Changes between Initial Version and Version 1 of Ticket #20553


Ignore:
Timestamp:
Jun 30, 2026, 9:41:17 AM (3 weeks ago)
Author:
Eric Pettersen
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #20553

    • Property Cc Eric Pettersen added
    • Property Component Unassigned → Sessions
    • Property Owner set to Zach Pearson
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → assigned
    • Property Summary ChimeraX bug report submission → Session save: 'BlastProteinResults' object has no attribute 'table'

  • Ticket #20553 – Description

    initial v1  
    31933193The above exception was the direct cause of the following exception: 
    31943194 
    3195 Traceback (most recent call last): 
    3196 File
    3197 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py",
    3198 line 1045, in _bootstrap_inner 
    3199 self.run() 
    3200 File
    3201 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py",
    3202 line 982, in run 
    3203 self._target(*self._args, **self._kwargs) 
    3204 File
    3205 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3206 packages/chimerax/core/tasks.py", line 323, in _run_function 
    3207 func(*args, **kw) 
    3208 File
    3209 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3210 packages/chimerax/webservices/cxservices_job.py", line 172, in run 
    3211 super().run() 
    3212 File
    3213 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3214 packages/chimerax/core/tasks.py", line 486, in run 
    3215 self.monitor() 
    3216 File
    3217 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3218 packages/chimerax/webservices/cxservices_job.py", line 207, in monitor 
    3219 result = self.chimerax_api.get_status(job_id=self.job_id) 
    3220 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    3221 File
    3222 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3223 packages/cxservices/api/default_api.py", line 954, in get_status 
    3224 (data) = self.get_status_with_http_info(job_id, **kwargs) # noqa: E501 
    3225 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    3226 File
    3227 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3228 packages/cxservices/api/default_api.py", line 1013, in
    3229 get_status_with_http_info 
    3230 return self.api_client.call_api( 
    3231 ^^^^^^^^^^^^^^^^^^^^^^^^^ 
    3232 File
    3233 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3234 packages/cxservices/api_client.py", line 319, in call_api 
    3235 return self.__call_api(resource_path, method, 
    3236 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    3237 File
    3238 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3239 packages/cxservices/api_client.py", line 151, in __call_api 
    3240 response_data = self.request( 
    3241 ^^^^^^^^^^^^^ 
    3242 File
    3243 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3244 packages/cxservices/api_client.py", line 341, in request 
    3245 return self.rest_client.GET(url, 
    3246 ^^^^^^^^^^^^^^^^^^^^^^^^^ 
    3247 File
    3248 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3249 packages/cxservices/rest.py", line 228, in GET 
    3250 return self.request("GET", url, 
    3251 ^^^^^^^^^^^^^^^^^^^^^^^^ 
    3252 File
    3253 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3254 packages/cxservices/rest.py", line 206, in request 
    3255 r = self.pool_manager.request(method, url, 
    3256 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    3257 File
    3258 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3259 packages/urllib3/_request_methods.py", line 135, in request 
    3260 return self.request_encode_url( 
    3261 ^^^^^^^^^^^^^^^^^^^^^^^^ 
    3262 File
    3263 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3264 packages/urllib3/_request_methods.py", line 182, in request_encode_url 
    3265 return self.urlopen(method, url, **extra_kw) 
    3266 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    3267 File
    3268 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3269 packages/urllib3/poolmanager.py", line 457, in urlopen 
    3270 response = conn.urlopen(method, u.request_uri, **kw) 
    3271 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    3272 File
    3273 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3274 packages/urllib3/connectionpool.py", line 872, in urlopen 
    3275 return self.urlopen( 
    3276 ^^^^^^^^^^^^^ 
    3277 File
    3278 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3279 packages/urllib3/connectionpool.py", line 872, in urlopen 
    3280 return self.urlopen( 
    3281 ^^^^^^^^^^^^^ 
    3282 File
    3283 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3284 packages/urllib3/connectionpool.py", line 872, in urlopen 
    3285 return self.urlopen( 
    3286 ^^^^^^^^^^^^^ 
    3287 File
    3288 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3289 packages/urllib3/connectionpool.py", line 842, in urlopen 
    3290 retries = retries.increment( 
    3291 ^^^^^^^^^^^^^^^^^^ 
    3292 File
    3293 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3294 packages/urllib3/util/retry.py", line 543, in increment 
    3295 raise MaxRetryError(_pool, url, reason) from reason # type: ignore[arg-type] 
    3296 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    3297 urllib3.exceptions.MaxRetryError:
    3298 HTTPConnectionPool(host='webservices.rbvi.ucsf.edu', port=80): Max retries
    3299 exceeded with url: /cxservices/api/v1/chimerax/jobs/FYN32J0BLRKN59QN/status
    3300 (Caused by
    3301 NewConnectionError("HTTPConnection(host='webservices.rbvi.ucsf.edu', port=80):
    3302 Failed to establish a new connection: [Errno 65] No route to host")) 
    3303 
    3304 > ui tool show H-Bonds
    3305 
    3306 > hbonds sel interModel false saltOnly true reveal true
    3307 
    3308 0 hydrogen bonds found 
    3309 
    3310 > ui tool show H-Bonds
    3311 
    3312 > hbonds sel interModel false saltOnly true reveal true
    3313 
    3314 0 hydrogen bonds found 
    3315 
    3316 > hide #!14 models
    3317 
    3318 > select ::name="GDP"
    3319 
    3320 168 atoms, 180 bonds, 6 residues, 6 models selected 
    3321 
    3322 > hbonds delete
    3323 
    3324 > ui tool show H-Bonds
    3325 
    3326 > hbonds sel interModel false saltOnly true reveal true
    3327 
    3328 8 hydrogen bonds found 
    3329 
    3330 > hide #!2 models
    3331 
    3332 > show #!14 models
    3333 
    3334 > hide #!14 models
    3335 
    3336 > show #!2 models
    3337 
    3338 > select #2/A:1
    3339 
    3340 8 atoms, 7 bonds, 1 residue, 1 model selected 
    3341 
    3342 > select #2/A
    3343 
    3344 3296 atoms, 3380 bonds, 404 residues, 1 model selected 
    3345 
    3346 > ui tool show H-Bonds
    3347 
    3348 > hbonds sel interModel false saltOnly true reveal true
    3349 
    3350 17 hydrogen bonds found 
    3351 
    3352 > hide #!2 models
    3353 
    3354 > show #!14 models
    3355 
    3356 > select #14/A:1
    3357 
    3358 8 atoms, 7 bonds, 1 residue, 1 model selected 
    3359 
    3360 > select #14/A:1-369
    3361 
    3362 3006 atoms, 3086 bonds, 369 residues, 1 model selected 
    3363 
    3364 > select #14/A:404
    3365 
    3366 7 atoms, 6 bonds, 1 residue, 1 model selected 
    3367 
    3368 > select #14/A:46-404
    3369 
    3370 2929 atoms, 3004 bonds, 359 residues, 1 model selected 
    3371 
    3372 > select #14/A:1
    3373 
    3374 8 atoms, 7 bonds, 1 residue, 1 model selected 
    3375 
    3376 > select #14/A
    3377 
    3378 3292 atoms, 3376 bonds, 404 residues, 1 model selected 
    3379 
    3380 > ui tool show H-Bonds
    3381 
    3382 > hbonds sel interModel false saltOnly true reveal true
    3383 
    3384 25 hydrogen bonds found 
    3385 
    3386 > show #!2 models
    3387 
    3388 > hide #!2 models
    3389 
    3390 > hide #!14 models
    3391 
    3392 > hide #2.1 models
    3393 
    3394 > show #2.1 models
    3395 
    3396 > hide #!2 models
    3397 
    3398 > show #!2 models
    3399 
    3400 > hbonds delete
    3401 
    3402 > ui tool show H-Bonds
    3403 
    3404 > hbonds sel interModel false saltOnly true reveal true
    3405 
    3406 25 hydrogen bonds found 
    3407 
    3408 > hide #14.1 models
    3409 
    3410 > show #!14 models
    3411 
    3412 > hide #!14 models
    3413 
    3414 > hide #2 models
    3415 
    3416 > show #2 models
    3417 
    3418 > select #2/A:404
    3419 
    3420 7 atoms, 6 bonds, 1 residue, 1 model selected 
    3421 
    3422 > select #2/A:291-404
    3423 
    3424 888 atoms, 901 bonds, 114 residues, 1 model selected 
    3425 
    3426 > select #2/A:404
    3427 
    3428 7 atoms, 6 bonds, 1 residue, 1 model selected 
    3429 
    3430 > select #2/A:184-404
    3431 
    3432 1778 atoms, 1822 bonds, 221 residues, 1 model selected 
    3433 
    3434 > select #2/A:1
    3435 
    3436 8 atoms, 7 bonds, 1 residue, 1 model selected 
    3437 
    3438 > select #2/A:1-216
    3439 
    3440 1785 atoms, 1836 bonds, 216 residues, 1 model selected 
    3441 
    3442 > select #2/A:1
    3443 
    3444 8 atoms, 7 bonds, 1 residue, 1 model selected 
    3445 
    3446 > select #2/A:1-395
    3447 
    3448 3221 atoms, 3305 bonds, 395 residues, 1 model selected 
    3449 
    3450 > select #2/A:404
    3451 
    3452 7 atoms, 6 bonds, 1 residue, 1 model selected 
    3453 
    3454 > select #2/A
    3455 
    3456 3296 atoms, 3380 bonds, 404 residues, 1 model selected 
    3457 
    3458 > ui tool show H-Bonds
    3459 
    3460 > hbonds sel interModel false saltOnly true reveal true
    3461 
    3462 17 hydrogen bonds found 
    3463 
    3464 > hide #!2 models
    3465 
    3466 > show #!14 models
    3467 
    3468 > show #14.1 models
    3469 
    3470 > show #!2 models
    3471 
    3472 > select add #2
    3473 
    3474 3324 atoms, 3410 bonds, 17 pseudobonds, 405 residues, 2 models selected 
    3475 
    3476 > select subtract #2
    3477 
    3478 Nothing selected 
    3479 
    3480 > open
    3481 > /Users/aleezamughal/Downloads/fold_gdp_bound_wbdp/fold_gdp_bound_wbdp_model_1.cif
    3482 
    3483 Chain information for fold_gdp_bound_wbdp_model_1.cif #15 
    3484 --- 
    3485 Chain | Description 
    3486 A | . 
    3487  
    3488 Associated fold_gdp_bound_wbdp_model_1.cif chain A to
    3489 fold_2026_05_15_15_51_model_1.cif, chain A with 0 mismatches 
    3490 Associated fold_gdp_bound_wbdp_model_1.cif chain A to
    3491 fold_2026_05_15_15_51_model_2.cif, chain A with 0 mismatches 
    3492 Associated fold_gdp_bound_wbdp_model_1.cif chain A to
    3493 fold_2026_05_15_15_51_model_3.cif, chain A with 0 mismatches 
    3494 Associated fold_gdp_bound_wbdp_model_1.cif chain A to
    3495 fold_2026_05_15_15_51_model_4.cif, chain A with 0 mismatches 
    3496 Associated fold_gdp_bound_wbdp_model_1.cif chain A to
    3497 fold_2026_06_01_00_39_model_0.cif, chain A with 0 mismatches 
    3498 Associated fold_gdp_bound_wbdp_model_1.cif chain A to
    3499 fold_2026_06_01_00_39_model_1.cif, chain A with 0 mismatches 
    3500 Associated fold_gdp_bound_wbdp_model_1.cif chain A to
    3501 fold_2026_06_01_00_39_model_2.cif, chain A with 0 mismatches 
    3502 Associated fold_gdp_bound_wbdp_model_1.cif chain A to
    3503 fold_2026_06_01_00_39_model_3.cif, chain A with 0 mismatches 
    3504 Associated fold_gdp_bound_wbdp_model_1.cif chain A to
    3505 fold_2026_06_01_00_39_model_4.cif, chain A with 0 mismatches 
    3506 Associated fold_gdp_bound_wbdp_model_1.cif chain A to
    3507 fold_2026_05_15_15_51_model_1.cif, chain A with 0 mismatches 
    3508 Chains used in RMSD evaluation for alignment 10: AlphaFold A0A9Q6ZED9 #!1/A,
    3509 fold_2026_05_15_15_51_model_1.cif #3/A, fold_gdp_bound_wbdp_model_1.cif #15/A 
    3510 Associated fold_gdp_bound_wbdp_model_1.cif chain A to
    3511 fold_2026_05_15_15_51_model_2.cif, chain A with 0 mismatches 
    3512 Chains used in RMSD evaluation for alignment 11: AlphaFold A0A9Q6ZED9 #!1/A,
    3513 fold_2026_05_15_15_51_model_2.cif #4/A, fold_gdp_bound_wbdp_model_1.cif #15/A 
    3514 Associated fold_gdp_bound_wbdp_model_1.cif chain A to
    3515 fold_2026_05_15_15_51_model_3.cif, chain A with 0 mismatches 
    3516 Chains used in RMSD evaluation for alignment 12: AlphaFold A0A9Q6ZED9 #!1/A,
    3517 fold_2026_05_15_15_51_model_3.cif #5/A, fold_gdp_bound_wbdp_model_1.cif #15/A 
    3518 Associated fold_gdp_bound_wbdp_model_1.cif chain A to
    3519 fold_2026_05_15_15_51_model_4.cif, chain A with 0 mismatches 
    3520 Chains used in RMSD evaluation for alignment 13: AlphaFold A0A9Q6ZED9 #!1/A,
    3521 fold_2026_05_15_15_51_model_4.cif #6/A, fold_gdp_bound_wbdp_model_1.cif #15/A 
    3522 Associated fold_gdp_bound_wbdp_model_1.cif chain A to
    3523 fold_2026_06_01_00_39_model_0.cif, chain A with 0 mismatches 
    3524 Chains used in RMSD evaluation for alignment 14: AlphaFold A0A9Q6ZED9 #!1/A,
    3525 fold_2026_06_01_00_39_model_0.cif #7/A, fold_gdp_bound_wbdp_model_1.cif #15/A 
    3526 Associated fold_gdp_bound_wbdp_model_1.cif chain A to
    3527 fold_2026_06_01_00_39_model_1.cif, chain A with 0 mismatches 
    3528 Chains used in RMSD evaluation for alignment 15: AlphaFold A0A9Q6ZED9 #!1/A,
    3529 fold_2026_06_01_00_39_model_1.cif #8/A, fold_gdp_bound_wbdp_model_1.cif #15/A 
    3530 Associated fold_gdp_bound_wbdp_model_1.cif chain A to
    3531 fold_2026_06_01_00_39_model_2.cif, chain A with 0 mismatches 
    3532 Chains used in RMSD evaluation for alignment 16: AlphaFold A0A9Q6ZED9 #!1/A,
    3533 fold_2026_06_01_00_39_model_2.cif #9/A, fold_gdp_bound_wbdp_model_1.cif #15/A 
    3534 Associated fold_gdp_bound_wbdp_model_1.cif chain A to
    3535 fold_2026_06_01_00_39_model_3.cif, chain A with 0 mismatches 
    3536 Chains used in RMSD evaluation for alignment 17: AlphaFold A0A9Q6ZED9 #!1/A,
    3537 fold_2026_06_01_00_39_model_3.cif #10/A, fold_gdp_bound_wbdp_model_1.cif #15/A 
    3538 Associated fold_gdp_bound_wbdp_model_1.cif chain A to
    3539 fold_2026_06_01_00_39_model_4.cif, chain A with 0 mismatches 
    3540 Chains used in RMSD evaluation for alignment 18: AlphaFold A0A9Q6ZED9 #!1/A,
    3541 fold_2026_06_01_00_39_model_4.cif #11/A, fold_gdp_bound_wbdp_model_1.cif #15/A 
    3542 Associated fold_gdp_bound_wbdp_model_1.cif chain A to AlphaFold A0A9Q6ZED9,
    3543 chain A with 0 mismatches 
    3544 Chains used in RMSD evaluation for alignment 19: AlphaFold A0A9Q6ZED9 #!1/A,
    3545 AlphaFold A0A9Q6ZED9 #12/A, fold_gdp_bound_wbdp_model_1.cif #15/A 
    3546 Associated fold_gdp_bound_wbdp_model_1.cif chain A to
    3547 fold_gdp_bound_wbdp_model_0.cif, chain A with 0 mismatches 
    3548 Chains used in RMSD evaluation for alignment 20: AlphaFold A0A9Q6ZED9 #!1/A,
    3549 fold_gdp_bound_wbdp_model_0.cif #14/A, fold_gdp_bound_wbdp_model_1.cif #15/A 
    3550 Computing secondary structure 
    3551 
    3552 > open
    3553 > /Users/aleezamughal/Downloads/fold_gdp_bound_wbdp/fold_gdp_bound_wbdp_model_2.cif
    3554 
    3555 Chain information for fold_gdp_bound_wbdp_model_2.cif #16 
    3556 --- 
    3557 Chain | Description 
    3558 A | . 
    3559  
    3560 Associated fold_gdp_bound_wbdp_model_2.cif chain A to
    3561 fold_2026_05_15_15_51_model_1.cif, chain A with 0 mismatches 
    3562 Associated fold_gdp_bound_wbdp_model_2.cif chain A to
    3563 fold_2026_05_15_15_51_model_2.cif, chain A with 0 mismatches 
    3564 Associated fold_gdp_bound_wbdp_model_2.cif chain A to
    3565 fold_2026_05_15_15_51_model_3.cif, chain A with 0 mismatches 
    3566 Associated fold_gdp_bound_wbdp_model_2.cif chain A to
    3567 fold_2026_05_15_15_51_model_4.cif, chain A with 0 mismatches 
    3568 Associated fold_gdp_bound_wbdp_model_2.cif chain A to
    3569 fold_2026_06_01_00_39_model_0.cif, chain A with 0 mismatches 
    3570 Associated fold_gdp_bound_wbdp_model_2.cif chain A to
    3571 fold_2026_06_01_00_39_model_1.cif, chain A with 0 mismatches 
    3572 Associated fold_gdp_bound_wbdp_model_2.cif chain A to
    3573 fold_2026_06_01_00_39_model_2.cif, chain A with 0 mismatches 
    3574 Associated fold_gdp_bound_wbdp_model_2.cif chain A to
    3575 fold_2026_06_01_00_39_model_3.cif, chain A with 0 mismatches 
    3576 Associated fold_gdp_bound_wbdp_model_2.cif chain A to
    3577 fold_2026_06_01_00_39_model_4.cif, chain A with 0 mismatches 
    3578 Associated fold_gdp_bound_wbdp_model_2.cif chain A to
    3579 fold_2026_05_15_15_51_model_1.cif, chain A with 0 mismatches 
    3580 Chains used in RMSD evaluation for alignment 10: AlphaFold A0A9Q6ZED9 #!1/A,
    3581 fold_2026_05_15_15_51_model_1.cif #3/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    3582 fold_gdp_bound_wbdp_model_2.cif #16/A 
    3583 Associated fold_gdp_bound_wbdp_model_2.cif chain A to
    3584 fold_2026_05_15_15_51_model_2.cif, chain A with 0 mismatches 
    3585 Chains used in RMSD evaluation for alignment 11: AlphaFold A0A9Q6ZED9 #!1/A,
    3586 fold_2026_05_15_15_51_model_2.cif #4/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    3587 fold_gdp_bound_wbdp_model_2.cif #16/A 
    3588 Associated fold_gdp_bound_wbdp_model_2.cif chain A to
    3589 fold_2026_05_15_15_51_model_3.cif, chain A with 0 mismatches 
    3590 Chains used in RMSD evaluation for alignment 12: AlphaFold A0A9Q6ZED9 #!1/A,
    3591 fold_2026_05_15_15_51_model_3.cif #5/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    3592 fold_gdp_bound_wbdp_model_2.cif #16/A 
    3593 Associated fold_gdp_bound_wbdp_model_2.cif chain A to
    3594 fold_2026_05_15_15_51_model_4.cif, chain A with 0 mismatches 
    3595 Chains used in RMSD evaluation for alignment 13: AlphaFold A0A9Q6ZED9 #!1/A,
    3596 fold_2026_05_15_15_51_model_4.cif #6/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    3597 fold_gdp_bound_wbdp_model_2.cif #16/A 
    3598 Associated fold_gdp_bound_wbdp_model_2.cif chain A to
    3599 fold_2026_06_01_00_39_model_0.cif, chain A with 0 mismatches 
    3600 Chains used in RMSD evaluation for alignment 14: AlphaFold A0A9Q6ZED9 #!1/A,
    3601 fold_2026_06_01_00_39_model_0.cif #7/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    3602 fold_gdp_bound_wbdp_model_2.cif #16/A 
    3603 Associated fold_gdp_bound_wbdp_model_2.cif chain A to
    3604 fold_2026_06_01_00_39_model_1.cif, chain A with 0 mismatches 
    3605 Chains used in RMSD evaluation for alignment 15: AlphaFold A0A9Q6ZED9 #!1/A,
    3606 fold_2026_06_01_00_39_model_1.cif #8/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    3607 fold_gdp_bound_wbdp_model_2.cif #16/A 
    3608 Associated fold_gdp_bound_wbdp_model_2.cif chain A to
    3609 fold_2026_06_01_00_39_model_2.cif, chain A with 0 mismatches 
    3610 Chains used in RMSD evaluation for alignment 16: AlphaFold A0A9Q6ZED9 #!1/A,
    3611 fold_2026_06_01_00_39_model_2.cif #9/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    3612 fold_gdp_bound_wbdp_model_2.cif #16/A 
    3613 Associated fold_gdp_bound_wbdp_model_2.cif chain A to
    3614 fold_2026_06_01_00_39_model_3.cif, chain A with 0 mismatches 
    3615 Chains used in RMSD evaluation for alignment 17: AlphaFold A0A9Q6ZED9 #!1/A,
    3616 fold_2026_06_01_00_39_model_3.cif #10/A, fold_gdp_bound_wbdp_model_1.cif
    3617 #15/A, fold_gdp_bound_wbdp_model_2.cif #16/A 
    3618 Associated fold_gdp_bound_wbdp_model_2.cif chain A to
    3619 fold_2026_06_01_00_39_model_4.cif, chain A with 0 mismatches 
    3620 Chains used in RMSD evaluation for alignment 18: AlphaFold A0A9Q6ZED9 #!1/A,
    3621 fold_2026_06_01_00_39_model_4.cif #11/A, fold_gdp_bound_wbdp_model_1.cif
    3622 #15/A, fold_gdp_bound_wbdp_model_2.cif #16/A 
    3623 Associated fold_gdp_bound_wbdp_model_2.cif chain A to AlphaFold A0A9Q6ZED9,
    3624 chain A with 0 mismatches 
    3625 Chains used in RMSD evaluation for alignment 19: AlphaFold A0A9Q6ZED9 #!1/A,
    3626 AlphaFold A0A9Q6ZED9 #12/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    3627 fold_gdp_bound_wbdp_model_2.cif #16/A 
    3628 Associated fold_gdp_bound_wbdp_model_2.cif chain A to
    3629 fold_gdp_bound_wbdp_model_0.cif, chain A with 0 mismatches 
    3630 Chains used in RMSD evaluation for alignment 20: AlphaFold A0A9Q6ZED9 #!1/A,
    3631 fold_gdp_bound_wbdp_model_0.cif #14/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    3632 fold_gdp_bound_wbdp_model_2.cif #16/A 
    3633 Computing secondary structure 
    3634 
    3635 > open
    3636 > /Users/aleezamughal/Downloads/fold_gdp_bound_wbdp/fold_gdp_bound_wbdp_model_3.cif
    3637 
    3638 Chain information for fold_gdp_bound_wbdp_model_3.cif #17 
    3639 --- 
    3640 Chain | Description 
    3641 A | . 
    3642  
    3643 Associated fold_gdp_bound_wbdp_model_3.cif chain A to
    3644 fold_2026_05_15_15_51_model_1.cif, chain A with 0 mismatches 
    3645 Associated fold_gdp_bound_wbdp_model_3.cif chain A to
    3646 fold_2026_05_15_15_51_model_2.cif, chain A with 0 mismatches 
    3647 Associated fold_gdp_bound_wbdp_model_3.cif chain A to
    3648 fold_2026_05_15_15_51_model_3.cif, chain A with 0 mismatches 
    3649 Associated fold_gdp_bound_wbdp_model_3.cif chain A to
    3650 fold_2026_05_15_15_51_model_4.cif, chain A with 0 mismatches 
    3651 Associated fold_gdp_bound_wbdp_model_3.cif chain A to
    3652 fold_2026_06_01_00_39_model_0.cif, chain A with 0 mismatches 
    3653 Associated fold_gdp_bound_wbdp_model_3.cif chain A to
    3654 fold_2026_06_01_00_39_model_1.cif, chain A with 0 mismatches 
    3655 Associated fold_gdp_bound_wbdp_model_3.cif chain A to
    3656 fold_2026_06_01_00_39_model_2.cif, chain A with 0 mismatches 
    3657 Associated fold_gdp_bound_wbdp_model_3.cif chain A to
    3658 fold_2026_06_01_00_39_model_3.cif, chain A with 0 mismatches 
    3659 Associated fold_gdp_bound_wbdp_model_3.cif chain A to
    3660 fold_2026_06_01_00_39_model_4.cif, chain A with 0 mismatches 
    3661 Associated fold_gdp_bound_wbdp_model_3.cif chain A to
    3662 fold_2026_05_15_15_51_model_1.cif, chain A with 0 mismatches 
    3663 Chains used in RMSD evaluation for alignment 10: AlphaFold A0A9Q6ZED9 #!1/A,
    3664 fold_2026_05_15_15_51_model_1.cif #3/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    3665 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A 
    3666 Associated fold_gdp_bound_wbdp_model_3.cif chain A to
    3667 fold_2026_05_15_15_51_model_2.cif, chain A with 0 mismatches 
    3668 Chains used in RMSD evaluation for alignment 11: AlphaFold A0A9Q6ZED9 #!1/A,
    3669 fold_2026_05_15_15_51_model_2.cif #4/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    3670 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A 
    3671 Associated fold_gdp_bound_wbdp_model_3.cif chain A to
    3672 fold_2026_05_15_15_51_model_3.cif, chain A with 0 mismatches 
    3673 Chains used in RMSD evaluation for alignment 12: AlphaFold A0A9Q6ZED9 #!1/A,
    3674 fold_2026_05_15_15_51_model_3.cif #5/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    3675 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A 
    3676 Associated fold_gdp_bound_wbdp_model_3.cif chain A to
    3677 fold_2026_05_15_15_51_model_4.cif, chain A with 0 mismatches 
    3678 Chains used in RMSD evaluation for alignment 13: AlphaFold A0A9Q6ZED9 #!1/A,
    3679 fold_2026_05_15_15_51_model_4.cif #6/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    3680 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A 
    3681 Associated fold_gdp_bound_wbdp_model_3.cif chain A to
    3682 fold_2026_06_01_00_39_model_0.cif, chain A with 0 mismatches 
    3683 Chains used in RMSD evaluation for alignment 14: AlphaFold A0A9Q6ZED9 #!1/A,
    3684 fold_2026_06_01_00_39_model_0.cif #7/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    3685 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A 
    3686 Associated fold_gdp_bound_wbdp_model_3.cif chain A to
    3687 fold_2026_06_01_00_39_model_1.cif, chain A with 0 mismatches 
    3688 Chains used in RMSD evaluation for alignment 15: AlphaFold A0A9Q6ZED9 #!1/A,
    3689 fold_2026_06_01_00_39_model_1.cif #8/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    3690 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A 
    3691 Associated fold_gdp_bound_wbdp_model_3.cif chain A to
    3692 fold_2026_06_01_00_39_model_2.cif, chain A with 0 mismatches 
    3693 Chains used in RMSD evaluation for alignment 16: AlphaFold A0A9Q6ZED9 #!1/A,
    3694 fold_2026_06_01_00_39_model_2.cif #9/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    3695 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A 
    3696 Associated fold_gdp_bound_wbdp_model_3.cif chain A to
    3697 fold_2026_06_01_00_39_model_3.cif, chain A with 0 mismatches 
    3698 Chains used in RMSD evaluation for alignment 17: AlphaFold A0A9Q6ZED9 #!1/A,
    3699 fold_2026_06_01_00_39_model_3.cif #10/A, fold_gdp_bound_wbdp_model_1.cif
    3700 #15/A, fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif
    3701 #17/A 
    3702 Associated fold_gdp_bound_wbdp_model_3.cif chain A to
    3703 fold_2026_06_01_00_39_model_4.cif, chain A with 0 mismatches 
    3704 Chains used in RMSD evaluation for alignment 18: AlphaFold A0A9Q6ZED9 #!1/A,
    3705 fold_2026_06_01_00_39_model_4.cif #11/A, fold_gdp_bound_wbdp_model_1.cif
    3706 #15/A, fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif
    3707 #17/A 
    3708 Associated fold_gdp_bound_wbdp_model_3.cif chain A to AlphaFold A0A9Q6ZED9,
    3709 chain A with 0 mismatches 
    3710 Chains used in RMSD evaluation for alignment 19: AlphaFold A0A9Q6ZED9 #!1/A,
    3711 AlphaFold A0A9Q6ZED9 #12/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    3712 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A 
    3713 Associated fold_gdp_bound_wbdp_model_3.cif chain A to
    3714 fold_gdp_bound_wbdp_model_0.cif, chain A with 0 mismatches 
    3715 Chains used in RMSD evaluation for alignment 20: AlphaFold A0A9Q6ZED9 #!1/A,
    3716 fold_gdp_bound_wbdp_model_0.cif #14/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    3717 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A 
    3718 Computing secondary structure 
    3719 
    3720 > open
    3721 > /Users/aleezamughal/Downloads/fold_gdp_bound_wbdp/fold_gdp_bound_wbdp_model_4.cif
    3722 
    3723 Chain information for fold_gdp_bound_wbdp_model_4.cif #18 
    3724 --- 
    3725 Chain | Description 
    3726 A | . 
    3727  
    3728 Associated fold_gdp_bound_wbdp_model_4.cif chain A to
    3729 fold_2026_05_15_15_51_model_1.cif, chain A with 0 mismatches 
    3730 Associated fold_gdp_bound_wbdp_model_4.cif chain A to
    3731 fold_2026_05_15_15_51_model_2.cif, chain A with 0 mismatches 
    3732 Associated fold_gdp_bound_wbdp_model_4.cif chain A to
    3733 fold_2026_05_15_15_51_model_3.cif, chain A with 0 mismatches 
    3734 Associated fold_gdp_bound_wbdp_model_4.cif chain A to
    3735 fold_2026_05_15_15_51_model_4.cif, chain A with 0 mismatches 
    3736 Associated fold_gdp_bound_wbdp_model_4.cif chain A to
    3737 fold_2026_06_01_00_39_model_0.cif, chain A with 0 mismatches 
    3738 Associated fold_gdp_bound_wbdp_model_4.cif chain A to
    3739 fold_2026_06_01_00_39_model_1.cif, chain A with 0 mismatches 
    3740 Associated fold_gdp_bound_wbdp_model_4.cif chain A to
    3741 fold_2026_06_01_00_39_model_2.cif, chain A with 0 mismatches 
    3742 Associated fold_gdp_bound_wbdp_model_4.cif chain A to
    3743 fold_2026_06_01_00_39_model_3.cif, chain A with 0 mismatches 
    3744 Associated fold_gdp_bound_wbdp_model_4.cif chain A to
    3745 fold_2026_06_01_00_39_model_4.cif, chain A with 0 mismatches 
    3746 Associated fold_gdp_bound_wbdp_model_4.cif chain A to
    3747 fold_2026_05_15_15_51_model_1.cif, chain A with 0 mismatches 
    3748 Chains used in RMSD evaluation for alignment 10: AlphaFold A0A9Q6ZED9 #!1/A,
    3749 fold_2026_05_15_15_51_model_1.cif #3/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    3750 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    3751 fold_gdp_bound_wbdp_model_4.cif #18/A 
    3752 Associated fold_gdp_bound_wbdp_model_4.cif chain A to
    3753 fold_2026_05_15_15_51_model_2.cif, chain A with 0 mismatches 
    3754 Chains used in RMSD evaluation for alignment 11: AlphaFold A0A9Q6ZED9 #!1/A,
    3755 fold_2026_05_15_15_51_model_2.cif #4/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    3756 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    3757 fold_gdp_bound_wbdp_model_4.cif #18/A 
    3758 Associated fold_gdp_bound_wbdp_model_4.cif chain A to
    3759 fold_2026_05_15_15_51_model_3.cif, chain A with 0 mismatches 
    3760 Chains used in RMSD evaluation for alignment 12: AlphaFold A0A9Q6ZED9 #!1/A,
    3761 fold_2026_05_15_15_51_model_3.cif #5/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    3762 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    3763 fold_gdp_bound_wbdp_model_4.cif #18/A 
    3764 Associated fold_gdp_bound_wbdp_model_4.cif chain A to
    3765 fold_2026_05_15_15_51_model_4.cif, chain A with 0 mismatches 
    3766 Chains used in RMSD evaluation for alignment 13: AlphaFold A0A9Q6ZED9 #!1/A,
    3767 fold_2026_05_15_15_51_model_4.cif #6/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    3768 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    3769 fold_gdp_bound_wbdp_model_4.cif #18/A 
    3770 Associated fold_gdp_bound_wbdp_model_4.cif chain A to
    3771 fold_2026_06_01_00_39_model_0.cif, chain A with 0 mismatches 
    3772 Chains used in RMSD evaluation for alignment 14: AlphaFold A0A9Q6ZED9 #!1/A,
    3773 fold_2026_06_01_00_39_model_0.cif #7/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    3774 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    3775 fold_gdp_bound_wbdp_model_4.cif #18/A 
    3776 Associated fold_gdp_bound_wbdp_model_4.cif chain A to
    3777 fold_2026_06_01_00_39_model_1.cif, chain A with 0 mismatches 
    3778 Chains used in RMSD evaluation for alignment 15: AlphaFold A0A9Q6ZED9 #!1/A,
    3779 fold_2026_06_01_00_39_model_1.cif #8/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    3780 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    3781 fold_gdp_bound_wbdp_model_4.cif #18/A 
    3782 Associated fold_gdp_bound_wbdp_model_4.cif chain A to
    3783 fold_2026_06_01_00_39_model_2.cif, chain A with 0 mismatches 
    3784 Chains used in RMSD evaluation for alignment 16: AlphaFold A0A9Q6ZED9 #!1/A,
    3785 fold_2026_06_01_00_39_model_2.cif #9/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    3786 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    3787 fold_gdp_bound_wbdp_model_4.cif #18/A 
    3788 Associated fold_gdp_bound_wbdp_model_4.cif chain A to
    3789 fold_2026_06_01_00_39_model_3.cif, chain A with 0 mismatches 
    3790 Chains used in RMSD evaluation for alignment 17: AlphaFold A0A9Q6ZED9 #!1/A,
    3791 fold_2026_06_01_00_39_model_3.cif #10/A, fold_gdp_bound_wbdp_model_1.cif
    3792 #15/A, fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif
    3793 #17/A, fold_gdp_bound_wbdp_model_4.cif #18/A 
    3794 Associated fold_gdp_bound_wbdp_model_4.cif chain A to
    3795 fold_2026_06_01_00_39_model_4.cif, chain A with 0 mismatches 
    3796 Chains used in RMSD evaluation for alignment 18: AlphaFold A0A9Q6ZED9 #!1/A,
    3797 fold_2026_06_01_00_39_model_4.cif #11/A, fold_gdp_bound_wbdp_model_1.cif
    3798 #15/A, fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif
    3799 #17/A, fold_gdp_bound_wbdp_model_4.cif #18/A 
    3800 Associated fold_gdp_bound_wbdp_model_4.cif chain A to AlphaFold A0A9Q6ZED9,
    3801 chain A with 0 mismatches 
    3802 Chains used in RMSD evaluation for alignment 19: AlphaFold A0A9Q6ZED9 #!1/A,
    3803 AlphaFold A0A9Q6ZED9 #12/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    3804 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    3805 fold_gdp_bound_wbdp_model_4.cif #18/A 
    3806 Associated fold_gdp_bound_wbdp_model_4.cif chain A to
    3807 fold_gdp_bound_wbdp_model_0.cif, chain A with 0 mismatches 
    3808 Chains used in RMSD evaluation for alignment 20: AlphaFold A0A9Q6ZED9 #!1/A,
    3809 fold_gdp_bound_wbdp_model_0.cif #14/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    3810 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    3811 fold_gdp_bound_wbdp_model_4.cif #18/A 
    3812 Computing secondary structure 
    3813 
    3814 > ui tool show Match→Align
    3815 
    3816 > ui tool show "Modeller Comparative"
    3817 
    3818 > ui tool show Match→Align
    3819 
    3820 > msa3d
    3821 > #!1/A#2/A#3/A#4/A#5/A#6/A#7/A#8/A#9/A#10/A#11/A#12/A#13/A#14/A#15/A#16/A#17/A#18/A
    3822 
    3823 Match→Align cutoff: 5.0, in column if within cutoff of: any 
    3824 0 fully populated columns 
    3825 Alignment identifier is MA-1 
    3826 Showing conservation header ("seq_conservation" residue attribute) for
    3827 alignment MA-1 
    3828 Chains used in RMSD evaluation for alignment MA-1: AlphaFold A0A9Q6ZED9 #!1/A,
    3829 fold_2026_05_15_15_51_model_0.cif #2/A, fold_2026_05_15_15_51_model_1.cif
    3830 #3/A, fold_2026_05_15_15_51_model_2.cif #4/A,
    3831 fold_2026_05_15_15_51_model_3.cif #5/A, fold_2026_05_15_15_51_model_4.cif
    3832 #6/A, fold_2026_06_01_00_39_model_0.cif #7/A,
    3833 fold_2026_06_01_00_39_model_1.cif #8/A, fold_2026_06_01_00_39_model_2.cif
    3834 #9/A, fold_2026_06_01_00_39_model_3.cif #10/A,
    3835 fold_2026_06_01_00_39_model_4.cif #11/A, AlphaFold A0A9Q6ZED9 #12/A, AlphaFold
    3836 A0A2W4UJ55 #13/A, fold_gdp_bound_wbdp_model_0.cif #14/A,
    3837 fold_gdp_bound_wbdp_model_1.cif #15/A, fold_gdp_bound_wbdp_model_2.cif #16/A,
    3838 fold_gdp_bound_wbdp_model_3.cif #17/A, fold_gdp_bound_wbdp_model_4.cif #18/A 
    3839 Showing rmsd header ("seq_rmsd" residue attribute) for alignment MA-1 
    3840 
    3841 > ui tool show Match→Align
    3842 
    3843 > msa3d
    3844 > #!1/A#2/A#3/A#4/A#5/A#6/A#7/A#8/A#9/A#10/A#11/A#12/A#13/A#14/A#15/A#16/A#17/A#18/A
    3845 
    3846 Match→Align cutoff: 5.0, in column if within cutoff of: any 
    3847 0 fully populated columns 
    3848 Alignment identifier is MA-1 
    3849 Showing conservation header ("seq_conservation" residue attribute) for
    3850 alignment MA-1 
    3851 Chains used in RMSD evaluation for alignment MA-1: AlphaFold A0A9Q6ZED9 #!1/A,
    3852 fold_2026_05_15_15_51_model_0.cif #2/A, fold_2026_05_15_15_51_model_1.cif
    3853 #3/A, fold_2026_05_15_15_51_model_2.cif #4/A,
    3854 fold_2026_05_15_15_51_model_3.cif #5/A, fold_2026_05_15_15_51_model_4.cif
    3855 #6/A, fold_2026_06_01_00_39_model_0.cif #7/A,
    3856 fold_2026_06_01_00_39_model_1.cif #8/A, fold_2026_06_01_00_39_model_2.cif
    3857 #9/A, fold_2026_06_01_00_39_model_3.cif #10/A,
    3858 fold_2026_06_01_00_39_model_4.cif #11/A, AlphaFold A0A9Q6ZED9 #12/A, AlphaFold
    3859 A0A2W4UJ55 #13/A, fold_gdp_bound_wbdp_model_0.cif #14/A,
    3860 fold_gdp_bound_wbdp_model_1.cif #15/A, fold_gdp_bound_wbdp_model_2.cif #16/A,
    3861 fold_gdp_bound_wbdp_model_3.cif #17/A, fold_gdp_bound_wbdp_model_4.cif #18/A 
    3862 Showing rmsd header ("seq_rmsd" residue attribute) for alignment MA-1 
    3863 
    3864 > ui tool show Match→Align
    3865 
    3866 > ui tool show Matchmaker
    3867 
    3868 > matchmaker #3-13,15-18#!2,14 to #1
    3869 
    3870 Parameters 
    3871 --- 
    3872 Chain pairing | bb 
    3873 Alignment algorithm | Needleman-Wunsch 
    3874 Similarity matrix | BLOSUM-62 
    3875 SS fraction | 0.3 
    3876 Gap open (HH/SS/other) | 18/18/6 
    3877 Gap extend | 1 
    3878 SS matrix |  |  | H | S | O 
    3879 ---|---|---|--- 
    3880 H | 6 | -9 | -6 
    3881 S |  | 6 | -6 
    3882 O |  |  | 4 
    3883 Iteration cutoff | 2 
    3884  
    3885 Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with
    3886 fold_2026_05_15_15_51_model_1.cif, chain A (#3), sequence alignment score =
    3887 2083.8 
    3888 RMSD between 351 pruned atom pairs is 0.790 angstroms; (across all 404 pairs:
    3889 2.779) 
    3890  
    3891 Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with
    3892 fold_2026_05_15_15_51_model_2.cif, chain A (#4), sequence alignment score =
    3893 2110.2 
    3894 Alignment identifier is 21 
    3895 Showing conservation header ("seq_conservation" residue attribute) for
    3896 alignment 21 
    3897 Hiding conservation header for alignment 21 
    3898 Chains used in RMSD evaluation for alignment 21: AlphaFold A0A9Q6ZED9 #!1/A,
    3899 fold_2026_05_15_15_51_model_2.cif #4/A 
    3900 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 21 
    3901 RMSD between 374 pruned atom pairs is 0.723 angstroms; (across all 404 pairs:
    3902 1.327) 
    3903  
    3904 Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with
    3905 fold_2026_05_15_15_51_model_3.cif, chain A (#5), sequence alignment score =
    3906 2121.6 
    3907 Alignment identifier is 22 
    3908 Showing conservation header ("seq_conservation" residue attribute) for
    3909 alignment 22 
    3910 Hiding conservation header for alignment 22 
    3911 Chains used in RMSD evaluation for alignment 22: AlphaFold A0A9Q6ZED9 #!1/A,
    3912 fold_2026_05_15_15_51_model_3.cif #5/A 
    3913 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 22 
    3914 RMSD between 367 pruned atom pairs is 0.649 angstroms; (across all 404 pairs:
    3915 2.750) 
    3916  
    3917 Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with
    3918 fold_2026_05_15_15_51_model_4.cif, chain A (#6), sequence alignment score =
    3919 2083.8 
    3920 Alignment identifier is 23 
    3921 Showing conservation header ("seq_conservation" residue attribute) for
    3922 alignment 23 
    3923 Hiding conservation header for alignment 23 
    3924 Chains used in RMSD evaluation for alignment 23: AlphaFold A0A9Q6ZED9 #!1/A,
    3925 fold_2026_05_15_15_51_model_4.cif #6/A 
    3926 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 23 
    3927 RMSD between 365 pruned atom pairs is 0.658 angstroms; (across all 404 pairs:
    3928 1.919) 
    3929  
    3930 Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with
    3931 fold_2026_06_01_00_39_model_0.cif, chain A (#7), sequence alignment score =
    3932 2110.8 
    3933 Alignment identifier is 24 
    3934 Showing conservation header ("seq_conservation" residue attribute) for
    3935 alignment 24 
    3936 Hiding conservation header for alignment 24 
    3937 Chains used in RMSD evaluation for alignment 24: AlphaFold A0A9Q6ZED9 #!1/A,
    3938 fold_2026_06_01_00_39_model_0.cif #7/A 
    3939 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 24 
    3940 RMSD between 371 pruned atom pairs is 0.326 angstroms; (across all 404 pairs:
    3941 1.148) 
    3942  
    3943 Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with
    3944 fold_2026_06_01_00_39_model_1.cif, chain A (#8), sequence alignment score =
    3945 2102.4 
    3946 Alignment identifier is 25 
    3947 Showing conservation header ("seq_conservation" residue attribute) for
    3948 alignment 25 
    3949 Hiding conservation header for alignment 25 
    3950 Chains used in RMSD evaluation for alignment 25: AlphaFold A0A9Q6ZED9 #!1/A,
    3951 fold_2026_06_01_00_39_model_1.cif #8/A 
    3952 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 25 
    3953 RMSD between 372 pruned atom pairs is 0.349 angstroms; (across all 404 pairs:
    3954 1.533) 
    3955  
    3956 Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with
    3957 fold_2026_06_01_00_39_model_2.cif, chain A (#9), sequence alignment score =
    3958 2115 
    3959 Alignment identifier is 26 
    3960 Showing conservation header ("seq_conservation" residue attribute) for
    3961 alignment 26 
    3962 Hiding conservation header for alignment 26 
    3963 Chains used in RMSD evaluation for alignment 26: AlphaFold A0A9Q6ZED9 #!1/A,
    3964 fold_2026_06_01_00_39_model_2.cif #9/A 
    3965 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 26 
    3966 RMSD between 374 pruned atom pairs is 0.420 angstroms; (across all 404 pairs:
    3967 2.359) 
    3968  
    3969 Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with
    3970 fold_2026_06_01_00_39_model_3.cif, chain A (#10), sequence alignment score =
    3971 2117.4 
    3972 Alignment identifier is 27 
    3973 Showing conservation header ("seq_conservation" residue attribute) for
    3974 alignment 27 
    3975 Hiding conservation header for alignment 27 
    3976 Chains used in RMSD evaluation for alignment 27: AlphaFold A0A9Q6ZED9 #!1/A,
    3977 fold_2026_06_01_00_39_model_3.cif #10/A 
    3978 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 27 
    3979 RMSD between 370 pruned atom pairs is 0.363 angstroms; (across all 404 pairs:
    3980 1.682) 
    3981  
    3982 Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with
    3983 fold_2026_06_01_00_39_model_4.cif, chain A (#11), sequence alignment score =
    3984 2098.8 
    3985 Alignment identifier is 28 
    3986 Showing conservation header ("seq_conservation" residue attribute) for
    3987 alignment 28 
    3988 Hiding conservation header for alignment 28 
    3989 Chains used in RMSD evaluation for alignment 28: AlphaFold A0A9Q6ZED9 #!1/A,
    3990 fold_2026_06_01_00_39_model_4.cif #11/A 
    3991 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 28 
    3992 RMSD between 373 pruned atom pairs is 0.398 angstroms; (across all 404 pairs:
    3993 1.169) 
    3994  
    3995 Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with AlphaFold A0A9Q6ZED9, chain
    3996 A (#12), sequence alignment score = 2144.4 
    3997 Alignment identifier is 29 
    3998 Showing conservation header ("seq_conservation" residue attribute) for
    3999 alignment 29 
    4000 Hiding conservation header for alignment 29 
    4001 Chains used in RMSD evaluation for alignment 29: AlphaFold A0A9Q6ZED9 #!1/A,
    4002 AlphaFold A0A9Q6ZED9 #12/A 
    4003 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 29 
    4004 RMSD between 404 pruned atom pairs is 0.000 angstroms; (across all 404 pairs:
    4005 0.000) 
    4006  
    4007 Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with AlphaFold A0A2W4UJ55, chain
    4008 A (#13), sequence alignment score = 661.2 
    4009 RMSD between 180 pruned atom pairs is 1.086 angstroms; (across all 383 pairs:
    4010 10.536) 
    4011  
    4012 Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with
    4013 fold_gdp_bound_wbdp_model_1.cif, chain A (#15), sequence alignment score =
    4014 2094.6 
    4015 Alignment identifier is 30 
    4016 Showing conservation header ("seq_conservation" residue attribute) for
    4017 alignment 30 
    4018 Hiding conservation header for alignment 30 
    4019 Chains used in RMSD evaluation for alignment 30: AlphaFold A0A9Q6ZED9 #!1/A,
    4020 fold_gdp_bound_wbdp_model_1.cif #15/A 
    4021 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 30 
    4022 RMSD between 363 pruned atom pairs is 0.611 angstroms; (across all 404 pairs:
    4023 1.462) 
    4024  
    4025 Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with
    4026 fold_gdp_bound_wbdp_model_2.cif, chain A (#16), sequence alignment score =
    4027 2105.4 
    4028 Alignment identifier is 31 
    4029 Showing conservation header ("seq_conservation" residue attribute) for
    4030 alignment 31 
    4031 Hiding conservation header for alignment 31 
    4032 Chains used in RMSD evaluation for alignment 31: AlphaFold A0A9Q6ZED9 #!1/A,
    4033 fold_gdp_bound_wbdp_model_2.cif #16/A 
    4034 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 31 
    4035 RMSD between 382 pruned atom pairs is 0.616 angstroms; (across all 404 pairs:
    4036 0.985) 
    4037  
    4038 Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with
    4039 fold_gdp_bound_wbdp_model_3.cif, chain A (#17), sequence alignment score =
    4040 2109 
    4041 Alignment identifier is 32 
    4042 Showing conservation header ("seq_conservation" residue attribute) for
    4043 alignment 32 
    4044 Hiding conservation header for alignment 32 
    4045 Chains used in RMSD evaluation for alignment 32: AlphaFold A0A9Q6ZED9 #!1/A,
    4046 fold_gdp_bound_wbdp_model_3.cif #17/A 
    4047 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 32 
    4048 RMSD between 385 pruned atom pairs is 0.703 angstroms; (across all 404 pairs:
    4049 0.901) 
    4050  
    4051 Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with
    4052 fold_gdp_bound_wbdp_model_4.cif, chain A (#18), sequence alignment score =
    4053 2109 
    4054 Alignment identifier is 33 
    4055 Showing conservation header ("seq_conservation" residue attribute) for
    4056 alignment 33 
    4057 Hiding conservation header for alignment 33 
    4058 Chains used in RMSD evaluation for alignment 33: AlphaFold A0A9Q6ZED9 #!1/A,
    4059 fold_gdp_bound_wbdp_model_4.cif #18/A 
    4060 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 33 
    4061 RMSD between 369 pruned atom pairs is 0.525 angstroms; (across all 404 pairs:
    4062 1.281) 
    4063  
    4064 Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with
    4065 fold_2026_05_15_15_51_model_0.cif, chain A (#2), sequence alignment score =
    4066 2101.2 
    4067 Alignment identifier is 34 
    4068 Showing conservation header ("seq_conservation" residue attribute) for
    4069 alignment 34 
    4070 Hiding conservation header for alignment 34 
    4071 Chains used in RMSD evaluation for alignment 34: AlphaFold A0A9Q6ZED9 #!1/A,
    4072 fold_2026_05_15_15_51_model_0.cif #2/A 
    4073 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 34 
    4074 RMSD between 366 pruned atom pairs is 0.687 angstroms; (across all 404 pairs:
    4075 2.582) 
    4076  
    4077 Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with
    4078 fold_gdp_bound_wbdp_model_0.cif, chain A (#14), sequence alignment score =
    4079 2105.4 
    4080 Alignment identifier is 35 
    4081 Showing conservation header ("seq_conservation" residue attribute) for
    4082 alignment 35 
    4083 Hiding conservation header for alignment 35 
    4084 Chains used in RMSD evaluation for alignment 35: AlphaFold A0A9Q6ZED9 #!1/A,
    4085 fold_gdp_bound_wbdp_model_0.cif #14/A 
    4086 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 35 
    4087 RMSD between 366 pruned atom pairs is 0.514 angstroms; (across all 404 pairs:
    4088 1.657) 
    4089  
    4090 
    4091 > hide #!14 models
    4092 
    4093 > hide #!2 models
    4094 
    4095 > hide #15 models
    4096 
    4097 > show #15 models
    4098 
    4099 > hide #16 models
    4100 
    4101 > hide #17 models
    4102 
    4103 > hide #18 models
    4104 
    4105 > ui tool show "Show Sequence Viewer"
    4106 
    4107 > sequence chain #15/A
    4108 
    4109 Alignment identifier is 15/A 
    4110 
    4111 > sequence chain #16/A
    4112 
    4113 Alignment identifier is 16/A 
    4114 
    4115 > sequence chain #17/A
    4116 
    4117 Alignment identifier is 17/A 
    4118 
    4119 > sequence chain #18/A
    4120 
    4121 Alignment identifier is 18/A 
    4122 
    4123 > select #15/A:404
    4124 
    4125 7 atoms, 6 bonds, 1 residue, 1 model selected 
    4126 
    4127 > select #15/A
    4128 
    4129 3292 atoms, 3376 bonds, 404 residues, 1 model selected 
    4130 
    4131 > ui tool show H-Bonds
    4132 
    4133 > hbonds sel interModel false saltOnly true reveal true
    4134 
    4135 25 hydrogen bonds found 
    4136 
    4137 > show #!14 models
    4138 
    4139 > hide #!14 models
    4140 
    4141 > hide #!15 models
    4142 
    4143 > show #!14 models
    4144 
    4145 > select add #15
    4146 
    4147 3320 atoms, 3406 bonds, 25 pseudobonds, 405 residues, 2 models selected 
    4148 
    4149 > select subtract #15
    4150 
    4151 Nothing selected 
    4152 
    4153 > show #!15 models
    4154 
    4155 > select add #15
    4156 
    4157 3320 atoms, 3406 bonds, 25 pseudobonds, 405 residues, 2 models selected 
    4158 
    4159 > select subtract #15
    4160 
    4161 Nothing selected 
    4162 
    4163 > hide #14.1 models
    4164 
    4165 > hide #!15 models
    4166 
    4167 > show #16 models
    4168 
    4169 > hide #!14 models
    4170 
    4171 > ui tool show H-Bonds
    4172 
    4173 > hbonds sel interModel false saltOnly true reveal true
    4174 
    4175 Atom specifier selects no atoms 
    4176 
    4177 > select #16/A:404
    4178 
    4179 7 atoms, 6 bonds, 1 residue, 1 model selected 
    4180 
    4181 > select #16/A:148-404
    4182 
    4183 2065 atoms, 2113 bonds, 257 residues, 1 model selected 
    4184 
    4185 > select #16/A:404
    4186 
    4187 7 atoms, 6 bonds, 1 residue, 1 model selected 
    4188 
    4189 > select #16/A
    4190 
    4191 3292 atoms, 3376 bonds, 404 residues, 1 model selected 
    4192 
    4193 > ui tool show H-Bonds
    4194 
    4195 > hbonds sel interModel false saltOnly true reveal true
    4196 
    4197 21 hydrogen bonds found 
    4198 
    4199 > hide #!16 models
    4200 
    4201 > show #17 models
    4202 
    4203 > select #17/A:404
    4204 
    4205 7 atoms, 6 bonds, 1 residue, 1 model selected 
    4206 
    4207 > select #17/A
    4208 
    4209 3292 atoms, 3376 bonds, 404 residues, 1 model selected 
    4210 
    4211 > ui tool show H-Bonds
    4212 
    4213 > hbonds sel interModel false saltOnly true reveal true
    4214 
    4215 18 hydrogen bonds found 
    4216 
    4217 > hide #!17 models
    4218 
    4219 > show #18 models
    4220 
    4221 > hide #18 models
    4222 
    4223 > show #18 models
    4224 
    4225 > show #!17 models
    4226 
    4227 > select #17/A:191
    4228 
    4229 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4230 
    4231 > select #17/A:191
    4232 
    4233 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4234 
    4235 > show #!16 models
    4236 
    4237 > show #!15 models
    4238 
    4239 > show #!14 models
    4240 
    4241 > ui mousemode right translate
    4242 
    4243 > show #!2 models
    4244 
    4245 > ui mousemode right zoom
    4246 
    4247 > hide #!15 models
    4248 
    4249 > hide #!16 models
    4250 
    4251 > hide #!17 models
    4252 
    4253 > hide #18 models
    4254 
    4255 > show #14.1 models
    4256 
    4257 > ui tool show "Selection Inspector"
    4258 
    4259 > hide #!2 models
    4260 
    4261 > select ::name="GDP"
    4262 
    4263 280 atoms, 300 bonds, 10 residues, 10 models selected 
    4264 
    4265 > select #14/A:54
    4266 
    4267 7 atoms, 7 bonds, 1 residue, 1 model selected 
    4268 
    4269 > select #14/A:54
    4270 
    4271 7 atoms, 7 bonds, 1 residue, 1 model selected 
    4272 
    4273 > ui tool show Distances
    4274 
    4275 Exactly two atoms must be selected! 
    4276 
    4277 > select #14/A:54
    4278 
    4279 7 atoms, 7 bonds, 1 residue, 1 model selected 
    4280 
    4281 > select #14/A:54
    4282 
    4283 7 atoms, 7 bonds, 1 residue, 1 model selected 
    4284 
    4285 > select #14/A:54
    4286 
    4287 7 atoms, 7 bonds, 1 residue, 1 model selected 
    4288 
    4289 > select #14/A:54
    4290 
    4291 7 atoms, 7 bonds, 1 residue, 1 model selected 
    4292 
    4293 > select #14/A:54-55
    4294 
    4295 18 atoms, 19 bonds, 2 residues, 1 model selected 
    4296 
    4297 > select #14/A:54
    4298 
    4299 7 atoms, 7 bonds, 1 residue, 1 model selected 
    4300 Exactly two atoms must be selected! 
    4301 [Repeated 2 time(s)]
    4302 
    4303 > select #14:GDP@O1
    4304 
    4305 Nothing selected 
    4306 
    4307 > select #14:54@CA and #14:GDP@O1
    4308 
    4309 Expected a keyword 
    4310 
    4311 > select #14:54@CA #14:GDP@O1
    4312 
    4313 1 atom, 1 residue, 1 model selected 
    4314 
    4315 > select ::name="GDP"
    4316 
    4317 280 atoms, 300 bonds, 10 residues, 10 models selected 
    4318 
    4319 > select #14:54@CA #14:GDP 1 PB @O1B
    4320 
    4321 Expected a keyword 
    4322 
    4323 > select #14:54@CA #14:GDP 1 @O1B
    4324 
    4325 Expected a keyword 
    4326 
    4327 > select #14:54@CA #14:GDP1 @O1B
    4328 
    4329 1 atom, 1 residue, 1 model selected 
    4330 
    4331 > select #14:GDP1 @O1B
    4332 
    4333 Nothing selected 
    4334 
    4335 > select #14:B GDP 1 PB O1B
    4336 
    4337 Expected a keyword 
    4338 
    4339 > select ligand
    4340 
    4341 280 atoms, 300 bonds, 10 residues, 10 models selected 
    4342 
    4343 > select #14:GDP@O1
    4344 
    4345 Nothing selected 
    4346 
    4347 > select #14:GDP@P
    4348 
    4349 Nothing selected 
    4350 
    4351 > select #14/B:GDP@PB
    4352 
    4353 1 atom, 1 residue, 1 model selected 
    4354 
    4355 > select select #14:54@CA #14/B:GDP@PB
    4356 
    4357 Expected an objects specifier or a keyword 
    4358 
    4359 > select select #14:54@CA and #14/B:GDP@PB
    4360 
    4361 Expected an objects specifier or a keyword 
    4362 
    4363 > select select #14:54@CA, #14/B:GDP@PB
    4364 
    4365 Expected an objects specifier or a keyword 
    4366 
    4367 > select select #14:54@CA,B:GDP@PB
    4368 
    4369 Expected an objects specifier or a keyword 
    4370 
    4371 > select select #14:54@CA,#14/B:GDP@PB
    4372 
    4373 Expected an objects specifier or a keyword 
    4374 
    4375 > select #14:54@CA,#14/B:GDP@PB
    4376 
    4377 Expected an objects specifier or a keyword 
    4378 
    4379 > select #14:54@CA and #14/B:GDP@PB
    4380 
    4381 Expected a keyword 
    4382 
    4383 > select #14:54@CA, #14/B:GDP@PB
    4384 
    4385 Expected an objects specifier or a keyword 
    4386 
    4387 > select #14:54@CA & #14/B:GDP@PB
    4388 
    4389 Nothing selected 
    4390 
    4391 > ui mousemode right translate
    4392 
    4393 > rmsd #2 to #14
    4394 
    4395 Number of atoms from first atom spec (3324) differs from number in second
    4396 (3320) 
    4397 
    4398 > rmsd #2 to #14
    4399 
    4400 Number of atoms from first atom spec (3324) differs from number in second
    4401 (3320) 
    4402 
    4403 > rmsd #2 to #14 residues
    4404 
    4405 Expected a keyword 
    4406 
    4407 > rmsd #2 to #14 residue
    4408 
    4409 Expected a keyword 
    4410 
    4411 > rmsd #2 to #14
    4412 
    4413 Number of atoms from first atom spec (3324) differs from number in second
    4414 (3320) 
    4415 
    4416 > ui tool show "Minimize Structure"
    4417 
    4418 > minimize #12
    4419 
    4420 Starting dock prep 
    4421 Deleting solvent 
    4422 Deleting non-metal-complex ions 
    4423 Deleting non-current alt locs 
    4424 Deleting residues with incomplete backbones 
    4425 Summary of feedback from adding hydrogens to AlphaFold A0A9Q6ZED9 #12 
    4426 --- 
    4427 notes | Termini for AlphaFold A0A9Q6ZED9 (#12) chain A determined from SEQRES records 
    4428 Chain-initial residues that are actual N termini: AlphaFold A0A9Q6ZED9 #12/A
    4429 MET 1 
    4430 Chain-initial residues that are not actual N termini: 
    4431 Chain-final residues that are actual C termini: AlphaFold A0A9Q6ZED9 #12/A SER
    4432 404 
    4433 Chain-final residues that are not actual C termini: 
    4434 394 hydrogen bonds 
    4435 3276 hydrogens added 
    4436  
    4437 Using Amber 20 recommended default charges and atom types for standard
    4438 residues 
    4439 Dock prep finished 
    4440 
    4441 > show #12 models
    4442 
    4443 > hide #!14 models
    4444 
    4445 > show #!1 models
    4446 
    4447 > hide #!1 models
    4448 
    4449 > show #!1 models
    4450 
    4451 > hide #!1 models
    4452 
    4453 > show #!1 models
    4454 
    4455 > hide #!1 models
    4456 
    4457 > show #!2 models
    4458 
    4459 > hide #!2 models
    4460 
    4461 > hide #12 models
    4462 
    4463 > show #!2 models
    4464 
    4465 > show #12 models
    4466 
    4467 > hide #!2 models
    4468 
    4469 > delete minimize #12
    4470 
    4471 Missing or invalid "atoms" argument: invalid atoms specifier 
    4472 
    4473 > undo minimize #12
    4474 
    4475 Expected fewer arguments 
    4476 
    4477 > undo
    4478 
    4479 [Repeated 9 time(s)]
    4480 
    4481 > show #!1 models
    4482 
    4483 > hide #!1 models
    4484 
    4485 > undo minimize #12
    4486 
    4487 Expected fewer arguments 
    4488 
    4489 > delete minimize #12
    4490 
    4491 Missing or invalid "atoms" argument: invalid atoms specifier 
    4492 
    4493 > minimize #12
    4494 
    4495 Starting dock prep 
    4496 Deleting solvent 
    4497 Deleting non-metal-complex ions 
    4498 Deleting non-current alt locs 
    4499 Deleting residues with incomplete backbones 
    4500 Summary of feedback from adding hydrogens to AlphaFold A0A9Q6ZED9 #12 
    4501 --- 
    4502 notes | Termini for AlphaFold A0A9Q6ZED9 (#12) chain A determined from SEQRES records 
    4503 Chain-initial residues that are actual N termini: AlphaFold A0A9Q6ZED9 #12/A
    4504 MET 1 
    4505 Chain-initial residues that are not actual N termini: 
    4506 Chain-final residues that are actual C termini: AlphaFold A0A9Q6ZED9 #12/A SER
    4507 404 
    4508 Chain-final residues that are not actual C termini: 
    4509 481 hydrogen bonds 
    4510 0 hydrogens added 
    4511  
    4512 Using Amber 20 recommended default charges and atom types for standard
    4513 residues 
    4514 Dock prep finished 
    4515 
    4516 > open
    4517 > /Users/aleezamughal/Downloads/fold_gdp_bound_wbdp/fold_gdp_bound_wbdp_model_0.cif
    4518 
    4519 Chain information for fold_gdp_bound_wbdp_model_0.cif #19 
    4520 --- 
    4521 Chain | Description 
    4522 A | . 
    4523  
    4524 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    4525 fold_2026_05_15_15_51_model_1.cif, chain A with 0 mismatches 
    4526 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    4527 fold_2026_05_15_15_51_model_2.cif, chain A with 0 mismatches 
    4528 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    4529 fold_2026_05_15_15_51_model_3.cif, chain A with 0 mismatches 
    4530 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    4531 fold_2026_05_15_15_51_model_4.cif, chain A with 0 mismatches 
    4532 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    4533 fold_2026_06_01_00_39_model_0.cif, chain A with 0 mismatches 
    4534 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    4535 fold_2026_06_01_00_39_model_1.cif, chain A with 0 mismatches 
    4536 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    4537 fold_2026_06_01_00_39_model_2.cif, chain A with 0 mismatches 
    4538 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    4539 fold_2026_06_01_00_39_model_3.cif, chain A with 0 mismatches 
    4540 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    4541 fold_2026_06_01_00_39_model_4.cif, chain A with 0 mismatches 
    4542 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    4543 fold_2026_05_15_15_51_model_1.cif, chain A with 0 mismatches 
    4544 Chains used in RMSD evaluation for alignment 10: AlphaFold A0A9Q6ZED9 #!1/A,
    4545 fold_2026_05_15_15_51_model_1.cif #3/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    4546 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    4547 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A 
    4548 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    4549 fold_2026_05_15_15_51_model_2.cif, chain A with 0 mismatches 
    4550 Chains used in RMSD evaluation for alignment 11: AlphaFold A0A9Q6ZED9 #!1/A,
    4551 fold_2026_05_15_15_51_model_2.cif #4/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    4552 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    4553 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A 
    4554 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    4555 fold_2026_05_15_15_51_model_3.cif, chain A with 0 mismatches 
    4556 Chains used in RMSD evaluation for alignment 12: AlphaFold A0A9Q6ZED9 #!1/A,
    4557 fold_2026_05_15_15_51_model_3.cif #5/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    4558 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    4559 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A 
    4560 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    4561 fold_2026_05_15_15_51_model_4.cif, chain A with 0 mismatches 
    4562 Chains used in RMSD evaluation for alignment 13: AlphaFold A0A9Q6ZED9 #!1/A,
    4563 fold_2026_05_15_15_51_model_4.cif #6/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    4564 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    4565 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A 
    4566 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    4567 fold_2026_06_01_00_39_model_0.cif, chain A with 0 mismatches 
    4568 Chains used in RMSD evaluation for alignment 14: AlphaFold A0A9Q6ZED9 #!1/A,
    4569 fold_2026_06_01_00_39_model_0.cif #7/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    4570 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    4571 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A 
    4572 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    4573 fold_2026_06_01_00_39_model_1.cif, chain A with 0 mismatches 
    4574 Chains used in RMSD evaluation for alignment 15: AlphaFold A0A9Q6ZED9 #!1/A,
    4575 fold_2026_06_01_00_39_model_1.cif #8/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    4576 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    4577 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A 
    4578 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    4579 fold_2026_06_01_00_39_model_2.cif, chain A with 0 mismatches 
    4580 Chains used in RMSD evaluation for alignment 16: AlphaFold A0A9Q6ZED9 #!1/A,
    4581 fold_2026_06_01_00_39_model_2.cif #9/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    4582 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    4583 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A 
    4584 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    4585 fold_2026_06_01_00_39_model_3.cif, chain A with 0 mismatches 
    4586 Chains used in RMSD evaluation for alignment 17: AlphaFold A0A9Q6ZED9 #!1/A,
    4587 fold_2026_06_01_00_39_model_3.cif #10/A, fold_gdp_bound_wbdp_model_1.cif
    4588 #15/A, fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif
    4589 #17/A, fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif
    4590 #19/A 
    4591 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    4592 fold_2026_06_01_00_39_model_4.cif, chain A with 0 mismatches 
    4593 Chains used in RMSD evaluation for alignment 18: AlphaFold A0A9Q6ZED9 #!1/A,
    4594 fold_2026_06_01_00_39_model_4.cif #11/A, fold_gdp_bound_wbdp_model_1.cif
    4595 #15/A, fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif
    4596 #17/A, fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif
    4597 #19/A 
    4598 Associated fold_gdp_bound_wbdp_model_0.cif chain A to AlphaFold A0A9Q6ZED9,
    4599 chain A with 0 mismatches 
    4600 Chains used in RMSD evaluation for alignment 19: AlphaFold A0A9Q6ZED9 #!1/A,
    4601 AlphaFold A0A9Q6ZED9 #12/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    4602 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    4603 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A 
    4604 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    4605 fold_gdp_bound_wbdp_model_0.cif, chain A with 0 mismatches 
    4606 Chains used in RMSD evaluation for alignment 20: AlphaFold A0A9Q6ZED9 #!1/A,
    4607 fold_gdp_bound_wbdp_model_0.cif #14/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    4608 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    4609 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A 
    4610 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    4611 fold_2026_05_15_15_51_model_2.cif, chain A with 0 mismatches 
    4612 Chains used in RMSD evaluation for alignment 21: AlphaFold A0A9Q6ZED9 #!1/A,
    4613 fold_2026_05_15_15_51_model_2.cif #4/A, fold_gdp_bound_wbdp_model_0.cif #19/A 
    4614 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    4615 fold_2026_05_15_15_51_model_3.cif, chain A with 0 mismatches 
    4616 Chains used in RMSD evaluation for alignment 22: AlphaFold A0A9Q6ZED9 #!1/A,
    4617 fold_2026_05_15_15_51_model_3.cif #5/A, fold_gdp_bound_wbdp_model_0.cif #19/A 
    4618 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    4619 fold_2026_05_15_15_51_model_4.cif, chain A with 0 mismatches 
    4620 Chains used in RMSD evaluation for alignment 23: AlphaFold A0A9Q6ZED9 #!1/A,
    4621 fold_2026_05_15_15_51_model_4.cif #6/A, fold_gdp_bound_wbdp_model_0.cif #19/A 
    4622 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    4623 fold_2026_06_01_00_39_model_0.cif, chain A with 0 mismatches 
    4624 Chains used in RMSD evaluation for alignment 24: AlphaFold A0A9Q6ZED9 #!1/A,
    4625 fold_2026_06_01_00_39_model_0.cif #7/A, fold_gdp_bound_wbdp_model_0.cif #19/A 
    4626 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    4627 fold_2026_06_01_00_39_model_1.cif, chain A with 0 mismatches 
    4628 Chains used in RMSD evaluation for alignment 25: AlphaFold A0A9Q6ZED9 #!1/A,
    4629 fold_2026_06_01_00_39_model_1.cif #8/A, fold_gdp_bound_wbdp_model_0.cif #19/A 
    4630 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    4631 fold_2026_06_01_00_39_model_2.cif, chain A with 0 mismatches 
    4632 Chains used in RMSD evaluation for alignment 26: AlphaFold A0A9Q6ZED9 #!1/A,
    4633 fold_2026_06_01_00_39_model_2.cif #9/A, fold_gdp_bound_wbdp_model_0.cif #19/A 
    4634 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    4635 fold_2026_06_01_00_39_model_3.cif, chain A with 0 mismatches 
    4636 Chains used in RMSD evaluation for alignment 27: AlphaFold A0A9Q6ZED9 #!1/A,
    4637 fold_2026_06_01_00_39_model_3.cif #10/A, fold_gdp_bound_wbdp_model_0.cif #19/A 
    4638 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    4639 fold_2026_06_01_00_39_model_4.cif, chain A with 0 mismatches 
    4640 Chains used in RMSD evaluation for alignment 28: AlphaFold A0A9Q6ZED9 #!1/A,
    4641 fold_2026_06_01_00_39_model_4.cif #11/A, fold_gdp_bound_wbdp_model_0.cif #19/A 
    4642 Associated fold_gdp_bound_wbdp_model_0.cif chain A to AlphaFold A0A9Q6ZED9,
    4643 chain A with 0 mismatches 
    4644 Chains used in RMSD evaluation for alignment 29: AlphaFold A0A9Q6ZED9 #!1/A,
    4645 AlphaFold A0A9Q6ZED9 #12/A, fold_gdp_bound_wbdp_model_0.cif #19/A 
    4646 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    4647 fold_gdp_bound_wbdp_model_1.cif, chain A with 0 mismatches 
    4648 Chains used in RMSD evaluation for alignment 30: AlphaFold A0A9Q6ZED9 #!1/A,
    4649 fold_gdp_bound_wbdp_model_1.cif #15/A, fold_gdp_bound_wbdp_model_0.cif #19/A 
    4650 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    4651 fold_gdp_bound_wbdp_model_2.cif, chain A with 0 mismatches 
    4652 Chains used in RMSD evaluation for alignment 31: AlphaFold A0A9Q6ZED9 #!1/A,
    4653 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_0.cif #19/A 
    4654 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    4655 fold_gdp_bound_wbdp_model_3.cif, chain A with 0 mismatches 
    4656 Chains used in RMSD evaluation for alignment 32: AlphaFold A0A9Q6ZED9 #!1/A,
    4657 fold_gdp_bound_wbdp_model_3.cif #17/A, fold_gdp_bound_wbdp_model_0.cif #19/A 
    4658 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    4659 fold_gdp_bound_wbdp_model_4.cif, chain A with 0 mismatches 
    4660 Chains used in RMSD evaluation for alignment 33: AlphaFold A0A9Q6ZED9 #!1/A,
    4661 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A 
    4662 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    4663 fold_2026_05_15_15_51_model_0.cif, chain A with 0 mismatches 
    4664 Chains used in RMSD evaluation for alignment 34: AlphaFold A0A9Q6ZED9 #!1/A,
    4665 fold_2026_05_15_15_51_model_0.cif #2/A, fold_gdp_bound_wbdp_model_0.cif #19/A 
    4666 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    4667 fold_gdp_bound_wbdp_model_0.cif, chain A with 0 mismatches 
    4668 Chains used in RMSD evaluation for alignment 35: AlphaFold A0A9Q6ZED9 #!1/A,
    4669 fold_gdp_bound_wbdp_model_0.cif #14/A, fold_gdp_bound_wbdp_model_0.cif #19/A 
    4670 Computing secondary structure 
    4671 
    4672 > hide #14.1 models
    4673 
    4674 > show #14.1 models
    4675 
    4676 > hide #14.1 models
    4677 
    4678 > hide #!14 models
    4679 
    4680 > hide #12 models
    4681 
    4682 > open "/Users/aleezamughal/Downloads/fold_2026_05_15_15_51
    4683 > 2/fold_2026_05_15_15_51_model_0.cif"
    4684 
    4685 Chain information for fold_2026_05_15_15_51_model_0.cif #20 
    4686 --- 
    4687 Chain | Description 
    4688 A | . 
    4689  
    4690 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    4691 fold_2026_05_15_15_51_model_1.cif, chain A with 0 mismatches 
    4692 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    4693 fold_2026_05_15_15_51_model_2.cif, chain A with 0 mismatches 
    4694 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    4695 fold_2026_05_15_15_51_model_3.cif, chain A with 0 mismatches 
    4696 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    4697 fold_2026_05_15_15_51_model_4.cif, chain A with 0 mismatches 
    4698 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    4699 fold_2026_06_01_00_39_model_0.cif, chain A with 0 mismatches 
    4700 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    4701 fold_2026_06_01_00_39_model_1.cif, chain A with 0 mismatches 
    4702 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    4703 fold_2026_06_01_00_39_model_2.cif, chain A with 0 mismatches 
    4704 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    4705 fold_2026_06_01_00_39_model_3.cif, chain A with 0 mismatches 
    4706 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    4707 fold_2026_06_01_00_39_model_4.cif, chain A with 0 mismatches 
    4708 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    4709 fold_2026_05_15_15_51_model_1.cif, chain A with 0 mismatches 
    4710 Chains used in RMSD evaluation for alignment 10: AlphaFold A0A9Q6ZED9 #!1/A,
    4711 fold_2026_05_15_15_51_model_1.cif #3/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    4712 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    4713 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    4714 fold_2026_05_15_15_51_model_0.cif #20/A 
    4715 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    4716 fold_2026_05_15_15_51_model_2.cif, chain A with 0 mismatches 
    4717 Chains used in RMSD evaluation for alignment 11: AlphaFold A0A9Q6ZED9 #!1/A,
    4718 fold_2026_05_15_15_51_model_2.cif #4/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    4719 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    4720 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    4721 fold_2026_05_15_15_51_model_0.cif #20/A 
    4722 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    4723 fold_2026_05_15_15_51_model_3.cif, chain A with 0 mismatches 
    4724 Chains used in RMSD evaluation for alignment 12: AlphaFold A0A9Q6ZED9 #!1/A,
    4725 fold_2026_05_15_15_51_model_3.cif #5/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    4726 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    4727 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    4728 fold_2026_05_15_15_51_model_0.cif #20/A 
    4729 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    4730 fold_2026_05_15_15_51_model_4.cif, chain A with 0 mismatches 
    4731 Chains used in RMSD evaluation for alignment 13: AlphaFold A0A9Q6ZED9 #!1/A,
    4732 fold_2026_05_15_15_51_model_4.cif #6/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    4733 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    4734 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    4735 fold_2026_05_15_15_51_model_0.cif #20/A 
    4736 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    4737 fold_2026_06_01_00_39_model_0.cif, chain A with 0 mismatches 
    4738 Chains used in RMSD evaluation for alignment 14: AlphaFold A0A9Q6ZED9 #!1/A,
    4739 fold_2026_06_01_00_39_model_0.cif #7/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    4740 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    4741 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    4742 fold_2026_05_15_15_51_model_0.cif #20/A 
    4743 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    4744 fold_2026_06_01_00_39_model_1.cif, chain A with 0 mismatches 
    4745 Chains used in RMSD evaluation for alignment 15: AlphaFold A0A9Q6ZED9 #!1/A,
    4746 fold_2026_06_01_00_39_model_1.cif #8/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    4747 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    4748 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    4749 fold_2026_05_15_15_51_model_0.cif #20/A 
    4750 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    4751 fold_2026_06_01_00_39_model_2.cif, chain A with 0 mismatches 
    4752 Chains used in RMSD evaluation for alignment 16: AlphaFold A0A9Q6ZED9 #!1/A,
    4753 fold_2026_06_01_00_39_model_2.cif #9/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    4754 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    4755 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    4756 fold_2026_05_15_15_51_model_0.cif #20/A 
    4757 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    4758 fold_2026_06_01_00_39_model_3.cif, chain A with 0 mismatches 
    4759 Chains used in RMSD evaluation for alignment 17: AlphaFold A0A9Q6ZED9 #!1/A,
    4760 fold_2026_06_01_00_39_model_3.cif #10/A, fold_gdp_bound_wbdp_model_1.cif
    4761 #15/A, fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif
    4762 #17/A, fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif
    4763 #19/A, fold_2026_05_15_15_51_model_0.cif #20/A 
    4764 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    4765 fold_2026_06_01_00_39_model_4.cif, chain A with 0 mismatches 
    4766 Chains used in RMSD evaluation for alignment 18: AlphaFold A0A9Q6ZED9 #!1/A,
    4767 fold_2026_06_01_00_39_model_4.cif #11/A, fold_gdp_bound_wbdp_model_1.cif
    4768 #15/A, fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif
    4769 #17/A, fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif
    4770 #19/A, fold_2026_05_15_15_51_model_0.cif #20/A 
    4771 Associated fold_2026_05_15_15_51_model_0.cif chain A to AlphaFold A0A9Q6ZED9,
    4772 chain A with 0 mismatches 
    4773 Chains used in RMSD evaluation for alignment 19: AlphaFold A0A9Q6ZED9 #!1/A,
    4774 AlphaFold A0A9Q6ZED9 #12/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    4775 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    4776 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    4777 fold_2026_05_15_15_51_model_0.cif #20/A 
    4778 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    4779 fold_gdp_bound_wbdp_model_0.cif, chain A with 0 mismatches 
    4780 Chains used in RMSD evaluation for alignment 20: AlphaFold A0A9Q6ZED9 #!1/A,
    4781 fold_gdp_bound_wbdp_model_0.cif #14/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    4782 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    4783 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    4784 fold_2026_05_15_15_51_model_0.cif #20/A 
    4785 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    4786 fold_2026_05_15_15_51_model_2.cif, chain A with 0 mismatches 
    4787 Chains used in RMSD evaluation for alignment 21: AlphaFold A0A9Q6ZED9 #!1/A,
    4788 fold_2026_05_15_15_51_model_2.cif #4/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    4789 fold_2026_05_15_15_51_model_0.cif #20/A 
    4790 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    4791 fold_2026_05_15_15_51_model_3.cif, chain A with 0 mismatches 
    4792 Chains used in RMSD evaluation for alignment 22: AlphaFold A0A9Q6ZED9 #!1/A,
    4793 fold_2026_05_15_15_51_model_3.cif #5/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    4794 fold_2026_05_15_15_51_model_0.cif #20/A 
    4795 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    4796 fold_2026_05_15_15_51_model_4.cif, chain A with 0 mismatches 
    4797 Chains used in RMSD evaluation for alignment 23: AlphaFold A0A9Q6ZED9 #!1/A,
    4798 fold_2026_05_15_15_51_model_4.cif #6/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    4799 fold_2026_05_15_15_51_model_0.cif #20/A 
    4800 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    4801 fold_2026_06_01_00_39_model_0.cif, chain A with 0 mismatches 
    4802 Chains used in RMSD evaluation for alignment 24: AlphaFold A0A9Q6ZED9 #!1/A,
    4803 fold_2026_06_01_00_39_model_0.cif #7/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    4804 fold_2026_05_15_15_51_model_0.cif #20/A 
    4805 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    4806 fold_2026_06_01_00_39_model_1.cif, chain A with 0 mismatches 
    4807 Chains used in RMSD evaluation for alignment 25: AlphaFold A0A9Q6ZED9 #!1/A,
    4808 fold_2026_06_01_00_39_model_1.cif #8/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    4809 fold_2026_05_15_15_51_model_0.cif #20/A 
    4810 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    4811 fold_2026_06_01_00_39_model_2.cif, chain A with 0 mismatches 
    4812 Chains used in RMSD evaluation for alignment 26: AlphaFold A0A9Q6ZED9 #!1/A,
    4813 fold_2026_06_01_00_39_model_2.cif #9/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    4814 fold_2026_05_15_15_51_model_0.cif #20/A 
    4815 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    4816 fold_2026_06_01_00_39_model_3.cif, chain A with 0 mismatches 
    4817 Chains used in RMSD evaluation for alignment 27: AlphaFold A0A9Q6ZED9 #!1/A,
    4818 fold_2026_06_01_00_39_model_3.cif #10/A, fold_gdp_bound_wbdp_model_0.cif
    4819 #19/A, fold_2026_05_15_15_51_model_0.cif #20/A 
    4820 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    4821 fold_2026_06_01_00_39_model_4.cif, chain A with 0 mismatches 
    4822 Chains used in RMSD evaluation for alignment 28: AlphaFold A0A9Q6ZED9 #!1/A,
    4823 fold_2026_06_01_00_39_model_4.cif #11/A, fold_gdp_bound_wbdp_model_0.cif
    4824 #19/A, fold_2026_05_15_15_51_model_0.cif #20/A 
    4825 Associated fold_2026_05_15_15_51_model_0.cif chain A to AlphaFold A0A9Q6ZED9,
    4826 chain A with 0 mismatches 
    4827 Chains used in RMSD evaluation for alignment 29: AlphaFold A0A9Q6ZED9 #!1/A,
    4828 AlphaFold A0A9Q6ZED9 #12/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    4829 fold_2026_05_15_15_51_model_0.cif #20/A 
    4830 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    4831 fold_gdp_bound_wbdp_model_1.cif, chain A with 0 mismatches 
    4832 Chains used in RMSD evaluation for alignment 30: AlphaFold A0A9Q6ZED9 #!1/A,
    4833 fold_gdp_bound_wbdp_model_1.cif #15/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    4834 fold_2026_05_15_15_51_model_0.cif #20/A 
    4835 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    4836 fold_gdp_bound_wbdp_model_2.cif, chain A with 0 mismatches 
    4837 Chains used in RMSD evaluation for alignment 31: AlphaFold A0A9Q6ZED9 #!1/A,
    4838 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    4839 fold_2026_05_15_15_51_model_0.cif #20/A 
    4840 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    4841 fold_gdp_bound_wbdp_model_3.cif, chain A with 0 mismatches 
    4842 Chains used in RMSD evaluation for alignment 32: AlphaFold A0A9Q6ZED9 #!1/A,
    4843 fold_gdp_bound_wbdp_model_3.cif #17/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    4844 fold_2026_05_15_15_51_model_0.cif #20/A 
    4845 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    4846 fold_gdp_bound_wbdp_model_4.cif, chain A with 0 mismatches 
    4847 Chains used in RMSD evaluation for alignment 33: AlphaFold A0A9Q6ZED9 #!1/A,
    4848 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    4849 fold_2026_05_15_15_51_model_0.cif #20/A 
    4850 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    4851 fold_2026_05_15_15_51_model_0.cif, chain A with 0 mismatches 
    4852 Chains used in RMSD evaluation for alignment 34: AlphaFold A0A9Q6ZED9 #!1/A,
    4853 fold_2026_05_15_15_51_model_0.cif #2/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    4854 fold_2026_05_15_15_51_model_0.cif #20/A 
    4855 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    4856 fold_gdp_bound_wbdp_model_0.cif, chain A with 0 mismatches 
    4857 Chains used in RMSD evaluation for alignment 35: AlphaFold A0A9Q6ZED9 #!1/A,
    4858 fold_gdp_bound_wbdp_model_0.cif #14/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    4859 fold_2026_05_15_15_51_model_0.cif #20/A 
    4860 Computing secondary structure 
    4861 
    4862 > hide #19 models
    4863 
    4864 > show #19 models
    4865 
    4866 > ui tool show Match→Align
    4867 
    4868 > msa3d #19/A#20/A
    4869 
    4870 Match→Align cutoff: 5.0, in column if within cutoff of: any 
    4871 32 residue pairs aligned 
    4872 404 fully populated columns 
    4873 Pairwise RMSDs across all fully populated columns 
    4874 --- 
    4875 Model | 19 | 20 
    4876 19 | 0.000 | 33.602 
    4877 20 | 33.602 | 0.000 
    4878  
    4879 Overall RMSD: 33.602 
    4880 Sequence lengths: 404 404 
    4881 SDM (cutoff 5.0): -282.503 
    4882 Q-score: 0.008 
    4883 Alignment identifier is MA-1 
    4884 Showing conservation header ("seq_conservation" residue attribute) for
    4885 alignment MA-1 
    4886 Chains used in RMSD evaluation for alignment MA-1:
    4887 fold_gdp_bound_wbdp_model_0.cif #19/A, fold_2026_05_15_15_51_model_0.cif #20/A 
    4888 Showing rmsd header ("seq_rmsd" residue attribute) for alignment MA-1 
    4889 
    4890 > ui tool show Matchmaker
    4891 
    4892 > matchmaker #19-20 to #1
    4893 
    4894 Parameters 
    4895 --- 
    4896 Chain pairing | bb 
    4897 Alignment algorithm | Needleman-Wunsch 
    4898 Similarity matrix | BLOSUM-62 
    4899 SS fraction | 0.3 
    4900 Gap open (HH/SS/other) | 18/18/6 
    4901 Gap extend | 1 
    4902 SS matrix |  |  | H | S | O 
    4903 ---|---|---|--- 
    4904 H | 6 | -9 | -6 
    4905 S |  | 6 | -6 
    4906 O |  |  | 4 
    4907 Iteration cutoff | 2 
    4908  
    4909 Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with
    4910 fold_gdp_bound_wbdp_model_0.cif, chain A (#19), sequence alignment score =
    4911 2105.4 
    4912 RMSD between 366 pruned atom pairs is 0.514 angstroms; (across all 404 pairs:
    4913 1.657) 
    4914  
    4915 Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with
    4916 fold_2026_05_15_15_51_model_0.cif, chain A (#20), sequence alignment score =
    4917 2101.2 
    4918 Alignment identifier is 36 
    4919 Showing conservation header ("seq_conservation" residue attribute) for
    4920 alignment 36 
    4921 Hiding conservation header for alignment 36 
    4922 Chains used in RMSD evaluation for alignment 36: AlphaFold A0A9Q6ZED9 #!1/A,
    4923 fold_2026_05_15_15_51_model_0.cif #20/A 
    4924 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 36 
    4925 RMSD between 366 pruned atom pairs is 0.687 angstroms; (across all 404 pairs:
    4926 2.582) 
    4927  
    4928 
    4929 > minimize #19
    4930 
    4931 Starting dock prep 
    4932 Deleting solvent 
    4933 Deleting non-metal-complex ions 
    4934 Deleting non-current alt locs 
    4935 Deleting residues with incomplete backbones 
    4936 Summary of feedback from adding hydrogens to fold_gdp_bound_wbdp_model_0.cif
    4937 #19 
    4938 --- 
    4939 notes | Termini for fold_gdp_bound_wbdp_model_0.cif (#19) chain A determined from SEQRES records 
    4940 Chain-initial residues that are actual N termini:
    4941 fold_gdp_bound_wbdp_model_0.cif #19/A MET 1 
    4942 Chain-initial residues that are not actual N termini: 
    4943 Chain-final residues that are actual C termini:
    4944 fold_gdp_bound_wbdp_model_0.cif #19/A SER 404 
    4945 Chain-final residues that are not actual C termini: 
    4946 393 hydrogen bonds 
    4947 3288 hydrogens added 
    4948  
    4949 Using Amber 20 recommended default charges and atom types for standard
    4950 residues 
    4951 Dock prep finished 
    4952 
    4953 > ui mousemode right zoom
    4954 
    4955 > select ::name="GDP"
    4956 
    4957 348 atoms, 372 bonds, 12 residues, 12 models selected 
    4958 
    4959 > open
    4960 > /Users/aleezamughal/Downloads/fold_2026_05_15_15_51/fold_2026_05_15_15_51_model_0.cif
    4961 
    4962 Chain information for fold_2026_05_15_15_51_model_0.cif #21 
    4963 --- 
    4964 Chain | Description 
    4965 A | . 
    4966  
    4967 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    4968 fold_2026_05_15_15_51_model_1.cif, chain A with 0 mismatches 
    4969 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    4970 fold_2026_05_15_15_51_model_2.cif, chain A with 0 mismatches 
    4971 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    4972 fold_2026_05_15_15_51_model_3.cif, chain A with 0 mismatches 
    4973 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    4974 fold_2026_05_15_15_51_model_4.cif, chain A with 0 mismatches 
    4975 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    4976 fold_2026_06_01_00_39_model_0.cif, chain A with 0 mismatches 
    4977 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    4978 fold_2026_06_01_00_39_model_1.cif, chain A with 0 mismatches 
    4979 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    4980 fold_2026_06_01_00_39_model_2.cif, chain A with 0 mismatches 
    4981 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    4982 fold_2026_06_01_00_39_model_3.cif, chain A with 0 mismatches 
    4983 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    4984 fold_2026_06_01_00_39_model_4.cif, chain A with 0 mismatches 
    4985 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    4986 fold_2026_05_15_15_51_model_1.cif, chain A with 0 mismatches 
    4987 Chains used in RMSD evaluation for alignment 10: AlphaFold A0A9Q6ZED9 #!1/A,
    4988 fold_2026_05_15_15_51_model_1.cif #3/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    4989 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    4990 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    4991 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    4992 #21/A 
    4993 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    4994 fold_2026_05_15_15_51_model_2.cif, chain A with 0 mismatches 
    4995 Chains used in RMSD evaluation for alignment 11: AlphaFold A0A9Q6ZED9 #!1/A,
    4996 fold_2026_05_15_15_51_model_2.cif #4/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    4997 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    4998 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    4999 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    5000 #21/A 
    5001 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    5002 fold_2026_05_15_15_51_model_3.cif, chain A with 0 mismatches 
    5003 Chains used in RMSD evaluation for alignment 12: AlphaFold A0A9Q6ZED9 #!1/A,
    5004 fold_2026_05_15_15_51_model_3.cif #5/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    5005 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    5006 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    5007 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    5008 #21/A 
    5009 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    5010 fold_2026_05_15_15_51_model_4.cif, chain A with 0 mismatches 
    5011 Chains used in RMSD evaluation for alignment 13: AlphaFold A0A9Q6ZED9 #!1/A,
    5012 fold_2026_05_15_15_51_model_4.cif #6/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    5013 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    5014 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    5015 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    5016 #21/A 
    5017 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    5018 fold_2026_06_01_00_39_model_0.cif, chain A with 0 mismatches 
    5019 Chains used in RMSD evaluation for alignment 14: AlphaFold A0A9Q6ZED9 #!1/A,
    5020 fold_2026_06_01_00_39_model_0.cif #7/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    5021 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    5022 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    5023 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    5024 #21/A 
    5025 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    5026 fold_2026_06_01_00_39_model_1.cif, chain A with 0 mismatches 
    5027 Chains used in RMSD evaluation for alignment 15: AlphaFold A0A9Q6ZED9 #!1/A,
    5028 fold_2026_06_01_00_39_model_1.cif #8/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    5029 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    5030 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    5031 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    5032 #21/A 
    5033 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    5034 fold_2026_06_01_00_39_model_2.cif, chain A with 0 mismatches 
    5035 Chains used in RMSD evaluation for alignment 16: AlphaFold A0A9Q6ZED9 #!1/A,
    5036 fold_2026_06_01_00_39_model_2.cif #9/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    5037 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    5038 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    5039 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    5040 #21/A 
    5041 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    5042 fold_2026_06_01_00_39_model_3.cif, chain A with 0 mismatches 
    5043 Chains used in RMSD evaluation for alignment 17: AlphaFold A0A9Q6ZED9 #!1/A,
    5044 fold_2026_06_01_00_39_model_3.cif #10/A, fold_gdp_bound_wbdp_model_1.cif
    5045 #15/A, fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif
    5046 #17/A, fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif
    5047 #19/A, fold_2026_05_15_15_51_model_0.cif #20/A,
    5048 fold_2026_05_15_15_51_model_0.cif #21/A 
    5049 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    5050 fold_2026_06_01_00_39_model_4.cif, chain A with 0 mismatches 
    5051 Chains used in RMSD evaluation for alignment 18: AlphaFold A0A9Q6ZED9 #!1/A,
    5052 fold_2026_06_01_00_39_model_4.cif #11/A, fold_gdp_bound_wbdp_model_1.cif
    5053 #15/A, fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif
    5054 #17/A, fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif
    5055 #19/A, fold_2026_05_15_15_51_model_0.cif #20/A,
    5056 fold_2026_05_15_15_51_model_0.cif #21/A 
    5057 Associated fold_2026_05_15_15_51_model_0.cif chain A to AlphaFold A0A9Q6ZED9,
    5058 chain A with 0 mismatches 
    5059 Chains used in RMSD evaluation for alignment 19: AlphaFold A0A9Q6ZED9 #!1/A,
    5060 AlphaFold A0A9Q6ZED9 #12/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    5061 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    5062 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    5063 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    5064 #21/A 
    5065 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    5066 fold_gdp_bound_wbdp_model_0.cif, chain A with 0 mismatches 
    5067 Chains used in RMSD evaluation for alignment 20: AlphaFold A0A9Q6ZED9 #!1/A,
    5068 fold_gdp_bound_wbdp_model_0.cif #14/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    5069 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    5070 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    5071 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    5072 #21/A 
    5073 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    5074 fold_2026_05_15_15_51_model_2.cif, chain A with 0 mismatches 
    5075 Chains used in RMSD evaluation for alignment 21: AlphaFold A0A9Q6ZED9 #!1/A,
    5076 fold_2026_05_15_15_51_model_2.cif #4/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    5077 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    5078 #21/A 
    5079 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    5080 fold_2026_05_15_15_51_model_3.cif, chain A with 0 mismatches 
    5081 Chains used in RMSD evaluation for alignment 22: AlphaFold A0A9Q6ZED9 #!1/A,
    5082 fold_2026_05_15_15_51_model_3.cif #5/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    5083 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    5084 #21/A 
    5085 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    5086 fold_2026_05_15_15_51_model_4.cif, chain A with 0 mismatches 
    5087 Chains used in RMSD evaluation for alignment 23: AlphaFold A0A9Q6ZED9 #!1/A,
    5088 fold_2026_05_15_15_51_model_4.cif #6/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    5089 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    5090 #21/A 
    5091 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    5092 fold_2026_06_01_00_39_model_0.cif, chain A with 0 mismatches 
    5093 Chains used in RMSD evaluation for alignment 24: AlphaFold A0A9Q6ZED9 #!1/A,
    5094 fold_2026_06_01_00_39_model_0.cif #7/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    5095 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    5096 #21/A 
    5097 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    5098 fold_2026_06_01_00_39_model_1.cif, chain A with 0 mismatches 
    5099 Chains used in RMSD evaluation for alignment 25: AlphaFold A0A9Q6ZED9 #!1/A,
    5100 fold_2026_06_01_00_39_model_1.cif #8/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    5101 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    5102 #21/A 
    5103 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    5104 fold_2026_06_01_00_39_model_2.cif, chain A with 0 mismatches 
    5105 Chains used in RMSD evaluation for alignment 26: AlphaFold A0A9Q6ZED9 #!1/A,
    5106 fold_2026_06_01_00_39_model_2.cif #9/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    5107 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    5108 #21/A 
    5109 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    5110 fold_2026_06_01_00_39_model_3.cif, chain A with 0 mismatches 
    5111 Chains used in RMSD evaluation for alignment 27: AlphaFold A0A9Q6ZED9 #!1/A,
    5112 fold_2026_06_01_00_39_model_3.cif #10/A, fold_gdp_bound_wbdp_model_0.cif
    5113 #19/A, fold_2026_05_15_15_51_model_0.cif #20/A,
    5114 fold_2026_05_15_15_51_model_0.cif #21/A 
    5115 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    5116 fold_2026_06_01_00_39_model_4.cif, chain A with 0 mismatches 
    5117 Chains used in RMSD evaluation for alignment 28: AlphaFold A0A9Q6ZED9 #!1/A,
    5118 fold_2026_06_01_00_39_model_4.cif #11/A, fold_gdp_bound_wbdp_model_0.cif
    5119 #19/A, fold_2026_05_15_15_51_model_0.cif #20/A,
    5120 fold_2026_05_15_15_51_model_0.cif #21/A 
    5121 Associated fold_2026_05_15_15_51_model_0.cif chain A to AlphaFold A0A9Q6ZED9,
    5122 chain A with 0 mismatches 
    5123 Chains used in RMSD evaluation for alignment 29: AlphaFold A0A9Q6ZED9 #!1/A,
    5124 AlphaFold A0A9Q6ZED9 #12/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    5125 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    5126 #21/A 
    5127 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    5128 fold_gdp_bound_wbdp_model_1.cif, chain A with 0 mismatches 
    5129 Chains used in RMSD evaluation for alignment 30: AlphaFold A0A9Q6ZED9 #!1/A,
    5130 fold_gdp_bound_wbdp_model_1.cif #15/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    5131 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    5132 #21/A 
    5133 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    5134 fold_gdp_bound_wbdp_model_2.cif, chain A with 0 mismatches 
    5135 Chains used in RMSD evaluation for alignment 31: AlphaFold A0A9Q6ZED9 #!1/A,
    5136 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    5137 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    5138 #21/A 
    5139 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    5140 fold_gdp_bound_wbdp_model_3.cif, chain A with 0 mismatches 
    5141 Chains used in RMSD evaluation for alignment 32: AlphaFold A0A9Q6ZED9 #!1/A,
    5142 fold_gdp_bound_wbdp_model_3.cif #17/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    5143 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    5144 #21/A 
    5145 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    5146 fold_gdp_bound_wbdp_model_4.cif, chain A with 0 mismatches 
    5147 Chains used in RMSD evaluation for alignment 33: AlphaFold A0A9Q6ZED9 #!1/A,
    5148 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    5149 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    5150 #21/A 
    5151 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    5152 fold_2026_05_15_15_51_model_0.cif, chain A with 0 mismatches 
    5153 Chains used in RMSD evaluation for alignment 34: AlphaFold A0A9Q6ZED9 #!1/A,
    5154 fold_2026_05_15_15_51_model_0.cif #2/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    5155 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    5156 #21/A 
    5157 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    5158 fold_gdp_bound_wbdp_model_0.cif, chain A with 0 mismatches 
    5159 Chains used in RMSD evaluation for alignment 35: AlphaFold A0A9Q6ZED9 #!1/A,
    5160 fold_gdp_bound_wbdp_model_0.cif #14/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    5161 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    5162 #21/A 
    5163 Associated fold_2026_05_15_15_51_model_0.cif chain A to
    5164 fold_2026_05_15_15_51_model_0.cif, chain A with 0 mismatches 
    5165 Chains used in RMSD evaluation for alignment 36: AlphaFold A0A9Q6ZED9 #!1/A,
    5166 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    5167 #21/A 
    5168 Computing secondary structure 
    5169 
    5170 > hide #20 models
    5171 
    5172 > hide #19 models
    5173 
    5174 > select ::name="TYR"
    5175 
    5176 5970 atoms, 6011 bonds, 463 residues, 21 models selected 
    5177 
    5178 > show (#21 & sel-residues & sidechain) target ab
    5179 
    5180 > show #19 models
    5181 
    5182 > hide #21 models
    5183 
    5184 > show (#19 & sel-residues & sidechain) target ab
    5185 
    5186 > select add #19
    5187 
    5188 12095 atoms, 12220 bonds, 845 residues, 21 models selected 
    5189 
    5190 > select subtract #19
    5191 
    5192 5487 atoms, 5526 bonds, 440 residues, 20 models selected 
    5193 
    5194 > hide #19 models
    5195 
    5196 > show #20 models
    5197 
    5198 > show (#20 & sel-residues & sidechain) target ab
    5199 
    5200 > ui tool show "Show Sequence Viewer"
    5201 
    5202 > sequence chain #20/A
    5203 
    5204 Alignment identifier is 20/A 
    5205 
    5206 > select
    5207 > #20/A:14-29,44-63,78-84,101-110,125-129,140-142,145-147,150-165,175-184,203-206,210-216,231-233,235-247,268-279,282-284,293-301,318-326,339-341,355-365,374-403
    5208 
    5209 1593 atoms, 1608 bonds, 194 residues, 1 model selected 
    5210 
    5211 > select #20/A:245
    5212 
    5213 16 atoms, 16 bonds, 1 residue, 1 model selected 
    5214 
    5215 > select #20/A:245
    5216 
    5217 16 atoms, 16 bonds, 1 residue, 1 model selected 
    5218 
    5219 > show (sel-residues & sidechain) target ab
    5220 
    5221 > show #18 models
    5222 
    5223 > hide #18 models
    5224 
    5225 > show #19 models
    5226 
    5227 > hide #19 models
    5228 
    5229 > show #19 models
    5230 
    5231 > hide #19 models
    5232 
    5233 > minimize #20
    5234 
    5235 Starting dock prep 
    5236 Deleting solvent 
    5237 Deleting non-metal-complex ions 
    5238 Deleting non-current alt locs 
    5239 Deleting residues with incomplete backbones 
    5240 Summary of feedback from adding hydrogens to fold_2026_05_15_15_51_model_0.cif
    5241 #20 
    5242 --- 
    5243 notes | Termini for fold_2026_05_15_15_51_model_0.cif (#20) chain A determined from SEQRES records 
    5244 Chain-initial residues that are actual N termini:
    5245 fold_2026_05_15_15_51_model_0.cif #20/A MET 1 
    5246 Chain-initial residues that are not actual N termini: 
    5247 Chain-final residues that are actual C termini:
    5248 fold_2026_05_15_15_51_model_0.cif #20/A SER 404 
    5249 Chain-final residues that are not actual C termini: 
    5250 385 hydrogen bonds 
    5251 3287 hydrogens added 
    5252  
    5253 Using Amber 20 recommended default charges and atom types for standard
    5254 residues 
    5255 Assigning partial charges to residue PTR (net charge -2) with am1-bcc method 
    5256 Running ANTECHAMBER command:
    5257 /Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/bin/amber20/bin/antechamber
    5258 -ek qm_theory='AM1', -i
    5259 /var/folders/zc/bn4qs3894m51jrw9pmkqnvlm0000gn/T/tmp4dgf5z2b/ante.in.mol2 -fi
    5260 mol2 -o
    5261 /var/folders/zc/bn4qs3894m51jrw9pmkqnvlm0000gn/T/tmp4dgf5z2b/ante.out.mol2 -fo
    5262 mol2 -c bcc -nc -2 -j 5 -s 2 -dr n 
    5263 (PTR) `` 
    5264 (PTR) `Welcome to antechamber 20.0: molecular input file processor.` 
    5265 (PTR) `` 
    5266 (PTR) `Info: Finished reading file
    5267 (/var/folders/zc/bn4qs3894m51jrw9pmkqnvlm0000gn/T/tmp4dgf5z2b/ante.in.mol2);
    5268 atoms read (36), bonds read (36).` 
    5269 (PTR) `Info: Determining atomic numbers from atomic symbols which are case
    5270 sensitive.` 
    5271 (PTR) `Running:
    5272 /Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/bin/amber20/bin/bondtype
    5273 -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` 
    5274 (PTR) `` 
    5275 (PTR) `` 
    5276 (PTR) `Running:
    5277 /Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/bin/amber20/bin/atomtype
    5278 -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` 
    5279 (PTR) `Info: Total number of electrons: 166; net charge: -2` 
    5280 (PTR) `` 
    5281 (PTR) `Running:
    5282 /Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/bin/amber20/bin/sqm -O
    5283 -i sqm.in -o sqm.out` 
    5284 (PTR) `` 
    5285 (PTR) `Running:
    5286 /Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/bin/amber20/bin/am1bcc
    5287 -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
    5288 /Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
    5289 -s 2 -j 1` 
    5290 (PTR) `` 
    5291 (PTR) `Running:
    5292 /Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/bin/amber20/bin/atomtype
    5293 -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` 
    5294 (PTR) `` 
    5295 Charges for residue PTR determined 
    5296 Dock prep finished 
    5297 
    5298 > show #19 models
    5299 
    5300 > rmsd #19 to #20
    5301 
    5302 Number of atoms from first atom spec (6608) differs from number in second
    5303 (6611) 
    5304 
    5305 > rmsd #19:GDP to #20:GDP
    5306 
    5307 RMSD between 40 atom pairs is 1.255 
    5308 
    5309 > ui tool show H-Bonds
    5310 
    5311 > hbonds sel interModel false saltOnly true reveal true
    5312 
    5313 0 hydrogen bonds found 
    5314 
    5315 > hide #!20 models
    5316 
    5317 > show #!20 models
    5318 
    5319 > select #20/A:1-2
    5320 
    5321 41 atoms, 40 bonds, 2 residues, 1 model selected 
    5322 
    5323 > select #20/A
    5324 
    5325 6571 atoms, 6655 bonds, 404 residues, 1 model selected 
    5326 
    5327 > ui tool show H-Bonds
    5328 
    5329 > hbonds sel interModel false saltOnly true reveal true
    5330 
    5331 50 hydrogen bonds found 
    5332 
    5333 > hide #19 models
    5334 
    5335 > show #19 models
    5336 
    5337 > hide #19 models
    5338 
    5339 > hide #!20 models
    5340 
    5341 > show #!20 models
    5342 
    5343 > select add #20
    5344 
    5345 6611 atoms, 6697 bonds, 50 pseudobonds, 405 residues, 2 models selected 
    5346 
    5347 > select subtract #20
    5348 
    5349 Nothing selected 
    5350 
    5351 > show #19 models
    5352 
    5353 > show #21 models
    5354 
    5355 > hide #21 models
    5356 
    5357 > hide #!20 models
    5358 
    5359 > show #!20 models
    5360 
    5361 > hide #!20 models
    5362 
    5363 > show #!20 models
    5364 
    5365 > hide #19 models
    5366 
    5367 > hide #!20 models
    5368 
    5369 > show #19 models
    5370 
    5371 > ui tool show H-Bonds
    5372 
    5373 > hbonds sel interModel false saltOnly true reveal true
    5374 
    5375 Atom specifier selects no atoms 
    5376 
    5377 > ui tool show "Show Sequence Viewer"
    5378 
    5379 > sequence chain #19/A
    5380 
    5381 Alignment identifier is 19/A 
    5382 
    5383 > select #19/A:404
    5384 
    5385 12 atoms, 11 bonds, 1 residue, 1 model selected 
    5386 
    5387 > select #19/A
    5388 
    5389 6568 atoms, 6652 bonds, 404 residues, 1 model selected 
    5390 
    5391 > ui tool show H-Bonds
    5392 
    5393 > hbonds sel interModel false saltOnly true reveal true
    5394 
    5395 53 hydrogen bonds found 
    5396 
    5397 > select add #19
    5398 
    5399 6608 atoms, 6694 bonds, 53 pseudobonds, 405 residues, 2 models selected 
    5400 
    5401 > select subtract #19
    5402 
    5403 Nothing selected 
    5404 
    5405 > show #!20 models
    5406 
    5407 > hide #!19 models
    5408 
    5409 > rmsd #19:GDP to #20:GDP
    5410 
    5411 RMSD between 40 atom pairs is 1.255 
    5412 
    5413 > rmsd #14:GDP to #2:GDP
    5414 
    5415 RMSD between 28 atom pairs is 0.700 
    5416 
    5417 > hide #!20 models
    5418 
    5419 > show #!2 models
    5420 
    5421 > show #7 models
    5422 
    5423 > hide #7 models
    5424 
    5425 > show #7 models
    5426 
    5427 > show #!14 models
    5428 
    5429 > ui mousemode right translate
    5430 
    5431 > hide #!14 models
    5432 
    5433 > show #!14 models
    5434 
    5435 > hide #!2 models
    5436 
    5437 > show #!2 models
    5438 
    5439 > show #!1 models
    5440 
    5441 > hide #!1 models
    5442 
    5443 > hide #7 models
    5444 
    5445 > show #21 models
    5446 
    5447 > hide #21 models
    5448 
    5449 > show #21 models
    5450 
    5451 > hide #21 models
    5452 
    5453 > hide #!2 models
    5454 
    5455 > hide #2.1 models
    5456 
    5457 > hide #!14 models
    5458 
    5459 > show #21 models
    5460 
    5461 > show #!20 models
    5462 
    5463 > hide #21 models
    5464 
    5465 > show #21 models
    5466 
    5467 > hide #21 models
    5468 
    5469 > hide #!20 models
    5470 
    5471 > show #21 models
    5472 
    5473 > hide #21 models
    5474 
    5475 > show #!19 models
    5476 
    5477 > hide #!19 models
    5478 
    5479 > show #21 models
    5480 
    5481 > hide #21 models
    5482 
    5483 > open
    5484 > /Users/aleezamughal/Downloads/fold_gdp_bound_wbdp/fold_gdp_bound_wbdp_model_0.cif
    5485 
    5486 Chain information for fold_gdp_bound_wbdp_model_0.cif #22 
    5487 --- 
    5488 Chain | Description 
    5489 A | . 
    5490  
    5491 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    5492 fold_2026_05_15_15_51_model_1.cif, chain A with 0 mismatches 
    5493 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    5494 fold_2026_05_15_15_51_model_2.cif, chain A with 0 mismatches 
    5495 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    5496 fold_2026_05_15_15_51_model_3.cif, chain A with 0 mismatches 
    5497 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    5498 fold_2026_05_15_15_51_model_4.cif, chain A with 0 mismatches 
    5499 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    5500 fold_2026_06_01_00_39_model_0.cif, chain A with 0 mismatches 
    5501 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    5502 fold_2026_06_01_00_39_model_1.cif, chain A with 0 mismatches 
    5503 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    5504 fold_2026_06_01_00_39_model_2.cif, chain A with 0 mismatches 
    5505 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    5506 fold_2026_06_01_00_39_model_3.cif, chain A with 0 mismatches 
    5507 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    5508 fold_2026_06_01_00_39_model_4.cif, chain A with 0 mismatches 
    5509 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    5510 fold_2026_05_15_15_51_model_1.cif, chain A with 0 mismatches 
    5511 Chains used in RMSD evaluation for alignment 10: AlphaFold A0A9Q6ZED9 #!1/A,
    5512 fold_2026_05_15_15_51_model_1.cif #3/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    5513 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    5514 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    5515 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    5516 #21/A, fold_gdp_bound_wbdp_model_0.cif #22/A 
    5517 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    5518 fold_2026_05_15_15_51_model_2.cif, chain A with 0 mismatches 
    5519 Chains used in RMSD evaluation for alignment 11: AlphaFold A0A9Q6ZED9 #!1/A,
    5520 fold_2026_05_15_15_51_model_2.cif #4/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    5521 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    5522 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    5523 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    5524 #21/A, fold_gdp_bound_wbdp_model_0.cif #22/A 
    5525 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    5526 fold_2026_05_15_15_51_model_3.cif, chain A with 0 mismatches 
    5527 Chains used in RMSD evaluation for alignment 12: AlphaFold A0A9Q6ZED9 #!1/A,
    5528 fold_2026_05_15_15_51_model_3.cif #5/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    5529 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    5530 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    5531 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    5532 #21/A, fold_gdp_bound_wbdp_model_0.cif #22/A 
    5533 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    5534 fold_2026_05_15_15_51_model_4.cif, chain A with 0 mismatches 
    5535 Chains used in RMSD evaluation for alignment 13: AlphaFold A0A9Q6ZED9 #!1/A,
    5536 fold_2026_05_15_15_51_model_4.cif #6/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    5537 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    5538 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    5539 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    5540 #21/A, fold_gdp_bound_wbdp_model_0.cif #22/A 
    5541 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    5542 fold_2026_06_01_00_39_model_0.cif, chain A with 0 mismatches 
    5543 Chains used in RMSD evaluation for alignment 14: AlphaFold A0A9Q6ZED9 #!1/A,
    5544 fold_2026_06_01_00_39_model_0.cif #7/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    5545 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    5546 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    5547 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    5548 #21/A, fold_gdp_bound_wbdp_model_0.cif #22/A 
    5549 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    5550 fold_2026_06_01_00_39_model_1.cif, chain A with 0 mismatches 
    5551 Chains used in RMSD evaluation for alignment 15: AlphaFold A0A9Q6ZED9 #!1/A,
    5552 fold_2026_06_01_00_39_model_1.cif #8/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    5553 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    5554 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    5555 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    5556 #21/A, fold_gdp_bound_wbdp_model_0.cif #22/A 
    5557 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    5558 fold_2026_06_01_00_39_model_2.cif, chain A with 0 mismatches 
    5559 Chains used in RMSD evaluation for alignment 16: AlphaFold A0A9Q6ZED9 #!1/A,
    5560 fold_2026_06_01_00_39_model_2.cif #9/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    5561 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    5562 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    5563 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    5564 #21/A, fold_gdp_bound_wbdp_model_0.cif #22/A 
    5565 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    5566 fold_2026_06_01_00_39_model_3.cif, chain A with 0 mismatches 
    5567 Chains used in RMSD evaluation for alignment 17: AlphaFold A0A9Q6ZED9 #!1/A,
    5568 fold_2026_06_01_00_39_model_3.cif #10/A, fold_gdp_bound_wbdp_model_1.cif
    5569 #15/A, fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif
    5570 #17/A, fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif
    5571 #19/A, fold_2026_05_15_15_51_model_0.cif #20/A,
    5572 fold_2026_05_15_15_51_model_0.cif #21/A, fold_gdp_bound_wbdp_model_0.cif #22/A 
    5573 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    5574 fold_2026_06_01_00_39_model_4.cif, chain A with 0 mismatches 
    5575 Chains used in RMSD evaluation for alignment 18: AlphaFold A0A9Q6ZED9 #!1/A,
    5576 fold_2026_06_01_00_39_model_4.cif #11/A, fold_gdp_bound_wbdp_model_1.cif
    5577 #15/A, fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif
    5578 #17/A, fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif
    5579 #19/A, fold_2026_05_15_15_51_model_0.cif #20/A,
    5580 fold_2026_05_15_15_51_model_0.cif #21/A, fold_gdp_bound_wbdp_model_0.cif #22/A 
    5581 Associated fold_gdp_bound_wbdp_model_0.cif chain A to AlphaFold A0A9Q6ZED9,
    5582 chain A with 0 mismatches 
    5583 Chains used in RMSD evaluation for alignment 19: AlphaFold A0A9Q6ZED9 #!1/A,
    5584 AlphaFold A0A9Q6ZED9 #12/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    5585 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    5586 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    5587 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    5588 #21/A, fold_gdp_bound_wbdp_model_0.cif #22/A 
    5589 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    5590 fold_gdp_bound_wbdp_model_0.cif, chain A with 0 mismatches 
    5591 Chains used in RMSD evaluation for alignment 20: AlphaFold A0A9Q6ZED9 #!1/A,
    5592 fold_gdp_bound_wbdp_model_0.cif #14/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    5593 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    5594 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    5595 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    5596 #21/A, fold_gdp_bound_wbdp_model_0.cif #22/A 
    5597 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    5598 fold_2026_05_15_15_51_model_2.cif, chain A with 0 mismatches 
    5599 Chains used in RMSD evaluation for alignment 21: AlphaFold A0A9Q6ZED9 #!1/A,
    5600 fold_2026_05_15_15_51_model_2.cif #4/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    5601 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    5602 #21/A, fold_gdp_bound_wbdp_model_0.cif #22/A 
    5603 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    5604 fold_2026_05_15_15_51_model_3.cif, chain A with 0 mismatches 
    5605 Chains used in RMSD evaluation for alignment 22: AlphaFold A0A9Q6ZED9 #!1/A,
    5606 fold_2026_05_15_15_51_model_3.cif #5/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    5607 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    5608 #21/A, fold_gdp_bound_wbdp_model_0.cif #22/A 
    5609 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    5610 fold_2026_05_15_15_51_model_4.cif, chain A with 0 mismatches 
    5611 Chains used in RMSD evaluation for alignment 23: AlphaFold A0A9Q6ZED9 #!1/A,
    5612 fold_2026_05_15_15_51_model_4.cif #6/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    5613 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    5614 #21/A, fold_gdp_bound_wbdp_model_0.cif #22/A 
    5615 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    5616 fold_2026_06_01_00_39_model_0.cif, chain A with 0 mismatches 
    5617 Chains used in RMSD evaluation for alignment 24: AlphaFold A0A9Q6ZED9 #!1/A,
    5618 fold_2026_06_01_00_39_model_0.cif #7/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    5619 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    5620 #21/A, fold_gdp_bound_wbdp_model_0.cif #22/A 
    5621 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    5622 fold_2026_06_01_00_39_model_1.cif, chain A with 0 mismatches 
    5623 Chains used in RMSD evaluation for alignment 25: AlphaFold A0A9Q6ZED9 #!1/A,
    5624 fold_2026_06_01_00_39_model_1.cif #8/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    5625 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    5626 #21/A, fold_gdp_bound_wbdp_model_0.cif #22/A 
    5627 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    5628 fold_2026_06_01_00_39_model_2.cif, chain A with 0 mismatches 
    5629 Chains used in RMSD evaluation for alignment 26: AlphaFold A0A9Q6ZED9 #!1/A,
    5630 fold_2026_06_01_00_39_model_2.cif #9/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    5631 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    5632 #21/A, fold_gdp_bound_wbdp_model_0.cif #22/A 
    5633 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    5634 fold_2026_06_01_00_39_model_3.cif, chain A with 0 mismatches 
    5635 Chains used in RMSD evaluation for alignment 27: AlphaFold A0A9Q6ZED9 #!1/A,
    5636 fold_2026_06_01_00_39_model_3.cif #10/A, fold_gdp_bound_wbdp_model_0.cif
    5637 #19/A, fold_2026_05_15_15_51_model_0.cif #20/A,
    5638 fold_2026_05_15_15_51_model_0.cif #21/A, fold_gdp_bound_wbdp_model_0.cif #22/A 
    5639 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    5640 fold_2026_06_01_00_39_model_4.cif, chain A with 0 mismatches 
    5641 Chains used in RMSD evaluation for alignment 28: AlphaFold A0A9Q6ZED9 #!1/A,
    5642 fold_2026_06_01_00_39_model_4.cif #11/A, fold_gdp_bound_wbdp_model_0.cif
    5643 #19/A, fold_2026_05_15_15_51_model_0.cif #20/A,
    5644 fold_2026_05_15_15_51_model_0.cif #21/A, fold_gdp_bound_wbdp_model_0.cif #22/A 
    5645 Associated fold_gdp_bound_wbdp_model_0.cif chain A to AlphaFold A0A9Q6ZED9,
    5646 chain A with 0 mismatches 
    5647 Chains used in RMSD evaluation for alignment 29: AlphaFold A0A9Q6ZED9 #!1/A,
    5648 AlphaFold A0A9Q6ZED9 #12/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    5649 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    5650 #21/A, fold_gdp_bound_wbdp_model_0.cif #22/A 
    5651 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    5652 fold_gdp_bound_wbdp_model_1.cif, chain A with 0 mismatches 
    5653 Chains used in RMSD evaluation for alignment 30: AlphaFold A0A9Q6ZED9 #!1/A,
    5654 fold_gdp_bound_wbdp_model_1.cif #15/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    5655 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    5656 #21/A, fold_gdp_bound_wbdp_model_0.cif #22/A 
    5657 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    5658 fold_gdp_bound_wbdp_model_2.cif, chain A with 0 mismatches 
    5659 Chains used in RMSD evaluation for alignment 31: AlphaFold A0A9Q6ZED9 #!1/A,
    5660 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    5661 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    5662 #21/A, fold_gdp_bound_wbdp_model_0.cif #22/A 
    5663 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    5664 fold_gdp_bound_wbdp_model_3.cif, chain A with 0 mismatches 
    5665 Chains used in RMSD evaluation for alignment 32: AlphaFold A0A9Q6ZED9 #!1/A,
    5666 fold_gdp_bound_wbdp_model_3.cif #17/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    5667 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    5668 #21/A, fold_gdp_bound_wbdp_model_0.cif #22/A 
    5669 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    5670 fold_gdp_bound_wbdp_model_4.cif, chain A with 0 mismatches 
    5671 Chains used in RMSD evaluation for alignment 33: AlphaFold A0A9Q6ZED9 #!1/A,
    5672 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    5673 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    5674 #21/A, fold_gdp_bound_wbdp_model_0.cif #22/A 
    5675 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    5676 fold_2026_05_15_15_51_model_0.cif, chain A with 0 mismatches 
    5677 Chains used in RMSD evaluation for alignment 34: AlphaFold A0A9Q6ZED9 #!1/A,
    5678 fold_2026_05_15_15_51_model_0.cif #2/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    5679 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    5680 #21/A, fold_gdp_bound_wbdp_model_0.cif #22/A 
    5681 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    5682 fold_gdp_bound_wbdp_model_0.cif, chain A with 0 mismatches 
    5683 Chains used in RMSD evaluation for alignment 35: AlphaFold A0A9Q6ZED9 #!1/A,
    5684 fold_gdp_bound_wbdp_model_0.cif #14/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    5685 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    5686 #21/A, fold_gdp_bound_wbdp_model_0.cif #22/A 
    5687 Associated fold_gdp_bound_wbdp_model_0.cif chain A to
    5688 fold_2026_05_15_15_51_model_0.cif, chain A with 0 mismatches 
    5689 Chains used in RMSD evaluation for alignment 36: AlphaFold A0A9Q6ZED9 #!1/A,
    5690 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    5691 #21/A, fold_gdp_bound_wbdp_model_0.cif #22/A 
    5692 Computing secondary structure 
    5693 
    5694 > show #21 models
    5695 
    5696 > hide #21 models
    5697 
    5698 > show #21 models
    5699 
    5700 > ui tool show Matchmaker
    5701 
    5702 > matchmaker #21-22 to #1
    5703 
    5704 Parameters 
    5705 --- 
    5706 Chain pairing | bb 
    5707 Alignment algorithm | Needleman-Wunsch 
    5708 Similarity matrix | BLOSUM-62 
    5709 SS fraction | 0.3 
    5710 Gap open (HH/SS/other) | 18/18/6 
    5711 Gap extend | 1 
    5712 SS matrix |  |  | H | S | O 
    5713 ---|---|---|--- 
    5714 H | 6 | -9 | -6 
    5715 S |  | 6 | -6 
    5716 O |  |  | 4 
    5717 Iteration cutoff | 2 
    5718  
    5719 Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with
    5720 fold_2026_05_15_15_51_model_0.cif, chain A (#21), sequence alignment score =
    5721 2101.2 
    5722 RMSD between 366 pruned atom pairs is 0.687 angstroms; (across all 404 pairs:
    5723 2.582) 
    5724  
    5725 Matchmaker AlphaFold A0A9Q6ZED9, chain A (#1) with
    5726 fold_gdp_bound_wbdp_model_0.cif, chain A (#22), sequence alignment score =
    5727 2105.4 
    5728 Alignment identifier is 37 
    5729 Showing conservation header ("seq_conservation" residue attribute) for
    5730 alignment 37 
    5731 Hiding conservation header for alignment 37 
    5732 Chains used in RMSD evaluation for alignment 37: AlphaFold A0A9Q6ZED9 #!1/A,
    5733 fold_gdp_bound_wbdp_model_0.cif #22/A 
    5734 Showing rmsd header ("seq_rmsd" residue attribute) for alignment 37 
    5735 RMSD between 366 pruned atom pairs is 0.514 angstroms; (across all 404 pairs:
    5736 1.657) 
    5737  
    5738 
    5739 > coulombic #21-22
    5740 
    5741 Using Amber 20 recommended default charges and atom types for standard
    5742 residues 
    5743 Assigning partial charges to residue PTR (net charge -2) with am1-bcc method 
    5744 Running ANTECHAMBER command:
    5745 /Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/bin/amber20/bin/antechamber
    5746 -ek qm_theory='AM1', -i
    5747 /var/folders/zc/bn4qs3894m51jrw9pmkqnvlm0000gn/T/tmp49mlus_s/ante.in.mol2 -fi
    5748 mol2 -o
    5749 /var/folders/zc/bn4qs3894m51jrw9pmkqnvlm0000gn/T/tmp49mlus_s/ante.out.mol2 -fo
    5750 mol2 -c bcc -nc -2 -j 5 -s 2 -dr n 
    5751 (PTR) `` 
    5752 (PTR) `Welcome to antechamber 20.0: molecular input file processor.` 
    5753 (PTR) `` 
    5754 (PTR) `Info: Finished reading file
    5755 (/var/folders/zc/bn4qs3894m51jrw9pmkqnvlm0000gn/T/tmp49mlus_s/ante.in.mol2);
    5756 atoms read (36), bonds read (36).` 
    5757 (PTR) `Info: Determining atomic numbers from atomic symbols which are case
    5758 sensitive.` 
    5759 (PTR) `Running:
    5760 /Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/bin/amber20/bin/bondtype
    5761 -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` 
    5762 (PTR) `` 
    5763 (PTR) `` 
    5764 (PTR) `Running:
    5765 /Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/bin/amber20/bin/atomtype
    5766 -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` 
    5767 (PTR) `Info: Total number of electrons: 166; net charge: -2` 
    5768 (PTR) `` 
    5769 (PTR) `Running:
    5770 /Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/bin/amber20/bin/sqm -O
    5771 -i sqm.in -o sqm.out` 
    5772 (PTR) `` 
    5773 (PTR) `Running:
    5774 /Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/bin/amber20/bin/am1bcc
    5775 -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
    5776 /Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
    5777 -s 2 -j 1` 
    5778 (PTR) `` 
    5779 (PTR) `Running:
    5780 /Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/bin/amber20/bin/atomtype
    5781 -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` 
    5782 (PTR) `` 
    5783 Charges for residue PTR determined 
    5784 Using Amber 20 recommended default charges and atom types for standard
    5785 residues 
    5786 Coulombic values for fold_2026_05_15_15_51_model_0.cif_A SES surface #21.1:
    5787 minimum, -20.05, mean -0.12, maximum 18.22 
    5788 Coulombic values for fold_gdp_bound_wbdp_model_0.cif_A SES surface #22.1:
    5789 minimum, -12.92, mean -0.15, maximum 18.97 
    5790 To also show corresponding color key, enter the above coulombic command and
    5791 add key true 
    5792 
    5793 > hide #!21 models
    5794 
    5795 > hide #!22 models
    5796 
    5797 > show #!22 models
    5798 
    5799 > hide #!22 models
    5800 
    5801 > show #!21 models
    5802 
    5803 > hide #!21 models
    5804 
    5805 > show #!22 models
    5806 
    5807 > hide #!22 models
    5808 
    5809 > show #!21 models
    5810 
    5811 > hide #!21 models
    5812 
    5813 > show #!22 models
    5814 
    5815 > hide #!22 models
    5816 
    5817 > show #!21 models
    5818 
    5819 > hide #21.1 models
    5820 
    5821 > show #21.1 models
    5822 
    5823 > hide #21.1 models
    5824 
    5825 > show #21.1 models
    5826 
    5827 > show #!22 models
    5828 
    5829 > hide #21.1 models
    5830 
    5831 > show #21.1 models
    5832 
    5833 > hide #!22 models
    5834 
    5835 > hide #21.1 models
    5836 
    5837 > show #21.1 models
    5838 
    5839 > show #!22 models
    5840 
    5841 > hide #!21 models
    5842 
    5843 > ui mousemode right zoom
    5844 
    5845 > hide #21.1 models
    5846 
    5847 > show #21.1 models
    5848 
    5849 > hide #!21 models
    5850 
    5851 > show #!21 models
    5852 
    5853 > hide #!21 models
    5854 
    5855 > hide #!22 models
    5856 
    5857 > show #!21 models
    5858 
    5859 > hide #!21 models
    5860 
    5861 > show #!22 models
    5862 
    5863 > hide #!22 models
    5864 
    5865 > show #!21 models
    5866 
    5867 > view
    5868 
    5869 [Repeated 2 time(s)]
    5870 
    5871 > save /Users/aleezamughal/Desktop/image1.png supersample 3
    5872 
    5873 > save /Users/aleezamughal/Desktop/image2.png supersample 3
    5874 
    5875 > view
    5876 
    5877 [Repeated 1 time(s)]
    5878 
    5879 > movie record
    5880 
    5881 > turn y 2 180
    5882 
    5883 > wait 180
    5884 
    5885 > movie encode /Users/aleezamughal/Desktop/movie1.mp4
    5886 
    5887 Movie saved to /Users/aleezamughal/Desktop/movie1.mp4 
    5888  
    5889 
    5890 > hide #!21 models
    5891 
    5892 > show #!21 models
    5893 
    5894 > hide #!21 models
    5895 
    5896 > show #!21 models
    5897 
    5898 > hide #!21 models
    5899 
    5900 > show #!21 models
    5901 
    5902 > show #!22 models
    5903 
    5904 > hide #!21 models
    5905 
    5906 > show #!21 models
    5907 
    5908 > hide #!21 models
    5909 
    5910 > show #!21 models
    5911 
    5912 > hide #!21 models
    5913 
    5914 > hide #!22 models
    5915 
    5916 > show #!21 models
    5917 
    5918 > hide #!21 models
    5919 
    5920 > show #!22 models
    5921 
    5922 > hide #!22 models
    5923 
    5924 > show #!21 models
    5925 
    5926 > show #!22 models
    5927 
    5928 > hide #22.1 models
    5929 
    5930 > hide #21.1 models
    5931 
    5932 > show #21.1 models
    5933 
    5934 > show #22.1 models
    5935 
    5936 > hide #!21 models
    5937 
    5938 > movie record
    5939 
    5940 > turn y 2 180
    5941 
    5942 > wait 180
    5943 
    5944 > movie encode /Users/aleezamughal/Desktop/movie1.mp4
    5945 
    5946 Movie saved to /Users/aleezamughal/Desktop/movie1.mp4 
    5947  
    5948 
    5949 > show #!21 models
    5950 
    5951 > hide #!21 models
    5952 
    5953 > show #!21 models
    5954 
    5955 > hide #!21 models
    5956 
    5957 > show #!21 models
    5958 
    5959 > hide #!21 models
    5960 
    5961 > show #!21 models
    5962 
    5963 > hide #!21 models
    5964 
    5965 > hide #!22 models
    5966 
    5967 > show #!21 models
    5968 
    5969 > hide #!21 models
    5970 
    5971 > show #!22 models
    5972 
    5973 > hide #!22 models
    5974 
    5975 > show #!21 models
    5976 
    5977 > hide #!21 models
    5978 
    5979 > show #!22 models
    5980 
    5981 > show #!21 models
    5982 
    5983 > hide #!21 models
    5984 
    5985 > hide #!22 models
    5986 
    5987 > show #!21 models
    5988 
    5989 > hide #!21 models
    5990 
    5991 > show #!22 models
    5992 
    5993 > save /Users/aleezamughal/Desktop/image1.png supersample 3
    5994 
    5995 > hide #!22 models
    5996 
    5997 > show #!21 models
    5998 
    5999 > save /Users/aleezamughal/Desktop/image1.png supersample 3
    6000 
    6001 > hide #!21 models
    6002 
    6003 > show #!21 models
    6004 
    6005 > hide #!21 models
    6006 
    6007 > show #!21 models
    6008 
    6009 > hide #!21 models
    6010 
    6011 > hide #22.1 models
    6012 
    6013 > show #!22 models
    6014 
    6015 > show #22.1 models
    6016 
    6017 > hide #!22 models
    6018 
    6019 > show #!21 models
    6020 
    6021 > hide #!21 models
    6022 
    6023 > show #!22 models
    6024 
    6025 > hide #!22 models
    6026 
    6027 > show #!21 models
    6028 
    6029 > hide #!21 models
    6030 
    6031 > show #!21 models
    6032 
    6033 > ui tool show ViewDock
    6034 
    6035 > ui tool show "Find Cavities"
    6036 
    6037 > kvfinder #21-22
    6038 
    6039 13 cavities found for fold_2026_05_15_15_51_model_0.cif #21 
    6040 fold_2026_05_15_15_51_model_0.cif Cavities 
    6041 --- 
    6042 ID |  | Volume | Area | Points | Maximum 
    6043 Depth | Average 
    6044 Depth 
    6045 21.2.1 |  | 2150.28 | 1212.7 | 9955 | 9.49 | 3.39 
    6046 21.2.11 |  | 318.6 | 265.45 | 1475 | 8.03 | 2.57 
    6047 21.2.12 |  | 236.09 | 213 | 1093 | 3.7 | 1.08 
    6048 21.2.5 |  | 115.78 | 121.01 | 536 | 5.09 | 1.78 
    6049 21.2.8 |  | 96.98 | 114.53 | 449 | 4.2 | 1.59 
    6050 21.2.2 |  | 60.26 | 80.88 | 279 | 3.06 | 0.91 
    6051 21.2.4 |  | 34.99 | 47.21 | 162 | 1.9 | 0.55 
    6052 21.2.10 |  | 34.56 | 53.42 | 160 | 0 | 0 
    6053 21.2.9 |  | 30.46 | 38.72 | 141 | 2.24 | 0.96 
    6054 21.2.3 |  | 23.33 | 37.11 | 108 | 1.34 | 0.42 
    6055 21.2.13 |  | 21.38 | 34.14 | 99 | 3 | 1.2 
    6056 21.2.7 |  | 20.95 | 31.69 | 97 | 1.8 | 0.57 
    6057 21.2.6 |  | 11.88 | 22.51 | 55 | 0.6 | 0.16 
    6058  
    6059 15 cavities found for fold_gdp_bound_wbdp_model_0.cif #22 
    6060 fold_gdp_bound_wbdp_model_0.cif Cavities 
    6061 --- 
    6062 ID |  | Volume | Area | Points | Maximum 
    6063 Depth | Average 
    6064 Depth 
    6065 22.2.4 |  | 1932.12 | 1131.17 | 8945 | 9.1 | 3.35 
    6066 22.2.8 |  | 249.7 | 203.45 | 1156 | 4.24 | 1.37 
    6067 22.2.3 |  | 159.41 | 160.61 | 738 | 4.84 | 1.18 
    6068 22.2.12 |  | 91.58 | 106.5 | 424 | 5.16 | 1.8 
    6069 22.2.6 |  | 42.98 | 62.43 | 199 | 2.47 | 0.69 
    6070 22.2.13 |  | 33.7 | 49.87 | 156 | 3.84 | 1.55 
    6071 22.2.9 |  | 29.81 | 49.21 | 138 | 4.24 | 2.13 
    6072 22.2.1 |  | 26.35 | 44.29 | 122 | 0 | 0 
    6073 22.2.10 |  | 20.74 | 41.19 | 96 | 0 | 0 
    6074 22.2.14 |  | 20.52 | 29.2 | 95 | 1.8 | 0.53 
    6075 22.2.7 |  | 19.66 | 27.87 | 91 | 2.16 | 0.68 
    6076 22.2.15 |  | 18.79 | 30.53 | 87 | 1.8 | 0.5 
    6077 22.2.11 |  | 12.31 | 29.54 | 57 | 0 | 0 
    6078 22.2.2 |  | 9.5 | 20.34 | 44 | 0.85 | 0.34 
    6079 22.2.5 |  | 6.26 | 13.53 | 29 | 0.6 | 0.08 
    6080  
    6081 
    6082 > hide #21.2.1 models
    6083 
    6084 > show #21.2.1 models
    6085 
    6086 > hide #!21.2 models
    6087 
    6088 > show #!21.2 models
    6089 
    6090 > hide #!21.2 models
    6091 
    6092 > show #!21.2 models
    6093 
    6094 > hide #21.2.2 models
    6095 
    6096 > show #21.2.2 models
    6097 
    6098 > hide #!21.2 models
    6099 
    6100 > hide #21.2.1 models
    6101 
    6102 > show #21.2.1 models
    6103 
    6104 > hide #21.2.2 models
    6105 
    6106 > hide #21.2.3 models
    6107 
    6108 > hide #21.2.4 models
    6109 
    6110 > hide #21.2.5 models
    6111 
    6112 > hide #21.2.6 models
    6113 
    6114 > hide #21.2.7 models
    6115 
    6116 > hide #21.2.8 models
    6117 
    6118 > hide #21.2.9 models
    6119 
    6120 > hide #21.2.10 models
    6121 
    6122 > hide #21.2.11 models
    6123 
    6124 > hide #21.2.12 models
    6125 
    6126 > hide #21.2.13 models
    6127 
    6128 > show #!22 models
    6129 
    6130 > hide #!22 models
    6131 
    6132 > hide #!21 models
    6133 
    6134 > show #!22 models
    6135 
    6136 > hide #22.2.4 models
    6137 
    6138 > show #22.2.4 models
    6139 
    6140 > hide #22.2.5 models
    6141 
    6142 > hide #22.2.6 models
    6143 
    6144 > hide #22.2.7 models
    6145 
    6146 > hide #22.2.8 models
    6147 
    6148 > hide #22.2.9 models
    6149 
    6150 > hide #22.2.10 models
    6151 
    6152 > hide #22.2.11 models
    6153 
    6154 > hide #22.2.12 models
    6155 
    6156 > hide #22.2.13 models
    6157 
    6158 > hide #22.2.14 models
    6159 
    6160 > hide #22.2.15 models
    6161 
    6162 > hide #22.2.3 models
    6163 
    6164 > hide #22.2.2 models
    6165 
    6166 > hide #22.2.1 models
    6167 
    6168 > show #22.2.1 models
    6169 
    6170 > hide #22.2.1 models
    6171 
    6172 > show #22.2.1 models
    6173 
    6174 > hide #22.2.1 models
    6175 
    6176 > show #22.2.2 models
    6177 
    6178 > hide #22.2.2 models
    6179 
    6180 > show #22.2.3 models
    6181 
    6182 > hide #22.2.3 models
    6183 
    6184 > show #22.2.5 models
    6185 
    6186 > hide #22.2.5 models
    6187 
    6188 > show #22.2.6 models
    6189 
    6190 > hide #22.2.6 models
    6191 
    6192 > show #22.2.7 models
    6193 
    6194 > hide #22.2.7 models
    6195 
    6196 > show #22.2.8 models
    6197 
    6198 > hide #22.2.8 models
    6199 
    6200 > show #22.2.9 models
    6201 
    6202 > hide #22.2.9 models
    6203 
    6204 > show #22.2.10 models
    6205 
    6206 > hide #22.2.10 models
    6207 
    6208 > show #22.2.11 models
    6209 
    6210 > hide #22.2.11 models
    6211 
    6212 > show #22.2.12 models
    6213 
    6214 > hide #22.2.12 models
    6215 
    6216 > show #22.2.13 models
    6217 
    6218 > hide #22.2.13 models
    6219 
    6220 > show #22.2.14 models
    6221 
    6222 > hide #22.2.14 models
    6223 
    6224 > show #22.2.15 models
    6225 
    6226 > hide #22.2.15 models
    6227 
    6228 > hide #!22 models
    6229 
    6230 > select add #22
    6231 
    6232 15697 atoms, 3406 bonds, 420 residues, 17 models selected 
    6233 
    6234 > select subtract #22
    6235 
    6236 1 model selected 
    6237 
    6238 > show #!22 models
    6239 
    6240 > show #!21 models
    6241 
    6242 > hide #!21 models
    6243 
    6244 Cell requested for row 23 is out of bounds for table with 28 rows! Resizing
    6245 table model. 
    6246 
    6247 > hide #!22 models
    6248 
    6249 > show #!21 models
    6250 
    6251 > hide #!21 models
    6252 
    6253 > show #!22 models
    6254 
    6255 > hide #!22 models
    6256 
    6257 > show #!21 models
    6258 
    6259 > hide #!21 models
    6260 
    6261 > show #!22 models
    6262 
    6263 > hide #!22 models
    6264 
    6265 > show #!21 models
    6266 
    6267 > hide #!21 models
    6268 
    6269 > show #!22 models
    6270 
    6271 > hide #!22 models
    6272 
    6273 > show #!21 models
    6274 
    6275 > hide #!21 models
    6276 
    6277 > show #!22 models
    6278 
    6279 > show #!21 models
    6280 
    6281 > hide #!22 models
    6282 
    6283 > hide #!21 models
    6284 
    6285 > show #!22 models
    6286 
    6287 > show #!21 models
    6288 
    6289 > hide #!21 models
    6290 
    6291 > hide #!22 models
    6292 
    6293 > show #!21 models
    6294 
    6295 > hide #!21 models
    6296 
    6297 > show #!22 models
    6298 
    6299 > hide #!22 models
    6300 
    6301 > show #!21 models
    6302 
    6303 > hide #!21 models
    6304 
    6305 > show #!22 models
    6306 
    6307 > hide #!22 models
    6308 
    6309 > show #!21 models
    6310 
    6311 > hide #!21 models
    6312 
    6313 > show #!22 models
    6314 
    6315 > show #!21 models
    6316 
    6317 > hide #!21 models
    6318 
    6319 > show #!21 models
    6320 
    6321 > hide #!22 models
    6322 
    6323 > hide #!21 models
    6324 
    6325 > show #!22 models
    6326 
    6327 > hide #!22 models
    6328 
    6329 > show #!21 models
    6330 
    6331 > hide #!21 models
    6332 
    6333 > show #!22 models
    6334 
    6335 > ui tool show H-Bonds
    6336 
    6337 > hbonds sel interModel false saltOnly true reveal true
    6338 
    6339 Atom specifier selects no atoms 
    6340 
    6341 > ui tool show "Show Sequence Viewer"
    6342 
    6343 > sequence chain #20/A
    6344 
    6345 Destroying pre-existing alignment with identifier 20/A 
    6346 Alignment identifier is 20/A 
    6347 
    6348 > sequence chain #!21/A
    6349 
    6350 Alignment identifier is 21/A 
    6351 
    6352 > sequence chain #!22/A
    6353 
    6354 Alignment identifier is 22/A 
    6355 
    6356 > select #!22/A:404
    6357 
    6358 7 atoms, 6 bonds, 1 residue, 1 model selected 
    6359 
    6360 > select #!22/A:181-404
    6361 
    6362 1796 atoms, 1840 bonds, 224 residues, 1 model selected 
    6363 
    6364 > select #!22/A:1
    6365 
    6366 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6367 
    6368 > select #!22/A
    6369 
    6370 3292 atoms, 3376 bonds, 404 residues, 1 model selected 
    6371 
    6372 > ui tool show H-Bonds
    6373 
    6374 > hbonds sel interModel false saltOnly true reveal true
    6375 
    6376 25 hydrogen bonds found 
    6377 
    6378 > hide #!22.2 models
    6379 
    6380 > hide #!22 models
    6381 
    6382 > show #!21 models
    6383 
    6384 > hide #!21 models
    6385 
    6386 > show #!22 models
    6387 
    6388 > show #!22.2 models
    6389 
    6390 > hide #!22.2 models
    6391 
    6392 > hide #!22 models
    6393 
    6394 > show #!21 models
    6395 
    6396 > hide #!21.2 models
    6397 
    6398 > select #!21/A:404
    6399 
    6400 7 atoms, 6 bonds, 1 residue, 1 model selected 
    6401 
    6402 > select #!21/A
    6403 
    6404 3296 atoms, 3380 bonds, 404 residues, 1 model selected 
    6405 
    6406 > ui tool show H-Bonds
    6407 
    6408 > hbonds sel interModel false saltOnly true reveal true
    6409 
    6410 17 hydrogen bonds found 
    6411 
    6412 > hide #!21 models
    6413 
    6414 > show #!21 models
    6415 
    6416 > hide #!21 models
    6417 
    6418 > show #!22 models
    6419 
    6420 > show #!21 models
    6421 
    6422 > hide #!21 models
    6423 
    6424 > show #!21 models
    6425 
    6426 > hide #!21 models
    6427 
    6428 > show #!21 models
    6429 
    6430 > hide #!21 models
    6431 
    6432 > show #!21 models
    6433 
    6434 > hide #!21 models
    6435 
    6436 > show #!21 models
    6437 
    6438 > hide #!22 models
    6439 
    6440 > ui tool show "Modeller Comparative"
    6441 
    6442 > hide #!21 models
    6443 
    6444 > show #!1 models
    6445 
    6446 > show #!1.1 models
    6447 
    6448 > hide #!1.1 models
    6449 
    6450 > show #!1.1 models
    6451 
    6452 > hide #!1.1 models
    6453 
    6454 > show #!21 models
    6455 
    6456 > hide #!1 models
    6457 
    6458 > hide #21.1 models
    6459 
    6460 > show #!21.2 models
    6461 
    6462 > hide #21.2.1 models
    6463 
    6464 > show #21.2.1 models
    6465 
    6466 > hide #!21.2 models
    6467 
    6468 > show #21.1 models
    6469 
    6470 > hide #!21 models
    6471 
    6472 > show #!1 models
    6473 
    6474 > show #!2 models
    6475 
    6476 > hide #!2 models
    6477 
    6478 > ui tool show "Blast Protein"
    6479 
    6480 > blastprotein #!1/A database alphafold cutoff 1e-3 matrix BLOSUM62 maxSeqs
    6481 > 100 version 4 name bp4
    6482 
    6483 Webservices job id: 18VPL69O9YDHF6OF 
    6484 Webservices job finished: 18VPL69O9YDHF6OF 
    6485 Traceback (most recent call last): 
    6486 File
    6487 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6488 packages/chimerax/ui/gui.py", line 937, in customEvent 
    6489 func(*args, **kw) 
    6490 File
    6491 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6492 packages/chimerax/blastprotein/job.py", line 132, in on_finish 
    6493 BlastProteinResults.from_job( 
    6494 File
    6495 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6496 packages/chimerax/blastprotein/ui/results.py", line 118, in from_job 
    6497 return cls(session, tool_name, from_restore=False, params=params, job=job,
    6498 **kw) 
    6499 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    6500 File
    6501 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6502 packages/chimerax/blastprotein/ui/results.py", line 100, in __init__ 
    6503 self._build_ui() 
    6504 File
    6505 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6506 packages/chimerax/blastprotein/ui/results.py", line 262, in _build_ui 
    6507 param_str = self._format_param_str() 
    6508 ^^^^^^^^^^^^^^^^^^^^^^^^ 
    6509 File
    6510 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6511 packages/chimerax/blastprotein/ui/results.py", line 222, in _format_param_str 
    6512 model_no = int(float(values[0].split("/")[0][1:])) 
    6513 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    6514 ValueError: could not convert string to float: '!1' 
    6515  
    6516 ValueError: could not convert string to float: '!1' 
    6517  
    6518 File
    6519 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6520 packages/chimerax/blastprotein/ui/results.py", line 222, in _format_param_str 
    6521 model_no = int(float(values[0].split("/")[0][1:])) 
    6522 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    6523  
    6524 See log for complete Python traceback. 
    6525  
    6526 
    6527 > ui tool show "Blast Protein"
    6528 
    6529 > blastprotein #12/A database alphafold cutoff 1e-3 matrix BLOSUM62 maxSeqs
    6530 > 100 version 4 name bp5
    6531 
    6532 Webservices job id: KHHXL2DK7SH44YG9 
    6533 Exception in thread Thread-5295 (_run_function): 
    6534 Traceback (most recent call last): 
    6535 File
    6536 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6537 packages/urllib3/connection.py", line 204, in _new_conn 
    6538 sock = connection.create_connection( 
    6539 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    6540 File
    6541 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6542 packages/urllib3/util/connection.py", line 85, in create_connection 
    6543 raise err 
    6544 File
    6545 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6546 packages/urllib3/util/connection.py", line 73, in create_connection 
    6547 sock.connect(sa) 
    6548 OSError: [Errno 65] No route to host 
    6549  
    6550 The above exception was the direct cause of the following exception: 
    6551  
    6552 Traceback (most recent call last): 
    6553 File
    6554 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6555 packages/urllib3/connectionpool.py", line 788, in urlopen 
    6556 response = self._make_request( 
    6557 ^^^^^^^^^^^^^^^^^^^ 
    6558 File
    6559 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6560 packages/urllib3/connectionpool.py", line 488, in _make_request 
    6561 raise new_e 
    6562 File
    6563 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6564 packages/urllib3/connectionpool.py", line 464, in _make_request 
    6565 self._validate_conn(conn) 
    6566 File
    6567 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6568 packages/urllib3/connectionpool.py", line 1106, in _validate_conn 
    6569 conn.connect() 
    6570 File
    6571 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6572 packages/urllib3/connection.py", line 759, in connect 
    6573 self.sock = sock = self._new_conn() 
    6574 ^^^^^^^^^^^^^^^^ 
    6575 File
    6576 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6577 packages/urllib3/connection.py", line 219, in _new_conn 
    6578 raise NewConnectionError( 
    6579 urllib3.exceptions.NewConnectionError:
    6580 HTTPSConnection(host='webservices.rbvi.ucsf.edu', port=443): Failed to
    6581 establish a new connection: [Errno 65] No route to host 
    6582  
    6583 The above exception was the direct cause of the following exception: 
    6584  
    6585 Traceback (most recent call last): 
    6586 File
    6587 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py",
    6588 line 1045, in _bootstrap_inner 
    6589 self.run() 
    6590 File
    6591 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py",
    6592 line 982, in run 
    6593 self._target(*self._args, **self._kwargs) 
    6594 File
    6595 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6596 packages/chimerax/core/tasks.py", line 323, in _run_function 
    6597 func(*args, **kw) 
    6598 File
    6599 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6600 packages/chimerax/webservices/cxservices_job.py", line 172, in run 
    6601 super().run() 
    6602 File
    6603 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6604 packages/chimerax/core/tasks.py", line 486, in run 
    6605 self.monitor() 
    6606 File
    6607 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6608 packages/chimerax/webservices/cxservices_job.py", line 207, in monitor 
    6609 result = self.chimerax_api.get_status(job_id=self.job_id) 
    6610 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    6611 File
    6612 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6613 packages/cxservices/api/default_api.py", line 954, in get_status 
    6614 (data) = self.get_status_with_http_info(job_id, **kwargs) # noqa: E501 
    6615 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    6616 File
    6617 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6618 packages/cxservices/api/default_api.py", line 1013, in
    6619 get_status_with_http_info 
    6620 return self.api_client.call_api( 
    6621 ^^^^^^^^^^^^^^^^^^^^^^^^^ 
    6622 File
    6623 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6624 packages/cxservices/api_client.py", line 319, in call_api 
    6625 return self.__call_api(resource_path, method, 
    6626 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    6627 File
    6628 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6629 packages/cxservices/api_client.py", line 151, in __call_api 
    6630 response_data = self.request( 
    6631 ^^^^^^^^^^^^^ 
    6632 File
    6633 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6634 packages/cxservices/api_client.py", line 341, in request 
    6635 return self.rest_client.GET(url, 
    6636 ^^^^^^^^^^^^^^^^^^^^^^^^^ 
    6637 File
    6638 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6639 packages/cxservices/rest.py", line 228, in GET 
    6640 return self.request("GET", url, 
    6641 ^^^^^^^^^^^^^^^^^^^^^^^^ 
    6642 File
    6643 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6644 packages/cxservices/rest.py", line 206, in request 
    6645 r = self.pool_manager.request(method, url, 
    6646 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    6647 File
    6648 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6649 packages/urllib3/_request_methods.py", line 135, in request 
    6650 return self.request_encode_url( 
    6651 ^^^^^^^^^^^^^^^^^^^^^^^^ 
    6652 File
    6653 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6654 packages/urllib3/_request_methods.py", line 182, in request_encode_url 
    6655 return self.urlopen(method, url, **extra_kw) 
    6656 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    6657 File
    6658 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6659 packages/urllib3/poolmanager.py", line 503, in urlopen 
    6660 return self.urlopen(method, redirect_location, **kw) 
    6661 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    6662 File
    6663 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6664 packages/urllib3/poolmanager.py", line 457, in urlopen 
    6665 response = conn.urlopen(method, u.request_uri, **kw) 
    6666 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    6667 File
    6668 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6669 packages/urllib3/connectionpool.py", line 872, in urlopen 
    6670 return self.urlopen( 
    6671 ^^^^^^^^^^^^^ 
    6672 File
    6673 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6674 packages/urllib3/connectionpool.py", line 872, in urlopen 
    6675 return self.urlopen( 
    6676 ^^^^^^^^^^^^^ 
    6677 File
    6678 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6679 packages/urllib3/connectionpool.py", line 842, in urlopen 
    6680 retries = retries.increment( 
    6681 ^^^^^^^^^^^^^^^^^^ 
    6682 File
    6683 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6684 packages/urllib3/util/retry.py", line 543, in increment 
    6685 raise MaxRetryError(_pool, url, reason) from reason # type: ignore[arg-type] 
    6686 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    6687 urllib3.exceptions.MaxRetryError:
    6688 HTTPSConnectionPool(host='webservices.rbvi.ucsf.edu', port=443): Max retries
    6689 exceeded with url: /cxservices/api/v1/chimerax/jobs/KHHXL2DK7SH44YG9/status
    6690 (Caused by
    6691 NewConnectionError("HTTPSConnection(host='webservices.rbvi.ucsf.edu',
    6692 port=443): Failed to establish a new connection: [Errno 65] No route to
    6693 host")) 
    6694 
    6695 > ui tool show "Blast Protein"
    6696 
    6697 > blastprotein #5/A database alphafold cutoff 1e-3 matrix BLOSUM62 maxSeqs 100
    6698 > version 4 name bp6
    6699 
    6700 Webservices job id: 6O86EWCZ2TXMDOQW 
    6701 
    6702 > save "/Users/aleezamughal/Desktop/WbdP analysis.cxs"
    6703 
    6704 Traceback (most recent call last): 
    6705 File
    6706 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6707 packages/chimerax/core/session.py", line 322, in process 
    6708 data = sm.take_snapshot(obj, session, self.state_flags) 
    6709 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    6710 File
    6711 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6712 packages/chimerax/blastprotein/ui/results.py", line 189, in take_snapshot 
    6713 "table_session": self.table.session_info(), 
    6714 ^^^^^^^^^^ 
    6715 AttributeError: 'BlastProteinResults' object has no attribute 'table' 
    6716  
    6717 The above exception was the direct cause of the following exception: 
    6718  
    6719 Traceback (most recent call last): 
    6720 File
    6721 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6722 packages/chimerax/core/session.py", line 297, in discovery 
    6723 self.processed[key] = self.process(obj, parents) 
    6724 ^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    6725 File
    6726 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6727 packages/chimerax/core/session.py", line 329, in process 
    6728 raise RuntimeError(msg) from e 
    6729 RuntimeError: Error while saving session data for 'tools' ->
    6730 [<chimerax.seq_view.tool.SequenceViewer object at 0x154fe2010>,
    6731 <chimerax.seq_view.tool.SequenceViewer object at 0x149607c50>,
    6732 <chimerax.toolbar.tool.ToolbarTool object at 0x1324b2890>,
    6733 <chimerax.model_panel.tool.ModelPanel object at 0x101024cd0>,
    6734 <chimerax.seq_view.tool.SequenceViewer object at 0x1551c74d0>,
    6735 <chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x14f2d3d10>,
    6736 <chimerax.modeller.tool.ModellerLauncher object at 0x14964d910>,
    6737 <chimerax.log.tool.Log object at 0x12c89b950>,
    6738 <chimerax.seq_view.tool.SequenceViewer object at 0x1551b7610>,
    6739 <chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x16abfbe10>,
    6740 <chimerax.cmd_line.tool.CommandLine object at 0x12c8afa90>,
    6741 <chimerax.seq_view.tool.SequenceViewer object at 0x15d231a90>,
    6742 <chimerax.blastprotein.ui.results.BlastProteinResults object at 0x34c3cc690>,
    6743 <chimerax.seq_view.tool.SequenceViewer object at 0x1491dc710>,
    6744 <chimerax.seq_view.tool.SequenceViewer object at 0x15d21c710>,
    6745 <chimerax.blastprotein.ui.results.BlastProteinResults object at 0x14cd1af50>,
    6746 <chimerax.seq_view.tool.SequenceViewer object at 0x1551d6350>,
    6747 <chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x34c3fb350>] ->
    6748 <chimerax.blastprotein.ui.results.BlastProteinResults object at 0x14cd1af50> 
    6749  
    6750 During handling of the above exception, another exception occurred: 
    6751  
    6752 Traceback (most recent call last): 
    6753 File
    6754 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6755 packages/chimerax/core/session.py", line 1048, in save 
    6756 session.save(output, version=version, include_maps=include_maps) 
    6757 File
    6758 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6759 packages/chimerax/core/session.py", line 731, in save 
    6760 mgr.discovery(self._state_containers) 
    6761 File
    6762 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6763 packages/chimerax/core/session.py", line 301, in discovery 
    6764 raise ValueError( 
    6765 ValueError: error processing: 'tools' ->
    6766 [<chimerax.seq_view.tool.SequenceViewer object at 0x154fe2010>,
    6767 <chimerax.seq_view.tool.SequenceViewer object at 0x149607c50>,
    6768 <chimerax.toolbar.tool.ToolbarTool object at 0x1324b2890>,
    6769 <chimerax.model_panel.tool.ModelPanel object at 0x101024cd0>,
    6770 <chimerax.seq_view.tool.SequenceViewer object at 0x1551c74d0>,
    6771 <chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x14f2d3d10>,
    6772 <chimerax.modeller.tool.ModellerLauncher object at 0x14964d910>,
    6773 <chimerax.log.tool.Log object at 0x12c89b950>,
    6774 <chimerax.seq_view.tool.SequenceViewer object at 0x1551b7610>,
    6775 <chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x16abfbe10>,
    6776 <chimerax.cmd_line.tool.CommandLine object at 0x12c8afa90>,
    6777 <chimerax.seq_view.tool.SequenceViewer object at 0x15d231a90>,
    6778 <chimerax.blastprotein.ui.results.BlastProteinResults object at 0x34c3cc690>,
    6779 <chimerax.seq_view.tool.SequenceViewer object at 0x1491dc710>,
    6780 <chimerax.seq_view.tool.SequenceViewer object at 0x15d21c710>,
    6781 <chimerax.blastprotein.ui.results.BlastProteinResults object at 0x14cd1af50>,
    6782 <chimerax.seq_view.tool.SequenceViewer object at 0x1551d6350>,
    6783 <chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x34c3fb350>] ->
    6784 <chimerax.blastprotein.ui.results.BlastProteinResults object at 0x14cd1af50>:
    6785 Error while saving session data for 'tools' ->
    6786 [<chimerax.seq_view.tool.SequenceViewer object at 0x154fe2010>,
    6787 <chimerax.seq_view.tool.SequenceViewer object at 0x149607c50>,
    6788 <chimerax.toolbar.tool.ToolbarTool object at 0x1324b2890>,
    6789 <chimerax.model_panel.tool.ModelPanel object at 0x101024cd0>,
    6790 <chimerax.seq_view.tool.SequenceViewer object at 0x1551c74d0>,
    6791 <chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x14f2d3d10>,
    6792 <chimerax.modeller.tool.ModellerLauncher object at 0x14964d910>,
    6793 <chimerax.log.tool.Log object at 0x12c89b950>,
    6794 <chimerax.seq_view.tool.SequenceViewer object at 0x1551b7610>,
    6795 <chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x16abfbe10>,
    6796 <chimerax.cmd_line.tool.CommandLine object at 0x12c8afa90>,
    6797 <chimerax.seq_view.tool.SequenceViewer object at 0x15d231a90>,
    6798 <chimerax.blastprotein.ui.results.BlastProteinResults object at 0x34c3cc690>,
    6799 <chimerax.seq_view.tool.SequenceViewer object at 0x1491dc710>,
    6800 <chimerax.seq_view.tool.SequenceViewer object at 0x15d21c710>,
    6801 <chimerax.blastprotein.ui.results.BlastProteinResults object at 0x14cd1af50>,
    6802 <chimerax.seq_view.tool.SequenceViewer object at 0x1551d6350>,
    6803 <chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x34c3fb350>] ->
    6804 <chimerax.blastprotein.ui.results.BlastProteinResults object at 0x14cd1af50> 
    6805  
    6806 ValueError: error processing: 'tools' -> [, , , , , , , , , , , , , , , , , ]
    6807 -> : Error while saving session data for 'tools' -> [, , , , , , , , , , , , ,
    6808 , , , , ] -> 
    6809  
    6810 File
    6811 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6812 packages/chimerax/core/session.py", line 301, in discovery 
    6813 raise ValueError( 
    6814  
    6815 See log for complete Python traceback. 
    6816  
    6817 Traceback (most recent call last): 
    6818 File
    6819 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6820 packages/chimerax/core/session.py", line 322, in process 
    6821 data = sm.take_snapshot(obj, session, self.state_flags) 
    6822 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    6823 File
    6824 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6825 packages/chimerax/blastprotein/ui/results.py", line 189, in take_snapshot 
    6826 "table_session": self.table.session_info(), 
    6827 ^^^^^^^^^^ 
    6828 AttributeError: 'BlastProteinResults' object has no attribute 'table' 
    6829  
    6830 The above exception was the direct cause of the following exception: 
    6831  
    6832 Traceback (most recent call last): 
    6833 File
    6834 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6835 packages/chimerax/core/session.py", line 297, in discovery 
    6836 self.processed[key] = self.process(obj, parents) 
    6837 ^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    6838 File
    6839 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6840 packages/chimerax/core/session.py", line 329, in process 
    6841 raise RuntimeError(msg) from e 
    6842 RuntimeError: Error while saving session data for 'tools' ->
    6843 [<chimerax.seq_view.tool.SequenceViewer object at 0x154fe2010>,
    6844 <chimerax.seq_view.tool.SequenceViewer object at 0x149607c50>,
    6845 <chimerax.toolbar.tool.ToolbarTool object at 0x1324b2890>,
    6846 <chimerax.model_panel.tool.ModelPanel object at 0x101024cd0>,
    6847 <chimerax.seq_view.tool.SequenceViewer object at 0x1551c74d0>,
    6848 <chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x14f2d3d10>,
    6849 <chimerax.modeller.tool.ModellerLauncher object at 0x14964d910>,
    6850 <chimerax.log.tool.Log object at 0x12c89b950>,
    6851 <chimerax.seq_view.tool.SequenceViewer object at 0x1551b7610>,
    6852 <chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x16abfbe10>,
    6853 <chimerax.cmd_line.tool.CommandLine object at 0x12c8afa90>,
    6854 <chimerax.seq_view.tool.SequenceViewer object at 0x15d231a90>,
    6855 <chimerax.blastprotein.ui.results.BlastProteinResults object at 0x34c3cc690>,
    6856 <chimerax.seq_view.tool.SequenceViewer object at 0x1491dc710>,
    6857 <chimerax.seq_view.tool.SequenceViewer object at 0x15d21c710>,
    6858 <chimerax.blastprotein.ui.results.BlastProteinResults object at 0x14cd1af50>,
    6859 <chimerax.seq_view.tool.SequenceViewer object at 0x1551d6350>,
    6860 <chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x34c3fb350>] ->
    6861 <chimerax.blastprotein.ui.results.BlastProteinResults object at 0x14cd1af50> 
    6862  
    6863 During handling of the above exception, another exception occurred: 
    6864  
    6865 Traceback (most recent call last): 
    6866 File
    6867 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6868 packages/chimerax/save_command/dialog.py", line 133, in <lambda> 
    6869 lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
    6870 file", 
    6871 ^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    6872 File
    6873 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6874 packages/chimerax/save_command/dialog.py", line 144, in show_save_file_dialog 
    6875 _dlg.display(session, **kw) 
    6876 File
    6877 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6878 packages/chimerax/save_command/dialog.py", line 68, in display 
    6879 run(session, cmd) 
    6880 File
    6881 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6882 packages/chimerax/core/commands/run.py", line 49, in run 
    6883 results = command.run(text, log=log, return_json=return_json) 
    6884 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    6885 File
    6886 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6887 packages/chimerax/core/commands/cli.py", line 3245, in run 
    6888 result = ci.function(session, **kw_args) 
    6889 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    6890 File
    6891 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6892 packages/chimerax/save_command/cmd.py", line 86, in cmd_save 
    6893 Command(session, registry=registry).run(provider_cmd_text, log=log) 
    6894 File
    6895 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6896 packages/chimerax/core/commands/cli.py", line 3245, in run 
    6897 result = ci.function(session, **kw_args) 
    6898 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    6899 File
    6900 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6901 packages/chimerax/save_command/cmd.py", line 101, in provider_save 
    6902 saver_info.save(session, path, **provider_kw) 
    6903 File
    6904 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6905 packages/chimerax/core_formats/__init__.py", line 95, in save 
    6906 return cxs_save(session, path, **kw) 
    6907 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    6908 File
    6909 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6910 packages/chimerax/core/session.py", line 1048, in save 
    6911 session.save(output, version=version, include_maps=include_maps) 
    6912 File
    6913 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6914 packages/chimerax/core/session.py", line 731, in save 
    6915 mgr.discovery(self._state_containers) 
    6916 File
    6917 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6918 packages/chimerax/core/session.py", line 301, in discovery 
    6919 raise ValueError( 
    6920 ValueError: error processing: 'tools' ->
    6921 [<chimerax.seq_view.tool.SequenceViewer object at 0x154fe2010>,
    6922 <chimerax.seq_view.tool.SequenceViewer object at 0x149607c50>,
    6923 <chimerax.toolbar.tool.ToolbarTool object at 0x1324b2890>,
    6924 <chimerax.model_panel.tool.ModelPanel object at 0x101024cd0>,
    6925 <chimerax.seq_view.tool.SequenceViewer object at 0x1551c74d0>,
    6926 <chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x14f2d3d10>,
    6927 <chimerax.modeller.tool.ModellerLauncher object at 0x14964d910>,
    6928 <chimerax.log.tool.Log object at 0x12c89b950>,
    6929 <chimerax.seq_view.tool.SequenceViewer object at 0x1551b7610>,
    6930 <chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x16abfbe10>,
    6931 <chimerax.cmd_line.tool.CommandLine object at 0x12c8afa90>,
    6932 <chimerax.seq_view.tool.SequenceViewer object at 0x15d231a90>,
    6933 <chimerax.blastprotein.ui.results.BlastProteinResults object at 0x34c3cc690>,
    6934 <chimerax.seq_view.tool.SequenceViewer object at 0x1491dc710>,
    6935 <chimerax.seq_view.tool.SequenceViewer object at 0x15d21c710>,
    6936 <chimerax.blastprotein.ui.results.BlastProteinResults object at 0x14cd1af50>,
    6937 <chimerax.seq_view.tool.SequenceViewer object at 0x1551d6350>,
    6938 <chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x34c3fb350>] ->
    6939 <chimerax.blastprotein.ui.results.BlastProteinResults object at 0x14cd1af50>:
    6940 Error while saving session data for 'tools' ->
    6941 [<chimerax.seq_view.tool.SequenceViewer object at 0x154fe2010>,
    6942 <chimerax.seq_view.tool.SequenceViewer object at 0x149607c50>,
    6943 <chimerax.toolbar.tool.ToolbarTool object at 0x1324b2890>,
    6944 <chimerax.model_panel.tool.ModelPanel object at 0x101024cd0>,
    6945 <chimerax.seq_view.tool.SequenceViewer object at 0x1551c74d0>,
    6946 <chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x14f2d3d10>,
    6947 <chimerax.modeller.tool.ModellerLauncher object at 0x14964d910>,
    6948 <chimerax.log.tool.Log object at 0x12c89b950>,
    6949 <chimerax.seq_view.tool.SequenceViewer object at 0x1551b7610>,
    6950 <chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x16abfbe10>,
    6951 <chimerax.cmd_line.tool.CommandLine object at 0x12c8afa90>,
    6952 <chimerax.seq_view.tool.SequenceViewer object at 0x15d231a90>,
    6953 <chimerax.blastprotein.ui.results.BlastProteinResults object at 0x34c3cc690>,
    6954 <chimerax.seq_view.tool.SequenceViewer object at 0x1491dc710>,
    6955 <chimerax.seq_view.tool.SequenceViewer object at 0x15d21c710>,
    6956 <chimerax.blastprotein.ui.results.BlastProteinResults object at 0x14cd1af50>,
    6957 <chimerax.seq_view.tool.SequenceViewer object at 0x1551d6350>,
    6958 <chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x34c3fb350>] ->
    6959 <chimerax.blastprotein.ui.results.BlastProteinResults object at 0x14cd1af50> 
    6960  
    6961 ValueError: error processing: 'tools' -> [, , , , , , , , , , , , , , , , , ]
    6962 -> : Error while saving session data for 'tools' -> [, , , , , , , , , , , , ,
    6963 , , , , ] -> 
    6964  
    6965 File
    6966 "/Applications/ChimeraX-1.12-rc2026.05.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6967 packages/chimerax/core/session.py", line 301, in discovery 
    6968 raise ValueError( 
    6969  
    6970 See log for complete Python traceback. 
    6971  
    6972 Webservices job finished: 6O86EWCZ2TXMDOQW 
    6973 Alignment identifier is bp6 [1] 
    6974 Associated AlphaFold A0A9Q6ZED9 chain A to #5/A with 0 mismatches 
    6975 Associated fold_2026_05_15_15_51_model_0.cif chain A to #5/A with 0 mismatches 
    6976 Associated fold_2026_05_15_15_51_model_1.cif chain A to #5/A with 0 mismatches 
    6977 Associated fold_2026_05_15_15_51_model_2.cif chain A to #5/A with 0 mismatches 
    6978 Associated fold_2026_05_15_15_51_model_3.cif chain A to #5/A with 0 mismatches 
    6979 Associated fold_2026_05_15_15_51_model_4.cif chain A to #5/A with 0 mismatches 
    6980 Associated fold_2026_06_01_00_39_model_0.cif chain A to #5/A with 0 mismatches 
    6981 Associated fold_2026_06_01_00_39_model_1.cif chain A to #5/A with 0 mismatches 
    6982 Associated fold_2026_06_01_00_39_model_2.cif chain A to #5/A with 0 mismatches 
    6983 Associated fold_2026_06_01_00_39_model_3.cif chain A to #5/A with 0 mismatches 
    6984 Associated fold_2026_06_01_00_39_model_4.cif chain A to #5/A with 0 mismatches 
    6985 Associated AlphaFold A0A9Q6ZED9 chain A to #5/A with 0 mismatches 
    6986 Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A with 0 mismatches 
    6987 Associated fold_gdp_bound_wbdp_model_1.cif chain A to #5/A with 0 mismatches 
    6988 Associated fold_gdp_bound_wbdp_model_2.cif chain A to #5/A with 0 mismatches 
    6989 Associated fold_gdp_bound_wbdp_model_3.cif chain A to #5/A with 0 mismatches 
    6990 Associated fold_gdp_bound_wbdp_model_4.cif chain A to #5/A with 0 mismatches 
    6991 Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A with 0 mismatches 
    6992 Associated fold_2026_05_15_15_51_model_0.cif chain A to #5/A with 0 mismatches 
    6993 [Repeated 1 time(s)]Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A
    6994 with 0 mismatches 
    6995 Showing conservation header ("seq_conservation" residue attribute) for
    6996 alignment bp6 [1] 
    6997 
    6998 > alphafold fetch Q2QKP2 version 4 alignTo #5/A
    6999 
    7000 Fetching compressed AlphaFold database settings from
    7001 https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database6.json 
    7002 Fetching compressed AlphaFold Q2QKP2 from
    7003 https://alphafold.ebi.ac.uk/files/AF-Q2QKP2-F1-model_v6.cif 
    7004 AlphaFold prediction matching chain A 
    7005 --- 
    7006 Chain| UniProt Id| RMSD| Length| Seen| % Id 
    7007 A | Q2QKP2 | 2.45 | 404 | 404 | 100   
    7008  
    7009 Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_1.cif,
    7010 chain A with 1 mismatch 
    7011 Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_2.cif,
    7012 chain A with 1 mismatch 
    7013 Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_3.cif,
    7014 chain A with 1 mismatch 
    7015 Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_4.cif,
    7016 chain A with 1 mismatch 
    7017 Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_0.cif,
    7018 chain A with 1 mismatch 
    7019 Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_1.cif,
    7020 chain A with 1 mismatch 
    7021 Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_2.cif,
    7022 chain A with 1 mismatch 
    7023 Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_3.cif,
    7024 chain A with 1 mismatch 
    7025 Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_4.cif,
    7026 chain A with 1 mismatch 
    7027 Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_1.cif,
    7028 chain A with 1 mismatch 
    7029 Chains used in RMSD evaluation for alignment 10: AlphaFold A0A9Q6ZED9 #!1/A,
    7030 fold_2026_05_15_15_51_model_1.cif #3/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    7031 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    7032 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    7033 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    7034 #!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A 
    7035 Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_2.cif,
    7036 chain A with 1 mismatch 
    7037 Chains used in RMSD evaluation for alignment 11: AlphaFold A0A9Q6ZED9 #!1/A,
    7038 fold_2026_05_15_15_51_model_2.cif #4/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    7039 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    7040 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    7041 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    7042 #!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A 
    7043 Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_3.cif,
    7044 chain A with 1 mismatch 
    7045 Chains used in RMSD evaluation for alignment 12: AlphaFold A0A9Q6ZED9 #!1/A,
    7046 fold_2026_05_15_15_51_model_3.cif #5/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    7047 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    7048 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    7049 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    7050 #!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A 
    7051 Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_4.cif,
    7052 chain A with 1 mismatch 
    7053 Chains used in RMSD evaluation for alignment 13: AlphaFold A0A9Q6ZED9 #!1/A,
    7054 fold_2026_05_15_15_51_model_4.cif #6/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    7055 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    7056 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    7057 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    7058 #!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A 
    7059 Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_0.cif,
    7060 chain A with 1 mismatch 
    7061 Chains used in RMSD evaluation for alignment 14: AlphaFold A0A9Q6ZED9 #!1/A,
    7062 fold_2026_06_01_00_39_model_0.cif #7/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    7063 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    7064 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    7065 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    7066 #!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A 
    7067 Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_1.cif,
    7068 chain A with 1 mismatch 
    7069 Chains used in RMSD evaluation for alignment 15: AlphaFold A0A9Q6ZED9 #!1/A,
    7070 fold_2026_06_01_00_39_model_1.cif #8/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    7071 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    7072 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    7073 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    7074 #!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A 
    7075 Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_2.cif,
    7076 chain A with 1 mismatch 
    7077 Chains used in RMSD evaluation for alignment 16: AlphaFold A0A9Q6ZED9 #!1/A,
    7078 fold_2026_06_01_00_39_model_2.cif #9/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    7079 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    7080 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    7081 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    7082 #!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A 
    7083 Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_3.cif,
    7084 chain A with 1 mismatch 
    7085 Chains used in RMSD evaluation for alignment 17: AlphaFold A0A9Q6ZED9 #!1/A,
    7086 fold_2026_06_01_00_39_model_3.cif #10/A, fold_gdp_bound_wbdp_model_1.cif
    7087 #15/A, fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif
    7088 #17/A, fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif
    7089 #19/A, fold_2026_05_15_15_51_model_0.cif #20/A,
    7090 fold_2026_05_15_15_51_model_0.cif #!21/A, fold_gdp_bound_wbdp_model_0.cif
    7091 #!22/A, AlphaFold Q2QKP2 #23/A 
    7092 Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_4.cif,
    7093 chain A with 1 mismatch 
    7094 Chains used in RMSD evaluation for alignment 18: AlphaFold A0A9Q6ZED9 #!1/A,
    7095 fold_2026_06_01_00_39_model_4.cif #11/A, fold_gdp_bound_wbdp_model_1.cif
    7096 #15/A, fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif
    7097 #17/A, fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif
    7098 #19/A, fold_2026_05_15_15_51_model_0.cif #20/A,
    7099 fold_2026_05_15_15_51_model_0.cif #!21/A, fold_gdp_bound_wbdp_model_0.cif
    7100 #!22/A, AlphaFold Q2QKP2 #23/A 
    7101 Associated AlphaFold Q2QKP2 chain A to AlphaFold A0A9Q6ZED9, chain A with 1
    7102 mismatch 
    7103 Chains used in RMSD evaluation for alignment 19: AlphaFold A0A9Q6ZED9 #!1/A,
    7104 AlphaFold A0A9Q6ZED9 #12/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    7105 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    7106 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    7107 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    7108 #!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A 
    7109 Associated AlphaFold Q2QKP2 chain A to fold_gdp_bound_wbdp_model_0.cif, chain
    7110 A with 1 mismatch 
    7111 Chains used in RMSD evaluation for alignment 20: AlphaFold A0A9Q6ZED9 #!1/A,
    7112 fold_gdp_bound_wbdp_model_0.cif #14/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    7113 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    7114 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    7115 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    7116 #!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A 
    7117 Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_2.cif,
    7118 chain A with 1 mismatch 
    7119 Chains used in RMSD evaluation for alignment 21: AlphaFold A0A9Q6ZED9 #!1/A,
    7120 fold_2026_05_15_15_51_model_2.cif #4/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    7121 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    7122 #!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A 
    7123 Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_3.cif,
    7124 chain A with 1 mismatch 
    7125 Chains used in RMSD evaluation for alignment 22: AlphaFold A0A9Q6ZED9 #!1/A,
    7126 fold_2026_05_15_15_51_model_3.cif #5/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    7127 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    7128 #!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A 
    7129 Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_4.cif,
    7130 chain A with 1 mismatch 
    7131 Chains used in RMSD evaluation for alignment 23: AlphaFold A0A9Q6ZED9 #!1/A,
    7132 fold_2026_05_15_15_51_model_4.cif #6/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    7133 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    7134 #!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A 
    7135 Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_0.cif,
    7136 chain A with 1 mismatch 
    7137 Chains used in RMSD evaluation for alignment 24: AlphaFold A0A9Q6ZED9 #!1/A,
    7138 fold_2026_06_01_00_39_model_0.cif #7/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    7139 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    7140 #!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A 
    7141 Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_1.cif,
    7142 chain A with 1 mismatch 
    7143 Chains used in RMSD evaluation for alignment 25: AlphaFold A0A9Q6ZED9 #!1/A,
    7144 fold_2026_06_01_00_39_model_1.cif #8/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    7145 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    7146 #!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A 
    7147 Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_2.cif,
    7148 chain A with 1 mismatch 
    7149 Chains used in RMSD evaluation for alignment 26: AlphaFold A0A9Q6ZED9 #!1/A,
    7150 fold_2026_06_01_00_39_model_2.cif #9/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    7151 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    7152 #!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A 
    7153 Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_3.cif,
    7154 chain A with 1 mismatch 
    7155 Chains used in RMSD evaluation for alignment 27: AlphaFold A0A9Q6ZED9 #!1/A,
    7156 fold_2026_06_01_00_39_model_3.cif #10/A, fold_gdp_bound_wbdp_model_0.cif
    7157 #19/A, fold_2026_05_15_15_51_model_0.cif #20/A,
    7158 fold_2026_05_15_15_51_model_0.cif #!21/A, fold_gdp_bound_wbdp_model_0.cif
    7159 #!22/A, AlphaFold Q2QKP2 #23/A 
    7160 Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_4.cif,
    7161 chain A with 1 mismatch 
    7162 Chains used in RMSD evaluation for alignment 28: AlphaFold A0A9Q6ZED9 #!1/A,
    7163 fold_2026_06_01_00_39_model_4.cif #11/A, fold_gdp_bound_wbdp_model_0.cif
    7164 #19/A, fold_2026_05_15_15_51_model_0.cif #20/A,
    7165 fold_2026_05_15_15_51_model_0.cif #!21/A, fold_gdp_bound_wbdp_model_0.cif
    7166 #!22/A, AlphaFold Q2QKP2 #23/A 
    7167 Associated AlphaFold Q2QKP2 chain A to AlphaFold A0A9Q6ZED9, chain A with 1
    7168 mismatch 
    7169 Chains used in RMSD evaluation for alignment 29: AlphaFold A0A9Q6ZED9 #!1/A,
    7170 AlphaFold A0A9Q6ZED9 #12/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    7171 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    7172 #!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A 
    7173 Associated AlphaFold Q2QKP2 chain A to fold_gdp_bound_wbdp_model_1.cif, chain
    7174 A with 1 mismatch 
    7175 Chains used in RMSD evaluation for alignment 30: AlphaFold A0A9Q6ZED9 #!1/A,
    7176 fold_gdp_bound_wbdp_model_1.cif #15/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    7177 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    7178 #!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A 
    7179 Associated AlphaFold Q2QKP2 chain A to fold_gdp_bound_wbdp_model_2.cif, chain
    7180 A with 1 mismatch 
    7181 Chains used in RMSD evaluation for alignment 31: AlphaFold A0A9Q6ZED9 #!1/A,
    7182 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    7183 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    7184 #!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A 
    7185 Associated AlphaFold Q2QKP2 chain A to fold_gdp_bound_wbdp_model_3.cif, chain
    7186 A with 1 mismatch 
    7187 Chains used in RMSD evaluation for alignment 32: AlphaFold A0A9Q6ZED9 #!1/A,
    7188 fold_gdp_bound_wbdp_model_3.cif #17/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    7189 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    7190 #!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A 
    7191 Associated AlphaFold Q2QKP2 chain A to fold_gdp_bound_wbdp_model_4.cif, chain
    7192 A with 1 mismatch 
    7193 Chains used in RMSD evaluation for alignment 33: AlphaFold A0A9Q6ZED9 #!1/A,
    7194 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    7195 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    7196 #!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A 
    7197 Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_0.cif,
    7198 chain A with 1 mismatch 
    7199 Chains used in RMSD evaluation for alignment 34: AlphaFold A0A9Q6ZED9 #!1/A,
    7200 fold_2026_05_15_15_51_model_0.cif #2/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    7201 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    7202 #!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A 
    7203 Associated AlphaFold Q2QKP2 chain A to fold_gdp_bound_wbdp_model_0.cif, chain
    7204 A with 1 mismatch 
    7205 Chains used in RMSD evaluation for alignment 35: AlphaFold A0A9Q6ZED9 #!1/A,
    7206 fold_gdp_bound_wbdp_model_0.cif #14/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    7207 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    7208 #!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A 
    7209 Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_0.cif,
    7210 chain A with 1 mismatch 
    7211 Chains used in RMSD evaluation for alignment 36: AlphaFold A0A9Q6ZED9 #!1/A,
    7212 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    7213 #!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A 
    7214 Associated AlphaFold Q2QKP2 chain A to fold_gdp_bound_wbdp_model_0.cif, chain
    7215 A with 1 mismatch 
    7216 Chains used in RMSD evaluation for alignment 37: AlphaFold A0A9Q6ZED9 #!1/A,
    7217 fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A 
    7218 Associated AlphaFold Q2QKP2 chain A to Q2QKP2 with 0 mismatches 
    7219 
    7220 > matchmaker #23 to #5/A
    7221 
    7222 Parameters 
    7223 --- 
    7224 Chain pairing | bb 
    7225 Alignment algorithm | Needleman-Wunsch 
    7226 Similarity matrix | BLOSUM-62 
    7227 SS fraction | 0.3 
    7228 Gap open (HH/SS/other) | 18/18/6 
    7229 Gap extend | 1 
    7230 SS matrix |  |  | H | S | O 
    7231 ---|---|---|--- 
    7232 H | 6 | -9 | -6 
    7233 S |  | 6 | -6 
    7234 O |  |  | 4 
    7235 Iteration cutoff | 2 
    7236  
    7237 Matchmaker fold_2026_05_15_15_51_model_3.cif, chain A (#5) with AlphaFold
    7238 Q2QKP2, chain A (#23), sequence alignment score = 2105.3 
    7239 RMSD between 367 pruned atom pairs is 0.622 angstroms; (across all 404 pairs:
    7240 2.454) 
    7241  
    7242 
    7243 > select #!1/A:62 #2/A:62 #3/A:62 #4/A:62 #5/A:62 #6/A:62 #7/A:62 #8/A:62
    7244 > #9/A:62 #10/A:62 #11/A:62 #12/A:62 #14/A:62 #15/A:62 #16/A:62 #17/A:62
    7245 > #18/A:62 #19/A:62 #20/A:62 #!21/A:62 #!22/A:62
    7246 
    7247 201 atoms, 180 bonds, 21 residues, 21 models selected 
    7248 
    7249 > select #!1/A:62 #2/A:62 #3/A:62 #4/A:62 #5/A:62 #6/A:62 #7/A:62 #8/A:62
    7250 > #9/A:62 #10/A:62 #11/A:62 #12/A:62 #14/A:62 #15/A:62 #16/A:62 #17/A:62
    7251 > #18/A:62 #19/A:62 #20/A:62 #!21/A:62 #!22/A:62
    7252 
    7253 201 atoms, 180 bonds, 21 residues, 21 models selected 
    7254 Bp6 [1] [ID: bp6 [1]] region #5/A [62] RMSD: 8.615 
    7255  
    7256 
    7257 > alphafold fetch Q2QKP2 version 4 alignTo #5/A
    7258 
    7259 AlphaFold prediction matching chain A 
    7260 --- 
    7261 Chain| UniProt Id| RMSD| Length| Seen| % Id 
    7262 A | Q2QKP2 | 2.45 | 404 | 404 | 100   
    7263  
    7264 Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_1.cif,
    7265 chain A with 1 mismatch 
    7266 Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_2.cif,
    7267 chain A with 1 mismatch 
    7268 Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_3.cif,
    7269 chain A with 1 mismatch 
    7270 Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_4.cif,
    7271 chain A with 1 mismatch 
    7272 Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_0.cif,
    7273 chain A with 1 mismatch 
    7274 Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_1.cif,
    7275 chain A with 1 mismatch 
    7276 Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_2.cif,
    7277 chain A with 1 mismatch 
    7278 Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_3.cif,
    7279 chain A with 1 mismatch 
    7280 Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_4.cif,
    7281 chain A with 1 mismatch 
    7282 Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_1.cif,
    7283 chain A with 1 mismatch 
    7284 Chains used in RMSD evaluation for alignment 10: AlphaFold A0A9Q6ZED9 #!1/A,
    7285 fold_2026_05_15_15_51_model_1.cif #3/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    7286 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    7287 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    7288 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    7289 #!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A,
    7290 AlphaFold Q2QKP2 #24/A 
    7291 Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_2.cif,
    7292 chain A with 1 mismatch 
    7293 Chains used in RMSD evaluation for alignment 11: AlphaFold A0A9Q6ZED9 #!1/A,
    7294 fold_2026_05_15_15_51_model_2.cif #4/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    7295 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    7296 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    7297 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    7298 #!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A,
    7299 AlphaFold Q2QKP2 #24/A 
    7300 Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_3.cif,
    7301 chain A with 1 mismatch 
    7302 Chains used in RMSD evaluation for alignment 12: AlphaFold A0A9Q6ZED9 #!1/A,
    7303 fold_2026_05_15_15_51_model_3.cif #5/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    7304 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    7305 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    7306 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    7307 #!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A,
    7308 AlphaFold Q2QKP2 #24/A 
    7309 Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_4.cif,
    7310 chain A with 1 mismatch 
    7311 Chains used in RMSD evaluation for alignment 13: AlphaFold A0A9Q6ZED9 #!1/A,
    7312 fold_2026_05_15_15_51_model_4.cif #6/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    7313 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    7314 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    7315 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    7316 #!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A,
    7317 AlphaFold Q2QKP2 #24/A 
    7318 Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_0.cif,
    7319 chain A with 1 mismatch 
    7320 Chains used in RMSD evaluation for alignment 14: AlphaFold A0A9Q6ZED9 #!1/A,
    7321 fold_2026_06_01_00_39_model_0.cif #7/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    7322 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    7323 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    7324 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    7325 #!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A,
    7326 AlphaFold Q2QKP2 #24/A 
    7327 Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_1.cif,
    7328 chain A with 1 mismatch 
    7329 Chains used in RMSD evaluation for alignment 15: AlphaFold A0A9Q6ZED9 #!1/A,
    7330 fold_2026_06_01_00_39_model_1.cif #8/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    7331 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    7332 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    7333 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    7334 #!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A,
    7335 AlphaFold Q2QKP2 #24/A 
    7336 Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_2.cif,
    7337 chain A with 1 mismatch 
    7338 Chains used in RMSD evaluation for alignment 16: AlphaFold A0A9Q6ZED9 #!1/A,
    7339 fold_2026_06_01_00_39_model_2.cif #9/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    7340 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    7341 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    7342 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    7343 #!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A,
    7344 AlphaFold Q2QKP2 #24/A 
    7345 Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_3.cif,
    7346 chain A with 1 mismatch 
    7347 Chains used in RMSD evaluation for alignment 17: AlphaFold A0A9Q6ZED9 #!1/A,
    7348 fold_2026_06_01_00_39_model_3.cif #10/A, fold_gdp_bound_wbdp_model_1.cif
    7349 #15/A, fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif
    7350 #17/A, fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif
    7351 #19/A, fold_2026_05_15_15_51_model_0.cif #20/A,
    7352 fold_2026_05_15_15_51_model_0.cif #!21/A, fold_gdp_bound_wbdp_model_0.cif
    7353 #!22/A, AlphaFold Q2QKP2 #23/A, AlphaFold Q2QKP2 #24/A 
    7354 Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_4.cif,
    7355 chain A with 1 mismatch 
    7356 Chains used in RMSD evaluation for alignment 18: AlphaFold A0A9Q6ZED9 #!1/A,
    7357 fold_2026_06_01_00_39_model_4.cif #11/A, fold_gdp_bound_wbdp_model_1.cif
    7358 #15/A, fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif
    7359 #17/A, fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif
    7360 #19/A, fold_2026_05_15_15_51_model_0.cif #20/A,
    7361 fold_2026_05_15_15_51_model_0.cif #!21/A, fold_gdp_bound_wbdp_model_0.cif
    7362 #!22/A, AlphaFold Q2QKP2 #23/A, AlphaFold Q2QKP2 #24/A 
    7363 Associated AlphaFold Q2QKP2 chain A to AlphaFold A0A9Q6ZED9, chain A with 1
    7364 mismatch 
    7365 Chains used in RMSD evaluation for alignment 19: AlphaFold A0A9Q6ZED9 #!1/A,
    7366 AlphaFold A0A9Q6ZED9 #12/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    7367 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    7368 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    7369 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    7370 #!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A,
    7371 AlphaFold Q2QKP2 #24/A 
    7372 Associated AlphaFold Q2QKP2 chain A to fold_gdp_bound_wbdp_model_0.cif, chain
    7373 A with 1 mismatch 
    7374 Chains used in RMSD evaluation for alignment 20: AlphaFold A0A9Q6ZED9 #!1/A,
    7375 fold_gdp_bound_wbdp_model_0.cif #14/A, fold_gdp_bound_wbdp_model_1.cif #15/A,
    7376 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_3.cif #17/A,
    7377 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    7378 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    7379 #!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A,
    7380 AlphaFold Q2QKP2 #24/A 
    7381 Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_2.cif,
    7382 chain A with 1 mismatch 
    7383 Chains used in RMSD evaluation for alignment 21: AlphaFold A0A9Q6ZED9 #!1/A,
    7384 fold_2026_05_15_15_51_model_2.cif #4/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    7385 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    7386 #!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A,
    7387 AlphaFold Q2QKP2 #24/A 
    7388 Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_3.cif,
    7389 chain A with 1 mismatch 
    7390 Chains used in RMSD evaluation for alignment 22: AlphaFold A0A9Q6ZED9 #!1/A,
    7391 fold_2026_05_15_15_51_model_3.cif #5/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    7392 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    7393 #!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A,
    7394 AlphaFold Q2QKP2 #24/A 
    7395 Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_4.cif,
    7396 chain A with 1 mismatch 
    7397 Chains used in RMSD evaluation for alignment 23: AlphaFold A0A9Q6ZED9 #!1/A,
    7398 fold_2026_05_15_15_51_model_4.cif #6/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    7399 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    7400 #!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A,
    7401 AlphaFold Q2QKP2 #24/A 
    7402 Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_0.cif,
    7403 chain A with 1 mismatch 
    7404 Chains used in RMSD evaluation for alignment 24: AlphaFold A0A9Q6ZED9 #!1/A,
    7405 fold_2026_06_01_00_39_model_0.cif #7/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    7406 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    7407 #!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A,
    7408 AlphaFold Q2QKP2 #24/A 
    7409 Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_1.cif,
    7410 chain A with 1 mismatch 
    7411 Chains used in RMSD evaluation for alignment 25: AlphaFold A0A9Q6ZED9 #!1/A,
    7412 fold_2026_06_01_00_39_model_1.cif #8/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    7413 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    7414 #!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A,
    7415 AlphaFold Q2QKP2 #24/A 
    7416 Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_2.cif,
    7417 chain A with 1 mismatch 
    7418 Chains used in RMSD evaluation for alignment 26: AlphaFold A0A9Q6ZED9 #!1/A,
    7419 fold_2026_06_01_00_39_model_2.cif #9/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    7420 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    7421 #!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A,
    7422 AlphaFold Q2QKP2 #24/A 
    7423 Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_3.cif,
    7424 chain A with 1 mismatch 
    7425 Chains used in RMSD evaluation for alignment 27: AlphaFold A0A9Q6ZED9 #!1/A,
    7426 fold_2026_06_01_00_39_model_3.cif #10/A, fold_gdp_bound_wbdp_model_0.cif
    7427 #19/A, fold_2026_05_15_15_51_model_0.cif #20/A,
    7428 fold_2026_05_15_15_51_model_0.cif #!21/A, fold_gdp_bound_wbdp_model_0.cif
    7429 #!22/A, AlphaFold Q2QKP2 #23/A, AlphaFold Q2QKP2 #24/A 
    7430 Associated AlphaFold Q2QKP2 chain A to fold_2026_06_01_00_39_model_4.cif,
    7431 chain A with 1 mismatch 
    7432 Chains used in RMSD evaluation for alignment 28: AlphaFold A0A9Q6ZED9 #!1/A,
    7433 fold_2026_06_01_00_39_model_4.cif #11/A, fold_gdp_bound_wbdp_model_0.cif
    7434 #19/A, fold_2026_05_15_15_51_model_0.cif #20/A,
    7435 fold_2026_05_15_15_51_model_0.cif #!21/A, fold_gdp_bound_wbdp_model_0.cif
    7436 #!22/A, AlphaFold Q2QKP2 #23/A, AlphaFold Q2QKP2 #24/A 
    7437 Associated AlphaFold Q2QKP2 chain A to AlphaFold A0A9Q6ZED9, chain A with 1
    7438 mismatch 
    7439 Chains used in RMSD evaluation for alignment 29: AlphaFold A0A9Q6ZED9 #!1/A,
    7440 AlphaFold A0A9Q6ZED9 #12/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    7441 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    7442 #!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A,
    7443 AlphaFold Q2QKP2 #24/A 
    7444 Associated AlphaFold Q2QKP2 chain A to fold_gdp_bound_wbdp_model_1.cif, chain
    7445 A with 1 mismatch 
    7446 Chains used in RMSD evaluation for alignment 30: AlphaFold A0A9Q6ZED9 #!1/A,
    7447 fold_gdp_bound_wbdp_model_1.cif #15/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    7448 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    7449 #!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A,
    7450 AlphaFold Q2QKP2 #24/A 
    7451 Associated AlphaFold Q2QKP2 chain A to fold_gdp_bound_wbdp_model_2.cif, chain
    7452 A with 1 mismatch 
    7453 Chains used in RMSD evaluation for alignment 31: AlphaFold A0A9Q6ZED9 #!1/A,
    7454 fold_gdp_bound_wbdp_model_2.cif #16/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    7455 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    7456 #!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A,
    7457 AlphaFold Q2QKP2 #24/A 
    7458 Associated AlphaFold Q2QKP2 chain A to fold_gdp_bound_wbdp_model_3.cif, chain
    7459 A with 1 mismatch 
    7460 Chains used in RMSD evaluation for alignment 32: AlphaFold A0A9Q6ZED9 #!1/A,
    7461 fold_gdp_bound_wbdp_model_3.cif #17/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    7462 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    7463 #!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A,
    7464 AlphaFold Q2QKP2 #24/A 
    7465 Associated AlphaFold Q2QKP2 chain A to fold_gdp_bound_wbdp_model_4.cif, chain
    7466 A with 1 mismatch 
    7467 Chains used in RMSD evaluation for alignment 33: AlphaFold A0A9Q6ZED9 #!1/A,
    7468 fold_gdp_bound_wbdp_model_4.cif #18/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    7469 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    7470 #!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A,
    7471 AlphaFold Q2QKP2 #24/A 
    7472 Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_0.cif,
    7473 chain A with 1 mismatch 
    7474 Chains used in RMSD evaluation for alignment 34: AlphaFold A0A9Q6ZED9 #!1/A,
    7475 fold_2026_05_15_15_51_model_0.cif #2/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    7476 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    7477 #!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A,
    7478 AlphaFold Q2QKP2 #24/A 
    7479 Associated AlphaFold Q2QKP2 chain A to fold_gdp_bound_wbdp_model_0.cif, chain
    7480 A with 1 mismatch 
    7481 Chains used in RMSD evaluation for alignment 35: AlphaFold A0A9Q6ZED9 #!1/A,
    7482 fold_gdp_bound_wbdp_model_0.cif #14/A, fold_gdp_bound_wbdp_model_0.cif #19/A,
    7483 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    7484 #!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A,
    7485 AlphaFold Q2QKP2 #24/A 
    7486 Associated AlphaFold Q2QKP2 chain A to fold_2026_05_15_15_51_model_0.cif,
    7487 chain A with 1 mismatch 
    7488 Chains used in RMSD evaluation for alignment 36: AlphaFold A0A9Q6ZED9 #!1/A,
    7489 fold_2026_05_15_15_51_model_0.cif #20/A, fold_2026_05_15_15_51_model_0.cif
    7490 #!21/A, fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A,
    7491 AlphaFold Q2QKP2 #24/A 
    7492 Associated AlphaFold Q2QKP2 chain A to fold_gdp_bound_wbdp_model_0.cif, chain
    7493 A with 1 mismatch 
    7494 Chains used in RMSD evaluation for alignment 37: AlphaFold A0A9Q6ZED9 #!1/A,
    7495 fold_gdp_bound_wbdp_model_0.cif #!22/A, AlphaFold Q2QKP2 #23/A, AlphaFold
    7496 Q2QKP2 #24/A 
    7497 
    7498 > matchmaker #24 to #5/A
    7499 
    7500 Parameters 
    7501 --- 
    7502 Chain pairing | bb 
    7503 Alignment algorithm | Needleman-Wunsch 
    7504 Similarity matrix | BLOSUM-62 
    7505 SS fraction | 0.3 
    7506 Gap open (HH/SS/other) | 18/18/6 
    7507 Gap extend | 1 
    7508 SS matrix |  |  | H | S | O 
    7509 ---|---|---|--- 
    7510 H | 6 | -9 | -6 
    7511 S |  | 6 | -6 
    7512 O |  |  | 4 
    7513 Iteration cutoff | 2 
    7514  
    7515 Matchmaker fold_2026_05_15_15_51_model_3.cif, chain A (#5) with AlphaFold
    7516 Q2QKP2, chain A (#24), sequence alignment score = 2105.3 
    7517 RMSD between 367 pruned atom pairs is 0.622 angstroms; (across all 404 pairs:
    7518 2.454) 
    7519  
    7520 
    7521 > hide #24 models
    7522 
    7523 > rename #23 "AlphaFold Q2QKP2_ESCFE - WbdP - Escherichia fergusonii"
    7524 
    7525 Alignment identifier is bp6 [2] 
    7526 Associated AlphaFold A0A9Q6ZED9 chain A to #5/A with 0 mismatches 
    7527 Associated fold_2026_05_15_15_51_model_0.cif chain A to #5/A with 0 mismatches 
    7528 Associated fold_2026_05_15_15_51_model_1.cif chain A to #5/A with 0 mismatches 
    7529 Associated fold_2026_05_15_15_51_model_2.cif chain A to #5/A with 0 mismatches 
    7530 Associated fold_2026_05_15_15_51_model_3.cif chain A to #5/A with 0 mismatches 
    7531 Associated fold_2026_05_15_15_51_model_4.cif chain A to #5/A with 0 mismatches 
    7532 Associated fold_2026_06_01_00_39_model_0.cif chain A to #5/A with 0 mismatches 
    7533 Associated fold_2026_06_01_00_39_model_1.cif chain A to #5/A with 0 mismatches 
    7534 Associated fold_2026_06_01_00_39_model_2.cif chain A to #5/A with 0 mismatches 
    7535 Associated fold_2026_06_01_00_39_model_3.cif chain A to #5/A with 0 mismatches 
    7536 Associated fold_2026_06_01_00_39_model_4.cif chain A to #5/A with 0 mismatches 
    7537 Associated AlphaFold A0A9Q6ZED9 chain A to #5/A with 0 mismatches 
    7538 Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A with 0 mismatches 
    7539 Associated fold_gdp_bound_wbdp_model_1.cif chain A to #5/A with 0 mismatches 
    7540 Associated fold_gdp_bound_wbdp_model_2.cif chain A to #5/A with 0 mismatches 
    7541 Associated fold_gdp_bound_wbdp_model_3.cif chain A to #5/A with 0 mismatches 
    7542 Associated fold_gdp_bound_wbdp_model_4.cif chain A to #5/A with 0 mismatches 
    7543 Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A with 0 mismatches 
    7544 Associated fold_2026_05_15_15_51_model_0.cif chain A to #5/A with 0 mismatches 
    7545 [Repeated 1 time(s)]Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A
    7546 with 0 mismatches 
    7547 Associated AlphaFold Q2QKP2_ESCFE - WbdP - Escherichia fergusonii chain A to
    7548 A0A4B9BQ02 with 0 mismatches 
    7549 Associated AlphaFold Q2QKP2 chain A to A0A4B9BQ02 with 0 mismatches 
    7550 Showing conservation header ("seq_conservation" residue attribute) for
    7551 alignment bp6 [2] 
    7552 
    7553 > alphafold fetch A0A4B9BQ02 version 4 alignTo #5/A
    7554 
    7555 Fetching url https://alphafold.ebi.ac.uk/files/AF-A0A4B9BQ02-F1-model_v6.cif
    7556 failed: 
    7557 HTTP Error 404: Not Found 
    7558 
    7559 > alphafold fetch A0A4B9BQ02 version 4 alignTo #5/A
    7560 
    7561 Fetching url https://alphafold.ebi.ac.uk/files/AF-A0A4B9BQ02-F1-model_v6.cif
    7562 failed: 
    7563 HTTP Error 404: Not Found 
    7564 
    7565 > alphafold fetch A0A4B9BQ02 version 4 alignTo #5/A
    7566 
    7567 Fetching url https://alphafold.ebi.ac.uk/files/AF-A0A4B9BQ02-F1-model_v6.cif
    7568 failed: 
    7569 HTTP Error 404: Not Found 
    7570 
    7571 > alphafold fetch A0A4B9BQ02 version 4 alignTo #5/A
    7572 
    7573 Fetching url https://alphafold.ebi.ac.uk/files/AF-A0A4B9BQ02-F1-model_v6.cif
    7574 failed: 
    7575 HTTP Error 404: Not Found 
    7576 
    7577 > alphafold fetch A0A4B9BQ02 version 4 alignTo #5/A
    7578 
    7579 Fetching url https://alphafold.ebi.ac.uk/files/AF-A0A4B9BQ02-F1-model_v6.cif
    7580 failed: 
    7581 HTTP Error 404: Not Found 
    7582 
    7583 > alphafold fetch A0A4B9BQ02 version 4 alignTo #5/A
    7584 
    7585 Fetching url https://alphafold.ebi.ac.uk/files/AF-A0A4B9BQ02-F1-model_v6.cif
    7586 failed: 
    7587 HTTP Error 404: Not Found 
    7588 
    7589 > alphafold fetch A0A4B9BQ02 version 4 alignTo #5/A
    7590 
    7591 Fetching url https://alphafold.ebi.ac.uk/files/AF-A0A4B9BQ02-F1-model_v6.cif
    7592 failed: 
    7593 HTTP Error 404: Not Found 
    7594 Alignment identifier is bp6 [3] 
    7595 Associated AlphaFold A0A9Q6ZED9 chain A to #5/A with 0 mismatches 
    7596 Associated fold_2026_05_15_15_51_model_0.cif chain A to #5/A with 0 mismatches 
    7597 Associated fold_2026_05_15_15_51_model_1.cif chain A to #5/A with 0 mismatches 
    7598 Associated fold_2026_05_15_15_51_model_2.cif chain A to #5/A with 0 mismatches 
    7599 Associated fold_2026_05_15_15_51_model_3.cif chain A to #5/A with 0 mismatches 
    7600 Associated fold_2026_05_15_15_51_model_4.cif chain A to #5/A with 0 mismatches 
    7601 Associated fold_2026_06_01_00_39_model_0.cif chain A to #5/A with 0 mismatches 
    7602 Associated fold_2026_06_01_00_39_model_1.cif chain A to #5/A with 0 mismatches 
    7603 Associated fold_2026_06_01_00_39_model_2.cif chain A to #5/A with 0 mismatches 
    7604 Associated fold_2026_06_01_00_39_model_3.cif chain A to #5/A with 0 mismatches 
    7605 Associated fold_2026_06_01_00_39_model_4.cif chain A to #5/A with 0 mismatches 
    7606 Associated AlphaFold A0A9Q6ZED9 chain A to #5/A with 0 mismatches 
    7607 Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A with 0 mismatches 
    7608 Associated fold_gdp_bound_wbdp_model_1.cif chain A to #5/A with 0 mismatches 
    7609 Associated fold_gdp_bound_wbdp_model_2.cif chain A to #5/A with 0 mismatches 
    7610 Associated fold_gdp_bound_wbdp_model_3.cif chain A to #5/A with 0 mismatches 
    7611 Associated fold_gdp_bound_wbdp_model_4.cif chain A to #5/A with 0 mismatches 
    7612 Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A with 0 mismatches 
    7613 Associated fold_2026_05_15_15_51_model_0.cif chain A to #5/A with 0 mismatches 
    7614 [Repeated 1 time(s)]Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A
    7615 with 0 mismatches 
    7616 Associated AlphaFold Q2QKP2_ESCFE - WbdP - Escherichia fergusonii chain A to
    7617 #5/A with 1 mismatch 
    7618 Associated AlphaFold Q2QKP2 chain A to #5/A with 1 mismatch 
    7619 Showing conservation header ("seq_conservation" residue attribute) for
    7620 alignment bp6 [3] 
    7621 
    7622 > surface (#!1 & sel)
    7623 
    7624 > hide #!1 models
    7625 
    7626 > show #!1 models
    7627 
    7628 > hide #!1 models
    7629 
    7630 > show #!1 models
    7631 
    7632 > hide #1.2 models
    7633 
    7634 > hide #!1 models
    7635 
    7636 > select add #24
    7637 
    7638 3492 atoms, 3555 bonds, 425 residues, 25 models selected 
    7639 
    7640 > select subtract #24
    7641 
    7642 201 atoms, 180 bonds, 21 residues, 24 models selected 
    7643 
    7644 > select add #24
    7645 
    7646 3492 atoms, 3555 bonds, 425 residues, 25 models selected 
    7647 
    7648 > show #24 models
    7649 
    7650 > hide #23 models
    7651 
    7652 > surface (#24 & sel)
    7653 
    7654 > ui tool show "Color Actions"
    7655 
    7656 > coulombic sel & #!24
    7657 
    7658 Using Amber 20 recommended default charges and atom types for standard
    7659 residues 
    7660 Coulombic values for AlphaFold Q2QKP2_A SES surface #24.1: minimum, -14.42,
    7661 mean 0.04, maximum 14.67 
    7662 To also show corresponding color key, enter the above coulombic command and
    7663 add key true 
    7664 
    7665 > hide #24.1 models
    7666 
    7667 > select subtract #24
    7668 
    7669 201 atoms, 180 bonds, 21 residues, 25 models selected 
    7670 
    7671 > hide #!24 models
    7672 
    7673 > alphafold fetch A0A737Y3F8 version 4 alignTo #5/A
    7674 
    7675 Fetching compressed AlphaFold A0A737Y3F8 from
    7676 https://alphafold.ebi.ac.uk/files/AF-A0A737Y3F8-F1-model_v6.cif 
    7677 AlphaFold prediction matching chain A 
    7678 --- 
    7679 Chain| UniProt Id| RMSD| Length| Seen| % Id 
    7680 A | A0A737Y3F8 | 1.92 | 404 | 404 | 67   
    7681  
    7682 Associated AlphaFold A0A737Y3F8 chain A to A0A737Y3F8 with 0 mismatches 
    7683 
    7684 > matchmaker #25 to #5/A
    7685 
    7686 Parameters 
    7687 --- 
    7688 Chain pairing | bb 
    7689 Alignment algorithm | Needleman-Wunsch 
    7690 Similarity matrix | BLOSUM-62 
    7691 SS fraction | 0.3 
    7692 Gap open (HH/SS/other) | 18/18/6 
    7693 Gap extend | 1 
    7694 SS matrix |  |  | H | S | O 
    7695 ---|---|---|--- 
    7696 H | 6 | -9 | -6 
    7697 S |  | 6 | -6 
    7698 O |  |  | 4 
    7699 Iteration cutoff | 2 
    7700  
    7701 Matchmaker fold_2026_05_15_15_51_model_3.cif, chain A (#5) with AlphaFold
    7702 A0A737Y3F8, chain A (#25), sequence alignment score = 1613.7 
    7703 RMSD between 371 pruned atom pairs is 0.726 angstroms; (across all 404 pairs:
    7704 1.918) 
    7705  
    7706 
    7707 > rename #25 "AlphaFold A0A737Y3F8_SALER - Glycosyltransferase family 4
    7708 > protein - Salmonella enterica subsp. salamae serovar 30:1, z28:z6"
    7709 
    7710 > alphafold fetch G5RX88 version 4 alignTo #5/A
    7711 
    7712 Fetching compressed AlphaFold G5RX88 from
    7713 https://alphafold.ebi.ac.uk/files/AF-G5RX88-F1-model_v6.cif 
    7714 AlphaFold prediction matching chain A 
    7715 --- 
    7716 Chain| UniProt Id| RMSD| Length| Seen| % Id 
    7717 A | G5RX88 | 2.16 | 404 | 404 | 67   
    7718  
    7719 Associated AlphaFold G5RX88 chain A to G5RX88 with 0 mismatches 
    7720 
    7721 > matchmaker #26 to #5/A
    7722 
    7723 Parameters 
    7724 --- 
    7725 Chain pairing | bb 
    7726 Alignment algorithm | Needleman-Wunsch 
    7727 Similarity matrix | BLOSUM-62 
    7728 SS fraction | 0.3 
    7729 Gap open (HH/SS/other) | 18/18/6 
    7730 Gap extend | 1 
    7731 SS matrix |  |  | H | S | O 
    7732 ---|---|---|--- 
    7733 H | 6 | -9 | -6 
    7734 S |  | 6 | -6 
    7735 O |  |  | 4 
    7736 Iteration cutoff | 2 
    7737  
    7738 Matchmaker fold_2026_05_15_15_51_model_3.cif, chain A (#5) with AlphaFold
    7739 G5RX88, chain A (#26), sequence alignment score = 1621.6 
    7740 RMSD between 367 pruned atom pairs is 0.659 angstroms; (across all 404 pairs:
    7741 2.156) 
    7742  
    7743 
    7744 > rename #26 "AlphaFold G5RX88_SALET - Mannosyltransferase - Salmonella"
    7745 
    7746 > rename #26 "AlphaFold G5RX88_SALET - Mannosyltransferase - Salmonella
    7747 > enterica subsp. enterica serovar Urbana str. R8-2977"
    7748 
    7749 > alphafold fetch A0A5X6ERK5 version 4 alignTo #5/A
    7750 
    7751 Fetching compressed AlphaFold A0A5X6ERK5 from
    7752 https://alphafold.ebi.ac.uk/files/AF-A0A5X6ERK5-F1-model_v6.cif 
    7753 AlphaFold prediction matching chain A 
    7754 --- 
    7755 Chain| UniProt Id| RMSD| Length| Seen| % Id 
    7756 A | A0A5X6ERK5 | 2.42 | 404 | 404 | 67   
    7757  
    7758 Associated AlphaFold A0A5X6ERK5 chain A to A0A5X6ERK5 with 0 mismatches 
    7759 
    7760 > matchmaker #27 to #5/A
    7761 
    7762 Parameters 
    7763 --- 
    7764 Chain pairing | bb 
    7765 Alignment algorithm | Needleman-Wunsch 
    7766 Similarity matrix | BLOSUM-62 
    7767 SS fraction | 0.3 
    7768 Gap open (HH/SS/other) | 18/18/6 
    7769 Gap extend | 1 
    7770 SS matrix |  |  | H | S | O 
    7771 ---|---|---|--- 
    7772 H | 6 | -9 | -6 
    7773 S |  | 6 | -6 
    7774 O |  |  | 4 
    7775 Iteration cutoff | 2 
    7776  
    7777 Matchmaker fold_2026_05_15_15_51_model_3.cif, chain A (#5) with AlphaFold
    7778 A0A5X6ERK5, chain A (#27), sequence alignment score = 1625 
    7779 RMSD between 369 pruned atom pairs is 0.690 angstroms; (across all 404 pairs:
    7780 2.422) 
    7781  
    7782 
    7783 > rename #27 "AlphaFold A0A5X6ERK5_SALET - Glycosyltransferase - Salmonella
    7784 > enterica subsp. enterica serovar Aqua"
    7785 
    7786 > alphafold fetch Q5UHC2 version 4 alignTo #5/A
    7787 
    7788 AlphaFold prediction matching chain A 
    7789 --- 
    7790 Chain| UniProt Id| RMSD| Length| Seen| % Id 
    7791 A | Q5UHC2 | 2.05 | 404 | 404 | 67   
    7792  
    7793 Associated AlphaFold Q5UHC2 chain A to Q5UHC2 with 0 mismatches 
    7794 
    7795 > matchmaker #28 to #5/A
    7796 
    7797 Parameters 
    7798 --- 
    7799 Chain pairing | bb 
    7800 Alignment algorithm | Needleman-Wunsch 
    7801 Similarity matrix | BLOSUM-62 
    7802 SS fraction | 0.3 
    7803 Gap open (HH/SS/other) | 18/18/6 
    7804 Gap extend | 1 
    7805 SS matrix |  |  | H | S | O 
    7806 ---|---|---|--- 
    7807 H | 6 | -9 | -6 
    7808 S |  | 6 | -6 
    7809 O |  |  | 4 
    7810 Iteration cutoff | 2 
    7811  
    7812 Matchmaker fold_2026_05_15_15_51_model_3.cif, chain A (#5) with AlphaFold
    7813 Q5UHC2, chain A (#28), sequence alignment score = 1602.3 
    7814 RMSD between 372 pruned atom pairs is 0.652 angstroms; (across all 404 pairs:
    7815 2.049) 
    7816  
    7817 
    7818 > rename #28 "AlphaFold Q5UHC2_SALET - Glycosyltransferase - Salmonella
    7819 > enterica subsp. enterica serovar Urbana"
    7820 
    7821 Alignment identifier is bp6 [4] 
    7822 Associated AlphaFold A0A9Q6ZED9 chain A to #5/A with 0 mismatches 
    7823 Associated fold_2026_05_15_15_51_model_0.cif chain A to #5/A with 0 mismatches 
    7824 Associated fold_2026_05_15_15_51_model_1.cif chain A to #5/A with 0 mismatches 
    7825 Associated fold_2026_05_15_15_51_model_2.cif chain A to #5/A with 0 mismatches 
    7826 Associated fold_2026_05_15_15_51_model_3.cif chain A to #5/A with 0 mismatches 
    7827 Associated fold_2026_05_15_15_51_model_4.cif chain A to #5/A with 0 mismatches 
    7828 Associated fold_2026_06_01_00_39_model_0.cif chain A to #5/A with 0 mismatches 
    7829 Associated fold_2026_06_01_00_39_model_1.cif chain A to #5/A with 0 mismatches 
    7830 Associated fold_2026_06_01_00_39_model_2.cif chain A to #5/A with 0 mismatches 
    7831 Associated fold_2026_06_01_00_39_model_3.cif chain A to #5/A with 0 mismatches 
    7832 Associated fold_2026_06_01_00_39_model_4.cif chain A to #5/A with 0 mismatches 
    7833 Associated AlphaFold A0A9Q6ZED9 chain A to #5/A with 0 mismatches 
    7834 Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A with 0 mismatches 
    7835 Associated fold_gdp_bound_wbdp_model_1.cif chain A to #5/A with 0 mismatches 
    7836 Associated fold_gdp_bound_wbdp_model_2.cif chain A to #5/A with 0 mismatches 
    7837 Associated fold_gdp_bound_wbdp_model_3.cif chain A to #5/A with 0 mismatches 
    7838 Associated fold_gdp_bound_wbdp_model_4.cif chain A to #5/A with 0 mismatches 
    7839 Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A with 0 mismatches 
    7840 Associated fold_2026_05_15_15_51_model_0.cif chain A to #5/A with 0 mismatches 
    7841 [Repeated 1 time(s)]Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A
    7842 with 0 mismatches 
    7843 Associated AlphaFold Q2QKP2_ESCFE - WbdP - Escherichia fergusonii chain A to
    7844 #5/A with 1 mismatch 
    7845 Associated AlphaFold Q2QKP2 chain A to #5/A with 1 mismatch 
    7846 Showing conservation header ("seq_conservation" residue attribute) for
    7847 alignment bp6 [4] 
    7848 
    7849 > alphafold fetch Q5UHD5 version 4 alignTo #5/A
    7850 
    7851 Fetching compressed AlphaFold Q5UHD5 from
    7852 https://alphafold.ebi.ac.uk/files/AF-Q5UHD5-F1-model_v6.cif 
    7853 AlphaFold prediction matching chain A 
    7854 --- 
    7855 Chain| UniProt Id| RMSD| Length| Seen| % Id 
    7856 A | Q5UHD5 | 1.93 | 404 | 404 | 60   
    7857  
    7858 Associated AlphaFold Q5UHD5 chain A to Q5UHD5 with 0 mismatches 
    7859 
    7860 > matchmaker #29 to #5/A
    7861 
    7862 Parameters 
    7863 --- 
    7864 Chain pairing | bb 
    7865 Alignment algorithm | Needleman-Wunsch 
    7866 Similarity matrix | BLOSUM-62 
    7867 SS fraction | 0.3 
    7868 Gap open (HH/SS/other) | 18/18/6 
    7869 Gap extend | 1 
    7870 SS matrix |  |  | H | S | O 
    7871 ---|---|---|--- 
    7872 H | 6 | -9 | -6 
    7873 S |  | 6 | -6 
    7874 O |  |  | 4 
    7875 Iteration cutoff | 2 
    7876  
    7877 Matchmaker fold_2026_05_15_15_51_model_3.cif, chain A (#5) with AlphaFold
    7878 Q5UHD5, chain A (#29), sequence alignment score = 1498.7 
    7879 RMSD between 367 pruned atom pairs is 0.730 angstroms; (across all 404 pairs:
    7880 1.932) 
    7881  
    7882 
    7883 > rename #29 "AlphaFold Q5UHD5_CITFR - Glycosyltransferase - Citrobacter
    7884 > freundii"
    7885 
    7886 Alignment identifier is bp6 [5] 
    7887 Associated AlphaFold A0A9Q6ZED9 chain A to #5/A with 0 mismatches 
    7888 Associated fold_2026_05_15_15_51_model_0.cif chain A to #5/A with 0 mismatches 
    7889 Associated fold_2026_05_15_15_51_model_1.cif chain A to #5/A with 0 mismatches 
    7890 Associated fold_2026_05_15_15_51_model_2.cif chain A to #5/A with 0 mismatches 
    7891 Associated fold_2026_05_15_15_51_model_3.cif chain A to #5/A with 0 mismatches 
    7892 Associated fold_2026_05_15_15_51_model_4.cif chain A to #5/A with 0 mismatches 
    7893 Associated fold_2026_06_01_00_39_model_0.cif chain A to #5/A with 0 mismatches 
    7894 Associated fold_2026_06_01_00_39_model_1.cif chain A to #5/A with 0 mismatches 
    7895 Associated fold_2026_06_01_00_39_model_2.cif chain A to #5/A with 0 mismatches 
    7896 Associated fold_2026_06_01_00_39_model_3.cif chain A to #5/A with 0 mismatches 
    7897 Associated fold_2026_06_01_00_39_model_4.cif chain A to #5/A with 0 mismatches 
    7898 Associated AlphaFold A0A9Q6ZED9 chain A to #5/A with 0 mismatches 
    7899 Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A with 0 mismatches 
    7900 Associated fold_gdp_bound_wbdp_model_1.cif chain A to #5/A with 0 mismatches 
    7901 Associated fold_gdp_bound_wbdp_model_2.cif chain A to #5/A with 0 mismatches 
    7902 Associated fold_gdp_bound_wbdp_model_3.cif chain A to #5/A with 0 mismatches 
    7903 Associated fold_gdp_bound_wbdp_model_4.cif chain A to #5/A with 0 mismatches 
    7904 Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A with 0 mismatches 
    7905 Associated fold_2026_05_15_15_51_model_0.cif chain A to #5/A with 0 mismatches 
    7906 [Repeated 1 time(s)]Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A
    7907 with 0 mismatches 
    7908 Associated AlphaFold Q2QKP2_ESCFE - WbdP - Escherichia fergusonii chain A to
    7909 #5/A with 1 mismatch 
    7910 Associated AlphaFold Q2QKP2 chain A to #5/A with 1 mismatch 
    7911 Showing conservation header ("seq_conservation" residue attribute) for
    7912 alignment bp6 [5] 
    7913 
    7914 > alphafold fetch A4SVM0 version 4 alignTo #5/A
    7915 
    7916 AlphaFold prediction matching chain A 
    7917 --- 
    7918 Chain| UniProt Id| RMSD| Length| Seen| % Id 
    7919 A | A4SVM0 | 1.71 | 409 | 404 | 44   
    7920  
    7921 Associated AlphaFold A4SVM0 chain A to A4SVM0 with 0 mismatches 
    7922 
    7923 > matchmaker #30 to #5/A
    7924 
    7925 Parameters 
    7926 --- 
    7927 Chain pairing | bb 
    7928 Alignment algorithm | Needleman-Wunsch 
    7929 Similarity matrix | BLOSUM-62 
    7930 SS fraction | 0.3 
    7931 Gap open (HH/SS/other) | 18/18/6 
    7932 Gap extend | 1 
    7933 SS matrix |  |  | H | S | O 
    7934 ---|---|---|--- 
    7935 H | 6 | -9 | -6 
    7936 S |  | 6 | -6 
    7937 O |  |  | 4 
    7938 Iteration cutoff | 2 
    7939  
    7940 Matchmaker fold_2026_05_15_15_51_model_3.cif, chain A (#5) with AlphaFold
    7941 A4SVM0, chain A (#30), sequence alignment score = 1151.6 
    7942 RMSD between 348 pruned atom pairs is 0.893 angstroms; (across all 403 pairs:
    7943 1.714) 
    7944  
    7945 
    7946 > rename #30 "AlphaFold A4SVM0_POLAQ - Glycosyltransferase group 1 - "
    7947 
    7948 > rename #30 "AlphaFold A4SVM0_POLAQ - Glycosyltransferase group 1 -
    7949 > Polynucelobacter asymbioticus (strain DSM 18221 / CIP 109841 /
    7950 > QLW-P1DMWA-1)"
    7951 
    7952 Alignment identifier is bp6 [6] 
    7953 Associated AlphaFold A0A9Q6ZED9 chain A to #5/A with 0 mismatches 
    7954 Associated fold_2026_05_15_15_51_model_0.cif chain A to #5/A with 0 mismatches 
    7955 Associated fold_2026_05_15_15_51_model_1.cif chain A to #5/A with 0 mismatches 
    7956 Associated fold_2026_05_15_15_51_model_2.cif chain A to #5/A with 0 mismatches 
    7957 Associated fold_2026_05_15_15_51_model_3.cif chain A to #5/A with 0 mismatches 
    7958 Associated fold_2026_05_15_15_51_model_4.cif chain A to #5/A with 0 mismatches 
    7959 Associated fold_2026_06_01_00_39_model_0.cif chain A to #5/A with 0 mismatches 
    7960 Associated fold_2026_06_01_00_39_model_1.cif chain A to #5/A with 0 mismatches 
    7961 Associated fold_2026_06_01_00_39_model_2.cif chain A to #5/A with 0 mismatches 
    7962 Associated fold_2026_06_01_00_39_model_3.cif chain A to #5/A with 0 mismatches 
    7963 Associated fold_2026_06_01_00_39_model_4.cif chain A to #5/A with 0 mismatches 
    7964 Associated AlphaFold A0A9Q6ZED9 chain A to #5/A with 0 mismatches 
    7965 Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A with 0 mismatches 
    7966 Associated fold_gdp_bound_wbdp_model_1.cif chain A to #5/A with 0 mismatches 
    7967 Associated fold_gdp_bound_wbdp_model_2.cif chain A to #5/A with 0 mismatches 
    7968 Associated fold_gdp_bound_wbdp_model_3.cif chain A to #5/A with 0 mismatches 
    7969 Associated fold_gdp_bound_wbdp_model_4.cif chain A to #5/A with 0 mismatches 
    7970 Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A with 0 mismatches 
    7971 Associated fold_2026_05_15_15_51_model_0.cif chain A to #5/A with 0 mismatches 
    7972 [Repeated 1 time(s)]Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A
    7973 with 0 mismatches 
    7974 Associated AlphaFold Q2QKP2_ESCFE - WbdP - Escherichia fergusonii chain A to
    7975 #5/A with 1 mismatch 
    7976 Associated AlphaFold Q2QKP2 chain A to #5/A with 1 mismatch 
    7977 Showing conservation header ("seq_conservation" residue attribute) for
    7978 alignment bp6 [6] 
    7979 
    7980 > alphafold fetch A0A2M8K035 version 4 alignTo #5/A
    7981 
    7982 Fetching compressed AlphaFold A0A2M8K035 from
    7983 https://alphafold.ebi.ac.uk/files/AF-A0A2M8K035-F1-model_v6.cif 
    7984 AlphaFold prediction matching chain A 
    7985 --- 
    7986 Chain| UniProt Id| RMSD| Length| Seen| % Id 
    7987 A | A0A2M8K035 | 2.33 | 406 | 404 | 46   
    7988  
    7989 Associated AlphaFold A0A2M8K035 chain A to A0A2M8K035 with 0 mismatches 
    7990 
    7991 > matchmaker #31 to #5/A
    7992 
    7993 Parameters 
    7994 --- 
    7995 Chain pairing | bb 
    7996 Alignment algorithm | Needleman-Wunsch 
    7997 Similarity matrix | BLOSUM-62 
    7998 SS fraction | 0.3 
    7999 Gap open (HH/SS/other) | 18/18/6 
    8000 Gap extend | 1 
    8001 SS matrix |  |  | H | S | O 
    8002 ---|---|---|--- 
    8003 H | 6 | -9 | -6 
    8004 S |  | 6 | -6 
    8005 O |  |  | 4 
    8006 Iteration cutoff | 2 
    8007  
    8008 Matchmaker fold_2026_05_15_15_51_model_3.cif, chain A (#5) with AlphaFold
    8009 A0A2M8K035, chain A (#31), sequence alignment score = 1160.9 
    8010 RMSD between 327 pruned atom pairs is 0.874 angstroms; (across all 400 pairs:
    8011 2.327) 
    8012  
    8013 
    8014 > hide #30 models
    8015 
    8016 > hide #29 models
    8017 
    8018 > hide #28 models
    8019 
    8020 > hide #27 models
    8021 
    8022 > hide #26 models
    8023 
    8024 > hide #25 models
    8025 
    8026 > show #!1 models
    8027 
    8028 > rename #31 "AlphaFold A0A2M8K035_9GAMM - Glycosyltransferase 1 domain-
    8029 > containing protein - Marinomonas sp. BSi20584"
    8030 
    8031 Alignment identifier is bp6 [7] 
    8032 Associated AlphaFold A0A9Q6ZED9 chain A to #5/A with 0 mismatches 
    8033 Associated fold_2026_05_15_15_51_model_0.cif chain A to #5/A with 0 mismatches 
    8034 Associated fold_2026_05_15_15_51_model_1.cif chain A to #5/A with 0 mismatches 
    8035 Associated fold_2026_05_15_15_51_model_2.cif chain A to #5/A with 0 mismatches 
    8036 Associated fold_2026_05_15_15_51_model_3.cif chain A to #5/A with 0 mismatches 
    8037 Associated fold_2026_05_15_15_51_model_4.cif chain A to #5/A with 0 mismatches 
    8038 Associated fold_2026_06_01_00_39_model_0.cif chain A to #5/A with 0 mismatches 
    8039 Associated fold_2026_06_01_00_39_model_1.cif chain A to #5/A with 0 mismatches 
    8040 Associated fold_2026_06_01_00_39_model_2.cif chain A to #5/A with 0 mismatches 
    8041 Associated fold_2026_06_01_00_39_model_3.cif chain A to #5/A with 0 mismatches 
    8042 Associated fold_2026_06_01_00_39_model_4.cif chain A to #5/A with 0 mismatches 
    8043 Associated AlphaFold A0A9Q6ZED9 chain A to #5/A with 0 mismatches 
    8044 Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A with 0 mismatches 
    8045 Associated fold_gdp_bound_wbdp_model_1.cif chain A to #5/A with 0 mismatches 
    8046 Associated fold_gdp_bound_wbdp_model_2.cif chain A to #5/A with 0 mismatches 
    8047 Associated fold_gdp_bound_wbdp_model_3.cif chain A to #5/A with 0 mismatches 
    8048 Associated fold_gdp_bound_wbdp_model_4.cif chain A to #5/A with 0 mismatches 
    8049 Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A with 0 mismatches 
    8050 Associated fold_2026_05_15_15_51_model_0.cif chain A to #5/A with 0 mismatches 
    8051 [Repeated 1 time(s)]Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A
    8052 with 0 mismatches 
    8053 Associated AlphaFold Q2QKP2_ESCFE - WbdP - Escherichia fergusonii chain A to
    8054 #5/A with 1 mismatch 
    8055 Associated AlphaFold Q2QKP2 chain A to #5/A with 1 mismatch 
    8056 Showing conservation header ("seq_conservation" residue attribute) for
    8057 alignment bp6 [7] 
    8058 
    8059 > alphafold fetch A0A1A3L386 version 4 alignTo #5/A
    8060 
    8061 Fetching compressed AlphaFold A0A1A3L386 from
    8062 https://alphafold.ebi.ac.uk/files/AF-A0A1A3L386-F1-model_v6.cif 
    8063 AlphaFold prediction matching chain A 
    8064 --- 
    8065 Chain| UniProt Id| RMSD| Length| Seen| % Id 
    8066 A | A0A1A3L386 | 5.42 | 409 | 404 | 38   
    8067  
    8068 Associated AlphaFold A0A1A3L386 chain A to A0A1A3L386 with 0 mismatches 
    8069 
    8070 > matchmaker #32 to #5/A
    8071 
    8072 Parameters 
    8073 --- 
    8074 Chain pairing | bb 
    8075 Alignment algorithm | Needleman-Wunsch 
    8076 Similarity matrix | BLOSUM-62 
    8077 SS fraction | 0.3 
    8078 Gap open (HH/SS/other) | 18/18/6 
    8079 Gap extend | 1 
    8080 SS matrix |  |  | H | S | O 
    8081 ---|---|---|--- 
    8082 H | 6 | -9 | -6 
    8083 S |  | 6 | -6 
    8084 O |  |  | 4 
    8085 Iteration cutoff | 2 
    8086  
    8087 Matchmaker fold_2026_05_15_15_51_model_3.cif, chain A (#5) with AlphaFold
    8088 A0A1A3L386, chain A (#32), sequence alignment score = 988.6 
    8089 RMSD between 310 pruned atom pairs is 0.918 angstroms; (across all 397 pairs:
    8090 5.422) 
    8091  
    8092 
    8093 > rename #32 "AlphaFold A0A1A3L386_MYCAS - Glycosyltransferase 1 domain-
    8094 > containing protein - Mycobacterium asiaticum"
    8095 
    8096 Alignment identifier is bp6 [8] 
    8097 Associated AlphaFold A0A9Q6ZED9 chain A to #5/A with 0 mismatches 
    8098 Associated fold_2026_05_15_15_51_model_0.cif chain A to #5/A with 0 mismatches 
    8099 Associated fold_2026_05_15_15_51_model_1.cif chain A to #5/A with 0 mismatches 
    8100 Associated fold_2026_05_15_15_51_model_2.cif chain A to #5/A with 0 mismatches 
    8101 Associated fold_2026_05_15_15_51_model_3.cif chain A to #5/A with 0 mismatches 
    8102 Associated fold_2026_05_15_15_51_model_4.cif chain A to #5/A with 0 mismatches 
    8103 Associated fold_2026_06_01_00_39_model_0.cif chain A to #5/A with 0 mismatches 
    8104 Associated fold_2026_06_01_00_39_model_1.cif chain A to #5/A with 0 mismatches 
    8105 Associated fold_2026_06_01_00_39_model_2.cif chain A to #5/A with 0 mismatches 
    8106 Associated fold_2026_06_01_00_39_model_3.cif chain A to #5/A with 0 mismatches 
    8107 Associated fold_2026_06_01_00_39_model_4.cif chain A to #5/A with 0 mismatches 
    8108 Associated AlphaFold A0A9Q6ZED9 chain A to #5/A with 0 mismatches 
    8109 Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A with 0 mismatches 
    8110 Associated fold_gdp_bound_wbdp_model_1.cif chain A to #5/A with 0 mismatches 
    8111 Associated fold_gdp_bound_wbdp_model_2.cif chain A to #5/A with 0 mismatches 
    8112 Associated fold_gdp_bound_wbdp_model_3.cif chain A to #5/A with 0 mismatches 
    8113 Associated fold_gdp_bound_wbdp_model_4.cif chain A to #5/A with 0 mismatches 
    8114 Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A with 0 mismatches 
    8115 Associated fold_2026_05_15_15_51_model_0.cif chain A to #5/A with 0 mismatches 
    8116 [Repeated 1 time(s)]Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A
    8117 with 0 mismatches 
    8118 Associated AlphaFold Q2QKP2_ESCFE - WbdP - Escherichia fergusonii chain A to
    8119 #5/A with 1 mismatch 
    8120 Associated AlphaFold Q2QKP2 chain A to #5/A with 1 mismatch 
    8121 Showing conservation header ("seq_conservation" residue attribute) for
    8122 alignment bp6 [8] 
    8123 Alignment identifier is bp6 [9] 
    8124 Associated AlphaFold A0A9Q6ZED9 chain A to #5/A with 0 mismatches 
    8125 Associated fold_2026_05_15_15_51_model_0.cif chain A to #5/A with 0 mismatches 
    8126 Associated fold_2026_05_15_15_51_model_1.cif chain A to #5/A with 0 mismatches 
    8127 Associated fold_2026_05_15_15_51_model_2.cif chain A to #5/A with 0 mismatches 
    8128 Associated fold_2026_05_15_15_51_model_3.cif chain A to #5/A with 0 mismatches 
    8129 Associated fold_2026_05_15_15_51_model_4.cif chain A to #5/A with 0 mismatches 
    8130 Associated fold_2026_06_01_00_39_model_0.cif chain A to #5/A with 0 mismatches 
    8131 Associated fold_2026_06_01_00_39_model_1.cif chain A to #5/A with 0 mismatches 
    8132 Associated fold_2026_06_01_00_39_model_2.cif chain A to #5/A with 0 mismatches 
    8133 Associated fold_2026_06_01_00_39_model_3.cif chain A to #5/A with 0 mismatches 
    8134 Associated fold_2026_06_01_00_39_model_4.cif chain A to #5/A with 0 mismatches 
    8135 Associated AlphaFold A0A9Q6ZED9 chain A to #5/A with 0 mismatches 
    8136 Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A with 0 mismatches 
    8137 Associated fold_gdp_bound_wbdp_model_1.cif chain A to #5/A with 0 mismatches 
    8138 Associated fold_gdp_bound_wbdp_model_2.cif chain A to #5/A with 0 mismatches 
    8139 Associated fold_gdp_bound_wbdp_model_3.cif chain A to #5/A with 0 mismatches 
    8140 Associated fold_gdp_bound_wbdp_model_4.cif chain A to #5/A with 0 mismatches 
    8141 Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A with 0 mismatches 
    8142 Associated fold_2026_05_15_15_51_model_0.cif chain A to #5/A with 0 mismatches 
    8143 [Repeated 1 time(s)]Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A
    8144 with 0 mismatches 
    8145 Associated AlphaFold Q2QKP2_ESCFE - WbdP - Escherichia fergusonii chain A to
    8146 #5/A with 1 mismatch 
    8147 Associated AlphaFold Q2QKP2 chain A to #5/A with 1 mismatch 
    8148 Showing conservation header ("seq_conservation" residue attribute) for
    8149 alignment bp6 [9] 
    8150 Alignment identifier is bp6 [10] 
    8151 Associated AlphaFold A0A9Q6ZED9 chain A to #5/A with 0 mismatches 
    8152 Associated fold_2026_05_15_15_51_model_0.cif chain A to #5/A with 0 mismatches 
    8153 Associated fold_2026_05_15_15_51_model_1.cif chain A to #5/A with 0 mismatches 
    8154 Associated fold_2026_05_15_15_51_model_2.cif chain A to #5/A with 0 mismatches 
    8155 Associated fold_2026_05_15_15_51_model_3.cif chain A to #5/A with 0 mismatches 
    8156 Associated fold_2026_05_15_15_51_model_4.cif chain A to #5/A with 0 mismatches 
    8157 Associated fold_2026_06_01_00_39_model_0.cif chain A to #5/A with 0 mismatches 
    8158 Associated fold_2026_06_01_00_39_model_1.cif chain A to #5/A with 0 mismatches 
    8159 Associated fold_2026_06_01_00_39_model_2.cif chain A to #5/A with 0 mismatches 
    8160 Associated fold_2026_06_01_00_39_model_3.cif chain A to #5/A with 0 mismatches 
    8161 Associated fold_2026_06_01_00_39_model_4.cif chain A to #5/A with 0 mismatches 
    8162 Associated AlphaFold A0A9Q6ZED9 chain A to #5/A with 0 mismatches 
    8163 Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A with 0 mismatches 
    8164 Associated fold_gdp_bound_wbdp_model_1.cif chain A to #5/A with 0 mismatches 
    8165 Associated fold_gdp_bound_wbdp_model_2.cif chain A to #5/A with 0 mismatches 
    8166 Associated fold_gdp_bound_wbdp_model_3.cif chain A to #5/A with 0 mismatches 
    8167 Associated fold_gdp_bound_wbdp_model_4.cif chain A to #5/A with 0 mismatches 
    8168 Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A with 0 mismatches 
    8169 Associated fold_2026_05_15_15_51_model_0.cif chain A to #5/A with 0 mismatches 
    8170 [Repeated 1 time(s)]Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A
    8171 with 0 mismatches 
    8172 Associated AlphaFold Q2QKP2_ESCFE - WbdP - Escherichia fergusonii chain A to
    8173 #5/A with 1 mismatch 
    8174 Associated AlphaFold Q2QKP2 chain A to #5/A with 1 mismatch 
    8175 Showing conservation header ("seq_conservation" residue attribute) for
    8176 alignment bp6 [10] 
    8177 
    8178 > alphafold fetch C6E0L3 version 4 alignTo #5/A
    8179 
    8180 Fetching compressed AlphaFold C6E0L3 from
    8181 https://alphafold.ebi.ac.uk/files/AF-C6E0L3-F1-model_v6.cif 
    8182 AlphaFold prediction matching chain A 
    8183 --- 
    8184 Chain| UniProt Id| RMSD| Length| Seen| % Id 
    8185 A | C6E0L3 | 3.38 | 413 | 404 | 38   
    8186  
    8187 Associated AlphaFold C6E0L3 chain A to C6E0L3 with 0 mismatches 
    8188 
    8189 > matchmaker #33 to #5/A
    8190 
    8191 Parameters 
    8192 --- 
    8193 Chain pairing | bb 
    8194 Alignment algorithm | Needleman-Wunsch 
    8195 Similarity matrix | BLOSUM-62 
    8196 SS fraction | 0.3 
    8197 Gap open (HH/SS/other) | 18/18/6 
    8198 Gap extend | 1 
    8199 SS matrix |  |  | H | S | O 
    8200 ---|---|---|--- 
    8201 H | 6 | -9 | -6 
    8202 S |  | 6 | -6 
    8203 O |  |  | 4 
    8204 Iteration cutoff | 2 
    8205  
    8206 Matchmaker fold_2026_05_15_15_51_model_3.cif, chain A (#5) with AlphaFold
    8207 C6E0L3, chain A (#33), sequence alignment score = 954.7 
    8208 RMSD between 293 pruned atom pairs is 1.058 angstroms; (across all 401 pairs:
    8209 3.394) 
    8210  
    8211 
    8212 > rename #33 "AlphaFold C6E0L3_GEOSM - Glycosyltransferase group 1 - Geobacter
    8213 > sp. (strain M21)"
    8214 
    8215 Alignment identifier is bp6 [11] 
    8216 Associated AlphaFold A0A9Q6ZED9 chain A to #5/A with 0 mismatches 
    8217 Associated fold_2026_05_15_15_51_model_0.cif chain A to #5/A with 0 mismatches 
    8218 Associated fold_2026_05_15_15_51_model_1.cif chain A to #5/A with 0 mismatches 
    8219 Associated fold_2026_05_15_15_51_model_2.cif chain A to #5/A with 0 mismatches 
    8220 Associated fold_2026_05_15_15_51_model_3.cif chain A to #5/A with 0 mismatches 
    8221 Associated fold_2026_05_15_15_51_model_4.cif chain A to #5/A with 0 mismatches 
    8222 Associated fold_2026_06_01_00_39_model_0.cif chain A to #5/A with 0 mismatches 
    8223 Associated fold_2026_06_01_00_39_model_1.cif chain A to #5/A with 0 mismatches 
    8224 Associated fold_2026_06_01_00_39_model_2.cif chain A to #5/A with 0 mismatches 
    8225 Associated fold_2026_06_01_00_39_model_3.cif chain A to #5/A with 0 mismatches 
    8226 Associated fold_2026_06_01_00_39_model_4.cif chain A to #5/A with 0 mismatches 
    8227 Associated AlphaFold A0A9Q6ZED9 chain A to #5/A with 0 mismatches 
    8228 Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A with 0 mismatches 
    8229 Associated fold_gdp_bound_wbdp_model_1.cif chain A to #5/A with 0 mismatches 
    8230 Associated fold_gdp_bound_wbdp_model_2.cif chain A to #5/A with 0 mismatches 
    8231 Associated fold_gdp_bound_wbdp_model_3.cif chain A to #5/A with 0 mismatches 
    8232 Associated fold_gdp_bound_wbdp_model_4.cif chain A to #5/A with 0 mismatches 
    8233 Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A with 0 mismatches 
    8234 Associated fold_2026_05_15_15_51_model_0.cif chain A to #5/A with 0 mismatches 
    8235 [Repeated 1 time(s)]Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A
    8236 with 0 mismatches 
    8237 Associated AlphaFold Q2QKP2_ESCFE - WbdP - Escherichia fergusonii chain A to
    8238 #5/A with 1 mismatch 
    8239 Associated AlphaFold Q2QKP2 chain A to #5/A with 1 mismatch 
    8240 Showing conservation header ("seq_conservation" residue attribute) for
    8241 alignment bp6 [11] 
    8242 
    8243 > hide #31 models
    8244 
    8245 > hide #32 models
    8246 
    8247 > hide #33 models
    8248 
    8249 Alignment identifier is bp6 [12] 
    8250 Associated AlphaFold A0A9Q6ZED9 chain A to #5/A with 0 mismatches 
    8251 Associated fold_2026_05_15_15_51_model_0.cif chain A to #5/A with 0 mismatches 
    8252 Associated fold_2026_05_15_15_51_model_1.cif chain A to #5/A with 0 mismatches 
    8253 Associated fold_2026_05_15_15_51_model_2.cif chain A to #5/A with 0 mismatches 
    8254 Associated fold_2026_05_15_15_51_model_3.cif chain A to #5/A with 0 mismatches 
    8255 Associated fold_2026_05_15_15_51_model_4.cif chain A to #5/A with 0 mismatches 
    8256 Associated fold_2026_06_01_00_39_model_0.cif chain A to #5/A with 0 mismatches 
    8257 Associated fold_2026_06_01_00_39_model_1.cif chain A to #5/A with 0 mismatches 
    8258 Associated fold_2026_06_01_00_39_model_2.cif chain A to #5/A with 0 mismatches 
    8259 Associated fold_2026_06_01_00_39_model_3.cif chain A to #5/A with 0 mismatches 
    8260 Associated fold_2026_06_01_00_39_model_4.cif chain A to #5/A with 0 mismatches 
    8261 Associated AlphaFold A0A9Q6ZED9 chain A to #5/A with 0 mismatches 
    8262 Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A with 0 mismatches 
    8263 Associated fold_gdp_bound_wbdp_model_1.cif chain A to #5/A with 0 mismatches 
    8264 Associated fold_gdp_bound_wbdp_model_2.cif chain A to #5/A with 0 mismatches 
    8265 Associated fold_gdp_bound_wbdp_model_3.cif chain A to #5/A with 0 mismatches 
    8266 Associated fold_gdp_bound_wbdp_model_4.cif chain A to #5/A with 0 mismatches 
    8267 Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A with 0 mismatches 
    8268 Associated fold_2026_05_15_15_51_model_0.cif chain A to #5/A with 0 mismatches 
    8269 [Repeated 1 time(s)]Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A
    8270 with 0 mismatches 
    8271 Associated AlphaFold Q2QKP2_ESCFE - WbdP - Escherichia fergusonii chain A to
    8272 #5/A with 1 mismatch 
    8273 Associated AlphaFold Q2QKP2 chain A to #5/A with 1 mismatch 
    8274 Showing conservation header ("seq_conservation" residue attribute) for
    8275 alignment bp6 [12] 
    8276 
    8277 > alphafold fetch A0A4R7CL53 version 4 alignTo #5/A
    8278 
    8279 Fetching url https://alphafold.ebi.ac.uk/files/AF-A0A4R7CL53-F1-model_v6.cif
    8280 failed: 
    8281 HTTP Error 404: Not Found 
    8282 
    8283 > alphafold fetch A0A4R7CL53 version 4 alignTo #5/A
    8284 
    8285 Fetching url https://alphafold.ebi.ac.uk/files/AF-A0A4R7CL53-F1-model_v6.cif
    8286 failed: 
    8287 HTTP Error 404: Not Found 
    8288 Alignment identifier is bp6 [13] 
    8289 Associated AlphaFold A0A9Q6ZED9 chain A to #5/A with 0 mismatches 
    8290 Associated fold_2026_05_15_15_51_model_0.cif chain A to #5/A with 0 mismatches 
    8291 Associated fold_2026_05_15_15_51_model_1.cif chain A to #5/A with 0 mismatches 
    8292 Associated fold_2026_05_15_15_51_model_2.cif chain A to #5/A with 0 mismatches 
    8293 Associated fold_2026_05_15_15_51_model_3.cif chain A to #5/A with 0 mismatches 
    8294 Associated fold_2026_05_15_15_51_model_4.cif chain A to #5/A with 0 mismatches 
    8295 Associated fold_2026_06_01_00_39_model_0.cif chain A to #5/A with 0 mismatches 
    8296 Associated fold_2026_06_01_00_39_model_1.cif chain A to #5/A with 0 mismatches 
    8297 Associated fold_2026_06_01_00_39_model_2.cif chain A to #5/A with 0 mismatches 
    8298 Associated fold_2026_06_01_00_39_model_3.cif chain A to #5/A with 0 mismatches 
    8299 Associated fold_2026_06_01_00_39_model_4.cif chain A to #5/A with 0 mismatches 
    8300 Associated AlphaFold A0A9Q6ZED9 chain A to #5/A with 0 mismatches 
    8301 Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A with 0 mismatches 
    8302 Associated fold_gdp_bound_wbdp_model_1.cif chain A to #5/A with 0 mismatches 
    8303 Associated fold_gdp_bound_wbdp_model_2.cif chain A to #5/A with 0 mismatches 
    8304 Associated fold_gdp_bound_wbdp_model_3.cif chain A to #5/A with 0 mismatches 
    8305 Associated fold_gdp_bound_wbdp_model_4.cif chain A to #5/A with 0 mismatches 
    8306 Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A with 0 mismatches 
    8307 Associated fold_2026_05_15_15_51_model_0.cif chain A to #5/A with 0 mismatches 
    8308 [Repeated 1 time(s)]Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A
    8309 with 0 mismatches 
    8310 Associated AlphaFold Q2QKP2_ESCFE - WbdP - Escherichia fergusonii chain A to
    8311 #5/A with 1 mismatch 
    8312 Associated AlphaFold Q2QKP2 chain A to #5/A with 1 mismatch 
    8313 Showing conservation header ("seq_conservation" residue attribute) for
    8314 alignment bp6 [13] 
    8315 
    8316 > alphafold fetch A0A257L694 version 4 alignTo #5/A
    8317 
    8318 Fetching compressed AlphaFold A0A257L694 from
    8319 https://alphafold.ebi.ac.uk/files/AF-A0A257L694-F1-model_v6.cif 
    8320 AlphaFold prediction matching chain A 
    8321 --- 
    8322 Chain| UniProt Id| RMSD| Length| Seen| % Id 
    8323 A | A0A257L694 | 4.03 | 397 | 404 | 34   
    8324  
    8325 Associated AlphaFold A0A257L694 chain A to A0A257L694 with 0 mismatches 
    8326 
    8327 > matchmaker #34 to #5/A
    8328 
    8329 Parameters 
    8330 --- 
    8331 Chain pairing | bb 
    8332 Alignment algorithm | Needleman-Wunsch 
    8333 Similarity matrix | BLOSUM-62 
    8334 SS fraction | 0.3 
    8335 Gap open (HH/SS/other) | 18/18/6 
    8336 Gap extend | 1 
    8337 SS matrix |  |  | H | S | O 
    8338 ---|---|---|--- 
    8339 H | 6 | -9 | -6 
    8340 S |  | 6 | -6 
    8341 O |  |  | 4 
    8342 Iteration cutoff | 2 
    8343  
    8344 Matchmaker fold_2026_05_15_15_51_model_3.cif, chain A (#5) with AlphaFold
    8345 A0A257L694, chain A (#34), sequence alignment score = 916.9 
    8346 RMSD between 257 pruned atom pairs is 0.949 angstroms; (across all 393 pairs:
    8347 4.032) 
    8348  
    8349 
    8350 > rename #34 "AlphaFold A0A257L694_9BACT - Glycosyltransferase 1 domain-
    8351 > containing protein - Bacteroidetes bacterium B1(2017)"
    8352 
    8353 Alignment identifier is bp6 [14] 
    8354 Associated AlphaFold A0A9Q6ZED9 chain A to #5/A with 0 mismatches 
    8355 Associated fold_2026_05_15_15_51_model_0.cif chain A to #5/A with 0 mismatches 
    8356 Associated fold_2026_05_15_15_51_model_1.cif chain A to #5/A with 0 mismatches 
    8357 Associated fold_2026_05_15_15_51_model_2.cif chain A to #5/A with 0 mismatches 
    8358 Associated fold_2026_05_15_15_51_model_3.cif chain A to #5/A with 0 mismatches 
    8359 Associated fold_2026_05_15_15_51_model_4.cif chain A to #5/A with 0 mismatches 
    8360 Associated fold_2026_06_01_00_39_model_0.cif chain A to #5/A with 0 mismatches 
    8361 Associated fold_2026_06_01_00_39_model_1.cif chain A to #5/A with 0 mismatches 
    8362 Associated fold_2026_06_01_00_39_model_2.cif chain A to #5/A with 0 mismatches 
    8363 Associated fold_2026_06_01_00_39_model_3.cif chain A to #5/A with 0 mismatches 
    8364 Associated fold_2026_06_01_00_39_model_4.cif chain A to #5/A with 0 mismatches 
    8365 Associated AlphaFold A0A9Q6ZED9 chain A to #5/A with 0 mismatches 
    8366 Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A with 0 mismatches 
    8367 Associated fold_gdp_bound_wbdp_model_1.cif chain A to #5/A with 0 mismatches 
    8368 Associated fold_gdp_bound_wbdp_model_2.cif chain A to #5/A with 0 mismatches 
    8369 Associated fold_gdp_bound_wbdp_model_3.cif chain A to #5/A with 0 mismatches 
    8370 Associated fold_gdp_bound_wbdp_model_4.cif chain A to #5/A with 0 mismatches 
    8371 Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A with 0 mismatches 
    8372 Associated fold_2026_05_15_15_51_model_0.cif chain A to #5/A with 0 mismatches 
    8373 [Repeated 1 time(s)]Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A
    8374 with 0 mismatches 
    8375 Associated AlphaFold Q2QKP2_ESCFE - WbdP - Escherichia fergusonii chain A to
    8376 #5/A with 1 mismatch 
    8377 Associated AlphaFold Q2QKP2 chain A to #5/A with 1 mismatch 
    8378 Showing conservation header ("seq_conservation" residue attribute) for
    8379 alignment bp6 [14] 
    8380 
    8381 > alphafold fetch R6HU74 version 4 alignTo #5/A
    8382 
    8383 Fetching url https://alphafold.ebi.ac.uk/files/AF-R6HU74-F1-model_v6.cif
    8384 failed: 
    8385 HTTP Error 404: Not Found 
    8386 
    8387 > alphafold fetch R6HU74 version 4 alignTo #5/A
    8388 
    8389 Fetching url https://alphafold.ebi.ac.uk/files/AF-R6HU74-F1-model_v6.cif
    8390 failed: 
    8391 HTTP Error 404: Not Found 
    8392 
    8393 > alphafold fetch R6HU74 version 4 alignTo #5/A
    8394 
    8395 Fetching url https://alphafold.ebi.ac.uk/files/AF-R6HU74-F1-model_v6.cif
    8396 failed: 
    8397 HTTP Error 404: Not Found 
    8398 
    8399 > alphafold fetch K2ACG0 version 4 alignTo #5/A
    8400 
    8401 Fetching compressed AlphaFold K2ACG0 from
    8402 https://alphafold.ebi.ac.uk/files/AF-K2ACG0-F1-model_v6.cif 
    8403 AlphaFold prediction matching chain A 
    8404 --- 
    8405 Chain| UniProt Id| RMSD| Length| Seen| % Id 
    8406 A | K2ACG0 | 4.98 | 405 | 404 | 36   
    8407  
    8408 
    8409 > matchmaker #35 to #5/A
    8410 
    8411 Parameters 
    8412 --- 
    8413 Chain pairing | bb 
    8414 Alignment algorithm | Needleman-Wunsch 
    8415 Similarity matrix | BLOSUM-62 
    8416 SS fraction | 0.3 
    8417 Gap open (HH/SS/other) | 18/18/6 
    8418 Gap extend | 1 
    8419 SS matrix |  |  | H | S | O 
    8420 ---|---|---|--- 
    8421 H | 6 | -9 | -6 
    8422 S |  | 6 | -6 
    8423 O |  |  | 4 
    8424 Iteration cutoff | 2 
    8425  
    8426 Matchmaker fold_2026_05_15_15_51_model_3.cif, chain A (#5) with AlphaFold
    8427 K2ACG0, chain A (#35), sequence alignment score = 866.8 
    8428 RMSD between 279 pruned atom pairs is 1.136 angstroms; (across all 387 pairs:
    8429 4.977) 
    8430  
    8431 
    8432 > delete #35
    8433 
    8434 > hide #34 models
    8435 
    8436 Alignment identifier is bp6 [15] 
    8437 Associated AlphaFold A0A9Q6ZED9 chain A to #5/A with 0 mismatches 
    8438 Associated fold_2026_05_15_15_51_model_0.cif chain A to #5/A with 0 mismatches 
    8439 Associated fold_2026_05_15_15_51_model_1.cif chain A to #5/A with 0 mismatches 
    8440 Associated fold_2026_05_15_15_51_model_2.cif chain A to #5/A with 0 mismatches 
    8441 Associated fold_2026_05_15_15_51_model_3.cif chain A to #5/A with 0 mismatches 
    8442 Associated fold_2026_05_15_15_51_model_4.cif chain A to #5/A with 0 mismatches 
    8443 Associated fold_2026_06_01_00_39_model_0.cif chain A to #5/A with 0 mismatches 
    8444 Associated fold_2026_06_01_00_39_model_1.cif chain A to #5/A with 0 mismatches 
    8445 Associated fold_2026_06_01_00_39_model_2.cif chain A to #5/A with 0 mismatches 
    8446 Associated fold_2026_06_01_00_39_model_3.cif chain A to #5/A with 0 mismatches 
    8447 Associated fold_2026_06_01_00_39_model_4.cif chain A to #5/A with 0 mismatches 
    8448 Associated AlphaFold A0A9Q6ZED9 chain A to #5/A with 0 mismatches 
    8449 Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A with 0 mismatches 
    8450 Associated fold_gdp_bound_wbdp_model_1.cif chain A to #5/A with 0 mismatches 
    8451 Associated fold_gdp_bound_wbdp_model_2.cif chain A to #5/A with 0 mismatches 
    8452 Associated fold_gdp_bound_wbdp_model_3.cif chain A to #5/A with 0 mismatches 
    8453 Associated fold_gdp_bound_wbdp_model_4.cif chain A to #5/A with 0 mismatches 
    8454 Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A with 0 mismatches 
    8455 Associated fold_2026_05_15_15_51_model_0.cif chain A to #5/A with 0 mismatches 
     3195[deleted to fit within ticket limits]
     3196
    84563197[Repeated 1 time(s)]Associated fold_gdp_bound_wbdp_model_0.cif chain A to #5/A
    84573198with 0 mismatches