    4324 > show #14 models
    4325 
    4326 > ui tool show Contacts
    4327 
    4328 > contacts saveFile "/Users/taic/OneDrive - National Institutes of
    4329 > Health/MacBookPro021/project/SusanG/HqbA_Ni/AF3/HqbA_UbiU_Fe.contacts.txt"
    4330 > resSeparation 5 interModel false intraMol false ignoreHiddenModels true
    4331 > color #ed5ffc radius 0.06 reveal true
    4332 
    4333 430 contacts 
    4334 
    4335 > hide #9 models
    4336 
    4337 > hide #10 models
    4338 
    4339 > hide #11 models
    4340 
    4341 > hide #12 models
    4342 
    4343 > hide #14 models
    4344 
    4345 > show #2 models
    4346 
    4347 > select #8/A:68,70,36,102,38,103,61
    4348 
    4349 57 atoms, 53 bonds, 7 residues, 1 model selected 
    4350 
    4351 > select #8/A:68,70,36,102,38,103,61,37,67,105
    4352 
    4353 86 atoms, 83 bonds, 10 residues, 1 model selected 
    4354 
    4355 > color sel magenta
    4356 
    4357 > ui tool show "Color Actions"
    4358 
    4359 > color sel thistle target acsp
    4360 
    4361 > hide #2 models
    4362 
    4363 > show #2 models
    4364 
    4365 > hide #2 models
    4366 
    4367 > show #10 models
    4368 
    4369 > hide #10 models
    4370 
    4371 > show #10 models
    4372 
    4373 > hide #10 models
    4374 
    4375 > select clear
    4376 
    4377 > select #8/A
    4378 
    4379 1311 atoms, 1341 bonds, 167 residues, 1 model selected 
    4380 
    4381 > color sel thistle target acsp
    4382 
    4383 > select #8/A:68,70,36,102,38,103,61,37,67,105
    4384 
    4385 86 atoms, 83 bonds, 10 residues, 1 model selected 
    4386 
    4387 > color sel medium purple target acsp
    4388 
    4389 > select clear
    4390 
    4391 > select #8/A:68,70,36,102,38,103,61,37,67,105
    4392 
    4393 86 atoms, 83 bonds, 10 residues, 1 model selected 
    4394 
    4395 > color sel thistle target acsp
    4396 
    4397 > select #8/A:68,70,36,102,38,103,61,37,67,105
    4398 
    4399 86 atoms, 83 bonds, 10 residues, 1 model selected 
    4400 
    4401 > select #8/A:37
    4402 
    4403 8 atoms, 7 bonds, 1 residue, 1 model selected 
    4404 
    4405 > select #8/A:165,37,63,68,149,70,36,67,102,162,38,32,40,29,39,103,61,105
    4406 
    4407 157 atoms, 150 bonds, 18 residues, 1 model selected 
    4408 
    4409 > color sel medium purple target acsp
    4410 
    4411 > color sel pale violet red target acsp
    4412 
    4413 > select #8/A:37,68,70,36,67,102,38,103,61,105
    4414 
    4415 86 atoms, 83 bonds, 10 residues, 1 model selected 
    4416 
    4417 > color sel dark orchid target acsp
    4418 
    4419 > select clear
    4420 
    4421 > select #8/A:61
    4422 
    4423 7 atoms, 7 bonds, 1 residue, 1 model selected 
    4424 
    4425 > select add #8/A:162
    4426 
    4427 16 atoms, 15 bonds, 2 residues, 1 model selected 
    4428 
    4429 > select add #8/A:165
    4430 
    4431 24 atoms, 22 bonds, 3 residues, 1 model selected 
    4432 
    4433 > show sel atoms
    4434 
    4435 > select #8/A:62
    4436 
    4437 7 atoms, 6 bonds, 1 residue, 1 model selected 
    4438 
    4439 > select clear
    4440 
    4441 > show #9 models
    4442 
    4443 > hide #8 models
    4444 
    4445 > show #10 models
    4446 
    4447 > hide #9 models
    4448 
    4449 > show #11 models
    4450 
    4451 > hide #10 models
    4452 
    4453 > show #12 models
    4454 
    4455 > hide #11 models
    4456 
    4457 > show #!6 models
    4458 
    4459 > hide #12 models
    4460 
    4461 > show #!1 models
    4462 
    4463 > hide #!1 models
    4464 
    4465 > show #!3 models
    4466 
    4467 > show #12 models
    4468 
    4469 > show #12#!3,6 surfaces
    4470 
    4471 > hide #!3,6,12 surfaces
    4472 
    4473 > hide #!12 models
    4474 
    4475 > show #11 models
    4476 
    4477 > hide #!6 models
    4478 
    4479 > show #!6 models
    4480 
    4481 > hide #!3 models
    4482 
    4483 > show #!3 models
    4484 
    4485 > hide #11 models
    4486 
    4487 > hide #!6 models
    4488 
    4489 > show #11 models
    4490 
    4491 > show #!6 models
    4492 
    4493 > hide #11 models
    4494 
    4495 > hide #!6 models
    4496 
    4497 > show #!6 models
    4498 
    4499 > show #11 models
    4500 
    4501 > hide #!6 models
    4502 
    4503 > select #11/A#12/A
    4504 
    4505 2622 atoms, 2682 bonds, 334 residues, 2 models selected 
    4506 
    4507 > show #!12 models
    4508 
    4509 > ui tool show "Color Actions"
    4510 
    4511 > color sel thistle target acsp
    4512 
    4513 > select clear
    4514 
    4515 > hide #!12 models
    4516 
    4517 > select #11/B:193,232,169,176
    4518 
    4519 24 atoms, 20 bonds, 4 residues, 1 model selected 
    4520 
    4521 > ui tool show "Color Actions"
    4522 
    4523 > color sel dark goldenrod target acsp
    4524 
    4525 > color sel sienna target acsp
    4526 
    4527 > select clear
    4528 
    4529 > select #12/B:193,232,169,176
    4530 
    4531 24 atoms, 20 bonds, 4 residues, 1 model selected 
    4532 
    4533 > show #!12 models
    4534 
    4535 > hide #11 models
    4536 
    4537 > hide #!3 models
    4538 
    4539 > delete atoms (#!12 & sel)
    4540 
    4541 > delete bonds (#!12 & sel)
    4542 
    4543 > hide #!3 models
    4544 
    4545 > select clear
    4546 
    4547 > delete atoms #12
    4548 
    4549 > delete bonds #12
    4550 
    4551 > show #14 models
    4552 
    4553 > select #14/B:193,232,169,176
    4554 
    4555 24 atoms, 20 bonds, 4 residues, 1 model selected 
    4556 
    4557 > show #10 models
    4558 
    4559 > hide #14 models
    4560 
    4561 > select #10/B:193,232,169,176
    4562 
    4563 24 atoms, 20 bonds, 4 residues, 1 model selected 
    4564 
    4565 > show #9 models
    4566 
    4567 > hide #10 models
    4568 
    4569 > show #8 models
    4570 
    4571 > hide #9 models
    4572 
    4573 > select #8/B:193,232,169,176
    4574 
    4575 24 atoms, 20 bonds, 4 residues, 1 model selected 
    4576 
    4577 > hide #8 models
    4578 
    4579 > show #8 models
    4580 
    4581 > show #10 models
    4582 
    4583 > hide #8 models
    4584 
    4585 > show #14 models
    4586 
    4587 > delete atoms #10,14
    4588 
    4589 > delete bonds #10,14
    4590 
    4591 > show #11 models
    4592 
    4593 > show #!3 models
    4594 
    4595 > color #3 #9ff996ff
    4596 
    4597 > color #3 #b9f992ff
    4598 
    4599 > color #3 #9af98eff
    4600 
    4601 > color #3 #96f99cff
    4602 
    4603 > color #3 #aef9bfff
    4604 
    4605 > show #4 models
    4606 
    4607 > hide #11 models
    4608 
    4609 > show #!6 models
    4610 
    4611 > hide #4 models
    4612 
    4613 > show #11 models
    4614 
    4615 > hide #!6 models
    4616 
    4617 > select clear
    4618 
    4619 > select #11/A:23
    4620 
    4621 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4622 
    4623 > select add #11/A:24
    4624 
    4625 15 atoms, 13 bonds, 2 residues, 1 model selected 
    4626 
    4627 > show #!6 models
    4628 
    4629 > hide #!6 models
    4630 
    4631 > select add #11/A:27
    4632 
    4633 24 atoms, 21 bonds, 3 residues, 1 model selected 
    4634 
    4635 > select add #11/A:167
    4636 
    4637 36 atoms, 33 bonds, 4 residues, 1 model selected 
    4638 
    4639 > show sel atoms
    4640 
    4641 > color sel cyan
    4642 
    4643 > select clear
    4644 
    4645 > show #!6 models
    4646 
    4647 > hide #11 models
    4648 
    4649 > show #11 models
    4650 
    4651 > hide #!6 models
    4652 
    4653 > show #!6 models
    4654 
    4655 > hide #11 models
    4656 
    4657 > show #2 models
    4658 
    4659 > ui tool show Contacts
    4660 
    4661 > hide #!3 models
    4662 
    4663 > ui tool show Contacts
    4664 
    4665 > contacts saveFile /Users/taic/Library/CloudStorage/OneDrive-
    4666 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfqx6_co/HqbA_Hfqx6.contacts.txt
    4667 > resSeparation 5 interModel false intraMol false ignoreHiddenModels true
    4668 > color #fdd4f6 radius 0.06 reveal true
    4669 
    4670 542 contacts 
    4671 
    4672 > hide #!6 models
    4673 
    4674 > show #!3 models
    4675 
    4676 > hide #2 models
    4677 
    4678 > show #!3 cartoons
    4679 
    4680 > select #3/A
    4681 
    4682 1678 atoms, 1491 bonds, 404 residues, 1 model selected 
    4683 
    4684 > delete atoms (#!3 & sel)
    4685 
    4686 > delete bonds (#!3 & sel)
    4687 
    4688 > ui tool show Contacts
    4689 
    4690 > contacts saveFile /Users/taic/Library/CloudStorage/OneDrive-
    4691 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/HqbA_CoA.4rs2.contact.txt
    4692 > resSeparation 5 interModel false intraMol false ignoreHiddenModels true
    4693 > color #fdd4f6 radius 0.06 reveal true
    4694 
    4695 668 contacts 
    4696 
    4697 > select ::name="HOH"
    4698 
    4699 235 atoms, 112 pseudobonds, 235 residues, 2 models selected 
    4700 
    4701 > hide sel atoms
    4702 
    4703 > show #2 models
    4704 
    4705 > select ::name="COA"
    4706 
    4707 48 atoms, 50 bonds, 1 residue, 1 model selected 
    4708 
    4709 > select #3/B
    4710 
    4711 1720 atoms, 1524 bonds, 668 pseudobonds, 419 residues, 2 models selected 
    4712 
    4713 > hide sel cartoons
    4714 
    4715 > hide sel atoms
    4716 
    4717 > show sel cartoons
    4718 
    4719 > show sel atoms
    4720 
    4721 > select ::name="COA"
    4722 
    4723 48 atoms, 50 bonds, 1 residue, 1 model selected 
    4724 
    4725 > select ~sel & ##selected
    4726 
    4727 1672 atoms, 1474 bonds, 668 pseudobonds, 418 residues, 2 models selected 
    4728 
    4729 > color sel gray target acsp
    4730 
    4731 > color sel light gray target acsp
    4732 
    4733 > select #3/B:74@SD
    4734 
    4735 1 atom, 1 residue, 1 model selected 
    4736 
    4737 > color #2 white models
    4738 
    4739 > color #2 #ffe0fcff models
    4740 
    4741 > select #3/B:75
    4742 
    4743 5 atoms, 4 bonds, 1 residue, 1 model selected 
    4744 
    4745 > ui tool show "Side View"
    4746 
    4747 > select clear
    4748 
    4749 > select #3/B:22,23,84,90,113,116,119,120
    4750 
    4751 80 atoms, 76 bonds, 8 residues, 1 model selected 
    4752 
    4753 > color sel indian red target acsp
    4754 
    4755 > color sel tomato target acsp
    4756 
    4757 > select #3/B:24, 27, 167
    4758 
    4759 26 atoms, 24 bonds, 3 residues, 1 model selected 
    4760 
    4761 > color sel coral target acsp
    4762 
    4763 > color sel sienna target acsp
    4764 
    4765 > color sel dark orange target acsp
    4766 
    4767 > color sel goldenrod target acsp
    4768 
    4769 > color sel peru target acsp
    4770 
    4771 > color sel dark goldenrod target acsp
    4772 
    4773 > select clear
    4774 
    4775 > show #9 models
    4776 
    4777 > hide #!3 models
    4778 
    4779 > show #!3 models
    4780 
    4781 > hide #9 models
    4782 
    4783 > show #8 models
    4784 
    4785 > hide #!3 models
    4786 
    4787 > show #!3 models
    4788 
    4789 > hide #!3 models
    4790 
    4791 > show #!3 models
    4792 
    4793 > hide #8 models
    4794 
    4795 > show #!6 models
    4796 
    4797 > hide #!3 models
    4798 
    4799 > show #!3 models
    4800 
    4801 > hide #2 models
    4802 
    4803 > hide #!6 models
    4804 
    4805 > select ::name="COA"
    4806 
    4807 48 atoms, 50 bonds, 1 residue, 1 model selected 
    4808 
    4809 > select ~sel & ##selected
    4810 
    4811 1672 atoms, 1474 bonds, 668 pseudobonds, 418 residues, 2 models selected 
    4812 
    4813 > hide sel cartoons
    4814 
    4815 > hide sel atoms
    4816 
    4817 > show #!6 models
    4818 
    4819 > show #2 models
    4820 
    4821 > hide #!6 models
    4822 
    4823 > show #!6 models
    4824 
    4825 > select #3/B
    4826 
    4827 1720 atoms, 1524 bonds, 668 pseudobonds, 419 residues, 2 models selected 
    4828 
    4829 > show sel cartoons
    4830 
    4831 > hide #!6 models
    4832 
    4833 > show sel atoms
    4834 
    4835 > show #!6 models
    4836 
    4837 > select #6/A:23
    4838 
    4839 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4840 
    4841 > color sel medium purple target acsp
    4842 
    4843 > hide #!3 models
    4844 
    4845 > color sel medium slate blue target acsp
    4846 
    4847 > color sel medium purple target acsp
    4848 
    4849 > color sel plum target acsp
    4850 
    4851 > color sel thistle target acsp
    4852 
    4853 > color sel lavender target acsp
    4854 
    4855 > color sel medium slate blue target acsp
    4856 
    4857 > select clear
    4858 
    4859 > select #6/A:22,23,84,90,113,116,119,120
    4860 
    4861 80 atoms, 76 bonds, 8 residues, 1 model selected 
    4862 
    4863 > show sel atoms
    4864 
    4865 > ui tool show "Color Actions"
    4866 
    4867 > color sel medium slate blue target acsp
    4868 
    4869 > select clear
    4870 
    4871 > show #!3 models
    4872 
    4873 > select #3/B
    4874 
    4875 1720 atoms, 1524 bonds, 668 pseudobonds, 419 residues, 2 models selected 
    4876 
    4877 > select ::name="COA"
    4878 
    4879 48 atoms, 50 bonds, 1 residue, 1 model selected 
    4880 
    4881 > select ~sel & ##selected
    4882 
    4883 1672 atoms, 1474 bonds, 668 pseudobonds, 418 residues, 2 models selected 
    4884 
    4885 > hide sel atoms
    4886 
    4887 > hide sel cartoons
    4888 
    4889 > show sel cartoons
    4890 
    4891 > hide sel cartoons
    4892 
    4893 > select #6/A:22,23,84,90,113,116,119,120
    4894 
    4895 80 atoms, 76 bonds, 8 residues, 1 model selected 
    4896 
    4897 > color sel dark turquoise target acsp
    4898 
    4899 > color sel spring green target acsp
    4900 
    4901 > select clear
    4902 
    4903 > show #11 models
    4904 
    4905 > hide #!6 models
    4906 
    4907 > select #11/A:22,23,84,90,113,116,119,120
    4908 
    4909 80 atoms, 76 bonds, 8 residues, 1 model selected 
    4910 
    4911 > color sel lime target acsp
    4912 
    4913 > select clear
    4914 
    4915 > select #11/A:22,23,84,90,113,116,119,120
    4916 
    4917 80 atoms, 76 bonds, 8 residues, 1 model selected 
    4918 
    4919 > show sel atoms
    4920 
    4921 > select clear
    4922 
    4923 > select #11/A:286,87,88
    4924 
    4925 12 atoms, 11 bonds, 2 residues, 1 model selected 
    4926 
    4927 > select #11/A:86,87,88
    4928 
    4929 21 atoms, 20 bonds, 3 residues, 1 model selected 
    4930 
    4931 > show sel atoms
    4932 
    4933 > show #!6 models
    4934 
    4935 > hide #11 models
    4936 
    4937 > select #3/B
    4938 
    4939 1720 atoms, 1524 bonds, 668 pseudobonds, 419 residues, 2 models selected 
    4940 
    4941 > hide #!6 models
    4942 
    4943 > show sel cartoons
    4944 
    4945 > show sel atoms
    4946 
    4947 > hide sel cartoons
    4948 
    4949 > hide sel atoms
    4950 
    4951 > select ::name="COA"
    4952 
    4953 48 atoms, 50 bonds, 1 residue, 1 model selected 
    4954 
    4955 > show sel cartoons
    4956 
    4957 > show sel atoms
    4958 
    4959 > show #!6 models
    4960 
    4961 > show #11 models
    4962 
    4963 > hide #!6 models
    4964 
    4965 > select #11/A:86,87,88,77,21
    4966 
    4967 35 atoms, 32 bonds, 5 residues, 1 model selected 
    4968 
    4969 > show sel atoms
    4970 
    4971 > color sel yellow green target acsp
    4972 
    4973 > select #6/A:86,87,88,77,21
    4974 
    4975 35 atoms, 32 bonds, 5 residues, 1 model selected 
    4976 
    4977 > show #!6 models
    4978 
    4979 > hide #11 models
    4980 
    4981 > show sel atoms
    4982 
    4983 > color sel yellow green target acsp
    4984 
    4985 > select clear
    4986 
    4987 > save /Users/taic/Library/CloudStorage/OneDrive-
    4988 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/HqbA_Ni.csx.cxs
    4989 
    4990 > select #6/A:2,4,5,7,8,9,35,38,41,42,70,98,102,103,104,105
    4991 
    4992 132 atoms, 126 bonds, 16 residues, 1 model selected 
    4993 
    4994 > show sel atoms
    4995 
    4996 > color (#!6 & sel) magenta
    4997 
    4998 > select clear
    4999 
    5000 > show #11 models
    5001 
    5002 > hide #!6 models
    5003 
    5004 > select #11/A:32,36,37,38,61,67,68,70,102,103,105
    5005 
    5006 96 atoms, 93 bonds, 11 residues, 1 model selected 
    5007 
    5008 > select #11/A:32,36,37,38,61,67,68,70,102,103,105,162,165
    5009 
    5010 113 atoms, 108 bonds, 13 residues, 1 model selected 
    5011 
    5012 > ui tool show "Color Actions"
    5013 
    5014 > color sel goldenrod target acsp
    5015 
    5016 > color sel dark khaki target acsp
    5017 
    5018 > color sel tan target acsp
    5019 
    5020 > select clear
    5021 
    5022 > show #7 models
    5023 
    5024 > hide #11 models
    5025 
    5026 > show #4 models
    5027 
    5028 > hide #4 models
    5029 
    5030 > show #4 models
    5031 
    5032 > hide #7 models
    5033 
    5034 > show #7 models
    5035 
    5036 > hide #4 models
    5037 
    5038 > ui tool show Contacts
    5039 
    5040 > contacts saveFile /Users/taic/Library/CloudStorage/OneDrive-
    5041 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/HqbA_YhbQ_Co.contacts.txt
    5042 > resSeparation 5 interModel false intraMol false ignoreHiddenModels true
    5043 > color #fdd4f6 radius 0.06 reveal true
    5044 
    5045 710 contacts 
    5046 
    5047 > ui tool show Contacts
    5048 
    5049 > hide #!3 models
    5050 
    5051 > ui tool show Contacts
    5052 
    5053 > contacts saveFile /Users/taic/Library/CloudStorage/OneDrive-
    5054 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/HqbA_YhbQ_Co.contacts.txt
    5055 > resSeparation 5 interModel false intraMol false ignoreHiddenModels true
    5056 > color #fdd4f6 radius 0.06 reveal true
    5057 
    5058 42 contacts 
    5059 
    5060 > select #7/A
    5061 
    5062 1311 atoms, 1341 bonds, 167 residues, 1 model selected 
    5063 
    5064 > ui tool show "Color Actions"
    5065 
    5066 > color sel medium purple target acsp
    5067 
    5068 > color sel plum target acsp
    5069 
    5070 > color sel rosy brown target acsp
    5071 
    5072 > color sel medium purple target acsp
    5073 
    5074 > color sel medium orchid target acsp
    5075 
    5076 > color sel medium slate blue target acsp
    5077 
    5078 > color sel medium purple target acsp
    5079 
    5080 > color sel thistle target acsp
    5081 
    5082 > color sel medium purple target acsp
    5083 
    5084 > color #7 #d97ae2ff
    5085 
    5086 > color #7 #e291dcff
    5087 
    5088 > color #7 #9f6ee2ff
    5089 
    5090 > color #7 #bfade2ff
    5091 
    5092 > color #7 #bc9de2ff
    5093 
    5094 > color #7 #c7bce2ff
    5095 
    5096 > color #7 #ccbde2ff
    5097 
    5098 > color #7 #c6b0e2ff
    5099 
    5100 > color #7 #bea9e2ff
    5101 
    5102 > color #7 #ce9be2ff
    5103 
    5104 > color #7 #d7b0e2ff
    5105 
    5106 > color #7 #be92e2ff
    5107 
    5108 > color #7 #ab8be2ff
    5109 
    5110 > color #7 #e1bce2ff
    5111 
    5112 > color #7 #c8aae2ff
    5113 
    5114 > color #7 #c6a7e2ff
    5115 
    5116 > color #7 #bf95e2ff
    5117 
    5118 > color #7 #d18ee2ff
    5119 
    5120 > color #7 #deaee2ff
    5121 
    5122 > color #7 #e2aadfff
    5123 
    5124 > color #7 #d3a1e2ff
    5125 
    5126 > color #7 #d6b4e2ff
    5127 
    5128 > color #7 #c5b4e2ff
    5129 
    5130 > color #7 #bdafe2ff
    5131 
    5132 > show #8 models
    5133 
    5134 > hide #8 models
    5135 
    5136 > select #7/B
    5137 
    5138 795 atoms, 807 bonds, 100 residues, 1 model selected 
    5139 
    5140 > rainbow sel
    5141 
    5142 > select clear
    5143 
    5144 > select #7/C:1@CO
    5145 
    5146 1 atom, 1 residue, 1 model selected 
    5147 
    5148 > ui tool show "Color Actions"
    5149 
    5150 > color sel medium aquamarine target acsp
    5151 
    5152 > color sel cadet blue target acsp
    5153 
    5154 > color sel medium turquoise target acsp
    5155 
    5156 > color sel light sea green target acsp
    5157 
    5158 > color sel cadet blue target acsp
    5159 
    5160 > color sel medium sea green target acsp
    5161 
    5162 > color sel cadet blue target acsp
    5163 
    5164 > select clear
    5165 
    5166 > select #7/A:7
    5167 
    5168 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5169 
    5170 > show #!6 models
    5171 
    5172 > hide #7 models
    5173 
    5174 > show #7 models
    5175 
    5176 > hide #!6 models
    5177 
    5178 > select #7/A:2,4,5,7,32,94,98,102,103,144
    5179 
    5180 94 atoms, 90 bonds, 10 residues, 1 model selected 
    5181 
    5182 > show #8 models
    5183 
    5184 > hide #7 models
    5185 
    5186 > show #7 models
    5187 
    5188 > hide #8 models
    5189 
    5190 > ui tool show "Color Actions"
    5191 
    5192 > color sel medium slate blue target acsp
    5193 
    5194 > help help:user/tools/coloractions.html
    5195 
    5196 > color sel purple target acsp
    5197 
    5198 > select clear
    5199 
    5200 > select #7/A:2,4,5,7,32,94,98,102,103,144
    5201 
    5202 94 atoms, 90 bonds, 10 residues, 1 model selected 
    5203 
    5204 > show #11 models
    5205 
    5206 > hide #7 models
    5207 
    5208 > show #8 models
    5209 
    5210 > hide #8 models
    5211 
    5212 > show #!6 models
    5213 
    5214 > hide #11 models
    5215 
    5216 > show #7 models
    5217 
    5218 > hide #!6 models
    5219 
    5220 > show #4 models
    5221 
    5222 > show #!6 models
    5223 
    5224 > hide #!6 models
    5225 
    5226 > hide #4 models
    5227 
    5228 > show #!3 models
    5229 
    5230 > hide #!3 models
    5231 
    5232 > select ::name="COA"
    5233 
    5234 48 atoms, 50 bonds, 1 residue, 1 model selected 
    5235 
    5236 > show #7 atoms
    5237 
    5238 > hide #7 atoms
    5239 
    5240 > select ::name="COA"
    5241 
    5242 48 atoms, 50 bonds, 1 residue, 1 model selected 
    5243 
    5244 > show #7 atoms
    5245 
    5246 > undo
    5247 
    5248 > select #7/A:2,4,5,7,32,94,98,102,103,144
    5249 
    5250 94 atoms, 90 bonds, 10 residues, 1 model selected 
    5251 
    5252 > show sel atoms
    5253 
    5254 > select ::name="CO"
    5255 
    5256 4 atoms, 4 residues, 4 models selected 
    5257 
    5258 > show sel & #7 atoms
    5259 
    5260 > hide #2 models
    5261 
    5262 > show #2 models
    5263 
    5264 > ui tool show Contacts
    5265 
    5266 > contacts resSeparation 5 interModel false intraMol false ignoreHiddenModels
    5267 > true color #fdd4f6 radius 0.06 reveal true
    5268 
    5269 42 contacts 
    5270 
    5271 > show #!3 models
    5272 
    5273 > hide #!3 models
    5274 
    5275 > show #!3 models
    5276 
    5277 > select ::name="COA"
    5278 
    5279 48 atoms, 50 bonds, 1 residue, 1 model selected 
    5280 
    5281 > select ~sel & ##selected
    5282 
    5283 1672 atoms, 1474 bonds, 9 pseudobonds, 418 residues, 2 models selected 
    5284 
    5285 > hide sel atoms
    5286 
    5287 > select #7/A:86,87,88
    5288 
    5289 21 atoms, 20 bonds, 3 residues, 1 model selected 
    5290 
    5291 > select #7/A:86,87,88
    5292 
    5293 21 atoms, 20 bonds, 3 residues, 1 model selected 
    5294 
    5295 > show #!6 models
    5296 
    5297 > hide #7 models
    5298 
    5299 > show #7 models
    5300 
    5301 > hide #!6 models
    5302 
    5303 > select #7/A:24,27,167
    5304 
    5305 27 atoms, 25 bonds, 3 residues, 1 model selected 
    5306 
    5307 > show sel atoms
    5308 
    5309 > color sel cyan
    5310 
    5311 > select clear
    5312 
    5313 > select #7/A:22,23,84,90,113,116,119,120
    5314 
    5315 80 atoms, 76 bonds, 8 residues, 1 model selected 
    5316 
    5317 > show #!6 models
    5318 
    5319 > hide #7 models
    5320 
    5321 > show #7 models
    5322 
    5323 > hide #!6 models
    5324 
    5325 > color sel lime target acsp
    5326 
    5327 > select clear
    5328 
    5329 > select #7/A:22,23,84,90,113,116,119,120
    5330 
    5331 80 atoms, 76 bonds, 8 residues, 1 model selected 
    5332 
    5333 > show sel atoms
    5334 
    5335 > show #!6 models
    5336 
    5337 > hide #7 models
    5338 
    5339 Drag select of 1 atoms, 6 residues, 1 bonds 
    5340 
    5341 > select clear
    5342 
    5343 > show #7 models
    5344 
    5345 > hide #!6 models
    5346 
    5347 > select clear
    5348 
    5349 > select #7/A:2,4,5,7,32,94,98,102,103,144
    5350 
    5351 94 atoms, 90 bonds, 10 residues, 1 model selected 
    5352 
    5353 > color sel medium violet red target acsp
    5354 
    5355 > color sel deep pink target acsp
    5356 
    5357 > help help:user/tools/coloractions.html
    5358 
    5359 > show #!6 models
    5360 
    5361 > hide #7 models
    5362 
    5363 > select #6/A
    5364 
    5365 1311 atoms, 1341 bonds, 167 residues, 1 model selected 
    5366 
    5367 > select ~sel & ##selected
    5368 
    5369 4717 atoms, 4800 bonds, 613 residues, 1 model selected 
    5370 
    5371 > hide sel atoms
    5372 
    5373 > select #6/C:57
    5374 
    5375 10 atoms, 10 bonds, 1 residue, 1 model selected 
    5376 
    5377 > select #6/C:31
    5378 
    5379 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5380 
    5381 > show sel atoms
    5382 
    5383 > select clear
    5384 
    5385 > select #6/A
    5386 
    5387 1311 atoms, 1341 bonds, 167 residues, 1 model selected 
    5388 
    5389 > select ~sel & ##selected
    5390 
    5391 4717 atoms, 4800 bonds, 613 residues, 1 model selected 
    5392 
    5393 > show sel surfaces
    5394 
    5395 > select clear
    5396 
    5397 > select ::name="COA"
    5398 
    5399 48 atoms, 50 bonds, 1 residue, 1 model selected 
    5400 
    5401 > color sel pale green target acsp
    5402 
    5403 > color sel honeydew target acsp
    5404 
    5405 > select clear
    5406 
    5407 > show #7 models
    5408 
    5409 > hide #!6 models
    5410 
    5411 > save /Users/taic/Library/CloudStorage/OneDrive-
    5412 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/HqbA_Ni.csx.cxs
    5413 
    5414 > preset "overall look" "publication 1 (silhouettes)"
    5415 
    5416 Using preset: Overall Look / Publication 1 (Silhouettes) 
    5417 Preset expands to these ChimeraX commands:
    5418 
    5419 
    5420 
    5421    set bg white
    5422    graphics silhouettes t
    5423    lighting depthCue f
    5424 
    5425 
    5426 
    5427 > preset "overall look" "publication 2 (depth-cued)"
    5428 
    5429 Using preset: Overall Look / Publication 2 (Depth-Cued) 
    5430 Preset expands to these ChimeraX commands:
    5431 
    5432 
    5433 
    5434    set bg white
    5435    graphics silhouettes f
    5436    lighting depthCue t
    5437 
    5438 
    5439 
    5440 > preset "overall look" "publication 1 (silhouettes)"
    5441 
    5442 Using preset: Overall Look / Publication 1 (Silhouettes) 
    5443 Preset expands to these ChimeraX commands:
    5444 
    5445 
    5446 
    5447    set bg white
    5448    graphics silhouettes t
    5449    lighting depthCue f
    5450 
    5451 
    5452 
    5453 > preset cartoons/nucleotides ribbons/slabs
    5454 
    5455 Using preset: Cartoons/Nucleotides / Ribbons/Slabs 
    5456 Changed 0 atom styles 
    5457 Preset expands to these ChimeraX commands:
    5458 
    5459 
    5460 
    5461    show nucleic
    5462    hide protein|solvent|H
    5463    surf hide
    5464    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    5465    ~worm
    5466    cartoon
    5467    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    5468    cartoon style ~(nucleic|strand) x round
    5469    cartoon style (nucleic|strand) x rect
    5470    nucleotides tube/slab shape box
    5471 
    5472 
    5473 
    5474 > hide #!3 models
    5475 
    5476 > preset "initial styles" "original look"
    5477 
    5478 Using preset: Initial Styles / Original Look 
    5479 Preset implemented in Python; no expansion to individual ChimeraX commands
    5480 available. 
    5481 
    5482 > preset "initial styles" "space-filling (chain colors)"
    5483 
    5484 Using preset: Initial Styles / Space-Filling (Chain Colors) 
    5485 Preset implemented in Python; no expansion to individual ChimeraX commands
    5486 available. 
    5487 
    5488 > preset "molecular surfaces" "ghostly white"
    5489 
    5490 Using preset: Molecular Surfaces / Ghostly White 
    5491 Changed 33098 atom styles 
    5492 Preset expands to these ChimeraX commands:
    5493 
    5494 
    5495 
    5496    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    5497    surface
    5498    color white targ s trans 80
    5499 
    5500 
    5501 
    5502 > preset "molecular surfaces" "atomic coloring (transparent)"
    5503 
    5504 Using preset: Molecular Surfaces / Atomic Coloring (Transparent) 
    5505 Changed 0 atom styles 
    5506 Preset expands to these ChimeraX commands:
    5507 
    5508 
    5509 
    5510    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    5511    surface
    5512    color fromatoms targ s trans 70
    5513 
    5514 
    5515 
    5516 > preset "molecular surfaces" "chain id coloring (opaque)"
    5517 
    5518 Using preset: Molecular Surfaces / Chain ID Coloring (Opaque) 
    5519 Changed 0 atom styles 
    5520 Preset expands to these ChimeraX commands:
    5521 
    5522 
    5523 
    5524    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    5525    surface
    5526    color bychain targ s trans 0
    5527 
    5528 
    5529 
    5530 > preset "molecular surfaces" "ghostly white"
    5531 
    5532 Using preset: Molecular Surfaces / Ghostly White 
    5533 Changed 0 atom styles 
    5534 Preset expands to these ChimeraX commands:
    5535 
    5536 
    5537 
    5538    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    5539    surface
    5540    color white targ s trans 80
    5541 
    5542 
    5543 
    5544 > preset "molecular surfaces" "chain id coloring (opaque)"
    5545 
    5546 Using preset: Molecular Surfaces / Chain ID Coloring (Opaque) 
    5547 Changed 0 atom styles 
    5548 Preset expands to these ChimeraX commands:
    5549 
    5550 
    5551 
    5552    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    5553    surface
    5554    color bychain targ s trans 0
    5555 
    5556 
    5557 
    5558 > preset "initial styles" cartoon
    5559 
    5560 Using preset: Initial Styles / Cartoon 
    5561 Preset implemented in Python; no expansion to individual ChimeraX commands
    5562 available. 
    5563 
    5564 > preset "overall look" "publication 2 (depth-cued)"
    5565 
    5566 Using preset: Overall Look / Publication 2 (Depth-Cued) 
    5567 Preset expands to these ChimeraX commands:
    5568 
    5569 
    5570 
    5571    set bg white
    5572    graphics silhouettes f
    5573    lighting depthCue t
    5574 
    5575 
    5576 
    5577 > preset "overall look" "publication 1 (silhouettes)"
    5578 
    5579 Using preset: Overall Look / Publication 1 (Silhouettes) 
    5580 Preset expands to these ChimeraX commands:
    5581 
    5582 
    5583 
    5584    set bg white
    5585    graphics silhouettes t
    5586    lighting depthCue f
    5587 
    5588 
    5589 
    5590 > preset "overall look" interactive
    5591 
    5592 Using preset: Overall Look / Interactive 
    5593 
    5594 > set bgColor transparent
    5595 
    5596 Preset expands to these ChimeraX commands:
    5597 
    5598 
    5599 
    5600    ~set bg
    5601    graphics silhouettes f
    5602    lighting depthCue t
    5603 
    5604 
    5605 
    5606 > preset "overall look" interactive
    5607 
    5608 Using preset: Overall Look / Interactive 
    5609 Preset expands to these ChimeraX commands:
    5610 
    5611 
    5612 
    5613    ~set bg
    5614    graphics silhouettes f
    5615    lighting depthCue t
    5616 
    5617 
    5618 
    5619 > preset "overall look" "publication 2 (depth-cued)"
    5620 
    5621 Using preset: Overall Look / Publication 2 (Depth-Cued) 
    5622 
    5623 > set bgColor #ffffff00
    5624 
    5625 Preset expands to these ChimeraX commands:
    5626 
    5627 
    5628 
    5629    set bg white
    5630    graphics silhouettes f
    5631    lighting depthCue t
    5632 
    5633 
    5634 
    5635 > show #!5 models
    5636 
    5637 > close session
    5638 
    5639 > open /Users/taic/Library/CloudStorage/OneDrive-
    5640 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/HqbA_Ni.cxs
    5641 
    5642 opened ChimeraX session 
    5643 
    5644 > show #!6 models
    5645 
    5646 > hide #7 models
    5647 
    5648 > select #6/A
    5649 
    5650 1311 atoms, 1341 bonds, 167 residues, 1 model selected 
    5651 
    5652 > show sel surfaces
    5653 
    5654 > select clear
    5655 
    5656 > show #7 models
    5657 
    5658 > hide #!6 models
    5659 
    5660 > show #!6 models
    5661 
    5662 > hide #7 models
    5663 
    5664 > hide #!3,6 surfaces
    5665 
    5666 > show #7 models
    5667 
    5668 > hide #!6 models
    5669 
    5670 > select #7/B
    5671 
    5672 795 atoms, 807 bonds, 100 residues, 1 model selected 
    5673 
    5674 > color sel light sky blue target acsp
    5675 
    5676 > select clear
    5677 
    5678 > select #7/B
    5679 
    5680 795 atoms, 807 bonds, 100 residues, 1 model selected 
    5681 
    5682 > color sel powder blue target acsp
    5683 
    5684 > select clear
    5685 
    5686 > select ::name="COA"
    5687 
    5688 48 atoms, 50 bonds, 1 residue, 1 model selected 
    5689 
    5690 > preset "overall look" "publication 2 (depth-cued)"
    5691 
    5692 Using preset: Overall Look / Publication 2 (Depth-Cued) 
    5693 Preset expands to these ChimeraX commands:
    5694 
    5695 
    5696 
    5697    set bg white
    5698    graphics silhouettes f
    5699    lighting depthCue t
    5700 
    5701 
    5702 
    5703 > preset "overall look" "publication 1 (silhouettes)"
    5704 
    5705 Using preset: Overall Look / Publication 1 (Silhouettes) 
    5706 Preset expands to these ChimeraX commands:
    5707 
    5708 
    5709 
    5710    set bg white
    5711    graphics silhouettes t
    5712    lighting depthCue f
    5713 
    5714 
    5715 
    5716 > select clear
    5717 
    5718 > select ::name="COA"
    5719 
    5720 48 atoms, 50 bonds, 1 residue, 1 model selected 
    5721 
    5722 > style sel ball
    5723 
    5724 Changed 48 atom styles 
    5725 
    5726 > select clear
    5727 
    5728 > show #!6 models
    5729 
    5730 > hide #7 models
    5731 
    5732 > select clear
    5733 
    5734 > select #6/A:23
    5735 
    5736 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5737 
    5738 > style sel stick
    5739 
    5740 Changed 9 atom styles 
    5741 
    5742 > select #6/A:103
    5743 
    5744 11 atoms, 11 bonds, 1 residue, 1 model selected 
    5745 
    5746 > style sel ball
    5747 
    5748 Changed 11 atom styles 
    5749 
    5750 > undo
    5751 
    5752 > select clear
    5753 
    5754 > show #7 models
    5755 
    5756 > hide #!6 models
    5757 
    5758 > show #11 models
    5759 
    5760 > show #!6 models
    5761 
    5762 > hide #!6 models
    5763 
    5764 > hide #7 models
    5765 
    5766 > show #8 models
    5767 
    5768 > hide #8 models
    5769 
    5770 > select #1/B
    5771 
    5772 688 atoms, 701 bonds, 87 residues, 1 model selected 
    5773 
    5774 > select #11/B
    5775 
    5776 2361 atoms, 2413 bonds, 300 residues, 1 model selected 
    5777 
    5778 > color sel khaki target acsp
    5779 
    5780 > color sel wheat target acsp
    5781 
    5782 > color sel beige target acsp
    5783 
    5784 > color sel antique white target acsp
    5785 
    5786 > select clear
    5787 
    5788 > select #11/B
    5789 
    5790 2361 atoms, 2413 bonds, 300 residues, 1 model selected 
    5791 
    5792 > color sel pale goldenrod target acsp
    5793 
    5794 > color sel light gray target acsp
    5795 
    5796 > color sel burly wood target acsp
    5797 
    5798 > color sel tan target acsp
    5799 
    5800 > color sel navajo white target acsp
    5801 
    5802 > color sel beige target acsp
    5803 
    5804 > color sel wheat target acsp
    5805 
    5806 > color sel beige target acsp
    5807 
    5808 > color sel antique white target acsp
    5809 
    5810 > select clear
    5811 
    5812 > lighting soft
    5813 
    5814 > lighting simple
    5815 
    5816 > lighting soft
    5817 
    5818 > lighting simple
    5819 
    5820 > lighting full
    5821 
    5822 > lighting soft
    5823 
    5824 > show #!6 models
    5825 
    5826 > hide #11 models
    5827 
    5828 > lighting full
    5829 
    5830 > lighting soft
    5831 
    5832 > lighting simple
    5833 
    5834 > show #11 models
    5835 
    5836 > hide #!6 models
    5837 
    5838 > select #11/B
    5839 
    5840 2361 atoms, 2413 bonds, 300 residues, 1 model selected 
    5841 
    5842 > color sel wheat target acsp
    5843 
    5844 > select clear
    5845 
    5846 > select #11/A:32,36,37,38,61,67,68,70,102,103,105,162,165
    5847 
    5848 113 atoms, 108 bonds, 13 residues, 1 model selected 
    5849 
    5850 > color sel dark orange target acsp
    5851 
    5852 > select clear
    5853 
    5854 > select #11/B165
    5855 
    5856 Nothing selected 
    5857 
    5858 > select #11/B
    5859 
    5860 2361 atoms, 2413 bonds, 300 residues, 1 model selected 
    5861 
    5862 > hide sel atoms
    5863 
    5864 > select clear
    5865 
    5866 > show #8 models
    5867 
    5868 > hide #8 models
    5869 
    5870 > select #11/B:176
    5871 
    5872 6 atoms, 5 bonds, 1 residue, 1 model selected 
    5873 
    5874 > select #11/B:232,169,176,193
    5875 
    5876 24 atoms, 20 bonds, 4 residues, 1 model selected 
    5877 
    5878 > show sel atoms
    5879 
    5880 > color sel yellow
    5881 
    5882 > select clear
    5883 
    5884 > show #8 models
    5885 
    5886 > hide #11 models
    5887 
    5888 > show #11 models
    5889 
    5890 > hide #8 models
    5891 
    5892 > show #9 models
    5893 
    5894 > hide #9 models
    5895 
    5896 > show #7 models
    5897 
    5898 > hide #11 models
    5899 
    5900 > show #!6 models
    5901 
    5902 > hide #7 models
    5903 
    5904 > show #8 models
    5905 
    5906 > hide #!6 models
    5907 
    5908 > show #11 models
    5909 
    5910 > hide #8 models
    5911 
    5912 > show #!6 models
    5913 
    5914 > show #7 models
    5915 
    5916 > hide #!6 models
    5917 
    5918 > hide #11 models
    5919 
    5920 > show #!6 models
    5921 
    5922 > hide #7 models
    5923 
    5924 > show #7 models
    5925 
    5926 > hide #!6 models
    5927 
    5928 > show #!6 models
    5929 
    5930 > hide #7 models
    5931 
    5932 > show #7 models
    5933 
    5934 > hide #!6 models
    5935 
    5936 > hide #2 models
    5937 
    5938 > show #2 models
    5939 
    5940 > hide #2 models
    5941 
    5942 > show #2 models
    5943 
    5944 > show #!6 models
    5945 
    5946 > hide #7 models
    5947 
    5948 > show #7 models
    5949 
    5950 > hide #!6 models
    5951 
    5952 > show #!6 models
    5953 
    5954 > hide #7 models
    5955 
    5956 > show #7 models
    5957 
    5958 > hide #7 models
    5959 
    5960 > show #7 models
    5961 
    5962 > show #11 models
    5963 
    5964 > hide #!6 models
    5965 
    5966 > hide #7 models
    5967 
    5968 > show #!6 models
    5969 
    5970 > show #7 models
    5971 
    5972 > hide #11 models
    5973 
    5974 > hide #7 models
    5975 
    5976 > show #7 models
    5977 
    5978 > hide #7 models
    5979 
    5980 > show #7 models
    5981 
    5982 > hide #!6 models
    5983 
    5984 > show #!6 models
    5985 
    5986 > hide #7 models
    5987 
    5988 > select ::name="CO"
    5989 
    5990 4 atoms, 4 residues, 4 models selected 
    5991 
    5992 > show sel & #!6 atoms
    5993 
    5994 > ui tool show "Color Actions"
    5995 
    5996 > color sel light steel blue target acsp
    5997 
    5998 > color sel silver target acsp
    5999 
    6000 > color sel dark blue target acsp
    6001 
    6002 > select clear
    6003 
    6004 > select ::name="CO"
    6005 
    6006 4 atoms, 4 residues, 4 models selected 
    6007 
    6008 > color sel medium blue target acsp
    6009 
    6010 > select clear
    6011 
    6012 > select #6/A:144
    6013 
    6014 10 atoms, 10 bonds, 1 residue, 1 model selected 
    6015 
    6016 > color sel deep sky blue target acsp
    6017 
    6018 > color sel royal blue target acsp
    6019 
    6020 > select clear
    6021 
    6022 > show #7 models
    6023 
    6024 > hide #!6 models
    6025 
    6026 > select #7/A:32
    6027 
    6028 10 atoms, 10 bonds, 1 residue, 1 model selected 
    6029 
    6030 > color sel royal blue target acsp
    6031 
    6032 > select clear
    6033 
    6034 > show #!6 models
    6035 
    6036 > hide #7 models
    6037 
    6038 > select clear
    6039 
    6040 > show #7 models
    6041 
    6042 > hide #!6 models
    6043 
    6044 > show #!6 models
    6045 
    6046 > hide #7 models
    6047 
    6048 > show #7 models
    6049 
    6050 > hide #!6 models
    6051 
    6052 > show #!6 models
    6053 
    6054 > hide #7 models
    6055 
    6056 > hide #!6 models
    6057 
    6058 > show #!6 models
    6059 
    6060 > show #7 models
    6061 
    6062 > hide #!6 models
    6063 
    6064 > show #!6 models
    6065 
    6066 > hide #7 models
    6067 
    6068 > show #7 models
    6069 
    6070 > hide #!6 models
    6071 
    6072 > show #!6 models
    6073 
    6074 > hide #7 models
    6075 
    6076 > show #7 models
    6077 
    6078 > hide #!6 models
    6079 
    6080 > show #!6 models
    6081 
    6082 > hide #7 models
    6083 
    6084 > show #7 models
    6085 
    6086 > hide #!6 models
    6087 
    6088 > show #11 models
    6089 
    6090 > hide #7 models
    6091 
    6092 > show #!6 models
    6093 
    6094 > show #7 models
    6095 
    6096 > hide #7 models
    6097 
    6098 > hide #!6 models
    6099 
    6100 > show #!6 models
    6101 
    6102 > hide #11 models
    6103 
    6104 > save /Users/taic/Library/CloudStorage/OneDrive-
    6105 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/HqbA_Hfq_Co.png
    6106 > width 900 height 668 supersample 4 transparentBackground true
    6107 
    6108 > show #7 models
    6109 
    6110 > hide #!6 models
    6111 
    6112 > save /Users/taic/Library/CloudStorage/OneDrive-
    6113 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/HqbA_YhbQ_Co.png
    6114 > width 900 height 668 supersample 4 transparentBackground true
    6115 
    6116 > show #11 models
    6117 
    6118 > hide #7 models
    6119 
    6120 > save /Users/taic/Library/CloudStorage/OneDrive-
    6121 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/HqbA_UbiU_Co.png
    6122 > width 900 height 668 supersample 4 transparentBackground true
    6123 
    6124 > select #11/B
    6125 
    6126 2361 atoms, 2413 bonds, 300 residues, 1 model selected 
    6127 
    6128 > show sel surfaces
    6129 
    6130 > select clear
    6131 
    6132 > hide #!3,11 surfaces
    6133 
    6134 > select clear
    6135 
    6136 > select #11/A
    6137 
    6138 1311 atoms, 1341 bonds, 167 residues, 1 model selected 
    6139 
    6140 > show sel surfaces
    6141 
    6142 > hide sel surfaces
    6143 
    6144 > select clear
    6145 
    6146 > show #!6 models
    6147 
    6148 > hide #!11 models
    6149 
    6150 > show #7 models
    6151 
    6152 > hide #!6 models
    6153 
    6154 > show #!11 models
    6155 
    6156 > hide #7 models
    6157 
    6158 > select #11/A:33
    6159 
    6160 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6161 
    6162 > select add #11/A:39
    6163 
    6164 19 atoms, 18 bonds, 2 residues, 2 models selected 
    6165 
    6166 > select add #11/A:66
    6167 
    6168 23 atoms, 21 bonds, 3 residues, 2 models selected 
    6169 
    6170 > select #11/A:62
    6171 
    6172 7 atoms, 6 bonds, 1 residue, 1 model selected 
    6173 
    6174 > select #11/A:63
    6175 
    6176 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6177 
    6178 > select add #11/A:39
    6179 
    6180 19 atoms, 18 bonds, 2 residues, 2 models selected 
    6181 
    6182 > select add #11/A:33
    6183 
    6184 27 atoms, 25 bonds, 3 residues, 2 models selected 
    6185 
    6186 > hide sel atoms
    6187 
    6188 > select #11/A:69
    6189 
    6190 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6191 
    6192 > hide sel atoms
    6193 
    6194 > select clear
    6195 
    6196 > show #!6 models
    6197 
    6198 > hide #!11 models
    6199 
    6200 > show #!11 models
    6201 
    6202 > hide #!6 models
    6203 
    6204 > show #!6 models
    6205 
    6206 > hide #!11 models
    6207 
    6208 > show #!11 models
    6209 
    6210 > hide #!6 models
    6211 
    6212 > select #11/B
    6213 
    6214 2361 atoms, 2413 bonds, 300 residues, 1 model selected 
    6215 
    6216 > show sel surfaces
    6217 
    6218 > select clear
    6219 
    6220 > hide #!3,11 surfaces
    6221 
    6222 > show #!6 models
    6223 
    6224 > hide #!11 models
    6225 
    6226 > show #!11 models
    6227 
    6228 > hide #!6 models
    6229 
    6230 > show #!6 models
    6231 
    6232 > hide #!11 models
    6233 
    6234 > show #7 models
    6235 
    6236 > hide #!6 models
    6237 
    6238 > show #!6 models
    6239 
    6240 > hide #7 models
    6241 
    6242 > select #6/A
    6243 
    6244 1311 atoms, 1341 bonds, 167 residues, 1 model selected 
    6245 
    6246 > show sel surfaces
    6247 
    6248 > select clear
    6249 
    6250 > hide #!6 models
    6251 
    6252 > show #7 models
    6253 
    6254 > show #!11 models
    6255 
    6256 > hide #7 models
    6257 
    6258 > select #11/A
    6259 
    6260 1311 atoms, 1341 bonds, 167 residues, 1 model selected 
    6261 
    6262 > show sel surfaces
    6263 
    6264 > select clear
    6265 
    6266 > show #!6 models
    6267 
    6268 > hide #!11 models
    6269 
    6270 > transparency #2-3,6 30
    6271 
    6272 > transparency #2-3,6 10
    6273 
    6274 > select clear
    6275 
    6276 > show #!11 models
    6277 
    6278 > hide #!11 models
    6279 
    6280 > show #!11 models
    6281 
    6282 > hide #!11 models
    6283 
    6284 > show #!11 models
    6285 
    6286 > hide #!11 models
    6287 
    6288 > show #!11 models
    6289 
    6290 > hide #!6 models
    6291 
    6292 > hide #!3,11 surfaces
    6293 
    6294 > select #11/C:1@FE
    6295 
    6296 1 atom, 1 residue, 1 model selected 
    6297 
    6298 > select #11/B
    6299 
    6300 2361 atoms, 2413 bonds, 300 residues, 1 model selected 
    6301 
    6302 > rainbow sel
    6303 
    6304 > select clear
    6305 
    6306 > save /Users/taic/Library/CloudStorage/OneDrive-
    6307 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/HqbA_UbiU_Fe.rainbow.png
    6308 > width 900 height 668 supersample 4 transparentBackground true
    6309 
    6310 > show #7 models
    6311 
    6312 > hide #!11 models
    6313 
    6314 > save /Users/taic/Library/CloudStorage/OneDrive-
    6315 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/HqbA_Ni.cxs
    6316 
    6317 > close session
    6318 
    6319 > open /Users/taic/Library/CloudStorage/OneDrive-
    6320 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR.cxs
    6321 
    6322 opened ChimeraX session 
    6323 
    6324 > show #1 models
    6325 
    6326 > hide #!13 models
    6327 
    6328 > show #!2 models
    6329 
    6330 > hide #!2 models
    6331 
    6332 > show #!3 models
    6333 
    6334 > ui tool show Matchmaker
    6335 
    6336 > matchmaker #!3 to #1
    6337 
    6338 Parameters 
    6339 --- 
    6340 Chain pairing | bb 
    6341 Alignment algorithm | Needleman-Wunsch 
    6342 Similarity matrix | BLOSUM-62 
    6343 SS fraction | 0.3 
    6344 Gap open (HH/SS/other) | 18/18/6 
    6345 Gap extend | 1 
    6346 SS matrix |  |  | H | S | O 
    6347 ---|---|---|--- 
    6348 H | 6 | -9 | -6 
    6349 S |  | 6 | -6 
    6350 O |  |  | 4 
    6351 Iteration cutoff | 2 
    6352 
    6353 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    6354 fold_azor_dimer_fad_model_0.cif, chain A (#3), sequence alignment score =
    6355 1077.8 
    6356 RMSD between 208 pruned atom pairs is 0.467 angstroms; (across all 208 pairs:
    6357 0.467) 
    6358 
    6359 
    6360 > show #!2 models
    6361 
    6362 > hide #!3 models
    6363 
    6364 > matchmaker #!2 to #1
    6365 
    6366 Parameters 
    6367 --- 
    6368 Chain pairing | bb 
    6369 Alignment algorithm | Needleman-Wunsch 
    6370 Similarity matrix | BLOSUM-62 
    6371 SS fraction | 0.3 
    6372 Gap open (HH/SS/other) | 18/18/6 
    6373 Gap extend | 1 
    6374 SS matrix |  |  | H | S | O 
    6375 ---|---|---|--- 
    6376 H | 6 | -9 | -6 
    6377 S |  | 6 | -6 
    6378 O |  |  | 4 
    6379 Iteration cutoff | 2 
    6380 
    6381 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    6382 fold_azor_dimer_model_0.cif, chain A (#2), sequence alignment score = 1074.2 
    6383 RMSD between 208 pruned atom pairs is 0.403 angstroms; (across all 208 pairs:
    6384 0.403) 
    6385 
    6386 
    6387 > hide #!2 models
    6388 
    6389 > show #!2 models
    6390 
    6391 > hide #1 models
    6392 
    6393 > show #1 models
    6394 
    6395 > show #!3 models
    6396 
    6397 > hide #!2 models
    6398 
    6399 > hide #1 models
    6400 
    6401 > show #1 models
    6402 
    6403 > hide #!3 models
    6404 
    6405 > show #!19 models
    6406 
    6407 > hide #1 models
    6408 
    6409 > show #1 models
    6410 
    6411 > select #19/B
    6412 
    6413 2028 atoms, 1951 bonds, 4 pseudobonds, 365 residues, 2 models selected 
    6414 
    6415 > rainbow sel
    6416 
    6417 > hide #1 models
    6418 
    6419 > show #1 models
    6420 
    6421 > hide #!19 models
    6422 
    6423 > show #!19 models
    6424 
    6425 > hide #1 models
    6426 
    6427 > show #1 models
    6428 
    6429 > hide #!19 models
    6430 
    6431 > show #!19 models
    6432 
    6433 > hide #1 models
    6434 
    6435 > select #19/A
    6436 
    6437 2063 atoms, 1951 bonds, 4 pseudobonds, 400 residues, 2 models selected 
    6438 
    6439 > hide sel cartoons
    6440 
    6441 > select clear
    6442 
    6443 > show #1 models
    6444 
    6445 > hide #!19 models
    6446 
    6447 > show #!18 models
    6448 
    6449 > show #!17 models
    6450 
    6451 > hide #!18 models
    6452 
    6453 > show #!19 models
    6454 
    6455 > hide #!17 models
    6456 
    6457 > hide #1 models
    6458 
    6459 > show #1 models
    6460 
    6461 > hide #!19 models
    6462 
    6463 > show #!19 models
    6464 
    6465 > show #1#!19 cartoons
    6466 
    6467 > hide #!19 models
    6468 
    6469 > show #!19 models
    6470 
    6471 > hide #1 models
    6472 
    6473 > select #19
    6474 
    6475 4091 atoms, 3902 bonds, 8 pseudobonds, 765 residues, 2 models selected 
    6476 
    6477 > color sel bychain
    6478 
    6479 > show #1 models
    6480 
    6481 > select clear
    6482 
    6483 > select #1/A:169
    6484 
    6485 11 atoms, 11 bonds, 1 residue, 1 model selected 
    6486 
    6487 > show sel atoms
    6488 
    6489 > select #1/A:122
    6490 
    6491 11 atoms, 11 bonds, 1 residue, 1 model selected 
    6492 
    6493 > show sel atoms
    6494 
    6495 > show #!2 models
    6496 
    6497 > hide #1 models
    6498 
    6499 > select #2/A:169
    6500 
    6501 11 atoms, 11 bonds, 1 residue, 1 model selected 
    6502 
    6503 > show sel atoms
    6504 
    6505 > select #2/A:122
    6506 
    6507 11 atoms, 11 bonds, 1 residue, 1 model selected 
    6508 
    6509 > show sel atoms
    6510 
    6511 > select ::name="FAD"
    6512 
    6513 583 atoms, 638 bonds, 11 residues, 7 models selected 
    6514 
    6515 > ui tool show "Color Actions"
    6516 
    6517 > color sel wheat target acsp
    6518 
    6519 > select clear
    6520 
    6521 > show #1 models
    6522 
    6523 > hide #!2 models
    6524 
    6525 > ui tool show "Show Sequence Viewer"
    6526 
    6527 > sequence chain #1/A
    6528 
    6529 Alignment identifier is 1/A 
    6530 
    6531 > select #1/A:10
    6532 
    6533 10 atoms, 10 bonds, 1 residue, 1 model selected 
    6534 
    6535 > show sel atoms
    6536 
    6537 > select #1/A:18
    6538 
    6539 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6540 
    6541 > select #1/A:18-19
    6542 
    6543 14 atoms, 13 bonds, 2 residues, 1 model selected 
    6544 
    6545 > show sel atoms
    6546 
    6547 > select #1/A:26
    6548 
    6549 11 atoms, 11 bonds, 1 residue, 1 model selected 
    6550 
    6551 > select #1/A:26
    6552 
    6553 11 atoms, 11 bonds, 1 residue, 1 model selected 
    6554 
    6555 > select #1/A:18
    6556 
    6557 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6558 
    6559 > select add #1/A:19
    6560 
    6561 14 atoms, 12 bonds, 2 residues, 1 model selected 
    6562 
    6563 > hide sel atoms
    6564 
    6565 > ui tool show "Show Sequence Viewer"
    6566 
    6567 > sequence chain #19/B
    6568 
    6569 Alignment identifier is 19/B 
    6570 
    6571 > select #19/B:16
    6572 
    6573 6 atoms, 5 bonds, 1 residue, 1 model selected 
    6574 
    6575 > select add #19/B:15
    6576 
    6577 15 atoms, 13 bonds, 2 residues, 1 model selected 
    6578 
    6579 > select add #19/B:17
    6580 
    6581 26 atoms, 24 bonds, 3 residues, 1 model selected 
    6582 
    6583 > select add #19/B:18
    6584 
    6585 34 atoms, 31 bonds, 4 residues, 1 model selected 
    6586 
    6587 > select #1/A:24
    6588 
    6589 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6590 
    6591 > select #1/A:24-27
    6592 
    6593 33 atoms, 33 bonds, 4 residues, 1 model selected 
    6594 
    6595 > select #19/B:15
    6596 
    6597 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6598 
    6599 > select #19/B:15-18
    6600 
    6601 34 atoms, 34 bonds, 4 residues, 1 model selected 
    6602 
    6603 > select #1/A:194
    6604 
    6605 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6606 
    6607 > show sel atoms
    6608 
    6609 Drag select of 12 residues 
    6610 
    6611 > select clear
    6612 
    6613 > select #19/B:212
    6614 
    6615 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6616 
    6617 > select #19/B:212
    6618 
    6619 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6620 
    6621 > select #19/B:193
    6622 
    6623 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6624 
    6625 > select #1/A:181
    6626 
    6627 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6628 
    6629 > select #1/A:181
    6630 
    6631 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6632 
    6633 > select #1/A:192
    6634 
    6635 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6636 
    6637 > select #1/A:192
    6638 
    6639 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6640 
    6641 > select #1/A:191
    6642 
    6643 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6644 
    6645 > select #1/A:191
    6646 
    6647 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6648 
    6649 > select #1/A:186
    6650 
    6651 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6652 
    6653 > select #1/A:186
    6654 
    6655 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6656 
    6657 > open /Users/taic/Library/CloudStorage/OneDrive-
    6658 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    6659 > Predictions/azor_monomer_fad/fold_azor_monomer_fad_model_0.cif
    6660 > /Users/taic/Library/CloudStorage/OneDrive-
    6661 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    6662 > Predictions/azor_monomer_fad/fold_azor_monomer_fad_model_1.cif
    6663 > /Users/taic/Library/CloudStorage/OneDrive-
    6664 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    6665 > Predictions/azor_monomer_fad/fold_azor_monomer_fad_model_2.cif
    6666 > /Users/taic/Library/CloudStorage/OneDrive-
    6667 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    6668 > Predictions/azor_monomer_fad/fold_azor_monomer_fad_model_3.cif
    6669 > /Users/taic/Library/CloudStorage/OneDrive-
    6670 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    6671 > Predictions/azor_monomer_fad/fold_azor_monomer_fad_model_4.cif
    6672 > /Users/taic/Library/CloudStorage/OneDrive-
    6673 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    6674 > Predictions/azor_monomer/fold_azor_monomer_model_1.cif
    6675 > /Users/taic/Library/CloudStorage/OneDrive-
    6676 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    6677 > Predictions/azor_monomer/fold_azor_monomer_model_2.cif
    6678 > /Users/taic/Library/CloudStorage/OneDrive-
    6679 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    6680 > Predictions/azor_monomer/fold_azor_monomer_model_3.cif
    6681 > /Users/taic/Library/CloudStorage/OneDrive-
    6682 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    6683 > Predictions/azor_monomer/fold_azor_monomer_model_4.cif
    6684 
    6685 Chain information for fold_azor_monomer_fad_model_0.cif #22 
    6686 --- 
    6687 Chain | Description 
    6688 A | . 
    6689 
    6690 Chain information for fold_azor_monomer_fad_model_1.cif #23 
    6691 --- 
    6692 Chain | Description 
    6693 A | . 
    6694 
    6695 Chain information for fold_azor_monomer_fad_model_2.cif #24 
    6696 --- 
    6697 Chain | Description 
    6698 A | . 
    6699 
    6700 Chain information for fold_azor_monomer_fad_model_3.cif #25 
    6701 --- 
    6702 Chain | Description 
    6703 A | . 
    6704 
    6705 Chain information for fold_azor_monomer_fad_model_4.cif #26 
    6706 --- 
    6707 Chain | Description 
    6708 A | . 
    6709 
    6710 Chain information for fold_azor_monomer_model_1.cif #27 
    6711 --- 
    6712 Chain | Description 
    6713 A | . 
    6714 
    6715 Chain information for fold_azor_monomer_model_2.cif #28 
    6716 --- 
    6717 Chain | Description 
    6718 A | . 
    6719 
    6720 Chain information for fold_azor_monomer_model_3.cif #29 
    6721 --- 
    6722 Chain | Description 
    6723 A | . 
    6724 
    6725 Chain information for fold_azor_monomer_model_4.cif #30 
    6726 --- 
    6727 Chain | Description 
    6728 A | . 
    6729 
    6730 Computing secondary structure 
    6731 
    6732 > ui tool show Matchmaker
    6733 
    6734 > matchmaker #22-30 to #1
    6735 
    6736 Computing secondary structure 
    6737 Parameters 
    6738 --- 
    6739 Chain pairing | bb 
    6740 Alignment algorithm | Needleman-Wunsch 
    6741 Similarity matrix | BLOSUM-62 
    6742 SS fraction | 0.3 
    6743 Gap open (HH/SS/other) | 18/18/6 
    6744 Gap extend | 1 
    6745 SS matrix |  |  | H | S | O 
    6746 ---|---|---|--- 
    6747 H | 6 | -9 | -6 
    6748 S |  | 6 | -6 
    6749 O |  |  | 4 
    6750 Iteration cutoff | 2 
    6751 
    6752 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    6753 fold_azor_monomer_fad_model_0.cif, chain A (#22), sequence alignment score =
    6754 1083.8 
    6755 RMSD between 208 pruned atom pairs is 0.351 angstroms; (across all 208 pairs:
    6756 0.351) 
    6757 
    6758 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    6759 fold_azor_monomer_fad_model_1.cif, chain A (#23), sequence alignment score =
    6760 1080.2 
    6761 RMSD between 208 pruned atom pairs is 0.403 angstroms; (across all 208 pairs:
    6762 0.403) 
    6763 
    6764 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    6765 fold_azor_monomer_fad_model_2.cif, chain A (#24), sequence alignment score =
    6766 1083.8 
    6767 RMSD between 208 pruned atom pairs is 0.447 angstroms; (across all 208 pairs:
    6768 0.447) 
    6769 
    6770 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    6771 fold_azor_monomer_fad_model_3.cif, chain A (#25), sequence alignment score =
    6772 1083.8 
    6773 RMSD between 208 pruned atom pairs is 0.420 angstroms; (across all 208 pairs:
    6774 0.420) 
    6775 
    6776 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    6777 fold_azor_monomer_fad_model_4.cif, chain A (#26), sequence alignment score =
    6778 1083.8 
    6779 RMSD between 208 pruned atom pairs is 0.291 angstroms; (across all 208 pairs:
    6780 0.291) 
    6781 
    6782 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    6783 fold_azor_monomer_model_1.cif, chain A (#27), sequence alignment score =
    6784 1086.8 
    6785 RMSD between 208 pruned atom pairs is 0.117 angstroms; (across all 208 pairs:
    6786 0.117) 
    6787 
    6788 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    6789 fold_azor_monomer_model_2.cif, chain A (#28), sequence alignment score =
    6790 1086.8 
    6791 RMSD between 208 pruned atom pairs is 0.103 angstroms; (across all 208 pairs:
    6792 0.103) 
    6793 
    6794 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    6795 fold_azor_monomer_model_3.cif, chain A (#29), sequence alignment score =
    6796 1086.8 
    6797 RMSD between 208 pruned atom pairs is 0.129 angstroms; (across all 208 pairs:
    6798 0.129) 
    6799 
    6800 Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
    6801 fold_azor_monomer_model_4.cif, chain A (#30), sequence alignment score =
    6802 1086.8 
    6803 RMSD between 208 pruned atom pairs is 0.121 angstroms; (across all 208 pairs:
    6804 0.121) 
    6805 
    6806 
    6807 > hide #!19 models
    6808 
    6809 > hide #23 models
    6810 
    6811 > hide #22 models
    6812 
    6813 > hide #24 models
    6814 
    6815 > hide #25 models
    6816 
    6817 > hide #26 models
    6818 
    6819 > hide #1 models
    6820 
    6821 > delete atoms #27-30
    6822 
    6823 > delete bonds #27-30
    6824 
    6825 > show #1 models
    6826 
    6827 > show #22 models
    6828 
    6829 > show #23 models
    6830 
    6831 > show #24 models
    6832 
    6833 > show #25 models
    6834 
    6835 > show #26 models
    6836 
    6837 > select ::name="FAD"
    6838 
    6839 848 atoms, 928 bonds, 16 residues, 12 models selected 
    6840 
    6841 > color sel gray target acsp
    6842 
    6843 > select clear
    6844 
    6845 > hide #22 models
    6846 
    6847 > hide #1 models
    6848 
    6849 > show #22 models
    6850 
    6851 > hide #22 models
    6852 
    6853 > show #22 models
    6854 
    6855 > hide #22 models
    6856 
    6857 > show #22 models
    6858 
    6859 > hide #22 models
    6860 
    6861 > delete atoms #23-26
    6862 
    6863 > delete bonds #23-26
    6864 
    6865 > show #22 models
    6866 
    6867 > show #1 models
    6868 
    6869 > select #1/A:12
    6870 
    6871 11 atoms, 11 bonds, 1 residue, 1 model selected 
    6872 
    6873 > show sel atoms
    6874 
    6875 > hide #1 models
    6876 
    6877 > select #22/A
    6878 
    6879 1646 atoms, 1685 bonds, 208 residues, 1 model selected 
    6880 
    6881 > rainbow sel
    6882 
    6883 > select clear
    6884 
    6885 > select #1/A:16
    6886 
    6887 7 atoms, 6 bonds, 1 residue, 1 model selected 
    6888 
    6889 > select #1/A:16-19
    6890 
    6891 27 atoms, 26 bonds, 4 residues, 1 model selected 
    6892 
    6893 > show #1 models
    6894 
    6895 > show sel atoms
    6896 
    6897 > hide #1 models
    6898 
    6899 > show #!19 models
    6900 
    6901 > hide #!19 models
    6902 
    6903 > show #!19 models
    6904 
    6905 
    6906 ===== Log before crash end =====
    6907 
    6908 Log:
    6909 UCSF ChimeraX version: 1.9 (2024-12-11) 
    6910 © 2016-2024 Regents of the University of California. All rights reserved. 
    6911 
    6912 > open /Users/taic/Library/CloudStorage/OneDrive-
    6913 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR.cxs
    6914 
    6915 Log from Wed Mar 11 15:25:43 2026UCSF ChimeraX version: 1.9 (2024-12-11) 
    6916 © 2016-2024 Regents of the University of California. All rights reserved. 
    6917 
    6918 > open /Users/taic/Library/CloudStorage/OneDrive-
    6919 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR.cxs
    6920 
    6921 Log from Wed Feb 18 08:19:31 2026UCSF ChimeraX version: 1.9 (2024-12-11) 
    6922 © 2016-2024 Regents of the University of California. All rights reserved. 
    6923 
    6924 > open /Users/taic/Library/CloudStorage/OneDrive-
    6925 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/IgaA_RcsF_RcsDx2.af3_contacts.cxs
    6926 
    6927 Log from Mon Jun 24 12:21:56 2024UCSF ChimeraX version: 1.7.1 (2024-01-23) 
    6928 © 2016-2023 Regents of the University of California. All rights reserved. 
    6929 
    6930 > open /Users/taic/Library/CloudStorage/OneDrive-
    6931 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsf_rcsdx2/IgaA_RcsF_RcsDx2.AF3vsAF2.cxs
    6932 > format session
    6933 
    6934 Log from Thu Jun 20 17:06:26 2024UCSF ChimeraX version: 1.7.1 (2024-01-23) 
    6935 © 2016-2023 Regents of the University of California. All rights reserved. 
    6936 
    6937 > open /Users/taic/Library/CloudStorage/OneDrive-
    6938 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsf_rcsdx2/IgaA_RcsF_RcsDx2.AF3vsAF2.cxs
    6939 > format session
    6940 
    6941 Log from Thu Jun 20 14:21:45 2024UCSF ChimeraX version: 1.7.1 (2024-01-23) 
    6942 © 2016-2023 Regents of the University of California. All rights reserved. 
    6943 
    6944 > open /Users/taic/Library/CloudStorage/OneDrive-
    6945 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/IgaA_RcsF_RcsD.AF3vsAF2.cxs
    6946 
    6947 Log from Thu Jun 20 13:37:04 2024UCSF ChimeraX version: 1.7.1 (2024-01-23) 
    6948 © 2016-2023 Regents of the University of California. All rights reserved. 
    6949 
    6950 > set bgColor #ffffff00
    6951 
    6952 Log from Wed May 22 02:35:17 2024UCSF ChimeraX version: 1.7.1 (2024-01-23) 
    6953 © 2016-2023 Regents of the University of California. All rights reserved. 
    6954 
    6955 > open /Users/taic/Desktop/Smf1MrkD_model0.cxs
    6956 
    6957 Log from Wed May 22 02:14:18 2024 Startup Messages 
    6958 --- 
    6959 warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle 
    6960 
    6961 You can double click a model's Name or ID in the model panel to edit those
    6962 fields 
    6963 UCSF ChimeraX version: 1.7.1 (2024-01-23) 
    6964 © 2016-2023 Regents of the University of California. All rights reserved. 
    6965 How to cite UCSF ChimeraX 
    6966 2024-05-22 01:52:01,857 WARNING Retrying (Retry(total=2, connect=None,
    6967 read=None, redirect=None, status=None)) after connection broken by
    6968 'NameResolutionError("<urllib3.connection.HTTPConnection object at
    6969 0x30b3499d0>: Failed to resolve 'webservices.rbvi.ucsf.edu' ([Errno 8]
    6970 nodename nor servname provided, or not known)")':
    6971 /cxservices/api/v1/chimerax/updates?uuid=76645f75-4e6d-5780-8383-9cae5a361a94&OS=macosx&OSVersion=14.4.1&ChimeraXVersion=1.7.1 
    6972 2024-05-22 01:52:01,859 WARNING Retrying (Retry(total=1, connect=None,
    6973 read=None, redirect=None, status=None)) after connection broken by
    6974 'NameResolutionError("<urllib3.connection.HTTPConnection object at
    6975 0x30b3480d0>: Failed to resolve 'webservices.rbvi.ucsf.edu' ([Errno 8]
    6976 nodename nor servname provided, or not known)")':
    6977 /cxservices/api/v1/chimerax/updates?uuid=76645f75-4e6d-5780-8383-9cae5a361a94&OS=macosx&OSVersion=14.4.1&ChimeraXVersion=1.7.1 
    6978 2024-05-22 01:52:01,863 WARNING Retrying (Retry(total=0, connect=None,
    6979 read=None, redirect=None, status=None)) after connection broken by
    6980 'NameResolutionError("<urllib3.connection.HTTPConnection object at
    6981 0x30b34b490>: Failed to resolve 'webservices.rbvi.ucsf.edu' ([Errno 8]
    6982 nodename nor servname provided, or not known)")':
    6983 /cxservices/api/v1/chimerax/updates?uuid=76645f75-4e6d-5780-8383-9cae5a361a94&OS=macosx&OSVersion=14.4.1&ChimeraXVersion=1.7.1 
    6984 
    6985 > open /Users/taic/Library/CloudStorage/OneDrive-
    6986 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_smf1_mrkd/fold_smf1_mrkd_model_0.cif
    6987 
    6988 Chain information for fold_smf1_mrkd_model_0.cif #1 
    6989 --- 
    6990 Chain | Description 
    6991 A | . 
    6992 B | . 
    6993 
    6994 
    6995 > open /Users/taic/Library/CloudStorage/OneDrive-
    6996 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_smf1_mrkd/fold_smf1_mrkd_model_4.cif
    6997 
    6998 Chain information for fold_smf1_mrkd_model_4.cif #2 
    6999 --- 
    7000 Chain | Description 
    7001 A | . 
    7002 B | . 
    7003 
    7004 
    7005 > open /Users/taic/Library/CloudStorage/OneDrive-
    7006 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_smf1_mrkd/fold_smf1_mrkd_model_1.cif
    7007 
    7008 Chain information for fold_smf1_mrkd_model_1.cif #3 
    7009 --- 
    7010 Chain | Description 
    7011 A | . 
    7012 B | . 
    7013 
    7014 
    7015 > open /Users/taic/Library/CloudStorage/OneDrive-
    7016 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_smf1_mrkd/fold_smf1_mrkd_model_2.cif
    7017 
    7018 Chain information for fold_smf1_mrkd_model_2.cif #4 
    7019 --- 
    7020 Chain | Description 
    7021 A | . 
    7022 B | . 
    7023 
    7024 
    7025 > open /Users/taic/Library/CloudStorage/OneDrive-
    7026 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_smf1_mrkd/fold_smf1_mrkd_model_3.cif
    7027 
    7028 Chain information for fold_smf1_mrkd_model_3.cif #5 
    7029 --- 
    7030 Chain | Description 
    7031 A | . 
    7032 B | . 
    7033 
    7034 
    7035 > hide #2 models
    7036 
    7037 > hide #3 models
    7038 
    7039 > hide #4 models
    7040 
    7041 > hide #5 models
    7042 
    7043 > select /B:1-344
    7044 
    7045 12720 atoms, 12915 bonds, 1720 residues, 5 models selected 
    7046 
    7047 > select /B:1-344
    7048 
    7049 12720 atoms, 12915 bonds, 1720 residues, 5 models selected 
    7050 
    7051 > select /B:1-344
    7052 
    7053 12720 atoms, 12915 bonds, 1720 residues, 5 models selected 
    7054 
    7055 > select /A:1-179
    7056 
    7057 6440 atoms, 6545 bonds, 895 residues, 5 models selected 
    7058 
    7059 > select /B:1-344
    7060 
    7061 12720 atoms, 12915 bonds, 1720 residues, 5 models selected 
    7062 
    7063 > color (#1 & sel) blue
    7064 
    7065 > preset "overall look" "publication 1 (silhouettes)"
    7066 
    7067 Using preset: Overall Look / Publication 1 (Silhouettes) 
    7068 Preset expands to these ChimeraX commands:
    7069 
    7070 
    7071 
    7072    set bg white
    7073    graphics silhouettes t
    7074    lighting depthCue f
    7075 
    7076 
    7077 
    7078 > select clear
    7079 
    7080 [Repeated 1 time(s)]
    7081 
    7082 > preset "overall look" "publication 2 (depth-cued)"
    7083 
    7084 Using preset: Overall Look / Publication 2 (Depth-Cued) 
    7085 Preset expands to these ChimeraX commands:
    7086 
    7087 
    7088 
    7089    set bg white
    7090    graphics silhouettes f
    7091    lighting depthCue t
    7092 
    7093 
    7094 
    7095 > preset cartoons/nucleotides ribbons/slabs
    7096 
    7097 Using preset: Cartoons/Nucleotides / Ribbons/Slabs 
    7098 Changed 0 atom styles 
    7099 Preset expands to these ChimeraX commands:
    7100 
    7101 
    7102 
    7103    show nucleic
    7104    hide protein|solvent|H
    7105    surf hide
    7106    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    7107    cartoon
    7108    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    7109    cartoon style ~(nucleic|strand) x round
    7110    cartoon style (nucleic|strand) x rect
    7111    nucleotides tube/slab shape box
    7112 
    7113 
    7114 
    7115 > preset "overall look" "publication 2 (depth-cued)"
    7116 
    7117 Using preset: Overall Look / Publication 2 (Depth-Cued) 
    7118 Preset expands to these ChimeraX commands:
    7119 
    7120 
    7121 
    7122    set bg white
    7123    graphics silhouettes f
    7124    lighting depthCue t
    7125 
    7126 
    7127 
    7128 > select /A:1-179
    7129 
    7130 6440 atoms, 6545 bonds, 895 residues, 5 models selected 
    7131 
    7132 > color (#1 & sel) hot pink
    7133 
    7134 > ui tool show "Color Actions"
    7135 
    7136 > color sel tomato
    7137 
    7138 > color sel light salmon
    7139 
    7140 > color sel hot pink
    7141 
    7142 > select clear
    7143 
    7144 Drag select of 3 residues 
    7145 
    7146 > select clear
    7147 
    7148 [Repeated 1 time(s)]
    7149 
    7150 > select /B:1-344
    7151 
    7152 12720 atoms, 12915 bonds, 1720 residues, 5 models selected 
    7153 
    7154 > color (#1 & sel) cornflower blue
    7155 
    7156 > select clear
    7157 
    7158 Drag select of 5 residues 
    7159 
    7160 > select clear
    7161 
    7162 [Repeated 1 time(s)]
    7163 
    7164 > save /Users/taic/Desktop/Smf1MrkD_model0.cxs
    7165 
    7166 \u2014\u2014\u2014 End of log from Wed May 22 02:14:18 2024 \u2014\u2014\u2014
    7167 
    7168 opened ChimeraX session 
    7169 
    7170 > select add #2
    7171 
    7172 3832 atoms, 3892 bonds, 523 residues, 1 model selected 
    7173 
    7174 > select add #3
    7175 
    7176 7664 atoms, 7784 bonds, 1046 residues, 2 models selected 
    7177 
    7178 > select add #4
    7179 
    7180 11496 atoms, 11676 bonds, 1569 residues, 3 models selected 
    7181 
    7182 > select add #5
    7183 
    7184 15328 atoms, 15568 bonds, 2092 residues, 4 models selected 
    7185 
    7186 > select add #1
    7187 
    7188 19160 atoms, 19460 bonds, 2615 residues, 5 models selected 
    7189 
    7190 > select subtract #1
    7191 
    7192 15328 atoms, 15568 bonds, 2092 residues, 4 models selected 
    7193 
    7194 > hide #1 target a
    7195 
    7196 > show #5 models
    7197 
    7198 > hide #5 models
    7199 
    7200 > show #5 models
    7201 
    7202 > delete atoms (#5 & sel)
    7203 
    7204 > delete bonds (#5 & sel)
    7205 
    7206 > show #4 models
    7207 
    7208 > delete atoms (#4 & sel)
    7209 
    7210 > delete bonds (#4 & sel)
    7211 
    7212 > show #2 models
    7213 
    7214 > delete atoms (#2 & sel)
    7215 
    7216 > delete bonds (#2 & sel)
    7217 
    7218 > show #3 models
    7219 
    7220 > delete atoms sel
    7221 
    7222 > delete bonds sel
    7223 
    7224 > select 24-33
    7225 
    7226 Expected an objects specifier or a keyword 
    7227 
    7228 > select .24-33
    7229 
    7230 Expected an objects specifier or a keyword 
    7231 
    7232 > select /A:24
    7233 
    7234 4 atoms, 3 bonds, 1 residue, 1 model selected 
    7235 
    7236 > select /A:26
    7237 
    7238 8 atoms, 7 bonds, 1 residue, 1 model selected 
    7239 
    7240 > select /A24-33
    7241 
    7242 Nothing selected 
    7243 
    7244 > select /A:24-33
    7245 
    7246 72 atoms, 72 bonds, 10 residues, 1 model selected 
    7247 
    7248 > color sel magenta
    7249 
    7250 [Repeated 1 time(s)]
    7251 
    7252 > select clear
    7253 
    7254 [Repeated 1 time(s)]
    7255 
    7256 > save /Users/taic/Desktop/Smf1MrkD_model0.cxs
    7257 
    7258 \u2014\u2014\u2014 End of log from Wed May 22 02:35:17 2024 \u2014\u2014\u2014
    7259 
    7260 opened ChimeraX session 
    7261 
    7262 > save /Users/taic/Library/CloudStorage/OneDrive-
    7263 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_smf1_mrkd/Smf1_MrkD.af3.pdb
    7264 > relModel #1
    7265 
    7266 > open /Users/taic/Library/CloudStorage/OneDrive-
    7267 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_smf1_mrkd/fold_smf1_mrkd_model_1.cif
    7268 > /Users/taic/Library/CloudStorage/OneDrive-
    7269 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_smf1_mrkd/fold_smf1_mrkd_model_2.cif
    7270 > /Users/taic/Library/CloudStorage/OneDrive-
    7271 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_smf1_mrkd/fold_smf1_mrkd_model_3.cif
    7272 > /Users/taic/Library/CloudStorage/OneDrive-
    7273 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_smf1_mrkd/fold_smf1_mrkd_model_4.cif
    7274 
    7275 Chain information for fold_smf1_mrkd_model_1.cif #2 
    7276 --- 
    7277 Chain | Description 
    7278 A | . 
    7279 B | . 
    7280 
    7281 Chain information for fold_smf1_mrkd_model_2.cif #3 
    7282 --- 
    7283 Chain | Description 
    7284 A | . 
    7285 B | . 
    7286 
    7287 Chain information for fold_smf1_mrkd_model_3.cif #4 
    7288 --- 
    7289 Chain | Description 
    7290 A | . 
    7291 B | . 
    7292 
    7293 Chain information for fold_smf1_mrkd_model_4.cif #5 
    7294 --- 
    7295 Chain | Description 
    7296 A | . 
    7297 B | . 
    7298 
    7299 
    7300 > toolshed show
    7301 
    7302 > select add #1
    7303 
    7304 3832 atoms, 3892 bonds, 523 residues, 1 model selected 
    7305 
    7306 > ui tool show Matchmaker
    7307 
    7308 > matchmaker #3-5 to #1
    7309 
    7310 Parameters 
    7311 --- 
    7312 Chain pairing | bb 
    7313 Alignment algorithm | Needleman-Wunsch 
    7314 Similarity matrix | BLOSUM-62 
    7315 SS fraction | 0.3 
    7316 Gap open (HH/SS/other) | 18/18/6 
    7317 Gap extend | 1 
    7318 SS matrix |  |  | H | S | O 
    7319 ---|---|---|--- 
    7320 H | 6 | -9 | -6 
    7321 S |  | 6 | -6 
    7322 O |  |  | 4 
    7323 Iteration cutoff | 2 
    7324 
    7325 Matchmaker fold_smf1_mrkd_model_0.cif, chain B (#1) with
    7326 fold_smf1_mrkd_model_2.cif, chain B (#3), sequence alignment score = 1735.3 
    7327 RMSD between 300 pruned atom pairs is 0.511 angstroms; (across all 344 pairs:
    7328 4.630) 
    7329 
    7330 Matchmaker fold_smf1_mrkd_model_0.cif, chain B (#1) with
    7331 fold_smf1_mrkd_model_3.cif, chain B (#4), sequence alignment score = 1735.3 
    7332 RMSD between 297 pruned atom pairs is 0.704 angstroms; (across all 344 pairs:
    7333 6.718) 
    7334 
    7335 Matchmaker fold_smf1_mrkd_model_0.cif, chain B (#1) with
    7336 fold_smf1_mrkd_model_4.cif, chain B (#5), sequence alignment score = 1735.3 
    7337 RMSD between 300 pruned atom pairs is 0.417 angstroms; (across all 344 pairs:
    7338 4.893) 
    7339 
    7340 
    7341 > hide #2 models
    7342 
    7343 > hide #3 models
    7344 
    7345 > hide #4 models
    7346 
    7347 > hide #5 models
    7348 
    7349 > select clear
    7350 
    7351 > show #2 models
    7352 
    7353 > toolshed show
    7354 
    7355 > ui tool show Matchmaker
    7356 
    7357 > select /A
    7358 
    7359 6440 atoms, 6545 bonds, 895 residues, 5 models selected 
    7360 
    7361 > hide #2 models
    7362 
    7363 > select /B
    7364 
    7365 12720 atoms, 12915 bonds, 1720 residues, 5 models selected 
    7366 
    7367 > show #2 models
    7368 
    7369 > matchmaker #2-5 & sel to #1 & sel
    7370 
    7371 Parameters 
    7372 --- 
    7373 Chain pairing | bb 
    7374 Alignment algorithm | Needleman-Wunsch 
    7375 Similarity matrix | BLOSUM-62 
    7376 SS fraction | 0.3 
    7377 Gap open (HH/SS/other) | 18/18/6 
    7378 Gap extend | 1 
    7379 SS matrix |  |  | H | S | O 
    7380 ---|---|---|--- 
    7381 H | 6 | -9 | -6 
    7382 S |  | 6 | -6 
    7383 O |  |  | 4 
    7384 Iteration cutoff | 2 
    7385 
    7386 Matchmaker fold_smf1_mrkd_model_0.cif, chain B (#1) with
    7387 fold_smf1_mrkd_model_1.cif, chain B (#2), sequence alignment score = 1726.3 
    7388 RMSD between 298 pruned atom pairs is 0.483 angstroms; (across all 344 pairs:
    7389 3.904) 
    7390 
    7391 Matchmaker fold_smf1_mrkd_model_0.cif, chain B (#1) with
    7392 fold_smf1_mrkd_model_2.cif, chain B (#3), sequence alignment score = 1735.3 
    7393 RMSD between 300 pruned atom pairs is 0.511 angstroms; (across all 344 pairs:
    7394 4.630) 
    7395 
    7396 Matchmaker fold_smf1_mrkd_model_0.cif, chain B (#1) with
    7397 fold_smf1_mrkd_model_3.cif, chain B (#4), sequence alignment score = 1735.3 
    7398 RMSD between 297 pruned atom pairs is 0.704 angstroms; (across all 344 pairs:
    7399 6.718) 
    7400 
    7401 Matchmaker fold_smf1_mrkd_model_0.cif, chain B (#1) with
    7402 fold_smf1_mrkd_model_4.cif, chain B (#5), sequence alignment score = 1735.3 
    7403 RMSD between 300 pruned atom pairs is 0.417 angstroms; (across all 344 pairs:
    7404 4.893) 
    7405 
    7406 
    7407 > select clear
    7408 
    7409 > show #3 models
    7410 
    7411 > hide #2 models
    7412 
    7413 Drag select of 32 residues 
    7414 Drag select of 26 residues 
    7415 
    7416 > show #4 models
    7417 
    7418 > hide #3 models
    7419 
    7420 > show #5 models
    7421 
    7422 > hide #4 models
    7423 
    7424 > show #2 models
    7425 
    7426 > show #3 models
    7427 
    7428 > show #4 models
    7429 
    7430 > select add #1
    7431 
    7432 4031 atoms, 3892 bonds, 550 residues, 2 models selected 
    7433 
    7434 > select subtract #1
    7435 
    7436 199 atoms, 27 residues, 1 model selected 
    7437 
    7438 > select add #2
    7439 
    7440 4031 atoms, 3892 bonds, 550 residues, 2 models selected 
    7441 
    7442 > select add #3
    7443 
    7444 7664 atoms, 7784 bonds, 1046 residues, 2 models selected 
    7445 
    7446 > select add #4
    7447 
    7448 11496 atoms, 11676 bonds, 1569 residues, 3 models selected 
    7449 
    7450 > select add #5
    7451 
    7452 15328 atoms, 15568 bonds, 2092 residues, 4 models selected 
    7453 
    7454 > delete atoms sel
    7455 
    7456 > delete bonds sel
    7457 
    7458 > open /Users/taic/Library/CloudStorage/OneDrive-
    7459 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_mrkd/fold_mrkd_model_0.cif
    7460 > /Users/taic/Library/CloudStorage/OneDrive-
    7461 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_mrkd/fold_mrkd_model_1.cif
    7462 > /Users/taic/Library/CloudStorage/OneDrive-
    7463 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_mrkd/fold_mrkd_model_2.cif
    7464 > /Users/taic/Library/CloudStorage/OneDrive-
    7465 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_mrkd/fold_mrkd_model_3.cif
    7466 > /Users/taic/Library/CloudStorage/OneDrive-
    7467 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_mrkd/fold_mrkd_model_4.cif
    7468 
    7469 Chain information for fold_mrkd_model_0.cif #2 
    7470 --- 
    7471 Chain | Description 
    7472 A | . 
    7473 
    7474 Chain information for fold_mrkd_model_1.cif #3 
    7475 --- 
    7476 Chain | Description 
    7477 A | . 
    7478 
    7479 Chain information for fold_mrkd_model_2.cif #4 
    7480 --- 
    7481 Chain | Description 
    7482 A | . 
    7483 
    7484 Chain information for fold_mrkd_model_3.cif #5 
    7485 --- 
    7486 Chain | Description 
    7487 A | . 
    7488 
    7489 Chain information for fold_mrkd_model_4.cif #6 
    7490 --- 
    7491 Chain | Description 
    7492 A | . 
    7493 
    7494 
    7495 > ui tool show Matchmaker
    7496 
    7497 > matchmaker #3-6 to #2
    7498 
    7499 Parameters 
    7500 --- 
    7501 Chain pairing | bb 
    7502 Alignment algorithm | Needleman-Wunsch 
    7503 Similarity matrix | BLOSUM-62 
    7504 SS fraction | 0.3 
    7505 Gap open (HH/SS/other) | 18/18/6 
    7506 Gap extend | 1 
    7507 SS matrix |  |  | H | S | O 
    7508 ---|---|---|--- 
    7509 H | 6 | -9 | -6 
    7510 S |  | 6 | -6 
    7511 O |  |  | 4 
    7512 Iteration cutoff | 2 
    7513 
    7514 Matchmaker fold_mrkd_model_0.cif, chain A (#2) with fold_mrkd_model_1.cif,
    7515 chain A (#3), sequence alignment score = 1734.1 
    7516 RMSD between 301 pruned atom pairs is 0.546 angstroms; (across all 344 pairs:
    7517 5.711) 
    7518 
    7519 Matchmaker fold_mrkd_model_0.cif, chain A (#2) with fold_mrkd_model_2.cif,
    7520 chain A (#4), sequence alignment score = 1680.1 
    7521 RMSD between 308 pruned atom pairs is 0.938 angstroms; (across all 344 pairs:
    7522 3.574) 
    7523 
    7524 Matchmaker fold_mrkd_model_0.cif, chain A (#2) with fold_mrkd_model_3.cif,
    7525 chain A (#5), sequence alignment score = 1705.3 
    7526 RMSD between 316 pruned atom pairs is 0.705 angstroms; (across all 344 pairs:
    7527 2.935) 
    7528 
    7529 Matchmaker fold_mrkd_model_0.cif, chain A (#2) with fold_mrkd_model_4.cif,
    7530 chain A (#6), sequence alignment score = 1737.1 
    7531 RMSD between 300 pruned atom pairs is 0.954 angstroms; (across all 344 pairs:
    7532 2.984) 
    7533 
    7534 
    7535 > hide #1 models
    7536 
    7537 > hide #3 models
    7538 
    7539 > show #3 models
    7540 
    7541 > hide #2 models
    7542 
    7543 > show #2 models
    7544 
    7545 > select #3/A:1
    7546 
    7547 8 atoms, 7 bonds, 1 residue, 1 model selected 
    7548 
    7549 > select #3/A:1
    7550 
    7551 8 atoms, 7 bonds, 1 residue, 1 model selected 
    7552 
    7553 > select add #3
    7554 
    7555 2544 atoms, 2583 bonds, 344 residues, 1 model selected 
    7556 
    7557 > select clear
    7558 
    7559 [Repeated 1 time(s)]
    7560 
    7561 > select add #3
    7562 
    7563 2544 atoms, 2583 bonds, 344 residues, 1 model selected 
    7564 
    7565 > select add #4
    7566 
    7567 5088 atoms, 5166 bonds, 688 residues, 2 models selected 
    7568 
    7569 > select add #5
    7570 
    7571 7632 atoms, 7749 bonds, 1032 residues, 3 models selected 
    7572 
    7573 > select add #6
    7574 
    7575 10176 atoms, 10332 bonds, 1376 residues, 4 models selected 
    7576 
    7577 > delete atoms sel
    7578 
    7579 > delete bonds sel
    7580 
    7581 > show #1 models
    7582 
    7583 > ui tool show Matchmaker
    7584 
    7585 > matchmaker #2 to #1
    7586 
    7587 Parameters 
    7588 --- 
    7589 Chain pairing | bb 
    7590 Alignment algorithm | Needleman-Wunsch 
    7591 Similarity matrix | BLOSUM-62 
    7592 SS fraction | 0.3 
    7593 Gap open (HH/SS/other) | 18/18/6 
    7594 Gap extend | 1 
    7595 SS matrix |  |  | H | S | O 
    7596 ---|---|---|--- 
    7597 H | 6 | -9 | -6 
    7598 S |  | 6 | -6 
    7599 O |  |  | 4 
    7600 Iteration cutoff | 2 
    7601 
    7602 Matchmaker fold_smf1_mrkd_model_0.cif, chain B (#1) with
    7603 fold_mrkd_model_0.cif, chain A (#2), sequence alignment score = 1629.1 
    7604 RMSD between 170 pruned atom pairs is 0.392 angstroms; (across all 344 pairs:
    7605 10.184) 
    7606 
    7607 
    7608 > hide #2 models
    7609 
    7610 > show #2 models
    7611 
    7612 > hide #2 models
    7613 
    7614 > show #2 models
    7615 
    7616 > hide #2 models
    7617 
    7618 > show #2 models
    7619 
    7620 > hide #2 models
    7621 
    7622 > show #2 models
    7623 
    7624 > save /Users/taic/Library/CloudStorage/OneDrive-
    7625 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_mrkd/af3.MrkD_Smf1.cxs
    7626 
    7627 > hide #1 models
    7628 
    7629 > show #1 models
    7630 
    7631 > hide #2 models
    7632 
    7633 > show #2 models
    7634 
    7635 > hide #1 models
    7636 
    7637 > show #1 models
    7638 
    7639 > hide #2 models
    7640 
    7641 > show #2 models
    7642 
    7643 > open /Users/taic/Library/CloudStorage/OneDrive-
    7644 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_smf1/fold_smf1_model_0.cif
    7645 > /Users/taic/Library/CloudStorage/OneDrive-
    7646 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_smf1/fold_smf1_model_1.cif
    7647 > /Users/taic/Library/CloudStorage/OneDrive-
    7648 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_smf1/fold_smf1_model_2.cif
    7649 > /Users/taic/Library/CloudStorage/OneDrive-
    7650 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_smf1/fold_smf1_model_3.cif
    7651 > /Users/taic/Library/CloudStorage/OneDrive-
    7652 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_smf1/fold_smf1_model_4.cif
    7653 
    7654 Chain information for fold_smf1_model_0.cif #3 
    7655 --- 
    7656 Chain | Description 
    7657 A | . 
    7658 
    7659 Chain information for fold_smf1_model_1.cif #4 
    7660 --- 
    7661 Chain | Description 
    7662 A | . 
    7663 
    7664 Chain information for fold_smf1_model_2.cif #5 
    7665 --- 
    7666 Chain | Description 
    7667 A | . 
    7668 
    7669 Chain information for fold_smf1_model_3.cif #6 
    7670 --- 
    7671 Chain | Description 
    7672 A | . 
    7673 
    7674 Chain information for fold_smf1_model_4.cif #7 
    7675 --- 
    7676 Chain | Description 
    7677 A | . 
    7678 
    7679 
    7680 > hide #1 models
    7681 
    7682 > hide #2 models
    7683 
    7684 > ui tool show Matchmaker
    7685 
    7686 > matchmaker #4-7 to #3
    7687 
    7688 Parameters 
    7689 --- 
    7690 Chain pairing | bb 
    7691 Alignment algorithm | Needleman-Wunsch 
    7692 Similarity matrix | BLOSUM-62 
    7693 SS fraction | 0.3 
    7694 Gap open (HH/SS/other) | 18/18/6 
    7695 Gap extend | 1 
    7696 SS matrix |  |  | H | S | O 
    7697 ---|---|---|--- 
    7698 H | 6 | -9 | -6 
    7699 S |  | 6 | -6 
    7700 O |  |  | 4 
    7701 Iteration cutoff | 2 
    7702 
    7703 Matchmaker fold_smf1_model_0.cif, chain A (#3) with fold_smf1_model_1.cif,
    7704 chain A (#4), sequence alignment score = 874.3 
    7705 RMSD between 151 pruned atom pairs is 0.152 angstroms; (across all 179 pairs:
    7706 4.075) 
    7707 
    7708 Matchmaker fold_smf1_model_0.cif, chain A (#3) with fold_smf1_model_2.cif,
    7709 chain A (#5), sequence alignment score = 874.3 
    7710 RMSD between 167 pruned atom pairs is 0.473 angstroms; (across all 179 pairs:
    7711 1.868) 
    7712 
    7713 Matchmaker fold_smf1_model_0.cif, chain A (#3) with fold_smf1_model_3.cif,
    7714 chain A (#6), sequence alignment score = 874.3 
    7715 RMSD between 141 pruned atom pairs is 0.157 angstroms; (across all 179 pairs:
    7716 6.954) 
    7717 
    7718 Matchmaker fold_smf1_model_0.cif, chain A (#3) with fold_smf1_model_4.cif,
    7719 chain A (#7), sequence alignment score = 874.3 
    7720 RMSD between 149 pruned atom pairs is 0.191 angstroms; (across all 179 pairs:
    7721 5.505) 
    7722 
    7723 
    7724 > select clear
    7725 
    7726 [Repeated 1 time(s)]
    7727 
    7728 > select add #4
    7729 
    7730 1288 atoms, 1309 bonds, 179 residues, 1 model selected 
    7731 
    7732 > select add #5
    7733 
    7734 2576 atoms, 2618 bonds, 358 residues, 2 models selected 
    7735 
    7736 > select add #6
    7737 
    7738 3864 atoms, 3927 bonds, 537 residues, 3 models selected 
    7739 
    7740 > select add #7
    7741 
    7742 5152 atoms, 5236 bonds, 716 residues, 4 models selected 
    7743 
    7744 > delete atoms sel
    7745 
    7746 > delete bonds sel
    7747 
    7748 > select #1/A
    7749 
    7750 1288 atoms, 1309 bonds, 179 residues, 1 model selected 
    7751 
    7752 > show #1 models
    7753 
    7754 > hide #3 models
    7755 
    7756 > matchmaker #3 to #1 & sel
    7757 
    7758 Parameters 
    7759 --- 
    7760 Chain pairing | bb 
    7761 Alignment algorithm | Needleman-Wunsch 
    7762 Similarity matrix | BLOSUM-62 
    7763 SS fraction | 0.3 
    7764 Gap open (HH/SS/other) | 18/18/6 
    7765 Gap extend | 1 
    7766 SS matrix |  |  | H | S | O 
    7767 ---|---|---|--- 
    7768 H | 6 | -9 | -6 
    7769 S |  | 6 | -6 
    7770 O |  |  | 4 
    7771 Iteration cutoff | 2 
    7772 
    7773 Matchmaker fold_smf1_mrkd_model_0.cif, chain A (#1) with
    7774 fold_smf1_model_0.cif, chain A (#3), sequence alignment score = 847.3 
    7775 RMSD between 146 pruned atom pairs is 0.267 angstroms; (across all 179 pairs:
    7776 7.118) 
    7777 
    7778 
    7779 > show #3 models
    7780 
    7781 > hide #1 models
    7782 
    7783 > select clear
    7784 
    7785 > show #1 models
    7786 
    7787 > hide #1 models
    7788 
    7789 > show #1 models
    7790 
    7791 > select #1/A:34
    7792 
    7793 8 atoms, 7 bonds, 1 residue, 1 model selected 
    7794 
    7795 > select #3/A:33
    7796 
    7797 7 atoms, 6 bonds, 1 residue, 1 model selected 
    7798 
    7799 > select #3/A:34
    7800 
    7801 8 atoms, 7 bonds, 1 residue, 1 model selected 
    7802 
    7803 > select #1/A:33
    7804 
    7805 7 atoms, 6 bonds, 1 residue, 1 model selected 
    7806 
    7807 > select #3/A:32
    7808 
    7809 7 atoms, 6 bonds, 1 residue, 1 model selected 
    7810 
    7811 > hide #3 models
    7812 
    7813 > show #2 models
    7814 
    7815 > hide #2 models
    7816 
    7817 > show #2 models
    7818 
    7819 > hide #1 models
    7820 
    7821 > show #3 models
    7822 
    7823 > show #1 models
    7824 
    7825 > hide #1 models
    7826 
    7827 > hide #3 models
    7828 
    7829 > show #1 models
    7830 
    7831 Drag select of 2 residues 
    7832 [Repeated 1 time(s)]Drag select of 5 residues 
    7833 
    7834 > select clear
    7835 
    7836 > select #1/B:197
    7837 
    7838 7 atoms, 7 bonds, 1 residue, 1 model selected 
    7839 
    7840 > select add #2/A:197
    7841 
    7842 14 atoms, 14 bonds, 2 residues, 2 models selected 
    7843 
    7844 > style sel stick
    7845 
    7846 Changed 14 atom styles 
    7847 
    7848 > show sel cartoons
    7849 
    7850 > show sel atoms
    7851 
    7852 > select clear
    7853 
    7854 [Repeated 1 time(s)]
    7855 
    7856 > hide #1-2 atoms
    7857 
    7858 > select #1/B:197
    7859 
    7860 7 atoms, 7 bonds, 1 residue, 1 model selected 
    7861 
    7862 > select add #2/A:197
    7863 
    7864 14 atoms, 14 bonds, 2 residues, 2 models selected 
    7865 
    7866 > show sel atoms
    7867 
    7868 > select clear
    7869 
    7870 [Repeated 1 time(s)]
    7871 
    7872 > hide #2 models
    7873 
    7874 > show #2 models
    7875 
    7876 > hide #1 models
    7877 
    7878 > show #1 models
    7879 
    7880 > open /Users/taic/Library/CloudStorage/OneDrive-
    7881 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_mrkd_smf1x2/fold_mrkd_smf1x2_model_0.cif
    7882 > /Users/taic/Library/CloudStorage/OneDrive-
    7883 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_mrkd_smf1x2/fold_mrkd_smf1x2_model_1.cif
    7884 > /Users/taic/Library/CloudStorage/OneDrive-
    7885 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_mrkd_smf1x2/fold_mrkd_smf1x2_model_2.cif
    7886 > /Users/taic/Library/CloudStorage/OneDrive-
    7887 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_mrkd_smf1x2/fold_mrkd_smf1x2_model_3.cif
    7888 > /Users/taic/Library/CloudStorage/OneDrive-
    7889 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_mrkd_smf1x2/fold_mrkd_smf1x2_model_4.cif
    7890 
    7891 Chain information for fold_mrkd_smf1x2_model_0.cif #4 
    7892 --- 
    7893 Chain | Description 
    7894 A | . 
    7895 B C | . 
    7896 
    7897 Chain information for fold_mrkd_smf1x2_model_1.cif #5 
    7898 --- 
    7899 Chain | Description 
    7900 A | . 
    7901 B C | . 
    7902 
    7903 Chain information for fold_mrkd_smf1x2_model_2.cif #6 
    7904 --- 
    7905 Chain | Description 
    7906 A | . 
    7907 B C | . 
    7908 
    7909 Chain information for fold_mrkd_smf1x2_model_3.cif #7 
    7910 --- 
    7911 Chain | Description 
    7912 A | . 
    7913 B C | . 
    7914 
    7915 Chain information for fold_mrkd_smf1x2_model_4.cif #8 
    7916 --- 
    7917 Chain | Description 
    7918 A | . 
    7919 B C | . 
    7920 
    7921 
    7922 > hide #2 models
    7923 
    7924 > save /Users/taic/Library/CloudStorage/OneDrive-
    7925 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_MarkD_Smf1.cxs
    7926 
    7927 > ui tool show Matchmaker
    7928 
    7929 > matchmaker #4-8 to #1
    7930 
    7931 Parameters 
    7932 --- 
    7933 Chain pairing | bb 
    7934 Alignment algorithm | Needleman-Wunsch 
    7935 Similarity matrix | BLOSUM-62 
    7936 SS fraction | 0.3 
    7937 Gap open (HH/SS/other) | 18/18/6 
    7938 Gap extend | 1 
    7939 SS matrix |  |  | H | S | O 
    7940 ---|---|---|--- 
    7941 H | 6 | -9 | -6 
    7942 S |  | 6 | -6 
    7943 O |  |  | 4 
    7944 Iteration cutoff | 2 
    7945 
    7946 Matchmaker fold_smf1_mrkd_model_0.cif, chain B (#1) with
    7947 fold_mrkd_smf1x2_model_0.cif, chain A (#4), sequence alignment score = 1735.3 
    7948 RMSD between 317 pruned atom pairs is 0.717 angstroms; (across all 344 pairs:
    7949 1.803) 
    7950 
    7951 Matchmaker fold_smf1_mrkd_model_0.cif, chain B (#1) with
    7952 fold_mrkd_smf1x2_model_1.cif, chain A (#5), sequence alignment score = 1735.3 
    7953 RMSD between 317 pruned atom pairs is 0.658 angstroms; (across all 344 pairs:
    7954 2.621) 
    7955 
    7956 Matchmaker fold_smf1_mrkd_model_0.cif, chain B (#1) with
    7957 fold_mrkd_smf1x2_model_2.cif, chain A (#6), sequence alignment score = 1735.3 
    7958 RMSD between 323 pruned atom pairs is 0.662 angstroms; (across all 344 pairs:
    7959 1.119) 
    7960 
    7961 Matchmaker fold_smf1_mrkd_model_0.cif, chain B (#1) with
    7962 fold_mrkd_smf1x2_model_3.cif, chain A (#7), sequence alignment score = 1726.3 
    7963 RMSD between 326 pruned atom pairs is 0.578 angstroms; (across all 344 pairs:
    7964 1.658) 
    7965 
    7966 Matchmaker fold_smf1_mrkd_model_0.cif, chain B (#1) with
    7967 fold_mrkd_smf1x2_model_4.cif, chain A (#8), sequence alignment score = 1735.3 
    7968 RMSD between 320 pruned atom pairs is 0.580 angstroms; (across all 344 pairs:
    7969 2.113) 
    7970 
    7971 
    7972 > save /Users/taic/Library/CloudStorage/OneDrive-
    7973 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_MarkD_Smf1.cxs
    7974 
    7975 > hide #4 models
    7976 
    7977 > hide #5 models
    7978 
    7979 > hide #6 models
    7980 
    7981 > hide #7 models
    7982 
    7983 > hide #8 models
    7984 
    7985 > show #4 models
    7986 
    7987 > hide #1 models
    7988 
    7989 > show #1 models
    7990 
    7991 > hide #1 models
    7992 
    7993 > show #5 models
    7994 
    7995 > show #6 models
    7996 
    7997 > show #7 models
    7998 
    7999 > show #8 models
    8000 
    8001 > show #2 models
    8002 
    8003 > hide #2 models
    8004 
    8005 > show #1 models
    8006 
    8007 > hide #1 models
    8008 
    8009 Drag select of 50 residues 
    8010 
    8011 > select add #4
    8012 
    8013 5409 atoms, 5201 bonds, 741 residues, 5 models selected 
    8014 
    8015 > select subtract #4
    8016 
    8017 289 atoms, 39 residues, 4 models selected 
    8018 
    8019 > select add #5
    8020 
    8021 5328 atoms, 5201 bonds, 730 residues, 4 models selected 
    8022 
    8023 > select add #6
    8024 
    8025 10376 atoms, 10402 bonds, 1422 residues, 4 models selected 
    8026 
    8027 > select add #7
    8028 
    8029 15415 atoms, 15603 bonds, 2113 residues, 4 models selected 
    8030 
    8031 > select add #8
    8032 
    8033 20480 atoms, 20804 bonds, 2808 residues, 4 models selected 
    8034 
    8035 > delete atoms sel
    8036 
    8037 > delete bonds sel
    8038 
    8039 > open /Users/taic/Library/CloudStorage/OneDrive-
    8040 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_mrkd_smf1x2_chaperone/fold_mrkd_smf1x2_chaperone_model_0.cif
    8041 > /Users/taic/Library/CloudStorage/OneDrive-
    8042 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_mrkd_smf1x2_chaperone/fold_mrkd_smf1x2_chaperone_model_1.cif
    8043 > /Users/taic/Library/CloudStorage/OneDrive-
    8044 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_mrkd_smf1x2_chaperone/fold_mrkd_smf1x2_chaperone_model_2.cif
    8045 > /Users/taic/Library/CloudStorage/OneDrive-
    8046 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_mrkd_smf1x2_chaperone/fold_mrkd_smf1x2_chaperone_model_3.cif
    8047 > /Users/taic/Library/CloudStorage/OneDrive-
    8048 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_mrkd_smf1x2_chaperone/fold_mrkd_smf1x2_chaperone_model_4.cif
    8049 
    8050 Chain information for fold_mrkd_smf1x2_chaperone_model_0.cif #5 
    8051 --- 
    8052 Chain | Description 
    8053 A | . 
    8054 B C | . 
    8055 D | . 
    8056 
    8057 Chain information for fold_mrkd_smf1x2_chaperone_model_1.cif #6 
    8058 --- 
    8059 Chain | Description 
    8060 A | . 
    8061 B C | . 
    8062 D | . 
    8063 
    8064 Chain information for fold_mrkd_smf1x2_chaperone_model_2.cif #7 
    8065 --- 
    8066 Chain | Description 
    8067 A | . 
    8068 B C | . 
    8069 D | . 
    8070 
    8071 Chain information for fold_mrkd_smf1x2_chaperone_model_3.cif #8 
    8072 --- 
    8073 Chain | Description 
    8074 A | . 
    8075 B C | . 
    8076 D | . 
    8077 
    8078 Chain information for fold_mrkd_smf1x2_chaperone_model_4.cif #9 
    8079 --- 
    8080 Chain | Description 
    8081 A | . 
    8082 B C | . 
    8083 D | . 
    8084 
    8085 
    8086 > ui tool show Matchmaker
    8087 
    8088 > matchmaker #5-9 to #4
    8089 
    8090 Parameters 
    8091 --- 
    8092 Chain pairing | bb 
    8093 Alignment algorithm | Needleman-Wunsch 
    8094 Similarity matrix | BLOSUM-62 
    8095 SS fraction | 0.3 
    8096 Gap open (HH/SS/other) | 18/18/6 
    8097 Gap extend | 1 
    8098 SS matrix |  |  | H | S | O 
    8099 ---|---|---|--- 
    8100 H | 6 | -9 | -6 
    8101 S |  | 6 | -6 
    8102 O |  |  | 4 
    8103 Iteration cutoff | 2 
    8104 
    8105 Matchmaker fold_mrkd_smf1x2_model_0.cif, chain A (#4) with
    8106 fold_mrkd_smf1x2_chaperone_model_0.cif, chain A (#5), sequence alignment score
    8107 = 1684.9 
    8108 RMSD between 174 pruned atom pairs is 0.454 angstroms; (across all 344 pairs:
    8109 13.892) 
    8110 
    8111 Matchmaker fold_mrkd_smf1x2_model_0.cif, chain A (#4) with
    8112 fold_mrkd_smf1x2_chaperone_model_1.cif, chain A (#6), sequence alignment score
    8113 = 1690.3 
    8114 RMSD between 170 pruned atom pairs is 0.422 angstroms; (across all 344 pairs:
    8115 13.078) 
    8116 
    8117 Matchmaker fold_mrkd_smf1x2_model_0.cif, chain A (#4) with
    8118 fold_mrkd_smf1x2_chaperone_model_2.cif, chain A (#7), sequence alignment score
    8119 = 1679.5 
    8120 RMSD between 162 pruned atom pairs is 0.341 angstroms; (across all 344 pairs:
    8121 14.032) 
    8122 
    8123 Matchmaker fold_mrkd_smf1x2_model_0.cif, chain A (#4) with
    8124 fold_mrkd_smf1x2_chaperone_model_3.cif, chain A (#8), sequence alignment score
    8125 = 1688.5 
    8126 RMSD between 171 pruned atom pairs is 0.409 angstroms; (across all 344 pairs:
    8127 14.387) 
    8128 
    8129 Matchmaker fold_mrkd_smf1x2_model_0.cif, chain A (#4) with
    8130 fold_mrkd_smf1x2_chaperone_model_4.cif, chain A (#9), sequence alignment score
    8131 = 1670.5 
    8132 RMSD between 167 pruned atom pairs is 0.440 angstroms; (across all 344 pairs:
    8133 13.538) 
    8134 
    8135 
    8136 > hide #4 models
    8137 
    8138 > ui tool show Matchmaker
    8139 
    8140 > matchmaker #6-9 to #5
    8141 
    8142 Parameters 
    8143 --- 
    8144 Chain pairing | bb 
    8145 Alignment algorithm | Needleman-Wunsch 
    8146 Similarity matrix | BLOSUM-62 
    8147 SS fraction | 0.3 
    8148 Gap open (HH/SS/other) | 18/18/6 
    8149 Gap extend | 1 
    8150 SS matrix |  |  | H | S | O 
    8151 ---|---|---|--- 
    8152 H | 6 | -9 | -6 
    8153 S |  | 6 | -6 
    8154 O |  |  | 4 
    8155 Iteration cutoff | 2 
    8156 
    8157 Matchmaker fold_mrkd_smf1x2_chaperone_model_0.cif, chain A (#5) with
    8158 fold_mrkd_smf1x2_chaperone_model_1.cif, chain A (#6), sequence alignment score
    8159 = 1705.9 
    8160 RMSD between 285 pruned atom pairs is 1.036 angstroms; (across all 344 pairs:
    8161 3.694) 
    8162 
    8163 Matchmaker fold_mrkd_smf1x2_chaperone_model_0.cif, chain A (#5) with
    8164 fold_mrkd_smf1x2_chaperone_model_2.cif, chain A (#7), sequence alignment score
    8165 = 1714.9 
    8166 RMSD between 142 pruned atom pairs is 0.412 angstroms; (across all 344 pairs:
    8167 7.789) 
    8168 
    8169 Matchmaker fold_mrkd_smf1x2_chaperone_model_0.cif, chain A (#5) with
    8170 fold_mrkd_smf1x2_chaperone_model_3.cif, chain A (#8), sequence alignment score
    8171 = 1723.9 
    8172 RMSD between 321 pruned atom pairs is 0.448 angstroms; (across all 344 pairs:
    8173 2.302) 
    8174 
    8175 Matchmaker fold_mrkd_smf1x2_chaperone_model_0.cif, chain A (#5) with
    8176 fold_mrkd_smf1x2_chaperone_model_4.cif, chain A (#9), sequence alignment score
    8177 = 1705.9 
    8178 RMSD between 300 pruned atom pairs is 0.999 angstroms; (across all 344 pairs:
    8179 4.300) 
    8180 
    8181 
    8182 > hide #6 models
    8183 
    8184 > hide #7 models
    8185 
    8186 > hide #8 models
    8187 
    8188 > hide #9 models
    8189 
    8190 > show #4 models
    8191 
    8192 > hide #5 models
    8193 
    8194 > show #1 models
    8195 
    8196 > hide #1 models
    8197 
    8198 > select #4/A
    8199 
    8200 2544 atoms, 2583 bonds, 344 residues, 1 model selected 
    8201 
    8202 > matchmaker #5-9 to #4 & sel
    8203 
    8204 Parameters 
    8205 --- 
    8206 Chain pairing | bb 
    8207 Alignment algorithm | Needleman-Wunsch 
    8208 Similarity matrix | BLOSUM-62 
    8209 SS fraction | 0.3 
    8210 Gap open (HH/SS/other) | 18/18/6 
    8211 Gap extend | 1 
    8212 SS matrix |  |  | H | S | O 
    8213 ---|---|---|--- 
    8214 H | 6 | -9 | -6 
    8215 S |  | 6 | -6 
    8216 O |  |  | 4 
    8217 Iteration cutoff | 2 
    8218 
    8219 Matchmaker fold_mrkd_smf1x2_model_0.cif, chain A (#4) with
    8220 fold_mrkd_smf1x2_chaperone_model_0.cif, chain A (#5), sequence alignment score
    8221 = 1684.9 
    8222 RMSD between 174 pruned atom pairs is 0.454 angstroms; (across all 344 pairs:
    8223 13.892) 
    8224 
    8225 Matchmaker fold_mrkd_smf1x2_model_0.cif, chain A (#4) with
    8226 fold_mrkd_smf1x2_chaperone_model_1.cif, chain A (#6), sequence alignment score
    8227 = 1690.3 
    8228 RMSD between 170 pruned atom pairs is 0.422 angstroms; (across all 344 pairs:
    8229 13.078) 
    8230 
    8231 Matchmaker fold_mrkd_smf1x2_model_0.cif, chain A (#4) with
    8232 fold_mrkd_smf1x2_chaperone_model_2.cif, chain A (#7), sequence alignment score
    8233 = 1679.5 
    8234 RMSD between 162 pruned atom pairs is 0.341 angstroms; (across all 344 pairs:
    8235 14.032) 
    8236 
    8237 Matchmaker fold_mrkd_smf1x2_model_0.cif, chain A (#4) with
    8238 fold_mrkd_smf1x2_chaperone_model_3.cif, chain A (#8), sequence alignment score
    8239 = 1688.5 
    8240 RMSD between 171 pruned atom pairs is 0.409 angstroms; (across all 344 pairs:
    8241 14.387) 
    8242 
    8243 Matchmaker fold_mrkd_smf1x2_model_0.cif, chain A (#4) with
    8244 fold_mrkd_smf1x2_chaperone_model_4.cif, chain A (#9), sequence alignment score
    8245 = 1670.5 
    8246 RMSD between 167 pruned atom pairs is 0.440 angstroms; (across all 344 pairs:
    8247 13.538) 
    8248 
    8249 
    8250 > show #5 models
    8251 
    8252 > show #6 models
    8253 
    8254 > show #7 models
    8255 
    8256 > show #8 models
    8257 
    8258 > show #9 models
    8259 
    8260 > hide #9 models
    8261 
    8262 > hide #5 models
    8263 
    8264 > hide #6 models
    8265 
    8266 > hide #7 models
    8267 
    8268 > hide #8 models
    8269 
    8270 > show #5 models
    8271 
    8272 > hide #4 models
    8273 
    8274 > show #6 models
    8275 
    8276 > select #5/D
    8277 
    8278 1844 atoms, 1886 bonds, 242 residues, 1 model selected 
    8279 
    8280 > rainbow sel
    8281 
    8282 > hide #5 models
    8283 
    8284 > hide #6 models
    8285 
    8286 > show #5 models
    8287 
    8288 > select add #5
    8289 
    8290 6964 atoms, 7087 bonds, 944 residues, 1 model selected 
    8291 
    8292 > rainbow sel
    8293 
    8294 > select clear
    8295 
    8296 > color #5 bychain
    8297 
    8298 > show #6 models
    8299 
    8300 > hide #5 models
    8301 
    8302 > color #6 bychain
    8303 
    8304 > show #5 models
    8305 
    8306 > hide #5 models
    8307 
    8308 > show #7 models
    8309 
    8310 > hide #6 models
    8311 
    8312 > color #7 bychain
    8313 
    8314 > show #8 models
    8315 
    8316 > hide #7 models
    8317 
    8318 > color #8 bychain
    8319 
    8320 > show #9 models
    8321 
    8322 > hide #8 models
    8323 
    8324 > color #9 bychain
    8325 
    8326 > show #8 models
    8327 
    8328 > show #7 models
    8329 
    8330 > show #6 models
    8331 
    8332 > show #5 models
    8333 
    8334 > hide #6 models
    8335 
    8336 > hide #7 models
    8337 
    8338 > hide #8 models
    8339 
    8340 > hide #9 models
    8341 
    8342 > show #6 models
    8343 
    8344 > show #7 models
    8345 
    8346 > show #8 models
    8347 
    8348 > show #9 models
    8349 
    8350 > hide #6 models
    8351 
    8352 > hide #7 models
    8353 
    8354 > hide #9 models
    8355 
    8356 > hide #8 models
    8357 
    8358 > show #1 models
    8359 
    8360 > hide #5 models
    8361 
    8362 > show #4 models
    8363 
    8364 > hide #1 models
    8365 
    8366 > select #5/A
    8367 
    8368 2544 atoms, 2583 bonds, 344 residues, 1 model selected 
    8369 
    8370 > select #4/A
    8371 
    8372 2544 atoms, 2583 bonds, 344 residues, 1 model selected 
    8373 
    8374 > ui tool show "Color Actions"
    8375 
    8376 > color sel cornflower blue
    8377 
    8378 > select #4/B
    8379 
    8380 1288 atoms, 1309 bonds, 179 residues, 1 model selected 
    8381 
    8382 > color sel hot pink
    8383 
    8384 > select #4/B:24
    8385 
    8386 4 atoms, 3 bonds, 1 residue, 1 model selected 
    8387 
    8388 > select /B:24-33
    8389 
    8390 501 atoms, 502 bonds, 70 residues, 7 models selected 
    8391 
    8392 > color sel magenta
    8393 
    8394 > select /C:24-33
    8395 
    8396 432 atoms, 432 bonds, 60 residues, 6 models selected 
    8397 
    8398 > color sel forest green
    8399 
    8400 > color sel lime green
    8401 
    8402 > color sel sea green
    8403 
    8404 > select #4/A:306
    8405 
    8406 7 atoms, 6 bonds, 1 residue, 1 model selected 
    8407 
    8408 > select /C:24-33
    8409 
    8410 432 atoms, 432 bonds, 60 residues, 6 models selected 
    8411 
    8412 > color sel magenta
    8413 
    8414 > color sel green
    8415 
    8416 > select clear
    8417 
    8418 > select add #3
    8419 
    8420 1288 atoms, 1309 bonds, 179 residues, 1 model selected 
    8421 
    8422 > save /Users/taic/Library/CloudStorage/OneDrive-
    8423 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_smf1/Smf1.af3.pdb
    8424 > models #3
    8425 
    8426 > select subtract #3
    8427 
    8428 Nothing selected 
    8429 
    8430 > save /Users/taic/Library/CloudStorage/OneDrive-
    8431 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_mrkd/MrkD.af3.pdb
    8432 > models #2
    8433 
    8434 > hide #4 models
    8435 
    8436 > show #2 models
    8437 
    8438 > show #3 models
    8439 
    8440 > hide #2 models
    8441 
    8442 > show #1 models
    8443 
    8444 > hide #3 models
    8445 
    8446 > show #4 models
    8447 
    8448 > hide #1 models
    8449 
    8450 > show #5 models
    8451 
    8452 > hide #4 models
    8453 
    8454 > open /Users/taic/Library/CloudStorage/OneDrive-
    8455 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_smlt_rs03360chaperone/fold_smlt_rs03360chaperone_model_0.cif
    8456 
    8457 Chain information for fold_smlt_rs03360chaperone_model_0.cif #10 
    8458 --- 
    8459 Chain | Description 
    8460 A | . 
    8461 
    8462 
    8463 > hide #5 models
    8464 
    8465 > show #5 models
    8466 
    8467 > hide #10 models
    8468 
    8469 > save /Users/taic/Library/CloudStorage/OneDrive-
    8470 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/MrkDSmf1/af3_MarkD_Smf1.cxs
    8471 
    8472 > close session
    8473 
    8474 > open /Users/taic/Library/CloudStorage/OneDrive-
    8475 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsf/fold_igaa_rcsf_model_0.cif
    8476 > /Users/taic/Library/CloudStorage/OneDrive-
    8477 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsf/fold_igaa_rcsf_model_1.cif
    8478 > /Users/taic/Library/CloudStorage/OneDrive-
    8479 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsf/fold_igaa_rcsf_model_2.cif
    8480 > /Users/taic/Library/CloudStorage/OneDrive-
    8481 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsf/fold_igaa_rcsf_model_3.cif
    8482 > /Users/taic/Library/CloudStorage/OneDrive-
    8483 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsf/fold_igaa_rcsf_model_4.cif
    8484 
    8485 Chain information for fold_igaa_rcsf_model_0.cif #1 
    8486 --- 
    8487 Chain | Description 
    8488 A | . 
    8489 B | . 
    8490 
    8491 Chain information for fold_igaa_rcsf_model_1.cif #2 
    8492 --- 
    8493 Chain | Description 
    8494 A | . 
    8495 B | . 
    8496 
    8497 Chain information for fold_igaa_rcsf_model_2.cif #3 
    8498 --- 
    8499 Chain | Description 
    8500 A | . 
    8501 B | . 
    8502 
    8503 Chain information for fold_igaa_rcsf_model_3.cif #4 
    8504 --- 
    8505 Chain | Description 
    8506 A | . 
    8507 B | . 
    8508 
    8509 Chain information for fold_igaa_rcsf_model_4.cif #5 
    8510 --- 
    8511 Chain | Description 
    8512 A | . 
    8513 B | . 
    8514 
    8515 
    8516 > ui tool show Matchmaker
    8517 
    8518 > matchmaker #2-5 to #1
    8519 
    8520 Parameters 
    8521 --- 
    8522 Chain pairing | bb 
    8523 Alignment algorithm | Needleman-Wunsch 
    8524 Similarity matrix | BLOSUM-62 
    8525 SS fraction | 0.3 
    8526 Gap open (HH/SS/other) | 18/18/6 
    8527 Gap extend | 1 
    8528 SS matrix |  |  | H | S | O 
    8529 ---|---|---|--- 
    8530 H | 6 | -9 | -6 
    8531 S |  | 6 | -6 
    8532 O |  |  | 4 
    8533 Iteration cutoff | 2 
    8534 
    8535 Matchmaker fold_igaa_rcsf_model_0.cif, chain A (#1) with
    8536 fold_igaa_rcsf_model_1.cif, chain A (#2), sequence alignment score = 3685.9 
    8537 RMSD between 521 pruned atom pairs is 0.855 angstroms; (across all 711 pairs:
    8538 4.046) 
    8539 
    8540 Matchmaker fold_igaa_rcsf_model_0.cif, chain A (#1) with
    8541 fold_igaa_rcsf_model_2.cif, chain A (#3), sequence alignment score = 3684.1 
    8542 RMSD between 476 pruned atom pairs is 1.001 angstroms; (across all 711 pairs:
    8543 4.084) 
    8544 
    8545 Matchmaker fold_igaa_rcsf_model_0.cif, chain A (#1) with
    8546 fold_igaa_rcsf_model_3.cif, chain A (#4), sequence alignment score = 3674.5 
    8547 RMSD between 588 pruned atom pairs is 0.972 angstroms; (across all 711 pairs:
    8548 2.309) 
    8549 
    8550 Matchmaker fold_igaa_rcsf_model_0.cif, chain A (#1) with
    8551 fold_igaa_rcsf_model_4.cif, chain A (#5), sequence alignment score = 3630.7 
    8552 RMSD between 513 pruned atom pairs is 0.831 angstroms; (across all 711 pairs:
    8553 7.825) 
    8554 
    8555 
    8556 > color bychain
    8557 
    8558 > open /Users/taic/Library/CloudStorage/OneDrive-
    8559 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/af2.3.1/IgaA_RcsF.full/IgaA_RcsF.full.ranked_0.pdb
    8560 
    8561 [Repeated 1 time(s)]Cannot open files: [Errno 60] Operation timed out 
    8562 
    8563 > open /Users/taic/Library/CloudStorage/OneDrive-
    8564 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/af2.3.1/IgaA_RcsF.full/IgaA_RcsF.full.ranked_0.pdb
    8565 
    8566 Cannot open files: [Errno 60] Operation timed out 
    8567 
    8568 > open /Users/taic/Library/CloudStorage/OneDrive-
    8569 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsf/IgaA_RcsF.full.af2.pdb
    8570 
    8571 Chain information for IgaA_RcsF.full.af2.pdb #6 
    8572 --- 
    8573 Chain | Description 
    8574 A | No description available 
    8575 B | No description available 
    8576 
    8577 
    8578 > matchmaker #6 to #1
    8579 
    8580 Parameters 
    8581 --- 
    8582 Chain pairing | bb 
    8583 Alignment algorithm | Needleman-Wunsch 
    8584 Similarity matrix | BLOSUM-62 
    8585 SS fraction | 0.3 
    8586 Gap open (HH/SS/other) | 18/18/6 
    8587 Gap extend | 1 
    8588 SS matrix |  |  | H | S | O 
    8589 ---|---|---|--- 
    8590 H | 6 | -9 | -6 
    8591 S |  | 6 | -6 
    8592 O |  |  | 4 
    8593 Iteration cutoff | 2 
    8594 
    8595 Matchmaker fold_igaa_rcsf_model_0.cif, chain A (#1) with
    8596 IgaA_RcsF.full.af2.pdb, chain A (#6), sequence alignment score = 3610.6 
    8597 RMSD between 211 pruned atom pairs is 0.633 angstroms; (across all 711 pairs:
    8598 11.108) 
    8599 
    8600 
    8601 > select #1/B
    8602 
    8603 984 atoms, 1001 bonds, 134 residues, 1 model selected 
    8604 
    8605 > matchmaker #2-6 to #1 & sel
    8606 
    8607 Parameters 
    8608 --- 
    8609 Chain pairing | bb 
    8610 Alignment algorithm | Needleman-Wunsch 
    8611 Similarity matrix | BLOSUM-62 
    8612 SS fraction | 0.3 
    8613 Gap open (HH/SS/other) | 18/18/6 
    8614 Gap extend | 1 
    8615 SS matrix |  |  | H | S | O 
    8616 ---|---|---|--- 
    8617 H | 6 | -9 | -6 
    8618 S |  | 6 | -6 
    8619 O |  |  | 4 
    8620 Iteration cutoff | 2 
    8621 
    8622 Matchmaker fold_igaa_rcsf_model_0.cif, chain B (#1) with
    8623 fold_igaa_rcsf_model_1.cif, chain B (#2), sequence alignment score = 678 
    8624 RMSD between 50 pruned atom pairs is 0.070 angstroms; (across all 134 pairs:
    8625 23.597) 
    8626 
    8627 Matchmaker fold_igaa_rcsf_model_0.cif, chain B (#1) with
    8628 fold_igaa_rcsf_model_2.cif, chain B (#3), sequence alignment score = 678 
    8629 RMSD between 68 pruned atom pairs is 0.125 angstroms; (across all 134 pairs:
    8630 21.352) 
    8631 
    8632 Matchmaker fold_igaa_rcsf_model_0.cif, chain B (#1) with
    8633 fold_igaa_rcsf_model_3.cif, chain B (#4), sequence alignment score = 678 
    8634 RMSD between 94 pruned atom pairs is 0.411 angstroms; (across all 134 pairs:
    8635 6.659) 
    8636 
    8637 Matchmaker fold_igaa_rcsf_model_0.cif, chain B (#1) with
    8638 fold_igaa_rcsf_model_4.cif, chain B (#5), sequence alignment score = 670.8 
    8639 RMSD between 69 pruned atom pairs is 0.174 angstroms; (across all 134 pairs:
    8640 14.431) 
    8641 
    8642 Matchmaker fold_igaa_rcsf_model_0.cif, chain B (#1) with
    8643 IgaA_RcsF.full.af2.pdb, chain B (#6), sequence alignment score = 678 
    8644 RMSD between 10 pruned atom pairs is 1.339 angstroms; (across all 134 pairs:
    8645 22.199) 
    8646 
    8647 
    8648 > select #6/A
    8649 
    8650 11187 atoms, 11321 bonds, 711 residues, 1 model selected 
    8651 
    8652 > color sel blue
    8653 
    8654 > select #6/B
    8655 
    8656 2000 atoms, 2017 bonds, 134 residues, 1 model selected 
    8657 
    8658 > color sel red
    8659 
    8660 > select clear
    8661 
    8662 > select /B
    8663 
    8664 6920 atoms, 7022 bonds, 804 residues, 6 models selected 
    8665 
    8666 > matchmaker #2-6 & sel to #1 & sel
    8667 
    8668 Parameters 
    8669 --- 
    8670 Chain pairing | bb 
    8671 Alignment algorithm | Needleman-Wunsch 
    8672 Similarity matrix | BLOSUM-62 
    8673 SS fraction | 0.3 
    8674 Gap open (HH/SS/other) | 18/18/6 
    8675 Gap extend | 1 
    8676 SS matrix |  |  | H | S | O 
    8677 ---|---|---|--- 
    8678 H | 6 | -9 | -6 
    8679 S |  | 6 | -6 
    8680 O |  |  | 4 
    8681 Iteration cutoff | 2 
    8682 
    8683 Matchmaker fold_igaa_rcsf_model_0.cif, chain B (#1) with
    8684 fold_igaa_rcsf_model_1.cif, chain B (#2), sequence alignment score = 678 
    8685 RMSD between 50 pruned atom pairs is 0.070 angstroms; (across all 134 pairs:
    8686 23.597) 
    8687 
    8688 Matchmaker fold_igaa_rcsf_model_0.cif, chain B (#1) with
    8689 fold_igaa_rcsf_model_2.cif, chain B (#3), sequence alignment score = 678 
    8690 RMSD between 68 pruned atom pairs is 0.125 angstroms; (across all 134 pairs:
    8691 21.352) 
    8692 
    8693 Matchmaker fold_igaa_rcsf_model_0.cif, chain B (#1) with
    8694 fold_igaa_rcsf_model_3.cif, chain B (#4), sequence alignment score = 678 
    8695 RMSD between 94 pruned atom pairs is 0.411 angstroms; (across all 134 pairs:
    8696 6.659) 
    8697 
    8698 Matchmaker fold_igaa_rcsf_model_0.cif, chain B (#1) with
    8699 fold_igaa_rcsf_model_4.cif, chain B (#5), sequence alignment score = 670.8 
    8700 RMSD between 69 pruned atom pairs is 0.174 angstroms; (across all 134 pairs:
    8701 14.431) 
    8702 
    8703 Matchmaker fold_igaa_rcsf_model_0.cif, chain B (#1) with
    8704 IgaA_RcsF.full.af2.pdb, chain B (#6), sequence alignment score = 678 
    8705 RMSD between 10 pruned atom pairs is 1.339 angstroms; (across all 134 pairs:
    8706 22.199) 
    8707 
    8708 
    8709 > matchmaker #2-6 & sel to #1 & sel
    8710 
    8711 Parameters 
    8712 --- 
    8713 Chain pairing | bb 
    8714 Alignment algorithm | Needleman-Wunsch 
    8715 Similarity matrix | BLOSUM-62 
    8716 SS fraction | 0.3 
    8717 Gap open (HH/SS/other) | 18/18/6 
    8718 Gap extend | 1 
    8719 SS matrix |  |  | H | S | O 
    8720 ---|---|---|--- 
    8721 H | 6 | -9 | -6 
    8722 S |  | 6 | -6 
    8723 O |  |  | 4 
    8724 Iteration cutoff | 2 
    8725 
    8726 Matchmaker fold_igaa_rcsf_model_0.cif, chain B (#1) with
    8727 fold_igaa_rcsf_model_1.cif, chain B (#2), sequence alignment score = 678 
    8728 RMSD between 50 pruned atom pairs is 0.070 angstroms; (across all 134 pairs:
    8729 23.597) 
    8730 
    8731 Matchmaker fold_igaa_rcsf_model_0.cif, chain B (#1) with
    8732 fold_igaa_rcsf_model_2.cif, chain B (#3), sequence alignment score = 678 
    8733 RMSD between 68 pruned atom pairs is 0.125 angstroms; (across all 134 pairs:
    8734 21.352) 
    8735 
    8736 Matchmaker fold_igaa_rcsf_model_0.cif, chain B (#1) with
    8737 fold_igaa_rcsf_model_3.cif, chain B (#4), sequence alignment score = 678 
    8738 RMSD between 94 pruned atom pairs is 0.411 angstroms; (across all 134 pairs:
    8739 6.659) 
    8740 
    8741 Matchmaker fold_igaa_rcsf_model_0.cif, chain B (#1) with
    8742 fold_igaa_rcsf_model_4.cif, chain B (#5), sequence alignment score = 670.8 
    8743 RMSD between 69 pruned atom pairs is 0.174 angstroms; (across all 134 pairs:
    8744 14.431) 
    8745 
    8746 Matchmaker fold_igaa_rcsf_model_0.cif, chain B (#1) with
    8747 IgaA_RcsF.full.af2.pdb, chain B (#6), sequence alignment score = 678 
    8748 RMSD between 10 pruned atom pairs is 1.339 angstroms; (across all 134 pairs:
    8749 22.199) 
    8750 
    8751 
    8752 > matchmaker #2-6 & sel to #1 & sel
    8753 
    8754 Parameters 
    8755 --- 
    8756 Chain pairing | bb 
    8757 Alignment algorithm | Needleman-Wunsch 
    8758 Similarity matrix | BLOSUM-62 
    8759 SS fraction | 0.3 
    8760 Gap open (HH/SS/other) | 18/18/6 
    8761 Gap extend | 1 
    8762 SS matrix |  |  | H | S | O 
    8763 ---|---|---|--- 
    8764 H | 6 | -9 | -6 
    8765 S |  | 6 | -6 
    8766 O |  |  | 4 
    8767 Iteration cutoff | 2 
    8768 
    8769 Matchmaker fold_igaa_rcsf_model_0.cif, chain B (#1) with
    8770 fold_igaa_rcsf_model_1.cif, chain B (#2), sequence alignment score = 678 
    8771 RMSD between 50 pruned atom pairs is 0.070 angstroms; (across all 134 pairs:
    8772 23.597) 
    8773 
    8774 Matchmaker fold_igaa_rcsf_model_0.cif, chain B (#1) with
    8775 fold_igaa_rcsf_model_2.cif, chain B (#3), sequence alignment score = 678 
    8776 RMSD between 68 pruned atom pairs is 0.125 angstroms; (across all 134 pairs:
    8777 21.352) 
    8778 
    8779 Matchmaker fold_igaa_rcsf_model_0.cif, chain B (#1) with
    8780 fold_igaa_rcsf_model_3.cif, chain B (#4), sequence alignment score = 678 
    8781 RMSD between 94 pruned atom pairs is 0.411 angstroms; (across all 134 pairs:
    8782 6.659) 
    8783 
    8784 Matchmaker fold_igaa_rcsf_model_0.cif, chain B (#1) with
    8785 fold_igaa_rcsf_model_4.cif, chain B (#5), sequence alignment score = 670.8 
    8786 RMSD between 69 pruned atom pairs is 0.174 angstroms; (across all 134 pairs:
    8787 14.431) 
    8788 
    8789 Matchmaker fold_igaa_rcsf_model_0.cif, chain B (#1) with
    8790 IgaA_RcsF.full.af2.pdb, chain B (#6), sequence alignment score = 678 
    8791 RMSD between 10 pruned atom pairs is 1.339 angstroms; (across all 134 pairs:
    8792 22.199) 
    8793 
    8794 
    8795 > select /A
    8796 
    8797 39202 atoms, 40006 bonds, 4266 residues, 6 models selected 
    8798 
    8799 > matchmaker #2-6 & sel to #1 & sel
    8800 
    8801 Parameters 
    8802 --- 
    8803 Chain pairing | bb 
    8804 Alignment algorithm | Needleman-Wunsch 
    8805 Similarity matrix | BLOSUM-62 
    8806 SS fraction | 0.3 
    8807 Gap open (HH/SS/other) | 18/18/6 
    8808 Gap extend | 1 
    8809 SS matrix |  |  | H | S | O 
    8810 ---|---|---|--- 
    8811 H | 6 | -9 | -6 
    8812 S |  | 6 | -6 
    8813 O |  |  | 4 
    8814 Iteration cutoff | 2 
    8815 
    8816 Matchmaker fold_igaa_rcsf_model_0.cif, chain A (#1) with
    8817 fold_igaa_rcsf_model_1.cif, chain A (#2), sequence alignment score = 3685.9 
    8818 RMSD between 521 pruned atom pairs is 0.855 angstroms; (across all 711 pairs:
    8819 4.046) 
    8820 
    8821 Matchmaker fold_igaa_rcsf_model_0.cif, chain A (#1) with
    8822 fold_igaa_rcsf_model_2.cif, chain A (#3), sequence alignment score = 3684.1 
    8823 RMSD between 476 pruned atom pairs is 1.001 angstroms; (across all 711 pairs:
    8824 4.084) 
    8825 
    8826 Matchmaker fold_igaa_rcsf_model_0.cif, chain A (#1) with
    8827 fold_igaa_rcsf_model_3.cif, chain A (#4), sequence alignment score = 3674.5 
    8828 RMSD between 588 pruned atom pairs is 0.972 angstroms; (across all 711 pairs:
    8829 2.309) 
    8830 
    8831 Matchmaker fold_igaa_rcsf_model_0.cif, chain A (#1) with
    8832 fold_igaa_rcsf_model_4.cif, chain A (#5), sequence alignment score = 3630.7 
    8833 RMSD between 513 pruned atom pairs is 0.831 angstroms; (across all 711 pairs:
    8834 7.825) 
    8835 
    8836 Matchmaker fold_igaa_rcsf_model_0.cif, chain A (#1) with
    8837 IgaA_RcsF.full.af2.pdb, chain A (#6), sequence alignment score = 3610.6 
    8838 RMSD between 211 pruned atom pairs is 0.633 angstroms; (across all 711 pairs:
    8839 11.108) 
    8840 
    8841 
    8842 > select #1/A:508
    8843 
    8844 9 atoms, 8 bonds, 1 residue, 1 model selected 
    8845 
    8846 > hide #3 models
    8847 
    8848 > hide #4 models
    8849 
    8850 > hide #5 models
    8851 
    8852 > hide #2 models
    8853 
    8854 > select add #2
    8855 
    8856 6596 atoms, 6746 bonds, 846 residues, 2 models selected 
    8857 
    8858 > show #2 models
    8859 
    8860 > rainbow sel
    8861 
    8862 > hide #1 models
    8863 
    8864 > hide #6 models
    8865 
    8866 > select clear
    8867 
    8868 > select #2/A:645
    8869 
    8870 7 atoms, 7 bonds, 1 residue, 1 model selected 
    8871 
    8872 > select clear
    8873 
    8874 [Repeated 1 time(s)]
    8875 
    8876 > select #2/A:711
    8877 
    8878 10 atoms, 9 bonds, 1 residue, 1 model selected 
    8879 
    8880 > select subtract #2/A:711
    8881 
    8882 Nothing selected 
    8883 
    8884 > select /A:375-711
    8885 
    8886 18203 atoms, 18527 bonds, 2022 residues, 6 models selected 
    8887 
    8888 > matchmaker #2-6 & sel to #1 & sel
    8889 
    8890 Parameters 
    8891 --- 
    8892 Chain pairing | bb 
    8893 Alignment algorithm | Needleman-Wunsch 
    8894 Similarity matrix | BLOSUM-62 
    8895 SS fraction | 0.3 
    8896 Gap open (HH/SS/other) | 18/18/6 
    8897 Gap extend | 1 
    8898 SS matrix |  |  | H | S | O 
    8899 ---|---|---|--- 
    8900 H | 6 | -9 | -6 
    8901 S |  | 6 | -6 
    8902 O |  |  | 4 
    8903 Iteration cutoff | 2 
    8904 
    8905 Matchmaker fold_igaa_rcsf_model_0.cif, chain A (#1) with
    8906 fold_igaa_rcsf_model_1.cif, chain A (#2), sequence alignment score = 1758.2 
    8907 RMSD between 321 pruned atom pairs is 0.760 angstroms; (across all 337 pairs:
    8908 1.922) 
    8909 
    8910 Matchmaker fold_igaa_rcsf_model_0.cif, chain A (#1) with
    8911 fold_igaa_rcsf_model_2.cif, chain A (#3), sequence alignment score = 1754.6 
    8912 RMSD between 322 pruned atom pairs is 0.682 angstroms; (across all 337 pairs:
    8913 2.315) 
    8914 
    8915 Matchmaker fold_igaa_rcsf_model_0.cif, chain A (#1) with
    8916 fold_igaa_rcsf_model_3.cif, chain A (#4), sequence alignment score = 1754.6 
    8917 RMSD between 312 pruned atom pairs is 0.735 angstroms; (across all 337 pairs:
    8918 2.317) 
    8919 
    8920 Matchmaker fold_igaa_rcsf_model_0.cif, chain A (#1) with
    8921 fold_igaa_rcsf_model_4.cif, chain A (#5), sequence alignment score = 1751 
    8922 RMSD between 320 pruned atom pairs is 0.672 angstroms; (across all 337 pairs:
    8923 2.072) 
    8924 
    8925 Matchmaker fold_igaa_rcsf_model_0.cif, chain A (#1) with
    8926 IgaA_RcsF.full.af2.pdb, chain A (#6), sequence alignment score = 1742 
    8927 RMSD between 221 pruned atom pairs is 0.564 angstroms; (across all 337 pairs:
    8928 7.369) 
    8929 
    8930 
    8931 > show #1 models
    8932 
    8933 > show #6 models
    8934 
    8935 > select clear
    8936 
    8937 > hide #6 models
    8938 
    8939 > hide #2 models
    8940 
    8941 > show #2 models
    8942 
    8943 > hide #1 models
    8944 
    8945 > select add #3
    8946 
    8947 6587 atoms, 6738 bonds, 845 residues, 1 model selected 
    8948 
    8949 > select add #4
    8950 
    8951 13174 atoms, 13476 bonds, 1690 residues, 2 models selected 
    8952 
    8953 > select add #5
    8954 
    8955 19761 atoms, 20214 bonds, 2535 residues, 3 models selected 
    8956 
    8957 > select add #1
    8958 
    8959 26348 atoms, 26952 bonds, 3380 residues, 4 models selected 
    8960 
    8961 > select add #2
    8962 
    8963 32935 atoms, 33690 bonds, 4225 residues, 5 models selected 
    8964 
    8965 > rainbow sel & #2
    8966 
    8967 [Repeated 1 time(s)]
    8968 
    8969 > show #1 models
    8970 
    8971 > select subtract #1
    8972 
    8973 26348 atoms, 26952 bonds, 3380 residues, 4 models selected 
    8974 
    8975 > select subtract #2
    8976 
    8977 19761 atoms, 20214 bonds, 2535 residues, 3 models selected 
    8978 
    8979 > select subtract #3
    8980 
    8981 13174 atoms, 13476 bonds, 1690 residues, 2 models selected 
    8982 
    8983 > select add #3
    8984 
    8985 19761 atoms, 20214 bonds, 2535 residues, 3 models selected 
    8986 
    8987 > select subtract #4
    8988 
    8989 13174 atoms, 13476 bonds, 1690 residues, 2 models selected 
    8990 
    8991 > select subtract #3
    8992 
    8993 6587 atoms, 6738 bonds, 845 residues, 1 model selected 
    8994 
    8995 > select subtract #5
    8996 
    8997 Nothing selected 
    8998 
    8999 > select clear
    9000 
    9001 > hide #2 models
    9002 
    9003 > show #2 models
    9004 
    9005 > show #3 models
    9006 
    9007 > show #4 models
    9008 
    9009 > show #5 models
    9010 
    9011 > hide #2 models
    9012 
    9013 > hide #3 models
    9014 
    9015 > hide #4 models
    9016 
    9017 > hide #5 models
    9018 
    9019 > show #6 models
    9020 
    9021 > save /Users/taic/Library/CloudStorage/OneDrive-
    9022 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsf/IgaA_RcsF.AF3vs2.cxs
    9023 
    9024 > show #2 models
    9025 
    9026 > hide #1 models
    9027 
    9028 > save /Users/taic/Library/CloudStorage/OneDrive-
    9029 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsf/IgaA_RcsF.AF3vs2.cxs
    9030 
    9031 > close session
    9032 
    9033 > open /Users/taic/Library/CloudStorage/OneDrive-
    9034 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsd/fold_igaa_rcsd_model_0.cif
    9035 > /Users/taic/Library/CloudStorage/OneDrive-
    9036 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsd/fold_igaa_rcsd_model_1.cif
    9037 > /Users/taic/Library/CloudStorage/OneDrive-
    9038 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsd/fold_igaa_rcsd_model_2.cif
    9039 > /Users/taic/Library/CloudStorage/OneDrive-
    9040 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsd/fold_igaa_rcsd_model_3.cif
    9041 > /Users/taic/Library/CloudStorage/OneDrive-
    9042 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsd/fold_igaa_rcsd_model_4.cif
    9043 
    9044 Chain information for fold_igaa_rcsd_model_0.cif #1 
    9045 --- 
    9046 Chain | Description 
    9047 A | . 
    9048 B | . 
    9049 
    9050 Chain information for fold_igaa_rcsd_model_1.cif #2 
    9051 --- 
    9052 Chain | Description 
    9053 A | . 
    9054 B | . 
    9055 
    9056 Chain information for fold_igaa_rcsd_model_2.cif #3 
    9057 --- 
    9058 Chain | Description 
    9059 A | . 
    9060 B | . 
    9061 
    9062 Chain information for fold_igaa_rcsd_model_3.cif #4 
    9063 --- 
    9064 Chain | Description 
    9065 A | . 
    9066 B | . 
    9067 
    9068 Chain information for fold_igaa_rcsd_model_4.cif #5 
    9069 --- 
    9070 Chain | Description 
    9071 A | . 
    9072 B | . 
    9073 
    9074 
    9075 > ui tool show Matchmaker
    9076 
    9077 > select /A:375-711
    9078 
    9079 13020 atoms, 13290 bonds, 1685 residues, 5 models selected 
    9080 No reference and/or match structure/chain chosen 
    9081 
    9082 > matchmaker #2-5 & sel to #1 & sel
    9083 
    9084 Parameters 
    9085 --- 
    9086 Chain pairing | bb 
    9087 Alignment algorithm | Needleman-Wunsch 
    9088 Similarity matrix | BLOSUM-62 
    9089 SS fraction | 0.3 
    9090 Gap open (HH/SS/other) | 18/18/6 
    9091 Gap extend | 1 
    9092 SS matrix |  |  | H | S | O 
    9093 ---|---|---|--- 
    9094 H | 6 | -9 | -6 
    9095 S |  | 6 | -6 
    9096 O |  |  | 4 
    9097 Iteration cutoff | 2 
    9098 
    9099 Matchmaker fold_igaa_rcsd_model_0.cif, chain A (#1) with
    9100 fold_igaa_rcsd_model_1.cif, chain A (#2), sequence alignment score = 1746.2 
    9101 RMSD between 325 pruned atom pairs is 0.852 angstroms; (across all 337 pairs:
    9102 1.129) 
    9103 
    9104 Matchmaker fold_igaa_rcsd_model_0.cif, chain A (#1) with
    9105 fold_igaa_rcsd_model_2.cif, chain A (#3), sequence alignment score = 1737.2 
    9106 RMSD between 248 pruned atom pairs is 0.910 angstroms; (across all 337 pairs:
    9107 2.172) 
    9108 
    9109 Matchmaker fold_igaa_rcsd_model_0.cif, chain A (#1) with
    9110 fold_igaa_rcsd_model_3.cif, chain A (#4), sequence alignment score = 1746.2 
    9111 RMSD between 327 pruned atom pairs is 0.857 angstroms; (across all 337 pairs:
    9112 1.514) 
    9113 
    9114 Matchmaker fold_igaa_rcsd_model_0.cif, chain A (#1) with
    9115 fold_igaa_rcsd_model_4.cif, chain A (#5), sequence alignment score = 1754 
    9116 RMSD between 286 pruned atom pairs is 0.647 angstroms; (across all 337 pairs:
    9117 3.056) 
    9118 
    9119 
    9120 > hide #2 models
    9121 
    9122 > show #2 models
    9123 
    9124 > hide #3 models
    9125 
    9126 > hide #4 models
    9127 
    9128 > show #4 models
    9129 
    9130 > show #3 models
    9131 
    9132 > hide #5 models
    9133 
    9134 > hide #4 models
    9135 
    9136 > hide #3 models
    9137 
    9138 > hide #2 models
    9139 
    9140 > show #2 models
    9141 
    9142 > select add #1
    9143 
    9144 23077 atoms, 23545 bonds, 2949 residues, 5 models selected 
    9145 
    9146 > select add #2
    9147 
    9148 33134 atoms, 33800 bonds, 4213 residues, 5 models selected 
    9149 
    9150 > select subtract #1
    9151 
    9152 20473 atoms, 20887 bonds, 2612 residues, 4 models selected 
    9153 
    9154 > hide #1 models
    9155 
    9156 > rainbow sel & #2
    9157 
    9158 > select clear
    9159 
    9160 > show #1 models
    9161 
    9162 > hide #2 models
    9163 
    9164 > select add #1
    9165 
    9166 12661 atoms, 12913 bonds, 1601 residues, 1 model selected 
    9167 
    9168 > color sel bychain
    9169 
    9170 > show #2 models
    9171 
    9172 > hide #1 models
    9173 
    9174 > select subtract #1
    9175 
    9176 Nothing selected 
    9177 
    9178 > show #1 models
    9179 
    9180 > hide #1 models
    9181 
    9182 > open /Users/taic/Library/CloudStorage/OneDrive-
    9183 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsf/IgaA_RcsF.full.af2.pdb
    9184 
    9185 Chain information for IgaA_RcsF.full.af2.pdb #6 
    9186 --- 
    9187 Chain | Description 
    9188 A | No description available 
    9189 B | No description available 
    9190 
    9191 
    9192 > select add #6
    9193 
    9194 13187 atoms, 13338 bonds, 845 residues, 1 model selected 
    9195 
    9196 > open /Users/taic/Library/CloudStorage/OneDrive-
    9197 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsd/IgaA_RcsF.full.af2.pdb
    9198 
    9199 Chain information for IgaA_RcsF.full.af2.pdb #7 
    9200 --- 
    9201 Chain | Description 
    9202 A | No description available 
    9203 B | No description available 
    9204 
    9205 
    9206 > select add #7
    9207 
    9208 26374 atoms, 26676 bonds, 1690 residues, 2 models selected 
    9209 
    9210 > select subtract #6
    9211 
    9212 13187 atoms, 13338 bonds, 845 residues, 1 model selected 
    9213 
    9214 > delete atoms sel
    9215 
    9216 > delete bonds sel
    9217 
    9218 > open /Users/taic/Library/CloudStorage/OneDrive-
    9219 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsd/IgaA_RcsD.dm.af2.pdb
    9220 
    9221 Chain information for IgaA_RcsD.dm.af2.pdb #7 
    9222 --- 
    9223 Chain | Description 
    9224 A | No description available 
    9225 B | No description available 
    9226 
    9227 
    9228 > hide #6 models
    9229 
    9230 > select /A:375-711
    9231 
    9232 18203 atoms, 18527 bonds, 2022 residues, 6 models selected 
    9233 
    9234 > matchmaker #6-7 & sel to #1 & sel
    9235 
    9236 Parameters 
    9237 --- 
    9238 Chain pairing | bb 
    9239 Alignment algorithm | Needleman-Wunsch 
    9240 Similarity matrix | BLOSUM-62 
    9241 SS fraction | 0.3 
    9242 Gap open (HH/SS/other) | 18/18/6 
    9243 Gap extend | 1 
    9244 SS matrix |  |  | H | S | O 
    9245 ---|---|---|--- 
    9246 H | 6 | -9 | -6 
    9247 S |  | 6 | -6 
    9248 O |  |  | 4 
    9249 Iteration cutoff | 2 
    9250 
    9251 Matchmaker fold_igaa_rcsd_model_0.cif, chain A (#1) with
    9252 IgaA_RcsF.full.af2.pdb, chain A (#6), sequence alignment score = 1730 
    9253 RMSD between 165 pruned atom pairs is 0.793 angstroms; (across all 337 pairs:
    9254 8.672) 
    9255 
    9256 
    9257 > matchmaker #6-7 & sel to #1 & sel
    9258 
    9259 Parameters 
    9260 --- 
    9261 Chain pairing | bb 
    9262 Alignment algorithm | Needleman-Wunsch 
    9263 Similarity matrix | BLOSUM-62 
    9264 SS fraction | 0.3 
    9265 Gap open (HH/SS/other) | 18/18/6 
    9266 Gap extend | 1 
    9267 SS matrix |  |  | H | S | O 
    9268 ---|---|---|--- 
    9269 H | 6 | -9 | -6 
    9270 S |  | 6 | -6 
    9271 O |  |  | 4 
    9272 Iteration cutoff | 2 
    9273 
    9274 Matchmaker fold_igaa_rcsd_model_0.cif, chain A (#1) with
    9275 IgaA_RcsF.full.af2.pdb, chain A (#6), sequence alignment score = 1730 
    9276 RMSD between 165 pruned atom pairs is 0.793 angstroms; (across all 337 pairs:
    9277 8.672) 
    9278 
    9279 
    9280 > hide #2 models
    9281 
    9282 No reference and/or match structure/chain chosen 
    9283 
    9284 > matchmaker #7 to #1 & sel
    9285 
    9286 Parameters 
    9287 --- 
    9288 Chain pairing | bb 
    9289 Alignment algorithm | Needleman-Wunsch 
    9290 Similarity matrix | BLOSUM-62 
    9291 SS fraction | 0.3 
    9292 Gap open (HH/SS/other) | 18/18/6 
    9293 Gap extend | 1 
    9294 SS matrix |  |  | H | S | O 
    9295 ---|---|---|--- 
    9296 H | 6 | -9 | -6 
    9297 S |  | 6 | -6 
    9298 O |  |  | 4 
    9299 Iteration cutoff | 2 
    9300 
    9301 Matchmaker fold_igaa_rcsd_model_0.cif, chain A (#1) with IgaA_RcsD.dm.af2.pdb,
    9302 chain A (#7), sequence alignment score = 1470.3 
    9303 RMSD between 143 pruned atom pairs is 0.843 angstroms; (across all 285 pairs:
    9304 3.900) 
    9305 
    9306 
    9307 > show #1 models
    9308 
    9309 > show #6 models
    9310 
    9311 > open /Users/taic/Library/CloudStorage/OneDrive-
    9312 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsf/fold_igaa_rcsf_model_0.cif
    9313 
    9314 Chain information for fold_igaa_rcsf_model_0.cif #8 
    9315 --- 
    9316 Chain | Description 
    9317 A | . 
    9318 B | . 
    9319 
    9320 
    9321 > hide #6 models
    9322 
    9323 > hide #7 models
    9324 
    9325 > select /A:375-711
    9326 
    9327 20807 atoms, 21185 bonds, 2359 residues, 7 models selected 
    9328 
    9329 > matchmaker #8 & sel to #1 & sel
    9330 
    9331 Parameters 
    9332 --- 
    9333 Chain pairing | bb 
    9334 Alignment algorithm | Needleman-Wunsch 
    9335 Similarity matrix | BLOSUM-62 
    9336 SS fraction | 0.3 
    9337 Gap open (HH/SS/other) | 18/18/6 
    9338 Gap extend | 1 
    9339 SS matrix |  |  | H | S | O 
    9340 ---|---|---|--- 
    9341 H | 6 | -9 | -6 
    9342 S |  | 6 | -6 
    9343 O |  |  | 4 
    9344 Iteration cutoff | 2 
    9345 
    9346 Matchmaker fold_igaa_rcsd_model_0.cif, chain A (#1) with
    9347 fold_igaa_rcsf_model_0.cif, chain A (#8), sequence alignment score = 1746.2 
    9348 RMSD between 164 pruned atom pairs is 0.791 angstroms; (across all 337 pairs:
    9349 7.310) 
    9350 
    9351 
    9352 > save /Users/taic/Library/CloudStorage/OneDrive-
    9353 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsd/IgaA_RcsD.AF3vsAF2.cxs
    9354 
    9355 > save /Users/taic/Library/CloudStorage/OneDrive-
    9356 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/IgaA_RcsF_RcsD.AF3vsAF2.cxs
    9357 
    9358 \u2014\u2014\u2014 End of log from Thu Jun 20 13:37:04 2024 \u2014\u2014\u2014
    9359 
    9360 opened ChimeraX session 
    9361 
    9362 > hide #1 models
    9363 
    9364 > show #2 models
    9365 
    9366 > show #3 models
    9367 
    9368 > show #4 models
    9369 
    9370 > show #5 models
    9371 
    9372 > hide #8 models
    9373 
    9374 > select add #8
    9375 
    9376 24790 atoms, 25265 bonds, 2867 residues, 7 models selected 
    9377 
    9378 > select add #1
    9379 
    9380 34847 atoms, 35520 bonds, 4131 residues, 7 models selected 
    9381 
    9382 > select subtract #1
    9383 
    9384 22186 atoms, 22607 bonds, 2530 residues, 6 models selected 
    9385 
    9386 > select subtract #8
    9387 
    9388 15599 atoms, 15869 bonds, 1685 residues, 5 models selected 
    9389 
    9390 > select add #6
    9391 
    9392 23603 atoms, 23970 bonds, 2193 residues, 5 models selected 
    9393 
    9394 > select subtract #6
    9395 
    9396 10416 atoms, 10632 bonds, 1348 residues, 4 models selected 
    9397 
    9398 > select add #2
    9399 
    9400 20473 atoms, 20887 bonds, 2612 residues, 4 models selected 
    9401 
    9402 > select add #3
    9403 
    9404 30530 atoms, 31142 bonds, 3876 residues, 4 models selected 
    9405 
    9406 > select add #4
    9407 
    9408 40587 atoms, 41397 bonds, 5140 residues, 4 models selected 
    9409 
    9410 > select add #5
    9411 
    9412 50644 atoms, 51652 bonds, 6404 residues, 4 models selected 
    9413 
    9414 > delete atoms sel
    9415 
    9416 > delete bonds sel
    9417 
    9418 > show #1 models
    9419 
    9420 > show #6 models
    9421 
    9422 > hide #1 models
    9423 
    9424 > show #1 models
    9425 
    9426 > show #8 models
    9427 
    9428 > show #7 models
    9429 
    9430 > ui tool show Matchmaker
    9431 
    9432 > select /A:375-711
    9433 
    9434 10391 atoms, 10553 bonds, 1011 residues, 3 models selected 
    9435 
    9436 > hide #1 models
    9437 
    9438 > hide #7 models
    9439 
    9440 > hide #8 models
    9441 
    9442 > show #7 models
    9443 
    9444 > hide #6 models
    9445 
    9446 > show #6 models
    9447 
    9448 > matchmaker #6-8 to #1 & sel
    9449 
    9450 Parameters 
    9451 --- 
    9452 Chain pairing | bb 
    9453 Alignment algorithm | Needleman-Wunsch 
    9454 Similarity matrix | BLOSUM-62 
    9455 SS fraction | 0.3 
    9456 Gap open (HH/SS/other) | 18/18/6 
    9457 Gap extend | 1 
    9458 SS matrix |  |  | H | S | O 
    9459 ---|---|---|--- 
    9460 H | 6 | -9 | -6 
    9461 S |  | 6 | -6 
    9462 O |  |  | 4 
    9463 Iteration cutoff | 2 
    9464 
    9465 Matchmaker fold_igaa_rcsd_model_0.cif, chain A (#1) with
    9466 IgaA_RcsF.full.af2.pdb, chain A (#6), sequence alignment score = 1730 
    9467 RMSD between 165 pruned atom pairs is 0.793 angstroms; (across all 337 pairs:
    9468 8.672) 
    9469 
    9470 Matchmaker fold_igaa_rcsd_model_0.cif, chain A (#1) with IgaA_RcsD.dm.af2.pdb,
    9471 chain A (#7), sequence alignment score = 1470.3 
    9472 RMSD between 143 pruned atom pairs is 0.843 angstroms; (across all 285 pairs:
    9473 3.900) 
    9474 
    9475 Matchmaker fold_igaa_rcsd_model_0.cif, chain A (#1) with
    9476 fold_igaa_rcsf_model_0.cif, chain A (#8), sequence alignment score = 1746.2 
    9477 RMSD between 164 pruned atom pairs is 0.791 angstroms; (across all 337 pairs:
    9478 7.310) 
    9479 
    9480 
    9481 > show #1 models
    9482 
    9483 > show #8 models
    9484 
    9485 > hide #1 models
    9486 
    9487 > hide #8 models
    9488 
    9489 > select /A
    9490 
    9491 26974 atoms, 27426 bonds, 2434 residues, 4 models selected 
    9492 
    9493 > ui tool show "Color Actions"
    9494 
    9495 > color sel gold
    9496 
    9497 > color sel goldenrod
    9498 
    9499 > show #1 models
    9500 
    9501 > hide #6 models
    9502 
    9503 > hide #7 models
    9504 
    9505 > show #6 models
    9506 
    9507 > hide #1 models
    9508 
    9509 > show #1 models
    9510 
    9511 > hide #1 models
    9512 
    9513 > show #7 models
    9514 
    9515 > hide #6 models
    9516 
    9517 > show #6 models
    9518 
    9519 > show #8 models
    9520 
    9521 > hide #7 models
    9522 
    9523 > select #6/B
    9524 
    9525 2000 atoms, 2017 bonds, 134 residues, 1 model selected 
    9526 
    9527 > color sel navy
    9528 
    9529 > color sel medium purple
    9530 
    9531 > select clear
    9532 
    9533 > select #8/B
    9534 
    9535 984 atoms, 1001 bonds, 134 residues, 1 model selected 
    9536 
    9537 > color sel dark orchid
    9538 
    9539 > select clear
    9540 
    9541 > select #8/A
    9542 
    9543 5603 atoms, 5737 bonds, 711 residues, 1 model selected 
    9544 
    9545 > color sel orange
    9546 
    9547 > color sel gold
    9548 
    9549 > select clear
    9550 
    9551 > show #7 models
    9552 
    9553 > hide #8 models
    9554 
    9555 > show #1 models
    9556 
    9557 > hide #6 models
    9558 
    9559 > show #8 models
    9560 
    9561 > hide #7 models
    9562 
    9563 > save /Users/taic/Library/CloudStorage/OneDrive-
    9564 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/IgaA_RcsF_RcsD.AF3vsAF2.cxs
    9565 
    9566 > open /Users/taic/Library/CloudStorage/OneDrive-
    9567 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsf_rcsdx2/fold_igaa_rcsf_rcsdx2_model_0.cif
    9568 > /Users/taic/Library/CloudStorage/OneDrive-
    9569 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsf_rcsdx2/fold_igaa_rcsf_rcsdx2_model_1.cif
    9570 > /Users/taic/Library/CloudStorage/OneDrive-
    9571 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsf_rcsdx2/fold_igaa_rcsf_rcsdx2_model_2.cif
    9572 > /Users/taic/Library/CloudStorage/OneDrive-
    9573 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsf_rcsdx2/fold_igaa_rcsf_rcsdx2_model_3.cif
    9574 > /Users/taic/Library/CloudStorage/OneDrive-
    9575 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsf_rcsdx2/fold_igaa_rcsf_rcsdx2_model_4.cif
    9576 
    9577 Chain information for fold_igaa_rcsf_rcsdx2_model_0.cif #2 
    9578 --- 
    9579 Chain | Description 
    9580 A | . 
    9581 B | . 
    9582 C D | . 
    9583 
    9584 Chain information for fold_igaa_rcsf_rcsdx2_model_1.cif #3 
    9585 --- 
    9586 Chain | Description 
    9587 A | . 
    9588 B | . 
    9589 C D | . 
    9590 
    9591 Chain information for fold_igaa_rcsf_rcsdx2_model_2.cif #4 
    9592 --- 
    9593 Chain | Description 
    9594 A | . 
    9595 B | . 
    9596 C D | . 
    9597 
    9598 Chain information for fold_igaa_rcsf_rcsdx2_model_3.cif #5 
    9599 --- 
    9600 Chain | Description 
    9601 A | . 
    9602 B | . 
    9603 C D | . 
    9604 
    9605 Chain information for fold_igaa_rcsf_rcsdx2_model_4.cif #9 
    9606 --- 
    9607 Chain | Description 
    9608 A | . 
    9609 B | . 
    9610 C D | . 
    9611 
    9612 
    9613 > hide #1 models
    9614 
    9615 > hide #8 models
    9616 
    9617 > ui tool show Matchmaker
    9618 
    9619 > select /A:375-711
    9620 
    9621 23411 atoms, 23843 bonds, 2696 residues, 8 models selected 
    9622 
    9623 > matchmaker #2-5,9 to #1 & sel
    9624 
    9625 Parameters 
    9626 --- 
    9627 Chain pairing | bb 
    9628 Alignment algorithm | Needleman-Wunsch 
    9629 Similarity matrix | BLOSUM-62 
    9630 SS fraction | 0.3 
    9631 Gap open (HH/SS/other) | 18/18/6 
    9632 Gap extend | 1 
    9633 SS matrix |  |  | H | S | O 
    9634 ---|---|---|--- 
    9635 H | 6 | -9 | -6 
    9636 S |  | 6 | -6 
    9637 O |  |  | 4 
    9638 Iteration cutoff | 2 
    9639 
    9640 Matchmaker fold_igaa_rcsd_model_0.cif, chain A (#1) with
    9641 fold_igaa_rcsf_rcsdx2_model_0.cif, chain A (#2), sequence alignment score =
    9642 1750.4 
    9643 RMSD between 220 pruned atom pairs is 1.035 angstroms; (across all 337 pairs:
    9644 10.315) 
    9645 
    9646 Matchmaker fold_igaa_rcsd_model_0.cif, chain A (#1) with
    9647 fold_igaa_rcsf_rcsdx2_model_1.cif, chain A (#3), sequence alignment score =
    9648 1742.6 
    9649 RMSD between 235 pruned atom pairs is 1.120 angstroms; (across all 337 pairs:
    9650 5.345) 
    9651 
    9652 Matchmaker fold_igaa_rcsd_model_0.cif, chain A (#1) with
    9653 fold_igaa_rcsf_rcsdx2_model_2.cif, chain A (#4), sequence alignment score =
    9654 1754 
    9655 RMSD between 160 pruned atom pairs is 0.743 angstroms; (across all 337 pairs:
    9656 8.032) 
    9657 
    9658 Matchmaker fold_igaa_rcsd_model_0.cif, chain A (#1) with
    9659 fold_igaa_rcsf_rcsdx2_model_3.cif, chain A (#5), sequence alignment score =
    9660 1746.2 
    9661 RMSD between 228 pruned atom pairs is 1.069 angstroms; (across all 337 pairs:
    9662 9.420) 
    9663 
    9664 Matchmaker fold_igaa_rcsd_model_0.cif, chain A (#1) with
    9665 fold_igaa_rcsf_rcsdx2_model_4.cif, chain A (#9), sequence alignment score =
    9666 1750.4 
    9667 RMSD between 231 pruned atom pairs is 1.149 angstroms; (across all 337 pairs:
    9668 9.284) 
    9669 
    9670 
    9671 > show #1 models
    9672 
    9673 > hide #3 models
    9674 
    9675 > hide #4 models
    9676 
    9677 > hide #5 models
    9678 
    9679 > hide #9 models
    9680 
    9681 > hide #1 models
    9682 
    9683 > select add #2
    9684 
    9685 41510 atoms, 42275 bonds, 4984 residues, 8 models selected 
    9686 
    9687 > select add #1
    9688 
    9689 51567 atoms, 52530 bonds, 6248 residues, 8 models selected 
    9690 
    9691 > select add #3
    9692 
    9693 69666 atoms, 70962 bonds, 8536 residues, 8 models selected 
    9694 
    9695 > select add #4
    9696 
    9697 87765 atoms, 89394 bonds, 10824 residues, 8 models selected 
    9698 
    9699 > select subtract #1
    9700 
    9701 75104 atoms, 76481 bonds, 9223 residues, 7 models selected 
    9702 
    9703 > select subtract #3
    9704 
    9705 54401 atoms, 55391 bonds, 6598 residues, 6 models selected 
    9706 
    9707 > select subtract #4
    9708 
    9709 33698 atoms, 34301 bonds, 3973 residues, 5 models selected 
    9710 
    9711 > select add #5
    9712 
    9713 51797 atoms, 52733 bonds, 6261 residues, 5 models selected 
    9714 
    9715 > select add #6
    9716 
    9717 59801 atoms, 60834 bonds, 6769 residues, 5 models selected 
    9718 
    9719 > select subtract #5
    9720 
    9721 39098 atoms, 39744 bonds, 4144 residues, 4 models selected 
    9722 
    9723 > select subtract #6
    9724 
    9725 25911 atoms, 26406 bonds, 3299 residues, 3 models selected 
    9726 
    9727 > select add #8
    9728 
    9729 29894 atoms, 30486 bonds, 3807 residues, 3 models selected 
    9730 
    9731 > select add #9
    9732 
    9733 47993 atoms, 48918 bonds, 6095 residues, 3 models selected 
    9734 
    9735 > select subtract #8
    9736 
    9737 41406 atoms, 42180 bonds, 5250 residues, 2 models selected 
    9738 
    9739 > select subtract #9
    9740 
    9741 20703 atoms, 21090 bonds, 2625 residues, 1 model selected 
    9742 
    9743 > color sel bychain
    9744 
    9745 > select clear
    9746 
    9747 > show #1 models
    9748 
    9749 > hide #1 models
    9750 
    9751 > show #1 models
    9752 
    9753 > hide #1 models
    9754 
    9755 > show #1 models
    9756 
    9757 > hide #1 models
    9758 
    9759 > show #3 models
    9760 
    9761 > hide #2 models
    9762 
    9763 > show #2 models
    9764 
    9765 > hide #2 models
    9766 
    9767 > select add #3
    9768 
    9769 20703 atoms, 21090 bonds, 2625 residues, 1 model selected 
    9770 
    9771 > select add #4
    9772 
    9773 41406 atoms, 42180 bonds, 5250 residues, 2 models selected 
    9774 
    9775 > select add #5
    9776 
    9777 62109 atoms, 63270 bonds, 7875 residues, 3 models selected 
    9778 
    9779 > select add #9
    9780 
    9781 82812 atoms, 84360 bonds, 10500 residues, 4 models selected 
    9782 
    9783 > color sel & #3 bychain
    9784 
    9785 > select clear
    9786 
    9787 > show #2 models
    9788 
    9789 > show #4 models
    9790 
    9791 > hide #3 models
    9792 
    9793 > hide #2 models
    9794 
    9795 > select add #4
    9796 
    9797 20703 atoms, 21090 bonds, 2625 residues, 1 model selected 
    9798 
    9799 > color sel bychain
    9800 
    9801 > show #5 models
    9802 
    9803 > hide #4 models
    9804 
    9805 > select add #5
    9806 
    9807 41406 atoms, 42180 bonds, 5250 residues, 2 models selected 
    9808 
    9809 > select subtract #4
    9810 
    9811 20703 atoms, 21090 bonds, 2625 residues, 1 model selected 
    9812 
    9813 > color sel bychain
    9814 
    9815 > show #9 models
    9816 
    9817 > select add #9
    9818 
    9819 41406 atoms, 42180 bonds, 5250 residues, 2 models selected 
    9820 
    9821 > hide #5 models
    9822 
    9823 > select subtract #5
    9824 
    9825 20703 atoms, 21090 bonds, 2625 residues, 1 model selected 
    9826 
    9827 > color sel bychain
    9828 
    9829 > select clear
    9830 
    9831 > show #2 models
    9832 
    9833 > open /Users/taic/Library/CloudStorage/OneDrive-
    9834 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsf_rcsdx2/IgaAfull_RcsF_RcsDdimer.af2.pdb
    9835 
    9836 Chain information for IgaAfull_RcsF_RcsDdimer.af2.pdb #10 
    9837 --- 
    9838 Chain | Description 
    9839 A | No description available 
    9840 B | No description available 
    9841 C D | No description available 
    9842 
    9843 
    9844 > hide #2 models
    9845 
    9846 > hide #9 models
    9847 
    9848 > matchmaker #10 to #1 & sel
    9849 
    9850 No 'to' model specified 
    9851 
    9852 > select /A:375-711
    9853 
    9854 28594 atoms, 29080 bonds, 3033 residues, 9 models selected 
    9855 
    9856 > matchmaker #10 to #1 & 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 fold_igaa_rcsd_model_0.cif, chain A (#1) with
    9874 IgaAfull_RcsF_RcsDdimer.af2.pdb, chain A (#10), sequence alignment score =
    9875 1733.6 
    9876 RMSD between 185 pruned atom pairs is 0.860 angstroms; (across all 337 pairs:
    9877 7.525) 
    9878 
    9879 
    9880 > show #1 models
    9881 
    9882 > hide #1 models
    9883 
    9884 > select add #10
    9885 
    9886 45158 atoms, 45835 bonds, 4083 residues, 9 models selected 
    9887 
    9888 > color sel & #10 bychain
    9889 
    9890 > show #2 models
    9891 
    9892 > hide #10 models
    9893 
    9894 > show #6 models
    9895 
    9896 > hide #6 models
    9897 
    9898 > show #6 models
    9899 
    9900 > show #7 models
    9901 
    9902 > hide #7 models
    9903 
    9904 > hide #6 models
    9905 
    9906 > show #1 models
    9907 
    9908 > hide #2 models
    9909 
    9910 > show #2 models
    9911 
    9912 > hide #1 models
    9913 
    9914 > show #1 models
    9915 
    9916 > hide #2 models
    9917 
    9918 > select #1/B
    9919 
    9920 7058 atoms, 7176 bonds, 890 residues, 1 model selected 
    9921 
    9922 > color sel medium aquamarine
    9923 
    9924 > select clear
    9925 
    9926 > show #2 models
    9927 
    9928 > show #8 models
    9929 
    9930 > hide #1 models
    9931 
    9932 > hide #2 models
    9933 
    9934 > show #1 models
    9935 
    9936 > show #2 models
    9937 
    9938 > hide #1 models
    9939 
    9940 > hide #2 models
    9941 
    9942 > show #10 models
    9943 
    9944 > hide #8 models
    9945 
    9946 > show #2 models
    9947 
    9948 > show #1 models
    9949 
    9950 > hide #2 models
    9951 
    9952 > hide #10 models
    9953 
    9954 > show #8 models
    9955 
    9956 > save /Users/taic/Library/CloudStorage/OneDrive-
    9957 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsf_rcsdx2/IgaA_RcsF_RcsDx2.AF3vsAF2.cxs
    9958 
    9959 \u2014\u2014\u2014 End of log from Thu Jun 20 14:21:45 2024 \u2014\u2014\u2014
    9960 
    9961 opened ChimeraX session 
    9962 
    9963 > show #2 models
    9964 
    9965 > hide #1 models
    9966 
    9967 > hide #8 models
    9968 
    9969 Drag select of 16 residues 
    9970 
    9971 > select add #2/C:223
    9972 
    9973 121 atoms, 3 bonds, 17 residues, 1 model selected 
    9974 Drag select of 8 residues 
    9975 
    9976 > select add #2/C:187
    9977 
    9978 190 atoms, 10 bonds, 26 residues, 1 model selected 
    9979 
    9980 > select add #2/C:196
    9981 
    9982 201 atoms, 20 bonds, 27 residues, 1 model selected 
    9983 
    9984 > select add #2/C:197
    9985 
    9986 210 atoms, 28 bonds, 28 residues, 1 model selected 
    9987 
    9988 > ui tool show Contacts
    9989 
    9990 > select #2/C:224
    9991 
    9992 10 atoms, 10 bonds, 1 residue, 1 model selected 
    9993 
    9994 > show sel atoms
    9995 
    9996 > select #2/C:225
    9997 
    9998 8 atoms, 7 bonds, 1 residue, 1 model selected 
    9999 
    10000 > show sel atoms
    10001 
    10002 > select #2/B:60
    10003 
    10004 4 atoms, 3 bonds, 1 residue, 1 model selected 
    10005 
    10006 > select clear
    10007 
    10008 > select #2/B:61
    10009 
    10010 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10011 
    10012 > show sel atoms
    10013 
    10014 > select #2/C:225
    10015 
    10016 8 atoms, 7 bonds, 1 residue, 1 model selected 
    10017 
    10018 > select #2/B:60
    10019 
    10020 4 atoms, 3 bonds, 1 residue, 1 model selected 
    10021 
    10022 > show sel atoms
    10023 
    10024 > select #2/B:59
    10025 
    10026 7 atoms, 6 bonds, 1 residue, 1 model selected 
    10027 
    10028 > show sel atoms
    10029 
    10030 > select #2/A:538
    10031 
    10032 8 atoms, 7 bonds, 1 residue, 1 model selected 
    10033 
    10034 > show sel atoms
    10035 
    10036 > select #2/A:540
    10037 
    10038 11 atoms, 10 bonds, 1 residue, 1 model selected 
    10039 
    10040 > show sel atoms
    10041 
    10042 > select #2/C:224
    10043 
    10044 10 atoms, 10 bonds, 1 residue, 1 model selected 
    10045 
    10046 > select #2/C:223
    10047 
    10048 4 atoms, 3 bonds, 1 residue, 1 model selected 
    10049 
    10050 > show sel atoms
    10051 
    10052 > select #2/C:222
    10053 
    10054 7 atoms, 7 bonds, 1 residue, 1 model selected 
    10055 
    10056 > show sel atoms
    10057 
    10058 > select #2/B:57
    10059 
    10060 9 atoms, 8 bonds, 1 residue, 1 model selected 
    10061 
    10062 > show sel atoms
    10063 
    10064 Drag select of 20 residues 
    10065 
    10066 > select /D:411
    10067 
    10068 35 atoms, 30 bonds, 5 residues, 5 models selected 
    10069 
    10070 > select #2/D:411
    10071 
    10072 7 atoms, 6 bonds, 1 residue, 1 model selected 
    10073 
    10074 > show sel atoms
    10075 
    10076 > select /C:411
    10077 
    10078 35 atoms, 30 bonds, 5 residues, 5 models selected 
    10079 
    10080 > show sel & #2 atoms
    10081 
    10082 > select #2/A:98
    10083 
    10084 12 atoms, 12 bonds, 1 residue, 1 model selected 
    10085 
    10086 > show sel atoms
    10087 
    10088 > select #2/A:129
    10089 
    10090 8 atoms, 7 bonds, 1 residue, 1 model selected 
    10091 
    10092 > show sel atoms
    10093 
    10094 > select #2/A:98
    10095 
    10096 12 atoms, 12 bonds, 1 residue, 1 model selected 
    10097 
    10098 > select add #2/A:97
    10099 
    10100 23 atoms, 22 bonds, 2 residues, 1 model selected 
    10101 
    10102 > select add #2/A:96
    10103 
    10104 30 atoms, 28 bonds, 3 residues, 1 model selected 
    10105 
    10106 > show sel atoms
    10107 
    10108 > select clear
    10109 
    10110 > select #2/C:413
    10111 
    10112 8 atoms, 7 bonds, 1 residue, 1 model selected 
    10113 
    10114 > show sel atoms
    10115 
    10116 > select clear
    10117 
    10118 > select #2/C:414
    10119 
    10120 8 atoms, 7 bonds, 1 residue, 1 model selected 
    10121 
    10122 > show sel atoms
    10123 
    10124 > select clear
    10125 
    10126 > select /:94
    10127 
    10128 Expected an objects specifier or a keyword 
    10129 
    10130 > select /A:94
    10131 
    10132 70 atoms, 60 bonds, 10 residues, 10 models selected 
    10133 
    10134 > select #2/A:94
    10135 
    10136 5 atoms, 4 bonds, 1 residue, 1 model selected 
    10137 
    10138 > select #2/A:94
    10139 
    10140 5 atoms, 4 bonds, 1 residue, 1 model selected 
    10141 
    10142 > show sel atoms
    10143 
    10144 > select #2/A:98
    10145 
    10146 12 atoms, 12 bonds, 1 residue, 1 model selected 
    10147 
    10148 > select #2/A:99
    10149 
    10150 4 atoms, 3 bonds, 1 residue, 1 model selected 
    10151 
    10152 > select #2/A:100
    10153 
    10154 8 atoms, 7 bonds, 1 residue, 1 model selected 
    10155 
    10156 > show sel atoms
    10157 
    10158 > select #2/A:101
    10159 
    10160 6 atoms, 5 bonds, 1 residue, 1 model selected 
    10161 
    10162 > show sel atoms
    10163 
    10164 [Repeated 1 time(s)]
    10165 
    10166 > select #2/A:102
    10167 
    10168 7 atoms, 6 bonds, 1 residue, 1 model selected 
    10169 
    10170 > show sel atoms
    10171 
    10172 > select #2/A:103
    10173 
    10174 8 atoms, 7 bonds, 1 residue, 1 model selected 
    10175 
    10176 > show sel atoms
    10177 
    10178 > select #2/A:104
    10179 
    10180 8 atoms, 7 bonds, 1 residue, 1 model selected 
    10181 
    10182 > show sel atoms
    10183 
    10184 > select add #2
    10185 
    10186 20703 atoms, 21090 bonds, 2625 residues, 1 model selected 
    10187 
    10188 > surface sel
    10189 
    10190 > transparency (#!2 & sel) 70
    10191 
    10192 > select subtract #2
    10193 
    10194 4 models selected 
    10195 
    10196 > hide #!2 models
    10197 
    10198 > show #!2 models
    10199 
    10200 > surface hidePatches #2
    10201 
    10202 > select #2/C:411
    10203 
    10204 7 atoms, 6 bonds, 1 residue, 1 model selected 
    10205 
    10206 > color sel red
    10207 
    10208 > select clear
    10209 
    10210 > select add #2
    10211 
    10212 20703 atoms, 21090 bonds, 2625 residues, 1 model selected 
    10213 
    10214 > surface (#!2 & sel)
    10215 
    10216 > save /Users/taic/Library/CloudStorage/OneDrive-
    10217 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsf_rcsdx2/IgaA_RcsF_RcsDx2.AF3vsAF2.cxs
    10218 
    10219 \u2014\u2014\u2014 End of log from Thu Jun 20 17:06:26 2024 \u2014\u2014\u2014
    10220 
    10221 opened ChimeraX session 
    10222 
    10223 > select add #9
    10224 
    10225 41406 atoms, 42180 bonds, 5250 residues, 2 models selected 
    10226 
    10227 > select add #2
    10228 
    10229 41406 atoms, 42180 bonds, 5250 residues, 2 models selected 
    10230 
    10231 > select subtract #2
    10232 
    10233 20703 atoms, 21090 bonds, 2625 residues, 1 model selected 
    10234 
    10235 > hide #!2 models
    10236 
    10237 > show #9 models
    10238 
    10239 > show #5 models
    10240 
    10241 > select add #5
    10242 
    10243 41406 atoms, 42180 bonds, 5250 residues, 2 models selected 
    10244 
    10245 > show #4 models
    10246 
    10247 > select add #4
    10248 
    10249 62109 atoms, 63270 bonds, 7875 residues, 3 models selected 
    10250 
    10251 > show #3 models
    10252 
    10253 > select add #3
    10254 
    10255 82812 atoms, 84360 bonds, 10500 residues, 4 models selected 
    10256 
    10257 > delete atoms sel
    10258 
    10259 > delete bonds sel
    10260 
    10261 > show #1 models
    10262 
    10263 > show #!2 models
    10264 
    10265 > hide #1 models
    10266 
    10267 > show #1 models
    10268 
    10269 > hide #1 models
    10270 
    10271 > hide #!2 models
    10272 
    10273 > show #!2 models
    10274 
    10275 > hide #!2 surfaces
    10276 
    10277 > show #6 models
    10278 
    10279 > hide #!2 models
    10280 
    10281 > show #!2 models
    10282 
    10283 > hide #!2 models
    10284 
    10285 > show #!2 models
    10286 
    10287 > hide #6 models
    10288 
    10289 > show #6 models
    10290 
    10291 > hide #6 models
    10292 
    10293 > show #8 models
    10294 
    10295 > hide #!2 models
    10296 
    10297 > show #!2 models
    10298 
    10299 > hide #!2 models
    10300 
    10301 > show #!2 models
    10302 
    10303 > show #10 models
    10304 
    10305 > hide #8 models
    10306 
    10307 > hide #!2 models
    10308 
    10309 > show #1 models
    10310 
    10311 > select clear
    10312 
    10313 > ui tool show Contacts
    10314 
    10315 > contacts saveFile /Users/taic/Library/CloudStorage/OneDrive-
    10316 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/IgaA_Rcsf_RcsDx2.af3_contacts.txt
    10317 > interModel false intraMol false reveal true
    10318 
    10319 1756 contacts 
    10320 Drag select of 5 residues 
    10321 Drag select of 42 residues 
    10322 
    10323 > hide #10 models
    10324 
    10325 > select clear
    10326 
    10327 > show #!2 models
    10328 
    10329 > hide #1 models
    10330 
    10331 > save /Users/taic/Library/CloudStorage/OneDrive-
    10332 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/IgaA_RcsF_RcsDx2.af3_contacts.cxs
    10333 
    10334 [Repeated 1 time(s)]
    10335 
    10336 \u2014\u2014\u2014 End of log from Mon Jun 24 12:21:56 2024 \u2014\u2014\u2014
    10337 
    10338 opened ChimeraX session 
    10339 
    10340 > open /Users/taic/Library/CloudStorage/OneDrive-
    10341 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2/fold_rcsdx2_model_0.cif
    10342 
    10343 Chain information for fold_rcsdx2_model_0.cif #4 
    10344 --- 
    10345 Chain | Description 
    10346 A B | . 
    10347 
    10348 
    10349 > open /Users/taic/Library/CloudStorage/OneDrive-
    10350 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2/fold_rcsdx2_model_1.cif
    10351 
    10352 Chain information for fold_rcsdx2_model_1.cif #5 
    10353 --- 
    10354 Chain | Description 
    10355 A B | . 
    10356 
    10357 Computing secondary structure 
    10358 [Repeated 1 time(s)]
    10359 
    10360 > open /Users/taic/Library/CloudStorage/OneDrive-
    10361 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2/fold_rcsdx2_model_2.cif
    10362 
    10363 Chain information for fold_rcsdx2_model_2.cif #9 
    10364 --- 
    10365 Chain | Description 
    10366 A B | . 
    10367 
    10368 Computing secondary structure 
    10369 
    10370 > open /Users/taic/Library/CloudStorage/OneDrive-
    10371 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2/fold_rcsdx2_model_3.cif
    10372 
    10373 Chain information for fold_rcsdx2_model_3.cif #11 
    10374 --- 
    10375 Chain | Description 
    10376 A B | . 
    10377 
    10378 Computing secondary structure 
    10379 
    10380 > open /Users/taic/Library/CloudStorage/OneDrive-
    10381 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2/fold_rcsdx2_model_4.cif
    10382 
    10383 Chain information for fold_rcsdx2_model_4.cif #12 
    10384 --- 
    10385 Chain | Description 
    10386 A B | . 
    10387 
    10388 Computing secondary structure 
    10389 
    10390 > hide #!2 models
    10391 
    10392 > hide #3 models
    10393 
    10394 > hide #4 models
    10395 
    10396 > show #4 models
    10397 
    10398 > hide #5 models
    10399 
    10400 > hide #9 models
    10401 
    10402 > hide #11 models
    10403 
    10404 > hide #12 models
    10405 
    10406 > color #4 bychain
    10407 
    10408 > show #5 models
    10409 
    10410 > hide #4 models
    10411 
    10412 > hide #5 models
    10413 
    10414 > show #4 models
    10415 
    10416 > show #!2 models
    10417 
    10418 > hide #4 models
    10419 
    10420 > show #12 models
    10421 
    10422 > hide #!2 models
    10423 
    10424 > show #11 models
    10425 
    10426 > select add #11
    10427 
    10428 14116 atoms, 14352 bonds, 1780 residues, 1 model selected 
    10429 
    10430 > select add #12
    10431 
    10432 28232 atoms, 28704 bonds, 3560 residues, 2 models selected 
    10433 
    10434 > delete atoms sel
    10435 
    10436 > delete bonds sel
    10437 
    10438 > show #5 models
    10439 
    10440 > select add #5
    10441 
    10442 14116 atoms, 14352 bonds, 1780 residues, 1 model selected 
    10443 
    10444 > delete atoms sel
    10445 
    10446 > delete bonds sel
    10447 
    10448 > show #9 models
    10449 
    10450 > select add #9
    10451 
    10452 14116 atoms, 14352 bonds, 1780 residues, 1 model selected 
    10453 
    10454 > delete atoms sel
    10455 
    10456 > delete bonds sel
    10457 
    10458 > show #4 models
    10459 
    10460 > hide #4 models
    10461 
    10462 > show #!2 models
    10463 
    10464 > hide #!2 models
    10465 
    10466 > show #1 models
    10467 
    10468 > open /Users/taic/Library/CloudStorage/OneDrive-
    10469 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_1.json
    10470 
    10471 Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
    10472 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_1.json: 
    10473 Opening an AlphaFold PAE file requires first opening the predicted atomic
    10474 model. Did not find an open atomic model from the same directory. If the
    10475 atomic model is already open choose it using menu 
    10476 
    10477 Tools / Structure Prediction / AlphaFold Error Plot 
    10478 
    10479 or use the open command structure option, for example 
    10480 
    10481 open /Users/taic/Library/CloudStorage/OneDrive-
    10482 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_1.json
    10483 structure #1 
    10484 
    10485 If you are trying to open a JSON file that is not AlphaFold PAE data then you
    10486 need to specify the specific JSON format such as 
    10487 
    10488 open mole_channels.json format mole 
    10489 
    10490 > open /Users/taic/Library/CloudStorage/OneDrive-
    10491 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_2.json
    10492 
    10493 Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
    10494 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_2.json: 
    10495 Opening an AlphaFold PAE file requires first opening the predicted atomic
    10496 model. Did not find an open atomic model from the same directory. If the
    10497 atomic model is already open choose it using menu 
    10498 
    10499 Tools / Structure Prediction / AlphaFold Error Plot 
    10500 
    10501 or use the open command structure option, for example 
    10502 
    10503 open /Users/taic/Library/CloudStorage/OneDrive-
    10504 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_2.json
    10505 structure #1 
    10506 
    10507 If you are trying to open a JSON file that is not AlphaFold PAE data then you
    10508 need to specify the specific JSON format such as 
    10509 
    10510 open mole_channels.json format mole 
    10511 
    10512 > open /Users/taic/Library/CloudStorage/OneDrive-
    10513 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_3.json
    10514 
    10515 Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
    10516 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_3.json: 
    10517 Opening an AlphaFold PAE file requires first opening the predicted atomic
    10518 model. Did not find an open atomic model from the same directory. If the
    10519 atomic model is already open choose it using menu 
    10520 
    10521 Tools / Structure Prediction / AlphaFold Error Plot 
    10522 
    10523 or use the open command structure option, for example 
    10524 
    10525 open /Users/taic/Library/CloudStorage/OneDrive-
    10526 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_3.json
    10527 structure #1 
    10528 
    10529 If you are trying to open a JSON file that is not AlphaFold PAE data then you
    10530 need to specify the specific JSON format such as 
    10531 
    10532 open mole_channels.json format mole 
    10533 
    10534 > open /Users/taic/Library/CloudStorage/OneDrive-
    10535 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_4.json
    10536 
    10537 Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
    10538 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_4.json: 
    10539 Opening an AlphaFold PAE file requires first opening the predicted atomic
    10540 model. Did not find an open atomic model from the same directory. If the
    10541 atomic model is already open choose it using menu 
    10542 
    10543 Tools / Structure Prediction / AlphaFold Error Plot 
    10544 
    10545 or use the open command structure option, for example 
    10546 
    10547 open /Users/taic/Library/CloudStorage/OneDrive-
    10548 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_4.json
    10549 structure #1 
    10550 
    10551 If you are trying to open a JSON file that is not AlphaFold PAE data then you
    10552 need to specify the specific JSON format such as 
    10553 
    10554 open mole_channels.json format mole 
    10555 
    10556 > open /Users/taic/Library/CloudStorage/OneDrive-
    10557 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_0.json
    10558 
    10559 Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
    10560 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_0.json: 
    10561 Opening an AlphaFold PAE file requires first opening the predicted atomic
    10562 model. Did not find an open atomic model from the same directory. If the
    10563 atomic model is already open choose it using menu 
    10564 
    10565 Tools / Structure Prediction / AlphaFold Error Plot 
    10566 
    10567 or use the open command structure option, for example 
    10568 
    10569 open /Users/taic/Library/CloudStorage/OneDrive-
    10570 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_0.json
    10571 structure #1 
    10572 
    10573 If you are trying to open a JSON file that is not AlphaFold PAE data then you
    10574 need to specify the specific JSON format such as 
    10575 
    10576 open mole_channels.json format mole 
    10577 
    10578 > open /Users/taic/Library/CloudStorage/OneDrive-
    10579 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_4.json
    10580 
    10581 Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
    10582 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_4.json: 
    10583 Opening an AlphaFold PAE file requires first opening the predicted atomic
    10584 model. Did not find an open atomic model from the same directory. If the
    10585 atomic model is already open choose it using menu 
    10586 
    10587 Tools / Structure Prediction / AlphaFold Error Plot 
    10588 
    10589 or use the open command structure option, for example 
    10590 
    10591 open /Users/taic/Library/CloudStorage/OneDrive-
    10592 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_4.json
    10593 structure #1 
    10594 
    10595 If you are trying to open a JSON file that is not AlphaFold PAE data then you
    10596 need to specify the specific JSON format such as 
    10597 
    10598 open mole_channels.json format mole 
    10599 
    10600 > open /Users/taic/Library/CloudStorage/OneDrive-
    10601 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_3.json
    10602 
    10603 Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
    10604 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_3.json: 
    10605 Opening an AlphaFold PAE file requires first opening the predicted atomic
    10606 model. Did not find an open atomic model from the same directory. If the
    10607 atomic model is already open choose it using menu 
    10608 
    10609 Tools / Structure Prediction / AlphaFold Error Plot 
    10610 
    10611 or use the open command structure option, for example 
    10612 
    10613 open /Users/taic/Library/CloudStorage/OneDrive-
    10614 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_3.json
    10615 structure #1 
    10616 
    10617 If you are trying to open a JSON file that is not AlphaFold PAE data then you
    10618 need to specify the specific JSON format such as 
    10619 
    10620 open mole_channels.json format mole 
    10621 
    10622 > open /Users/taic/Library/CloudStorage/OneDrive-
    10623 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_2.json
    10624 
    10625 Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
    10626 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_2.json: 
    10627 Opening an AlphaFold PAE file requires first opening the predicted atomic
    10628 model. Did not find an open atomic model from the same directory. If the
    10629 atomic model is already open choose it using menu 
    10630 
    10631 Tools / Structure Prediction / AlphaFold Error Plot 
    10632 
    10633 or use the open command structure option, for example 
    10634 
    10635 open /Users/taic/Library/CloudStorage/OneDrive-
    10636 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_2.json
    10637 structure #1 
    10638 
    10639 If you are trying to open a JSON file that is not AlphaFold PAE data then you
    10640 need to specify the specific JSON format such as 
    10641 
    10642 open mole_channels.json format mole 
    10643 
    10644 > open /Users/taic/Library/CloudStorage/OneDrive-
    10645 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_1.json
    10646 
    10647 Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
    10648 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_1.json: 
    10649 Opening an AlphaFold PAE file requires first opening the predicted atomic
    10650 model. Did not find an open atomic model from the same directory. If the
    10651 atomic model is already open choose it using menu 
    10652 
    10653 Tools / Structure Prediction / AlphaFold Error Plot 
    10654 
    10655 or use the open command structure option, for example 
    10656 
    10657 open /Users/taic/Library/CloudStorage/OneDrive-
    10658 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_1.json
    10659 structure #1 
    10660 
    10661 If you are trying to open a JSON file that is not AlphaFold PAE data then you
    10662 need to specify the specific JSON format such as 
    10663 
    10664 open mole_channels.json format mole 
    10665 
    10666 > open /Users/taic/Library/CloudStorage/OneDrive-
    10667 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_0.json
    10668 
    10669 Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
    10670 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_0.json: 
    10671 Opening an AlphaFold PAE file requires first opening the predicted atomic
    10672 model. Did not find an open atomic model from the same directory. If the
    10673 atomic model is already open choose it using menu 
    10674 
    10675 Tools / Structure Prediction / AlphaFold Error Plot 
    10676 
    10677 or use the open command structure option, for example 
    10678 
    10679 open /Users/taic/Library/CloudStorage/OneDrive-
    10680 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_0.json
    10681 structure #1 
    10682 
    10683 If you are trying to open a JSON file that is not AlphaFold PAE data then you
    10684 need to specify the specific JSON format such as 
    10685 
    10686 open mole_channels.json format mole 
    10687 
    10688 > open /Users/taic/Library/CloudStorage/OneDrive-
    10689 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_4.json
    10690 
    10691 Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
    10692 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_4.json: 
    10693 Opening an AlphaFold PAE file requires first opening the predicted atomic
    10694 model. Did not find an open atomic model from the same directory. If the
    10695 atomic model is already open choose it using menu 
    10696 
    10697 Tools / Structure Prediction / AlphaFold Error Plot 
    10698 
    10699 or use the open command structure option, for example 
    10700 
    10701 open /Users/taic/Library/CloudStorage/OneDrive-
    10702 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_4.json
    10703 structure #1 
    10704 
    10705 If you are trying to open a JSON file that is not AlphaFold PAE data then you
    10706 need to specify the specific JSON format such as 
    10707 
    10708 open mole_channels.json format mole 
    10709 
    10710 > open /Users/taic/Library/CloudStorage/OneDrive-
    10711 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_3.json
    10712 
    10713 Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
    10714 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_3.json: 
    10715 Opening an AlphaFold PAE file requires first opening the predicted atomic
    10716 model. Did not find an open atomic model from the same directory. If the
    10717 atomic model is already open choose it using menu 
    10718 
    10719 Tools / Structure Prediction / AlphaFold Error Plot 
    10720 
    10721 or use the open command structure option, for example 
    10722 
    10723 open /Users/taic/Library/CloudStorage/OneDrive-
    10724 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_3.json
    10725 structure #1 
    10726 
    10727 If you are trying to open a JSON file that is not AlphaFold PAE data then you
    10728 need to specify the specific JSON format such as 
    10729 
    10730 open mole_channels.json format mole 
    10731 
    10732 > open /Users/taic/Library/CloudStorage/OneDrive-
    10733 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_2.json
    10734 
    10735 Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
    10736 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_2.json: 
    10737 Opening an AlphaFold PAE file requires first opening the predicted atomic
    10738 model. Did not find an open atomic model from the same directory. If the
    10739 atomic model is already open choose it using menu 
    10740 
    10741 Tools / Structure Prediction / AlphaFold Error Plot 
    10742 
    10743 or use the open command structure option, for example 
    10744 
    10745 open /Users/taic/Library/CloudStorage/OneDrive-
    10746 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_2.json
    10747 structure #1 
    10748 
    10749 If you are trying to open a JSON file that is not AlphaFold PAE data then you
    10750 need to specify the specific JSON format such as 
    10751 
    10752 open mole_channels.json format mole 
    10753 
    10754 > open /Users/taic/Library/CloudStorage/OneDrive-
    10755 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_1.json
    10756 
    10757 Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
    10758 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_1.json: 
    10759 Opening an AlphaFold PAE file requires first opening the predicted atomic
    10760 model. Did not find an open atomic model from the same directory. If the
    10761 atomic model is already open choose it using menu 
    10762 
    10763 Tools / Structure Prediction / AlphaFold Error Plot 
    10764 
    10765 or use the open command structure option, for example 
    10766 
    10767 open /Users/taic/Library/CloudStorage/OneDrive-
    10768 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_1.json
    10769 structure #1 
    10770 
    10771 If you are trying to open a JSON file that is not AlphaFold PAE data then you
    10772 need to specify the specific JSON format such as 
    10773 
    10774 open mole_channels.json format mole 
    10775 
    10776 > open /Users/taic/Library/CloudStorage/OneDrive-
    10777 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_0.json
    10778 
    10779 Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
    10780 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_0.json: 
    10781 Opening an AlphaFold PAE file requires first opening the predicted atomic
    10782 model. Did not find an open atomic model from the same directory. If the
    10783 atomic model is already open choose it using menu 
    10784 
    10785 Tools / Structure Prediction / AlphaFold Error Plot 
    10786 
    10787 or use the open command structure option, for example 
    10788 
    10789 open /Users/taic/Library/CloudStorage/OneDrive-
    10790 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_full_data_0.json
    10791 structure #1 
    10792 
    10793 If you are trying to open a JSON file that is not AlphaFold PAE data then you
    10794 need to specify the specific JSON format such as 
    10795 
    10796 open mole_channels.json format mole 
    10797 
    10798 > open /Users/taic/Library/CloudStorage/OneDrive-
    10799 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsdx2_rcsf/fold_igaa_rcsdx2_rcsf_full_data_0.json
    10800 > /Users/taic/Library/CloudStorage/OneDrive-
    10801 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsdx2_rcsf/fold_igaa_rcsdx2_rcsf_full_data_1.json
    10802 > /Users/taic/Library/CloudStorage/OneDrive-
    10803 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsdx2_rcsf/fold_igaa_rcsdx2_rcsf_full_data_2.json
    10804 > /Users/taic/Library/CloudStorage/OneDrive-
    10805 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsdx2_rcsf/fold_igaa_rcsdx2_rcsf_full_data_3.json
    10806 > /Users/taic/Library/CloudStorage/OneDrive-
    10807 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsdx2_rcsf/fold_igaa_rcsdx2_rcsf_full_data_4.json
    10808 
    10809 Opening an AlphaFold PAE file requires first opening the predicted atomic
    10810 model. Did not find an open atomic model from the same directory. If the
    10811 atomic model is already open choose it using menu 
    10812 
    10813 Tools / Structure Prediction / AlphaFold Error Plot 
    10814 
    10815 or use the open command structure option, for example 
    10816 
    10817 open /Users/taic/Library/CloudStorage/OneDrive-
    10818 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsdx2_rcsf/fold_igaa_rcsdx2_rcsf_full_data_0.json
    10819 structure #1 
    10820 
    10821 If you are trying to open a JSON file that is not AlphaFold PAE data then you
    10822 need to specify the specific JSON format such as 
    10823 
    10824 open mole_channels.json format mole 
    10825 
    10826 > open /Users/taic/Library/CloudStorage/OneDrive-
    10827 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsdx2_rcsf/fold_igaa_rcsdx2_rcsf_full_data_0.json
    10828 
    10829 Opening an AlphaFold PAE file requires first opening the predicted atomic
    10830 model. Did not find an open atomic model from the same directory. If the
    10831 atomic model is already open choose it using menu 
    10832 
    10833 Tools / Structure Prediction / AlphaFold Error Plot 
    10834 
    10835 or use the open command structure option, for example 
    10836 
    10837 open /Users/taic/Library/CloudStorage/OneDrive-
    10838 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsdx2_rcsf/fold_igaa_rcsdx2_rcsf_full_data_0.json
    10839 structure #1 
    10840 
    10841 If you are trying to open a JSON file that is not AlphaFold PAE data then you
    10842 need to specify the specific JSON format such as 
    10843 
    10844 open mole_channels.json format mole 
    10845 
    10846 > open /Users/taic/Library/CloudStorage/OneDrive-
    10847 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_model_0.cif
    10848 
    10849 Chain information for fold_igaa_rcscx2_rcsdx2_model_0.cif #5 
    10850 --- 
    10851 Chain | Description 
    10852 A | . 
    10853 B C | . 
    10854 D E | . 
    10855 
    10856 
    10857 > hide #1,5 surfaces
    10858 
    10859 [Repeated 1 time(s)]
    10860 
    10861 > show #1,5 cartoons
    10862 
    10863 Computing secondary structure 
    10864 
    10865 > hide #1,5 surfaces
    10866 
    10867 > select add #5
    10868 
    10869 34679 atoms, 35323 bonds, 4389 residues, 1 model selected 
    10870 
    10871 > hide sel surfaces
    10872 
    10873 > show sel cartoons
    10874 
    10875 > style sel stick
    10876 
    10877 Changed 34679 atom styles 
    10878 
    10879 > hide sel atoms
    10880 
    10881 > select clear
    10882 
    10883 > hide #1 models
    10884 
    10885 > color #5 bychain
    10886 
    10887 > open /Users/taic/Library/CloudStorage/OneDrive-
    10888 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_model_1.cif
    10889 
    10890 Chain information for fold_igaa_rcscx2_rcsdx2_model_1.cif #9 
    10891 --- 
    10892 Chain | Description 
    10893 A | . 
    10894 B C | . 
    10895 D E | . 
    10896 
    10897 
    10898 > open /Users/taic/Library/CloudStorage/OneDrive-
    10899 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_model_4.cif
    10900 
    10901 Chain information for fold_igaa_rcscx2_rcsdx2_model_4.cif #11 
    10902 --- 
    10903 Chain | Description 
    10904 A | . 
    10905 B C | . 
    10906 D E | . 
    10907 
    10908 
    10909 > open /Users/taic/Library/CloudStorage/OneDrive-
    10910 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_model_2.cif
    10911 
    10912 Chain information for fold_igaa_rcscx2_rcsdx2_model_2.cif #12 
    10913 --- 
    10914 Chain | Description 
    10915 A | . 
    10916 B C | . 
    10917 D E | . 
    10918 
    10919 
    10920 > show #5,9,11-12 cartoons
    10921 
    10922 Computing secondary structure 
    10923 [Repeated 2 time(s)]
    10924 
    10925 > open /Users/taic/Library/CloudStorage/OneDrive-
    10926 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcscx2_rcsdx2/fold_igaa_rcscx2_rcsdx2_model_3.cif
    10927 
    10928 Chain information for fold_igaa_rcscx2_rcsdx2_model_3.cif #13 
    10929 --- 
    10930 Chain | Description 
    10931 A | . 
    10932 B C | . 
    10933 D E | . 
    10934 
    10935 
    10936 > hide #5,9,11-13 atoms
    10937 
    10938 > hide #5 models
    10939 
    10940 > hide #9 models
    10941 
    10942 > show #9 models
    10943 
    10944 > hide #11 models
    10945 
    10946 > hide #12 models
    10947 
    10948 > hide #13 models
    10949 
    10950 > color #9 bychain
    10951 
    10952 > show #11 models
    10953 
    10954 > hide #9 models
    10955 
    10956 > color #11 bychain
    10957 
    10958 > show #12 models
    10959 
    10960 > hide #11 models
    10961 
    10962 > color #12 bychain
    10963 
    10964 > select add #12
    10965 
    10966 34679 atoms, 35323 bonds, 4389 residues, 1 model selected 
    10967 
    10968 > delete atoms sel
    10969 
    10970 > delete bonds sel
    10971 
    10972 > show #13 models
    10973 
    10974 > select add #13
    10975 
    10976 34679 atoms, 35323 bonds, 4389 residues, 1 model selected 
    10977 
    10978 > show #11 models
    10979 
    10980 > hide #13 models
    10981 
    10982 > select subtract #13
    10983 
    10984 Nothing selected 
    10985 
    10986 > show #13 models
    10987 
    10988 > hide #11 models
    10989 
    10990 > select add #13
    10991 
    10992 34679 atoms, 35323 bonds, 4389 residues, 1 model selected 
    10993 
    10994 > delete atoms sel
    10995 
    10996 > delete bonds sel
    10997 
    10998 > show #11 models
    10999 
    11000 > show #9 models
    11001 
    11002 > show #10 models
    11003 
    11004 > hide #9 models
    11005 
    11006 > hide #11 models
    11007 
    11008 > show #11 models
    11009 
    11010 > hide #10 models
    11011 
    11012 > show #!2 models
    11013 
    11014 > hide #11 models
    11015 
    11016 > show #10 models
    11017 
    11018 > hide #!2 models
    11019 
    11020 > show #9 models
    11021 
    11022 > hide #10 models
    11023 
    11024 > show #1 models
    11025 
    11026 > show #!2 models
    11027 
    11028 > hide #1 models
    11029 
    11030 > hide #9 models
    11031 
    11032 > show #9 models
    11033 
    11034 > hide #!2 models
    11035 
    11036 > show #4 models
    11037 
    11038 > hide #9 models
    11039 
    11040 > select add #4
    11041 
    11042 14116 atoms, 14352 bonds, 1780 residues, 1 model selected 
    11043 
    11044 > delete atoms sel
    11045 
    11046 > delete bonds sel
    11047 
    11048 > show #7 models
    11049 
    11050 > show #8 models
    11051 
    11052 > hide #8 models
    11053 
    11054 > hide #7 models
    11055 
    11056 > open /Users/taic/Library/CloudStorage/OneDrive-
    11057 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2/fold_rcsdx2_full_data_0.json
    11058 
    11059 Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
    11060 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2/fold_rcsdx2_full_data_0.json: 
    11061 Opening an AlphaFold PAE file requires first opening the predicted atomic
    11062 model. Did not find an open atomic model from the same directory. If the
    11063 atomic model is already open choose it using menu 
    11064 
    11065 Tools / Structure Prediction / AlphaFold Error Plot 
    11066 
    11067 or use the open command structure option, for example 
    11068 
    11069 open /Users/taic/Library/CloudStorage/OneDrive-
    11070 NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2/fold_rcsdx2_full_data_0.json
    11071 structure #1 
    11072 
    11073 If you are trying to open a JSON file that is not AlphaFold PAE data then you
    11074 need to specify the specific JSON format such as 
    11075 
    11076 open mole_channels.json format mole 
    11077 
    11078 > open /Users/taic/Library/CloudStorage/OneDrive-
    11079 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2_rcscx2/fold_rcsdx2_rcscx2_model_0.cif
    11080 
    11081 Chain information for fold_rcsdx2_rcscx2_model_0.cif #4 
    11082 --- 
    11083 Chain | Description 
    11084 A B | . 
    11085 C D | . 
    11086 
    11087 Computing secondary structure 
    11088 
    11089 > color #4 bychain
    11090 
    11091 > open /Users/taic/Library/CloudStorage/OneDrive-
    11092 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2_rcscx2/fold_rcsdx2_rcscx2_model_1.cif
    11093 
    11094 Chain information for fold_rcsdx2_rcscx2_model_1.cif #12 
    11095 --- 
    11096 Chain | Description 
    11097 A B | . 
    11098 C D | . 
    11099 
    11100 
    11101 > open /Users/taic/Library/CloudStorage/OneDrive-
    11102 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2_rcscx2/fold_rcsdx2_rcscx2_model_3.cif
    11103 
    11104 Chain information for fold_rcsdx2_rcscx2_model_3.cif #13 
    11105 --- 
    11106 Chain | Description 
    11107 A B | . 
    11108 C D | . 
    11109 
    11110 
    11111 > open /Users/taic/Library/CloudStorage/OneDrive-
    11112 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2_rcscx2/fold_rcsdx2_rcscx2_model_4.cif
    11113 
    11114 Chain information for fold_rcsdx2_rcscx2_model_4.cif #14 
    11115 --- 
    11116 Chain | Description 
    11117 A B | . 
    11118 C D | . 
    11119 
    11120 Computing secondary structure 
    11121 [Repeated 2 time(s)]
    11122 
    11123 > open /Users/taic/Library/CloudStorage/OneDrive-
    11124 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2_rcscx2/fold_rcsdx2_rcscx2_model_2.cif
    11125 
    11126 Chain information for fold_rcsdx2_rcscx2_model_2.cif #15 
    11127 --- 
    11128 Chain | Description 
    11129 A B | . 
    11130 C D | . 
    11131 
    11132 Computing secondary structure 
    11133 
    11134 > hide #4 models
    11135 
    11136 > hide #13 models
    11137 
    11138 > hide #14 models
    11139 
    11140 > hide #15 models
    11141 
    11142 > color #12 bychain
    11143 
    11144 > hide #12 models
    11145 
    11146 > show #13 models
    11147 
    11148 > color #13 bychain
    11149 
    11150 > show #14 models
    11151 
    11152 > hide #13 models
    11153 
    11154 > color #14 bychain
    11155 
    11156 > show #15 models
    11157 
    11158 > hide #14 models
    11159 
    11160 > color #15 bychain
    11161 
    11162 > show #14 models
    11163 
    11164 > hide #15 models
    11165 
    11166 > show #4 models
    11167 
    11168 > hide #14 models
    11169 
    11170 > show #12 models
    11171 
    11172 > hide #12 models
    11173 
    11174 > show #12 models
    11175 
    11176 > hide #4 models
    11177 
    11178 > show #13 models
    11179 
    11180 > hide #12 models
    11181 
    11182 > show #14 models
    11183 
    11184 > hide #13 models
    11185 
    11186 > show #15 models
    11187 
    11188 > hide #14 models
    11189 
    11190 > hide #15 models
    11191 
    11192 > show #15 models
    11193 
    11194 > show #4 models
    11195 
    11196 > hide #15 models
    11197 
    11198 > show #12 models
    11199 
    11200 > hide #4 models
    11201 
    11202 > show #9 models
    11203 
    11204 > hide #12 models
    11205 
    11206 > ui tool show "Show Sequence Viewer"
    11207 
    11208 > sequence chain #9/D
    11209 
    11210 Alignment identifier is 9/D 
    11211 
    11212 > select
    11213 > #9/D:91-96,99-103,110-114,144-148,155-159,197-199,203-205,210-219,227-234,248-252,270-274,278-285,290-297,367-372,377-381,407-412,415-423,430-437,525-528,550-555,562-565,589-596,603-610,657-663,667-675,695-699,719-721,734-737,747-751,757-761,764-768
    11214 
    11215 1522 atoms, 1520 bonds, 183 residues, 1 model selected 
    11216 
    11217 > hide #9 models
    11218 
    11219 > show #7 models
    11220 
    11221 > show #1 models
    11222 
    11223 > hide #7 models
    11224 
    11225 > color #1 bychain
    11226 
    11227 > select
    11228 > #1/B#2/C/D#4/A/B#5/D/E#7/B/C#9/D/E#10/C/D#11/D/E#12/A/B#13/A/B#14/A/B#15/A/B
    11229 
    11230 146942 atoms, 149325 bonds, 767 pseudobonds, 17723 residues, 13 models
    11231 selected 
    11232 
    11233 > rainbow sel & #1
    11234 
    11235 > select clear
    11236 
    11237 > show #4 models
    11238 
    11239 > hide #4 models
    11240 
    11241 > select
    11242 > #1/B#2/C/D#4/A/B#5/D/E#7/B/C#9/D/E#10/C/D#11/D/E#12/A/B#13/A/B#14/A/B#15/A/B
    11243 
    11244 146942 atoms, 149325 bonds, 767 pseudobonds, 17723 residues, 13 models
    11245 selected 
    11246 
    11247 > ui tool show Matchmaker
    11248 
    11249 > matchmaker #4-15#!2 & sel to #1 & sel
    11250 
    11251 Computing secondary structure 
    11252 [Repeated 7 time(s)]  Parameters 
    11253 --- 
    11254 Chain pairing | bb 
    11255 Alignment algorithm | Needleman-Wunsch 
    11256 Similarity matrix | BLOSUM-62 
    11257 SS fraction | 0.3 
    11258 Gap open (HH/SS/other) | 18/18/6 
    11259 Gap extend | 1 
    11260 SS matrix |  |  | H | S | O 
    11261 ---|---|---|--- 
    11262 H | 6 | -9 | -6 
    11263 S |  | 6 | -6 
    11264 O |  |  | 4 
    11265 Iteration cutoff | 2 
    11266 
    11267 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with IgaA_RcsD.dm.af2.pdb,
    11268 chain B (#7), sequence alignment score = 1372.7 
    11269 RMSD between 238 pruned atom pairs is 0.815 angstroms; (across all 271 pairs:
    11270 1.791) 
    11271 
    11272 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    11273 fold_igaa_rcsf_rcsdx2_model_0.cif, chain C (#2), sequence alignment score =
    11274 4552.2 
    11275 RMSD between 10 pruned atom pairs is 1.265 angstroms; (across all 890 pairs:
    11276 23.121) 
    11277 
    11278 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    11279 IgaAfull_RcsF_RcsDdimer.af2.pdb, chain D (#10), sequence alignment score =
    11280 1374.5 
    11281 RMSD between 252 pruned atom pairs is 0.841 angstroms; (across all 271 pairs:
    11282 1.531) 
    11283 
    11284 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    11285 fold_igaa_rcscx2_rcsdx2_model_0.cif, chain E (#5), sequence alignment score =
    11286 4504.2 
    11287 RMSD between 31 pruned atom pairs is 1.322 angstroms; (across all 890 pairs:
    11288 19.956) 
    11289 
    11290 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    11291 fold_igaa_rcscx2_rcsdx2_model_1.cif, chain D (#9), sequence alignment score =
    11292 4506.6 
    11293 RMSD between 117 pruned atom pairs is 0.564 angstroms; (across all 890 pairs:
    11294 45.059) 
    11295 
    11296 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    11297 fold_igaa_rcscx2_rcsdx2_model_4.cif, chain D (#11), sequence alignment score =
    11298 4461.6 
    11299 RMSD between 67 pruned atom pairs is 0.810 angstroms; (across all 890 pairs:
    11300 37.620) 
    11301 
    11302 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    11303 fold_rcsdx2_rcscx2_model_0.cif, chain B (#4), sequence alignment score =
    11304 4539.6 
    11305 RMSD between 38 pruned atom pairs is 1.321 angstroms; (across all 890 pairs:
    11306 22.279) 
    11307 
    11308 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    11309 fold_rcsdx2_rcscx2_model_1.cif, chain B (#12), sequence alignment score =
    11310 4538.4 
    11311 RMSD between 238 pruned atom pairs is 0.699 angstroms; (across all 890 pairs:
    11312 33.986) 
    11313 
    11314 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    11315 fold_rcsdx2_rcscx2_model_3.cif, chain A (#13), sequence alignment score =
    11316 4543.2 
    11317 RMSD between 270 pruned atom pairs is 0.662 angstroms; (across all 890 pairs:
    11318 51.173) 
    11319 
    11320 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    11321 fold_rcsdx2_rcscx2_model_4.cif, chain A (#14), sequence alignment score =
    11322 4535.4 
    11323 RMSD between 307 pruned atom pairs is 0.693 angstroms; (across all 890 pairs:
    11324 25.202) 
    11325 
    11326 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    11327 fold_rcsdx2_rcscx2_model_2.cif, chain B (#15), sequence alignment score =
    11328 4532.4 
    11329 RMSD between 64 pruned atom pairs is 0.846 angstroms; (across all 890 pairs:
    11330 32.264) 
    11331 
    11332 
    11333 > matchmaker #4-15#!2 & sel to #1 & sel
    11334 
    11335 Computing secondary structure 
    11336 [Repeated 7 time(s)]  Parameters 
    11337 --- 
    11338 Chain pairing | bb 
    11339 Alignment algorithm | Needleman-Wunsch 
    11340 Similarity matrix | BLOSUM-62 
    11341 SS fraction | 0.3 
    11342 Gap open (HH/SS/other) | 18/18/6 
    11343 Gap extend | 1 
    11344 SS matrix |  |  | H | S | O 
    11345 ---|---|---|--- 
    11346 H | 6 | -9 | -6 
    11347 S |  | 6 | -6 
    11348 O |  |  | 4 
    11349 Iteration cutoff | 2 
    11350 
    11351 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with IgaA_RcsD.dm.af2.pdb,
    11352 chain B (#7), sequence alignment score = 1372.7 
    11353 RMSD between 238 pruned atom pairs is 0.815 angstroms; (across all 271 pairs:
    11354 1.791) 
    11355 
    11356 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    11357 fold_igaa_rcsf_rcsdx2_model_0.cif, chain C (#2), sequence alignment score =
    11358 4552.2 
    11359 RMSD between 10 pruned atom pairs is 1.265 angstroms; (across all 890 pairs:
    11360 23.121) 
    11361 
    11362 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    11363 IgaAfull_RcsF_RcsDdimer.af2.pdb, chain D (#10), sequence alignment score =
    11364 1374.5 
    11365 RMSD between 252 pruned atom pairs is 0.841 angstroms; (across all 271 pairs:
    11366 1.531) 
    11367 
    11368 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    11369 fold_igaa_rcscx2_rcsdx2_model_0.cif, chain E (#5), sequence alignment score =
    11370 4504.2 
    11371 RMSD between 31 pruned atom pairs is 1.322 angstroms; (across all 890 pairs:
    11372 19.956) 
    11373 
    11374 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    11375 fold_igaa_rcscx2_rcsdx2_model_1.cif, chain D (#9), sequence alignment score =
    11376 4506.6 
    11377 RMSD between 117 pruned atom pairs is 0.564 angstroms; (across all 890 pairs:
    11378 45.059) 
    11379 
    11380 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    11381 fold_igaa_rcscx2_rcsdx2_model_4.cif, chain D (#11), sequence alignment score =
    11382 4461.6 
    11383 RMSD between 67 pruned atom pairs is 0.810 angstroms; (across all 890 pairs:
    11384 37.620) 
    11385 
    11386 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    11387 fold_rcsdx2_rcscx2_model_0.cif, chain B (#4), sequence alignment score =
    11388 4539.6 
    11389 RMSD between 38 pruned atom pairs is 1.321 angstroms; (across all 890 pairs:
    11390 22.279) 
    11391 
    11392 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    11393 fold_rcsdx2_rcscx2_model_1.cif, chain B (#12), sequence alignment score =
    11394 4538.4 
    11395 RMSD between 238 pruned atom pairs is 0.699 angstroms; (across all 890 pairs:
    11396 33.986) 
    11397 
    11398 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    11399 fold_rcsdx2_rcscx2_model_3.cif, chain A (#13), sequence alignment score =
    11400 4543.2 
    11401 RMSD between 270 pruned atom pairs is 0.662 angstroms; (across all 890 pairs:
    11402 51.173) 
    11403 
    11404 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    11405 fold_rcsdx2_rcscx2_model_4.cif, chain A (#14), sequence alignment score =
    11406 4535.4 
    11407 RMSD between 307 pruned atom pairs is 0.693 angstroms; (across all 890 pairs:
    11408 25.202) 
    11409 
    11410 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    11411 fold_rcsdx2_rcscx2_model_2.cif, chain B (#15), sequence alignment score =
    11412 4532.4 
    11413 RMSD between 64 pruned atom pairs is 0.846 angstroms; (across all 890 pairs:
    11414 32.264) 
    11415 
    11416 
    11417 > matchmaker #4-15#!2 & sel to #1 & sel
    11418 
    11419 Computing secondary structure 
    11420 [Repeated 7 time(s)]  Parameters 
    11421 --- 
    11422 Chain pairing | bb 
    11423 Alignment algorithm | Needleman-Wunsch 
    11424 Similarity matrix | BLOSUM-62 
    11425 SS fraction | 0.3 
    11426 Gap open (HH/SS/other) | 18/18/6 
    11427 Gap extend | 1 
    11428 SS matrix |  |  | H | S | O 
    11429 ---|---|---|--- 
    11430 H | 6 | -9 | -6 
    11431 S |  | 6 | -6 
    11432 O |  |  | 4 
    11433 Iteration cutoff | 2 
    11434 
    11435 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with IgaA_RcsD.dm.af2.pdb,
    11436 chain B (#7), sequence alignment score = 1372.7 
    11437 RMSD between 238 pruned atom pairs is 0.815 angstroms; (across all 271 pairs:
    11438 1.791) 
    11439 
    11440 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    11441 fold_igaa_rcsf_rcsdx2_model_0.cif, chain C (#2), sequence alignment score =
    11442 4552.2 
    11443 RMSD between 10 pruned atom pairs is 1.265 angstroms; (across all 890 pairs:
    11444 23.121) 
    11445 
    11446 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    11447 IgaAfull_RcsF_RcsDdimer.af2.pdb, chain D (#10), sequence alignment score =
    11448 1374.5 
    11449 RMSD between 252 pruned atom pairs is 0.841 angstroms; (across all 271 pairs:
    11450 1.531) 
    11451 
    11452 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    11453 fold_igaa_rcscx2_rcsdx2_model_0.cif, chain E (#5), sequence alignment score =
    11454 4504.2 
    11455 RMSD between 31 pruned atom pairs is 1.322 angstroms; (across all 890 pairs:
    11456 19.956) 
    11457 
    11458 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    11459 fold_igaa_rcscx2_rcsdx2_model_1.cif, chain D (#9), sequence alignment score =
    11460 4506.6 
    11461 RMSD between 117 pruned atom pairs is 0.564 angstroms; (across all 890 pairs:
    11462 45.059) 
    11463 
    11464 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    11465 fold_igaa_rcscx2_rcsdx2_model_4.cif, chain D (#11), sequence alignment score =
    11466 4461.6 
    11467 RMSD between 67 pruned atom pairs is 0.810 angstroms; (across all 890 pairs:
    11468 37.620) 
    11469 
    11470 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    11471 fold_rcsdx2_rcscx2_model_0.cif, chain B (#4), sequence alignment score =
    11472 4539.6 
    11473 RMSD between 38 pruned atom pairs is 1.321 angstroms; (across all 890 pairs:
    11474 22.279) 
    11475 
    11476 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    11477 fold_rcsdx2_rcscx2_model_1.cif, chain B (#12), sequence alignment score =
    11478 4538.4 
    11479 RMSD between 238 pruned atom pairs is 0.699 angstroms; (across all 890 pairs:
    11480 33.986) 
    11481 
    11482 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    11483 fold_rcsdx2_rcscx2_model_3.cif, chain A (#13), sequence alignment score =
    11484 4543.2 
    11485 RMSD between 270 pruned atom pairs is 0.662 angstroms; (across all 890 pairs:
    11486 51.173) 
    11487 
    11488 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    11489 fold_rcsdx2_rcscx2_model_4.cif, chain A (#14), sequence alignment score =
    11490 4535.4 
    11491 RMSD between 307 pruned atom pairs is 0.693 angstroms; (across all 890 pairs:
    11492 25.202) 
    11493 
    11494 Matchmaker fold_igaa_rcsd_model_0.cif, chain B (#1) with
    11495 fold_rcsdx2_rcscx2_model_2.cif, chain B (#15), sequence alignment score =
    11496 4532.4 
    11497 RMSD between 64 pruned atom pairs is 0.846 angstroms; (across all 890 pairs:
    11498 32.264) 
    11499 
    11500 
    11501 > show #!2 models
    11502 
    11503 > hide #1 models
    11504 
    11505 > show #1 models
    11506 
    11507 > show #3 models
    11508 
    11509 > show #4 models
    11510 
    11511 > show #5 models
    11512 
    11513 > show #6 models
    11514 
    11515 > show #7 models
    11516 
    11517 > show #8 models
    11518 
    11519 > show #9 models
    11520 
    11521 > show #10 models
    11522 
    11523 > show #11 models
    11524 
    11525 > show #12 models
    11526 
    11527 > show #13 models
    11528 
    11529 > show #14 models
    11530 
    11531 > show #15 models
    11532 
    11533 > select
    11534 > #1/B#2/C/D#4/A/B#5/D/E#7/B/C#9/D/E#10/C/D#11/D/E#12/A/B#13/A/B#14/A/B#15/A/B
    11535 
    11536 146942 atoms, 149325 bonds, 767 pseudobonds, 17723 residues, 13 models
    11537 selected 
    11538 
    11539 > rainbow sel
    11540 
    11541 > hide #!2 models
    11542 
    11543 > hide #3 models
    11544 
    11545 > hide #4 models
    11546 
    11547 > hide #5 models
    11548 
    11549 > hide #6 models
    11550 
    11551 > hide #7 models
    11552 
    11553 > hide #8 models
    11554 
    11555 > hide #9 models
    11556 
    11557 > hide #10 models
    11558 
    11559 > hide #11 models
    11560 
    11561 > hide #12 models
    11562 
    11563 > hide #13 models
    11564 
    11565 > hide #14 models
    11566 
    11567 > hide #15 models
    11568 
    11569 > select clear
    11570 
    11571 > show #!2 models
    11572 
    11573 > hide #1 models
    11574 
    11575 > show #1 models
    11576 
    11577 > hide #!2 models
    11578 
    11579 > hide #1 models
    11580 
    11581 > show #1 models
    11582 
    11583 > show #!2 models
    11584 
    11585 > hide #1 models
    11586 
    11587 > show #4 models
    11588 
    11589 > hide #!2 models
    11590 
    11591 > show #5 models
    11592 
    11593 > hide #4 models
    11594 
    11595 > hide #5 models
    11596 
    11597 > show #6 models
    11598 
    11599 > hide #6 models
    11600 
    11601 > show #7 models
    11602 
    11603 > hide #7 models
    11604 
    11605 > show #8 models
    11606 
    11607 > hide #8 models
    11608 
    11609 > show #9 models
    11610 
    11611 > show #5 models
    11612 
    11613 > hide #9 models
    11614 
    11615 > show #9 models
    11616 
    11617 > hide #9 models
    11618 
    11619 > show #10 models
    11620 
    11621 > hide #5 models
    11622 
    11623 > hide #10 models
    11624 
    11625 > show #11 models
    11626 
    11627 > hide #11 models
    11628 
    11629 > show #12 models
    11630 
    11631 > show #13 models
    11632 
    11633 > hide #12 models
    11634 
    11635 > show #14 models
    11636 
    11637 > hide #13 models
    11638 
    11639 > show #15 models
    11640 
    11641 > hide #14 models
    11642 
    11643 > show #!2 models
    11644 
    11645 > hide #15 models
    11646 
    11647 > show #5 models
    11648 
    11649 > hide #!2 models
    11650 
    11651 > show #12 models
    11652 
    11653 > hide #5 models
    11654 
    11655 > show #13 models
    11656 
    11657 > hide #12 models
    11658 
    11659 > hide #13 models
    11660 
    11661 > show #14 models
    11662 
    11663 > show #15 models
    11664 
    11665 > hide #14 models
    11666 
    11667 > show #!2 models
    11668 
    11669 > hide #15 models
    11670 
    11671 > select #2/A
    11672 
    11673 5603 atoms, 5737 bonds, 711 residues, 1 model selected 
    11674 
    11675 > rainbow sel
    11676 
    11677 > select clear
    11678 
    11679 > color #!2 bychain
    11680 
    11681 > select #2/A
    11682 
    11683 5603 atoms, 5737 bonds, 711 residues, 1 model selected 
    11684 
    11685 > rainbow sel
    11686 
    11687 > select clear
    11688 
    11689 > select #2/A
    11690 
    11691 5603 atoms, 5737 bonds, 711 residues, 1 model selected 
    11692 
    11693 > select ~sel & ##selected
    11694 
    11695 15100 atoms, 15353 bonds, 1028 pseudobonds, 1914 residues, 2 models selected 
    11696 
    11697 > hide sel cartoons
    11698 
    11699 > hide sel atoms
    11700 
    11701 > select #2/B
    11702 
    11703 984 atoms, 1001 bonds, 134 residues, 1 model selected 
    11704 
    11705 > show sel cartoons
    11706 
    11707 > select ~sel & ##selected
    11708 
    11709 19719 atoms, 20089 bonds, 1028 pseudobonds, 2491 residues, 2 models selected 
    11710 
    11711 > hide sel cartoons
    11712 
    11713 > hide sel atoms
    11714 
    11715 > select #2/B
    11716 
    11717 984 atoms, 1001 bonds, 134 residues, 1 model selected 
    11718 
    11719 > rainbow sel
    11720 
    11721 > hide sel cartoons
    11722 
    11723 > select #2/C/D
    11724 
    11725 14116 atoms, 14352 bonds, 638 pseudobonds, 1780 residues, 2 models selected 
    11726 
    11727 > show sel cartoons
    11728 
    11729 > rainbow sel
    11730 
    11731 > select clear
    11732 
    11733 > hide #!2 cartoons
    11734 
    11735 [Repeated 1 time(s)]
    11736 
    11737 > show #!2 cartoons
    11738 
    11739 > color #!2 bychain
    11740 
    11741 > select #2/A
    11742 
    11743 5603 atoms, 5737 bonds, 711 residues, 1 model selected 
    11744 
    11745 > rainbow sel
    11746 
    11747 > select clear
    11748 
    11749 > select #2/C
    11750 
    11751 7058 atoms, 7176 bonds, 890 residues, 1 model selected 
    11752 
    11753 > color sel bychain
    11754 
    11755 > select clear
    11756 
    11757 > color #!2 bychain
    11758 
    11759 > select #2/C
    11760 
    11761 7058 atoms, 7176 bonds, 890 residues, 1 model selected 
    11762 
    11763 > rainbow sel
    11764 
    11765 > select #2/B
    11766 
    11767 984 atoms, 1001 bonds, 134 residues, 1 model selected 
    11768 
    11769 > rainbow sel
    11770 
    11771 > select clear
    11772 
    11773 > show #9 models
    11774 
    11775 > hide #!2 models
    11776 
    11777 > show #!2 models
    11778 
    11779 > hide #9 models
    11780 
    11781 > open /Users/taic/Library/CloudStorage/OneDrive-
    11782 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2_rcsbx2/fold_rcsdx2_rcsbx2_model_3.cif
    11783 
    11784 Chain information for fold_rcsdx2_rcsbx2_model_3.cif #16 
    11785 --- 
    11786 Chain | Description 
    11787 A B | . 
    11788 C D | . 
    11789 
    11790 
    11791 > open /Users/taic/Library/CloudStorage/OneDrive-
    11792 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2_rcsbx2/fold_rcsdx2_rcsbx2_model_4.cif
    11793 
    11794 Chain information for fold_rcsdx2_rcsbx2_model_4.cif #17 
    11795 --- 
    11796 Chain | Description 
    11797 A B | . 
    11798 C D | . 
    11799 
    11800 Computing secondary structure 
    11801 [Repeated 1 time(s)]
    11802 
    11803 > open /Users/taic/Library/CloudStorage/OneDrive-
    11804 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2_rcsbx2/fold_rcsdx2_rcsbx2_model_0.cif
    11805 
    11806 Chain information for fold_rcsdx2_rcsbx2_model_0.cif #18 
    11807 --- 
    11808 Chain | Description 
    11809 A B | . 
    11810 C D | . 
    11811 
    11812 Computing secondary structure 
    11813 
    11814 > hide #!2 models
    11815 
    11816 > open /Users/taic/Library/CloudStorage/OneDrive-
    11817 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2_rcsbx2/fold_rcsdx2_rcsbx2_model_1.cif
    11818 
    11819 Chain information for fold_rcsdx2_rcsbx2_model_1.cif #19 
    11820 --- 
    11821 Chain | Description 
    11822 A B | . 
    11823 C D | . 
    11824 
    11825 Computing secondary structure 
    11826 
    11827 > open /Users/taic/Library/CloudStorage/OneDrive-
    11828 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_rcsdx2_rcsbx2/fold_rcsdx2_rcsbx2_model_2.cif
    11829 
    11830 Chain information for fold_rcsdx2_rcsbx2_model_2.cif #20 
    11831 --- 
    11832 Chain | Description 
    11833 A B | . 
    11834 C D | . 
    11835 
    11836 Computing secondary structure 
    11837 
    11838 > hide #16 models
    11839 
    11840 > hide #17 models
    11841 
    11842 > hide #19 models
    11843 
    11844 > hide #20 models
    11845 
    11846 > color #18 bychain
    11847 
    11848 > show #19 models
    11849 
    11850 > hide #18 models
    11851 
    11852 > color #19 bychain
    11853 
    11854 > show #20 models
    11855 
    11856 > hide #19 models
    11857 
    11858 > color #20 bychain
    11859 
    11860 > show #17 models
    11861 
    11862 > hide #20 models
    11863 
    11864 > color #17 bychain
    11865 
    11866 > show #1 models
    11867 
    11868 > hide #17 models
    11869 
    11870 > show #4 models
    11871 
    11872 > hide #1 models
    11873 
    11874 > show #1 models
    11875 
    11876 > hide #1 models
    11877 
    11878 > color #4 bychain
    11879 
    11880 > select #4/B
    11881 
    11882 7058 atoms, 7176 bonds, 890 residues, 1 model selected 
    11883 
    11884 > select #4/C
    11885 
    11886 7480 atoms, 7617 bonds, 949 residues, 1 model selected 
    11887 
    11888 > rainbow sel
    11889 
    11890 > select clear
    11891 
    11892 > select #4/A/B/C
    11893 
    11894 21596 atoms, 21969 bonds, 2729 residues, 1 model selected 
    11895 
    11896 > hide sel cartoons
    11897 
    11898 > undo
    11899 
    11900 > select #4/A/B/D
    11901 
    11902 21596 atoms, 21969 bonds, 2729 residues, 1 model selected 
    11903 
    11904 > hide sel cartoons
    11905 
    11906 > show sel cartoons
    11907 
    11908 > select clear
    11909 
    11910 > color #4 bychain
    11911 
    11912 > select #4/A
    11913 
    11914 7058 atoms, 7176 bonds, 890 residues, 1 model selected 
    11915 
    11916 > rainbow sel
    11917 
    11918 > select clear
    11919 
    11920 > select #4/B/C/D
    11921 
    11922 22018 atoms, 22410 bonds, 2788 residues, 1 model selected 
    11923 
    11924 > hide sel cartoons
    11925 
    11926 > show sel cartoons
    11927 
    11928 > select #4/D
    11929 
    11930 7480 atoms, 7617 bonds, 949 residues, 1 model selected 
    11931 
    11932 > rainbow sel
    11933 
    11934 > select clear
    11935 
    11936 > select #4/D
    11937 
    11938 7480 atoms, 7617 bonds, 949 residues, 1 model selected 
    11939 
    11940 > select clear
    11941 
    11942 > hide #4 models
    11943 
    11944 > show #1 models
    11945 
    11946 > color #1 bychain
    11947 
    11948 > select #1/A
    11949 
    11950 5603 atoms, 5737 bonds, 711 residues, 1 model selected 
    11951 
    11952 > rainbow sel
    11953 
    11954 > show #!2 models
    11955 
    11956 > hide #1 models
    11957 
    11958 > show #1 models
    11959 
    11960 > hide #!2 models
    11961 
    11962 > show #8 models
    11963 
    11964 > hide #1 models
    11965 
    11966 Drag select of 12 residues 
    11967 Drag select of 1 residues 
    11968 
    11969 > show #3 models
    11970 
    11971 Drag select of 3 atoms, 5 residues 
    11972 
    11973 > select #8/A:472
    11974 
    11975 8 atoms, 7 bonds, 1 residue, 1 model selected 
    11976 
    11977 > preset cartoons/nucleotides cylinders/stubs
    11978 
    11979 Using preset: Cartoons/Nucleotides / Cylinders/Stubs 
    11980 Changed 69358 atom styles 
    11981 Preset expands to these ChimeraX commands:
    11982 
    11983 
    11984 
    11985    show nucleic
    11986    hide protein|solvent|H
    11987    surf hide
    11988    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    11989    ~worm
    11990    cartoon
    11991    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    11992    cartoon style ~(nucleic|strand) x round
    11993    cartoon style (nucleic|strand) x rect
    11994    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    11995    cartoon style nucleic x round width 1.6 thick 1.6
    11996    nucleotides stubs
    11997 
    11998 
    11999 
    12000 > preset cartoons/nucleotides licorice/ovals
    12001 
    12002 Using preset: Cartoons/Nucleotides / Licorice/Ovals 
    12003 Changed 0 atom styles 
    12004 Preset expands to these ChimeraX commands:
    12005 
    12006 
    12007 
    12008    show nucleic
    12009    hide protein|solvent|H
    12010    surf hide
    12011    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    12012    ~worm
    12013    cartoon
    12014    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    12015    cartoon style ~(nucleic|strand) x round
    12016    cartoon style (nucleic|strand) x rect
    12017    cartoon style protein modeh default arrows f x round width 1 thick 1
    12018    cartoon style nucleic x round width 1.6 thick 1.6
    12019    nucleotides tube/slab shape ellipsoid
    12020 
    12021 
    12022 
    12023 > preset cartoons/nucleotides ribbons/slabs
    12024 
    12025 Using preset: Cartoons/Nucleotides / Ribbons/Slabs 
    12026 Changed 0 atom styles 
    12027 Preset expands to these ChimeraX commands:
    12028 
    12029 
    12030 
    12031    show nucleic
    12032    hide protein|solvent|H
    12033    surf hide
    12034    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    12035    ~worm
    12036    cartoon
    12037    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    12038    cartoon style ~(nucleic|strand) x round
    12039    cartoon style (nucleic|strand) x rect
    12040    nucleotides tube/slab shape box
    12041 
    12042 
    12043 
    12044 > hide #3 models
    12045 
    12046 > show #4 models
    12047 
    12048 > hide #8 models
    12049 
    12050 > select #4/A/B
    12051 
    12052 14116 atoms, 14352 bonds, 1780 residues, 1 model selected 
    12053 
    12054 > rainbow sel
    12055 
    12056 > select clear
    12057 
    12058 > color #4 bychain
    12059 
    12060 > select #4/A/B
    12061 
    12062 14116 atoms, 14352 bonds, 1780 residues, 1 model selected 
    12063 
    12064 > rainbow sel
    12065 
    12066 > select clear
    12067 
    12068 [Repeated 1 time(s)]
    12069 
    12070 > show #12 models
    12071 
    12072 > show #13 models
    12073 
    12074 > show #14 models
    12075 
    12076 > show #15 models
    12077 
    12078 > color #4,12-15 bychain
    12079 
    12080 > select #4/A/B#12/A/B#13/A/B#14/A/B#15/A/B
    12081 
    12082 70580 atoms, 71760 bonds, 8900 residues, 5 models selected 
    12083 
    12084 > rainbow sel
    12085 
    12086 > hide #12 models
    12087 
    12088 > hide #13 models
    12089 
    12090 > hide #14 models
    12091 
    12092 > hide #15 models
    12093 
    12094 > select clear
    12095 
    12096 > hide #4 models
    12097 
    12098 > show #12 models
    12099 
    12100 > show #13 models
    12101 
    12102 > hide #12 models
    12103 
    12104 > show #14 models
    12105 
    12106 > hide #13 models
    12107 
    12108 > show #15 models
    12109 
    12110 > hide #14 models
    12111 
    12112 > show #!2 models
    12113 
    12114 > hide #!2 models
    12115 
    12116 > show #5 models
    12117 
    12118 > hide #15 models
    12119 
    12120 > color #5 bychain
    12121 
    12122 > select #5/B/C
    12123 
    12124 14960 atoms, 15234 bonds, 1898 residues, 1 model selected 
    12125 
    12126 > rainbow sel
    12127 
    12128 > select clear
    12129 
    12130 > hide #5 models
    12131 
    12132 > show #4 models
    12133 
    12134 > show #!2 models
    12135 
    12136 > hide #4 models
    12137 
    12138 Drag select of 18 residues 
    12139 
    12140 > show #4 models
    12141 
    12142 > hide #!2 models
    12143 
    12144 > show #12 models
    12145 
    12146 > hide #4 models
    12147 
    12148 > show #13 models
    12149 
    12150 > hide #12 models
    12151 
    12152 > show #14 models
    12153 
    12154 > hide #13 models
    12155 
    12156 > show #15 models
    12157 
    12158 > hide #14 models
    12159 
    12160 > hide #15 models
    12161 
    12162 > show #12 models
    12163 
    12164 > show #4 models
    12165 
    12166 > hide #12 models
    12167 
    12168 > show #13 models
    12169 
    12170 > hide #4 models
    12171 
    12172 > show #14 models
    12173 
    12174 > hide #13 models
    12175 
    12176 > show #15 models
    12177 
    12178 > hide #14 models
    12179 
    12180 > show #12 models
    12181 
    12182 > hide #15 models
    12183 
    12184 > show #!2 models
    12185 
    12186 > hide #12 models
    12187 
    12188 Drag select of 6 residues 
    12189 
    12190 > select #2/C:411
    12191 
    12192 7 atoms, 6 bonds, 1 residue, 1 model selected 
    12193 
    12194 > select #2/C:411
    12195 
    12196 7 atoms, 6 bonds, 1 residue, 1 model selected 
    12197 
    12198 > show sel atoms
    12199 
    12200 > select #2/C:411
    12201 
    12202 7 atoms, 6 bonds, 1 residue, 1 model selected 
    12203 
    12204 > select #2/C:411
    12205 
    12206 7 atoms, 6 bonds, 1 residue, 1 model selected 
    12207 
    12208 > show sel atoms
    12209 
    12210 > select clear
    12211 
    12212 > color #2 magenta
    12213 
    12214 > undo
    12215 
    12216 > select #2/C:412
    12217 
    12218 8 atoms, 7 bonds, 1 residue, 1 model selected 
    12219 
    12220 > color (#!2 & sel) magenta
    12221 
    12222 > select #2/A:97
    12223 
    12224 11 atoms, 10 bonds, 1 residue, 1 model selected 
    12225 
    12226 > show sel atoms
    12227 
    12228 > show #3 models
    12229 
    12230 > select #2/C:412
    12231 
    12232 8 atoms, 7 bonds, 1 residue, 1 model selected 
    12233 
    12234 > rainbow sel
    12235 
    12236 > select #2/C:410
    12237 
    12238 5 atoms, 4 bonds, 1 residue, 1 model selected 
    12239 
    12240 > select #2/C
    12241 
    12242 7058 atoms, 7176 bonds, 890 residues, 1 model selected 
    12243 
    12244 > select #2/C
    12245 
    12246 7058 atoms, 7176 bonds, 890 residues, 1 model selected 
    12247 
    12248 > rainbow sel
    12249 
    12250 > select #2/C:411
    12251 
    12252 7 atoms, 6 bonds, 1 residue, 1 model selected 
    12253 
    12254 > color (#!2 & sel) magenta
    12255 
    12256 > select #2/A:97
    12257 
    12258 11 atoms, 10 bonds, 1 residue, 1 model selected 
    12259 
    12260 > color (#!2 & sel) cornflower blue
    12261 
    12262 > select #2/C:411
    12263 
    12264 7 atoms, 6 bonds, 1 residue, 1 model selected 
    12265 
    12266 > color (#!2 & sel) yellow
    12267 
    12268 > ui tool show "Color Actions"
    12269 
    12270 > color sel green yellow
    12271 
    12272 > select clear
    12273 
    12274 > select #2/C:411
    12275 
    12276 7 atoms, 6 bonds, 1 residue, 1 model selected 
    12277 
    12278 > ui tool show "Color Actions"
    12279 
    12280 > color sel yellow
    12281 
    12282 > select clear
    12283 
    12284 > select #2/C:413
    12285 
    12286 8 atoms, 7 bonds, 1 residue, 1 model selected 
    12287 
    12288 > select add #2/C:414
    12289 
    12290 16 atoms, 14 bonds, 2 residues, 2 models selected 
    12291 
    12292 > show sel atoms
    12293 
    12294 > select #2/A:94
    12295 
    12296 5 atoms, 4 bonds, 1 residue, 1 model selected 
    12297 
    12298 > show sel atoms
    12299 
    12300 > color (#!2 & sel) cornflower blue
    12301 
    12302 > select add #2/C:413
    12303 
    12304 13 atoms, 11 bonds, 2 residues, 2 models selected 
    12305 
    12306 > select add #2/C:414
    12307 
    12308 21 atoms, 18 bonds, 3 residues, 3 models selected 
    12309 
    12310 > color (#!2 & sel) yellow
    12311 
    12312 > select clear
    12313 
    12314 > select #2/A:94
    12315 
    12316 5 atoms, 4 bonds, 1 residue, 1 model selected 
    12317 
    12318 > color (#!2 & sel) cornflower blue
    12319 
    12320 > select clear
    12321 
    12322 [Repeated 2 time(s)]
    12323 
    12324 > select #2/A
    12325 
    12326 5603 atoms, 5737 bonds, 711 residues, 1 model selected 
    12327 
    12328 > rainbow sel
    12329 
    12330 > select clear
    12331 
    12332 > select #2/B
    12333 
    12334 984 atoms, 1001 bonds, 134 residues, 1 model selected 
    12335 
    12336 > color sel bychain
    12337 
    12338 > select #2/B
    12339 
    12340 984 atoms, 1001 bonds, 134 residues, 1 model selected 
    12341 
    12342 > ui tool show "Color Actions"
    12343 
    12344 > color sel light steel blue
    12345 
    12346 > select #2/B
    12347 
    12348 984 atoms, 1001 bonds, 134 residues, 1 model selected 
    12349 
    12350 > ui tool show "Color Actions"
    12351 
    12352 > color sel burly wood
    12353 
    12354 > color sel rosy brown
    12355 
    12356 > color sel tan
    12357 
    12358 > color sel dark salmon
    12359 
    12360 > color sel peru
    12361 
    12362 > color sel dark goldenrod
    12363 
    12364 > select #2/C
    12365 
    12366 7058 atoms, 7176 bonds, 890 residues, 1 model selected 
    12367 
    12368 > color sel light slate gray
    12369 
    12370 > select clear
    12371 
    12372 > select #2/D
    12373 
    12374 7058 atoms, 7176 bonds, 890 residues, 1 model selected 
    12375 
    12376 > ui tool show "Color Actions"
    12377 
    12378 > color sel light steel blue
    12379 
    12380 > select clear
    12381 
    12382 Drag select of 4 residues 
    12383 
    12384 > select clear
    12385 
    12386 > select #2/A:94
    12387 
    12388 5 atoms, 4 bonds, 1 residue, 1 model selected 
    12389 
    12390 > select add #2/A:96
    12391 
    12392 12 atoms, 10 bonds, 2 residues, 2 models selected 
    12393 
    12394 > select subtract #2/A:96
    12395 
    12396 5 atoms, 4 bonds, 1 residue, 2 models selected 
    12397 
    12398 > select add #2/A:96
    12399 
    12400 12 atoms, 10 bonds, 2 residues, 2 models selected 
    12401 
    12402 > ui tool show "Color Actions"
    12403 
    12404 > color sel cyan
    12405 
    12406 > select #2/A:96
    12407 
    12408 7 atoms, 6 bonds, 1 residue, 1 model selected 
    12409 
    12410 > undo
    12411 
    12412 [Repeated 2 time(s)]
    12413 
    12414 > select #2/A:97
    12415 
    12416 11 atoms, 10 bonds, 1 residue, 1 model selected 
    12417 
    12418 > select add #2/A:94
    12419 
    12420 16 atoms, 14 bonds, 2 residues, 2 models selected 
    12421 
    12422 > select #2/A
    12423 
    12424 5603 atoms, 5737 bonds, 711 residues, 1 model selected 
    12425 
    12426 > select #2/A
    12427 
    12428 5603 atoms, 5737 bonds, 711 residues, 1 model selected 
    12429 
    12430 > color sel gray
    12431 
    12432 > color sel silver
    12433 
    12434 > color sel dark gray
    12435 
    12436 > select clear
    12437 
    12438 > select #2/A:96
    12439 
    12440 7 atoms, 6 bonds, 1 residue, 1 model selected 
    12441 
    12442 > select #2/A:95
    12443 
    12444 8 atoms, 7 bonds, 1 residue, 1 model selected 
    12445 
    12446 > select #2/A:94
    12447 
    12448 5 atoms, 4 bonds, 1 residue, 1 model selected 
    12449 
    12450 > select #2/A:94
    12451 
    12452 5 atoms, 4 bonds, 1 residue, 1 model selected 
    12453 
    12454 > select #2/A:96
    12455 
    12456 7 atoms, 6 bonds, 1 residue, 1 model selected 
    12457 
    12458 > select #2/A:96
    12459 
    12460 7 atoms, 6 bonds, 1 residue, 1 model selected 
    12461 
    12462 > select #2/A:97
    12463 
    12464 11 atoms, 10 bonds, 1 residue, 1 model selected 
    12465 
    12466 > select add #2/A:94
    12467 
    12468 16 atoms, 14 bonds, 2 residues, 2 models selected 
    12469 
    12470 > color sel deep sky blue
    12471 
    12472 > select add #2/C:411
    12473 
    12474 23 atoms, 20 bonds, 3 residues, 2 models selected 
    12475 
    12476 > select add #2/C:413
    12477 
    12478 31 atoms, 27 bonds, 4 residues, 3 models selected 
    12479 
    12480 > select add #2/C:414
    12481 
    12482 39 atoms, 34 bonds, 5 residues, 3 models selected 
    12483 
    12484 > color sel plum
    12485 
    12486 > color sel pale violet red
    12487 
    12488 > color sel magenta
    12489 
    12490 > select #2/A:97
    12491 
    12492 11 atoms, 10 bonds, 1 residue, 1 model selected 
    12493 
    12494 > select clear
    12495 
    12496 > select #2/A:97
    12497 
    12498 11 atoms, 10 bonds, 1 residue, 1 model selected 
    12499 
    12500 > select add #2/A:94
    12501 
    12502 16 atoms, 14 bonds, 2 residues, 2 models selected 
    12503 
    12504 > color sel deep sky blue
    12505 
    12506 > select clear
    12507 
    12508 > select add #2/C:411
    12509 
    12510 7 atoms, 6 bonds, 1 residue, 1 model selected 
    12511 
    12512 > select add #2/C:413
    12513 
    12514 15 atoms, 13 bonds, 2 residues, 2 models selected 
    12515 
    12516 > select add #2/C:414
    12517 
    12518 23 atoms, 20 bonds, 3 residues, 2 models selected 
    12519 
    12520 > select add #2/A:97
    12521 
    12522 34 atoms, 30 bonds, 4 residues, 2 models selected 
    12523 
    12524 > select add #2/A:94
    12525 
    12526 39 atoms, 34 bonds, 5 residues, 3 models selected 
    12527 
    12528 > label (#!2 & sel) text "{0.label_one_letter_code}
    12529 > {0.number}{0.insertion_code}"
    12530 
    12531 > label height 1
    12532 
    12533 > select clear
    12534 
    12535 [Repeated 1 time(s)]
    12536 
    12537 > hide #3 models
    12538 
    12539 > show #3 models
    12540 
    12541 > close session
    12542 
    12543 > open /Users/taic/Library/CloudStorage/OneDrive-
    12544 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq_co/fold_hqba_yhbq_co_model_0.cif
    12545 
    12546 Summary of feedback from opening /Users/taic/Library/CloudStorage/OneDrive-
    12547 NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq_co/fold_hqba_yhbq_co_model_0.cif 
    12548 --- 
    12549 note | Fetching CCD CO from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/CO/CO.cif 
    12550 
    12551 Chain information for fold_hqba_yhbq_co_model_0.cif #1 
    12552 --- 
    12553 Chain | Description 
    12554 A | . 
    12555 B | . 
    12556 
    12557 Computing secondary structure 
    12558 
    12559 > open /Users/taic/Library/CloudStorage/OneDrive-
    12560 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq_co/fold_hqba_yhbq_co_model_1.cif
    12561 
    12562 Chain information for fold_hqba_yhbq_co_model_1.cif #2 
    12563 --- 
    12564 Chain | Description 
    12565 A | . 
    12566 B | . 
    12567 
    12568 
    12569 > open /Users/taic/Library/CloudStorage/OneDrive-
    12570 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq_co/fold_hqba_yhbq_co_model_2.cif
    12571 
    12572 Chain information for fold_hqba_yhbq_co_model_2.cif #3 
    12573 --- 
    12574 Chain | Description 
    12575 A | . 
    12576 B | . 
    12577 
    12578 
    12579 > open /Users/taic/Library/CloudStorage/OneDrive-
    12580 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq_co/fold_hqba_yhbq_co_model_3.cif
    12581 
    12582 Chain information for fold_hqba_yhbq_co_model_3.cif #4 
    12583 --- 
    12584 Chain | Description 
    12585 A | . 
    12586 B | . 
    12587 
    12588 
    12589 > open /Users/taic/Library/CloudStorage/OneDrive-
    12590 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq_co/fold_hqba_yhbq_co_model_4.cif
    12591 
    12592 Chain information for fold_hqba_yhbq_co_model_4.cif #5 
    12593 --- 
    12594 Chain | Description 
    12595 A | . 
    12596 B | . 
    12597 
    12598 Computing secondary structure 
    12599 [Repeated 3 time(s)]
    12600 
    12601 > color bychain
    12602 
    12603 > open /Users/taic/Library/CloudStorage/OneDrive-
    12604 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbp_co/fold_hqba_yhbp_co_model_0.cif
    12605 
    12606 Chain information for fold_hqba_yhbp_co_model_0.cif #6 
    12607 --- 
    12608 Chain | Description 
    12609 A | . 
    12610 B | . 
    12611 
    12612 
    12613 > open /Users/taic/Library/CloudStorage/OneDrive-
    12614 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbp_co/fold_hqba_yhbp_co_model_1.cif
    12615 
    12616 Chain information for fold_hqba_yhbp_co_model_1.cif #7 
    12617 --- 
    12618 Chain | Description 
    12619 A | . 
    12620 B | . 
    12621 
    12622 
    12623 > open /Users/taic/Library/CloudStorage/OneDrive-
    12624 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbp_co/fold_hqba_yhbp_co_model_2.cif
    12625 
    12626 Chain information for fold_hqba_yhbp_co_model_2.cif #8 
    12627 --- 
    12628 Chain | Description 
    12629 A | . 
    12630 B | . 
    12631 
    12632 
    12633 > open /Users/taic/Library/CloudStorage/OneDrive-
    12634 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbp_co/fold_hqba_yhbp_co_model_3.cif
    12635 
    12636 Chain information for fold_hqba_yhbp_co_model_3.cif #9 
    12637 --- 
    12638 Chain | Description 
    12639 A | . 
    12640 B | . 
    12641 
    12642 
    12643 > open /Users/taic/Library/CloudStorage/OneDrive-
    12644 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbp_co/fold_hqba_yhbp_co_model_4.cif
    12645 
    12646 Chain information for fold_hqba_yhbp_co_model_4.cif #10 
    12647 --- 
    12648 Chain | Description 
    12649 A | . 
    12650 B | . 
    12651 
    12652 Computing secondary structure 
    12653 [Repeated 4 time(s)]
    12654 
    12655 > color bychain
    12656 
    12657 > open /Users/taic/Library/CloudStorage/OneDrive-
    12658 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu/fold_hqba_ubiu_model_0.cif
    12659 
    12660 Chain information for fold_hqba_ubiu_model_0.cif #11 
    12661 --- 
    12662 Chain | Description 
    12663 A | . 
    12664 B | . 
    12665 
    12666 
    12667 > open /Users/taic/Library/CloudStorage/OneDrive-
    12668 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu/fold_hqba_ubiu_model_1.cif
    12669 
    12670 Chain information for fold_hqba_ubiu_model_1.cif #12 
    12671 --- 
    12672 Chain | Description 
    12673 A | . 
    12674 B | . 
    12675 
    12676 
    12677 > open /Users/taic/Library/CloudStorage/OneDrive-
    12678 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu/fold_hqba_ubiu_model_2.cif
    12679 
    12680 Chain information for fold_hqba_ubiu_model_2.cif #13 
    12681 --- 
    12682 Chain | Description 
    12683 A | . 
    12684 B | . 
    12685 
    12686 
    12687 > open /Users/taic/Library/CloudStorage/OneDrive-
    12688 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu/fold_hqba_ubiu_model_3.cif
    12689 
    12690 Chain information for fold_hqba_ubiu_model_3.cif #14 
    12691 --- 
    12692 Chain | Description 
    12693 A | . 
    12694 B | . 
    12695 
    12696 
    12697 > open /Users/taic/Library/CloudStorage/OneDrive-
    12698 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu/fold_hqba_ubiu_model_4.cif
    12699 
    12700 Chain information for fold_hqba_ubiu_model_4.cif #15 
    12701 --- 
    12702 Chain | Description 
    12703 A | . 
    12704 B | . 
    12705 
    12706 Computing secondary structure 
    12707 [Repeated 4 time(s)]
    12708 
    12709 > color bychain
    12710 
    12711 > open /Users/taic/Library/CloudStorage/OneDrive-
    12712 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_nfua_fe4_co/fold_hqba_nfua_fe4_co_model_0.cif
    12713 
    12714 Summary of feedback from opening /Users/taic/Library/CloudStorage/OneDrive-
    12715 NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_nfua_fe4_co/fold_hqba_nfua_fe4_co_model_0.cif 
    12716 --- 
    12717 note | Fetching CCD FE from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/FE/FE.cif 
    12718 
    12719 Chain information for fold_hqba_nfua_fe4_co_model_0.cif #16 
    12720 --- 
    12721 Chain | Description 
    12722 A | . 
    12723 B | . 
    12724 
    12725 
    12726 > open /Users/taic/Library/CloudStorage/OneDrive-
    12727 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_nfua_fe4_co/fold_hqba_nfua_fe4_co_model_1.cif
    12728 
    12729 Chain information for fold_hqba_nfua_fe4_co_model_1.cif #17 
    12730 --- 
    12731 Chain | Description 
    12732 A | . 
    12733 B | . 
    12734 
    12735 
    12736 > open /Users/taic/Library/CloudStorage/OneDrive-
    12737 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_nfua_fe4_co/fold_hqba_nfua_fe4_co_model_2.cif
    12738 
    12739 Chain information for fold_hqba_nfua_fe4_co_model_2.cif #18 
    12740 --- 
    12741 Chain | Description 
    12742 A | . 
    12743 B | . 
    12744 
    12745 
    12746 > open /Users/taic/Library/CloudStorage/OneDrive-
    12747 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_nfua_fe4_co/fold_hqba_nfua_fe4_co_model_3.cif
    12748 
    12749 Chain information for fold_hqba_nfua_fe4_co_model_3.cif #19 
    12750 --- 
    12751 Chain | Description 
    12752 A | . 
    12753 B | . 
    12754 
    12755 
    12756 > open /Users/taic/Library/CloudStorage/OneDrive-
    12757 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_nfua_fe4_co/fold_hqba_nfua_fe4_co_model_4.cif
    12758 
    12759 Chain information for fold_hqba_nfua_fe4_co_model_4.cif #20 
    12760 --- 
    12761 Chain | Description 
    12762 A | . 
    12763 B | . 
    12764 
    12765 Computing secondary structure 
    12766 [Repeated 4 time(s)]
    12767 
    12768 > color bychain
    12769 
    12770 > select /AA
    12771 
    12772 Nothing selected 
    12773 
    12774 > select /A
    12775 
    12776 26220 atoms, 26820 bonds, 3340 residues, 20 models selected 
    12777 
    12778 > ui tool show Matchmaker
    12779 
    12780 > matchmaker #2-20 to #1 & sel
    12781 
    12782 Computing secondary structure 
    12783 [Repeated 19 time(s)]  Parameters 
    12784 --- 
    12785 Chain pairing | bb 
    12786 Alignment algorithm | Needleman-Wunsch 
    12787 Similarity matrix | BLOSUM-62 
    12788 SS fraction | 0.3 
    12789 Gap open (HH/SS/other) | 18/18/6 
    12790 Gap extend | 1 
    12791 SS matrix |  |  | H | S | O 
    12792 ---|---|---|--- 
    12793 H | 6 | -9 | -6 
    12794 S |  | 6 | -6 
    12795 O |  |  | 4 
    12796 Iteration cutoff | 2 
    12797 
    12798 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    12799 fold_hqba_yhbq_co_model_1.cif, chain A (#2), sequence alignment score = 875 
    12800 RMSD between 167 pruned atom pairs is 0.416 angstroms; (across all 167 pairs:
    12801 0.416) 
    12802 
    12803 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    12804 fold_hqba_yhbq_co_model_2.cif, chain A (#3), sequence alignment score = 871.4 
    12805 RMSD between 167 pruned atom pairs is 0.283 angstroms; (across all 167 pairs:
    12806 0.283) 
    12807 
    12808 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    12809 fold_hqba_yhbq_co_model_3.cif, chain A (#4), sequence alignment score = 875 
    12810 RMSD between 167 pruned atom pairs is 0.340 angstroms; (across all 167 pairs:
    12811 0.340) 
    12812 
    12813 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    12814 fold_hqba_yhbq_co_model_4.cif, chain A (#5), sequence alignment score = 875 
    12815 RMSD between 167 pruned atom pairs is 0.303 angstroms; (across all 167 pairs:
    12816 0.303) 
    12817 
    12818 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    12819 fold_hqba_yhbp_co_model_0.cif, chain A (#6), sequence alignment score = 853.4 
    12820 RMSD between 167 pruned atom pairs is 0.452 angstroms; (across all 167 pairs:
    12821 0.452) 
    12822 
    12823 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    12824 fold_hqba_yhbp_co_model_1.cif, chain A (#7), sequence alignment score = 871.4 
    12825 RMSD between 166 pruned atom pairs is 0.483 angstroms; (across all 167 pairs:
    12826 0.507) 
    12827 
    12828 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    12829 fold_hqba_yhbp_co_model_2.cif, chain A (#8), sequence alignment score = 871.4 
    12830 RMSD between 167 pruned atom pairs is 0.304 angstroms; (across all 167 pairs:
    12831 0.304) 
    12832 
    12833 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    12834 fold_hqba_yhbp_co_model_3.cif, chain A (#9), sequence alignment score = 871.4 
    12835 RMSD between 167 pruned atom pairs is 0.339 angstroms; (across all 167 pairs:
    12836 0.339) 
    12837 
    12838 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    12839 fold_hqba_yhbp_co_model_4.cif, chain A (#10), sequence alignment score = 867.8 
    12840 RMSD between 167 pruned atom pairs is 0.350 angstroms; (across all 167 pairs:
    12841 0.350) 
    12842 
    12843 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    12844 fold_hqba_ubiu_model_0.cif, chain A (#11), sequence alignment score = 871.4 
    12845 RMSD between 167 pruned atom pairs is 0.343 angstroms; (across all 167 pairs:
    12846 0.343) 
    12847 
    12848 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    12849 fold_hqba_ubiu_model_1.cif, chain A (#12), sequence alignment score = 871.4 
    12850 RMSD between 167 pruned atom pairs is 0.286 angstroms; (across all 167 pairs:
    12851 0.286) 
    12852 
    12853 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    12854 fold_hqba_ubiu_model_2.cif, chain A (#13), sequence alignment score = 875 
    12855 RMSD between 167 pruned atom pairs is 0.302 angstroms; (across all 167 pairs:
    12856 0.302) 
    12857 
    12858 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    12859 fold_hqba_ubiu_model_3.cif, chain A (#14), sequence alignment score = 871.4 
    12860 RMSD between 167 pruned atom pairs is 0.276 angstroms; (across all 167 pairs:
    12861 0.276) 
    12862 
    12863 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    12864 fold_hqba_ubiu_model_4.cif, chain A (#15), sequence alignment score = 875 
    12865 RMSD between 167 pruned atom pairs is 0.268 angstroms; (across all 167 pairs:
    12866 0.268) 
    12867 
    12868 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    12869 fold_hqba_nfua_fe4_co_model_0.cif, chain A (#16), sequence alignment score =
    12870 871.4 
    12871 RMSD between 167 pruned atom pairs is 0.331 angstroms; (across all 167 pairs:
    12872 0.331) 
    12873 
    12874 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    12875 fold_hqba_nfua_fe4_co_model_1.cif, chain A (#17), sequence alignment score =
    12876 871.4 
    12877 RMSD between 167 pruned atom pairs is 0.226 angstroms; (across all 167 pairs:
    12878 0.226) 
    12879 
    12880 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    12881 fold_hqba_nfua_fe4_co_model_2.cif, chain A (#18), sequence alignment score =
    12882 871.4 
    12883 RMSD between 166 pruned atom pairs is 0.568 angstroms; (across all 167 pairs:
    12884 0.589) 
    12885 
    12886 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    12887 fold_hqba_nfua_fe4_co_model_3.cif, chain A (#19), sequence alignment score =
    12888 871.4 
    12889 RMSD between 167 pruned atom pairs is 0.390 angstroms; (across all 167 pairs:
    12890 0.390) 
    12891 
    12892 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    12893 fold_hqba_nfua_fe4_co_model_4.cif, chain A (#20), sequence alignment score =
    12894 849.8 
    12895 RMSD between 167 pruned atom pairs is 0.211 angstroms; (across all 167 pairs:
    12896 0.211) 
    12897 
    12898 
    12899 > hide #6 models
    12900 
    12901 > hide #7 models
    12902 
    12903 > hide #8 models
    12904 
    12905 > hide #9 models
    12906 
    12907 > hide #10 models
    12908 
    12909 > hide #11 models
    12910 
    12911 > hide #12 models
    12912 
    12913 > hide #13 models
    12914 
    12915 > hide #14 models
    12916 
    12917 > hide #15 models
    12918 
    12919 > hide #16 models
    12920 
    12921 > hide #17 models
    12922 
    12923 > hide #18 models
    12924 
    12925 > hide #19 models
    12926 
    12927 > hide #20 models
    12928 
    12929 > open 4RS2 fromDatabase pdb format mmcif
    12930 
    12931 Summary of feedback from opening 4RS2 fetched from pdb 
    12932 --- 
    12933 notes | Fetching compressed mmCIF 4rs2 from http://files.rcsb.org/download/4rs2.cif 
    12934 Fetching CCD COA from
    12935 https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/COA/COA.cif 
    12936 
    12937 4rs2 title: 
    12938 1.55 Angstrom Crystal Structure of GNAT Family N-acetyltransferase (YhbS) from
    12939 Escherichia coli in Complex with CoA [more info...] 
    12940 
    12941 Chain information for 4rs2 #21 
    12942 --- 
    12943 Chain | Description | UniProt 
    12944 A B | Predicted acyltransferase with acyl-CoA N-acyltransferase domain | H0QE96_ECOLI 2-167 
    12945 
    12946 Non-standard residues in 4rs2 #21 
    12947 --- 
    12948 COA \u2014 coenzyme A 
    12949 
    12950 4rs2 mmCIF Assemblies 
    12951 --- 
    12952 1| author_and_software_defined_assembly 
    12953 2| author_and_software_defined_assembly 
    12954 
    12955 331 atoms have alternate locations. Control/examine alternate locations with
    12956 Altloc Explorer [start tool...] or the altlocs command. 
    12957 
    12958 > select /A
    12959 
    12960 27898 atoms, 28311 bonds, 3744 residues, 21 models selected 
    12961 
    12962 > ui tool show Matchmaker
    12963 
    12964 > matchmaker #21 to #1 & sel
    12965 
    12966 Computing secondary structure 
    12967 [Repeated 1 time(s)]  Parameters 
    12968 --- 
    12969 Chain pairing | bb 
    12970 Alignment algorithm | Needleman-Wunsch 
    12971 Similarity matrix | BLOSUM-62 
    12972 SS fraction | 0.3 
    12973 Gap open (HH/SS/other) | 18/18/6 
    12974 Gap extend | 1 
    12975 SS matrix |  |  | H | S | O 
    12976 ---|---|---|--- 
    12977 H | 6 | -9 | -6 
    12978 S |  | 6 | -6 
    12979 O |  |  | 4 
    12980 Iteration cutoff | 2 
    12981 
    12982 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with 4rs2, chain B
    12983 (#21), sequence alignment score = 836 
    12984 RMSD between 166 pruned atom pairs is 0.628 angstroms; (across all 167 pairs:
    12985 0.670) 
    12986 
    12987 
    12988 > select clear
    12989 
    12990 > select #21/A
    12991 
    12992 1678 atoms, 1491 bonds, 404 residues, 1 model selected 
    12993 
    12994 > hide sel cartoons
    12995 
    12996 > hide sel atoms
    12997 
    12998 > select clear
    12999 
    13000 [Repeated 1 time(s)]
    13001 
    13002 > open /Users/taic/Library/CloudStorage/OneDrive-
    13003 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/YhbS/models/Hfq6_YhbS.af2.4rs2.pdb
    13004 
    13005 Summary of feedback from opening /Users/taic/Library/CloudStorage/OneDrive-
    13006 NationalInstitutesofHealth/MacBookPro021/project/SusanG/YhbS/models/Hfq6_YhbS.af2.4rs2.pdb 
    13007 --- 
    13008 warnings | Start residue of secondary structure not found: HELIX 8 8 GLN B 8 GLU B 18 1 11 
    13009 Start residue of secondary structure not found: HELIX 9 9 LYS B 56 ALA B 58 1
    13010 3 
    13011 Start residue of secondary structure not found: HELIX 10 10 GLN C 8 GLU C 18 1
    13012 11 
    13013 Start residue of secondary structure not found: HELIX 11 11 LYS C 56 ALA C 58
    13014 1 3 
    13015 Start residue of secondary structure not found: HELIX 12 12 SER C 72 ASN C 74
    13016 1 3 
    13017 39 messages similar to the above omitted 
    13018 
    13019 Chain information for Hfq6_YhbS.af2.4rs2.pdb 
    13020 --- 
    13021 Chain | Description 
    13022 22.1/A | No description available 
    13023 22.2/A | No description available 
    13024 22.1/B 22.1/C 22.1/D 22.1/E 22.1/F 22.1/G | No description available 
    13025 22.2/B | No description available 
    13026 
    13027 331 atoms have alternate locations. Control/examine alternate locations with
    13028 Altloc Explorer [start tool...] or the altlocs command. 
    13029 
    13030 > hide #1-5,21#!22.1-2 atoms
    13031 
    13032 > hide #!22.2 models
    13033 
    13034 > show #!22.2 models
    13035 
    13036 > hide #!22.1 models
    13037 
    13038 > show #!22.1 models
    13039 
    13040 > select #1/A
    13041 
    13042 1311 atoms, 1341 bonds, 167 residues, 1 model selected 
    13043 
    13044 > ui tool show Matchmaker
    13045 
    13046 > matchmaker #!22.2 to #1 & sel
    13047 
    13048 Computing secondary structure 
    13049 [Repeated 1 time(s)]  Parameters 
    13050 --- 
    13051 Chain pairing | bb 
    13052 Alignment algorithm | Needleman-Wunsch 
    13053 Similarity matrix | BLOSUM-62 
    13054 SS fraction | 0.3 
    13055 Gap open (HH/SS/other) | 18/18/6 
    13056 Gap extend | 1 
    13057 SS matrix |  |  | H | S | O 
    13058 ---|---|---|--- 
    13059 H | 6 | -9 | -6 
    13060 S |  | 6 | -6 
    13061 O |  |  | 4 
    13062 Iteration cutoff | 2 
    13063 
    13064 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    13065 Hfq6_YhbS.af2.4rs2.pdb, chain B (#22.2), sequence alignment score = 836 
    13066 RMSD between 166 pruned atom pairs is 0.628 angstroms; (across all 167 pairs:
    13067 0.670) 
    13068 
    13069 
    13070 > hide #21 models
    13071 
    13072 > show #21 models
    13073 
    13074 > ui tool show Matchmaker
    13075 
    13076 > matchmaker #!22.1-2 to #1 & sel
    13077 
    13078 Computing secondary structure 
    13079 [Repeated 2 time(s)]  Parameters 
    13080 --- 
    13081 Chain pairing | bb 
    13082 Alignment algorithm | Needleman-Wunsch 
    13083 Similarity matrix | BLOSUM-62 
    13084 SS fraction | 0.3 
    13085 Gap open (HH/SS/other) | 18/18/6 
    13086 Gap extend | 1 
    13087 SS matrix |  |  | H | S | O 
    13088 ---|---|---|--- 
    13089 H | 6 | -9 | -6 
    13090 S |  | 6 | -6 
    13091 O |  |  | 4 
    13092 Iteration cutoff | 2 
    13093 
    13094 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    13095 Hfq6_YhbS.af2.4rs2.pdb, chain A (#22.1), sequence alignment score = 875 
    13096 RMSD between 167 pruned atom pairs is 0.339 angstroms; (across all 167 pairs:
    13097 0.339) 
    13098 
    13099 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    13100 Hfq6_YhbS.af2.4rs2.pdb, chain B (#22.2), sequence alignment score = 836 
    13101 RMSD between 166 pruned atom pairs is 0.628 angstroms; (across all 167 pairs:
    13102 0.670) 
    13103 
    13104 
    13105 > hide #21 models
    13106 
    13107 > show #21 models
    13108 
    13109 > hide #21 models
    13110 
    13111 > show #21 models
    13112 
    13113 > hide #1 models
    13114 
    13115 > hide #2 models
    13116 
    13117 > hide #3 models
    13118 
    13119 > hide #4 models
    13120 
    13121 > hide #5 models
    13122 
    13123 > hide #21 models
    13124 
    13125 > select add #22
    13126 
    13127 16588 atoms, 16330 bonds, 40 pseudobonds, 1769 residues, 6 models selected 
    13128 
    13129 > delete atoms (#!22.1-2 & sel)
    13130 
    13131 > delete bonds (#!22.1-2 & sel)
    13132 
    13133 > show #21 models
    13134 
    13135 > select add #21
    13136 
    13137 4709 atoms, 4356 bonds, 990 residues, 3 models selected 
    13138 
    13139 > select subtract #21
    13140 
    13141 1311 atoms, 1341 bonds, 167 residues, 2 models selected 
    13142 
    13143 > hide #22 models
    13144 
    13145 > hide #21 models
    13146 
    13147 > select subtract #22
    13148 
    13149 1311 atoms, 1341 bonds, 167 residues, 1 model selected 
    13150 
    13151 > show #22 models
    13152 
    13153 > select add #22
    13154 
    13155 1311 atoms, 1341 bonds, 167 residues, 2 models selected 
    13156 
    13157 > select add #1
    13158 
    13159 2107 atoms, 2148 bonds, 268 residues, 2 models selected 
    13160 
    13161 > select subtract #1
    13162 
    13163 1 model selected 
    13164 
    13165 > show #1 models
    13166 
    13167 > hide #1 models
    13168 
    13169 > delete atoms #22
    13170 
    13171 > delete bonds #22
    13172 
    13173 > open /Users/taic/Library/CloudStorage/OneDrive-
    13174 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/YhbS/models/AF2-multi/Hfq6mer_YhbS/YhbS-
    13175 > Hfq6mer.ranked_0.pdb
    13176 
    13177 Chain information for YhbS-Hfq6mer.ranked_0.pdb #23 
    13178 --- 
    13179 Chain | Description 
    13180 A | No description available 
    13181 B C D E F G | No description available 
    13182 
    13183 
    13184 > hide #23 atoms
    13185 
    13186 > show #23 cartoons
    13187 
    13188 Computing secondary structure 
    13189 
    13190 > select #1/A
    13191 
    13192 1311 atoms, 1341 bonds, 167 residues, 1 model selected 
    13193 
    13194 > ui tool show Matchmaker
    13195 
    13196 > matchmaker #2-21,23 to #1 & sel
    13197 
    13198 Computing secondary structure 
    13199 [Repeated 21 time(s)]  Parameters 
    13200 --- 
    13201 Chain pairing | bb 
    13202 Alignment algorithm | Needleman-Wunsch 
    13203 Similarity matrix | BLOSUM-62 
    13204 SS fraction | 0.3 
    13205 Gap open (HH/SS/other) | 18/18/6 
    13206 Gap extend | 1 
    13207 SS matrix |  |  | H | S | O 
    13208 ---|---|---|--- 
    13209 H | 6 | -9 | -6 
    13210 S |  | 6 | -6 
    13211 O |  |  | 4 
    13212 Iteration cutoff | 2 
    13213 
    13214 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    13215 fold_hqba_yhbq_co_model_1.cif, chain A (#2), sequence alignment score = 875 
    13216 RMSD between 167 pruned atom pairs is 0.416 angstroms; (across all 167 pairs:
    13217 0.416) 
    13218 
    13219 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    13220 fold_hqba_yhbq_co_model_2.cif, chain A (#3), sequence alignment score = 871.4 
    13221 RMSD between 167 pruned atom pairs is 0.283 angstroms; (across all 167 pairs:
    13222 0.283) 
    13223 
    13224 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    13225 fold_hqba_yhbq_co_model_3.cif, chain A (#4), sequence alignment score = 875 
    13226 RMSD between 167 pruned atom pairs is 0.340 angstroms; (across all 167 pairs:
    13227 0.340) 
    13228 
    13229 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    13230 fold_hqba_yhbq_co_model_4.cif, chain A (#5), sequence alignment score = 875 
    13231 RMSD between 167 pruned atom pairs is 0.303 angstroms; (across all 167 pairs:
    13232 0.303) 
    13233 
    13234 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    13235 fold_hqba_yhbp_co_model_0.cif, chain A (#6), sequence alignment score = 853.4 
    13236 RMSD between 167 pruned atom pairs is 0.452 angstroms; (across all 167 pairs:
    13237 0.452) 
    13238 
    13239 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    13240 fold_hqba_yhbp_co_model_1.cif, chain A (#7), sequence alignment score = 871.4 
    13241 RMSD between 166 pruned atom pairs is 0.483 angstroms; (across all 167 pairs:
    13242 0.507) 
    13243 
    13244 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    13245 fold_hqba_yhbp_co_model_2.cif, chain A (#8), sequence alignment score = 871.4 
    13246 RMSD between 167 pruned atom pairs is 0.304 angstroms; (across all 167 pairs:
    13247 0.304) 
    13248 
    13249 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    13250 fold_hqba_yhbp_co_model_3.cif, chain A (#9), sequence alignment score = 871.4 
    13251 RMSD between 167 pruned atom pairs is 0.339 angstroms; (across all 167 pairs:
    13252 0.339) 
    13253 
    13254 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    13255 fold_hqba_yhbp_co_model_4.cif, chain A (#10), sequence alignment score = 867.8 
    13256 RMSD between 167 pruned atom pairs is 0.350 angstroms; (across all 167 pairs:
    13257 0.350) 
    13258 
    13259 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    13260 fold_hqba_ubiu_model_0.cif, chain A (#11), sequence alignment score = 871.4 
    13261 RMSD between 167 pruned atom pairs is 0.343 angstroms; (across all 167 pairs:
    13262 0.343) 
    13263 
    13264 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    13265 fold_hqba_ubiu_model_1.cif, chain A (#12), sequence alignment score = 871.4 
    13266 RMSD between 167 pruned atom pairs is 0.286 angstroms; (across all 167 pairs:
    13267 0.286) 
    13268 
    13269 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    13270 fold_hqba_ubiu_model_2.cif, chain A (#13), sequence alignment score = 875 
    13271 RMSD between 167 pruned atom pairs is 0.302 angstroms; (across all 167 pairs:
    13272 0.302) 
    13273 
    13274 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    13275 fold_hqba_ubiu_model_3.cif, chain A (#14), sequence alignment score = 871.4 
    13276 RMSD between 167 pruned atom pairs is 0.276 angstroms; (across all 167 pairs:
    13277 0.276) 
    13278 
    13279 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    13280 fold_hqba_ubiu_model_4.cif, chain A (#15), sequence alignment score = 875 
    13281 RMSD between 167 pruned atom pairs is 0.268 angstroms; (across all 167 pairs:
    13282 0.268) 
    13283 
    13284 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    13285 fold_hqba_nfua_fe4_co_model_0.cif, chain A (#16), sequence alignment score =
    13286 871.4 
    13287 RMSD between 167 pruned atom pairs is 0.331 angstroms; (across all 167 pairs:
    13288 0.331) 
    13289 
    13290 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    13291 fold_hqba_nfua_fe4_co_model_1.cif, chain A (#17), sequence alignment score =
    13292 871.4 
    13293 RMSD between 167 pruned atom pairs is 0.226 angstroms; (across all 167 pairs:
    13294 0.226) 
    13295 
    13296 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    13297 fold_hqba_nfua_fe4_co_model_2.cif, chain A (#18), sequence alignment score =
    13298 871.4 
    13299 RMSD between 166 pruned atom pairs is 0.568 angstroms; (across all 167 pairs:
    13300 0.589) 
    13301 
    13302 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    13303 fold_hqba_nfua_fe4_co_model_3.cif, chain A (#19), sequence alignment score =
    13304 871.4 
    13305 RMSD between 167 pruned atom pairs is 0.390 angstroms; (across all 167 pairs:
    13306 0.390) 
    13307 
    13308 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    13309 fold_hqba_nfua_fe4_co_model_4.cif, chain A (#20), sequence alignment score =
    13310 849.8 
    13311 RMSD between 167 pruned atom pairs is 0.211 angstroms; (across all 167 pairs:
    13312 0.211) 
    13313 
    13314 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with 4rs2, chain B
    13315 (#21), sequence alignment score = 836 
    13316 RMSD between 166 pruned atom pairs is 0.628 angstroms; (across all 167 pairs:
    13317 0.670) 
    13318 
    13319 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with YhbS-
    13320 Hfq6mer.ranked_0.pdb, chain A (#23), sequence alignment score = 875 
    13321 RMSD between 167 pruned atom pairs is 0.339 angstroms; (across all 167 pairs:
    13322 0.339) 
    13323 
    13324 
    13325 > hide #22 models
    13326 
    13327 > show #1 models
    13328 
    13329 > hide #1 models
    13330 
    13331 > select #23/B
    13332 
    13333 1552 atoms, 1566 bonds, 102 residues, 1 model selected 
    13334 
    13335 > Sel #23/B/C/D/E/F/G
    13336 
    13337 Unknown command: Sel #23/B/C/D/E/F/G 
    13338 
    13339 > Sel #23/B#23/C#23/D#23/E#23/F#23/G
    13340 
    13341 Unknown command: Sel #23/B#23/C#23/D#23/E#23/F#23/G 
    13342 
    13343 > select #23/B#23/C#23/D#23/E#23/F#23/G
    13344 
    13345 9312 atoms, 9396 bonds, 612 residues, 1 model selected 
    13346 
    13347 > ui tool show "Color Actions"
    13348 
    13349 > color sel deep sky blue
    13350 
    13351 > color sel royal blue
    13352 
    13353 > color sel dodger blue
    13354 
    13355 > color sel royal blue
    13356 
    13357 > select clear
    13358 
    13359 > show #21 models
    13360 
    13361 > select #21
    13362 
    13363 3398 atoms, 3015 bonds, 823 residues, 1 model selected 
    13364 
    13365 > show sel atoms
    13366 
    13367 > hide sel atoms
    13368 
    13369 > hide #23 models
    13370 
    13371 > delete atoms sel
    13372 
    13373 > delete bonds sel
    13374 
    13375 > open 4RS2 fromDatabase pdb format mmcif
    13376 
    13377 4rs2 title: 
    13378 1.55 Angstrom Crystal Structure of GNAT Family N-acetyltransferase (YhbS) from
    13379 Escherichia coli in Complex with CoA [more info...] 
    13380 
    13381 Chain information for 4rs2 #21 
    13382 --- 
    13383 Chain | Description | UniProt 
    13384 A B | Predicted acyltransferase with acyl-CoA N-acyltransferase domain | H0QE96_ECOLI 2-167 
    13385 
    13386 Non-standard residues in 4rs2 #21 
    13387 --- 
    13388 COA \u2014 coenzyme A 
    13389 
    13390 4rs2 mmCIF Assemblies 
    13391 --- 
    13392 1| author_and_software_defined_assembly 
    13393 2| author_and_software_defined_assembly 
    13394 
    13395 331 atoms have alternate locations. Control/examine alternate locations with
    13396 Altloc Explorer [start tool...] or the altlocs command. 
    13397 
    13398 > select #1/A
    13399 
    13400 1311 atoms, 1341 bonds, 167 residues, 1 model selected 
    13401 
    13402 > ui tool show Matchmaker
    13403 
    13404 > matchmaker #23 to #1 & sel
    13405 
    13406 Computing secondary structure 
    13407 [Repeated 1 time(s)]  Parameters 
    13408 --- 
    13409 Chain pairing | bb 
    13410 Alignment algorithm | Needleman-Wunsch 
    13411 Similarity matrix | BLOSUM-62 
    13412 SS fraction | 0.3 
    13413 Gap open (HH/SS/other) | 18/18/6 
    13414 Gap extend | 1 
    13415 SS matrix |  |  | H | S | O 
    13416 ---|---|---|--- 
    13417 H | 6 | -9 | -6 
    13418 S |  | 6 | -6 
    13419 O |  |  | 4 
    13420 Iteration cutoff | 2 
    13421 
    13422 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with YhbS-
    13423 Hfq6mer.ranked_0.pdb, chain A (#23), sequence alignment score = 875 
    13424 RMSD between 167 pruned atom pairs is 0.339 angstroms; (across all 167 pairs:
    13425 0.339) 
    13426 
    13427 
    13428 > matchmaker #23 to #1 & sel
    13429 
    13430 Computing secondary structure 
    13431 [Repeated 1 time(s)]  Parameters 
    13432 --- 
    13433 Chain pairing | bb 
    13434 Alignment algorithm | Needleman-Wunsch 
    13435 Similarity matrix | BLOSUM-62 
    13436 SS fraction | 0.3 
    13437 Gap open (HH/SS/other) | 18/18/6 
    13438 Gap extend | 1 
    13439 SS matrix |  |  | H | S | O 
    13440 ---|---|---|--- 
    13441 H | 6 | -9 | -6 
    13442 S |  | 6 | -6 
    13443 O |  |  | 4 
    13444 Iteration cutoff | 2 
    13445 
    13446 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with YhbS-
    13447 Hfq6mer.ranked_0.pdb, chain A (#23), sequence alignment score = 875 
    13448 RMSD between 167 pruned atom pairs is 0.339 angstroms; (across all 167 pairs:
    13449 0.339) 
    13450 
    13451 
    13452 > show #1 models
    13453 
    13454 > select #1/A
    13455 
    13456 1311 atoms, 1341 bonds, 167 residues, 1 model selected 
    13457 
    13458 > matchmaker #21 to #1 & sel
    13459 
    13460 Computing secondary structure 
    13461 [Repeated 1 time(s)]  Parameters 
    13462 --- 
    13463 Chain pairing | bb 
    13464 Alignment algorithm | Needleman-Wunsch 
    13465 Similarity matrix | BLOSUM-62 
    13466 SS fraction | 0.3 
    13467 Gap open (HH/SS/other) | 18/18/6 
    13468 Gap extend | 1 
    13469 SS matrix |  |  | H | S | O 
    13470 ---|---|---|--- 
    13471 H | 6 | -9 | -6 
    13472 S |  | 6 | -6 
    13473 O |  |  | 4 
    13474 Iteration cutoff | 2 
    13475 
    13476 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with 4rs2, chain B
    13477 (#21), sequence alignment score = 836 
    13478 RMSD between 166 pruned atom pairs is 0.628 angstroms; (across all 167 pairs:
    13479 0.670) 
    13480 
    13481 
    13482 > select #21/A
    13483 
    13484 1678 atoms, 1491 bonds, 404 residues, 1 model selected 
    13485 
    13486 > hide sel cartoons
    13487 
    13488 > hide sel atoms
    13489 
    13490 > hide #21 models
    13491 
    13492 > select #1
    13493 
    13494 2107 atoms, 2148 bonds, 268 residues, 1 model selected 
    13495 
    13496 > show sel atoms
    13497 
    13498 > select #1/C:1@CO
    13499 
    13500 1 atom, 1 residue, 1 model selected 
    13501 
    13502 > select ~sel & ##selected
    13503 
    13504 2106 atoms, 2148 bonds, 267 residues, 1 model selected 
    13505 
    13506 > hide sel atoms
    13507 
    13508 > select clear
    13509 
    13510 > select #1/C:1@CO
    13511 
    13512 1 atom, 1 residue, 1 model selected 
    13513 
    13514 > select ::name="CO"
    13515 
    13516 15 atoms, 15 residues, 15 models selected 
    13517 
    13518 > ui tool show "Color Actions"
    13519 
    13520 > color sel dim gray
    13521 
    13522 > select clear
    13523 
    13524 > show #21 models
    13525 
    13526 > show #23 models
    13527 
    13528 > hide #23 models
    13529 
    13530 > show #23 models
    13531 
    13532 > hide #23 models
    13533 
    13534 > open /Users/taic/Library/CloudStorage/OneDrive-
    13535 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfq1_65x6_co/fold_hqba_hfq1_65x6_co_model_0.cif
    13536 
    13537 Chain information for fold_hqba_hfq1_65x6_co_model_0.cif #24 
    13538 --- 
    13539 Chain | Description 
    13540 A | . 
    13541 B C D E F G | . 
    13542 
    13543 
    13544 > open /Users/taic/Library/CloudStorage/OneDrive-
    13545 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfq1_65x6_co/fold_hqba_hfq1_65x6_co_model_1.cif
    13546 
    13547 Chain information for fold_hqba_hfq1_65x6_co_model_1.cif #25 
    13548 --- 
    13549 Chain | Description 
    13550 A | . 
    13551 B C D E F G | . 
    13552 
    13553 
    13554 > open /Users/taic/Library/CloudStorage/OneDrive-
    13555 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfq1_65x6_co/fold_hqba_hfq1_65x6_co_model_2.cif
    13556 
    13557 Chain information for fold_hqba_hfq1_65x6_co_model_2.cif #26 
    13558 --- 
    13559 Chain | Description 
    13560 A | . 
    13561 B C D E F G | . 
    13562 
    13563 
    13564 > open /Users/taic/Library/CloudStorage/OneDrive-
    13565 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfq1_65x6_co/fold_hqba_hfq1_65x6_co_model_3.cif
    13566 
    13567 Chain information for fold_hqba_hfq1_65x6_co_model_3.cif #27 
    13568 --- 
    13569 Chain | Description 
    13570 A | . 
    13571 B C D E F G | . 
    13572 
    13573 
    13574 > open /Users/taic/Library/CloudStorage/OneDrive-
    13575 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfq1_65x6_co/fold_hqba_hfq1_65x6_co_model_4.cif
    13576 
    13577 Chain information for fold_hqba_hfq1_65x6_co_model_4.cif #28 
    13578 --- 
    13579 Chain | Description 
    13580 A | . 
    13581 B C D E F G | . 
    13582 
    13583 
    13584 > hide #21 models
    13585 
    13586 > select #24#25#26#27#28
    13587 
    13588 22010 atoms, 22395 bonds, 2790 residues, 5 models selected 
    13589 
    13590 > hide sel atoms
    13591 
    13592 > show sel cartoons
    13593 
    13594 Computing secondary structure 
    13595 [Repeated 4 time(s)]
    13596 
    13597 > open /Users/taic/Library/CloudStorage/OneDrive-
    13598 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfqx6_co/fold_hqba_hfqx6_co_model_0.cif
    13599 
    13600 Chain information for fold_hqba_hfqx6_co_model_0.cif #29 
    13601 --- 
    13602 Chain | Description 
    13603 A | . 
    13604 B C D E F G | . 
    13605 
    13606 
    13607 > open /Users/taic/Library/CloudStorage/OneDrive-
    13608 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfqx6_co/fold_hqba_hfqx6_co_model_1.cif
    13609 
    13610 Chain information for fold_hqba_hfqx6_co_model_1.cif #30 
    13611 --- 
    13612 Chain | Description 
    13613 A | . 
    13614 B C D E F G | . 
    13615 
    13616 
    13617 > open /Users/taic/Library/CloudStorage/OneDrive-
    13618 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfqx6_co/fold_hqba_hfqx6_co_model_2.cif
    13619 
    13620 Chain information for fold_hqba_hfqx6_co_model_2.cif #31 
    13621 --- 
    13622 Chain | Description 
    13623 A | . 
    13624 B C D E F G | . 
    13625 
    13626 
    13627 > open /Users/taic/Library/CloudStorage/OneDrive-
    13628 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfqx6_co/fold_hqba_hfqx6_co_model_3.cif
    13629 
    13630 Chain information for fold_hqba_hfqx6_co_model_3.cif #32 
    13631 --- 
    13632 Chain | Description 
    13633 A | . 
    13634 B C D E F G | . 
    13635 
    13636 
    13637 > open /Users/taic/Library/CloudStorage/OneDrive-
    13638 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_hfqx6_co/fold_hqba_hfqx6_co_model_4.cif
    13639 
    13640 Chain information for fold_hqba_hfqx6_co_model_4.cif #33 
    13641 --- 
    13642 Chain | Description 
    13643 A | . 
    13644 B C D E F G | . 
    13645 
    13646 
    13647 > select add #29
    13648 
    13649 28038 atoms, 28536 bonds, 3570 residues, 6 models selected 
    13650 
    13651 > select add #30
    13652 
    13653 34066 atoms, 34677 bonds, 4350 residues, 7 models selected 
    13654 
    13655 > select add #31
    13656 
    13657 40094 atoms, 40818 bonds, 5130 residues, 8 models selected 
    13658 
    13659 > select add #32
    13660 
    13661 46122 atoms, 46959 bonds, 5910 residues, 9 models selected 
    13662 
    13663 > select add #33
    13664 
    13665 52150 atoms, 53100 bonds, 6690 residues, 10 models selected 
    13666 
    13667 > hide sel atoms
    13668 
    13669 > show sel cartoons
    13670 
    13671 Computing secondary structure 
    13672 [Repeated 4 time(s)]
    13673 
    13674 > select #1
    13675 
    13676 2107 atoms, 2148 bonds, 268 residues, 1 model selected 
    13677 
    13678 > select #1/A
    13679 
    13680 1311 atoms, 1341 bonds, 167 residues, 1 model selected 
    13681 
    13682 > ui tool show Matchmaker
    13683 
    13684 > matchmaker #24-33 to #1 & sel
    13685 
    13686 Computing secondary structure 
    13687 [Repeated 10 time(s)]  Parameters 
    13688 --- 
    13689 Chain pairing | bb 
    13690 Alignment algorithm | Needleman-Wunsch 
    13691 Similarity matrix | BLOSUM-62 
    13692 SS fraction | 0.3 
    13693 Gap open (HH/SS/other) | 18/18/6 
    13694 Gap extend | 1 
    13695 SS matrix |  |  | H | S | O 
    13696 ---|---|---|--- 
    13697 H | 6 | -9 | -6 
    13698 S |  | 6 | -6 
    13699 O |  |  | 4 
    13700 Iteration cutoff | 2 
    13701 
    13702 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    13703 fold_hqba_hfq1_65x6_co_model_0.cif, chain A (#24), sequence alignment score =
    13704 867.8 
    13705 RMSD between 167 pruned atom pairs is 0.225 angstroms; (across all 167 pairs:
    13706 0.225) 
    13707 
    13708 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    13709 fold_hqba_hfq1_65x6_co_model_1.cif, chain A (#25), sequence alignment score =
    13710 867.8 
    13711 RMSD between 167 pruned atom pairs is 0.181 angstroms; (across all 167 pairs:
    13712 0.181) 
    13713 
    13714 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    13715 fold_hqba_hfq1_65x6_co_model_2.cif, chain A (#26), sequence alignment score =
    13716 867.8 
    13717 RMSD between 167 pruned atom pairs is 0.299 angstroms; (across all 167 pairs:
    13718 0.299) 
    13719 
    13720 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    13721 fold_hqba_hfq1_65x6_co_model_3.cif, chain A (#27), sequence alignment score =
    13722 867.8 
    13723 RMSD between 167 pruned atom pairs is 0.368 angstroms; (across all 167 pairs:
    13724 0.368) 
    13725 
    13726 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    13727 fold_hqba_hfq1_65x6_co_model_4.cif, chain A (#28), sequence alignment score =
    13728 867.8 
    13729 RMSD between 167 pruned atom pairs is 0.255 angstroms; (across all 167 pairs:
    13730 0.255) 
    13731 
    13732 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    13733 fold_hqba_hfqx6_co_model_0.cif, chain A (#29), sequence alignment score =
    13734 867.8 
    13735 RMSD between 167 pruned atom pairs is 0.202 angstroms; (across all 167 pairs:
    13736 0.202) 
    13737 
    13738 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    13739 fold_hqba_hfqx6_co_model_1.cif, chain A (#30), sequence alignment score =
    13740 864.8 
    13741 RMSD between 167 pruned atom pairs is 0.220 angstroms; (across all 167 pairs:
    13742 0.220) 
    13743 
    13744 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    13745 fold_hqba_hfqx6_co_model_2.cif, chain A (#31), sequence alignment score =
    13746 864.8 
    13747 RMSD between 167 pruned atom pairs is 0.288 angstroms; (across all 167 pairs:
    13748 0.288) 
    13749 
    13750 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    13751 fold_hqba_hfqx6_co_model_3.cif, chain A (#32), sequence alignment score =
    13752 868.4 
    13753 RMSD between 167 pruned atom pairs is 0.264 angstroms; (across all 167 pairs:
    13754 0.264) 
    13755 
    13756 Matchmaker fold_hqba_yhbq_co_model_0.cif, chain A (#1) with
    13757 fold_hqba_hfqx6_co_model_4.cif, chain A (#33), sequence alignment score =
    13758 864.8 
    13759 RMSD between 167 pruned atom pairs is 0.315 angstroms; (across all 167 pairs:
    13760 0.315) 
    13761 
    13762 
    13763 > show #23 models
    13764 
    13765 > hide #23 models
    13766 
    13767 > show #23 models
    13768 
    13769 > hide #23 models
    13770 
    13771 > hide #25 models
    13772 
    13773 > hide #26 models
    13774 
    13775 > hide #27 models
    13776 
    13777 > hide #28 models
    13778 
    13779 > hide #30 models
    13780 
    13781 > hide #31 models
    13782 
    13783 > show #31 models
    13784 
    13785 > show #30 models
    13786 
    13787 > show #25 models
    13788 
    13789 > show #26 models
    13790 
    13791 > show #27 models
    13792 
    13793 > show #28 models
    13794 
    13795 > hide #25 models
    13796 
    13797 > hide #24 models
    13798 
    13799 > hide #33 models
    13800 
    13801 > hide #29 models
    13802 
    13803 > show #25 models
    13804 
    13805 > show #33 models
    13806 
    13807 > select add #24
    13808 
    13809 5713 atoms, 5820 bonds, 725 residues, 2 models selected 
    13810 
    13811 > select subtract #24
    13812 
    13813 1311 atoms, 1341 bonds, 167 residues, 1 model selected 
    13814 
    13815 > select add #25
    13816 
    13817 5713 atoms, 5820 bonds, 725 residues, 2 models selected 
    13818 
    13819 > select add #26
    13820 
    13821 10115 atoms, 10299 bonds, 1283 residues, 3 models selected 
    13822 
    13823 > select add #27
    13824 
    13825 14517 atoms, 14778 bonds, 1841 residues, 4 models selected 
    13826 
    13827 > select add #28
    13828 
    13829 18919 atoms, 19257 bonds, 2399 residues, 5 models selected 
    13830 
    13831 > select add #30
    13832 
    13833 24947 atoms, 25398 bonds, 3179 residues, 6 models selected 
    13834 
    13835 > select add #31
    13836 
    13837 30975 atoms, 31539 bonds, 3959 residues, 7 models selected 
    13838 
    13839 > select add #32
    13840 
    13841 37003 atoms, 37680 bonds, 4739 residues, 8 models selected 
    13842 
    13843 > select add #33
    13844 
    13845 43031 atoms, 43821 bonds, 5519 residues, 9 models selected 
    13846 
    13847 > select add #1
    13848 
    13849 43827 atoms, 44628 bonds, 5620 residues, 9 models selected 
    13850 
    13851 > hide #1 models
    13852 
    13853 > select subtract #1
    13854 
    13855 41720 atoms, 42480 bonds, 5352 residues, 8 models selected 
    13856 
    13857 > delete atoms sel
    13858 
    13859 > delete bonds sel
    13860 
    13861 > show #1 models
    13862 
    13863 > show #21 models
    13864 
    13865 > hide #21 models
    13866 
    13867 > show #2 models
    13868 
    13869 > show #3 models
    13870 
    13871 > show #4 models
    13872 
    13873 > show #5 models
    13874 
    13875 > select ::name="CO"
    13876 
    13877 17 atoms, 17 residues, 17 models selected 
    13878 
    13879 > show sel & #1-5 atoms
    13880 
    13881 > select #4/A:32
    13882 
    13883 10 atoms, 10 bonds, 1 residue, 1 model selected 
    13884 
    13885 > style sel stick
    13886 
    13887 Changed 10 atom styles 
    13888 
    13889 > show sel atoms
    13890 
    13891 > ui tool show "Color Actions"
    13892 
    13893 > color sel magenta
    13894 
    13895 > select clear
    13896 
    13897 > select add #2
    13898 
    13899 2107 atoms, 2148 bonds, 268 residues, 1 model selected 
    13900 
    13901 > select add #3
    13902 
    13903 4214 atoms, 4296 bonds, 536 residues, 2 models selected 
    13904 
    13905 > select add #4
    13906 
    13907 6321 atoms, 6444 bonds, 804 residues, 3 models selected 
    13908 
    13909 > select add #5
    13910 
    13911 8428 atoms, 8592 bonds, 1072 residues, 4 models selected 
    13912 
    13913 > select clear
    13914 
    13915 > show #21 models
    13916 
    13917 > select #21/B:-10
    13918 
    13919 10 atoms, 10 bonds, 1 residue, 1 model selected 
    13920 
    13921 > select add #21/B:0
    13922 
    13923 21 atoms, 20 bonds, 2 residues, 1 model selected 
    13924 
    13925 > select add #21/B:-1
    13926 
    13927 29 atoms, 27 bonds, 3 residues, 1 model selected 
    13928 
    13929 > select add #21/B:-2
    13930 
    13931 34 atoms, 31 bonds, 4 residues, 1 model selected 
    13932 
    13933 > select add #21/B:-3
    13934 
    13935 41 atoms, 38 bonds, 5 residues, 1 model selected 
    13936 
    13937 > select add #21/B:-4
    13938 
    13939 49 atoms, 45 bonds, 6 residues, 1 model selected 
    13940 
    13941 > select add #21/B:-5
    13942 
    13943 56 atoms, 51 bonds, 7 residues, 1 model selected 
    13944 
    13945 > select add #21/B:-6
    13946 
    13947 66 atoms, 61 bonds, 8 residues, 1 model selected 
    13948 
    13949 > select add #21/B:-7
    13950 
    13951 76 atoms, 71 bonds, 9 residues, 1 model selected 
    13952 
    13953 > select add #21/B:-8
    13954 
    13955 86 atoms, 81 bonds, 10 residues, 1 model selected 
    13956 
    13957 > select add #21/B:-9
    13958 
    13959 96 atoms, 91 bonds, 11 residues, 1 model selected 
    13960 
    13961 > hide sel cartoons
    13962 
    13963 > select clear
    13964 
    13965 > select ::name="HIS"
    13966 
    13967 3382 atoms, 3436 bonds, 313 residues, 24 models selected 
    13968 
    13969 > hide #2 models
    13970 
    13971 > hide #3 models
    13972 
    13973 > hide #4 models
    13974 
    13975 > hide #5 models
    13976 
    13977 > hide #21 models
    13978 
    13979 > show #2 models
    13980 
    13981 > show #3 models
    13982 
    13983 > show #4 models
    13984 
    13985 > show #5 models
    13986 
    13987 > hide #4 models
    13988 
    13989 > hide #2 models
    13990 
    13991 > hide #3 models
    13992 
    13993 > hide #5 models
    13994 
    13995 > select #1/A:32
    13996 
    13997 10 atoms, 10 bonds, 1 residue, 1 model selected 
    13998 
    13999 > color sel magenta
    14000 
    14001 > hide sel atoms
    14002 
    14003 > show sel atoms
    14004 
    14005 > select clear
    14006 
    14007 > show #21 models
    14008 
    14009 > show #29 models
    14010 
    14011 > hide #21 models
    14012 
    14013 > hide #1 models
    14014 
    14015 > show #23 models
    14016 
    14017 > hide #29 models
    14018 
    14019 > select #23/G:30
    14020 
    14021 19 atoms, 18 bonds, 1 residue, 1 model selected 
    14022 
    14023 > select #23/G:31
    14024 
    14025 22 atoms, 21 bonds, 1 residue, 1 model selected 
    14026 
    14027 > show sel atoms
    14028 
    14029 > style sel stick
    14030 
    14031 Changed 22 atom styles 
    14032 
    14033 > show #29 models
    14034 
    14035 > hide #23 models
    14036 
    14037 > select #29/G:31
    14038 
    14039 9 atoms, 8 bonds, 1 residue, 1 model selected 
    14040 
    14041 > show sel atoms
    14042 
    14043 > style sel stick
    14044 
    14045 Changed 9 atom styles 
    14046 
    14047 > show #23 models
    14048 
    14049 > hide #23 models
    14050 
    14051 > show #1 models
    14052 
    14053 > hide #1 models
    14054 
    14055 > color sel cornflower blue
    14056 
    14057 > select clear
    14058 
    14059 > show #23 models
    14060 
    14061 > hide #29 models
    14062 
    14063 > show #29 models
    14064 
    14065 > hide #23 models
    14066 
    14067 > hide #29 models
    14068 
    14069 > show #29 models
    14070 
    14071 > select #29/G:31
    14072 
    14073 9 atoms, 8 bonds, 1 residue, 1 model selected 
    14074 
    14075 > undo
    14076 
    14077 [Repeated 9 time(s)]
    14078 
    14079 > ui tool show "Color Actions"
    14080 
    14081 > color sel pale violet red
    14082 
    14083 > color sel light pink
    14084 
    14085 > color sel hot pink
    14086 
    14087 > color sel plum
    14088 
    14089 > select clear
    14090 
    14091 > select #29/G:31
    14092 
    14093 9 atoms, 8 bonds, 1 residue, 1 model selected 
    14094 
    14095 > color sel plum
    14096 
    14097 > color sel violet
    14098 
    14099 > select clear
    14100 
    14101 > select #29/G:31
    14102 
    14103 9 atoms, 8 bonds, 1 residue, 1 model selected 
    14104 
    14105 > hide sel atoms
    14106 
    14107 > select #29/A:102
    14108 
    14109 9 atoms, 8 bonds, 1 residue, 1 model selected 
    14110 
    14111 > color sel red
    14112 
    14113 > style sel stick
    14114 
    14115 Changed 9 atom styles 
    14116 
    14117 > show sel atoms
    14118 
    14119 > select #29/A:98
    14120 
    14121 8 atoms, 7 bonds, 1 residue, 1 model selected 
    14122 
    14123 > style sel stick
    14124 
    14125 Changed 8 atom styles 
    14126 
    14127 > show sel atoms
    14128 
    14129 > color sel red
    14130 
    14131 Drag select of 3 residues 
    14132 
    14133 > select clear
    14134 
    14135 > select #29/C:31
    14136 
    14137 9 atoms, 8 bonds, 1 residue, 1 model selected 
    14138 
    14139 > color sel cornflower blue
    14140 
    14141 > style sel stick
    14142 
    14143 Changed 9 atom styles 
    14144 
    14145 > show sel atoms
    14146 
    14147 > select #29/A:98
    14148 
    14149 8 atoms, 7 bonds, 1 residue, 1 model selected 
    14150 
    14151 > select #29/C:31
    14152 
    14153 9 atoms, 8 bonds, 1 residue, 1 model selected 
    14154 
    14155 > color sel medium blue
    14156 
    14157 > select clear
    14158 
    14159 > select #29/C:31
    14160 
    14161 9 atoms, 8 bonds, 1 residue, 1 model selected 
    14162 
    14163 > ui tool show "Color Actions"
    14164 
    14165 > color sel royal blue
    14166 
    14167 > select clear
    14168 
    14169 > show #23 models
    14170 
    14171 > select #23/C:31
    14172 
    14173 22 atoms, 21 bonds, 1 residue, 1 model selected 
    14174 
    14175 > style sel stick
    14176 
    14177 Changed 22 atom styles 
    14178 
    14179 > show sel atoms
    14180 
    14181 > hide #23 models
    14182 
    14183 > select #29/A
    14184 
    14185 1311 atoms, 1341 bonds, 167 residues, 1 model selected 
    14186 
    14187 > select ~sel & ##selected
    14188 
    14189 4717 atoms, 4800 bonds, 613 residues, 1 model selected 
    14190 
    14191 > color sel tan
    14192 
    14193 > select clear
    14194 
    14195 > select #29/C:31
    14196 
    14197 9 atoms, 8 bonds, 1 residue, 1 model selected 
    14198 
    14199 > color sel royal blue
    14200 
    14201 > select #29/G:33
    14202 
    14203 9 atoms, 8 bonds, 1 residue, 1 model selected 
    14204 
    14205 > select clear
    14206 
    14207 > show #21 models
    14208 
    14209 > save /Users/taic/Library/CloudStorage/OneDrive-
    14210 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni.cxs
    14211 
    14212 > save /Users/taic/Library/CloudStorage/OneDrive-
    14213 > NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/HqbA_Ni.csx.cxs
    14214 
    14215 > close session
    14216 
    14217 > open /Users/taic/Library/CloudStorage/OneDrive-
    14218 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    14219 > Predictions/azor_monomer/fold_azor_monomer_model_0.cif
    14220 
    14221 Chain information for fold_azor_monomer_model_0.cif #1 
    14222 --- 
    14223 Chain | Description 
    14224 A | . 
    14225 
    14226 Computing secondary structure 
    14227 
    14228 > open /Users/taic/Library/CloudStorage/OneDrive-
    14229 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    14230 > Predictions/azor_monomer/fold_azor_monomer_model_1.cif
    14231 
    14232 Chain information for fold_azor_monomer_model_1.cif #2 
    14233 --- 
    14234 Chain | Description 
    14235 A | . 
    14236 
    14237 Computing secondary structure 
    14238 
    14239 > open /Users/taic/Library/CloudStorage/OneDrive-
    14240 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    14241 > Predictions/azor_monomer/fold_azor_monomer_model_2.cif
    14242 
    14243 Chain information for fold_azor_monomer_model_2.cif #3 
    14244 --- 
    14245 Chain | Description 
    14246 A | . 
    14247 
    14248 Computing secondary structure 
    14249 
    14250 > open /Users/taic/Library/CloudStorage/OneDrive-
    14251 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    14252 > Predictions/azor_monomer/fold_azor_monomer_model_3.cif
    14253 
    14254 Chain information for fold_azor_monomer_model_3.cif #4 
    14255 --- 
    14256 Chain | Description 
    14257 A | . 
    14258 
    14259 Computing secondary structure 
    14260 
    14261 > open /Users/taic/Library/CloudStorage/OneDrive-
    14262 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    14263 > Predictions/azor_monomer/fold_azor_monomer_model_4.cif
    14264 
    14265 Chain information for fold_azor_monomer_model_4.cif #5 
    14266 --- 
    14267 Chain | Description 
    14268 A | . 
    14269 
    14270 Computing secondary structure 
    14271 
    14272 > open /Users/taic/Library/CloudStorage/OneDrive-
    14273 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    14274 > Predictions/azor_monomer_fad/fold_azor_monomer_fad_model_0.cif
    14275 
    14276 Summary of feedback from opening /Users/taic/Library/CloudStorage/OneDrive-
    14277 NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    14278 Predictions/azor_monomer_fad/fold_azor_monomer_fad_model_0.cif 
    14279 --- 
    14280 note | Fetching CCD FAD from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/FAD/FAD.cif 
    14281 
    14282 Chain information for fold_azor_monomer_fad_model_0.cif #6 
    14283 --- 
    14284 Chain | Description 
    14285 A | . 
    14286 
    14287 Computing secondary structure 
    14288 
    14289 > rainbow
    14290 
    14291 > open /Users/taic/Library/CloudStorage/OneDrive-
    14292 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    14293 > Predictions/azor_monomer_fad/fold_azor_monomer_fad_model_1.cif
    14294 
    14295 Chain information for fold_azor_monomer_fad_model_1.cif #7 
    14296 --- 
    14297 Chain | Description 
    14298 A | . 
    14299 
    14300 Computing secondary structure 
    14301 
    14302 > open /Users/taic/Library/CloudStorage/OneDrive-
    14303 > NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
    14304 > Predictions/azor_monomer_fad/fold_azor_monomer_fad_model_2.cif
    14305 
    14306 Chain information for fold_azor_monomer_fad_model_2.cif #8 
    14307 --- 
    14308 Chain | Description 
    14309 A | . 
    14310 
    14311 Computing secondary structure 
     1494[deleted to fit within ticket limits]
     1495
    143121496
    143131497> open /Users/taic/Library/CloudStorage/OneDrive-