Changes between Initial Version and Version 1 of Ticket #16457


Ignore:
Timestamp:
Dec 12, 2024, 9:59:34 AM (12 months ago)
Author:
Eric Pettersen
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #16457

    • Property Cc chimera-programmers added
    • Property Component Unassigned → Sessions
    • Property Owner set to Greg Couch
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → assigned
    • Property Summary ChimeraX bug report submission → Session restore failed: decompression failure

  • Ticket #16457 – Description

    initial v1  
    32493249> #8,-0.84124,0.18697,-0.5073,309.25,0.53436,0.14474,-0.83277,-14.836,-0.082277,-0.97164,-0.22167,34.72
    32503250
    3251 > fitmap #8 inMap #1.2
    3252 
    3253 Fit molecule
    3254 HpyloripflB_4cab4_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb (#8) to
    3255 map HP-PflA-PflB-2.1A.mrc (#1.2) using 13645 atoms 
    3256 average map value = 2.741, steps = 180 
    3257 shifted from previous position = 21.9 
    3258 rotated from previous position = 11.2 degrees 
    3259 atoms outside contour = 5878, contour level = 0.78314 
    3260  
    3261 Position of
    3262 HpyloripflB_4cab4_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb (#8)
    3263 relative to HP-PflA-PflB-2.1A.mrc (#1.2) coordinates: 
    3264 Matrix rotation and translation 
    3265 -0.92150179 0.19288374 -0.33709094 111.18331880 
    3266 0.36424268 0.12804289 -0.92245989 8.00867933 
    3267 -0.13476540 -0.97283137 -0.18824822 -36.62916278 
    3268 Axis -0.18664195 -0.74967890 0.63493805 
    3269 Axis point 54.81507538 0.00000000 -10.31888937 
    3270 Rotation angle (degrees) 172.24476469 
    3271 Shift along axis -50.01265912 
    3272  
    3273 
    3274 > fitmap #8 inMap #1.2
    3275 
    3276 Fit molecule
    3277 HpyloripflB_4cab4_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb (#8) to
    3278 map HP-PflA-PflB-2.1A.mrc (#1.2) using 13645 atoms 
    3279 average map value = 2.741, steps = 120 
    3280 shifted from previous position = 0.00193 
    3281 rotated from previous position = 0.0173 degrees 
    3282 atoms outside contour = 5880, contour level = 0.78314 
    3283  
    3284 Position of
    3285 HpyloripflB_4cab4_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb (#8)
    3286 relative to HP-PflA-PflB-2.1A.mrc (#1.2) coordinates: 
    3287 Matrix rotation and translation 
    3288 -0.92139865 0.19310067 -0.33724865 111.18287890 
    3289 0.36444926 0.12809101 -0.92237161 8.00909646 
    3290 -0.13491205 -0.97278200 -0.18839825 -36.62878465 
    3291 Axis -0.18677990 -0.74969493 0.63487856 
    3292 Axis point 54.81382704 0.00000000 -10.31930172 
    3293 Rotation angle (degrees) 172.24450516 
    3294 Shift along axis -50.02593564 
    3295  
    3296 
    3297 > close #8
    3298 
    3299 > show #2 models
    3300 
    3301 > split #2
    3302 
    3303 Split fold_pylori_pfla_pflb_model_0.cif (#2) into 2 models 
    3304 Chain information for fold_pylori_pfla_pflb_model_0.cif A #2.1 
    3305 --- 
    3306 Chain | Description 
    3307 A | No description available 
    3308  
    3309 Chain information for fold_pylori_pfla_pflb_model_0.cif B #2.2 
    3310 --- 
    3311 Chain | Description 
    3312 B | No description available 
    3313  
    3314 
    3315 > hide #2.2 models
    3316 
    3317 > show #2.2 models
    3318 
    3319 > color #2.2 blue
    3320 
    3321 > select add #2.2
    3322 
    3323 6838 atoms, 6982 bonds, 844 residues, 1 model selected 
    3324 
    3325 > view matrix models
    3326 > #2.2,-0.52349,-0.78607,0.3287,441.45,-0.079043,-0.33932,-0.93735,88.749,0.84836,-0.51668,0.1155,131.88
    3327 
    3328 > view orient
    3329 
    3330 > select add #2.1
    3331 
    3332 13262 atoms, 13531 bonds, 1635 residues, 2 models selected 
    3333 
    3334 > view matrix models
    3335 > #2.1,-0.52349,-0.78607,0.3287,189.48,-0.079043,-0.33932,-0.93735,59.679,0.84836,-0.51668,0.1155,109.44,#2.2,-0.52349,-0.78607,0.3287,397.44,-0.079043,-0.33932,-0.93735,80.831,0.84836,-0.51668,0.1155,134.41
    3336 
    3337 > view matrix models
    3338 > #2.1,-0.45963,-0.81134,0.36121,189.78,-0.11115,-0.35096,-0.92977,56.989,0.88113,-0.4675,0.07113,116.18,#2.2,-0.45963,-0.81134,0.36121,398.34,-0.11115,-0.35096,-0.92977,83.537,0.88113,-0.4675,0.07113,126.92
    3339 
    3340 > view matrix models
    3341 > #2.1,-0.45963,-0.81134,0.36121,190.86,-0.11115,-0.35096,-0.92977,52.509,0.88113,-0.4675,0.07113,113.4,#2.2,-0.45963,-0.81134,0.36121,399.43,-0.11115,-0.35096,-0.92977,79.057,0.88113,-0.4675,0.07113,124.14
    3342 
    3343 > view matrix models
    3344 > #2.1,-0.45963,-0.81134,0.36121,191.15,-0.11115,-0.35096,-0.92977,58.876,0.88113,-0.4675,0.07113,105.18,#2.2,-0.45963,-0.81134,0.36121,399.71,-0.11115,-0.35096,-0.92977,85.424,0.88113,-0.4675,0.07113,115.92
    3345 
    3346 > view matrix models
    3347 > #2.1,-0.51826,-0.8512,-0.082782,192.38,0.098322,0.03685,-0.99447,104.57,0.84955,-0.52354,0.064594,98.777,#2.2,-0.51826,-0.8512,-0.082782,390.67,0.098322,0.03685,-0.99447,37.89,0.84955,-0.52354,0.064594,122.29
    3348 
    3349 > view matrix models
    3350 > #2.1,-0.51826,-0.8512,-0.082782,192.2,0.098322,0.03685,-0.99447,37.197,0.84955,-0.52354,0.064594,107.46,#2.2,-0.51826,-0.8512,-0.082782,390.5,0.098322,0.03685,-0.99447,-29.483,0.84955,-0.52354,0.064594,130.97
    3351 
    3352 > select clear
    3353 
    3354 > open "C:/Users/Jack Botting/Documents/alphafold
    3355 > results/fold_pylori_pflanob_pflc_flgy/fold_pylori_pflanob_pflc_flgy_model_0.cif"
    3356 
    3357 Chain information for fold_pylori_pflanob_pflc_flgy_model_0.cif #8 
    3358 --- 
    3359 Chain | Description 
    3360 A | . 
    3361 B | . 
    3362 C D | . 
    3363  
    3364 
    3365 > hide #!2 models
    3366 
    3367 > select add #8
    3368 
    3369 10870 atoms, 11060 bonds, 1340 residues, 1 model selected 
    3370 
    3371 > view matrix models #8,1,0,0,158.15,0,1,0,-73.011,0,0,1,67.312
    3372 
    3373 > view matrix models
    3374 > #8,-0.27447,-0.61292,-0.74094,165.59,0.69203,-0.6609,0.29036,-41.748,-0.66766,-0.43306,0.60556,73.191
    3375 
    3376 > view matrix models
    3377 > #8,-0.27447,-0.61292,-0.74094,181.29,0.69203,-0.6609,0.29036,-7.4341,-0.66766,-0.43306,0.60556,62.004
    3378 
    3379 > view matrix models
    3380 > #8,-0.28898,-0.6768,-0.67708,181.33,0.68329,-0.64118,0.34929,-8.6805,-0.67053,-0.3617,0.64774,60.179
    3381 
    3382 > view matrix models
    3383 > #8,-0.057524,-0.39642,-0.91627,182.33,0.028772,-0.91806,0.39539,-11.45,-0.99793,-0.0036181,0.064217,58.847
    3384 
    3385 > view matrix models
    3386 > #8,-0.057524,-0.39642,-0.91627,161.09,0.028772,-0.91806,0.39539,-5.1111,-0.99793,-0.0036181,0.064217,56.584
    3387 
    3388 > view matrix models
    3389 > #8,-0.057524,-0.39642,-0.91627,161.28,0.028772,-0.91806,0.39539,-9.74,-0.99793,-0.0036181,0.064217,56.41
    3390 
    3391 > view matrix models
    3392 > #8,-0.057524,-0.39642,-0.91627,163.28,0.028772,-0.91806,0.39539,-7.9025,-0.99793,-0.0036181,0.064217,49.2
    3393 
    3394 > view matrix models
    3395 > #8,-0.031343,-0.16412,-0.98594,160.59,-0.033496,-0.9857,0.16514,-4.1959,-0.99895,0.038201,0.025398,49.023
    3396 
    3397 > view matrix models
    3398 > #8,-0.20143,0.098503,-0.97454,154.22,-0.2213,-0.97378,-0.052687,-3.3154,-0.95418,0.20505,0.21795,43.981
    3399 
    3400 > view matrix models
    3401 > #8,-0.20143,0.098503,-0.97454,163.38,-0.2213,-0.97378,-0.052687,-1.2369,-0.95418,0.20505,0.21795,48.39
    3402 
    3403 > view matrix models
    3404 > #8,-0.33179,0.08528,-0.93949,161.76,-0.10075,-0.99341,-0.054594,0.37659,-0.93796,0.076541,0.33819,49.057
    3405 
    3406 > view matrix models
    3407 > #8,-0.33179,0.08528,-0.93949,166.1,-0.10075,-0.99341,-0.054594,2.6668,-0.93796,0.076541,0.33819,50.041
    3408 
    3409 > view matrix models
    3410 > #8,-0.28587,0.019868,-0.95806,167.95,-0.041422,-0.99911,-0.0083591,2.736,-0.95737,0.037295,0.28644,51.224
    3411 
    3412 > fitmap #8 inMap #1.2
    3413 
    3414 Fit molecule fold_pylori_pflanob_pflc_flgy_model_0.cif (#8) to map HP-PflA-
    3415 PflB-2.1A.mrc (#1.2) using 10870 atoms 
    3416 average map value = 1.073, steps = 276 
    3417 shifted from previous position = 36.4 
    3418 rotated from previous position = 25.3 degrees 
    3419 atoms outside contour = 8297, contour level = 0.78314 
    3420  
    3421 Position of fold_pylori_pflanob_pflc_flgy_model_0.cif (#8) relative to HP-
    3422 PflA-PflB-2.1A.mrc (#1.2) coordinates: 
    3423 Matrix rotation and translation 
    3424 -0.05996141 -0.25908761 -0.96399080 -20.57711302 
    3425 -0.24506312 -0.93235181 0.26582736 36.34047063 
    3426 -0.96765113 0.25217797 -0.00758769 -18.26006028 
    3427 Axis -0.68556995 0.18384827 0.70441015 
    3428 Axis point -19.29764091 20.49963346 0.00000000 
    3429 Rotation angle (degrees) 179.42962414 
    3430 Shift along axis 7.92561143 
    3431  
    3432 
    3433 > view matrix models
    3434 > #8,-0.059961,-0.25909,-0.96399,196.77,-0.24506,-0.93235,0.26583,-2.5626,-0.96765,0.25218,-0.0075877,50.483
    3435 
    3436 > view matrix models
    3437 > #8,-0.059961,-0.25909,-0.96399,160.39,-0.24506,-0.93235,0.26583,-10.563,-0.96765,0.25218,-0.0075877,49.163
    3438 
    3439 > show #!4 models
    3440 
    3441 > hide #!1.2 models
    3442 
    3443 > select #4.104
    3444 
    3445 1 model selected 
    3446 
    3447 > select add #4.28
    3448 
    3449 2 models selected 
    3450 Region has 13 adjacent regions 
    3451 
    3452 > select clear
    3453 
    3454 > show #!1.2 models
    3455 
    3456 > select #4.90
    3457 
    3458 1 model selected 
    3459 
    3460 > select add #4.141
    3461 
    3462 2 models selected 
    3463 
    3464 > select clear
    3465 
    3466 > select #4.86
    3467 
    3468 1 model selected 
    3469 
    3470 > select clear
    3471 
    3472 > hide #!1.2 models
    3473 
    3474 > show #!2 models
    3475 
    3476 > select add #2.2
    3477 
    3478 6838 atoms, 6982 bonds, 844 residues, 1 model selected 
    3479 
    3480 > hide #2.1 models
    3481 
    3482 > view matrix models
    3483 > #2.2,-0.51826,-0.8512,-0.082782,354.56,0.098322,0.03685,-0.99447,-9.004,0.84955,-0.52354,0.064594,140.23
    3484 
    3485 > view matrix models
    3486 > #2.2,-0.51826,-0.8512,-0.082782,339.3,0.098322,0.03685,-0.99447,23.329,0.84955,-0.52354,0.064594,0.18441
    3487 
    3488 > view matrix models
    3489 > #2.2,-0.51826,-0.8512,-0.082782,303.88,0.098322,0.03685,-0.99447,23.934,0.84955,-0.52354,0.064594,-5.5463
    3490 
    3491 > view matrix models
    3492 > #2.2,-0.2848,-0.95285,-0.10473,300.45,-0.64725,0.27174,-0.7122,37.798,0.70708,-0.13505,-0.69412,-14.044
    3493 
    3494 > select clear
    3495 
    3496 > select #4.46
    3497 
    3498 1 model selected 
    3499 
    3500 > select add #4.50
    3501 
    3502 2 models selected 
    3503 
    3504 > select add #4.28
    3505 
    3506 3 models selected 
    3507 
    3508 > select add #4.104
    3509 
    3510 4 models selected 
    3511 
    3512 > select add #4.31
    3513 
    3514 5 models selected 
    3515 
    3516 > select add #4.12
    3517 
    3518 6 models selected 
    3519 
    3520 > select add #4.126
    3521 
    3522 7 models selected 
    3523 
    3524 > select add #4.66
    3525 
    3526 8 models selected 
    3527 
    3528 > select clear
    3529 
    3530 > select #4.62
    3531 
    3532 1 model selected 
    3533 
    3534 > select add #4.228
    3535 
    3536 2 models selected 
    3537 
    3538 > select add #4.261
    3539 
    3540 3 models selected 
    3541 
    3542 > select clear
    3543 
    3544 > select add #2.2
    3545 
    3546 6838 atoms, 6982 bonds, 844 residues, 1 model selected 
    3547 
    3548 > view matrix models
    3549 > #2.2,-0.2848,-0.95285,-0.10473,294.39,-0.64725,0.27174,-0.7122,36.123,0.70708,-0.13505,-0.69412,-14.728
    3550 
    3551 > view matrix models
    3552 > #2.2,-0.2848,-0.95285,-0.10473,291.95,-0.64725,0.27174,-0.7122,37.261,0.70708,-0.13505,-0.69412,14.333
    3553 
    3554 > view matrix models
    3555 > #2.2,0.82698,-0.26986,0.49323,319.88,-0.44589,-0.84917,0.283,33.917,0.34246,-0.45396,-0.82258,4.5328
    3556 
    3557 > view matrix models
    3558 > #2.2,0.82698,-0.26986,0.49323,278.14,-0.44589,-0.84917,0.283,45.567,0.34246,-0.45396,-0.82258,19.687
    3559 
    3560 > view matrix models
    3561 > #2.2,0.82698,-0.26986,0.49323,278.02,-0.44589,-0.84917,0.283,44.078,0.34246,-0.45396,-0.82258,20.378
    3562 
    3563 > view matrix models
    3564 > #2.2,0.82698,-0.26986,0.49323,277.26,-0.44589,-0.84917,0.283,43.474,0.34246,-0.45396,-0.82258,19.847
    3565 
    3566 > select clear
    3567 
    3568 > hide #!4 models
    3569 
    3570 > hide #2.2:1-137
    3571 
    3572 > hide #2.2:1-137 cartoons
    3573 
    3574 > show #!1.2 models
    3575 
    3576 > fitmap #2.2 inMap #1.2
    3577 
    3578 Fit molecule fold_pylori_pfla_pflb_model_0.cif B (#2.2) to map HP-PflA-
    3579 PflB-2.1A.mrc (#1.2) using 6838 atoms 
    3580 average map value = 3.316, steps = 96 
    3581 shifted from previous position = 12.2 
    3582 rotated from previous position = 12.6 degrees 
    3583 atoms outside contour = 2362, contour level = 0.78314 
    3584  
    3585 Position of fold_pylori_pfla_pflb_model_0.cif B (#2.2) relative to HP-PflA-
    3586 PflB-2.1A.mrc (#1.2) coordinates: 
    3587 Matrix rotation and translation 
    3588 0.72134562 -0.34120996 0.60269087 64.14730073 
    3589 -0.48947677 -0.86681514 0.09510009 36.86395482 
    3590 0.48997247 -0.36360321 -0.79228765 -49.34849803 
    3591 Axis -0.92653683 0.22768040 -0.29948477 
    3592 Axis point 0.00000000 22.22858053 -38.10267412 
    3593 Rotation angle (degrees) 165.66821959 
    3594 Shift along axis -36.26251320 
    3595  
    3596 
    3597 > select #8:1-275
    3598 
    3599 7645 atoms, 7771 bonds, 948 residues, 1 model selected 
    3600 
    3601 > select #8:1-276
    3602 
    3603 7663 atoms, 7790 bonds, 950 residues, 1 model selected 
    3604 
    3605 > view matrix models
    3606 > #8,-0.081803,-0.39746,-0.91397,161.81,-0.42733,-0.81448,0.39244,-16.22,-0.90039,0.42267,-0.10322,48.311
    3607 
    3608 > undo
    3609 
    3610 > ui mousemode right "translate selected atoms"
    3611 
    3612 > undo
    3613 
    3614 > select clear
    3615 
    3616 > select #8:1-276
    3617 
    3618 7663 atoms, 7790 bonds, 950 residues, 1 model selected 
    3619 
    3620 > show #2.1 models
    3621 
    3622 > hide #8 models
    3623 
    3624 > select add #2.1
    3625 
    3626 14087 atoms, 14339 bonds, 1741 residues, 2 models selected 
    3627 
    3628 > select clear
    3629 
    3630 > select #2.1/A:720
    3631 
    3632 8 atoms, 7 bonds, 1 residue, 1 model selected 
    3633 
    3634 > select up
    3635 
    3636 97 atoms, 97 bonds, 12 residues, 1 model selected 
    3637 
    3638 > select up
    3639 
    3640 6424 atoms, 6549 bonds, 791 residues, 1 model selected 
    3641 
    3642 > select up
    3643 
    3644 13262 atoms, 13531 bonds, 1635 residues, 2 models selected 
    3645 
    3646 > select down
    3647 
    3648 6424 atoms, 6549 bonds, 791 residues, 1 model selected 
    3649 
    3650 > ui mousemode right "map eraser"
    3651 
    3652 > volume erase #1.2 center 238.91,8.9647,40.719 radius 119.7 outside true
    3653 
    3654 Opened HP-PflA-PflB-2.1A.mrc copy as #10, grid size 240,240,240, pixel 2.14,
    3655 shown at step 1, values float32 
    3656 
    3657 > ui mousemode right "translate selected models"
    3658 
    3659 > view matrix models
    3660 > #2.1,0.22265,-0.97427,-0.035071,211.1,0.21968,0.085187,-0.97185,38.401,0.94982,0.20868,0.233,89.342
    3661 
    3662 > view matrix models
    3663 > #2.1,0.22265,-0.97427,-0.035071,225.87,0.21968,0.085187,-0.97185,40.116,0.94982,0.20868,0.233,83.644
    3664 
    3665 > view matrix models
    3666 > #2.1,0.28295,-0.85523,-0.43419,217.62,0.14836,0.48626,-0.86113,27.999,0.94759,0.17924,0.26447,84.959
    3667 
    3668 > view matrix models
    3669 > #2.1,0.28295,-0.85523,-0.43419,240.58,0.14836,0.48626,-0.86113,31.095,0.94759,0.17924,0.26447,82.712
    3670 
    3671 > view matrix models
    3672 > #2.1,0.30516,-0.84748,-0.43434,240.77,0.090483,0.47983,-0.87268,29.999,0.94799,0.22701,0.22311,80.654
    3673 
    3674 > fitmap #2.1 inMap #1.2
    3675 
    3676 Fit molecule fold_pylori_pfla_pflb_model_0.cif A (#2.1) to map HP-PflA-
    3677 PflB-2.1A.mrc (#1.2) using 6424 atoms 
    3678 average map value = 3.025, steps = 108 
    3679 shifted from previous position = 12.2 
    3680 rotated from previous position = 18 degrees 
    3681 atoms outside contour = 2660, contour level = 0.78314 
    3682  
    3683 Position of fold_pylori_pfla_pflb_model_0.cif A (#2.1) relative to HP-PflA-
    3684 PflB-2.1A.mrc (#1.2) coordinates: 
    3685 Matrix rotation and translation 
    3686 0.11845427 -0.79763237 -0.59139765 13.21575514 
    3687 -0.13127716 0.57778284 -0.80556396 21.63069805 
    3688 0.98424331 0.17305950 -0.03627007 6.60123598 
    3689 Axis 0.49654076 -0.79945964 0.33809993 
    3690 Axis point 8.33436068 0.00000000 17.05899800 
    3691 Rotation angle (degrees) 99.78877722 
    3692 Shift along axis -8.49883154 
    3693  
    3694 
    3695 > view matrix models
    3696 > #2.1,0.11845,-0.79763,-0.5914,227.47,-0.13128,0.57778,-0.80556,18.659,0.98424,0.17306,-0.03627,74.679
    3697 
    3698 > show #!1.2 models
    3699 
    3700 > hide #!10 models
    3701 
    3702 > hide #!1.2 models
    3703 
    3704 > show #!10 models
    3705 
    3706 > show #8 models
    3707 
    3708 > mmaker #8 to #2.1
    3709 
    3710 Parameters 
    3711 --- 
    3712 Chain pairing | bb 
    3713 Alignment algorithm | Needleman-Wunsch 
    3714 Similarity matrix | BLOSUM-62 
    3715 SS fraction | 0.3 
    3716 Gap open (HH/SS/other) | 18/18/6 
    3717 Gap extend | 1 
    3718 SS matrix |  |  | H | S | O 
    3719 ---|---|---|--- 
    3720 H | 6 | -9 | -6 
    3721 S |  | 6 | -6 
    3722 O |  |  | 4 
    3723 Iteration cutoff | 2 
    3724  
    3725 Matchmaker fold_pylori_pfla_pflb_model_0.cif A, chain A (#2.1) with
    3726 fold_pylori_pflanob_pflc_flgy_model_0.cif, chain A (#8), sequence alignment
    3727 score = 3176.4 
    3728 RMSD between 188 pruned atom pairs is 0.565 angstroms; (across all 611 pairs:
    3729 11.355) 
    3730  
    3731 
    3732 > fitmap #8 inMap #10
    3733 
    3734 Fit molecule fold_pylori_pflanob_pflc_flgy_model_0.cif (#8) to map HP-PflA-
    3735 PflB-2.1A.mrc copy (#10) using 10870 atoms 
    3736 average map value = 1.325, steps = 448 
    3737 shifted from previous position = 5.63 
    3738 rotated from previous position = 12.7 degrees 
    3739 atoms outside contour = 7827, contour level = 0.78314 
    3740  
    3741 Position of fold_pylori_pflanob_pflc_flgy_model_0.cif (#8) relative to HP-
    3742 PflA-PflB-2.1A.mrc copy (#10) coordinates: 
    3743 Matrix rotation and translation 
    3744 -0.73780364 -0.29797262 -0.60568814 -40.97742596 
    3745 -0.67013134 0.43107792 0.60423160 58.29804599 
    3746 0.08105431 0.85169487 -0.51773165 -26.16309988 
    3747 Axis 0.30201917 -0.83814211 -0.45420505 
    3748 Axis point -3.77609840 0.00000000 -32.21009413 
    3749 Rotation angle (degrees) 155.81517811 
    3750 Shift along axis -49.35460328 
    3751  
    3752 
    3753 > hide #8 models
    3754 
    3755 > open "C:/Users/Jack Botting/Documents/alphafold
    3756 > results/flgY/fold_campy_flgy_pfla_nosig/fold_campy_flgy_pfla_nosig_model_0.cif"
    3757 
    3758 Chain information for fold_campy_flgy_pfla_nosig_model_0.cif #11 
    3759 --- 
    3760 Chain | Description 
    3761 A B | . 
    3762 C | . 
    3763  
    3764 
    3765 > select clear
    3766 
    3767 > mmaker #11 to #2.1
    3768 
    3769 Parameters 
    3770 --- 
    3771 Chain pairing | bb 
    3772 Alignment algorithm | Needleman-Wunsch 
    3773 Similarity matrix | BLOSUM-62 
    3774 SS fraction | 0.3 
    3775 Gap open (HH/SS/other) | 18/18/6 
    3776 Gap extend | 1 
    3777 SS matrix |  |  | H | S | O 
    3778 ---|---|---|--- 
    3779 H | 6 | -9 | -6 
    3780 S |  | 6 | -6 
    3781 O |  |  | 4 
    3782 Iteration cutoff | 2 
    3783  
    3784 Matchmaker fold_pylori_pfla_pflb_model_0.cif A, chain A (#2.1) with
    3785 fold_campy_flgy_pfla_nosig_model_0.cif, chain C (#11), sequence alignment
    3786 score = 1295.3 
    3787 RMSD between 75 pruned atom pairs is 1.084 angstroms; (across all 744 pairs:
    3788 42.656) 
    3789  
    3790 
    3791 > hide #11 models
    3792 
    3793 > open "C:/Users/Jack Botting/Documents/alphafold
    3794 > results/flgY/fold_pylori_flgy_pfla_nosig/fold_pylori_flgy_pfla_nosig_model_4.cif"
    3795 
    3796 Chain information for fold_pylori_flgy_pfla_nosig_model_4.cif #12 
    3797 --- 
    3798 Chain | Description 
    3799 A B | . 
    3800 C | . 
    3801  
    3802 
    3803 > open "C:/Users/Jack Botting/Documents/alphafold
    3804 > results/flgY/fold_pylori_flgy_pfla_nosig/fold_pylori_flgy_pfla_nosig_model_0.cif"
    3805 
    3806 Chain information for fold_pylori_flgy_pfla_nosig_model_0.cif #13 
    3807 --- 
    3808 Chain | Description 
    3809 A B | . 
    3810 C | . 
    3811  
    3812 
    3813 > open "C:/Users/Jack Botting/Documents/alphafold
    3814 > results/flgY/fold_pylori_flgy_pfla_nosig/fold_pylori_flgy_pfla_nosig_model_1.cif"
    3815 
    3816 Chain information for fold_pylori_flgy_pfla_nosig_model_1.cif #14 
    3817 --- 
    3818 Chain | Description 
    3819 A B | . 
    3820 C | . 
    3821  
    3822 
    3823 > open "C:/Users/Jack Botting/Documents/alphafold
    3824 > results/flgY/fold_pylori_flgy_pfla_nosig/fold_pylori_flgy_pfla_nosig_model_2.cif"
    3825 
    3826 Chain information for fold_pylori_flgy_pfla_nosig_model_2.cif #15 
    3827 --- 
    3828 Chain | Description 
    3829 A B | . 
    3830 C | . 
    3831  
    3832 
    3833 > open "C:/Users/Jack Botting/Documents/alphafold
    3834 > results/flgY/fold_pylori_flgy_pfla_nosig/fold_pylori_flgy_pfla_nosig_model_3.cif"
    3835 
    3836 Chain information for fold_pylori_flgy_pfla_nosig_model_3.cif #16 
    3837 --- 
    3838 Chain | Description 
    3839 A B | . 
    3840 C | . 
    3841  
    3842 
    3843 > mmaker #13-16 to #12
    3844 
    3845 Parameters 
    3846 --- 
    3847 Chain pairing | bb 
    3848 Alignment algorithm | Needleman-Wunsch 
    3849 Similarity matrix | BLOSUM-62 
    3850 SS fraction | 0.3 
    3851 Gap open (HH/SS/other) | 18/18/6 
    3852 Gap extend | 1 
    3853 SS matrix |  |  | H | S | O 
    3854 ---|---|---|--- 
    3855 H | 6 | -9 | -6 
    3856 S |  | 6 | -6 
    3857 O |  |  | 4 
    3858 Iteration cutoff | 2 
    3859  
    3860 Matchmaker fold_pylori_flgy_pfla_nosig_model_4.cif, chain C (#12) with
    3861 fold_pylori_flgy_pfla_nosig_model_0.cif, chain C (#13), sequence alignment
    3862 score = 4040 
    3863 RMSD between 606 pruned atom pairs is 1.093 angstroms; (across all 781 pairs:
    3864 7.682) 
    3865  
    3866 Matchmaker fold_pylori_flgy_pfla_nosig_model_4.cif, chain C (#12) with
    3867 fold_pylori_flgy_pfla_nosig_model_1.cif, chain C (#14), sequence alignment
    3868 score = 4023.2 
    3869 RMSD between 546 pruned atom pairs is 0.909 angstroms; (across all 781 pairs:
    3870 20.883) 
    3871  
    3872 Matchmaker fold_pylori_flgy_pfla_nosig_model_4.cif, chain C (#12) with
    3873 fold_pylori_flgy_pfla_nosig_model_2.cif, chain C (#15), sequence alignment
    3874 score = 4033.4 
    3875 RMSD between 390 pruned atom pairs is 1.016 angstroms; (across all 781 pairs:
    3876 15.670) 
    3877  
    3878 Matchmaker fold_pylori_flgy_pfla_nosig_model_4.cif, chain C (#12) with
    3879 fold_pylori_flgy_pfla_nosig_model_3.cif, chain C (#16), sequence alignment
    3880 score = 4035.2 
    3881 RMSD between 425 pruned atom pairs is 0.845 angstroms; (across all 781 pairs:
    3882 26.988) 
    3883  
    3884 
    3885 > mmaker #12-16 to #2.1
    3886 
    3887 Parameters 
    3888 --- 
    3889 Chain pairing | bb 
    3890 Alignment algorithm | Needleman-Wunsch 
    3891 Similarity matrix | BLOSUM-62 
    3892 SS fraction | 0.3 
    3893 Gap open (HH/SS/other) | 18/18/6 
    3894 Gap extend | 1 
    3895 SS matrix |  |  | H | S | O 
    3896 ---|---|---|--- 
    3897 H | 6 | -9 | -6 
    3898 S |  | 6 | -6 
    3899 O |  |  | 4 
    3900 Iteration cutoff | 2 
    3901  
    3902 Matchmaker fold_pylori_pfla_pflb_model_0.cif A, chain A (#2.1) with
    3903 fold_pylori_flgy_pfla_nosig_model_4.cif, chain C (#12), sequence alignment
    3904 score = 4005.2 
    3905 RMSD between 146 pruned atom pairs is 1.357 angstroms; (across all 781 pairs:
    3906 31.332) 
    3907  
    3908 Matchmaker fold_pylori_pfla_pflb_model_0.cif A, chain A (#2.1) with
    3909 fold_pylori_flgy_pfla_nosig_model_0.cif, chain C (#13), sequence alignment
    3910 score = 4008.2 
    3911 RMSD between 229 pruned atom pairs is 0.623 angstroms; (across all 781 pairs:
    3912 35.568) 
    3913  
    3914 Matchmaker fold_pylori_pfla_pflb_model_0.cif A, chain A (#2.1) with
    3915 fold_pylori_flgy_pfla_nosig_model_1.cif, chain C (#14), sequence alignment
    3916 score = 4004.6 
    3917 RMSD between 116 pruned atom pairs is 0.461 angstroms; (across all 781 pairs:
    3918 23.485) 
    3919  
    3920 Matchmaker fold_pylori_pfla_pflb_model_0.cif A, chain A (#2.1) with
    3921 fold_pylori_flgy_pfla_nosig_model_2.cif, chain C (#15), sequence alignment
    3922 score = 4001.6 
    3923 RMSD between 269 pruned atom pairs is 0.619 angstroms; (across all 781 pairs:
    3924 20.809) 
    3925  
    3926 Matchmaker fold_pylori_pfla_pflb_model_0.cif A, chain A (#2.1) with
    3927 fold_pylori_flgy_pfla_nosig_model_3.cif, chain C (#16), sequence alignment
    3928 score = 4003.4 
    3929 RMSD between 186 pruned atom pairs is 0.631 angstroms; (across all 781 pairs:
    3930 25.936) 
    3931  
    3932 
    3933 > close #12-16
    3934 
    3935 > show #11 models
    3936 
    3937 > hide #11 models
    3938 
    3939 > hide #!1 models
    3940 
    3941 > show #!1.1 models
    3942 
    3943 > hide #!1 models
    3944 
    3945 > hide #!1.1 models
    3946 
    3947 > show #!1.2 models
    3948 
    3949 > hide #!10 models
    3950 
    3951 > view orient
    3952 
    3953 > show #!1.1 models
    3954 
    3955 > select add #1.1
    3956 
    3957 2 models selected 
    3958 
    3959 > show #!5 models
    3960 
    3961 > hide #!5 models
    3962 
    3963 > show #!7 models
    3964 
    3965 > select add #7
    3966 
    3967 171450 atoms, 174330 bonds, 21222 residues, 75 models selected 
    3968 
    3969 > view orient
    3970 
    3971 > view matrix models
    3972 > #7,1,0,0,-40.839,0,1,0,-3.0251,0,0,1,0,#1.1,1,0,0,-40.839,0,1,0,-3.0251,0,0,1,0
    3973 
    3974 > view matrix models
    3975 > #7,1,0,0,-41.712,0,1,0,-3.6426,0,0,1,-18.652,#1.1,1,0,0,-41.712,0,1,0,-3.6426,0,0,1,-18.652
    3976 
    3977 > ui tool show "Side View"
    3978 
    3979 > view orient
    3980 
    3981 > view matrix models
    3982 > #7,-0.96983,-0.24379,0,-41.379,0.24379,-0.96983,0,-6.9085,0,0,1,-18.652,#1.1,-0.96983,-0.24379,0,-41.379,0.24379,-0.96983,0,-6.9085,0,0,1,-18.652
    3983 
    3984 > undo
    3985 
    3986 > view orient
    3987 
    3988 > select clear
    3989 
    3990 > syn #2 C18 center #1.1
    3991 
    3992 Unknown command: syn #2 C18 center #1.1 
    3993 
    3994 > sym #2 C18 center #1.1
    3995 
    3996 Made 18 graphical clones for fold_pylori_pfla_pflb_model_0.cif A,
    3997 fold_pylori_pfla_pflb_model_0.cif B symmetry C18 
    3998 
    3999 > hide #!7 models
    4000 
    4001 > show #!7 models
    4002 
    4003 > rename #7 FlgY
    4004 
    4005 > rename #6 pflC
    4006 
    4007 > rename #2.1 pflA
    4008 
    4009 > rename #2.2 pflB
    4010 
    4011 > show #!3 models
    4012 
    4013 > hide #!3 models
    4014 
    4015 > show #!3 models
    4016 
    4017 > select add #3
    4018 
    4019 112125 atoms, 113781 bonds, 14157 residues, 82 models selected 
    4020 
    4021 > view orient
    4022 
    4023 > view matrix models #3,1,0,0,-36.359,0,1,0,0.75258,0,0,1,97.215
    4024 
    4025 > view matrix models #3,1,0,0,-38.617,0,1,0,0.75258,0,0,1,97.215
    4026 
    4027 > hide #!1.2 models
    4028 
    4029 > view matrix models #3,1,0,0,-39.37,0,1,0,-1.5052,0,0,1,97.215
    4030 
    4031 > select clear
    4032 
    4033 > view orient
    4034 
    4035 > hide #!1.1 models
    4036 
    4037 > show #!1.2 models
    4038 
    4039 > sym clear #2.1
    4040 
    4041 > sym #2.1 C18 center #1.1 copies true
    4042 
    4043 Made 18 copies for pflA symmetry C18 
    4044 
    4045 > rename #9 "pflA no FlgY"
    4046 
    4047 > hide #!1 models
    4048 
    4049 > rename #1 maps
    4050 
    4051 > hide #9.1-18 target m
    4052 
    4053 > show #9.18 models
    4054 
    4055 > show #9.17 models
    4056 
    4057 > hide #9.17 models
    4058 
    4059 > show #9.14 models
    4060 
    4061 > show #9.10 models
    4062 
    4063 > show #9.7 models
    4064 
    4065 > show #9.3 models
    4066 
    4067 > close #9.1-2,4-6,8-9,11-13,15-17
    4068 
    4069 > show #2.1 models
    4070 
    4071 > hide #!9 models
    4072 
    4073 > show #!1 models
    4074 
    4075 > hide #!7 models
    4076 
    4077 > hide #!1 models
    4078 
    4079 > select # 2.1 1-580
    4080 
    4081 Expected a keyword 
    4082 
    4083 > select # 2.1:1-580
    4084 
    4085 4671 atoms, 4761 bonds, 580 residues, 1 model selected 
    4086 
    4087 > select clear
    4088 
    4089 > select # 2.1:580-end
    4090 
    4091 1758 atoms, 1792 bonds, 212 residues, 1 model selected 
    4092 
    4093 > show #!1 models
    4094 
    4095 > view matrix models
    4096 > #2.1,0.12292,-0.74376,-0.65705,224.95,-0.3617,0.58296,-0.72755,15.14,0.92415,0.32709,-0.19736,66.449
    4097 
    4098 > undo
    4099 
    4100 > ui mousemode right "translate selected atoms"
    4101 
    4102 > select clear
    4103 
    4104 > select # 2.1:580-end
    4105 
    4106 1758 atoms, 1792 bonds, 212 residues, 1 model selected 
    4107 
    4108 > select clear
    4109 
    4110 > hide #!1 models
    4111 
    4112 > select #2.1/A:581
    4113 
    4114 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4115 
    4116 > select clear
    4117 
    4118 > select #2.1/A:581
    4119 
    4120 9 atoms, 8 bonds, 1 residue, 1 model selected 
    4121 
    4122 > select #2.1/A:580
    4123 
    4124 5 atoms, 4 bonds, 1 residue, 1 model selected 
    4125 
    4126 > select clear
    4127 
    4128 > show #!1 models
    4129 
    4130 > view orient
    4131 
    4132 > sym #2.1 C18 center #1.1 copies true
    4133 
    4134 Made 18 copies for pflA symmetry C18 
    4135 
    4136 > rename #12 "pflA FlgY"
    4137 
    4138 > show #!9 models
    4139 
    4140 > hide #!1 models
    4141 
    4142 > hide #!3 models
    4143 
    4144 > close #12.3,7,10,14,18
    4145 
    4146 > rename #12.1 id #9.1
    4147 
    4148 > rename #12.2 id #9.2
    4149 
    4150 > rename #12.4 id #9.4
    4151 
    4152 > rename #12.5 id #9.5
    4153 
    4154 > rename #12.6 id #9.6
    4155 
    4156 > rename #12.8 id #9.8
    4157 
    4158 > rename #12.9 id #9.9
    4159 
    4160 > rename #12.11 id #9.11
    4161 
    4162 > rename #12.12 id #9.12
    4163 
    4164 > rename #12.13 id #9.13
    4165 
    4166 > rename #12.15 id #9.15
    4167 
    4168 > rename #12.16 id #9.16
    4169 
    4170 > rename #12.17 id #9.17
    4171 
    4172 > close #12
    4173 
    4174 > rename #9 "pflA "
    4175 
    4176 > show #!7 models
    4177 
    4178 > save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
    4179 > pflA pflB.cxs"
    4180 
    4181 ——— End of log from Mon Jun 3 14:11:08 2024 ———
    4182 
    4183 opened ChimeraX session 
    4184 Showing HP-PflA-PflB-2.1A.seg - 283 regions, 283 surfaces 
    4185 
    4186 > color #2.2 mediumslateblue
    4187 
    4188 > color #2.1 #ff5500ff
    4189 
    4190 > color #9 #ff5500ff models
    4191 
    4192 > color #7 deeppink models
    4193 
    4194 > hide #!4 models
    4195 
    4196 > save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
    4197 > pflA pflB.cxs"
    4198 
    4199 > select #7.1.1:116-end
    4200 
    4201 643 atoms, 657 bonds, 84 residues, 1 model selected 
    4202 
    4203 > select #7.1.1-2:116-end
    4204 
    4205 1286 atoms, 1314 bonds, 168 residues, 2 models selected 
    4206 
    4207 > view orient
    4208 
    4209 > undo
    4210 
    4211 [Repeated 1 time(s)]
    4212 
    4213 > select #7.1.1:116-end, #7.1.2:102-end
    4214 
    4215 Expected an objects specifier or a keyword 
    4216 
    4217 > select #7.1.1:116-end
    4218 
    4219 643 atoms, 657 bonds, 84 residues, 1 model selected 
    4220 
    4221 > select #7.1.2:102-end
    4222 
    4223 752 atoms, 767 bonds, 98 residues, 1 model selected 
    4224 
    4225 > select #7.1.1-2:116-end
    4226 
    4227 1286 atoms, 1314 bonds, 168 residues, 2 models selected 
    4228 
    4229 > select add #7.1.2/B:115
    4230 
    4231 1295 atoms, 1322 bonds, 169 residues, 2 models selected 
    4232 
    4233 > select add #7.1.2/B:114
    4234 
    4235 1303 atoms, 1329 bonds, 170 residues, 2 models selected 
    4236 
    4237 > select add #7.1.2/B:113
    4238 
    4239 1312 atoms, 1337 bonds, 171 residues, 2 models selected 
    4240 
    4241 > select add #7.1.2/B:112
    4242 
    4243 1318 atoms, 1342 bonds, 172 residues, 2 models selected 
    4244 
    4245 > select add #7.1.2/B:111
    4246 
    4247 1330 atoms, 1354 bonds, 173 residues, 2 models selected 
    4248 
    4249 > select add #7.1.2/B:110
    4250 
    4251 1337 atoms, 1360 bonds, 174 residues, 2 models selected 
    4252 
    4253 > select add #7.1.2/B:109
    4254 
    4255 1346 atoms, 1368 bonds, 175 residues, 2 models selected 
    4256 
    4257 > select add #7.1.2/B:108
    4258 
    4259 1350 atoms, 1371 bonds, 176 residues, 2 models selected 
    4260 
    4261 > select add #7.1.2/B:107
    4262 
    4263 1358 atoms, 1378 bonds, 177 residues, 2 models selected 
    4264 
    4265 > select add #7.1.2/B:106
    4266 
    4267 1367 atoms, 1386 bonds, 178 residues, 2 models selected 
    4268 
    4269 > select add #7.1.2/B:105
    4270 
    4271 1373 atoms, 1391 bonds, 179 residues, 2 models selected 
    4272 
    4273 > select add #7.1.2/B:104
    4274 
    4275 1381 atoms, 1398 bonds, 180 residues, 2 models selected 
    4276 
    4277 > select add #7.1.2/B:103
    4278 
    4279 1390 atoms, 1406 bonds, 181 residues, 2 models selected 
    4280 
    4281 > select add #7.1.2/B:102
    4282 
    4283 1395 atoms, 1410 bonds, 182 residues, 2 models selected 
    4284 
    4285 > view orient
    4286 
    4287 > select clear
    4288 
    4289 > view orient
    4290 
    4291 [Repeated 1 time(s)]
    4292 
    4293 > save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
    4294 > pflA pflB.cxs"
    4295 
    4296 ——— End of log from Mon Jun 3 14:21:22 2024 ———
    4297 
    4298 opened ChimeraX session 
    4299 Showing HP-PflA-PflB-2.1A.seg - 283 regions, 283 surfaces 
    4300 
    4301 > hide #!4 models
    4302 
    4303 > select #7.12.1-2:114-end
    4304 
    4305 1320 atoms, 1348 bonds, 172 residues, 2 models selected 
    4306 
    4307 > select add #7.12.2/B:113
    4308 
    4309 1329 atoms, 1356 bonds, 173 residues, 2 models selected 
    4310 
    4311 > select add #7.12.2/B:111
    4312 
    4313 1341 atoms, 1368 bonds, 174 residues, 2 models selected 
    4314 
    4315 > select add #7.12.2/B:112
    4316 
    4317 1347 atoms, 1373 bonds, 175 residues, 2 models selected 
    4318 
    4319 > select add #7.12.2/B:110
    4320 
    4321 1354 atoms, 1379 bonds, 176 residues, 2 models selected 
    4322 
    4323 > select subtract #7.12.2/B:110
    4324 
    4325 1347 atoms, 1373 bonds, 175 residues, 2 models selected 
    4326 
    4327 > select add #7.12.2/B:109
    4328 
    4329 1356 atoms, 1381 bonds, 176 residues, 2 models selected 
    4330 
    4331 > select add #7.12.2/B:110
    4332 
    4333 1363 atoms, 1387 bonds, 177 residues, 2 models selected 
    4334 
    4335 > select add #7.12.2/B:107
    4336 
    4337 1371 atoms, 1394 bonds, 178 residues, 2 models selected 
    4338 
    4339 > select add #7.12.2/B:108
    4340 
    4341 1375 atoms, 1397 bonds, 179 residues, 2 models selected 
    4342 
    4343 > select add #7.12.2/B:106
    4344 
    4345 1384 atoms, 1405 bonds, 180 residues, 2 models selected 
    4346 
    4347 > select add #7.12.2/B:105
    4348 
    4349 1390 atoms, 1410 bonds, 181 residues, 2 models selected 
    4350 
    4351 > view orient
    4352 
    4353 > select clear
    4354 
    4355 > view orient
    4356 
    4357 > select #9.*:1-180
    4358 
    4359 25848 atoms, 26424 bonds, 3240 residues, 18 models selected 
    4360 
    4361 > split sel
    4362 
    4363 Did not split pflA, has only one piece 
    4364 [Repeated 17 time(s)]
    4365 
    4366 > split #9.* atoms :180-end
    4367 
    4368 Split pflA (#9.1) into 2 models 
    4369 Split pflA (#9.2) into 2 models 
    4370 Split pflA (#9.3) into 2 models 
    4371 Split pflA (#9.4) into 2 models 
    4372 Split pflA (#9.5) into 2 models 
    4373 Split pflA (#9.6) into 2 models 
    4374 Split pflA (#9.7) into 2 models 
    4375 Split pflA (#9.8) into 2 models 
    4376 Split pflA (#9.9) into 2 models 
    4377 Split pflA (#9.10) into 2 models 
    4378 Split pflA (#9.11) into 2 models 
    4379 Split pflA (#9.12) into 2 models 
    4380 Split pflA (#9.13) into 2 models 
    4381 Split pflA (#9.14) into 2 models 
    4382 Split pflA (#9.15) into 2 models 
    4383 Split pflA (#9.16) into 2 models 
    4384 Split pflA (#9.17) into 2 models 
    4385 Split pflA (#9.18) into 2 models 
    4386 Chain information for pflA 1 #9.1.1 
    4387 --- 
    4388 Chain | Description 
    4389 A | No description available 
    4390  
    4391 Chain information for pflA 2 #9.1.2 
    4392 --- 
    4393 Chain | Description 
    4394 A | No description available 
    4395  
    4396 Chain information for pflA 1 #9.2.1 
    4397 --- 
    4398 Chain | Description 
    4399 A | No description available 
    4400  
    4401 Chain information for pflA 2 #9.2.2 
    4402 --- 
    4403 Chain | Description 
    4404 A | No description available 
    4405  
    4406 Chain information for pflA 1 #9.3.1 
    4407 --- 
    4408 Chain | Description 
    4409 A | No description available 
    4410  
    4411 Chain information for pflA 2 #9.3.2 
    4412 --- 
    4413 Chain | Description 
    4414 A | No description available 
    4415  
    4416 Chain information for pflA 1 #9.4.1 
    4417 --- 
    4418 Chain | Description 
    4419 A | No description available 
    4420  
    4421 Chain information for pflA 2 #9.4.2 
    4422 --- 
    4423 Chain | Description 
    4424 A | No description available 
    4425  
    4426 Chain information for pflA 1 #9.5.1 
    4427 --- 
    4428 Chain | Description 
    4429 A | No description available 
    4430  
    4431 Chain information for pflA 2 #9.5.2 
    4432 --- 
    4433 Chain | Description 
    4434 A | No description available 
    4435  
    4436 Chain information for pflA 1 #9.6.1 
    4437 --- 
    4438 Chain | Description 
    4439 A | No description available 
    4440  
    4441 Chain information for pflA 2 #9.6.2 
    4442 --- 
    4443 Chain | Description 
    4444 A | No description available 
    4445  
    4446 Chain information for pflA 1 #9.7.1 
    4447 --- 
    4448 Chain | Description 
    4449 A | No description available 
    4450  
    4451 Chain information for pflA 2 #9.7.2 
    4452 --- 
    4453 Chain | Description 
    4454 A | No description available 
    4455  
    4456 Chain information for pflA 1 #9.8.1 
    4457 --- 
    4458 Chain | Description 
    4459 A | No description available 
    4460  
    4461 Chain information for pflA 2 #9.8.2 
    4462 --- 
    4463 Chain | Description 
    4464 A | No description available 
    4465  
    4466 Chain information for pflA 1 #9.9.1 
    4467 --- 
    4468 Chain | Description 
    4469 A | No description available 
    4470  
    4471 Chain information for pflA 2 #9.9.2 
    4472 --- 
    4473 Chain | Description 
    4474 A | No description available 
    4475  
    4476 Chain information for pflA 1 #9.10.1 
    4477 --- 
    4478 Chain | Description 
    4479 A | No description available 
    4480  
    4481 Chain information for pflA 2 #9.10.2 
    4482 --- 
    4483 Chain | Description 
    4484 A | No description available 
    4485  
    4486 Chain information for pflA 1 #9.11.1 
    4487 --- 
    4488 Chain | Description 
    4489 A | No description available 
    4490  
    4491 Chain information for pflA 2 #9.11.2 
    4492 --- 
    4493 Chain | Description 
    4494 A | No description available 
    4495  
    4496 Chain information for pflA 1 #9.12.1 
    4497 --- 
    4498 Chain | Description 
    4499 A | No description available 
    4500  
    4501 Chain information for pflA 2 #9.12.2 
    4502 --- 
    4503 Chain | Description 
    4504 A | No description available 
    4505  
    4506 Chain information for pflA 1 #9.13.1 
    4507 --- 
    4508 Chain | Description 
    4509 A | No description available 
    4510  
    4511 Chain information for pflA 2 #9.13.2 
    4512 --- 
    4513 Chain | Description 
    4514 A | No description available 
    4515  
    4516 Chain information for pflA 1 #9.14.1 
    4517 --- 
    4518 Chain | Description 
    4519 A | No description available 
    4520  
    4521 Chain information for pflA 2 #9.14.2 
    4522 --- 
    4523 Chain | Description 
    4524 A | No description available 
    4525  
    4526 Chain information for pflA 1 #9.15.1 
    4527 --- 
    4528 Chain | Description 
    4529 A | No description available 
    4530  
    4531 Chain information for pflA 2 #9.15.2 
    4532 --- 
    4533 Chain | Description 
    4534 A | No description available 
    4535  
    4536 Chain information for pflA 1 #9.16.1 
    4537 --- 
    4538 Chain | Description 
    4539 A | No description available 
    4540  
    4541 Chain information for pflA 2 #9.16.2 
    4542 --- 
    4543 Chain | Description 
    4544 A | No description available 
    4545  
    4546 Chain information for pflA 1 #9.17.1 
    4547 --- 
    4548 Chain | Description 
    4549 A | No description available 
    4550  
    4551 Chain information for pflA 2 #9.17.2 
    4552 --- 
    4553 Chain | Description 
    4554 A | No description available 
    4555  
    4556 Chain information for pflA 1 #9.18.1 
    4557 --- 
    4558 Chain | Description 
    4559 A | No description available 
    4560  
    4561 Chain information for pflA 2 #9.18.2 
    4562 --- 
    4563 Chain | Description 
    4564 A | No description available 
    4565  
    4566 
    4567 > hide #9.*.2 cartoons
    4568 
    4569 > view orient
    4570 
    4571 > show #2.2 cartoons
    4572 
    4573 > split #2.2 atoms :1-137
    4574 
    4575 Split pflB (#2.2) into 2 models 
    4576 Chain information for pflB 1 #2.2.1 
    4577 --- 
    4578 Chain | Description 
    4579 B | No description available 
    4580  
    4581 Chain information for pflB 2 #2.2.2 
    4582 --- 
    4583 Chain | Description 
    4584 B | No description available 
    4585  
    4586 
    4587 > view orient
    4588 
    4589 > hide #2.2.2 models
    4590 
    4591 > show #2.2.2 models
    4592 
    4593 > close #2.2.1
    4594 
    4595 > sym #2.2 C18 center #1.1
    4596 
    4597 Invalid "center" argument: Center argument has no object bounds 
    4598 
    4599 > show #!1.1 models
    4600 
    4601 > hide #!1.1 models
    4602 
    4603 > show #!1.1 models
    4604 
    4605 > sym #2.2 C18 center #1.1
    4606 
    4607 Made 18 graphical clones for pflB 2 symmetry C18 
    4608 
    4609 > hide #!1 models
    4610 
    4611 > show
    4612 > #2.2.2#7.1.1-3#7.2.1-3#7.3.1-3#7.4.1-3#7.5.1-3#7.6.1-3#7.7.1-3#7.8.1-3#7.9.1-3#7.10.1-3#7.11.1-3#7.12.1-3#7.13.1-3#7.14.1-3#7.15.1-3#7.16.1-3#7.17.1-3#7.18.1-3#9.1.1-2#9.2.1-2#9.3.1-2#9.4.1-2#9.5.1-2#9.6.1-2#9.7.1-2#9.8.1-2#9.9.1-2#9.10.1-2#9.11.1-2#9.12.1-2#9.13.1-2#9.14.1-2#9.15.1-2#9.16.1-2#9.17.1-2#9.18.1-2
    4613 > surfaces
    4614 
    4615 > hide #9.*.2 surfaces
    4616 
    4617 > hide #7.*.3 surfaces
    4618 
    4619 > show #!3 models
    4620 
    4621 > color #3 #01543fff models
    4622 
    4623 > show
    4624 > #3.1-42#!3.43-81#!2.2.2#!7.1.1-3#!7.2.1-3#!7.3.1-3#!7.4.1-3#!7.5.1-3#!7.6.1-3#!7.7.1-3#!7.8.1-3#!7.9.1-3#!7.10.1-3#!7.11.1-3#!7.12.1-3#!7.13.1-3#!7.14.1-3#!7.15.1-3#!7.16.1-3#!7.17.1-3#!7.18.1-3#!9.1.1-2#!9.2.1-2#!9.3.1-2#!9.4.1-2#!9.5.1-2#!9.6.1-2#!9.7.1-2#!9.8.1-2#!9.9.1-2#!9.10.1-2#!9.11.1-2#!9.12.1-2#!9.13.1-2#!9.14.1-2#!9.15.1-2#!9.16.1-2#!9.17.1-2#!9.18.1-2
    4625 > surfaces
    4626 
    4627 > hide #7.*.3 surfaces
    4628 
    4629 > hide #9.*.2 surfaces
    4630 
    4631 > view orient
    4632 
    4633 > lighting soft
    4634 
    4635 > lighting simple
    4636 
    4637 > hide
    4638 > #!3.1-81#!2.2.2#!7.1.1-3#!7.2.1-3#!7.3.1-3#!7.4.1-3#!7.5.1-3#!7.6.1-3#!7.7.1-3#!7.8.1-3#!7.9.1-3#!7.10.1-3#!7.11.1-3#!7.12.1-3#!7.13.1-3#!7.14.1-3#!7.15.1-3#!7.16.1-3#!7.17.1-3#!7.18.1-3#!9.1.1-2#!9.2.1-2#!9.3.1-2#!9.4.1-2#!9.5.1-2#!9.6.1-2#!9.7.1-2#!9.8.1-2#!9.9.1-2#!9.10.1-2#!9.11.1-2#!9.12.1-2#!9.13.1-2#!9.14.1-2#!9.15.1-2#!9.16.1-2#!9.17.1-2#!9.18.1-2
    4639 > surfaces
    4640 
    4641 > view orient
    4642 
    4643 > save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
    4644 > pflA pflB.cxs"
    4645 
    4646 ——— End of log from Mon Jun 3 14:56:25 2024 ———
    4647 
    4648 opened ChimeraX session 
    4649 Showing HP-PflA-PflB-2.1A.seg - 283 regions, 283 surfaces 
    4650 
    4651 > hide #!4 models
    4652 
    4653 > open "C:/Users/Jack Botting/Documents/Chimera/PDB/stator.pdb"
    4654 
    4655 Summary of feedback from opening C:/Users/Jack
    4656 Botting/Documents/Chimera/PDB/stator.pdb 
    4657 --- 
    4658 warnings | Start residue of secondary structure not found: HELIX 1 1 SER A 85 VAL A 87 1 3 
    4659 Start residue of secondary structure not found: HELIX 2 2 ARG A 88 LYS A 107 1
    4660 20 
    4661 Start residue of secondary structure not found: HELIX 3 3 ALA A 128 ALA A 130
    4662 1 3 
    4663 Start residue of secondary structure not found: HELIX 4 4 LEU A 141 ALA A 152
    4664 1 12 
    4665 Start residue of secondary structure not found: HELIX 5 5 PHE A 154 PHE A 157
    4666 1 4 
    4667 247 messages similar to the above omitted 
    4668  
    4669 Chain information for stator.pdb 
    4670 --- 
    4671 Chain | Description 
    4672 12.3/? | No description available 
    4673 12.14/? 12.15/? 12.16/? 12.17/? 12.18/? 12.19/? 12.20/? 12.21/? 12.22/? 12.23/? | No description available 
    4674 12.1/A 12.2/A | No description available 
    4675 12.4/B 12.5/B 12.6/B 12.7/B 12.8/B 12.9/B 12.10/B 12.11/B 12.12/B 12.13/B | No description available 
    4676  
    4677 
    4678 > select add #12
    4679 
    4680 24669 atoms, 24971 bonds, 2802 residues, 24 models selected 
    4681 
    4682 > ui mousemode right "translate selected models"
    4683 
    4684 > view matrix models #12,1,0,0,-578.91,0,1,0,28.461,0,0,1,-3.6162
    4685 
    4686 > view matrix models #12,1,0,0,-563.77,0,1,0,48.676,0,0,1,-486.31
    4687 
    4688 > view matrix models #12,1,0,0,-585.84,0,1,0,-392.56,0,0,1,-568.02
    4689 
    4690 > view matrix models #12,1,0,0,-625.19,0,1,0,-401.85,0,0,1,-452.6
    4691 
    4692 > show #!1 models
    4693 
    4694 > hide #!2.2 models
    4695 
    4696 > hide #!3 models
    4697 
    4698 > hide #!7 models
    4699 
    4700 > hide #!9 models
    4701 
    4702 > hide #!1.1 models
    4703 
    4704 > view matrix models #12,1,0,0,-595.83,0,1,0,-407.42,0,0,1,-449.38
    4705 
    4706 > view matrix models #12,1,0,0,-589.75,0,1,0,-408.62,0,0,1,-485.85
    4707 
    4708 > select clear
    4709 
    4710 > view orient
    4711 
    4712 > color #12 #00aa00ff models
    4713 
    4714 > color #12 #008600ff models
    4715 
    4716 > show #!1.1 models
    4717 
    4718 > view orient
    4719 
    4720 > show #!2.2 models
    4721 
    4722 > show #2.1 models
    4723 
    4724 > hide #2.1 models
    4725 
    4726 > show #!9 models
    4727 
    4728 > show #!7 models
    4729 
    4730 > view orient
    4731 
    4732 > hide #!1.2 models
    4733 
    4734 > view orient
    4735 
    4736 > sym #12 C18 center #1.1
    4737 
    4738 Made 18 graphical clones for stator.pdb, stator.pdb, stator.pdb, stator.pdb,
    4739 stator.pdb, stator.pdb, stator.pdb, stator.pdb, stator.pdb, stator.pdb,
    4740 stator.pdb, stator.pdb, stator.pdb, stator.pdb, stator.pdb, stator.pdb,
    4741 stator.pdb, stator.pdb, stator.pdb, stator.pdb, stator.pdb, stator.pdb,
    4742 stator.pdb symmetry C18 
    4743 
    4744 > select clear
    4745 
    4746 [Repeated 1 time(s)]
    4747 
    4748 > color #12 #005400ff models
    4749 
    4750 > color #12 #004f00ff models
    4751 
    4752 > view orient
    4753 
    4754 > open "C:/Users/Jack Botting/Documents/alphafold
    4755 > results/fold_pylori_piln_pilo_pflb/fold_pylori_piln_pilo_pflb_model_0.cif"
    4756 
    4757 Chain information for fold_pylori_piln_pilo_pflb_model_0.cif #13 
    4758 --- 
    4759 Chain | Description 
    4760 A | . 
    4761 B | . 
    4762 C | . 
    4763  
    4764 
    4765 > mmaker #13 to #2.2
    4766 
    4767 Parameters 
    4768 --- 
    4769 Chain pairing | bb 
    4770 Alignment algorithm | Needleman-Wunsch 
    4771 Similarity matrix | BLOSUM-62 
    4772 SS fraction | 0.3 
    4773 Gap open (HH/SS/other) | 18/18/6 
    4774 Gap extend | 1 
    4775 SS matrix |  |  | H | S | O 
    4776 ---|---|---|--- 
    4777 H | 6 | -9 | -6 
    4778 S |  | 6 | -6 
    4779 O |  |  | 4 
    4780 Iteration cutoff | 2 
    4781  
    4782 Matchmaker pflB 2, chain B (#2.2.2) with
    4783 fold_pylori_piln_pilo_pflb_model_0.cif, chain B (#13), sequence alignment
    4784 score = 3635.5 
    4785 RMSD between 608 pruned atom pairs is 0.697 angstroms; (across all 707 pairs:
    4786 6.109) 
    4787  
    4788 
    4789 > hide #!12 models
    4790 
    4791 > hide #!9 models
    4792 
    4793 > hide #!7 models
    4794 
    4795 > hide #!1.1 models
    4796 
    4797 > show #!1.2 models
    4798 
    4799 > select add #13
    4800 
    4801 9256 atoms, 9455 bonds, 1136 residues, 1 model selected 
    4802 
    4803 > view matrix models
    4804 > #13,-0.63411,0.028196,-0.77273,298.14,-0.66839,0.48249,0.56609,10.698,0.38879,0.87545,-0.2871,-43.281
    4805 
    4806 > view matrix models
    4807 > #13,-0.65422,0.035133,-0.75549,297.83,-0.56433,0.64236,0.51856,11.914,0.50351,0.7656,-0.40042,-41.315
    4808 
    4809 > view matrix models
    4810 > #13,-0.65422,0.035133,-0.75549,315.66,-0.56433,0.64236,0.51856,-322.03,0.50351,0.7656,-0.40042,-56.272
    4811 
    4812 > split #13 atoms /B
    4813 
    4814 Split fold_pylori_piln_pilo_pflb_model_0.cif (#13) into 2 models 
    4815 Chain information for fold_pylori_piln_pilo_pflb_model_0.cif 1 #13.1 
    4816 --- 
    4817 Chain | Description 
    4818 B | No description available 
    4819  
    4820 Chain information for fold_pylori_piln_pilo_pflb_model_0.cif 2 #13.2 
    4821 --- 
    4822 Chain | Description 
    4823 A | No description available 
    4824 C | No description available 
    4825  
    4826 
    4827 > hide #13.1 models
    4828 
    4829 > close #13.1
    4830 
    4831 > select add #13.2
    4832 
    4833 2418 atoms, 2473 bonds, 292 residues, 1 model selected 
    4834 
    4835 > view matrix models
    4836 > #13.2,-0.65422,0.035133,-0.75549,298.03,-0.56433,0.64236,0.51856,-2.1929,0.50351,0.7656,-0.40042,-37.817
    4837 
    4838 > view matrix models
    4839 > #13.2,-0.65734,0.03675,-0.7527,298.07,-0.54523,0.6663,0.50869,-2.4932,0.52022,0.74477,-0.41795,-37.968
    4840 
    4841 > view orient
    4842 
    4843 > turn x -90
    4844 
    4845 > view matrix models
    4846 > #13.2,-0.65734,0.03675,-0.7527,298.08,-0.54523,0.6663,0.50869,1.2039,0.52022,0.74477,-0.41795,-13.096
    4847 
    4848 > view matrix models
    4849 > #13.2,-0.65734,0.03675,-0.7527,360.28,-0.54523,0.6663,0.50869,13.702,0.52022,0.74477,-0.41795,-17.781
    4850 
    4851 > view matrix models
    4852 > #13.2,-0.65734,0.03675,-0.7527,360.09,-0.54523,0.6663,0.50869,3.9914,0.52022,0.74477,-0.41795,-24.544
    4853 
    4854 > fitmap #13.2 inMap #1.2
    4855 
    4856 Fit molecule fold_pylori_piln_pilo_pflb_model_0.cif 2 (#13.2) to map HP-PflA-
    4857 PflB-2.1A.mrc (#1.2) using 2418 atoms 
    4858 average map value = 5.318, steps = 244 
    4859 shifted from previous position = 9.27 
    4860 rotated from previous position = 20.2 degrees 
    4861 atoms outside contour = 513, contour level = 0.78314 
    4862  
    4863 Position of fold_pylori_piln_pilo_pflb_model_0.cif 2 (#13.2) relative to HP-
    4864 PflA-PflB-2.1A.mrc (#1.2) coordinates: 
    4865 Matrix rotation and translation 
    4866 -0.38190509 0.03803185 -0.92341869 130.64005158 
    4867 -0.57941091 0.76856187 0.27128518 5.36319709 
    4868 0.72002188 0.63864406 -0.27148162 -93.36724892 
    4869 Axis 0.20481382 -0.91626845 -0.34424325 
    4870 Axis point 91.29210272 0.00000000 -7.11876351 
    4871 Rotation angle (degrees) 116.25790439 
    4872 Shift along axis 53.98380587 
    4873  
    4874 
    4875 > combine #13
    4876 
    4877 > select add #14
    4878 
    4879 4836 atoms, 4946 bonds, 584 residues, 2 models selected 
    4880 
    4881 > view matrix models
    4882 > #13.2,-0.38191,0.038032,-0.92342,343.93,-0.57941,0.76856,0.27129,3.1769,0.72002,0.63864,-0.27148,-29.695,#14,-0.38191,0.038032,-0.92342,343.93,-0.57941,0.76856,0.27129,3.1769,0.72002,0.63864,-0.27148,-29.695
    4883 
    4884 > undo
    4885 
    4886 > select subtract #13.2
    4887 
    4888 2418 atoms, 2473 bonds, 292 residues, 1 model selected 
    4889 
    4890 > view matrix models
    4891 > #14,-0.38191,0.038032,-0.92342,340.37,-0.57941,0.76856,0.27129,54.359,0.72002,0.63864,-0.27148,-44.455
    4892 
    4893 > select up
    4894 
    4895 34274 atoms, 34866 bonds, 4224 residues, 15 models selected 
    4896 
    4897 > select clear
    4898 
    4899 > fitmap #14 inMap #1.2
    4900 
    4901 Fit molecule copy of fold_pylori_piln_pilo_pflb_model_0.cif 2 (#14) to map HP-
    4902 PflA-PflB-2.1A.mrc (#1.2) using 2418 atoms 
    4903 average map value = 4.763, steps = 536 
    4904 shifted from previous position = 11.3 
    4905 rotated from previous position = 26.7 degrees 
    4906 atoms outside contour = 656, contour level = 0.78314 
    4907  
    4908 Position of copy of fold_pylori_piln_pilo_pflb_model_0.cif 2 (#14) relative to
    4909 HP-PflA-PflB-2.1A.mrc (#1.2) coordinates: 
    4910 Matrix rotation and translation 
    4911 -0.67020056 0.24615531 -0.70017053 144.21435003 
    4912 -0.23151960 0.82698178 0.51234736 47.22202715 
    4913 0.70514530 0.50547868 -0.49725387 -115.16981588 
    4914 Axis -0.00462757 -0.94678980 -0.32181928 
    4915 Axis point 99.64464218 0.00000000 -31.77890818 
    4916 Rotation angle (degrees) 132.08530707 
    4917 Shift along axis -8.31282746 
    4918  
    4919 
    4920 > combine #13.2,14
    4921 
    4922 > hide #14 models
    4923 
    4924 > hide #!13 models
    4925 
    4926 > show #!13 models
    4927 
    4928 > show #14 models
    4929 
    4930 > close #15
    4931 
    4932 > combine #13.2 #14
    4933 
    4934 Remapping chain ID 'A' in copy of fold_pylori_piln_pilo_pflb_model_0.cif 2 #14
    4935 to 'B' 
    4936 Remapping chain ID 'C' in copy of fold_pylori_piln_pilo_pflb_model_0.cif 2 #14
    4937 to 'D' 
    4938 
    4939 > hide #13.2 models
    4940 
    4941 > hide #14 models
    4942 
    4943 > hide #15 models
    4944 
    4945 > show #15 models
    4946 
    4947 > view orient
    4948 
    4949 > hide #!1.2 models
    4950 
    4951 > show #!1.1 models
    4952 
    4953 > show #!12 models
    4954 
    4955 > close #14#13
    4956 
    4957 > rename #15 pilNO
    4958 
    4959 > show #!9 models
    4960 
    4961 > close #10
    4962 
    4963 > show #!7 models
    4964 
    4965 > show #!3 models
    4966 
    4967 > view orient
    4968 
    4969 > sym #15 C18 center #1.1
    4970 
    4971 Made 18 graphical clones for pilNO symmetry C18 
    4972 
    4973 > save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
    4974 > pflA pflB.cxs"
    4975 
    4976 ——— End of log from Mon Jun 3 15:09:09 2024 ———
    4977 
    4978 opened ChimeraX session 
    4979 Showing HP-PflA-PflB-2.1A.seg - 283 regions, 283 surfaces 
    4980 
    4981 > hide #!4 models
    4982 
    4983 > color #12 #356a00ff models
    4984 
    4985 > color #15 #003600ff
    4986 
    4987 > hide #!1.1 models
    4988 
    4989 > save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
    4990 > pflA pflB.cxs"
    4991 
    4992 > lighting soft
    4993 
    4994 > show
    4995 > #15#12.1-23#!3.1-81#!2.2.2#!7.1.1-3#!7.2.1-3#!7.3.1-3#!7.4.1-3#!7.5.1-3#!7.6.1-3#!7.7.1-3#!7.8.1-3#!7.9.1-3#!7.10.1-3#!7.11.1-3#!7.12.1-3#!7.13.1-3#!7.14.1-3#!7.15.1-3#!7.16.1-3#!7.17.1-3#!7.18.1-3#!9.1.1-2#!9.2.1-2#!9.3.1-2#!9.4.1-2#!9.5.1-2#!9.6.1-2#!9.7.1-2#!9.8.1-2#!9.9.1-2#!9.10.1-2#!9.11.1-2#!9.12.1-2#!9.13.1-2#!9.14.1-2#!9.15.1-2#!9.16.1-2#!9.17.1-2#!9.18.1-2
    4996 > surfaces
    4997 
    4998 > hide #9.*.2 surfaces
    4999 
    5000 > hide #17.*.3 surfaces
    5001 
    5002 [Repeated 1 time(s)]
    5003 
    5004 > hide #7.*.3 surfaces
    5005 
    5006 > view orient
    5007 
    5008 > hide #!7.4 models
    5009 
    5010 > hide #!7.18 models
    5011 
    5012 > hide #!7.15 models
    5013 
    5014 > hide #!7.11 models
    5015 
    5016 > hide #!7.8 models
    5017 
    5018 > save "C:/Users/Jack Botting/Documents/Chimera/Images/pylori FlgY system.jpg"
    5019 > width 2848 height 1180 supersample 3
    5020 
    5021 > lighting simple
    5022 
    5023 > save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
    5024 > pflA pflB.cxs"
    5025 
    5026 ——— End of log from Mon Jun 3 15:19:25 2024 ———
    5027 
    5028 opened ChimeraX session 
    5029 Showing HP-PflA-PflB-2.1A.seg - 283 regions, 283 surfaces 
    5030 
    5031 > hide
    5032 > #!15#!3.1-81#!12.1-23#!2.2.2#!7.1.1-3#!7.2.1-3#!7.3.1-3#!7.5.1-3#!7.6.1-3#!7.7.1-3#!7.9.1-3#!7.10.1-3#!7.12.1-3#!7.13.1-3#!7.14.1-3#!7.16.1-3#!7.17.1-3#!9.1.1-2#!9.2.1-2#!9.3.1-2#!9.4.1-2#!9.5.1-2#!9.6.1-2#!9.7.1-2#!9.8.1-2#!9.9.1-2#!9.10.1-2#!9.11.1-2#!9.12.1-2#!9.13.1-2#!9.14.1-2#!9.15.1-2#!9.16.1-2#!9.17.1-2#!9.18.1-2
    5033 > surfaces
    5034 
    5035 > hide #!4 models
    5036 
    5037 > show #!1.2 models
    5038 
    5039 > color #1.2 #00000080 models
    5040 
    5041 > color #1.2 #a8a8a880 models
    5042 
    5043 > color #1.2 #adadad80 models
    5044 
    5045 > view orient
    5046 
    5047 > hide #!12 models
    5048 
    5049 > hide #!15 models
    5050 
    5051 > hide #!3 models
    5052 
    5053 > view orient
    5054 
    5055 > hide #!1.2 models
    5056 
    5057 > show #!1.1 models
    5058 
    5059 > view orient
    5060 
    5061 [Repeated 1 time(s)]
    5062 
    5063 > close #4
    5064 
    5065 > rename #3 id #13
    5066 
    5067 > rename #2.2 id #3
    5068 
    5069 > rename #5 id #16
    5070 
    5071 > rename #8 id #17
    5072 
    5073 > rename #11 id #18
    5074 
    5075 > close #2
    5076 
    5077 > hide #!1 models
    5078 
    5079 > show #!12 models
    5080 
    5081 > show #!13 models
    5082 
    5083 > show #!15 models
    5084 
    5085 > save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
    5086 > pflA pflB.cxs"
    5087 
    5088 > turn x -90
    5089 
    5090 > view orient
    5091 
    5092 > close #7.*.3
    5093 
    5094 > select #7.*:164-end
    5095 
    5096 9864 atoms, 10188 bonds, 1296 residues, 36 models selected 
    5097 
    5098 > view orient
    5099 
    5100 [Repeated 2 time(s)]
    5101 
    5102 > hide #7.*:164-end cartoons
    5103 
    5104 > view orient
    5105 
    5106 > turn x -90
    5107 
    5108 > show #!1 models
    5109 
    5110 > hide #!7 models
    5111 
    5112 > hide #!3 models
    5113 
    5114 > hide #!9 models
    5115 
    5116 > hide #!12 models
    5117 
    5118 > hide #!15 models
    5119 
    5120 > select add #13
    5121 
    5122 121989 atoms, 123969 bonds, 15453 residues, 154 models selected 
    5123 
    5124 > view matrix models
    5125 > #7.1.1,0.32864,0.93245,-0.15009,-186.67,-0.75761,0.35516,0.54762,-94.364,0.56394,-0.066262,0.82315,30.867,#7.1.2,0.32864,0.93245,-0.15009,-186.67,-0.75761,0.35516,0.54762,-94.364,0.56394,-0.066262,0.82315,30.867,#7.2.1,0.52473,0.79843,-0.29522,-145.29,-0.63767,0.59842,0.48504,-154.11,0.56394,-0.066262,0.82315,30.867,#7.2.2,0.52473,0.79843,-0.29522,-145.29,-0.63767,0.59842,0.48504,-154.11,0.56394,-0.066262,0.82315,30.867,#7.3.1,0.69449,0.57738,-0.42932,-81.712,-0.44682,0.81378,0.37163,-197.51,0.56394,-0.066262,0.82315,30.867,#7.3.2,0.69449,0.57738,-0.42932,-81.712,-0.44682,0.81378,0.37163,-197.51,0.56394,-0.066262,0.82315,30.867,#7.4.1,0.81186,0.22698,-0.53793,-13.526,-0.15119,0.97164,0.1818,-211.13,0.56394,-0.066262,0.82315,30.867,#7.4.2,0.81186,0.22698,-0.53793,-13.526,-0.15119,0.97164,0.1818,-211.13,0.56394,-0.066262,0.82315,30.867,#7.5.1,0.82059,-0.067022,-0.56758,45.023,0.092778,0.99555,0.016577,-207.23,0.56394,-0.066262,0.82315,30.867,#7.5.2,0.82059,-0.067022,-0.56758,45.023,0.092778,0.99555,0.016577,-207.23,0.56394,-0.066262,0.82315,30.867,#7.6.1,0.7191,-0.45069,-0.52894,124.06,0.40603,0.89022,-0.20651,-170.12,0.56394,-0.066262,0.82315,30.867,#7.6.2,0.7191,-0.45069,-0.52894,124.06,0.40603,0.89022,-0.20651,-170.12,0.56394,-0.066262,0.82315,30.867,#7.7.1,0.56372,-0.69752,-0.44236,175.15,0.60348,0.71349,-0.35601,-114.52,0.56394,-0.066262,0.82315,30.867,#7.7.2,0.56372,-0.69752,-0.44236,175.15,0.60348,0.71349,-0.35601,-114.52,0.56394,-0.066262,0.82315,30.867,#7.8.1,0.28987,-0.91747,-0.27245,203.1,0.77327,0.39225,-0.49819,-50.258,0.56394,-0.066262,0.82315,30.867,#7.8.2,0.28987,-0.91747,-0.27245,203.1,0.77327,0.39225,-0.49819,-50.258,0.56394,-0.066262,0.82315,30.867,#7.9.1,-0.0013443,-0.99685,-0.079323,204.97,0.82581,0.043627,-0.56225,16.669,0.56394,-0.066262,0.82315,30.867,#7.9.2,-0.0013443,-0.99685,-0.079323,204.97,0.82581,0.043627,-0.56225,16.669,0.56394,-0.066262,0.82315,30.867,#7.10.1,-0.26136,-0.95986,0.10179,182.41,0.78337,-0.27254,-0.55862,91.475,0.56394,-0.066262,0.82315,30.867,#7.10.2,-0.26136,-0.95986,0.10179,182.41,0.78337,-0.27254,-0.55862,91.475,0.56394,-0.066262,0.82315,30.867,#7.11.1,-0.52473,-0.79843,0.29522,143.14,0.63767,-0.59842,-0.48504,150.89,0.56394,-0.066262,0.82315,30.867,#7.11.2,-0.52473,-0.79843,0.29522,143.14,0.63767,-0.59842,-0.48504,150.89,0.56394,-0.066262,0.82315,30.867,#7.12.1,-0.74397,-0.47341,0.47159,80.282,0.35844,-0.87835,-0.31627,186.09,0.56394,-0.066262,0.82315,30.867,#7.12.2,-0.74397,-0.47341,0.47159,80.282,0.35844,-0.87835,-0.31627,186.09,0.56394,-0.066262,0.82315,30.867,#7.13.1,-0.81186,-0.22698,0.53793,11.377,0.15119,-0.97164,-0.1818,207.91,0.56394,-0.066262,0.82315,30.867,#7.13.2,-0.81186,-0.22698,0.53793,11.377,0.15119,-0.97164,-0.1818,207.91,0.56394,-0.066262,0.82315,30.867,#7.14.1,-0.82059,0.067022,0.56758,-65.836,-0.092778,-0.99555,-0.016577,197.58,0.56394,-0.066262,0.82315,30.867,#7.14.2,-0.82059,0.067022,0.56758,-65.836,-0.092778,-0.99555,-0.016577,197.58,0.56394,-0.066262,0.82315,30.867,#7.15.1,-0.7191,0.45069,0.52894,-126.21,-0.40603,-0.89022,0.20651,166.89,0.56394,-0.066262,0.82315,30.867,#7.15.2,-0.7191,0.45069,0.52894,-126.21,-0.40603,-0.89022,0.20651,166.89,0.56394,-0.066262,0.82315,30.867,#7.16.1,-0.50663,0.7594,0.40822,-175.3,-0.65215,-0.64725,0.39468,114.59,0.56394,-0.066262,0.82315,30.867,#7.16.2,-0.50663,0.7594,0.40822,-175.3,-0.65215,-0.64725,0.39468,114.59,0.56394,-0.066262,0.82315,30.867,#7.17.1,-0.32333,0.89948,0.29392,-205.34,-0.75989,-0.4319,0.48583,47.002,0.56394,-0.066262,0.82315,30.867,#7.17.2,-0.32333,0.89948,0.29392,-205.34,-0.75989,-0.4319,0.48583,47.002,0.56394,-0.066262,0.82315,30.867,#7.18.1,-0.0079177,0.9963,0.085624,-209.57,-0.82578,-0.054804,0.56133,-25.733,0.56394,-0.066262,0.82315,30.867,#7.18.2,-0.0079177,0.9963,0.085624,-209.57,-0.82578,-0.054804,0.56133,-25.733,0.56394,-0.066262,0.82315,30.867,#13,1,0,0,-40.813,0,1,0,-1.5052,0,0,1,70.377
    5126 
    5127 > select clear
    5128 
    5129 > select add #13
    5130 
    5131 112125 atoms, 113781 bonds, 14157 residues, 82 models selected 
    5132 
    5133 > view matrix models #13,1,0,0,-38.504,0,1,0,-1.5052,0,0,1,70.089
    5134 
    5135 > select clear
    5136 
    5137 > view orient
    5138 
    5139 > show #!3 models
    5140 
    5141 > show #!6 models
    5142 
    5143 > show #!7 models
    5144 
    5145 > hide #!6 models
    5146 
    5147 > show #!9 models
    5148 
    5149 > show #!12 models
    5150 
    5151 > show #!15 models
    5152 
    5153 > view orient
    5154 
    5155 > save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
    5156 > pflA pflB.cxs"
    5157 
    5158 > turn x -90
    5159 
    5160 > select add #1.1
    5161 
    5162 4 models selected 
    5163 
    5164 > select clear
    5165 
    5166 > select add #7
    5167 
    5168 57096 atoms, 57744 bonds, 7164 residues, 55 models selected 
    5169 
    5170 > view matrix models #7,1,0,0,-39.329,0,1,0,-3.6426,0,0,1,8.9225
    5171 
    5172 > view orient
    5173 
    5174 > hide #!1 models
    5175 
    5176 > show #!1.2 models
    5177 
    5178 > hide #!1.1 models
    5179 
    5180 > view orient
    5181 
    5182 > select clear
    5183 
    5184 > save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
    5185 > pflA pflB.cxs"
    5186 
    5187 ——— End of log from Mon Jun 3 16:15:41 2024 ———
    5188 
    5189 opened ChimeraX session 
    5190 
    5191 > hide #!1 models
    5192 
    5193 > show #18 models
    5194 
    5195 > hide #18/A,B cartoon'
    5196 
    5197 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
    5198 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword 
    5199 
    5200 > hide #18/A,B cartoons
    5201 
    5202 > view orient
    5203 
    5204 [Repeated 1 time(s)]
    5205 
    5206 > show #!1 models
    5207 
    5208 > show #!6 models
    5209 
    5210 > hide #18 models
    5211 
    5212 > select add #6
    5213 
    5214 2710 atoms, 2772 bonds, 331 residues, 1 model selected 
    5215 
    5216 > hide #!15 models
    5217 
    5218 > hide #!13 models
    5219 
    5220 > hide #!12 models
    5221 
    5222 > hide #!3 models
    5223 
    5224 > ui mousemode right "translate selected models"
    5225 
    5226 > view matrix models
    5227 > #6,-0.37725,-0.44737,0.81089,24.268,-0.91985,0.28263,-0.27202,170.26,-0.10749,-0.84852,-0.51814,187.19
    5228 
    5229 > view matrix models
    5230 > #6,-0.37725,-0.44737,0.81089,107.06,-0.91985,0.28263,-0.27202,188.71,-0.10749,-0.84852,-0.51814,107.82
    5231 
    5232 > hide sel surfaces
    5233 
    5234 > view matrix models
    5235 > #6,-0.37725,-0.44737,0.81089,166.96,-0.91985,0.28263,-0.27202,14.919,-0.10749,-0.84852,-0.51814,85.961
    5236 
    5237 > view matrix models
    5238 > #6,-0.37725,-0.44737,0.81089,165.76,-0.91985,0.28263,-0.27202,12.248,-0.10749,-0.84852,-0.51814,92.284
    5239 
    5240 > view matrix models
    5241 > #6,-0.37725,-0.44737,0.81089,165.55,-0.91985,0.28263,-0.27202,14.538,-0.10749,-0.84852,-0.51814,65.62
    5242 
    5243 > view matrix models
    5244 > #6,-0.37725,-0.44737,0.81089,178.07,-0.91985,0.28263,-0.27202,1.4718,-0.10749,-0.84852,-0.51814,52.601
    5245 
    5246 > open "C:/Users/Jack Botting/Documents/alphafold
    5247 > results/pflAB/fold_pylori_pfla_pflc/fold_pylori_pfla_pflc_model_0.cif"
    5248 
    5249 Chain information for fold_pylori_pfla_pflc_model_0.cif #2 
    5250 --- 
    5251 Chain | Description 
    5252 A | . 
    5253 B | . 
    5254  
    5255 
    5256 > mmaker #2 to #9.18.1
    5257 
    5258 Parameters 
    5259 --- 
    5260 Chain pairing | bb 
    5261 Alignment algorithm | Needleman-Wunsch 
    5262 Similarity matrix | BLOSUM-62 
    5263 SS fraction | 0.3 
    5264 Gap open (HH/SS/other) | 18/18/6 
    5265 Gap extend | 1 
    5266 SS matrix |  |  | H | S | O 
    5267 ---|---|---|--- 
    5268 H | 6 | -9 | -6 
    5269 S |  | 6 | -6 
    5270 O |  |  | 4 
    5271 Iteration cutoff | 2 
    5272  
    5273 Matchmaker pflA 1, chain A (#9.18.1) with fold_pylori_pfla_pflc_model_0.cif,
    5274 chain A (#2), sequence alignment score = 3183.5 
    5275 RMSD between 89 pruned atom pairs is 0.293 angstroms; (across all 612 pairs:
    5276 25.225) 
    5277  
    5278 
    5279 > close #2
    5280 
    5281 > view orient
    5282 
    5283 > ui tool show "Side View"
    5284 
    5285 > view matrix models
    5286 > #6,-0.37725,-0.44737,0.81089,178.41,-0.91985,0.28263,-0.27202,0.90513,-0.10749,-0.84852,-0.51814,52.601
    5287 
    5288 > view matrix models
    5289 > #6,-0.37725,-0.44737,0.81089,178.38,-0.91985,0.28263,-0.27202,2.9904,-0.10749,-0.84852,-0.51814,52.808
    5290 
    5291 > view matrix models
    5292 > #6,-0.37725,-0.44737,0.81089,178.85,-0.91985,0.28263,-0.27202,3.2499,-0.10749,-0.84852,-0.51814,53.36
    5293 
    5294 > view matrix models
    5295 > #6,-0.37725,-0.44737,0.81089,182.4,-0.91985,0.28263,-0.27202,-78.627,-0.10749,-0.84852,-0.51814,44.028
    5296 
    5297 > view matrix models
    5298 > #6,-0.37725,-0.44737,0.81089,161.35,-0.91985,0.28263,-0.27202,-73.059,-0.10749,-0.84852,-0.51814,40.963
    5299 
    5300 > view matrix models
    5301 > #6,-0.37725,-0.44737,0.81089,162,-0.91985,0.28263,-0.27202,-73.712,-0.10749,-0.84852,-0.51814,42.155
    5302 
    5303 > view matrix models
    5304 > #6,-0.37725,-0.44737,0.81089,165.22,-0.91985,0.28263,-0.27202,-74.73,-0.10749,-0.84852,-0.51814,46.859
    5305 
    5306 > select clear
    5307 
    5308 > fitmap #6 inMap #1.2 shift false
    5309 
    5310 Fit molecule pflC (#6) to map HP-PflA-PflB-2.1A.mrc (#1.2) using 2710 atoms 
    5311 average map value = 0.7647, steps = 64 
    5312 shifted from previous position = 5.68e-14 
    5313 rotated from previous position = 16.9 degrees 
    5314 atoms outside contour = 1781, contour level = 0.78314 
    5315  
    5316 Position of pflC (#6) relative to HP-PflA-PflB-2.1A.mrc (#1.2) coordinates: 
    5317 Matrix rotation and translation 
    5318 -0.30285245 -0.68737158 0.66015204 -48.52526860 
    5319 -0.95285864 0.23180699 -0.19577011 -67.98025203 
    5320 -0.01846105 -0.68832103 -0.72517127 -19.67829116 
    5321 Axis -0.56000429 0.77154712 -0.30184472 
    5322 Axis point -52.76429963 0.00000000 -14.22503516 
    5323 Rotation angle (degrees) 153.91052268 
    5324 Shift along axis -19.33582070 
    5325  
    5326 
    5327 > fitmap #6 inMap #1.2 rotate false
    5328 
    5329 Fit molecule pflC (#6) to map HP-PflA-PflB-2.1A.mrc (#1.2) using 2710 atoms 
    5330 average map value = 0.8716, steps = 44 
    5331 shifted from previous position = 5.91 
    5332 rotated from previous position = 0 degrees 
    5333 atoms outside contour = 1645, contour level = 0.78314 
    5334  
    5335 Position of pflC (#6) relative to HP-PflA-PflB-2.1A.mrc (#1.2) coordinates: 
    5336 Matrix rotation and translation 
    5337 -0.30285245 -0.68737158 0.66015204 -46.93764496 
    5338 -0.95285864 0.23180699 -0.19577011 -68.13717407 
    5339 -0.01846105 -0.68832103 -0.72517127 -25.36694166 
    5340 Axis -0.56000429 0.77154712 -0.30184472 
    5341 Axis point -52.84953027 0.00000000 -17.39787428 
    5342 Rotation angle (degrees) 153.91052268 
    5343 Shift along axis -18.62888040 
    5344  
    5345 
    5346 > fitmap #6 inMap #1.2
    5347 
    5348 Fit molecule pflC (#6) to map HP-PflA-PflB-2.1A.mrc (#1.2) using 2710 atoms 
    5349 average map value = 2.92, steps = 368 
    5350 shifted from previous position = 22.4 
    5351 rotated from previous position = 81.3 degrees 
    5352 atoms outside contour = 555, contour level = 0.78314 
    5353  
    5354 Position of pflC (#6) relative to HP-PflA-PflB-2.1A.mrc (#1.2) coordinates: 
    5355 Matrix rotation and translation 
    5356 -0.94371631 0.25400702 0.21184892 -46.09255130 
    5357 0.14453894 0.89281185 -0.42660932 -54.17654056 
    5358 -0.29750298 -0.37197775 -0.87927501 -41.60541004 
    5359 Axis 0.10429077 0.97234449 -0.20897278 
    5360 Axis point -23.69126255 0.00000000 -23.81405425 
    5361 Rotation angle (degrees) 164.81601291 
    5362 Shift along axis -48.79089015 
    5363  
    5364 
    5365 > view matrix models
    5366 > #6,-0.96972,-0.024248,-0.24302,169.11,0.048713,0.95586,-0.28975,-61.215,0.23932,-0.29282,-0.92573,24.399
    5367 
    5368 > view matrix models
    5369 > #6,-0.83191,0.48147,0.27588,164.23,0.43122,0.24802,0.86749,-38.79,0.34924,0.84064,-0.41395,8.0546
    5370 
    5371 > view matrix models
    5372 > #6,-0.87725,-0.48004,-0.0014224,179.39,-0.12758,0.236,-0.96334,-53.719,0.46278,-0.84491,-0.26827,39.861
    5373 
    5374 > view matrix models
    5375 > #6,-0.87725,-0.48004,-0.0014224,177.67,-0.12758,0.236,-0.96334,-75.32,0.46278,-0.84491,-0.26827,44.313
    5376 
    5377 > fitmap #6 inMap #1.2 rotate false
    5378 
    5379 Fit molecule pflC (#6) to map HP-PflA-PflB-2.1A.mrc (#1.2) using 2710 atoms 
    5380 average map value = 1.722, steps = 60 
    5381 shifted from previous position = 11.8 
    5382 rotated from previous position = 0 degrees 
    5383 atoms outside contour = 1307, contour level = 0.78314 
    5384  
    5385 Position of pflC (#6) relative to HP-PflA-PflB-2.1A.mrc (#1.2) coordinates: 
    5386 Matrix rotation and translation 
    5387 -0.87724573 -0.48003942 -0.00142242 -31.82690333 
    5388 -0.12757774 0.23599581 -0.96334306 -63.00722732 
    5389 0.46277834 -0.84490715 -0.26826866 -31.44548340 
    5390 Axis 0.19913251 -0.78048505 0.59261229 
    5391 Axis point -19.48872547 0.00000000 -43.21458388 
    5392 Rotation angle (degrees) 162.69971271 
    5393 Shift along axis 24.20344831 
    5394  
    5395 
    5396 > fitmap #6 inMap #1.2 shift false
    5397 
    5398 Fit molecule pflC (#6) to map HP-PflA-PflB-2.1A.mrc (#1.2) using 2710 atoms 
    5399 average map value = 1.796, steps = 56 
    5400 shifted from previous position = 3.26e-14 
    5401 rotated from previous position = 9.35 degrees 
    5402 atoms outside contour = 1250, contour level = 0.78314 
    5403  
    5404 Position of pflC (#6) relative to HP-PflA-PflB-2.1A.mrc (#1.2) coordinates: 
    5405 Matrix rotation and translation 
    5406 -0.85554718 -0.51036300 -0.08699756 -31.91291532 
    5407 -0.13260657 0.37845086 -0.91607336 -63.01025522 
    5408 0.50045426 -0.77220756 -0.39146005 -31.61608246 
    5409 Axis 0.20174994 -0.82381195 0.52974601 
    5410 Axis point -18.43270312 0.00000000 -40.28574201 
    5411 Rotation angle (degrees) 159.11184496 
    5412 Shift along axis 28.72167879 
    5413  
    5414 
    5415 > view matrix models
    5416 > #6,-0.85555,-0.51036,-0.086998,180.5,-0.13261,0.37845,-0.91607,-80.249,0.50045,-0.77221,-0.39146,36.14
    5417 
    5418 > fitmap #6 inMap #1.2 shift false
    5419 
    5420 Fit molecule pflC (#6) to map HP-PflA-PflB-2.1A.mrc (#1.2) using 2710 atoms 
    5421 average map value = 1.261, steps = 88 
    5422 shifted from previous position = 1.03e-13 
    5423 rotated from previous position = 21.5 degrees 
    5424 atoms outside contour = 1495, contour level = 0.78314 
    5425  
    5426 Position of pflC (#6) relative to HP-PflA-PflB-2.1A.mrc (#1.2) coordinates: 
    5427 Matrix rotation and translation 
    5428 -0.80394309 -0.58905015 -0.08182530 -33.13685232 
    5429 -0.35908216 0.59047996 -0.72276786 -73.30860251 
    5430 0.47406272 -0.55168224 -0.68622969 -30.39146180 
    5431 Axis 0.27354726 -0.88880436 0.36769376 
    5432 Axis point -23.61741436 0.00000000 -34.45768777 
    5433 Rotation angle (degrees) 161.77696883 
    5434 Shift along axis 44.91775978 
    5435  
    5436 
    5437 > fitmap #6 inMap #1.2 rotate false
    5438 
    5439 Fit molecule pflC (#6) to map HP-PflA-PflB-2.1A.mrc (#1.2) using 2710 atoms 
    5440 average map value = 1.655, steps = 72 
    5441 shifted from previous position = 12.3 
    5442 rotated from previous position = 0 degrees 
    5443 atoms outside contour = 1246, contour level = 0.78314 
    5444  
    5445 Position of pflC (#6) relative to HP-PflA-PflB-2.1A.mrc (#1.2) coordinates: 
    5446 Matrix rotation and translation 
    5447 -0.80394309 -0.58905015 -0.08182530 -30.97954999 
    5448 -0.35908216 0.59047996 -0.72276786 -62.45119875 
    5449 0.47406272 -0.55168224 -0.68622969 -35.68542061 
    5450 Axis 0.27354726 -0.88880436 0.36769376 
    5451 Axis point -20.75547151 0.00000000 -34.39256177 
    5452 Rotation angle (degrees) 161.77696883 
    5453 Shift along axis 33.91122049 
    5454  
    5455 
    5456 > view matrix models
    5457 > #6,-0.92898,0.17022,0.32866,171.62,-0.1264,0.68868,-0.71396,-70.114,-0.34787,-0.7048,-0.61826,31.402
    5458 
    5459 > view matrix models
    5460 > #6,-0.92898,0.17022,0.32866,167.27,-0.1264,0.68868,-0.71396,-78.744,-0.34787,-0.7048,-0.61826,59.742
    5461 
    5462 > view matrix models
    5463 > #6,-0.892,0.21544,0.39738,167.07,-0.26509,0.46276,-0.84592,-76.047,-0.36614,-0.8599,-0.35568,64.425
    5464 
    5465 > view matrix models
    5466 > #6,-0.892,0.21544,0.39738,165.74,-0.26509,0.46276,-0.84592,-76.153,-0.36614,-0.8599,-0.35568,60.256
    5467 
    5468 > fitmap #6 inMap #1.2 rotate false
    5469 
    5470 Fit molecule pflC (#6) to map HP-PflA-PflB-2.1A.mrc (#1.2) using 2710 atoms 
    5471 average map value = 1.498, steps = 76 
    5472 shifted from previous position = 30.9 
    5473 rotated from previous position = 0 degrees 
    5474 atoms outside contour = 1347, contour level = 0.78314 
    5475  
    5476 Position of pflC (#6) relative to HP-PflA-PflB-2.1A.mrc (#1.2) coordinates: 
    5477 Matrix rotation and translation 
    5478 -0.89200350 0.21544120 0.39738494 -49.29839561 
    5479 -0.26508574 0.46276321 -0.84591945 -60.14427182 
    5480 -0.36614104 -0.85990422 -0.35567603 -35.38181210 
    5481 Axis -0.01549970 0.84623693 -0.53258127 
    5482 Axis point -32.53055108 0.00000000 -29.60494458 
    5483 Rotation angle (degrees) 153.18378369 
    5484 Shift along axis -31.28850345 
    5485  
    5486 
    5487 > view matrix models
    5488 > #6,-0.892,0.21544,0.39738,164.74,-0.26509,0.46276,-0.84592,-74.836,-0.36614,-0.8599,-0.35568,55.972
    5489 
    5490 > fitmap #6 inMap #1.2 shift false
    5491 
    5492 Fit molecule pflC (#6) to map HP-PflA-PflB-2.1A.mrc (#1.2) using 2710 atoms 
    5493 average map value = 0.963, steps = 60 
    5494 shifted from previous position = 8.56e-14 
    5495 rotated from previous position = 23.7 degrees 
    5496 atoms outside contour = 1815, contour level = 0.78314 
    5497  
    5498 Position of pflC (#6) relative to HP-PflA-PflB-2.1A.mrc (#1.2) coordinates: 
    5499 Matrix rotation and translation 
    5500 -0.92577832 0.29237105 0.23969485 -49.01968455 
    5501 -0.22793582 0.07418241 -0.97084612 -68.21238874 
    5502 -0.30162844 -0.95342336 -0.00203464 -9.95055506 
    5503 Axis 0.02319834 0.72076965 -0.69278637 
    5504 Axis point -28.82316026 0.00000000 -31.26620913 
    5505 Rotation angle (degrees) 157.94369601 
    5506 Shift along axis -43.40898577 
    5507  
    5508 
    5509 > select clear
    5510 
    5511 > view orient
    5512 
    5513 [Repeated 2 time(s)]
    5514 
    5515 > hide #!1 models
    5516 
    5517 > hide #!1.2 models
    5518 
    5519 > show #!1.1 models
    5520 
    5521 > hide #!1 models
    5522 
    5523 > show #!1 models
    5524 
    5525 > show #7 cartoons
    5526 
    5527 > hide #!1 models
    5528 
    5529 > show #!1 models
    5530 
    5531 > hide #!1.1 models
    5532 
    5533 > show #!1.2 models
    5534 
    5535 > view orient
    5536 
    5537 > rename #1.1 FlgY-sym13-2.1A.mrc
    5538 
    5539 > hide #!1.2 models
    5540 
    5541 > view orient
    5542 
    5543 > show #!1.1 models
    5544 
    5545 > sym #6 C18 center #1.1
    5546 
    5547 Made 18 graphical clones for pflC symmetry C18 
    5548 
    5549 > hide #!1.1 models
    5550 
    5551 > show #!1.2 models
    5552 
    5553 > hide #!6 models
    5554 
    5555 > view orient
    5556 
    5557 > hide #!1 models
    5558 
    5559 > show #!6 models
    5560 
    5561 > show #!3 models
    5562 
    5563 > show #!12 models
    5564 
    5565 > show #!13 models
    5566 
    5567 > show #!15 models
    5568 
    5569 > save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
    5570 > pflA pflB.cxs"
    5571 
    5572 ——— End of log from Tue Jun 4 09:30:10 2024 ———
    5573 
    5574 opened ChimeraX session 
    5575 
    5576 > color #6 #aa0000ff
    5577 
    5578 > color #6 #aa007fff
    5579 
    5580 > color #6 #aa0003ff
    5581 
    5582 > color #6 #004daaff
    5583 
    5584 > color #6 #6300aaff
    5585 
    5586 > color #6 #001aaaff
    5587 
    5588 > color #6 #00158aff
    5589 
    5590 > view orient
    5591 
    5592 > save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
    5593 > pflA pflB.cxs"
    5594 
    5595 > set bgColor white
    5596 
    5597 > set bgColor black
    5598 
    5599 > set bgColor gray
    5600 
    5601 > set bgColor black
    5602 
    5603 > view orient
    5604 
    5605 > show #!1 models
    5606 
    5607 > ui tool show "Side View"
    5608 
    5609 > hide #!6 models
    5610 
    5611 > hide #!7 models
    5612 
    5613 > hide #!9 models
    5614 
    5615 > hide #!12 models
    5616 
    5617 > hide #!13 models
    5618 
    5619 > hide #!15 models
    5620 
    5621 > fitmap #3.2 inMap #1.2
    5622 
    5623 Fit molecule pflB 2 (#3.2) to map HP-PflA-PflB-2.1A.mrc (#1.2) using 5767
    5624 atoms 
    5625 average map value = 3.673, steps = 132 
    5626 shifted from previous position = 2.15 
    5627 rotated from previous position = 21.6 degrees 
    5628 atoms outside contour = 1634, contour level = 0.78314 
    5629  
    5630 Position of pflB 2 (#3.2) relative to HP-PflA-PflB-2.1A.mrc (#1.2)
    5631 coordinates: 
    5632 Matrix rotation and translation 
    5633 0.80291160 -0.52157229 0.28860930 60.18065259 
    5634 -0.56854588 -0.81555340 0.10783445 40.94646428 
    5635 0.17913284 -0.25066916 -0.95135505 -40.20640584 
    5636 Axis -0.94897880 0.28979025 -0.12434167 
    5637 Axis point 0.00000000 27.39177205 -26.68750735 
    5638 Rotation angle (degrees) 169.11203642 
    5639 Shift along axis -40.24494598 
    5640  
    5641 
    5642 > fitmap #3.2 inMap #1.2
    5643 
    5644 Fit molecule pflB 2 (#3.2) to map HP-PflA-PflB-2.1A.mrc (#1.2) using 5767
    5645 atoms 
    5646 average map value = 3.673, steps = 80 
    5647 shifted from previous position = 0.0367 
    5648 rotated from previous position = 0.0746 degrees 
    5649 atoms outside contour = 1631, contour level = 0.78314 
    5650  
    5651 Position of pflB 2 (#3.2) relative to HP-PflA-PflB-2.1A.mrc (#1.2)
    5652 coordinates: 
    5653 Matrix rotation and translation 
    5654 0.80327839 -0.52166751 0.28741411 60.12735411 
    5655 -0.56827441 -0.81577700 0.10757370 40.95182051 
    5656 0.17834811 -0.24974171 -0.95174632 -40.19180750 
    5657 Axis -0.94907957 0.28969450 -0.12379444 
    5658 Axis point 0.00000000 27.39239640 -26.64929415 
    5659 Rotation angle (degrees) 169.14972727 
    5660 Shift along axis -40.22660404 
    5661  
    5662 
    5663 > fitmap #3.2 inMap #1.2
    5664 
    5665 Fit molecule pflB 2 (#3.2) to map HP-PflA-PflB-2.1A.mrc (#1.2) using 5767
    5666 atoms 
    5667 average map value = 3.673, steps = 80 
    5668 shifted from previous position = 0.024 
    5669 rotated from previous position = 0.0303 degrees 
    5670 atoms outside contour = 1631, contour level = 0.78314 
    5671  
    5672 Position of pflB 2 (#3.2) relative to HP-PflA-PflB-2.1A.mrc (#1.2)
    5673 coordinates: 
    5674 Matrix rotation and translation 
    5675 0.80354108 -0.52137777 0.28720546 60.10572930 
    5676 -0.56799800 -0.81591769 0.10796587 40.96659533 
    5677 0.17804501 -0.24988714 -0.95176490 -40.18454753 
    5678 Axis -0.94914803 0.28953069 -0.12365273 
    5679 Axis point 0.00000000 27.38819739 -26.64343560 
    5680 Rotation angle (degrees) 169.13399735 
    5681 Shift along axis -40.21921879 
    5682  
    5683 
    5684 > fitmap #3.2 inMap #1.2
    5685 
    5686 Fit molecule pflB 2 (#3.2) to map HP-PflA-PflB-2.1A.mrc (#1.2) using 5767
    5687 atoms 
    5688 average map value = 3.673, steps = 64 
    5689 shifted from previous position = 0.0348 
    5690 rotated from previous position = 0.0278 degrees 
    5691 atoms outside contour = 1636, contour level = 0.78314 
    5692  
    5693 Position of pflB 2 (#3.2) relative to HP-PflA-PflB-2.1A.mrc (#1.2)
    5694 coordinates: 
    5695 Matrix rotation and translation 
    5696 0.80346674 -0.52137448 0.28741934 60.14388335 
    5697 -0.56797181 -0.81599222 0.10753953 40.96691971 
    5698 0.17846358 -0.24965051 -0.95174860 -40.19178707 
    5699 Axis -0.94913002 0.28951867 -0.12381903 
    5700 Axis point 0.00000000 27.39728385 -26.65040903 
    5701 Rotation angle (degrees) 169.15416414 
    5702 Shift along axis -40.24716905 
    5703  
    5704 
    5705 > fitmap #3.2 inMap #1.2
    5706 
    5707 Fit molecule pflB 2 (#3.2) to map HP-PflA-PflB-2.1A.mrc (#1.2) using 5767
    5708 atoms 
    5709 average map value = 3.673, steps = 76 
    5710 shifted from previous position = 0.0336 
    5711 rotated from previous position = 0.0166 degrees 
    5712 atoms outside contour = 1633, contour level = 0.78314 
    5713  
    5714 Position of pflB 2 (#3.2) relative to HP-PflA-PflB-2.1A.mrc (#1.2)
    5715 coordinates: 
    5716 Matrix rotation and translation 
    5717 0.80342788 -0.52130240 0.28765860 60.12353808 
    5718 -0.56798849 -0.81596225 0.10767872 40.95156780 
    5719 0.17858538 -0.24989885 -0.95166058 -40.21197705 
    5720 Axis -0.94911865 0.28951319 -0.12391895 
    5721 Axis point 0.00000000 27.38281428 -26.66426324 
    5722 Rotation angle (degrees) 169.14212239 
    5723 Shift along axis -40.22532595 
    5724  
    5725 
    5726 > fitmap #3.2 inMap #1.2
    5727 
    5728 Fit molecule pflB 2 (#3.2) to map HP-PflA-PflB-2.1A.mrc (#1.2) using 5767
    5729 atoms 
    5730 average map value = 3.673, steps = 84 
    5731 shifted from previous position = 0.0115 
    5732 rotated from previous position = 0.0325 degrees 
    5733 atoms outside contour = 1631, contour level = 0.78314 
    5734  
    5735 Position of pflB 2 (#3.2) relative to HP-PflA-PflB-2.1A.mrc (#1.2)
    5736 coordinates: 
    5737 Matrix rotation and translation 
    5738 0.80325146 -0.52136987 0.28802878 60.12732889 
    5739 -0.56821419 -0.81576401 0.10798956 40.95545529 
    5740 0.17866101 -0.25040481 -0.95151337 -40.20604415 
    5741 Axis -0.94906953 0.28961845 -0.12404915 
    5742 Axis point 0.00000000 27.38373734 -26.67254520 
    5743 Rotation angle (degrees) 169.11644776 
    5744 Shift along axis -40.21603469 
    5745  
    5746 
    5747 > show #!9 models
    5748 
    5749 > view orient
    5750 
    5751 > hide #!3 models
    5752 
    5753 > show #!3 models
    5754 
    5755 > hide #!1 models
    5756 
    5757 > show #!6 models
    5758 
    5759 > show #!7 models
    5760 
    5761 > show #!12 models
    5762 
    5763 > show #!13 models
    5764 
    5765 > show #!15 models
    5766 
    5767 > view orient
    5768 
    5769 [Repeated 1 time(s)]
    5770 
    5771 > open "C:/Users/Jack Botting/Documents/alphafold
    5772 > results/fold_pylori_flgy_pfla2_nosig(1)/fold_pylori_flgy_pfla2_nosig_model_0.cif"
    5773 
    5774 Chain information for fold_pylori_flgy_pfla2_nosig_model_0.cif #2 
    5775 --- 
    5776 Chain | Description 
    5777 A B | . 
    5778 C D | . 
    5779  
    5780 
    5781 > hide #2,A,B,C cartoon
    5782 
    5783 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
    5784 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword 
    5785 
    5786 > hide #2/A,B,C cartoons
    5787 
    5788 > mmaker #2/D to #9.10.1
    5789 
    5790 Parameters 
    5791 --- 
    5792 Chain pairing | bb 
    5793 Alignment algorithm | Needleman-Wunsch 
    5794 Similarity matrix | BLOSUM-62 
    5795 SS fraction | 0.3 
    5796 Gap open (HH/SS/other) | 18/18/6 
    5797 Gap extend | 1 
    5798 SS matrix |  |  | H | S | O 
    5799 ---|---|---|--- 
    5800 H | 6 | -9 | -6 
    5801 S |  | 6 | -6 
    5802 O |  |  | 4 
    5803 Iteration cutoff | 2 
    5804  
    5805 Matchmaker pflA 1, chain A (#9.10.1) with
    5806 fold_pylori_flgy_pfla2_nosig_model_0.cif, chain D (#2), sequence alignment
    5807 score = 3174.5 
    5808 RMSD between 277 pruned atom pairs is 0.741 angstroms; (across all 612 pairs:
    5809 11.168) 
    5810  
    5811 
    5812 > mmaker #2/D to #9.9.1
    5813 
    5814 Parameters 
    5815 --- 
    5816 Chain pairing | bb 
    5817 Alignment algorithm | Needleman-Wunsch 
    5818 Similarity matrix | BLOSUM-62 
    5819 SS fraction | 0.3 
    5820 Gap open (HH/SS/other) | 18/18/6 
    5821 Gap extend | 1 
    5822 SS matrix |  |  | H | S | O 
    5823 ---|---|---|--- 
    5824 H | 6 | -9 | -6 
    5825 S |  | 6 | -6 
    5826 O |  |  | 4 
    5827 Iteration cutoff | 2 
    5828  
    5829 Matchmaker pflA 1, chain A (#9.9.1) with
    5830 fold_pylori_flgy_pfla2_nosig_model_0.cif, chain D (#2), sequence alignment
    5831 score = 3170.9 
    5832 RMSD between 292 pruned atom pairs is 0.771 angstroms; (across all 612 pairs:
    5833 7.930) 
    5834  
    5835 
    5836 > show #!1 models
    5837 
    5838 > hide #!1 models
    5839 
    5840 > show #!1 models
    5841 
    5842 > mmaker #2/D to #9.1.1
    5843 
    5844 Parameters 
    5845 --- 
    5846 Chain pairing | bb 
    5847 Alignment algorithm | Needleman-Wunsch 
    5848 Similarity matrix | BLOSUM-62 
    5849 SS fraction | 0.3 
    5850 Gap open (HH/SS/other) | 18/18/6 
    5851 Gap extend | 1 
    5852 SS matrix |  |  | H | S | O 
    5853 ---|---|---|--- 
    5854 H | 6 | -9 | -6 
    5855 S |  | 6 | -6 
    5856 O |  |  | 4 
    5857 Iteration cutoff | 2 
    5858  
    5859 Matchmaker pflA 1, chain A (#9.1.1) with
    5860 fold_pylori_flgy_pfla2_nosig_model_0.cif, chain D (#2), sequence alignment
    5861 score = 3170.9 
    5862 RMSD between 292 pruned atom pairs is 0.771 angstroms; (across all 612 pairs:
    5863 7.930) 
    5864  
    5865 
    5866 > close #2
    5867 
    5868 > hide #!1 models
    5869 
    5870 > hide #!3.2 models
    5871 
    5872 > hide #!6 models
    5873 
    5874 > hide #!3 models
    5875 
    5876 > hide #!7 models
    5877 
    5878 > hide #!9 models
    5879 
    5880 > hide #!12 models
    5881 
    5882 > hide #!13 models
    5883 
    5884 > hide #!15 models
    5885 
    5886 > open "C:/Users/Jack Botting/Documents/alphafold
    5887 > results/fold_pylori_flgy_pfla2_nosig(1)/fold_pylori_flgy_pfla2_nosig_model_4.cif"
    5888 
    5889 Chain information for fold_pylori_flgy_pfla2_nosig_model_4.cif #2 
    5890 --- 
    5891 Chain | Description 
    5892 A B | . 
    5893 C D | . 
    5894  
    5895 
    5896 > open "C:/Users/Jack Botting/Documents/alphafold
    5897 > results/fold_pylori_flgy_pfla2_nosig(1)/fold_pylori_flgy_pfla2_nosig_model_0.cif"
    5898 
    5899 Chain information for fold_pylori_flgy_pfla2_nosig_model_0.cif #4 
    5900 --- 
    5901 Chain | Description 
    5902 A B | . 
    5903 C D | . 
    5904  
    5905 
    5906 > open "C:/Users/Jack Botting/Documents/alphafold
    5907 > results/fold_pylori_flgy_pfla2_nosig(1)/fold_pylori_flgy_pfla2_nosig_model_1.cif"
    5908 
    5909 Chain information for fold_pylori_flgy_pfla2_nosig_model_1.cif #5 
    5910 --- 
    5911 Chain | Description 
    5912 A B | . 
    5913 C D | . 
    5914  
    5915 
    5916 > open "C:/Users/Jack Botting/Documents/alphafold
    5917 > results/fold_pylori_flgy_pfla2_nosig(1)/fold_pylori_flgy_pfla2_nosig_model_2.cif"
    5918 
    5919 Chain information for fold_pylori_flgy_pfla2_nosig_model_2.cif #8 
    5920 --- 
    5921 Chain | Description 
    5922 A B | . 
    5923 C D | . 
    5924  
    5925 
    5926 > open "C:/Users/Jack Botting/Documents/alphafold
    5927 > results/fold_pylori_flgy_pfla2_nosig(1)/fold_pylori_flgy_pfla2_nosig_model_3.cif"
    5928 
    5929 Chain information for fold_pylori_flgy_pfla2_nosig_model_3.cif #10 
    5930 --- 
    5931 Chain | Description 
    5932 A B | . 
    5933 C D | . 
    5934  
    5935 
    5936 > mmaker #4,5,8,10 to #2
    5937 
    5938 Parameters 
    5939 --- 
    5940 Chain pairing | bb 
    5941 Alignment algorithm | Needleman-Wunsch 
    5942 Similarity matrix | BLOSUM-62 
    5943 SS fraction | 0.3 
    5944 Gap open (HH/SS/other) | 18/18/6 
    5945 Gap extend | 1 
    5946 SS matrix |  |  | H | S | O 
    5947 ---|---|---|--- 
    5948 H | 6 | -9 | -6 
    5949 S |  | 6 | -6 
    5950 O |  |  | 4 
    5951 Iteration cutoff | 2 
    5952  
    5953 Matchmaker fold_pylori_flgy_pfla2_nosig_model_4.cif, chain C (#2) with
    5954 fold_pylori_flgy_pfla2_nosig_model_0.cif, chain C (#4), sequence alignment
    5955 score = 4034.6 
    5956 RMSD between 143 pruned atom pairs is 1.084 angstroms; (across all 781 pairs:
    5957 15.051) 
    5958  
    5959 Matchmaker fold_pylori_flgy_pfla2_nosig_model_4.cif, chain D (#2) with
    5960 fold_pylori_flgy_pfla2_nosig_model_1.cif, chain C (#5), sequence alignment
    5961 score = 4037.6 
    5962 RMSD between 491 pruned atom pairs is 0.943 angstroms; (across all 781 pairs:
    5963 22.995) 
    5964  
    5965 Matchmaker fold_pylori_flgy_pfla2_nosig_model_4.cif, chain D (#2) with
    5966 fold_pylori_flgy_pfla2_nosig_model_2.cif, chain C (#8), sequence alignment
    5967 score = 4026.2 
    5968 RMSD between 473 pruned atom pairs is 1.081 angstroms; (across all 781 pairs:
    5969 3.295) 
    5970  
    5971 Matchmaker fold_pylori_flgy_pfla2_nosig_model_4.cif, chain D (#2) with
    5972 fold_pylori_flgy_pfla2_nosig_model_3.cif, chain D (#10), sequence alignment
    5973 score = 4011.8 
    5974 RMSD between 455 pruned atom pairs is 1.046 angstroms; (across all 781 pairs:
    5975 7.826) 
    5976  
    5977 
    5978 > hide #2 models
    5979 
    5980 > hide #8 models
    5981 
    5982 > hide #10 models
    5983 
    5984 > hide #5 models
    5985 
    5986 > show #5 models
    5987 
    5988 > show #2 models
    5989 
    5990 > hide #4 models
    5991 
    5992 > show #8 models
    5993 
    5994 > show #10 models
    5995 
    5996 > show #4 models
    5997 
    5998 > select add #4
    5999 
    6000 15878 atoms, 16162 bonds, 1960 residues, 1 model selected 
    6001 
    6002 > ui mousemode right "translate selected models"
    6003 
    6004 > view matrix models
    6005 > #4,-0.48287,0.82725,0.2872,-23.127,-0.86081,-0.50862,0.017761,-16.209,0.16077,-0.23865,0.9577,-76.601
    6006 
    6007 > select clear
    6008 
    6009 > mmaker #4/D to #4/C
    6010 
    6011 Must use different reference and match structures 
    6012 
    6013 > split #4
    6014 
    6015 Split fold_pylori_flgy_pfla2_nosig_model_0.cif (#4) into 4 models 
    6016 Chain information for fold_pylori_flgy_pfla2_nosig_model_0.cif A #4.1 
    6017 --- 
    6018 Chain | Description 
    6019 A | No description available 
    6020  
    6021 Chain information for fold_pylori_flgy_pfla2_nosig_model_0.cif B #4.2 
    6022 --- 
    6023 Chain | Description 
    6024 B | No description available 
    6025  
    6026 Chain information for fold_pylori_flgy_pfla2_nosig_model_0.cif C #4.3 
    6027 --- 
    6028 Chain | Description 
    6029 C | No description available 
    6030  
    6031 Chain information for fold_pylori_flgy_pfla2_nosig_model_0.cif D #4.4 
    6032 --- 
    6033 Chain | Description 
    6034 D | No description available 
    6035  
    6036 
    6037 > mmaker #4.3 to #4.4
    6038 
    6039 Parameters 
    6040 --- 
    6041 Chain pairing | bb 
    6042 Alignment algorithm | Needleman-Wunsch 
    6043 Similarity matrix | BLOSUM-62 
    6044 SS fraction | 0.3 
    6045 Gap open (HH/SS/other) | 18/18/6 
    6046 Gap extend | 1 
    6047 SS matrix |  |  | H | S | O 
    6048 ---|---|---|--- 
    6049 H | 6 | -9 | -6 
    6050 S |  | 6 | -6 
    6051 O |  |  | 4 
    6052 Iteration cutoff | 2 
    6053  
    6054 Matchmaker fold_pylori_flgy_pfla2_nosig_model_0.cif D, chain D (#4.4) with
    6055 fold_pylori_flgy_pfla2_nosig_model_0.cif C, chain C (#4.3), sequence alignment
    6056 score = 4058 
    6057 RMSD between 624 pruned atom pairs is 0.804 angstroms; (across all 781 pairs:
    6058 1.684) 
    6059  
    6060 
    6061 > close #4
    6062 
    6063 > split #5
    6064 
    6065 Split fold_pylori_flgy_pfla2_nosig_model_1.cif (#5) into 4 models 
    6066 Chain information for fold_pylori_flgy_pfla2_nosig_model_1.cif A #5.1 
    6067 --- 
    6068 Chain | Description 
    6069 A | No description available 
    6070  
    6071 Chain information for fold_pylori_flgy_pfla2_nosig_model_1.cif B #5.2 
    6072 --- 
    6073 Chain | Description 
    6074 B | No description available 
    6075  
    6076 Chain information for fold_pylori_flgy_pfla2_nosig_model_1.cif C #5.3 
    6077 --- 
    6078 Chain | Description 
    6079 C | No description available 
    6080  
    6081 Chain information for fold_pylori_flgy_pfla2_nosig_model_1.cif D #5.4 
    6082 --- 
    6083 Chain | Description 
    6084 D | No description available 
    6085  
    6086 
    6087 > mmaker #5e.3 to #5.4
    6088 
    6089 > matchmaker #5e.3 to #5.4
    6090 
    6091 Missing or invalid "matchAtoms" argument: invalid atoms specifier 
    6092 
    6093 > hide #8 models
    6094 
    6095 > hide #10 models
    6096 
    6097 > hide #2 models
    6098 
    6099 > mmaker #5.3 to #5.4
    6100 
    6101 Parameters 
    6102 --- 
    6103 Chain pairing | bb 
    6104 Alignment algorithm | Needleman-Wunsch 
    6105 Similarity matrix | BLOSUM-62 
    6106 SS fraction | 0.3 
    6107 Gap open (HH/SS/other) | 18/18/6 
    6108 Gap extend | 1 
    6109 SS matrix |  |  | H | S | O 
    6110 ---|---|---|--- 
    6111 H | 6 | -9 | -6 
    6112 S |  | 6 | -6 
    6113 O |  |  | 4 
    6114 Iteration cutoff | 2 
    6115  
    6116 Matchmaker fold_pylori_flgy_pfla2_nosig_model_1.cif D, chain D (#5.4) with
    6117 fold_pylori_flgy_pfla2_nosig_model_1.cif C, chain C (#5.3), sequence alignment
    6118 score = 4058.6 
    6119 RMSD between 553 pruned atom pairs is 0.951 angstroms; (across all 781 pairs:
    6120 4.311) 
    6121  
    6122 
    6123 > show #!9 models
    6124 
    6125 > select ~sel & ##selected
    6126 
    6127 Nothing selected 
    6128 
    6129 > mmaker #5.3 to #9.1.1
    6130 
    6131 Parameters 
    6132 --- 
    6133 Chain pairing | bb 
    6134 Alignment algorithm | Needleman-Wunsch 
    6135 Similarity matrix | BLOSUM-62 
    6136 SS fraction | 0.3 
    6137 Gap open (HH/SS/other) | 18/18/6 
    6138 Gap extend | 1 
    6139 SS matrix |  |  | H | S | O 
    6140 ---|---|---|--- 
    6141 H | 6 | -9 | -6 
    6142 S |  | 6 | -6 
    6143 O |  |  | 4 
    6144 Iteration cutoff | 2 
    6145  
    6146 Matchmaker pflA 1, chain A (#9.1.1) with
    6147 fold_pylori_flgy_pfla2_nosig_model_1.cif C, chain C (#5.3), sequence alignment
    6148 score = 3184.1 
    6149 RMSD between 177 pruned atom pairs is 0.625 angstroms; (across all 612 pairs:
    6150 18.352) 
    6151  
    6152 
    6153 > hide #5.1 models
    6154 
    6155 > hide #5.2 models
    6156 
    6157 > hide #5.4 models
    6158 
    6159 > show #!1 models
    6160 
    6161 > close #2,8,10#5
    6162 
    6163 > view orient
    6164 
    6165 [Repeated 1 time(s)]
    6166 
    6167 > show #!6 models
    6168 
    6169 > view orient
    6170 
    6171 > show #!3 models
    6172 
    6173 > show #!3.2 models
    6174 
    6175 > rename #3.2 id #4
    6176 
    6177 > close #3
    6178 
    6179 > rename #9 id #2
    6180 
    6181 > rename #7 id #3
    6182 
    6183 > rename #12 id #7
    6184 
    6185 > rename #13 id #8
    6186 
    6187 > rename #15 id #9
    6188 
    6189 > rename #4 "pflB "
    6190 
    6191 > show #!7 models
    6192 
    6193 > show #!8 models
    6194 
    6195 > show #!9 models
    6196 
    6197 > show #!3 models
    6198 
    6199 > save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
    6200 > pflA pflB.cxs"
    6201 
    6202 ——— End of log from Tue Jun 4 11:39:36 2024 ———
    6203 
    6204 opened ChimeraX session 
    6205 
    6206 > color #3.*.1 orchid
    6207 
    6208 > color #7 yellow
    6209 
    6210 > color #8 forest green
    6211 
    6212 > color #8 green
    6213 
    6214 > color #2 #7b68ee
    6215 
    6216 > color #2 mediumslateblue models
    6217 
    6218 > color #2 #6152bdff models
    6219 
    6220 > color #2 #40377eff models
    6221 
    6222 > color #2 #5a4db1ff models
    6223 
    6224 > color #2 #5f51baff models
    6225 
    6226 > hide #!6 models
    6227 
    6228 > hide #!4 models
    6229 
    6230 > hide #!3 models
    6231 
    6232 > hide #!2 models
    6233 
    6234 > hide #!1.2 models
    6235 
    6236 > show #!1.2 models
    6237 
    6238 > hide #!7 models
    6239 
    6240 > hide #!8 models
    6241 
    6242 > hide #!9 models
    6243 
    6244 Segmenting HP-PflA-PflB-2.1A.mrc, density threshold 0.783137 
    6245 Showing 283 region surfaces 
    6246 3344 watershed regions, grouped to 283 regions 
    6247 Showing HP-PflA-PflB-2.1A.seg - 283 regions, 283 surfaces 
    6248 
    6249 > select add #5
    6250 
    6251 284 models selected 
    6252 
    6253 > ui mousemode right "translate selected models"
    6254 
    6255 > view matrix models #5,1,0,0,209.3,0,1,0,-34.119,0,0,1,69.594
    6256 
    6257 > view matrix models #5,1,0,0,208.49,0,1,0,-8.9177,0,0,1,64.454
    6258 
    6259 > view matrix models #5,1,0,0,211.45,0,1,0,-9.0965,0,0,1,64.729
    6260 
    6261 > select clear
    6262 
    6263 > show #!6 models
    6264 
    6265 > select #5.190
    6266 
    6267 1 model selected 
    6268 
    6269 > select add #5.104
    6270 
    6271 2 models selected 
    6272 Ungrouped to 4 regions 
    6273 Ungrouped to 12 regions 
    6274 Ungrouped to 7 regions 
    6275 Ungrouped to 0 regions 
    6276 
    6277 > select add #5
    6278 
    6279 299 models selected 
    6280 
    6281 > view matrix models #5,1,0,0,212.19,0,1,0,-8.3139,0,0,1,65.137
    6282 
    6283 > select clear
    6284 
    6285 > show #!2 models
    6286 
    6287 > select #5.37
    6288 
    6289 1 model selected 
    6290 
    6291 > close #5
    6292 
    6293 > view orient
    6294 
    6295 > select clear
    6296 
    6297 > hide #!6 models
    6298 
    6299 > view orient
    6300 
    6301 > save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
    6302 > pflA pflB.cxs"
    6303 
    6304 ——— End of log from Tue Jun 4 16:15:45 2024 ———
    6305 
    6306 opened ChimeraX session 
    6307 Segmenting HP-PflA-PflB-2.1A.mrc, density threshold 0.783137 
    6308 Showing 283 region surfaces 
    6309 3344 watershed regions, grouped to 283 regions 
    6310 Showing HP-PflA-PflB-2.1A.seg - 283 regions, 283 surfaces 
    6311 
    6312 > select add #5
    6313 
    6314 284 models selected 
    6315 
    6316 > view matrix models #5,1,0,0,213.13,0,1,0,-12.179,0,0,1,64.138
    6317 
    6318 > view matrix models #5,1,0,0,214.02,0,1,0,-6.5896,0,0,1,64.448
    6319 
    6320 > select clear
    6321 
    6322 > ui tool show "Side View"
    6323 
    6324 > view orient
    6325 
    6326 > hide #!1.2 models
    6327 
    6328 > select #5.248
    6329 
    6330 1 model selected 
    6331 
    6332 > select add #5.37
    6333 
    6334 2 models selected 
    6335 
    6336 > select add #5.31
    6337 
    6338 3 models selected 
    6339 
    6340 > show #!4 models
    6341 
    6342 > select clear
    6343 
    6344 > show #!9 models
    6345 
    6346 > select #5.248
    6347 
    6348 1 model selected 
    6349 
    6350 > select add #5.37
    6351 
    6352 2 models selected 
    6353 
    6354 > select add #5.31
    6355 
    6356 3 models selected 
    6357 
    6358 > select add #5.90
    6359 
    6360 4 models selected 
    6361 
    6362 > select add #5.141
    6363 
    6364 5 models selected 
    6365 
    6366 > select add #5.104
    6367 
    6368 6 models selected 
    6369 
    6370 > view orient
    6371 
    6372 > sym clear #4
    6373 
    6374 > select add #5.28
    6375 
    6376 7 models selected 
    6377 
    6378 > select add #5.12
    6379 
    6380 8 models selected 
    6381 
    6382 > select add #5.62
    6383 
    6384 9 models selected 
    6385 
    6386 > select add #5.42
    6387 
    6388 10 models selected 
    6389 
    6390 > show #!7 models
    6391 
    6392 > hide #!7 models
    6393 
    6394 Region has 27 adjacent regions 
    6395 [Repeated 1 time(s)]
    6396 
    6397 > select add #5.75
    6398 
    6399 11 models selected 
    6400 
    6401 > select add #5.228
    6402 
    6403 12 models selected 
    6404 Region has 27 adjacent regions 
    6405 [Repeated 1 time(s)]Grouped 12 regions 
    6406 
    6407 > select clear
    6408 
    6409 Showing 272 region surfaces 
    6410 
    6411 > select #5.12
    6412 
    6413 1 model selected 
    6414 
    6415 > select add #5.174
    6416 
    6417 2 models selected 
    6418 
    6419 > select add #5.169
    6420 
    6421 3 models selected 
    6422 
    6423 > select add #5.46
    6424 
    6425 4 models selected 
    6426 Grouped 4 regions 
    6427 Ungrouped to 4 regions 
    6428 Ungrouped to 19 regions 
    6429 Ungrouped to 50 regions 
    6430 Ungrouped to 58 regions 
    6431 Ungrouped to 25 regions 
    6432 Ungrouped to 2 regions 
    6433 Ungrouped to 0 regions 
    6434 
    6435 > select #5.320
    6436 
    6437 1 model selected 
    6438 
    6439 > select add #5.364
    6440 
    6441 2 models selected 
    6442 
    6443 > select add #5.363
    6444 
    6445 3 models selected 
    6446 
    6447 > select add #5.291
    6448 
    6449 4 models selected 
    6450 
    6451 > select add #5.340
    6452 
    6453 5 models selected 
    6454 
    6455 > select add #5.324
    6456 
    6457 6 models selected 
    6458 
    6459 > select add #5.326
    6460 
    6461 7 models selected 
    6462 
    6463 > select add #5.339
    6464 
    6465 8 models selected 
    6466 
    6467 > select add #5.31
    6468 
    6469 9 models selected 
    6470 
    6471 > select add #5.28
    6472 
    6473 10 models selected 
    6474 
    6475 > select add #5.368
    6476 
    6477 11 models selected 
    6478 
    6479 > select add #5.369
    6480 
    6481 12 models selected 
    6482 
    6483 > select add #5.322
    6484 
    6485 13 models selected 
    6486 
    6487 > select add #5.367
    6488 
    6489 14 models selected 
    6490 
    6491 > select add #5.290
    6492 
    6493 15 models selected 
    6494 
    6495 > select add #5.321
    6496 
    6497 16 models selected 
    6498 
    6499 > select add #5.169
    6500 
    6501 17 models selected 
    6502 
    6503 > select add #5.141
    6504 
    6505 18 models selected 
    6506 
    6507 > select subtract #5.321
    6508 
    6509 17 models selected 
    6510 
    6511 > select subtract #5.169
    6512 
    6513 16 models selected 
    6514 
    6515 > select subtract #5.141
    6516 
    6517 15 models selected 
    6518 Grouped 15 regions 
    6519 
    6520 > select clear
    6521 
    6522 > select add #5.321
    6523 
    6524 1 model selected 
    6525 
    6526 > select add #5.169
    6527 
    6528 2 models selected 
    6529 
    6530 > select add #5.141
    6531 
    6532 3 models selected 
    6533 
    6534 > select add #5.349
    6535 
    6536 4 models selected 
    6537 
    6538 > select add #5.348
    6539 
    6540 5 models selected 
    6541 
    6542 > select add #5.342
    6543 
    6544 6 models selected 
    6545 
    6546 > select add #5.316
    6547 
    6548 7 models selected 
    6549 
    6550 > select add #5.344
    6551 
    6552 8 models selected 
    6553 
    6554 > select add #5.62
    6555 
    6556 9 models selected 
    6557 
    6558 > select add #5.104
    6559 
    6560 10 models selected 
    6561 
    6562 > select add #5.305
    6563 
    6564 11 models selected 
    6565 
    6566 > select subtract #5.62
    6567 
    6568 10 models selected 
    6569 
    6570 > select subtract #5.104
    6571 
    6572 9 models selected 
    6573 
    6574 > select add #5.297
    6575 
    6576 10 models selected 
    6577 
    6578 > select add #5.62
    6579 
    6580 11 models selected 
    6581 Region has 38 adjacent regions 
    6582 
    6583 > select add #5.104
    6584 
    6585 12 models selected 
    6586 Region has 38 adjacent regions 
    6587 Grouped 12 regions 
    6588 Region has 27 adjacent regions 
    6589 
    6590 > select add #5.314
    6591 
    6592 2 models selected 
    6593 Grouped 2 regions 
    6594 
    6595 > hide #!2 models
    6596 
    6597 Region has 26 adjacent regions 
    6598 
    6599 > select add #5.347
    6600 
    6601 2 models selected 
    6602 Region has 26 adjacent regions 
    6603 [Repeated 4 time(s)]
    6604 
    6605 > select add #5.295
    6606 
    6607 3 models selected 
    6608 Grouped 3 regions 
    6609 Region has 25 adjacent regions 
    6610 [Repeated 1 time(s)]
    6611 
    6612 > select clear
    6613 
    6614 > select #5.310
    6615 
    6616 1 model selected 
    6617 
    6618 > select add #5.330
    6619 
    6620 2 models selected 
    6621 
    6622 > select add #5.350
    6623 
    6624 3 models selected 
    6625 
    6626 > select add #5.351
    6627 
    6628 4 models selected 
    6629 
    6630 > select add #5.379
    6631 
    6632 5 models selected 
    6633 Grouped 5 regions 
    6634 Region has 10 adjacent regions 
    6635 
    6636 > select add #5.293
    6637 
    6638 2 models selected 
    6639 
    6640 > select add #5.378
    6641 
    6642 3 models selected 
    6643 
    6644 > select add #5.292
    6645 
    6646 4 models selected 
    6647 
    6648 > select add #5.380
    6649 
    6650 5 models selected 
    6651 
    6652 > select add #5.46
    6653 
    6654 6 models selected 
    6655 Grouped 6 regions 
    6656 Region has 7 adjacent regions 
    6657 
    6658 > select add #5.288
    6659 
    6660 2 models selected 
    6661 
    6662 > select add #5.309
    6663 
    6664 3 models selected 
    6665 Grouped 3 regions 
    6666 Region has 13 adjacent regions 
    6667 
    6668 > select add #5.304
    6669 
    6670 2 models selected 
    6671 Grouped 2 regions 
    6672 
    6673 > select add #5.303
    6674 
    6675 2 models selected 
    6676 
    6677 > select add #5.302
    6678 
    6679 3 models selected 
    6680 Grouped 3 regions 
    6681 Region has 12 adjacent regions 
    6682 [Repeated 1 time(s)]
    6683 
    6684 > select add #5.31
    6685 
    6686 2 models selected 
    6687 Region has 29 adjacent regions 
    6688 
    6689 > select add #5.28
    6690 
    6691 3 models selected 
    6692 Region has 38 adjacent regions 
    6693 [Repeated 1 time(s)]
    6694 
    6695 > select add #5.360
    6696 
    6697 4 models selected 
    6698 Region has 41 adjacent regions 
    6699 
    6700 > select #5.28
    6701 
    6702 1 model selected 
    6703 
    6704 > select add #5.31
    6705 
    6706 2 models selected 
    6707 
    6708 > select add #5.42
    6709 
    6710 3 models selected 
    6711 
    6712 > select clear
    6713 
    6714 > select #5.31
    6715 
    6716 1 model selected 
    6717 Ungrouped to 3 regions 
    6718 Ungrouped to 2 regions 
    6719 Ungrouped to 12 regions 
    6720 Ungrouped to 0 regions 
    6721 
    6722 > select #5.169
    6723 
    6724 1 model selected 
    6725 
    6726 > select add #5.291
    6727 
    6728 2 models selected 
    6729 
    6730 > select add #5.293
    6731 
    6732 3 models selected 
    6733 
    6734 > select add #5.31
    6735 
    6736 4 models selected 
    6737 
    6738 > select add #5.287
    6739 
    6740 5 models selected 
    6741 
    6742 > select add #5.302
    6743 
    6744 6 models selected 
    6745 
    6746 > select add #5.288
    6747 
    6748 7 models selected 
    6749 
    6750 > select add #5.104
    6751 
    6752 8 models selected 
    6753 
    6754 > select add #5.62
    6755 
    6756 9 models selected 
    6757 
    6758 > select add #5.297
    6759 
    6760 10 models selected 
    6761 
    6762 > select add #5.303
    6763 
    6764 11 models selected 
    6765 
    6766 > select add #5.46
    6767 
    6768 12 models selected 
    6769 
    6770 > select add #5.295
    6771 
    6772 13 models selected 
    6773 
    6774 > select add #5.290
    6775 
    6776 14 models selected 
    6777 
    6778 > select add #5.292
    6779 
    6780 15 models selected 
    6781 Grouped 15 regions 
    6782 Showing 329 region surfaces 
    6783 
    6784 > select #5.360
    6785 
    6786 1 model selected 
    6787 
    6788 > select add #5.359
    6789 
    6790 2 models selected 
    6791 
    6792 > select add #5.306
    6793 
    6794 3 models selected 
    6795 
    6796 > select add #5.318
    6797 
    6798 4 models selected 
    6799 Region has 13 adjacent regions 
    6800 
    6801 > select add #5.319
    6802 
    6803 5 models selected 
    6804 
    6805 > select add #5.371
    6806 
    6807 6 models selected 
    6808 
    6809 > select add #5.370
    6810 
    6811 7 models selected 
    6812 
    6813 > select add #5.374
    6814 
    6815 8 models selected 
    6816 
    6817 > select add #5.365
    6818 
    6819 9 models selected 
    6820 
    6821 > select add #5.354
    6822 
    6823 10 models selected 
    6824 
    6825 > select add #5.353
    6826 
    6827 11 models selected 
    6828 Grouped 11 regions 
    6829 Region has 11 adjacent regions 
    6830 
    6831 > select add #5.329
    6832 
    6833 2 models selected 
    6834 
    6835 > select add #5.328
    6836 
    6837 3 models selected 
    6838 
    6839 > select add #5.375
    6840 
    6841 4 models selected 
    6842 
    6843 > select add #5.327
    6844 
    6845 5 models selected 
    6846 
    6847 > select add #5.335
    6848 
    6849 6 models selected 
    6850 
    6851 > select add #5.336
    6852 
    6853 7 models selected 
    6854 
    6855 > select add #5.337
    6856 
    6857 8 models selected 
    6858 
    6859 > select add #5.334
    6860 
    6861 9 models selected 
    6862 Grouped 9 regions 
    6863 Region has 6 adjacent regions 
    6864 
    6865 > select add #5.312
    6866 
    6867 2 models selected 
    6868 
    6869 > select add #5.313
    6870 
    6871 3 models selected 
    6872 
    6873 > select add #5.343
    6874 
    6875 4 models selected 
    6876 
    6877 > select subtract #5.343
    6878 
    6879 3 models selected 
    6880 Grouped 3 regions 
    6881 Region has 4 adjacent regions 
    6882 [Repeated 1 time(s)]
    6883 
    6884 > select clear
    6885 
    6886 Showing 264 grouped regions 
    6887 
    6888 > select #5.28
    6889 
    6890 1 model selected 
    6891 
    6892 > select add #5.31
    6893 
    6894 2 models selected 
    6895 
    6896 > select add #5.46
    6897 
    6898 3 models selected 
    6899 
    6900 > select add #5.42
    6901 
    6902 4 models selected 
    6903 Deleted 305 regions 
    6904 
    6905 > save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori pfla
    6906 > asymm.seg" models #5
    6907 
    6908 > view orient
    6909 
    6910 [Repeated 1 time(s)]
    6911 
    6912 > open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori pfla
    6913 > asymm.seg"
    6914 
    6915 Summary of feedback from opening C:/Users/Jack Botting/Documents/Chimera/Saved
    6916 Sessions/pylori pfla asymm.seg 
    6917 --- 
    6918 note | Showing 4 region surfaces 
    6919  
    6920 Opened pylori pfla asymm.seg 
    6921 
    6922 > open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori pfla
    6923 > asymm.seg"
    6924 
    6925 Summary of feedback from opening C:/Users/Jack Botting/Documents/Chimera/Saved
    6926 Sessions/pylori pfla asymm.seg 
    6927 --- 
    6928 note | Showing 4 region surfaces 
    6929  
    6930 Opened pylori pfla asymm.seg 
    6931 
    6932 > open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori pfla
    6933 > asymm.seg"
    6934 
    6935 Summary of feedback from opening C:/Users/Jack Botting/Documents/Chimera/Saved
    6936 Sessions/pylori pfla asymm.seg 
    6937 --- 
    6938 note | Showing 4 region surfaces 
    6939  
    6940 Opened pylori pfla asymm.seg 
    6941 
    6942 > open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori pfla
    6943 > asymm.seg"
    6944 
    6945 Summary of feedback from opening C:/Users/Jack Botting/Documents/Chimera/Saved
    6946 Sessions/pylori pfla asymm.seg 
    6947 --- 
    6948 note | Showing 4 region surfaces 
    6949  
    6950 Opened pylori pfla asymm.seg 
    6951 
    6952 > open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori pfla
    6953 > asymm.seg"
    6954 
    6955 Summary of feedback from opening C:/Users/Jack Botting/Documents/Chimera/Saved
    6956 Sessions/pylori pfla asymm.seg 
    6957 --- 
    6958 note | Showing 4 region surfaces 
    6959  
    6960 Opened pylori pfla asymm.seg 
    6961 
    6962 > open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori pfla
    6963 > asymm.seg"
    6964 
    6965 Summary of feedback from opening C:/Users/Jack Botting/Documents/Chimera/Saved
    6966 Sessions/pylori pfla asymm.seg 
    6967 --- 
    6968 note | Showing 4 region surfaces 
    6969  
    6970 Opened pylori pfla asymm.seg 
    6971 
    6972 > open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori pfla
    6973 > asymm.seg"
    6974 
    6975 Summary of feedback from opening C:/Users/Jack Botting/Documents/Chimera/Saved
    6976 Sessions/pylori pfla asymm.seg 
    6977 --- 
    6978 note | Showing 4 region surfaces 
    6979  
    6980 Opened pylori pfla asymm.seg 
    6981 
    6982 > open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori pfla
    6983 > asymm.seg"
    6984 
    6985 Summary of feedback from opening C:/Users/Jack Botting/Documents/Chimera/Saved
    6986 Sessions/pylori pfla asymm.seg 
    6987 --- 
    6988 note | Showing 4 region surfaces 
    6989  
    6990 Opened pylori pfla asymm.seg 
    6991 
    6992 > open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori pfla
    6993 > asymm.seg"
    6994 
    6995 Summary of feedback from opening C:/Users/Jack Botting/Documents/Chimera/Saved
    6996 Sessions/pylori pfla asymm.seg 
    6997 --- 
    6998 note | Showing 4 region surfaces 
    6999  
    7000 Opened pylori pfla asymm.seg 
    7001 
    7002 > open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori pfla
    7003 > asymm.seg"
    7004 
    7005 Summary of feedback from opening C:/Users/Jack Botting/Documents/Chimera/Saved
    7006 Sessions/pylori pfla asymm.seg 
    7007 --- 
    7008 note | Showing 4 region surfaces 
    7009  
    7010 Opened pylori pfla asymm.seg 
    7011 
    7012 > open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori pfla
    7013 > asymm.seg"
    7014 
    7015 Summary of feedback from opening C:/Users/Jack Botting/Documents/Chimera/Saved
    7016 Sessions/pylori pfla asymm.seg 
    7017 --- 
    7018 note | Showing 4 region surfaces 
    7019  
    7020 Opened pylori pfla asymm.seg 
    7021 
    7022 > open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori pfla
    7023 > asymm.seg"
    7024 
    7025 Summary of feedback from opening C:/Users/Jack Botting/Documents/Chimera/Saved
    7026 Sessions/pylori pfla asymm.seg 
    7027 --- 
    7028 note | Showing 4 region surfaces 
    7029  
    7030 Opened pylori pfla asymm.seg 
    7031 
    7032 > open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori pfla
    7033 > asymm.seg"
    7034 
    7035 Summary of feedback from opening C:/Users/Jack Botting/Documents/Chimera/Saved
    7036 Sessions/pylori pfla asymm.seg 
    7037 --- 
    7038 note | Showing 4 region surfaces 
    7039  
    7040 Opened pylori pfla asymm.seg 
    7041 
    7042 > open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori pfla
    7043 > asymm.seg"
    7044 
    7045 Summary of feedback from opening C:/Users/Jack Botting/Documents/Chimera/Saved
    7046 Sessions/pylori pfla asymm.seg 
    7047 --- 
    7048 note | Showing 4 region surfaces 
    7049  
    7050 Opened pylori pfla asymm.seg 
    7051 
    7052 > open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori pfla
    7053 > asymm.seg"
    7054 
    7055 Summary of feedback from opening C:/Users/Jack Botting/Documents/Chimera/Saved
    7056 Sessions/pylori pfla asymm.seg 
    7057 --- 
    7058 note | Showing 4 region surfaces 
    7059  
    7060 Opened pylori pfla asymm.seg 
    7061 
    7062 > open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori pfla
    7063 > asymm.seg"
    7064 
    7065 Summary of feedback from opening C:/Users/Jack Botting/Documents/Chimera/Saved
    7066 Sessions/pylori pfla asymm.seg 
    7067 --- 
    7068 note | Showing 4 region surfaces 
    7069  
    7070 Opened pylori pfla asymm.seg 
    7071 
    7072 > open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori pfla
    7073 > asymm.seg"
    7074 
    7075 Summary of feedback from opening C:/Users/Jack Botting/Documents/Chimera/Saved
    7076 Sessions/pylori pfla asymm.seg 
    7077 --- 
    7078 note | Showing 4 region surfaces 
    7079  
    7080 Opened pylori pfla asymm.seg 
    7081 
    7082 > rename #10 id #30
    7083 
    7084 > rename #11 id #31
    7085 
    7086 > rename #12 id #32
    7087 
    7088 > rename #13 id #33
    7089 
    7090 > rename #14 id #34
    7091 
    7092 > rename #15 id #35
    7093 
    7094 > rename #16 id #10
    7095 
    7096 > rename #17 id #11
    7097 
    7098 > rename #18 id #12
    7099 
    7100 > rename #5 id #36
    7101 
    7102 > select #19-35
    7103 
    7104 85 models selected 
    7105 
    7106 > view matrix models
    7107 > #19,1,0,0,216.49,0,1,0,-5.851,0,0,1,0,#20,1,0,0,216.49,0,1,0,-5.851,0,0,1,0,#21,1,0,0,216.49,0,1,0,-5.851,0,0,1,0,#22,1,0,0,216.49,0,1,0,-5.851,0,0,1,0,#23,1,0,0,216.49,0,1,0,-5.851,0,0,1,0,#24,1,0,0,216.49,0,1,0,-5.851,0,0,1,0,#25,1,0,0,216.49,0,1,0,-5.851,0,0,1,0,#26,1,0,0,216.49,0,1,0,-5.851,0,0,1,0,#27,1,0,0,216.49,0,1,0,-5.851,0,0,1,0,#28,1,0,0,216.49,0,1,0,-5.851,0,0,1,0,#29,1,0,0,216.49,0,1,0,-5.851,0,0,1,0,#30,1,0,0,216.49,0,1,0,-5.851,0,0,1,0,#31,1,0,0,216.49,0,1,0,-5.851,0,0,1,0,#32,1,0,0,216.49,0,1,0,-5.851,0,0,1,0,#33,1,0,0,216.49,0,1,0,-5.851,0,0,1,0,#34,1,0,0,216.49,0,1,0,-5.851,0,0,1,0,#35,1,0,0,216.49,0,1,0,-5.851,0,0,1,0
    7108 
    7109 > view matrix models
    7110 > #19,1,0,0,216.19,0,1,0,-0.24819,0,0,1,64.137,#20,1,0,0,216.19,0,1,0,-0.24819,0,0,1,64.137,#21,1,0,0,216.19,0,1,0,-0.24819,0,0,1,64.137,#22,1,0,0,216.19,0,1,0,-0.24819,0,0,1,64.137,#23,1,0,0,216.19,0,1,0,-0.24819,0,0,1,64.137,#24,1,0,0,216.19,0,1,0,-0.24819,0,0,1,64.137,#25,1,0,0,216.19,0,1,0,-0.24819,0,0,1,64.137,#26,1,0,0,216.19,0,1,0,-0.24819,0,0,1,64.137,#27,1,0,0,216.19,0,1,0,-0.24819,0,0,1,64.137,#28,1,0,0,216.19,0,1,0,-0.24819,0,0,1,64.137,#29,1,0,0,216.19,0,1,0,-0.24819,0,0,1,64.137,#30,1,0,0,216.19,0,1,0,-0.24819,0,0,1,64.137,#31,1,0,0,216.19,0,1,0,-0.24819,0,0,1,64.137,#32,1,0,0,216.19,0,1,0,-0.24819,0,0,1,64.137,#33,1,0,0,216.19,0,1,0,-0.24819,0,0,1,64.137,#34,1,0,0,216.19,0,1,0,-0.24819,0,0,1,64.137,#35,1,0,0,216.19,0,1,0,-0.24819,0,0,1,64.137
    7111 
    7112 > hide #!9 models
    7113 
    7114 > view matrix models
    7115 > #19,1,0,0,213.49,0,1,0,-0.28232,0,0,1,63.952,#20,1,0,0,213.49,0,1,0,-0.28232,0,0,1,63.952,#21,1,0,0,213.49,0,1,0,-0.28232,0,0,1,63.952,#22,1,0,0,213.49,0,1,0,-0.28232,0,0,1,63.952,#23,1,0,0,213.49,0,1,0,-0.28232,0,0,1,63.952,#24,1,0,0,213.49,0,1,0,-0.28232,0,0,1,63.952,#25,1,0,0,213.49,0,1,0,-0.28232,0,0,1,63.952,#26,1,0,0,213.49,0,1,0,-0.28232,0,0,1,63.952,#27,1,0,0,213.49,0,1,0,-0.28232,0,0,1,63.952,#28,1,0,0,213.49,0,1,0,-0.28232,0,0,1,63.952,#29,1,0,0,213.49,0,1,0,-0.28232,0,0,1,63.952,#30,1,0,0,213.49,0,1,0,-0.28232,0,0,1,63.952,#31,1,0,0,213.49,0,1,0,-0.28232,0,0,1,63.952,#32,1,0,0,213.49,0,1,0,-0.28232,0,0,1,63.952,#33,1,0,0,213.49,0,1,0,-0.28232,0,0,1,63.952,#34,1,0,0,213.49,0,1,0,-0.28232,0,0,1,63.952,#35,1,0,0,213.49,0,1,0,-0.28232,0,0,1,63.952
    7116 
    7117 > view matrix models
    7118 > #19,1,0,0,213.59,0,1,0,-6.7631,0,0,1,64.403,#20,1,0,0,213.59,0,1,0,-6.7631,0,0,1,64.403,#21,1,0,0,213.59,0,1,0,-6.7631,0,0,1,64.403,#22,1,0,0,213.59,0,1,0,-6.7631,0,0,1,64.403,#23,1,0,0,213.59,0,1,0,-6.7631,0,0,1,64.403,#24,1,0,0,213.59,0,1,0,-6.7631,0,0,1,64.403,#25,1,0,0,213.59,0,1,0,-6.7631,0,0,1,64.403,#26,1,0,0,213.59,0,1,0,-6.7631,0,0,1,64.403,#27,1,0,0,213.59,0,1,0,-6.7631,0,0,1,64.403,#28,1,0,0,213.59,0,1,0,-6.7631,0,0,1,64.403,#29,1,0,0,213.59,0,1,0,-6.7631,0,0,1,64.403,#30,1,0,0,213.59,0,1,0,-6.7631,0,0,1,64.403,#31,1,0,0,213.59,0,1,0,-6.7631,0,0,1,64.403,#32,1,0,0,213.59,0,1,0,-6.7631,0,0,1,64.403,#33,1,0,0,213.59,0,1,0,-6.7631,0,0,1,64.403,#34,1,0,0,213.59,0,1,0,-6.7631,0,0,1,64.403,#35,1,0,0,213.59,0,1,0,-6.7631,0,0,1,64.403
    7119 
    7120 > view orient
    7121 
    7122 > show #!1.1 models
    7123 
    7124 > view orient
    7125 
    7126 > view matrix models
    7127 > #19,1,0,0,221.19,0,1,0,-6.2876,0,0,1,64.403,#20,1,0,0,221.19,0,1,0,-6.2876,0,0,1,64.403,#21,1,0,0,221.19,0,1,0,-6.2876,0,0,1,64.403,#22,1,0,0,221.19,0,1,0,-6.2876,0,0,1,64.403,#23,1,0,0,221.19,0,1,0,-6.2876,0,0,1,64.403,#24,1,0,0,221.19,0,1,0,-6.2876,0,0,1,64.403,#25,1,0,0,221.19,0,1,0,-6.2876,0,0,1,64.403,#26,1,0,0,221.19,0,1,0,-6.2876,0,0,1,64.403,#27,1,0,0,221.19,0,1,0,-6.2876,0,0,1,64.403,#28,1,0,0,221.19,0,1,0,-6.2876,0,0,1,64.403,#29,1,0,0,221.19,0,1,0,-6.2876,0,0,1,64.403,#30,1,0,0,221.19,0,1,0,-6.2876,0,0,1,64.403,#31,1,0,0,221.19,0,1,0,-6.2876,0,0,1,64.403,#32,1,0,0,221.19,0,1,0,-6.2876,0,0,1,64.403,#33,1,0,0,221.19,0,1,0,-6.2876,0,0,1,64.403,#34,1,0,0,221.19,0,1,0,-6.2876,0,0,1,64.403,#35,1,0,0,221.19,0,1,0,-6.2876,0,0,1,64.403
    7128 
    7129 > undo
    7130 
    7131 > select clear
    7132 
    7133 > turn z 20 1 models #19 center #1.1
    7134 
    7135 > turn z 20 2 models #20 center #1.1
    7136 
    7137 > turn z 20 3 models #21 center #1.1
    7138 
    7139 > turn z 20 4 models #22 center #1.1
    7140 
    7141 > turn z 20 5 models #23 center #1.1
    7142 
    7143 > turn z 20 6 models #24 center #1.1
    7144 
    7145 > turn z 20 7 models #25 center #1.1
    7146 
    7147 > turn z 20 8 models #26 center #1.1
    7148 
    7149 > turn z 20 9 models #27 center #1.1
    7150 
    7151 > turn z 20 10 models #28 center #1.1
    7152 
    7153 > turn z 20 11 models #29 center #1.1
    7154 
    7155 > turn z 20 12 models #30 center #1.1
    7156 
    7157 > turn z 20 13 models #31 center #1.1
    7158 
    7159 > turn z 20 14 models #32 center #1.1
    7160 
    7161 > turn z 20 15 models #33 center #1.1
    7162 
    7163 > turn z 20 16 models #34 center #1.1
    7164 
    7165 > turn z 20 17 models #35 center #1.1
    7166 
    7167 > view orient
    7168 
    7169 > hide #!1.1 models
    7170 
    7171 > show #!1.2 models
    7172 
    7173 > hide #!1.2 models
    7174 
    7175 > view orient
    7176 
    7177 > color #19-35.4 #5f51ba
    7178 
    7179 > color #19-35.1 #7b68ee
    7180 
    7181 > color #19-35.2 yellow
    7182 
    7183 > color #19-35.3 #003600
    7184 
    7185 > color #36.42 #003600
    7186 
    7187 > color #36.31 #7b68ee
    7188 
    7189 > color #36.28 #5f51ba
    7190 
    7191 > color #36.46 yellow
    7192 
    7193 Segmenting FlgY-sym13-2.1A.mrc, density threshold 0.997772 
    7194 Showing 229 region surfaces 
    7195 2534 watershed regions, grouped to 229 regions 
    7196 
    7197 > show #!19-28,30-36 target m
    7198 
    7199 > hide #!36 models
    7200 
    7201 > show #!36 models
    7202 
    7203 > hide #!5 models
    7204 
    7205 > show #!1.1 models
    7206 
    7207 > show #!5 models
    7208 
    7209 > select add #5
    7210 
    7211 230 models selected 
    7212 
    7213 > view orient
    7214 
    7215 > view matrix models #5,1,0,0,-41.306,0,1,0,-6.6385,0,0,1,0
    7216 
    7217 > view matrix models #5,1,0,0,-40.707,0,1,0,-6.0357,0,0,1,-14.746
    7218 
    7219 > hide #!19-28,30-36 target m
    7220 
    7221 > select clear
    7222 
    7223 > select #5.22
    7224 
    7225 1 model selected 
    7226 
    7227 > select add #5.20
    7228 
    7229 2 models selected 
    7230 
    7231 > select add #5.19
    7232 
    7233 3 models selected 
    7234 
    7235 > select add #5.23
    7236 
    7237 4 models selected 
    7238 
    7239 > select add #5.40
    7240 
    7241 5 models selected 
    7242 
    7243 > select add #5.1
    7244 
    7245 6 models selected 
    7246 
    7247 > select add #5.42
    7248 
    7249 7 models selected 
    7250 
    7251 > select add #5.2
    7252 
    7253 8 models selected 
    7254 
    7255 > select add #5.37
    7256 
    7257 9 models selected 
    7258 
    7259 > select add #5.3
    7260 
    7261 10 models selected 
    7262 
    7263 > select add #5.17
    7264 
    7265 11 models selected 
    7266 
    7267 > select add #5.18
    7268 
    7269 12 models selected 
    7270 
    7271 > select add #5.21
    7272 
    7273 13 models selected 
    7274 Ungrouped to 39 regions 
    7275 
    7276 > select #5.266
    7277 
    7278 1 model selected 
    7279 Ungrouped to 3 regions 
    7280 
    7281 > select #5.245
    7282 
    7283 1 model selected 
    7284 
    7285 > select #5.259
    7286 
    7287 1 model selected 
    7288 Ungrouped to 3 regions 
    7289 
    7290 > select #5.249
    7291 
    7292 1 model selected 
    7293 Ungrouped to 3 regions 
    7294 
    7295 > select #5.240
    7296 
    7297 1 model selected 
    7298 
    7299 > select #5.21
    7300 
    7301 1 model selected 
    7302 
    7303 > select #5.240
    7304 
    7305 1 model selected 
    7306 Ungrouped to 3 regions 
    7307 
    7308 > select #5.251
    7309 
    7310 1 model selected 
    7311 
    7312 > select add #5.242
    7313 
    7314 2 models selected 
    7315 
    7316 > select add #5.254
    7317 
    7318 3 models selected 
    7319 
    7320 > select add #5.234
    7321 
    7322 4 models selected 
    7323 
    7324 > select add #5.2
    7325 
    7326 5 models selected 
    7327 
    7328 > select add #5.3
    7329 
    7330 6 models selected 
    7331 
    7332 > select add #5.245
    7333 
    7334 7 models selected 
    7335 
    7336 > select add #5.263
    7337 
    7338 8 models selected 
    7339 
    7340 > select add #5.231
    7341 
    7342 9 models selected 
    7343 
    7344 > select add #5.18
    7345 
    7346 10 models selected 
    7347 
    7348 > select add #5.19
    7349 
    7350 11 models selected 
    7351 
    7352 > select add #5.261
    7353 
    7354 12 models selected 
    7355 
    7356 > select add #5.22
    7357 
    7358 13 models selected 
    7359 
    7360 > select add #5.236
    7361 
    7362 14 models selected 
    7363 
    7364 > select add #5.37
    7365 
    7366 15 models selected 
    7367 
    7368 > select add #5.40
    7369 
    7370 16 models selected 
    7371 Grouped 16 regions 
    7372 
    7373 > select add #5.241
    7374 
    7375 2 models selected 
    7376 
    7377 > select add #5.253
    7378 
    7379 3 models selected 
    7380 
    7381 > select add #5.244
    7382 
    7383 4 models selected 
    7384 
    7385 > select add #5.256
    7386 
    7387 5 models selected 
    7388 
    7389 > select add #5.235
    7390 
    7391 6 models selected 
    7392 
    7393 > select add #5.268
    7394 
    7395 7 models selected 
    7396 
    7397 > select add #5.246
    7398 
    7399 8 models selected 
    7400 
    7401 > select add #5.265
    7402 
    7403 9 models selected 
    7404 
    7405 > select add #5.232
    7406 
    7407 10 models selected 
    7408 
    7409 > select add #5.258
    7410 
    7411 11 models selected 
    7412 
    7413 > select add #5.262
    7414 
    7415 12 models selected 
    7416 
    7417 > select add #5.250
    7418 
    7419 13 models selected 
    7420 
    7421 > select add #5.238
    7422 
    7423 14 models selected 
    7424 
    7425 > select subtract #5.241
    7426 
    7427 13 models selected 
    7428 Grouped 13 regions 
    7429 
    7430 > show #!19-28,30-36 target m
    7431 
    7432 Region has 32 adjacent regions 
    7433 
    7434 > select add #5.241
    7435 
    7436 2 models selected 
    7437 Grouped 2 regions 
    7438 
    7439 > hide #!1.1 models
    7440 
    7441 > select clear
    7442 
    7443 > open "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori pfla
    7444 > asymm.seg"
    7445 
    7446 Summary of feedback from opening C:/Users/Jack Botting/Documents/Chimera/Saved
    7447 Sessions/pylori pfla asymm.seg 
    7448 --- 
    7449 note | Showing 4 region surfaces 
    7450  
    7451 Opened pylori pfla asymm.seg 
    7452 
    7453 > hide #!13 models
    7454 
    7455 > show #!13 models
    7456 
    7457 > select add #13
    7458 
    7459 5 models selected 
    7460 
    7461 > view orient
    7462 
    7463 > view matrix models #13,1,0,0,202.16,0,1,0,50.908,0,0,1,0
    7464 
    7465 > view matrix models #13,1,0,0,191.22,0,1,0,45.673,0,0,1,70.544
    7466 
    7467 > view matrix models #13,1,0,0,213.1,0,1,0,-5.5216,0,0,1,69.695
    7468 
    7469 > hide #!19-28,30-35 target m
    7470 
    7471 > view matrix models #13,1,0,0,214.22,0,1,0,-5.9712,0,0,1,64.639
    7472 
    7473 > view matrix models #13,1,0,0,214.33,0,1,0,-6.6974,0,0,1,64.637
    7474 
    7475 > show #!19-28,30-35 target m
    7476 
    7477 > view orient
    7478 
    7479 > turn z 11 20 models #13
    7480 
    7481 > select clear
    7482 
    7483 > rename #13 id #29
    7484 
    7485 > color #29.4 #5f51ba
    7486 
    7487 > color #29.1 #7b68ee
    7488 
    7489 > color #29.3 #003600
    7490 
    7491 > color #29.2 yellow
    7492 
    7493 > view orient
    7494 
    7495 > show #!9 models
    7496 
    7497 > show #!8 models
    7498 
    7499 > show #!7 models
    7500 
    7501 > show #!6 models
    7502 
    7503 > hide #!6 models
    7504 
    7505 > show #!3 models
    7506 
    7507 > show #!2 models
    7508 
    7509 > transparency #19-36 50
    7510 
    7511 > transparency #5 50
    7512 
    7513 > color #5 magenta
    7514 
    7515 > save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
    7516 > pflA pflB.cxs"
    7517 
    7518 ——— End of log from Wed Jun 5 14:36:12 2024 ———
    7519 
    7520 opened ChimeraX session 
    7521 
    7522 > hide #!5 models
    7523 
    7524 > show #!5 models
    7525 
    7526 > hide #5.1-234 target m
    7527 
    7528 > close #5.1-234
    7529 
    7530 > view orient
    7531 
    7532 [Repeated 1 time(s)]
    7533 
    7534 > sym #4 C18 center #1.1
    7535 
    7536 Invalid "center" argument: Center argument has no object bounds 
    7537 
    7538 > show #!1.1 models
    7539 
    7540 > sym #4 C18 center #1.1
    7541 
    7542 Made 18 graphical clones for pflB symmetry C18 
    7543 
    7544 > hide #!1.1 models
    7545 
    7546 > view orient
    7547 
    7548 > save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
    7549 > pflA pflB.cxs"
    7550 
    7551 ——— End of log from Thu Jun 6 10:26:44 2024 ———
    7552 
    7553 opened ChimeraX session 
    7554 
    7555 > open "C:/Users/Jack Botting/Documents/B burgdorferi/borrelia maps/IM_1.mrc"
    7556 
    7557 Opened IM_1.mrc as #13, grid size 121,121,39, pixel 4.2,4.2,4.2, shown at
    7558 level 0.0419, step 1, values float32 
    7559 
    7560 > open "C:/Users/Jack Botting/Documents/B burgdorferi/borrelia maps/IM_2.mrc"
    7561 
    7562 Opened IM_2.mrc as #14, grid size 207,207,129, pixel 5,5,0.6, shown at level
    7563 0.0708, step 1, values float32 
    7564 
    7565 > select add #13
    7566 
    7567 2 models selected 
    7568 
    7569 > select add #14
    7570 
    7571 4 models selected 
    7572 
    7573 > ui mousemode right "translate selected models"
    7574 
    7575 > view matrix models
    7576 > #13,1,0,0,-533.4,0,1,0,-492.94,0,0,1,8.0147,#14,1,0,0,-533.4,0,1,0,-492.94,0,0,1,8.0147
    7577 
    7578 > volume #13 level 0.001013
    7579 
    7580 > volume #14 level 0.002112
    7581 
    7582 > color #13,14 dark gray
    7583 
    7584 > view matrix models
    7585 > #13,1,0,0,-546.92,0,1,0,-487.29,0,0,1,-68.732,#14,1,0,0,-546.92,0,1,0,-487.29,0,0,1,-68.732
    7586 
    7587 > select subtract #13
    7588 
    7589 2 models selected 
    7590 
    7591 > select add #13
    7592 
    7593 4 models selected 
    7594 
    7595 > select subtract #14
    7596 
    7597 2 models selected 
    7598 
    7599 > view matrix models #13,1,0,0,-518.11,0,1,0,-451.13,0,0,1,-533.27
    7600 
    7601 > view matrix models #13,1,0,0,-499.41,0,1,0,-444.88,0,0,1,-531.97
    7602 
    7603 > view orient
    7604 
    7605 > select add #14
    7606 
    7607 4 models selected 
    7608 
    7609 > view matrix models
    7610 > #13,1,0,0,-509.51,0,1,0,-465.08,0,0,1,-531.97,#14,1,0,0,-557.01,0,1,0,-507.49,0,0,1,-68.732
    7611 
    7612 > select clear
    7613 
    7614 > view orient
    7615 
    7616 > select add #13
    7617 
    7618 2 models selected 
    7619 
    7620 > select add #14
    7621 
    7622 4 models selected 
    7623 
    7624 > view matrix models
    7625 > #13,1,0,0,-505.87,0,1,0,-468.72,0,0,1,-531.97,#14,1,0,0,-553.37,0,1,0,-511.13,0,0,1,-68.732
    7626 
    7627 > select clear
    7628 
    7629 > show #!1.2 models
    7630 
    7631 > ui tool show "Side View"
    7632 
    7633 > hide #!14 models
    7634 
    7635 > show #!14 models
    7636 
    7637 > hide #!14 models
    7638 
    7639 > show #!14 models
    7640 
    7641 > hide #!14 models
    7642 
    7643 > show #!14 models
    7644 
    7645 > view orient
    7646 
    7647 > turn x -90
    7648 
    7649 > select add #13
    7650 
    7651 2 models selected 
    7652 
    7653 > select add #14
    7654 
    7655 4 models selected 
    7656 
    7657 > view matrix models
    7658 > #13,1,0,0,-505.29,0,1,0,-468.72,0,0,1,-530.21,#14,1,0,0,-552.79,0,1,0,-511.13,0,0,1,-66.974
    7659 
    7660 > select clear
    7661 
    7662 > view orient
    7663 
    7664 > hide #!1.2 models
    7665 
    7666 > save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
    7667 > pflA pflB.cxs"
    7668 
    7669 ——— End of log from Fri Jun 7 16:12:49 2024 ———
    7670 
    7671 opened ChimeraX session 
    7672 
    7673 > hide #!2-3,5,7-9 target m
    7674 
    7675 > hide #19-36.1
    7676 
    7677 > hide #19-36.2
    7678 
    7679 > hide #19-36.4
    7680 
    7681 > sym clear #4
    7682 
    7683 > show #4 cartoons
    7684 
    7685 > show #!7 models
    7686 
    7687 > hide #!7 models
    7688 
    7689 > select #4/B:325
    7690 
    7691 9 atoms, 8 bonds, 1 residue, 1 model selected 
    7692 
    7693 > select up
    7694 
    7695 127 atoms, 131 bonds, 14 residues, 2 models selected 
    7696 
    7697 > select up
    7698 
    7699 5767 atoms, 5902 bonds, 707 residues, 2 models selected 
    7700 Alignment identifier is 4/B 
    7701 
    7702 > show #4/A cartoons
    7703 
    7704 > select #4/B:138
    7705 
    7706 6 atoms, 5 bonds, 1 residue, 1 model selected 
    7707 
    7708 > select #4/B
    7709 
    7710 5767 atoms, 5902 bonds, 707 residues, 1 model selected 
    7711 
    7712 > open "C:/Users/Jack Botting/Documents/alphafold
    7713 > results/HpyloripflB_4cab4/HpyloripflB_4cab4_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb"
    7714 
    7715 Chain information for
    7716 HpyloripflB_4cab4_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb #15 
    7717 --- 
    7718 Chain | Description 
    7719 A | No description available 
    7720  
    7721 
    7722 > mmaker #15 to #4
    7723 
    7724 Parameters 
    7725 --- 
    7726 Chain pairing | bb 
    7727 Alignment algorithm | Needleman-Wunsch 
    7728 Similarity matrix | BLOSUM-62 
    7729 SS fraction | 0.3 
    7730 Gap open (HH/SS/other) | 18/18/6 
    7731 Gap extend | 1 
    7732 SS matrix |  |  | H | S | O 
    7733 ---|---|---|--- 
    7734 H | 6 | -9 | -6 
    7735 S |  | 6 | -6 
    7736 O |  |  | 4 
    7737 Iteration cutoff | 2 
    7738  
    7739 Matchmaker pflB , chain B (#4) with
    7740 HpyloripflB_4cab4_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb, chain
    7741 A (#15), sequence alignment score = 3570.7 
    7742 RMSD between 467 pruned atom pairs is 1.012 angstroms; (across all 707 pairs:
    7743 6.069) 
    7744  
    7745 
    7746 > open "C:/Users/Jack Botting/Documents/alphafold
    7747 > results/pflAB/fold_pylori_pfla_pflb/fold_pylori_pfla_pflb_model_0.cif"
    7748 
    7749 Chain information for fold_pylori_pfla_pflb_model_0.cif #16 
    7750 --- 
    7751 Chain | Description 
    7752 A | . 
    7753 B | . 
    7754  
    7755 
    7756 > mmaker #16 to #4
    7757 
    7758 Parameters 
    7759 --- 
    7760 Chain pairing | bb 
    7761 Alignment algorithm | Needleman-Wunsch 
    7762 Similarity matrix | BLOSUM-62 
    7763 SS fraction | 0.3 
    7764 Gap open (HH/SS/other) | 18/18/6 
    7765 Gap extend | 1 
    7766 SS matrix |  |  | H | S | O 
    7767 ---|---|---|--- 
    7768 H | 6 | -9 | -6 
    7769 S |  | 6 | -6 
    7770 O |  |  | 4 
    7771 Iteration cutoff | 2 
    7772  
    7773 Matchmaker pflB , chain B (#4) with fold_pylori_pfla_pflb_model_0.cif, chain B
    7774 (#16), sequence alignment score = 3709.9 
    7775 RMSD between 707 pruned atom pairs is 0.000 angstroms; (across all 707 pairs:
    7776 0.000) 
    7777  
    7778 
    7779 > hide #15 models
    7780 
    7781 > hide #!4 models
    7782 
    7783 > show #!4 models
    7784 
    7785 > hide #!4 models
    7786 
    7787 > show #!4 models
    7788 
    7789 > hide #!4 models
    7790 
    7791 > show #!4 models
    7792 
    7793 > hide #!4 models
    7794 
    7795 > show #!4 models
    7796 
    7797 > hide #!4 models
    7798 
    7799 > show #!1.2 models
    7800 
    7801 > hide #!1.2 models
    7802 
    7803 > hide #16 models
    7804 
    7805 > show #!4 models
    7806 
    7807 > rename #4 "pflB (from pflA-pflB)"
    7808 
    7809 > view orient
    7810 
    7811 > sym #4 C18 center #1.1
    7812 
    7813 Invalid "center" argument: Center argument has no object bounds 
    7814 
    7815 > show #!1.1 models
    7816 
    7817 > sym #4 C18 center #1.1
    7818 
    7819 Made 18 graphical clones for pflB (from pflA-pflB) symmetry C18 
    7820 
    7821 > select clear
    7822 
    7823 > show #19-36
    7824 
    7825 > close #15-16
    7826 
    7827 > show #!9 models
    7828 
    7829 > show #!8 models
    7830 
    7831 > show #!7 models
    7832 
    7833 > show #!3 models
    7834 
    7835 > show #!2 models
    7836 
    7837 > save "C:/Users/Jack Botting/Documents/Chimera/Saved Sessions/pylori flgY
    7838 > pflA pflB.cxs"
    7839 
    7840 ——— End of log from Mon Jun 10 09:14:27 2024 ———
    7841 
    7842 opened ChimeraX session 
    7843 
    7844 > close session
    7845 
    7846 > open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    7847 > from_June2024/Sep11_2023/PflA-2.1A-230911.mrc
    7848 
    7849 Opened PflA-2.1A-230911.mrc as #1, grid size 240,240,240, pixel 2.1, shown at
    7850 level 4.29, step 1, values float32 
    7851 
    7852 > volume #1 level 0.04668
    7853 
    7854 > ui tool show "Segment Map"
    7855 
    7856 Segmenting PflA-2.1A-230911.mrc, density threshold 0.046682 
    7857 Showing 295 region surfaces 
    7858 3353 watershed regions, grouped to 295 regions 
    7859 Showing PflA-2.1A-230911.seg - 295 regions, 295 surfaces 
    7860 Drag select of 4917, 2456 of 27676 triangles, 4914, 4515 of 23484 triangles,
    7861 4777, 20659 of 21324 triangles, 4913, 4693, 9326 of 19524 triangles, 4688,
    7862 3362 of 20760 triangles, 4953, 9370 of 20004 triangles, 4898, 7845 of 20040
    7863 triangles, 4966, 8000 of 19788 triangles, 4947, 4324 of 18268 triangles, 4672,
    7864 6676 of 18776 triangles, 4958, 11735 of 19080 triangles, 4965, 7488 of 16572
    7865 triangles, 4923, 10655 of 19480 triangles, 4742, 6902 of 18496 triangles,
    7866 4969, 7819 of 16128 triangles, 4894, 5986 of 19516 triangles, 4915, 4711 of
    7867 16732 triangles, 4897, 6387 of 17880 triangles, 4971, 8820 of 18612 triangles,
    7868 4955, 6160 of 17068 triangles, 4960, 3460 of 15704 triangles, 4940, 5627 of
    7869 15616 triangles, 4957, 4194 of 15808 triangles, 4868, 7876 of 16436 triangles,
    7870 4905, 8875 of 16712 triangles, 4922, 4947 of 15528 triangles, 4674, 6630 of
    7871 14628 triangles, 4954, 3366 of 14652 triangles, 4951, 3686 of 14820 triangles,
    7872 4771, 705 of 15692 triangles, 4721, 5425 of 14464 triangles, 4941, 5325 of
    7873 15676 triangles, 4972, 6301 of 14184 triangles, 4759, 7430 of 13076 triangles,
    7874 4946, 8730 of 13764 triangles, 4743, 3311 of 13128 triangles, 4936, 7780 of
    7875 13408 triangles, 4798, 1997 of 14384 triangles, 4945, 4944, 5942 of 12836
    7876 triangles, 4896, 4904, 7882 of 13164 triangles, 4967, 4216 of 13064 triangles,
    7877 4800, 6473 of 13300 triangles, 4683, 5380 of 13212 triangles, 4797, 4958 of
    7878 12652 triangles, 4950, 4924, 7745 of 14044 triangles, 4860, 4700, 4131 of
    7879 12816 triangles, 4712, 3616 of 12332 triangles, 4714, 4338 of 13132 triangles,
    7880 4938, 2263 of 12916 triangles, 4918, 5703 of 11432 triangles, 4773, 8204 of
    7881 12228 triangles, 4722, 4122 of 11564 triangles, 4751, 4591 of 11416 triangles,
    7882 4772, 1690 of 11660 triangles, 4935, 6125 of 12532 triangles, 4849, 4682, 4995
    7883 of 10644 triangles, 4942, 6983 of 10200 triangles, 4943, 4515 of 10976
    7884 triangles, 4921, 3815 of 10060 triangles, 4853, 6928 of 10608 triangles, 4699,
    7885 710 of 11424 triangles, 4906, 3249 of 10540 triangles, 4902, 8613 of 12076
    7886 triangles, 4119, 4690 of 9840 triangles, 4843, 4704, 7216 of 9924 triangles,
    7887 4750, 5791 of 8764 triangles, 4710, 2416 of 9272 triangles, 4795, 6634 of 9780
    7888 triangles, 4864, 4696, 5466 of 9492 triangles, 4701, 5641 of 9124 triangles,
    7889 4307, 4170 of 8288 triangles, 4774, 4815 of 9908 triangles, 4839, 1788 of 8044
    7890 triangles, 4709, 3439 of 8564 triangles, 4702, 2046 of 9240 triangles, 4318,
    7891 5032 of 9276 triangles, 4724, 4563 of 8056 triangles, 4851, 2899 of 8268
    7892 triangles, 4837, 4194, 5032 of 7952 triangles, 4113, 1833 of 6928 triangles,
    7893 4767, 2476 of 7772 triangles, 4760, 4779 of 7528 triangles, 4749, 3903 of 7860
    7894 triangles, 4207, 1641 of 8160 triangles, 4270, 4484 of 7056 triangles, 4808,
    7895 3328 of 7512 triangles, 4414, 540 of 6884 triangles, 4345, 1609 of 6432
    7896 triangles, 4167, 854 of 4872 triangles, 4761, 4235 of 6232 triangles, 3403,
    7897 343 of 4816 triangles, 4601, 3703 of 4892 triangles, 4098, 1092 of 4880
    7898 triangles, 1 PflA-2.1A-230911.mrc 
    7899 Grouped 102 regions 
    7900 
    7901 > hide #!1 models
    7902 
    7903 Drag select of 4903, 8878 of 34032 triangles, 4752, 24936 of 31216 triangles,
    7904 4685, 4861, 8260 of 15472 triangles, 4757, 7852 of 15336 triangles, 4729, 4922
    7905 of 11360 triangles, 4779, 1926 of 11008 triangles, 4708, 4745, 2272 of 6484
    7906 triangles, 4620 
    7907 
    7908 > select add #2.107
    7909 
    7910 14 models selected 
    7911 Grouped 12 regions 
    7912 
    7913 > select add #2.83
    7914 
    7915 4 models selected 
    7916 
    7917 > select add #2.197
    7918 
    7919 5 models selected 
    7920 
    7921 > select add #2.106
    7922 
    7923 6 models selected 
    7924 
    7925 > select add #2.148
    7926 
    7927 7 models selected 
    7928 
    7929 > select add #2.229
    7930 
    7931 8 models selected 
    7932 
    7933 > select add #2.230
    7934 
    7935 9 models selected 
    7936 
    7937 > select add #2.191
    7938 
    7939 10 models selected 
    7940 
    7941 > select add #2.138
    7942 
    7943 11 models selected 
    7944 
    7945 > select add #2.228
    7946 
    7947 12 models selected 
    7948 
    7949 > select add #2.164
    7950 
    7951 13 models selected 
    7952 
    7953 > select add #2.216
    7954 
    7955 14 models selected 
    7956 Grouped 12 regions 
    7957 
    7958 > select add #2.1
    7959 
    7960 4 models selected 
    7961 
    7962 > select add #2.103
    7963 
    7964 5 models selected 
    7965 
    7966 > select add #2.7
    7967 
    7968 6 models selected 
    7969 
    7970 > select add #2.2
    7971 
    7972 7 models selected 
    7973 
    7974 > select add #2.206
    7975 
    7976 8 models selected 
    7977 
    7978 > select add #2.23
    7979 
    7980 9 models selected 
    7981 
    7982 > select add #2.11
    7983 
    7984 10 models selected 
    7985 
    7986 > select add #2.53
    7987 
    7988 11 models selected 
    7989 
    7990 > select add #2.9
    7991 
    7992 12 models selected 
    7993 
    7994 > select add #2.49
    7995 
    7996 13 models selected 
    7997 
    7998 > select subtract #2.49
    7999 
    8000 12 models selected 
    8001 
    8002 > select add #2.49
    8003 
    8004 13 models selected 
    8005 
    8006 > select add #2.20
    8007 
    8008 14 models selected 
    8009 
    8010 > select add #2.116
    8011 
    8012 15 models selected 
    8013 
    8014 > select add #2.212
    8015 
    8016 16 models selected 
    8017 
    8018 > select add #2.179
    8019 
    8020 17 models selected 
    8021 
    8022 > select subtract #2.179
    8023 
    8024 16 models selected 
    8025 
    8026 > select add #2.179
    8027 
    8028 17 models selected 
    8029 
    8030 > select add #2.176
    8031 
    8032 18 models selected 
    8033 
    8034 > select add #2.266
    8035 
    8036 19 models selected 
    8037 
    8038 > select add #2.177
    8039 
    8040 20 models selected 
    8041 
    8042 > select add #2.147
    8043 
    8044 21 models selected 
    8045 
    8046 > select add #2.209
    8047 
    8048 22 models selected 
    8049 
    8050 > select add #2.96
    8051 
    8052 23 models selected 
    8053 
    8054 > select add #2.125
    8055 
    8056 24 models selected 
    8057 
    8058 > select add #2.187
    8059 
    8060 25 models selected 
    8061 
    8062 > select add #2.113
    8063 
    8064 26 models selected 
    8065 
    8066 > select add #2.141
    8067 
    8068 27 models selected 
    8069 
    8070 > select add #2.259
    8071 
    8072 28 models selected 
    8073 
    8074 > select add #2.287
    8075 
    8076 29 models selected 
    8077 
    8078 > select add #2.104
    8079 
    8080 30 models selected 
    8081 
    8082 > select add #2.286
    8083 
    8084 31 models selected 
    8085 
    8086 > select add #2.196
    8087 
    8088 32 models selected 
    8089 
    8090 > select add #2.95
    8091 
    8092 33 models selected 
    8093 
    8094 > select add #2.10
    8095 
    8096 34 models selected 
    8097 
    8098 > select add #2.262
    8099 
    8100 35 models selected 
    8101 
    8102 > select add #2.221
    8103 
    8104 36 models selected 
    8105 
    8106 > select add #2.167
    8107 
    8108 37 models selected 
    8109 
    8110 > select add #2.264
    8111 
    8112 38 models selected 
    8113 
    8114 > select subtract #2.167
    8115 
    8116 37 models selected 
    8117 
    8118 > select subtract #2.221
    8119 
    8120 36 models selected 
    8121 
    8122 > select subtract #2.10
    8123 
    8124 35 models selected 
    8125 
    8126 > select add #2.271
    8127 
    8128 36 models selected 
    8129 
    8130 > select add #2.283
    8131 
    8132 37 models selected 
    8133 
    8134 > select add #2.199
    8135 
    8136 38 models selected 
    8137 
    8138 > select add #2.112
    8139 
    8140 39 models selected 
    8141 
    8142 > select subtract #2.112
    8143 
    8144 38 models selected 
    8145 
    8146 > select add #2.256
    8147 
    8148 39 models selected 
    8149 
    8150 > select add #2.236
    8151 
    8152 40 models selected 
    8153 
    8154 > select add #2.278
    8155 
    8156 41 models selected 
    8157 
    8158 > select add #2.289
    8159 
    8160 42 models selected 
    8161 
    8162 > select add #2.149
    8163 
    8164 43 models selected 
    8165 
    8166 > select add #2.198
    8167 
    8168 44 models selected 
    8169 
    8170 > select add #2.165
    8171 
    8172 45 models selected 
    8173 
    8174 > select add #2.250
    8175 
    8176 46 models selected 
    8177 
    8178 > select add #2.279
    8179 
    8180 47 models selected 
    8181 
    8182 > select add #2.181
    8183 
    8184 48 models selected 
    8185 
    8186 > select add #2.219
    8187 
    8188 49 models selected 
    8189 
    8190 > select add #2.294
    8191 
    8192 50 models selected 
    8193 Grouped 48 regions 
    8194 Opened PflA-2.1A-230911_imasked as #3, grid size 240,240,240, pixel 2.1, shown
    8195 at step 1, values float32 
    8196 Segmenting PflA-2.1A-230911_imasked, density threshold 0.046682 
    8197 Showing 122 region surfaces 
    8198 793 watershed regions, grouped to 122 regions 
    8199 Showing PflA-2.seg - 122 regions, 122 surfaces 
    8200 Showing 122 region surfaces 
    8201 
    8202 > select #2.105
    8203 
    8204 1 model selected 
    8205 
    8206 > select add #2.8
    8207 
    8208 2 models selected 
    8209 
    8210 > select add #2.21
    8211 
    8212 3 models selected 
    8213 
    8214 > select add #2.30
    8215 
    8216 4 models selected 
    8217 
    8218 > select add #2.25
    8219 
    8220 5 models selected 
    8221 Grouped 5 regions 
    8222 
    8223 > select add #2.22
    8224 
    8225 2 models selected 
    8226 Grouped 2 regions 
    8227 
    8228 > select add #2.61
    8229 
    8230 2 models selected 
    8231 
    8232 > select add #2.44
    8233 
    8234 3 models selected 
    8235 
    8236 > select add #2.75
    8237 
    8238 4 models selected 
    8239 
    8240 > close session
    8241 
    8242 > open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    8243 > from_June2024/For-FlgY-model_June2024/Rev-Hp-PflB.mrc
    8244 
    8245 Opened Rev-Hp-PflB.mrc as #1, grid size 220,220,220, pixel 4.3, shown at level
    8246 3.57, step 1, values float32 
    8247 
    8248 > volume #1 level 0.4885
    8249 
    8250 > volume #1 level 0.3839
    8251 
    8252 > ui tool show "Segment Map"
    8253 
    8254 Segmenting Rev-Hp-PflB.mrc, density threshold 0.383927 
    8255 Showing 764 region surfaces 
    8256 5878 watershed regions, grouped to 764 regions 
    8257 Showing Rev-Hp-PflB.seg - 764 regions, 764 surfaces 
    8258 Drag select of 8536, 57 of 28120 triangles, 8544, 8666 of 26268 triangles,
    8259 8653, 35203 of 39008 triangles, 8637, 8615, 8046, 8677, 8734, 6946 of 18500
    8260 triangles, 8562, 3040 of 19812 triangles, 8652, 10841 of 18308 triangles,
    8261 8740, 3627 of 16592 triangles, 8593, 8627, 8539, 7230 of 16668 triangles,
    8262 8655, 8678, 145 of 16336 triangles, 8634, 8669, 8181, 64 of 17716 triangles,
    8263 8012, 21724 of 22204 triangles, 8076, 4510 of 15852 triangles, 8712, 8665,
    8264 8533, 3272 of 14972 triangles, 8668, 8651, 8578, 8674, 8670, 8324, 8801, 8071,
    8265 1110 of 13696 triangles, 8599, 140 of 12148 triangles, 8426, 8565, 8586, 8263,
    8266 8644, 8727, 8540, 5474 of 12288 triangles, 8224, 5750 of 11444 triangles,
    8267 8774, 8058, 8777, 8115, 8711, 6132 of 11512 triangles, 8623, 8640, 8722, 8555,
    8268 3924 of 10388 triangles, 8091, 8528, 235 of 10756 triangles, 8325, 3952 of
    8269 11704 triangles, 8597, 8260, 8671, 8738, 8770, 8610, 860 of 12196 triangles,
    8270 8664, 8537, 8359, 5226 of 10624 triangles, 8621, 176 of 10412 triangles, 8110,
    8271 8735, 796 of 9768 triangles, 8374, 3298 of 9860 triangles, 8203, 29 of 9844
    8272 triangles, 8120, 8622, 15682 of 15772 triangles, 8701, 9932 of 10512
    8273 triangles, 8366, 8373, 1211 of 10100 triangles, 8721, 8629, 7219, 8541, 8002,
    8274 8243, 102 of 8284 triangles, 7452, 8538, 488 of 8584 triangles, 8710, 8370,
    8275 147 of 8780 triangles, 8096, 8617, 8694, 8518, 3708 of 8916 triangles, 8059,
    8276 8784, 8289, 8001, 545 of 8676 triangles, 8566, 6306 of 9552 triangles, 8093,
    8277 8730, 8089, 6124 of 8420 triangles, 8595, 1655 of 9352 triangles, 8084, 8545,
    8278 1084 of 8600 triangles, 8087, 397 of 9180 triangles, 8080, 6573 of 8792
    8279 triangles, 8164, 9847 of 10612 triangles, 8527, 3922 of 8004 triangles, 8682,
    8280 8350, 8500, 8147, 4490 of 7536 triangles, 8725, 8416, 8050, 8090, 8067, 3257
    8281 of 7488 triangles, 8590, 3285 of 7856 triangles, 7436, 7302, 3983 of 6620
    8282 triangles, 8479, 8709, 5093 of 7868 triangles, 8786, 8556, 1289 of 7084
    8283 triangles, 8395, 7624, 6762 of 7068 triangles, 8245, 3401 of 6688 triangles,
    8284 8258, 8225, 601 of 6612 triangles, 8762, 7082, 3213 of 6704 triangles, 8608,
    8285 8732, 7698, 2847 of 6596 triangles, 7287, 8543, 3440 of 6372 triangles, 7111,
    8286 1387 of 7252 triangles, 7167, 5034 of 6684 triangles, 7300, 13 of 7644
    8287 triangles, 7130, 3210 of 6448 triangles, 7638, 7281, 4201 of 6464 triangles,
    8288 8204, 648 of 6956 triangles, 7101, 8752, 8371, 4196 of 6748 triangles, 8375,
    8289 2301 of 7088 triangles, 7092, 8393, 3571 of 6144 triangles, 7151, 4724 of 6004
    8290 triangles, 8383, 7038, 2962 of 5624 triangles, 8364, 8016, 4479 of 5636
    8291 triangles, 8475, 8335, 402 of 6264 triangles, 8038, 8613, 8020, 8631, 8112,
    8292 464 of 5084 triangles, 7217, 7172, 3851 of 5596 triangles, 7678, 901 of 6008
    8293 triangles, 8354, 8619, 8448, 8009, 2956 of 5524 triangles, 8720, 7376, 8625,
    8294 8358, 7574, 8311, 4143, 6637, 3044 of 5024 triangles, 7129, 3273 of 4648
    8295 triangles, 7675, 488 of 5476 triangles, 7380, 8800, 7164, 1731 of 4936
    8296 triangles, 7607, 1357 of 5392 triangles, 7112, 2546 of 4920 triangles, 8776,
    8297 7294, 3017 of 5008 triangles, 8357, 8072, 2411 of 5240 triangles, 7387, 7591,
    8298 8184, 7234, 6746, 693 of 4172 triangles, 5914, 17 of 4436 triangles, 7896,
    8299 8508, 8799, 7657, 461 of 3992 triangles, 8739, 6734, 338 of 3520 triangles,
    8300 8097, 8620, 4489 of 4496 triangles, 8291, 7542, 8299, 8753, 8626, 3104 of 3140
    8301 triangles, 6816, 8294, 8248, 5313, 7960, 5865, 867 of 892 triangles, 7957,
    8302 5868, 1 Rev-Hp-PflB.mrc 
    8303 
    8304 > hide #!1 models
    8305 
    8306 > select add #2.134
    8307 
    8308 210 models selected 
    8309 
    8310 > select subtract #2.134
    8311 
    8312 209 models selected 
    8313 
    8314 > select add #2.89
    8315 
    8316 210 models selected 
    8317 
    8318 > select add #2.15
    8319 
    8320 211 models selected 
    8321 
    8322 > select add #2.5
    8323 
    8324 212 models selected 
    8325 
    8326 > select add #2.198
    8327 
    8328 213 models selected 
    8329 
    8330 > select add #2.178
    8331 
    8332 214 models selected 
    8333 
    8334 > select add #2.338
    8335 
    8336 215 models selected 
    8337 
    8338 > select add #2.248
    8339 
    8340 216 models selected 
    8341 
    8342 > select add #2.419
    8343 
    8344 217 models selected 
    8345 
    8346 > select add #2.134
    8347 
    8348 218 models selected 
    8349 
    8350 > select add #2.503
    8351 
    8352 219 models selected 
    8353 
    8354 > select add #2.49
    8355 
    8356 220 models selected 
    8357 
    8358 > select add #2.268
    8359 
    8360 221 models selected 
    8361 
    8362 > select add #2.250
    8363 
    8364 222 models selected 
    8365 
    8366 > select add #2.466
    8367 
    8368 223 models selected 
    8369 
    8370 > select add #2.478
    8371 
    8372 224 models selected 
    8373 
    8374 > select add #2.96
    8375 
    8376 225 models selected 
    8377 
    8378 > select add #2.131
    8379 
    8380 226 models selected 
    8381 
    8382 > select add #2.57
    8383 
    8384 227 models selected 
    8385 
    8386 > select add #2.298
    8387 
    8388 228 models selected 
    8389 
    8390 > select add #2.406
    8391 
    8392 229 models selected 
    8393 
    8394 > select add #2.426
    8395 
    8396 230 models selected 
    8397 
    8398 > select add #2.256
    8399 
    8400 231 models selected 
    8401 
    8402 > select add #2.286
    8403 
    8404 232 models selected 
    8405 
    8406 > select add #2.212
    8407 
    8408 233 models selected 
    8409 
    8410 > select add #2.398
    8411 
    8412 234 models selected 
    8413 
    8414 > select add #2.191
    8415 
    8416 235 models selected 
    8417 
    8418 > select add #2.352
    8419 
    8420 236 models selected 
    8421 
    8422 > select add #2.448
    8423 
    8424 237 models selected 
    8425 
    8426 > select add #2.342
    8427 
    8428 238 models selected 
    8429 
    8430 > select add #2.158
    8431 
    8432 239 models selected 
    8433 
    8434 > select add #2.200
    8435 
    8436 240 models selected 
    8437 
    8438 > select add #2.150
    8439 
    8440 241 models selected 
    8441 Drag select of 8658, 62 of 26828 triangles, 8743, 16616 of 20440 triangles,
    8442 8624, 55 of 26256 triangles, 8559, 8628, 95 of 20304 triangles, 8769, 12547 of
    8443 15180 triangles, 8706, 84 of 17300 triangles, 8515, 15 of 19696 triangles,
    8444 8750, 11009 of 13028 triangles, 8729, 9544 of 12292 triangles, 8125, 10602 of
    8445 11560 triangles, 8249, 8016 of 11676 triangles, 8787, 8524, 3485 of 10364
    8446 triangles, 8273, 9486 of 10444 triangles, 8723, 7844 of 10284 triangles, 8201,
    8447 8252, 8332, 7876 of 8376 triangles, 8352, 8657 of 8704 triangles, 7502, 8716,
    8448 7547 of 7940 triangles, 8529, 8639, 7878, 8635, 24 of 14008 triangles, 8339,
    8449 7437 of 10124 triangles, 8129, 6435 of 7852 triangles, 8583, 154 of 12500
    8450 triangles, 8605, 7420, 8612, 8574, 341 of 12536 triangles, 8764, 4049 of 7428
    8451 triangles, 8748, 8534, 8761, 1403 of 6948 triangles, 8768, 7741, 7602, 8347,
    8452 8523, 3210 of 7180 triangles, 8714, 8296, 7873, 1154 of 6540 triangles, 8233,
    8453 8007, 453 of 11036 triangles, 8319, 393 of 6688 triangles, 8765, 847 of 6412
    8454 triangles, 8477, 8277, 2540 of 7128 triangles, 8589, 3913 of 6304 triangles,
    8455 8428, 5592 of 6196 triangles, 8054, 1518 of 7100 triangles, 8356, 845 of 6604
    8456 triangles, 8118, 6114 of 7296 triangles, 8611, 5887 of 8228 triangles, 8679,
    8457 8253, 8642, 949 of 9196 triangles, 8318, 4620 of 5372 triangles, 8802, 8409,
    8458 8327, 2390 of 6412 triangles, 7178, 2642 of 5336 triangles, 7188, 2590 of 6288
    8459 triangles, 7752, 565 of 6664 triangles, 7447, 3881 of 6288 triangles, 6872,
    8460 1489 of 5080 triangles, 8334, 8785, 487 of 5752 triangles, 8042, 3057 of 5756
    8461 triangles, 8159, 898 of 5388 triangles, 8519, 2773 of 4980 triangles, 8797,
    8462 3138 of 5580 triangles, 8471, 1546 of 5312 triangles, 916, 1207 of 4716
    8463 triangles, 6864, 2546 of 4384 triangles, 8766, 3991 of 5488 triangles, 8525,
    8464 225 of 4368 triangles, 8489, 8737, 8064, 1399 of 4200 triangles, 7842, 2902 of
    8465 4644 triangles, 8469, 1189 of 4900 triangles, 8633, 8783, 6079, 906 of 4728
    8466 triangles, 8741, 908, 1810 of 3960 triangles, 907, 1695 of 3892 triangles,
    8467 6070, 1496 of 3916 triangles, 8713, 7705, 8043, 276 of 3812 triangles, 8452,
    8468 8742, 8648, 6212 of 7104 triangles, 7947, 179 of 3880 triangles, 8804, 4471 of
    8469 6556 triangles, 7199, 2014 of 3356 triangles, 6144, 25 of 3708 triangles,
    8470 8771, 5728 of 5820 triangles, 8381, 378 of 6144 triangles, 8660, 2059 of 7024
    8471 triangles, 922, 901 of 3532 triangles, 8521, 2933 of 6164 triangles, 8401,
    8472 7196, 2679 of 3556 triangles, 900, 2048 of 3584 triangles, 7849, 1716 of 3524
    8473 triangles, 8460, 959, 1645 of 3240 triangles, 448, 7847, 2089 of 3616
    8474 triangles, 7841, 2216 of 3624 triangles, 8681, 2801 of 5252 triangles, 7930,
    8475 8550, 897 of 5832 triangles, 7843, 1487 of 3536 triangles, 8782, 1132 of 5748
    8476 triangles, 7751, 888 of 3332 triangles, 8530, 8229, 8719, 4778 of 5096
    8477 triangles, 6064, 1530 of 2796 triangles, 8662, 1262 of 4756 triangles, 8548,
    8478 3024 of 3744 triangles, 8546, 223 of 4436 triangles, 8708, 6716, 1431 of 2684
    8479 triangles, 8542, 7589, 8328, 8747, 6941, 347 of 2496 triangles, 868, 2238 of
    8480 2536 triangles, 8531, 8520, 3436 of 3812 triangles, 6334, 2427 of 2632
    8481 triangles, 8788, 8704, 8789, 8636, 8577, 7899, 7257, 8213, 8790, 8705, 8717,
    8482 7742, 2008 of 2132 triangles, 8667, 2777 of 2864 triangles, 8297, 140 of 2780
    8483 triangles, 8576, 8803, 8155, 2292 of 2376 triangles, 8170, 1837 of 2068
    8484 triangles, 7710, 8794, 8609, 8758, 8798, 7865, 864 of 2092 triangles, 7733,
    8485 8215, 466, 8231, 6888, 8600, 1978 of 2256 triangles, 6678, 8715, 8603, 8481,
    8486 7709, 7718, 8449, 8700, 8269, 8746, 847, 781 of 1456 triangles, 6348, 7894,
    8487 54, 8773, 8618, 7713, 227, 6420, 6567, 6703, 82, 1040, 8698, 266, 8459, 8697,
    8488 8563, 8560, 8696, 8757, 1514 of 2232 triangles, 8047, 264, 240, 8270, 199,
    8489 8772, 1830 of 1960 triangles, 8792, 247, 8433, 621, 677, 8695, 202, 313, 8756,
    8490 8434, 289, 6824, 8441, 8440, 263, 417, 8404, 498, 537, 354, 7823, 8793, 18,
    8491 579, 737, 968 of 992 triangles, 385, 6099, 338, 326, 8699, 312, 418, 8060, 442
    8492 of 1148 triangles, 8554, 782, 698 of 832 triangles, 111, 297, 201, 8573, 314,
    8493 59, 8557, 965 of 1104 triangles, 8333, 8791, 419, 119, 200, 6809, 139, 8442,
    8494 293, 98, 242, 122, 342, 6846, 379, 554, 238, 239, 594, 176, 228, 53, 756, 437
    8495 of 588 triangles, 8755, 1169, 523 of 592 triangles, 77, 106, 378, 27, 146,
    8496 7457, 299 of 656 triangles, 7209, 399 of 632 triangles, 8109, 779, 365, 7210,
    8497 268, 48, 785, 790, 6817, 30, 473, 279, 580, 8726, 567, 1167, 50, 1101, 128 of
    8498 264 triangles, 273, 799, 77 of 216 triangles, 76 
    8499 
    8500 > select add #2.95
    8501 
    8502 544 models selected 
    8503 
    8504 > select add #2.173
    8505 
    8506 545 models selected 
    8507 
    8508 > select add #2.43
    8509 
    8510 546 models selected 
    8511 
    8512 > select add #2.565
    8513 
    8514 547 models selected 
    8515 
    8516 > select add #2.126
    8517 
    8518 548 models selected 
    8519 
    8520 > select add #2.18
    8521 
    8522 549 models selected 
    8523 
    8524 > select add #2.480
    8525 
    8526 550 models selected 
    8527 
    8528 > select add #2.387
    8529 
    8530 551 models selected 
    8531 
    8532 > select add #2.396
    8533 
    8534 552 models selected 
    8535 
    8536 > select add #2.454
    8537 
    8538 553 models selected 
    8539 
    8540 > select add #2.310
    8541 
    8542 554 models selected 
    8543 
    8544 > select add #2.117
    8545 
    8546 555 models selected 
    8547 
    8548 > select add #2.6
    8549 
    8550 556 models selected 
    8551 
    8552 > select add #2.328
    8553 
    8554 557 models selected 
    8555 
    8556 > select add #2.385
    8557 
    8558 558 models selected 
    8559 
    8560 > select add #2.434
    8561 
    8562 559 models selected 
    8563 
    8564 > select add #2.400
    8565 
    8566 560 models selected 
    8567 
    8568 > select add #2.403
    8569 
    8570 561 models selected 
    8571 
    8572 > select add #2.464
    8573 
    8574 562 models selected 
    8575 
    8576 > select add #2.337
    8577 
    8578 563 models selected 
    8579 
    8580 > select add #2.450
    8581 
    8582 564 models selected 
    8583 
    8584 > select add #2.77
    8585 
    8586 565 models selected 
    8587 
    8588 > select add #2.75
    8589 
    8590 566 models selected 
    8591 
    8592 > select add #2.213
    8593 
    8594 567 models selected 
    8595 
    8596 > select add #2.221
    8597 
    8598 568 models selected 
    8599 
    8600 > select add #2.234
    8601 
    8602 569 models selected 
    8603 
    8604 > select subtract #2.18
    8605 
    8606 568 models selected 
    8607 
    8608 > select add #2.18
    8609 
    8610 569 models selected 
    8611 
    8612 > select subtract #2.126
    8613 
    8614 568 models selected 
    8615 
    8616 > select add #2.65
    8617 
    8618 569 models selected 
    8619 
    8620 > select add #2.126
    8621 
    8622 570 models selected 
    8623 
    8624 > select subtract #2.43
    8625 
    8626 569 models selected 
    8627 
    8628 > select add #2.61
    8629 
    8630 570 models selected 
    8631 
    8632 > select subtract #2.95
    8633 
    8634 569 models selected 
    8635 
    8636 > select add #2.95
    8637 
    8638 570 models selected 
    8639 
    8640 > select add #2.161
    8641 
    8642 571 models selected 
    8643 
    8644 > select add #2.38
    8645 
    8646 572 models selected 
    8647 
    8648 > select add #2.22
    8649 
    8650 573 models selected 
    8651 
    8652 > select add #2.339
    8653 
    8654 574 models selected 
    8655 
    8656 > select add #2.349
    8657 
    8658 575 models selected 
    8659 
    8660 > select add #2.545
    8661 
    8662 576 models selected 
    8663 
    8664 > select add #2.535
    8665 
    8666 577 models selected 
    8667 
    8668 > select add #2.344
    8669 
    8670 578 models selected 
    8671 
    8672 > select add #2.361
    8673 
    8674 579 models selected 
    8675 
    8676 > select add #2.23
    8677 
    8678 580 models selected 
    8679 
    8680 > select add #2.382
    8681 
    8682 581 models selected 
    8683 
    8684 > select add #2.86
    8685 
    8686 582 models selected 
    8687 
    8688 > select add #2.39
    8689 
    8690 583 models selected 
    8691 Drag select of 8659, 82 of 18068 triangles, 8604, 6 of 12792 triangles, 8474,
    8692 69 of 9604 triangles, 7680, 46 of 4496 triangles, 3036, 41 of 3268 triangles 
    8693 
    8694 > select add #2.10
    8695 
    8696 589 models selected 
    8697 
    8698 > select add #2.460
    8699 
    8700 590 models selected 
    8701 Drag select of 8512, 189 of 23920 triangles, 8675, 534 of 17068 triangles,
    8702 8575, 532 of 13132 triangles, 8522, 6419 of 7876 triangles, 8779, 125 of 10904
    8703 triangles, 8396, 197 of 9736 triangles, 8582, 865 of 8368 triangles, 8034, 296
    8704 of 10924 triangles, 8535, 380 of 10464 triangles, 8736, 1762 of 10760
    8705 triangles, 8572, 229 of 8488 triangles, 8796, 83 of 8092 triangles, 8137, 10
    8706 of 7124 triangles, 7103, 927 of 7712 triangles, 8399, 326 of 6276 triangles,
    8707 8051, 3524 of 3968 triangles, 7961, 1060 of 3256 triangles, 7255, 2368 of 3080
    8708 triangles, 8754, 3639 of 4580 triangles, 989, 1904 of 2440 triangles, 1055,
    8709 943 of 2116 triangles, 8646, 7241, 931 of 1628 triangles, 1034, 7909, 8402,
    8710 1202 of 1924 triangles, 1092, 706 of 1092 triangles, 938, 8410, 628 of 1284
    8711 triangles, 1058, 608 of 1000 triangles, 1062, 697 of 904 triangles, 7280, 318
    8712 of 1032 triangles, 1228, 14 of 560 triangles, 836, 7137, 148 of 532 triangles,
    8713 807 
    8714 Grouped 624 regions 
    8715 
    8716 > select clear
    8717 
    8718 > select #2.225
    8719 
    8720 1 model selected 
    8721 
    8722 > select add #2.275
    8723 
    8724 2 models selected 
    8725 
    8726 > select add #2.422
    8727 
    8728 3 models selected 
    8729 
    8730 > select add #2.232
    8731 
    8732 4 models selected 
    8733 Grouped 4 regions 
    8734 
    8735 > select add #2.190
    8736 
    8737 2 models selected 
    8738 
    8739 > select add #2.227
    8740 
    8741 3 models selected 
    8742 
    8743 > select subtract #2.227
    8744 
    8745 2 models selected 
    8746 
    8747 > select add #2.227
    8748 
    8749 3 models selected 
    8750 
    8751 > select add #2.266
    8752 
    8753 4 models selected 
    8754 
    8755 > select add #2.258
    8756 
    8757 5 models selected 
    8758 
    8759 > select add #2.283
    8760 
    8761 6 models selected 
    8762 
    8763 > select add #2.290
    8764 
    8765 7 models selected 
    8766 
    8767 > select add #2.432
    8768 
    8769 8 models selected 
    8770 
    8771 > select add #2.249
    8772 
    8773 9 models selected 
    8774 
    8775 > select add #2.175
    8776 
    8777 10 models selected 
    8778 
    8779 > select add #2.254
    8780 
    8781 11 models selected 
    8782 
    8783 > select add #2.343
    8784 
    8785 12 models selected 
    8786 
    8787 > select add #2.233
    8788 
    8789 13 models selected 
    8790 
    8791 > select add #2.136
    8792 
    8793 14 models selected 
    8794 
    8795 > select add #2.220
    8796 
    8797 15 models selected 
    8798 
    8799 > select add #2.427
    8800 
    8801 16 models selected 
    8802 
    8803 > select add #2.500
    8804 
    8805 17 models selected 
    8806 
    8807 > select add #2.241
    8808 
    8809 18 models selected 
    8810 Grouped 18 regions 
    8811 
    8812 > select add #2.531
    8813 
    8814 2 models selected 
    8815 Grouped 2 regions 
    8816 
    8817 > select add #2.271
    8818 
    8819 2 models selected 
    8820 Grouped 2 regions 
    8821 
    8822 > select clear
    8823 
    8824 > select #2.2
    8825 
    8826 1 model selected 
    8827 Opened Rev-Hp-PflB_imasked as #3, grid size 220,220,220, pixel 4.3, shown at
    8828 step 1, values float32 
    8829 Segmenting Rev-Hp-PflB_imasked, density threshold 0.383927 
    8830 Showing 23 region surfaces 
    8831 103 watershed regions, grouped to 23 regions 
    8832 Showing Rev-Hp-PflB_imasked.seg - 23 regions, 23 surfaces 
    8833 
    8834 > open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    8835 > from_June2024/PDB-
    8836 > files/Hp_motElikeproteindimer_ed02a_unrelaxed_rank_004_alphafold2_multimer_v3_model_1_seed_000.pdb
    8837 
    8838 Chain information for
    8839 Hp_motElikeproteindimer_ed02a_unrelaxed_rank_004_alphafold2_multimer_v3_model_1_seed_000.pdb
    8840 #4 
    8841 --- 
    8842 Chain | Description 
    8843 A B | No description available 
    8844  
    8845 
    8846 > select add #4
    8847 
    8848 3420 atoms, 3458 bonds, 430 residues, 1 model selected 
    8849 
    8850 > select subtract #4
    8851 
    8852 Nothing selected 
    8853 
    8854 > select add #4
    8855 
    8856 3420 atoms, 3458 bonds, 430 residues, 1 model selected 
    8857 
    8858 > view matrix models #4,1,0,0,-18.183,0,1,0,119.32,0,0,1,25.036
    8859 
    8860 > view matrix models #4,1,0,0,-2.2723,0,1,0,128.67,0,0,1,-24.184
    8861 
    8862 > view matrix models #4,1,0,0,1.0942,0,1,0,124.99,0,0,1,-24.281
    8863 
    8864 > view matrix models #4,1,0,0,-16.19,0,1,0,121.95,0,0,1,-57.422
    8865 
    8866 > view matrix models #4,1,0,0,-13.434,0,1,0,120.81,0,0,1,-57.512
    8867 
    8868 > ui mousemode right "rotate selected models"
    8869 
    8870 > view matrix models
    8871 > #4,0.84172,-0.30814,0.44335,-8.8352,0.031429,0.84772,0.52951,120.21,-0.539,-0.43177,0.72323,-42.743
    8872 
    8873 > ui mousemode right "translate selected models"
    8874 
    8875 > view matrix models
    8876 > #4,0.84172,-0.30814,0.44335,-16.152,0.031429,0.84772,0.52951,122.98,-0.539,-0.43177,0.72323,-35.613
    8877 
    8878 > select clear
    8879 
    8880 > select #2.7
    8881 
    8882 1 model selected 
    8883 
    8884 > select add #2.19
    8885 
    8886 2 models selected 
    8887 
    8888 > select add #2.16
    8889 
    8890 3 models selected 
    8891 
    8892 > select add #2.21
    8893 
    8894 4 models selected 
    8895 
    8896 > select add #2.20
    8897 
    8898 5 models selected 
    8899 
    8900 > select add #2.18
    8901 
    8902 6 models selected 
    8903 
    8904 > select add #2.15
    8905 
    8906 7 models selected 
    8907 
    8908 > select add #2.17
    8909 
    8910 8 models selected 
    8911 Grouped 8 regions 
    8912 
    8913 > select #2.3
    8914 
    8915 1 model selected 
    8916 Ungrouped to 3 regions 
    8917 Ungrouped to 5 regions 
    8918 Ungrouped to 0 regions 
    8919 
    8920 > select #2.3
    8921 
    8922 1 model selected 
    8923 
    8924 > select add #2.20
    8925 
    8926 2 models selected 
    8927 
    8928 > select add #2.18
    8929 
    8930 3 models selected 
    8931 Grouped 3 regions 
    8932 
    8933 > select add #2.7
    8934 
    8935 2 models selected 
    8936 Grouped 2 regions 
    8937 
    8938 > select clear
    8939 
    8940 > select #2.8
    8941 
    8942 1 model selected 
    8943 Ungrouped to 3 regions 
    8944 Ungrouped to 6 regions 
    8945 Ungrouped to 0 regions 
    8946 
    8947 > select #2.16
    8948 
    8949 1 model selected 
    8950 
    8951 > select add #2.8
    8952 
    8953 2 models selected 
    8954 Grouped 2 regions 
    8955 
    8956 > select add #2.3
    8957 
    8958 2 models selected 
    8959 Grouped 2 regions 
    8960 
    8961 > select clear
    8962 
    8963 > select #2.6
    8964 
    8965 1 model selected 
    8966 Ungrouped to 4 regions 
    8967 Ungrouped to 2 regions 
    8968 
    8969 > select #2.17
    8970 
    8971 1 model selected 
    8972 
    8973 > select add #2.16
    8974 
    8975 2 models selected 
    8976 
    8977 > select add #2.7
    8978 
    8979 3 models selected 
    8980 Grouped 3 regions 
    8981 
    8982 > select #2.27
    8983 
    8984 1 model selected 
    8985 
    8986 > hide #!3 models
    8987 
    8988 > select clear
    8989 
    8990 > select #2.7
    8991 
    8992 1 model selected 
    8993 
    8994 > select add #2.3
    8995 
    8996 2 models selected 
    8997 Grouped 2 regions 
    8998 
    8999 > select #2.10
    9000 
    9001 1 model selected 
    9002 Ungrouped to 3 regions 
    9003 
    9004 > select clear
    9005 
    9006 > select #2.7
    9007 
    9008 1 model selected 
    9009 
    9010 > select add #2.16
    9011 
    9012 2 models selected 
    9013 
    9014 > select add #2.3
    9015 
    9016 3 models selected 
    9017 Grouped 3 regions 
    9018 
    9019 > select #2.5
    9020 
    9021 1 model selected 
    9022 Ungrouped to 4 regions 
    9023 
    9024 > select clear
    9025 
    9026 > select #2.17
    9027 
    9028 1 model selected 
    9029 
    9030 > select add #2.16
    9031 
    9032 2 models selected 
    9033 
    9034 > select add #2.7
    9035 
    9036 3 models selected 
    9037 Grouped 3 regions 
    9038 
    9039 > select add #2.3
    9040 
    9041 2 models selected 
    9042 Grouped 2 regions 
    9043 
    9044 > select #2.9
    9045 
    9046 1 model selected 
    9047 
    9048 > select #2.1
    9049 
    9050 1 model selected 
    9051 Ungrouped to 3 regions 
    9052 [Repeated 1 time(s)]Ungrouped to 5 regions 
    9053 Ungrouped to 0 regions 
    9054 
    9055 > select #2.3
    9056 
    9057 1 model selected 
    9058 
    9059 > select add #2.16
    9060 
    9061 2 models selected 
    9062 
    9063 > select add #2.31
    9064 
    9065 3 models selected 
    9066 
    9067 > select add #2.32
    9068 
    9069 4 models selected 
    9070 
    9071 > select add #2.1
    9072 
    9073 5 models selected 
    9074 Grouped 5 regions 
    9075 
    9076 > select clear
    9077 
    9078 > select #2.9
    9079 
    9080 1 model selected 
    9081 Ungrouped to 2 regions 
    9082 
    9083 > select clear
    9084 
    9085 > select #2.3
    9086 
    9087 1 model selected 
    9088 
    9089 > select add #2.1
    9090 
    9091 2 models selected 
    9092 Grouped 2 regions 
    9093 
    9094 > select #2.12
    9095 
    9096 1 model selected 
    9097 Ungrouped to 2 regions 
    9098 
    9099 > select clear
    9100 
    9101 > select #2.1
    9102 
    9103 1 model selected 
    9104 
    9105 > select add #2.9
    9106 
    9107 2 models selected 
    9108 Grouped 2 regions 
    9109 
    9110 > select #2.4
    9111 
    9112 1 model selected 
    9113 
    9114 > select clear
    9115 
    9116 > select #2.4
    9117 
    9118 1 model selected 
    9119 Ungrouped to 2 regions 
    9120 Ungrouped to 4 regions 
    9121 
    9122 > select clear
    9123 
    9124 > select #2.31
    9125 
    9126 1 model selected 
    9127 
    9128 > select add #2.32
    9129 
    9130 2 models selected 
    9131 
    9132 > select add #2.4
    9133 
    9134 3 models selected 
    9135 Grouped 3 regions 
    9136 
    9137 > select #2.11
    9138 
    9139 1 model selected 
    9140 Ungrouped to 2 regions 
    9141 [Repeated 1 time(s)]
    9142 
    9143 > select clear
    9144 
    9145 > select #2.1
    9146 
    9147 1 model selected 
    9148 
    9149 > select add #2.31
    9150 
    9151 2 models selected 
    9152 
    9153 > select add #2.11
    9154 
    9155 3 models selected 
    9156 Grouped 3 regions 
    9157 
    9158 > select clear
    9159 
    9160 > select #2.9
    9161 
    9162 1 model selected 
    9163 
    9164 > select #2.2
    9165 
    9166 1 model selected 
    9167 Ungrouped to 2 regions 
    9168 Ungrouped to 4 regions 
    9169 Ungrouped to 2 regions 
    9170 
    9171 > select clear
    9172 
    9173 > select #2.2
    9174 
    9175 1 model selected 
    9176 
    9177 > select add #2.33
    9178 
    9179 2 models selected 
    9180 
    9181 > select add #2.1
    9182 
    9183 3 models selected 
    9184 Grouped 3 regions 
    9185 
    9186 > select #2.13
    9187 
    9188 1 model selected 
    9189 Ungrouped to 2 regions 
    9190 Ungrouped to 0 regions 
    9191 
    9192 > select #2.32
    9193 
    9194 1 model selected 
    9195 
    9196 > select add #2.2
    9197 
    9198 2 models selected 
    9199 
    9200 > select add #2.1
    9201 
    9202 3 models selected 
    9203 Grouped 3 regions 
    9204 
    9205 > select clear
    9206 
    9207 > select #2.14
    9208 
    9209 1 model selected 
    9210 Ungrouped to 2 regions 
    9211 
    9212 > select clear
    9213 
    9214 > select #2.13
    9215 
    9216 1 model selected 
    9217 
    9218 > select add #2.1
    9219 
    9220 2 models selected 
    9221 
    9222 > select clear
    9223 
    9224 > select #2.13
    9225 
    9226 1 model selected 
    9227 Ungrouped to 2 regions 
    9228 Ungrouped to 3 regions 
    9229 
    9230 > select clear
    9231 
    9232 > select #2.13
    9233 
    9234 1 model selected 
    9235 
    9236 > select add #2.1
    9237 
    9238 2 models selected 
    9239 Grouped 2 regions 
    9240 
    9241 > select clear
    9242 
    9243 > select #2.4
    9244 
    9245 1 model selected 
    9246 
    9247 > select add #2.1
    9248 
    9249 2 models selected 
    9250 Grouped 2 regions 
    9251 Opened Rev-Hp-PflB_imasked_imasked as #5, grid size 220,220,220, pixel 4.3,
    9252 shown at step 1, values float32 
    9253 Segmenting Rev-Hp-PflB_imasked_imasked, density threshold 0.383927 
    9254 Showing 21 region surfaces 
    9255 71 watershed regions, grouped to 21 regions 
    9256 Showing Rev-Hp-PflB_imasked_imasked.seg - 21 regions, 21 surfaces 
    9257 
    9258 > select #2.2
    9259 
    9260 1 model selected 
    9261 Ungrouped to 2 regions 
    9262 Ungrouped to 0 regions 
    9263 
    9264 > hide #4 models
    9265 
    9266 > hide #!2 models
    9267 
    9268 > show #!2 models
    9269 
    9270 > save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    9271 > from_June2024/For-FlgY-model_June2024/Segments/FlgY-with-joints.mrc models
    9272 > #5
    9273 
    9274 > select #2.18
    9275 
    9276 1 model selected 
    9277 
    9278 > select add #2.13
    9279 
    9280 2 models selected 
    9281 
    9282 > select add #2.8
    9283 
    9284 3 models selected 
    9285 
    9286 > select add #2.9
    9287 
    9288 4 models selected 
    9289 
    9290 > select add #2.11
    9291 
    9292 5 models selected 
    9293 
    9294 > select add #2.12
    9295 
    9296 6 models selected 
    9297 
    9298 > select add #2.6
    9299 
    9300 7 models selected 
    9301 
    9302 > select add #2.17
    9303 
    9304 8 models selected 
    9305 
    9306 > select add #2.15
    9307 
    9308 9 models selected 
    9309 
    9310 > select add #2.23
    9311 
    9312 10 models selected 
    9313 
    9314 > select add #2.22
    9315 
    9316 11 models selected 
    9317 
    9318 > select add #2.16
    9319 
    9320 12 models selected 
    9321 
    9322 > select add #2.10
    9323 
    9324 13 models selected 
    9325 
    9326 > select add #2.5
    9327 
    9328 14 models selected 
    9329 Ungrouped to 24 regions 
    9330 Ungrouped to 18 regions 
    9331 Ungrouped to 0 regions 
    9332 
    9333 > select #2.24
    9334 
    9335 1 model selected 
    9336 
    9337 > select add #2.14
    9338 
    9339 2 models selected 
    9340 
    9341 > select add #2.33
    9342 
    9343 3 models selected 
    9344 
    9345 > select add #2.3
    9346 
    9347 4 models selected 
    9348 
    9349 > select add #2.7
    9350 
    9351 5 models selected 
    9352 
    9353 > select add #2.1
    9354 
    9355 6 models selected 
    9356 
    9357 > select add #2.19
    9358 
    9359 7 models selected 
    9360 
    9361 > select add #2.4
    9362 
    9363 8 models selected 
    9364 
    9365 > select add #2.21
    9366 
    9367 9 models selected 
    9368 
    9369 > select add #2.20
    9370 
    9371 10 models selected 
    9372 
    9373 > hide #!5 models
    9374 
    9375 > select subtract #2.12
    9376 
    9377 34 models selected 
    9378 
    9379 > select subtract #2.45
    9380 
    9381 33 models selected 
    9382 
    9383 > select subtract #2.46
    9384 
    9385 32 models selected 
    9386 
    9387 > select clear
    9388 
    9389 > select add #2.12
    9390 
    9391 1 model selected 
    9392 
    9393 > select add #2.45
    9394 
    9395 2 models selected 
    9396 
    9397 > select add #2.46
    9398 
    9399 3 models selected 
    9400 
    9401 > select add #2.21
    9402 
    9403 4 models selected 
    9404 
    9405 > select add #2.20
    9406 
    9407 5 models selected 
    9408 
    9409 > select add #2.14
    9410 
    9411 6 models selected 
    9412 
    9413 > select add #2.24
    9414 
    9415 7 models selected 
    9416 
    9417 > select add #2.48
    9418 
    9419 8 models selected 
    9420 
    9421 > select add #2.18
    9422 
    9423 9 models selected 
    9424 Grouped 9 regions 
    9425 
    9426 > select add #2.52
    9427 
    9428 2 models selected 
    9429 
    9430 > select add #2.8
    9431 
    9432 3 models selected 
    9433 
    9434 > select add #2.33
    9435 
    9436 4 models selected 
    9437 
    9438 > select add #2.3
    9439 
    9440 5 models selected 
    9441 
    9442 > select add #2.30
    9443 
    9444 6 models selected 
    9445 
    9446 > select add #2.7
    9447 
    9448 7 models selected 
    9449 
    9450 > select add #2.1
    9451 
    9452 8 models selected 
    9453 
    9454 > select add #2.19
    9455 
    9456 9 models selected 
    9457 
    9458 > select add #2.4
    9459 
    9460 10 models selected 
    9461 Grouped 10 regions 
    9462 
    9463 > select add #2.15
    9464 
    9465 2 models selected 
    9466 
    9467 > select clear
    9468 
    9469 > select #2.26
    9470 
    9471 1 model selected 
    9472 
    9473 > select add #2.11
    9474 
    9475 2 models selected 
    9476 Ungrouped to 0 regions 
    9477 Ungrouped to 10 regions 
    9478 
    9479 > save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    9480 > from_June2024/For-FlgY-
    9481 > model_June2024/Segments/Segmentation_FlgY_June2024.cxs includeMaps true
    9482 
    9483 > close session
    9484 
    9485 > open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    9486 > from_June2024/Sep11_2023/PflA-2.1A-230911.mrc
    9487 
    9488 Opened PflA-2.1A-230911.mrc as #1, grid size 240,240,240, pixel 2.1, shown at
    9489 level 4.29, step 1, values float32 
    9490 
    9491 > volume #1 level 0.04668
    9492 
    9493 > ui tool show "Segment Map"
    9494 
    9495 Segmenting PflA-2.1A-230911.mrc, density threshold 0.046682 
    9496 Showing 295 region surfaces 
    9497 3353 watershed regions, grouped to 295 regions 
    9498 Showing PflA-2.1A-230911.seg - 295 regions, 295 surfaces 
    9499 Drag select of 4912, 2073 of 27676 triangles, 4895, 1858 of 23484 triangles,
    9500 4753, 17818 of 21324 triangles, 4925, 16701 of 20336 triangles, 4688, 13072 of
    9501 19524 triangles, 4681, 62 of 20760 triangles, 4893, 3877 of 20004 triangles,
    9502 4965, 5486 of 20040 triangles, 4959, 8950 of 19788 triangles, 4921, 11627 of
    9503 18268 triangles, 4701, 11608 of 18776 triangles, 4958, 7623 of 19080
    9504 triangles, 4944, 12405 of 16572 triangles, 4930, 8286 of 19480 triangles,
    9505 4687, 10865 of 18496 triangles, 4927, 9131 of 16128 triangles, 4899, 15393 of
    9506 19516 triangles, 4905, 10808 of 16732 triangles, 4938, 9705 of 17880
    9507 triangles, 4945, 5453 of 18612 triangles, 4892, 15229 of 17068 triangles,
    9508 4937, 12209 of 15616 triangles, 4948, 9712 of 15808 triangles, 4828, 9026 of
    9509 16436 triangles, 4917, 7074 of 16712 triangles, 4946, 5740 of 15528 triangles,
    9510 4749, 6345 of 14628 triangles, 4953, 7293 of 14652 triangles, 4924, 5379 of
    9511 14820 triangles, 4814, 1274 of 15692 triangles, 4672, 7717 of 14464 triangles,
    9512 4943, 9823 of 15676 triangles, 4926, 7517 of 14184 triangles, 4790, 5831 of
    9513 13076 triangles, 4949, 5754 of 13764 triangles, 4779, 8226 of 13128 triangles,
    9514 4955, 1711 of 13408 triangles, 4878, 2869 of 14384 triangles, 4909, 4933, 7556
    9515 of 12836 triangles, 4939, 4919, 3987 of 13164 triangles, 4931, 9538 of 13064
    9516 triangles, 4787, 5468 of 13300 triangles, 4847, 8107 of 13212 triangles, 4774,
    9517 8059 of 12652 triangles, 4900, 4897, 718 of 14044 triangles, 4836, 4969, 196
    9518 of 11808 triangles, 4720, 6164 of 12816 triangles, 4706, 1125 of 12332
    9519 triangles, 4752, 8297 of 13132 triangles, 4918, 4384 of 12916 triangles, 4960,
    9520 3394 of 11432 triangles, 4668, 6980 of 12228 triangles, 4791, 7757 of 11564
    9521 triangles, 4879, 5193 of 11416 triangles, 4766, 3336 of 11660 triangles, 4964,
    9522 832 of 12532 triangles, 4730, 4865, 5181 of 10644 triangles, 4902, 592 of
    9523 10200 triangles, 4914, 6601 of 10976 triangles, 4952, 4941 of 10060 triangles,
    9524 4710, 3265 of 11424 triangles, 4932, 5705 of 10540 triangles, 4922, 2699 of
    9525 12076 triangles, 4146, 4602 of 9840 triangles, 4775, 4671, 3540 of 9924
    9526 triangles, 4729, 3033 of 8764 triangles, 4680, 1509 of 9780 triangles, 4829,
    9527 4823, 2999 of 9492 triangles, 4806, 2571 of 9124 triangles, 4409, 3902 of 8288
    9528 triangles, 4777, 4386 of 9908 triangles, 4690, 1212 of 8044 triangles, 4860,
    9529 7037 of 8564 triangles, 4858, 1787 of 9240 triangles, 4167, 5091 of 9276
    9530 triangles, 4744, 1927 of 8056 triangles, 4857, 5105 of 8268 triangles, 4783,
    9531 4427, 1470 of 7952 triangles, 4242, 5623 of 6928 triangles, 4793, 1778 of 7528
    9532 triangles, 4799, 3560 of 7860 triangles, 4526, 810 of 8160 triangles, 4156,
    9533 3036 of 7056 triangles, 4853, 3870 of 7512 triangles, 4393, 447 of 6884
    9534 triangles, 4505, 1549 of 6432 triangles, 4822, 3122 of 6232 triangles, 3688,
    9535 2024 of 4816 triangles, 4254, 220 of 4892 triangles, 4566, 1624 of 4880
    9536 triangles, 1 PflA-2.1A-230911.mrc 
    9537 
    9538 > hide #!1 models
    9539 
    9540 > select add #2.239
    9541 
    9542 101 models selected 
    9543 
    9544 > select add #2.41
    9545 
    9546 102 models selected 
    9547 
    9548 > select add #2.272
    9549 
    9550 103 models selected 
    9551 
    9552 > select add #2.166
    9553 
    9554 104 models selected 
    9555 
    9556 > select add #2.188
    9557 
    9558 105 models selected 
    9559 Drag select of 4894, 13014 of 34032 triangles, 4767, 4694, 13173 of 18900
    9560 triangles, 4711, 4723, 4712, 4760, 9477 of 11008 triangles, 4841, 4740, 4308 
    9561 Drag select of 4903, 5664 of 13508 triangles, 4904, 233 of 12368 triangles,
    9562 4896, 10603 of 11052 triangles, 4692, 3757 of 10748 triangles, 4934, 2285 of
    9563 10452 triangles, 4722, 8320 of 9168 triangles, 4966, 138 of 8844 triangles,
    9564 4446, 1502 of 8072 triangles, 4788, 4826, 4727, 7222 of 7424 triangles 
    9565 
    9566 > select add #2.278
    9567 
    9568 127 models selected 
    9569 Grouped 125 regions 
    9570 Opened PflA-2.1A-230911_imasked as #3, grid size 240,240,240, pixel 2.1, shown
    9571 at step 1, values float32 
    9572 Segmenting PflA-2.1A-230911_imasked, density threshold 0.046682 
    9573 Showing 170 region surfaces 
    9574 1322 watershed regions, grouped to 170 regions 
    9575 Showing PflA-2.seg - 170 regions, 170 surfaces 
    9576 
    9577 > select subtract #1
    9578 
    9579 Nothing selected 
    9580 
    9581 > hide #!2 models
    9582 
    9583 > open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    9584 > from_June2024/For-FlgY-model_June2024/Segments/FlgY-with-joints.mrc
    9585 
    9586 Opened FlgY-with-joints.mrc as #4, grid size 220,220,220, pixel 4.3, shown at
    9587 level 0.346, step 1, values float32 
    9588 
    9589 > select add #4
    9590 
    9591 2 models selected 
    9592 
    9593 > view matrix models #4,1,0,0,-273.89,0,1,0,-9.814,0,0,1,-18.309
    9594 
    9595 > volume #4 level 0.5615
    9596 
    9597 > view matrix models #4,1,0,0,-248.02,0,1,0,-8.3112,0,0,1,-16.835
    9598 
    9599 > view matrix models #4,1,0,0,-251.4,0,1,0,-10.631,0,0,1,-16.514
    9600 
    9601 > ui mousemode right "rotate selected models"
    9602 
    9603 > view matrix models
    9604 > #4,1,0.0014314,0.00027573,-251.39,-0.0014291,0.99996,-0.008294,-10.93,-0.00028759,0.0082936,0.99997,-16.509
    9605 
    9606 > ui mousemode right "translate selected models"
    9607 
    9608 > view orient
    9609 
    9610 > ui mousemode right "rotate selected models"
    9611 
    9612 > view matrix models
    9613 > #4,0.79655,0.60246,-0.05048,-254.13,-0.60188,0.7981,0.027742,-14.604,0.057002,0.0082847,0.99834,-16.115
    9614 
    9615 > close #4
    9616 
    9617 Segmenting PflA-2.1A-230911_imasked, density threshold 0.046682 
    9618 Showing 170 region surfaces 
    9619 1322 watershed regions, grouped to 170 regions 
    9620 Showing PflA-2.seg - 170 regions, 170 surfaces 
    9621 
    9622 > select #2.140
    9623 
    9624 1 model selected 
    9625 
    9626 > select add #2.15
    9627 
    9628 2 models selected 
    9629 
    9630 > select add #2.30
    9631 
    9632 3 models selected 
    9633 
    9634 > select add #2.61
    9635 
    9636 4 models selected 
    9637 
    9638 > select add #2.34
    9639 
    9640 5 models selected 
    9641 
    9642 > select add #2.58
    9643 
    9644 6 models selected 
    9645 
    9646 > select add #2.79
    9647 
    9648 7 models selected 
    9649 
    9650 > select add #2.102
    9651 
    9652 8 models selected 
    9653 Grouped 8 regions 
    9654 
    9655 > select add #2.11
    9656 
    9657 2 models selected 
    9658 
    9659 > select add #2.99
    9660 
    9661 3 models selected 
    9662 
    9663 > select subtract #2.99
    9664 
    9665 2 models selected 
    9666 
    9667 > select #2.11
    9668 
    9669 1 model selected 
    9670 
    9671 > select add #2.99
    9672 
    9673 2 models selected 
    9674 
    9675 > select add #2.109
    9676 
    9677 3 models selected 
    9678 Grouped 3 regions 
    9679 
    9680 > select clear
    9681 
    9682 > select #2.15
    9683 
    9684 1 model selected 
    9685 
    9686 > select add #2.74
    9687 
    9688 2 models selected 
    9689 
    9690 > select add #2.11
    9691 
    9692 3 models selected 
    9693 
    9694 > select add #2.111
    9695 
    9696 4 models selected 
    9697 
    9698 > select add #2.101
    9699 
    9700 5 models selected 
    9701 
    9702 > select add #2.167
    9703 
    9704 6 models selected 
    9705 Grouped 6 regions 
    9706 
    9707 > select add #2.31
    9708 
    9709 2 models selected 
    9710 
    9711 > select add #2.38
    9712 
    9713 3 models selected 
    9714 Grouped 3 regions 
    9715 
    9716 > select #2.11
    9717 
    9718 1 model selected 
    9719 
    9720 > hide #!3 models
    9721 
    9722 Opened PflA-2_imasked as #4, grid size 240,240,240, pixel 2.1, shown at step
    9723 1, values float32 
    9724 
    9725 > save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    9726 > from_June2024/Sep11_2023/Segment_june11_2024/1x_Cage-units.mrc models #4
    9727 
    9728 > save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    9729 > from_June2024/Sep11_2023/Segment_june11_2024/Segment-local-PflAB.cxs
    9730 > includeMaps true
    9731 
    9732 ——— End of log from Tue Jun 11 18:45:39 2024 ———
    9733 
    9734 opened ChimeraX session 
    9735 Showing PflA-2.seg - 154 regions, 154 surfaces 
    9736 
    9737 > hide #!2 models
    9738 
    9739 > hide #!4 models
    9740 
    9741 > show #!2 models
    9742 
    9743 > select #2.83
    9744 
    9745 1 model selected 
    9746 
    9747 > select add #2.96
    9748 
    9749 2 models selected 
    9750 
    9751 > select add #2.154
    9752 
    9753 3 models selected 
    9754 
    9755 > select subtract #2.17
    9756 
    9757 150 models selected 
    9758 
    9759 > select clear
    9760 
    9761 > select #2.17
    9762 
    9763 1 model selected 
    9764 
    9765 > select add #2.154
    9766 
    9767 2 models selected 
    9768 
    9769 > select add #2.96
    9770 
    9771 3 models selected 
    9772 
    9773 > select add #2.83
    9774 
    9775 4 models selected 
    9776 Grouped 4 regions 
    9777 Opened PflA-2_imasked as #5, grid size 240,240,240, pixel 2.1, shown at step
    9778 1, values float32 
    9779 Segmenting PflA-2_imasked, density threshold 0.046682 
    9780 Showing 20 region surfaces 
    9781 103 watershed regions, grouped to 20 regions 
    9782 Showing PflA-2_imasked.seg - 20 regions, 20 surfaces 
    9783 
    9784 > select #2.7
    9785 
    9786 1 model selected 
    9787 
    9788 > hide #!5 models
    9789 
    9790 Opened PflA-2_imasked_imasked as #6, grid size 240,240,240, pixel 2.1, shown
    9791 at step 1, values float32 
    9792 
    9793 > save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    9794 > from_June2024/Sep11_2023/Segment_june11_2024/MotB_PG.mrc models #6
    9795 
    9796 Opened PflA-2_imasked_imasked as #7, grid size 240,240,240, pixel 2.1, shown
    9797 at step 1, values float32 
    9798 Segmenting PflA-2_imasked_imasked, density threshold 0.046682 
    9799 Showing 19 region surfaces 
    9800 99 watershed regions, grouped to 19 regions 
    9801 Showing PflA-2_imasked_imasked.seg - 19 regions, 19 surfaces 
    9802 
    9803 > hide #!6 models
    9804 
    9805 > hide #!7 models
    9806 
    9807 > select #2.17
    9808 
    9809 1 model selected 
    9810 
    9811 > select add #2.2
    9812 
    9813 2 models selected 
    9814 
    9815 > select add #2.4
    9816 
    9817 3 models selected 
    9818 
    9819 > select add #2.10
    9820 
    9821 4 models selected 
    9822 Grouped 4 regions 
    9823 
    9824 > select #2.6
    9825 
    9826 1 model selected 
    9827 Ungrouped to 2 regions 
    9828 Ungrouped to 4 regions 
    9829 
    9830 > select clear
    9831 
    9832 > select #2.17
    9833 
    9834 1 model selected 
    9835 
    9836 > select add #2.2
    9837 
    9838 2 models selected 
    9839 
    9840 > select #2.17
    9841 
    9842 1 model selected 
    9843 Ungrouped to 2 regions 
    9844 
    9845 > select clear
    9846 
    9847 > select #2.2
    9848 
    9849 1 model selected 
    9850 
    9851 > select subtract #2.2
    9852 
    9853 Nothing selected 
    9854 
    9855 > select add #2.10
    9856 
    9857 1 model selected 
    9858 
    9859 > select clear
    9860 
    9861 Showing 20 region surfaces 
    9862 
    9863 > select clear
    9864 
    9865 > select #2.2
    9866 
    9867 1 model selected 
    9868 
    9869 > select add #2.10
    9870 
    9871 2 models selected 
    9872 Grouped 2 regions 
    9873 
    9874 > select clear
    9875 
    9876 > select #2.2
    9877 
    9878 1 model selected 
    9879 Ungrouped to 2 regions 
    9880 
    9881 > select #2.17
    9882 
    9883 1 model selected 
    9884 
    9885 > hide #!2 models
    9886 
    9887 > show #!7 models
    9888 
    9889 > ui tool show "Side View"
    9890 
    9891 > show #!2 models
    9892 
    9893 > select #2.17
    9894 
    9895 1 model selected 
    9896 
    9897 > select clear
    9898 
    9899 > select #2.17
    9900 
    9901 1 model selected 
    9902 Opened PflA-2_imasked_imasked_imasked as #8, grid size 240,240,240, pixel 2.1,
    9903 shown at step 1, values float32 
    9904 
    9905 > save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    9906 > from_June2024/Sep11_2023/Segment_june11_2024/PflA.mrc models #8
    9907 
    9908 Opened PflA-2_imasked_imasked_imasked as #9, grid size 240,240,240, pixel 2.1,
    9909 shown at step 1, values float32 
    9910 Segmenting PflA-2_imasked_imasked_imasked, density threshold 0.046682 
    9911 Showing 15 region surfaces 
    9912 71 watershed regions, grouped to 15 regions 
    9913 Showing PflA-2_imasked_imasked_imasked.seg - 15 regions, 15 surfaces 
    9914 
    9915 > hide #!7 models
    9916 
    9917 > hide #!8 models
    9918 
    9919 > select #2.9
    9920 
    9921 1 model selected 
    9922 
    9923 > select add #2.12
    9924 
    9925 2 models selected 
    9926 
    9927 > select add #2.7
    9928 
    9929 3 models selected 
    9930 
    9931 > select add #2.13
    9932 
    9933 4 models selected 
    9934 
    9935 > select add #2.15
    9936 
    9937 5 models selected 
    9938 
    9939 > select add #2.10
    9940 
    9941 6 models selected 
    9942 Grouped 6 regions 
    9943 Opened PflA-2_imasked_imasked_imasked_imasked as #10, grid size 240,240,240,
    9944 pixel 2.1, shown at step 1, values float32 
    9945 
    9946 > save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    9947 > from_June2024/Sep11_2023/Segment_june11_2024/Cage.mrc models #10
    9948 
    9949 Opened PflA-2_imasked_imasked_imasked_imasked as #11, grid size 240,240,240,
    9950 pixel 2.1, shown at step 1, values float32 
    9951 Segmenting PflA-2_imasked_imasked_imasked_imasked, density threshold 0.046682 
    9952 Showing 9 region surfaces 
    9953 50 watershed regions, grouped to 9 regions 
    9954 Showing PflA-2_imasked_imasked_imasked_imasked.seg - 9 regions, 9 surfaces 
    9955 
    9956 > hide #!9 models
    9957 
    9958 > hide #!10 models
    9959 
    9960 > hide #!11 models
    9961 
    9962 > select #2.4
    9963 
    9964 1 model selected 
    9965 
    9966 > select #2.1
    9967 
    9968 1 model selected 
    9969 
    9970 > select #2.1
    9971 
    9972 1 model selected 
    9973 Ungrouped to 2 regions 
    9974 Ungrouped to 4 regions 
    9975 
    9976 > select #2.1
    9977 
    9978 1 model selected 
    9979 
    9980 > select #2.1
    9981 
    9982 1 model selected 
    9983 Ungrouped to 4 regions 
    9984 Ungrouped to 2 regions 
    9985 Ungrouped to 0 regions 
    9986 
    9987 > select #2.4
    9988 
    9989 1 model selected 
    9990 
    9991 > select add #2.1
    9992 
    9993 2 models selected 
    9994 
    9995 > select add #2.11
    9996 
    9997 3 models selected 
    9998 
    9999 > select add #2.10
    10000 
    10001 4 models selected 
    10002 
    10003 > select add #2.16
    10004 
    10005 5 models selected 
    10006 Grouped 5 regions 
    10007 
    10008 > select #2.6
    10009 
    10010 1 model selected 
    10011 
    10012 > select add #2.1
    10013 
    10014 2 models selected 
    10015 Grouped 2 regions 
    10016 
    10017 > select clear
    10018 
    10019 > select #2.1
    10020 
    10021 1 model selected 
    10022 Opened PflA-2_imasked_imasked_imasked_imasked_imasked as #12, grid size
    10023 240,240,240, pixel 2.1, shown at step 1, values float32 
    10024 
    10025 > save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    10026 > from_June2024/Sep11_2023/Segment_june11_2024/PflB.mrc models #12
    10027 
    10028 Opened PflA-2_imasked_imasked_imasked_imasked_imasked as #13, grid size
    10029 240,240,240, pixel 2.1, shown at step 1, values float32 
    10030 Segmenting PflA-2_imasked_imasked_imasked_imasked_imasked, density threshold
    10031 0.046682 
    10032 Showing 7 region surfaces 
    10033 34 watershed regions, grouped to 7 regions 
    10034 Showing PflA-2_imasked_imasked_imasked_imasked_imasked.seg - 7 regions, 7
    10035 surfaces 
    10036 
    10037 > hide #!12 models
    10038 
    10039 > select add #2.7
    10040 
    10041 1 model selected 
    10042 Drag select of 51, 7 of 14852 triangles, 13
    10043 PflA-2_imasked_imasked_imasked_imasked_imasked 
    10044 
    10045 > select add #2.4
    10046 
    10047 5 models selected 
    10048 Opened PflA-2_imasked_imasked_imasked_imasked_imasked_imasked as #14, grid
    10049 size 240,240,240, pixel 2.1, shown at step 1, values float32 
    10050 
    10051 > save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    10052 > from_June2024/Sep11_2023/Segment_june11_2024/FliL.mrc models #14
    10053 
    10054 Opened PflA-2_imasked_imasked_imasked_imasked_imasked_imasked as #15, grid
    10055 size 240,240,240, pixel 2.1, shown at step 1, values float32 
    10056 Segmenting PflA-2_imasked_imasked_imasked_imasked_imasked_imasked, density
    10057 threshold 0.046682 
    10058 Showing 4 region surfaces 
    10059 18 watershed regions, grouped to 4 regions 
    10060 Showing PflA-2_imasked_imasked_imasked_imasked_imasked_imasked.seg - 4
    10061 regions, 4 surfaces 
    10062 
    10063 > select #2.3
    10064 
    10065 1 model selected 
    10066 
    10067 > select add #2.4
    10068 
    10069 2 models selected 
    10070 
    10071 > select add #2.1
    10072 
    10073 3 models selected 
    10074 
    10075 > select add #2.2
    10076 
    10077 4 models selected 
    10078 
    10079 > hide #!2 models
    10080 
    10081 > select add #2
    10082 
    10083 5 models selected 
    10084 
    10085 > hide #!13 models
    10086 
    10087 > hide #!14 models
    10088 
    10089 > save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    10090 > from_June2024/Sep11_2023/Segment_june11_2024/Other_Cage.mrc models #15
    10091 
    10092 > save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    10093 > from_June2024/Sep11_2023/Segment_june11_2024/Segment2-local-PflAB.cxs
    10094 > includeMaps true
    10095 
    10096 ——— End of log from Tue Jun 11 23:04:54 2024 ———
    10097 
    10098 opened ChimeraX session 
    10099 Showing PflA-2_imasked_imasked_imasked_imasked_imasked_imasked.seg - 4
    10100 regions, 4 surfaces 
    10101 
    10102 > show #!11 models
    10103 
    10104 > show #!12 models
    10105 
    10106 > show #!13 models
    10107 
    10108 > show #!14 models
    10109 
    10110 > show #!10 models
    10111 
    10112 > show #!9 models
    10113 
    10114 > show #!8 models
    10115 
    10116 > show #!6 models
    10117 
    10118 > show #!5 models
    10119 
    10120 > show #!4 models
    10121 
    10122 > show #!3 models
    10123 
    10124 > close session
    10125 
    10126 > open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    10127 > from_June2024/July_2024/Final-
    10128 > version_model/Flo_PflA_Local/PflA-2.1A-230911.mrc
    10129 
    10130 Opened PflA-2.1A-230911.mrc as #1, grid size 240,240,240, pixel 2.1, shown at
    10131 level 4.29, step 1, values float32 
    10132 
    10133 > volume #1 level 1.73
    10134 
    10135 > volume #1 level 0.1847
    10136 
    10137 > ui tool show "Segment Map"
    10138 
    10139 Segmenting PflA-2.1A-230911.mrc, density threshold 0.184695 
    10140 Showing 295 region surfaces 
    10141 3349 watershed regions, grouped to 295 regions 
    10142 Showing PflA-2.1A-230911.seg - 295 regions, 295 surfaces 
    10143 
    10144 > select add #2.110
    10145 
    10146 1 model selected 
    10147 
    10148 > select add #2.62
    10149 
    10150 2 models selected 
    10151 
    10152 > select add #2.5
    10153 
    10154 3 models selected 
    10155 
    10156 > select add #2.7
    10157 
    10158 4 models selected 
    10159 
    10160 > select add #2.15
    10161 
    10162 5 models selected 
    10163 
    10164 > select add #2.42
    10165 
    10166 6 models selected 
    10167 
    10168 > select add #2.104
    10169 
    10170 7 models selected 
    10171 
    10172 > select add #2.174
    10173 
    10174 8 models selected 
    10175 
    10176 > select add #2.165
    10177 
    10178 9 models selected 
    10179 
    10180 > select add #2.280
    10181 
    10182 10 models selected 
    10183 
    10184 > select add #2.176
    10185 
    10186 11 models selected 
    10187 
    10188 > select add #2.192
    10189 
    10190 12 models selected 
    10191 
    10192 > select add #2.86
    10193 
    10194 13 models selected 
    10195 
    10196 > select add #2.234
    10197 
    10198 14 models selected 
    10199 
    10200 > select add #2.144
    10201 
    10202 15 models selected 
    10203 
    10204 > select add #2.14
    10205 
    10206 16 models selected 
    10207 
    10208 > select add #2.207
    10209 
    10210 17 models selected 
    10211 
    10212 > select add #2.111
    10213 
    10214 18 models selected 
    10215 
    10216 > select add #2.18
    10217 
    10218 19 models selected 
    10219 
    10220 > select add #2.112
    10221 
    10222 20 models selected 
    10223 
    10224 > select add #2.263
    10225 
    10226 21 models selected 
    10227 
    10228 > select add #2.55
    10229 
    10230 22 models selected 
    10231 
    10232 > select add #2.82
    10233 
    10234 23 models selected 
    10235 
    10236 > select add #2.288
    10237 
    10238 24 models selected 
    10239 
    10240 > select add #2.143
    10241 
    10242 25 models selected 
    10243 
    10244 > select add #2.125
    10245 
    10246 26 models selected 
    10247 
    10248 > select add #2.175
    10249 
    10250 27 models selected 
    10251 
    10252 > select add #2.63
    10253 
    10254 28 models selected 
    10255 Drag select of 4753, 6 of 12864 triangles, 4945, 7 of 13180 triangles, 4867,
    10256 16 of 9972 triangles, 3781, 12 of 4436 triangles 
    10257 
    10258 > select add #2.30
    10259 
    10260 33 models selected 
    10261 
    10262 > select add #2.24
    10263 
    10264 34 models selected 
    10265 
    10266 > select add #2.70
    10267 
    10268 35 models selected 
    10269 
    10270 > select add #2.35
    10271 
    10272 36 models selected 
    10273 
    10274 > select add #2.236
    10275 
    10276 37 models selected 
    10277 
    10278 > select add #2.33
    10279 
    10280 38 models selected 
    10281 
    10282 > select add #2.40
    10283 
    10284 39 models selected 
    10285 
    10286 > select subtract #2.40
    10287 
    10288 38 models selected 
    10289 
    10290 > select add #2.40
    10291 
    10292 39 models selected 
    10293 
    10294 > select add #2.46
    10295 
    10296 40 models selected 
    10297 
    10298 > select add #2.84
    10299 
    10300 41 models selected 
    10301 
    10302 > select add #2.49
    10303 
    10304 42 models selected 
    10305 
    10306 > select add #2.137
    10307 
    10308 43 models selected 
    10309 
    10310 > select add #2.172
    10311 
    10312 44 models selected 
    10313 
    10314 > select add #2.61
    10315 
    10316 45 models selected 
    10317 Drag select of 4929, 12 of 27404 triangles, 4933, 6 of 16236 triangles, 4907,
    10318 6 of 14460 triangles, 1 PflA-2.1A-230911.mrc 
    10319 
    10320 > select subtract #2.60
    10321 
    10322 49 models selected 
    10323 
    10324 > select add #2.136
    10325 
    10326 50 models selected 
    10327 Grouped 48 regions 
    10328 
    10329 > select add #2.60
    10330 
    10331 4 models selected 
    10332 
    10333 > select clear
    10334 
    10335 > select #2.23
    10336 
    10337 1 model selected 
    10338 
    10339 > select add #2.89
    10340 
    10341 2 models selected 
    10342 
    10343 > select add #2.228
    10344 
    10345 3 models selected 
    10346 
    10347 > select add #2.34
    10348 
    10349 4 models selected 
    10350 
    10351 > select add #2.109
    10352 
    10353 5 models selected 
    10354 
    10355 > select add #2.221
    10356 
    10357 6 models selected 
    10358 
    10359 > select add #2.28
    10360 
    10361 7 models selected 
    10362 
    10363 > select add #2.96
    10364 
    10365 8 models selected 
    10366 
    10367 > select add #2.13
    10368 
    10369 9 models selected 
    10370 
    10371 > select add #2.157
    10372 
    10373 10 models selected 
    10374 
    10375 > select add #2.44
    10376 
    10377 11 models selected 
    10378 
    10379 > select add #2.32
    10380 
    10381 12 models selected 
    10382 
    10383 > select add #2.227
    10384 
    10385 13 models selected 
    10386 
    10387 > select add #2.134
    10388 
    10389 14 models selected 
    10390 
    10391 > select add #2.216
    10392 
    10393 15 models selected 
    10394 
    10395 > select add #2.212
    10396 
    10397 16 models selected 
    10398 Grouped 16 regions 
    10399 
    10400 > select add #2.99
    10401 
    10402 2 models selected 
    10403 
    10404 > select add #2.83
    10405 
    10406 3 models selected 
    10407 
    10408 > select add #2.19
    10409 
    10410 4 models selected 
    10411 
    10412 > select add #2.249
    10413 
    10414 5 models selected 
    10415 
    10416 > select subtract #2.249
    10417 
    10418 4 models selected 
    10419 
    10420 > select add #2.249
    10421 
    10422 5 models selected 
    10423 
    10424 > select add #2.171
    10425 
    10426 6 models selected 
    10427 
    10428 > select add #2.87
    10429 
    10430 7 models selected 
    10431 
    10432 > select add #2.51
    10433 
    10434 8 models selected 
    10435 
    10436 > select add #2.200
    10437 
    10438 9 models selected 
    10439 
    10440 > select add #2.76
    10441 
    10442 10 models selected 
    10443 
    10444 > select add #2.37
    10445 
    10446 11 models selected 
    10447 
    10448 > select add #2.211
    10449 
    10450 12 models selected 
    10451 
    10452 > select add #2.225
    10453 
    10454 13 models selected 
    10455 
    10456 > select add #2.79
    10457 
    10458 14 models selected 
    10459 
    10460 > select add #2.237
    10461 
    10462 15 models selected 
    10463 
    10464 > select add #2.181
    10465 
    10466 16 models selected 
    10467 
    10468 > select add #2.184
    10469 
    10470 17 models selected 
    10471 
    10472 > select add #2.26
    10473 
    10474 18 models selected 
    10475 
    10476 > select add #2.251
    10477 
    10478 19 models selected 
    10479 
    10480 > select add #2.271
    10481 
    10482 20 models selected 
    10483 Grouped 20 regions 
    10484 
    10485 > select add #2.77
    10486 
    10487 2 models selected 
    10488 
    10489 > select add #2.29
    10490 
    10491 3 models selected 
    10492 
    10493 > select add #2.154
    10494 
    10495 4 models selected 
    10496 
    10497 > select add #2.72
    10498 
    10499 5 models selected 
    10500 
    10501 > select add #2.60
    10502 
    10503 6 models selected 
    10504 
    10505 > select add #2.223
    10506 
    10507 7 models selected 
    10508 
    10509 > select add #2.258
    10510 
    10511 8 models selected 
    10512 
    10513 > select add #2.246
    10514 
    10515 9 models selected 
    10516 
    10517 > select add #2.108
    10518 
    10519 10 models selected 
    10520 
    10521 > select add #2.187
    10522 
    10523 11 models selected 
    10524 
    10525 > select add #2.239
    10526 
    10527 12 models selected 
    10528 Grouped 12 regions 
    10529 
    10530 > select add #2.214
    10531 
    10532 2 models selected 
    10533 
    10534 > select add #2.240
    10535 
    10536 3 models selected 
    10537 
    10538 > select add #2.5
    10539 
    10540 4 models selected 
    10541 Grouped 4 regions 
    10542 
    10543 > select add #2.56
    10544 
    10545 2 models selected 
    10546 
    10547 > select add #2.159
    10548 
    10549 3 models selected 
    10550 Grouped 3 regions 
    10551 
    10552 > select add #2.122
    10553 
    10554 2 models selected 
    10555 Grouped 2 regions 
    10556 
    10557 > hide #!1 models
    10558 
    10559 Ungrouped to 2 regions 
    10560 Ungrouped to 5 regions 
    10561 Ungrouped to 21 regions 
    10562 Ungrouped to 95 regions 
    10563 
    10564 > select clear
    10565 
    10566 Drag select of 2080, 1729 of 1900 triangles, 1908, 2947, 576 of 2072
    10567 triangles, 2865, 741 of 1336 triangles, 2719, 750 of 1448 triangles, 2779,
    10568 1077 of 2408 triangles, 1906, 2629, 1477 of 2104 triangles, 2784, 686 of 1524
    10569 triangles, 3769, 4739 of 5428 triangles, 2933, 1034 of 2308 triangles, 2066,
    10570 3151 of 3180 triangles, 4339, 4000 of 5896 triangles, 2938, 1082 of 2372
    10571 triangles, 2220, 3497, 3675, 3222 of 3340 triangles, 2216, 2057, 2880 of 2948
    10572 triangles, 3793, 3805 of 4752 triangles, 4442, 3379 of 3756 triangles, 4564,
    10573 2849 of 4116 triangles, 1964, 3592, 2076 of 2164 triangles, 4828, 1957 of 9008
    10574 triangles, 4922, 12932 of 19224 triangles, 4907, 9492 of 14460 triangles,
    10575 4737, 8287 of 12092 triangles, 4356, 5870 of 7912 triangles, 4969, 127818 of
    10576 215268 triangles, 4880, 5733 of 8936 triangles, 4474, 5217 of 6700 triangles,
    10577 4691, 11119 of 12868 triangles, 4958, 10083 of 14060 triangles, 4761, 8523 of
    10578 10476 triangles, 2698, 1601 of 2268 triangles, 3422, 3523 of 4204 triangles,
    10579 3007, 810 of 1864 triangles, 3785, 3399 of 4136 triangles, 2927, 1037 of 1388
    10580 triangles, 2687, 1760 of 2584 triangles, 2186, 2835, 891 of 1416 triangles,
    10581 3129, 457 of 864 triangles, 2699, 2140 of 2492 triangles, 1939, 4203, 5095 of
    10582 6192 triangles, 3571, 1958 of 1996 triangles, 3671, 2079, 2949, 444 of 1212
    10583 triangles, 2403, 1794 of 2060 triangles, 4966, 7398 of 10228 triangles, 4941,
    10584 8976 of 12716 triangles, 4753, 8772 of 12864 triangles, 4944, 10068 of 15236
    10585 triangles, 4932, 5328 of 14104 triangles, 4705, 10933 of 17972 triangles,
    10586 4956, 9840 of 15096 triangles, 4096, 4933 of 6712 triangles, 4904, 4964 of
    10587 27220 triangles, 4584, 3198 of 4632 triangles, 4685, 4916 of 11200 triangles,
    10588 4965, 6846 of 12440 triangles, 4940, 12763 of 18084 triangles, 4939, 3067 of
    10589 12096 triangles, 4799, 2637 of 15236 triangles, 4898, 788 of 13532 triangles,
    10590 4301, 2382 of 4648 triangles, 4902, 6167 of 23188 triangles, 4485, 5113 of
    10591 6248 triangles, 4919, 12179 of 19796 triangles, 4870, 449 of 10328 triangles,
    10592 4906, 13362 of 19236 triangles, 4843, 8271 of 11168 triangles, 4943, 11254 of
    10593 15304 triangles, 4910, 10584 of 15396 triangles, 4953, 11774 of 16520
    10594 triangles, 4927, 7564 of 13064 triangles, 4758, 4696 of 20372 triangles, 4896,
    10595 6893 of 11756 triangles, 4783, 8099 of 11256 triangles, 4935, 2929 of 9736
    10596 triangles, 4908, 13910 of 19788 triangles, 4281, 4328 of 7764 triangles, 4946,
    10597 10147 of 16072 triangles, 4831, 9103 of 14224 triangles, 4862, 5320 of 9596
    10598 triangles, 4804, 10005 of 14140 triangles, 4794, 883 of 10880 triangles 
    10599 Grouped 90 regions 
    10600 
    10601 > select add #2.105
    10602 
    10603 2 models selected 
    10604 
    10605 > select add #2.211
    10606 
    10607 3 models selected 
    10608 
    10609 > select add #2.299
    10610 
    10611 4 models selected 
    10612 Grouped 4 regions 
    10613 Opened PflA-2.1A-230911_imasked as #3, grid size 240,240,240, pixel 2.1, shown
    10614 at step 1, values float32 
    10615 
    10616 > save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    10617 > from_June2024/July_2024/Final-
    10618 > version_model/Flo_PflA_Local/Segment_July_26/Disk.mrc models #3
    10619 
    10620 Opened PflA-2.1A-230911_imasked as #4, grid size 240,240,240, pixel 2.1, shown
    10621 at step 1, values float32 
    10622 Segmenting PflA-2.1A-230911_imasked, density threshold 0.184695 
    10623 Showing 204 region surfaces 
    10624 1746 watershed regions, grouped to 204 regions 
    10625 Showing PflA-2.seg - 204 regions, 204 surfaces 
    10626 
    10627 > hide #!2 models
    10628 
    10629 > show #!2 models
    10630 
    10631 > hide #!3 models
    10632 
    10633 > hide #!4 models
    10634 
    10635 Drag select of 2455, 14642 of 20620 triangles, 2589, 9697 of 19436 triangles,
    10636 2598, 2618, 2522, 11189 of 11436 triangles, 2606, 7432 of 11344 triangles,
    10637 2508, 2519, 2521, 2507, 2125, 3803 of 4348 triangles 
    10638 Grouped 11 regions 
    10639 
    10640 > select clear
    10641 
    10642 > select add #2.165
    10643 
    10644 1 model selected 
    10645 
    10646 > select add #2.22
    10647 
    10648 2 models selected 
    10649 
    10650 > select add #2.24
    10651 
    10652 3 models selected 
    10653 
    10654 > select add #2.78
    10655 
    10656 4 models selected 
    10657 
    10658 > select add #2.11
    10659 
    10660 5 models selected 
    10661 
    10662 > select add #2.90
    10663 
    10664 6 models selected 
    10665 
    10666 > select add #2.170
    10667 
    10668 7 models selected 
    10669 
    10670 > select add #2.4
    10671 
    10672 8 models selected 
    10673 
    10674 > select add #2.86
    10675 
    10676 9 models selected 
    10677 
    10678 > select add #2.3
    10679 
    10680 10 models selected 
    10681 Grouped 10 regions 
    10682 
    10683 > select add #2.7
    10684 
    10685 2 models selected 
    10686 
    10687 > select subtract #2.7
    10688 
    10689 1 model selected 
    10690 
    10691 > select add #2.7
    10692 
    10693 2 models selected 
    10694 
    10695 > select add #2.187
    10696 
    10697 3 models selected 
    10698 Grouped 3 regions 
    10699 
    10700 > select add #2.115
    10701 
    10702 2 models selected 
    10703 
    10704 > select add #2.149
    10705 
    10706 3 models selected 
    10707 
    10708 > select clear
    10709 
    10710 > select #2.3
    10711 
    10712 1 model selected 
    10713 Opened PflA-2_imasked as #5, grid size 240,240,240, pixel 2.1, shown at step
    10714 1, values float32 
    10715 Segmenting PflA-2_imasked, density threshold 0.184695 
    10716 Showing 182 region surfaces 
    10717 1409 watershed regions, grouped to 182 regions 
    10718 Showing PflA-2_imasked.seg - 182 regions, 182 surfaces 
    10719 
    10720 > select add #2.151
    10721 
    10722 1 model selected 
    10723 
    10724 > select add #2.15
    10725 
    10726 2 models selected 
    10727 
    10728 > select add #2.16
    10729 
    10730 3 models selected 
    10731 
    10732 > select add #2.161
    10733 
    10734 4 models selected 
    10735 
    10736 > select add #2.13
    10737 
    10738 5 models selected 
    10739 
    10740 > select add #2.30
    10741 
    10742 6 models selected 
    10743 
    10744 > select add #2.38
    10745 
    10746 7 models selected 
    10747 
    10748 > select add #2.33
    10749 
    10750 8 models selected 
    10751 
    10752 > select add #2.29
    10753 
    10754 9 models selected 
    10755 
    10756 > select add #2.40
    10757 
    10758 10 models selected 
    10759 
    10760 > select add #2.39
    10761 
    10762 11 models selected 
    10763 
    10764 > select add #2.31
    10765 
    10766 12 models selected 
    10767 
    10768 > select subtract #2.29
    10769 
    10770 11 models selected 
    10771 
    10772 > select add #2.29
    10773 
    10774 12 models selected 
    10775 
    10776 > select add #2.106
    10777 
    10778 13 models selected 
    10779 
    10780 > select add #2.93
    10781 
    10782 14 models selected 
    10783 
    10784 > select add #2.92
    10785 
    10786 15 models selected 
    10787 
    10788 > select add #2.77
    10789 
    10790 16 models selected 
    10791 
    10792 > select add #2.53
    10793 
    10794 17 models selected 
    10795 
    10796 > select add #2.91
    10797 
    10798 18 models selected 
    10799 
    10800 > select add #2.66
    10801 
    10802 19 models selected 
    10803 
    10804 > select add #2.101
    10805 
    10806 20 models selected 
    10807 
    10808 > select add #2.59
    10809 
    10810 21 models selected 
    10811 
    10812 > select add #2.42
    10813 
    10814 22 models selected 
    10815 
    10816 > select add #2.128
    10817 
    10818 23 models selected 
    10819 
    10820 > select add #2.124
    10821 
    10822 24 models selected 
    10823 
    10824 > select add #2.109
    10825 
    10826 25 models selected 
    10827 
    10828 > select add #2.112
    10829 
    10830 26 models selected 
    10831 
    10832 > select add #2.10
    10833 
    10834 27 models selected 
    10835 
    10836 > hide #!5 models
    10837 
    10838 > select add #2.88
    10839 
    10840 28 models selected 
    10841 
    10842 > show #!5 models
    10843 
    10844 > select add #2.72
    10845 
    10846 29 models selected 
    10847 
    10848 > select add #2.9
    10849 
    10850 30 models selected 
    10851 
    10852 > select add #2.27
    10853 
    10854 31 models selected 
    10855 Grouped 31 regions 
    10856 
    10857 > select add #2.32
    10858 
    10859 2 models selected 
    10860 
    10861 > select add #2.102
    10862 
    10863 3 models selected 
    10864 
    10865 > select add #2.62
    10866 
    10867 4 models selected 
    10868 
    10869 > select add #2.83
    10870 
    10871 5 models selected 
    10872 
    10873 > select add #2.110
    10874 
    10875 6 models selected 
    10876 
    10877 > select add #2.105
    10878 
    10879 7 models selected 
    10880 
    10881 > select add #2.34
    10882 
    10883 8 models selected 
    10884 
    10885 > select add #2.64
    10886 
    10887 9 models selected 
    10888 
    10889 > select subtract #2.32
    10890 
    10891 8 models selected 
    10892 Grouped 8 regions 
    10893 
    10894 > select add #2.46
    10895 
    10896 2 models selected 
    10897 
    10898 > select add #2.26
    10899 
    10900 3 models selected 
    10901 
    10902 > select add #2.121
    10903 
    10904 4 models selected 
    10905 
    10906 > select add #2.57
    10907 
    10908 5 models selected 
    10909 
    10910 > select add #2.24
    10911 
    10912 6 models selected 
    10913 Grouped 6 regions 
    10914 
    10915 > select add #2.171
    10916 
    10917 2 models selected 
    10918 Grouped 2 regions 
    10919 
    10920 > select add #2.32
    10921 
    10922 2 models selected 
    10923 Grouped 2 regions 
    10924 
    10925 > select add #2.107
    10926 
    10927 2 models selected 
    10928 Grouped 2 regions 
    10929 
    10930 > select add #2.63
    10931 
    10932 2 models selected 
    10933 
    10934 > select add #2.170
    10935 
    10936 3 models selected 
    10937 
    10938 > select add #2.117
    10939 
    10940 4 models selected 
    10941 
    10942 > select add #2.139
    10943 
    10944 5 models selected 
    10945 
    10946 > select add #2.179
    10947 
    10948 6 models selected 
    10949 
    10950 > select add #2.61
    10951 
    10952 7 models selected 
    10953 
    10954 > select subtract #2.139
    10955 
    10956 6 models selected 
    10957 
    10958 > select add #2.139
    10959 
    10960 7 models selected 
    10961 Grouped 7 regions 
    10962 
    10963 > select clear
    10964 
    10965 > select #2.9
    10966 
    10967 1 model selected 
    10968 
    10969 > hide #!5 models
    10970 
    10971 > show #!1 models
    10972 
    10973 > hide #!1 models
    10974 
    10975 > select clear
    10976 
    10977 [Repeated 1 time(s)]
    10978 
    10979 > select #2.9
    10980 
    10981 1 model selected 
    10982 Opened PflA-2_imasked_imasked as #6, grid size 240,240,240, pixel 2.1, shown
    10983 at step 1, values float32 
    10984 
    10985 > save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    10986 > from_June2024/July_2024/Final-
    10987 > version_model/Flo_PflA_Local/Segment_July_26/3Xunits.mrc models #6
    10988 
    10989 Opened PflA-2_imasked_imasked as #7, grid size 240,240,240, pixel 2.1, shown
    10990 at step 1, values float32 
    10991 Segmenting PflA-2_imasked_imasked, density threshold 0.184695 
    10992 Showing 130 region surfaces 
    10993 1128 watershed regions, grouped to 130 regions 
    10994 Showing PflA-2_imasked_imasked.seg - 130 regions, 130 surfaces 
    10995 
    10996 > hide #!6 models
    10997 
    10998 > hide #!7 models
    10999 
    11000 > select #2.50
    11001 
    11002 1 model selected 
    11003 
    11004 > select add #2.16
    11005 
    11006 2 models selected 
    11007 
    11008 > select add #2.85
    11009 
    11010 3 models selected 
    11011 
    11012 > select add #2.103
    11013 
    11014 4 models selected 
    11015 
    11016 > select add #2.24
    11017 
    11018 5 models selected 
    11019 
    11020 > select add #2.15
    11021 
    11022 6 models selected 
    11023 
    11024 > select add #2.12
    11025 
    11026 7 models selected 
    11027 
    11028 > select add #2.88
    11029 
    11030 8 models selected 
    11031 
    11032 > select add #2.67
    11033 
    11034 9 models selected 
    11035 
    11036 > show #!6 models
    11037 
    11038 > close #6-7
    11039 
    11040 Segmenting PflA-2_imasked, density threshold 0.184695 
    11041 Showing 182 region surfaces 
    11042 1409 watershed regions, grouped to 182 regions 
    11043 Showing PflA-2_imasked.seg - 182 regions, 182 surfaces 
    11044 
    11045 > select add #2.16
    11046 
    11047 1 model selected 
    11048 
    11049 > select add #2.161
    11050 
    11051 2 models selected 
    11052 
    11053 > select add #2.15
    11054 
    11055 3 models selected 
    11056 
    11057 > select add #2.151
    11058 
    11059 4 models selected 
    11060 
    11061 > select add #2.57
    11062 
    11063 5 models selected 
    11064 
    11065 > select add #2.121
    11066 
    11067 6 models selected 
    11068 
    11069 > select add #2.171
    11070 
    11071 7 models selected 
    11072 
    11073 > select add #2.24
    11074 
    11075 8 models selected 
    11076 
    11077 > select add #2.26
    11078 
    11079 9 models selected 
    11080 
    11081 > select add #2.30
    11082 
    11083 10 models selected 
    11084 
    11085 > select add #2.13
    11086 
    11087 11 models selected 
    11088 Grouped 11 regions 
    11089 
    11090 > select add #2.32
    11091 
    11092 2 models selected 
    11093 
    11094 > select add #2.102
    11095 
    11096 3 models selected 
    11097 
    11098 > select add #2.28
    11099 
    11100 4 models selected 
    11101 
    11102 > select add #2.106
    11103 
    11104 5 models selected 
    11105 
    11106 > select add #2.77
    11107 
    11108 6 models selected 
    11109 
    11110 > select add #2.53
    11111 
    11112 7 models selected 
    11113 
    11114 > select add #2.33
    11115 
    11116 8 models selected 
    11117 
    11118 > select add #2.38
    11119 
    11120 9 models selected 
    11121 
    11122 > select subtract #2.102
    11123 
    11124 8 models selected 
    11125 
    11126 > select add #2.102
    11127 
    11128 9 models selected 
    11129 
    11130 > select add #2.62
    11131 
    11132 10 models selected 
    11133 
    11134 > select add #2.83
    11135 
    11136 11 models selected 
    11137 
    11138 > select add #2.34
    11139 
    11140 12 models selected 
    11141 Grouped 12 regions 
    11142 
    11143 > select add #2.46
    11144 
    11145 2 models selected 
    11146 
    11147 > select add #2.64
    11148 
    11149 3 models selected 
    11150 
    11151 > select add #2.70
    11152 
    11153 4 models selected 
    11154 
    11155 > select add #2.110
    11156 
    11157 5 models selected 
    11158 
    11159 > select add #2.105
    11160 
    11161 6 models selected 
    11162 
    11163 > select add #2.112
    11164 
    11165 7 models selected 
    11166 
    11167 > select add #2.163
    11168 
    11169 8 models selected 
    11170 
    11171 > select add #2.101
    11172 
    11173 9 models selected 
    11174 
    11175 > select add #2.109
    11176 
    11177 10 models selected 
    11178 
    11179 > select add #2.66
    11180 
    11181 11 models selected 
    11182 
    11183 > select add #2.124
    11184 
    11185 12 models selected 
    11186 
    11187 > select add #2.91
    11188 
    11189 13 models selected 
    11190 
    11191 > select add #2.128
    11192 
    11193 14 models selected 
    11194 Grouped 14 regions 
    11195 
    11196 > select add #2.39
    11197 
    11198 2 models selected 
    11199 
    11200 > select add #2.42
    11201 
    11202 3 models selected 
    11203 
    11204 > select add #2.92
    11205 
    11206 4 models selected 
    11207 
    11208 > select add #2.93
    11209 
    11210 5 models selected 
    11211 
    11212 > select add #2.31
    11213 
    11214 6 models selected 
    11215 
    11216 > select add #2.40
    11217 
    11218 7 models selected 
    11219 Grouped 7 regions 
    11220 
    11221 > select add #2.9
    11222 
    11223 2 models selected 
    11224 
    11225 > select add #2.72
    11226 
    11227 3 models selected 
    11228 
    11229 > select add #2.59
    11230 
    11231 4 models selected 
    11232 
    11233 > select add #2.10
    11234 
    11235 5 models selected 
    11236 
    11237 > select add #2.88
    11238 
    11239 6 models selected 
    11240 
    11241 > select add #2.27
    11242 
    11243 7 models selected 
    11244 Grouped 7 regions 
    11245 
    11246 > select #2.18
    11247 
    11248 1 model selected 
    11249 Ungrouped to 5 regions 
    11250 
    11251 > select clear
    11252 
    11253 > select #2.10
    11254 
    11255 1 model selected 
    11256 
    11257 > select add #2.13
    11258 
    11259 2 models selected 
    11260 
    11261 > select add #2.24
    11262 
    11263 3 models selected 
    11264 
    11265 > select subtract #2.24
    11266 
    11267 2 models selected 
    11268 Grouped 2 regions 
    11269 
    11270 > select add #2.9
    11271 
    11272 2 models selected 
    11273 Grouped 2 regions 
    11274 
    11275 > select clear
    11276 
    11277 > select #2.9
    11278 
    11279 1 model selected 
    11280 
    11281 > select add #2.107
    11282 
    11283 2 models selected 
    11284 Grouped 2 regions 
    11285 Ungrouped to 2 regions 
    11286 
    11287 > select clear
    11288 
    11289 > select #2.10
    11290 
    11291 1 model selected 
    11292 Ungrouped to 2 regions 
    11293 Ungrouped to 9 regions 
    11294 Ungrouped to 21 regions 
    11295 Ungrouped to 63 regions 
    11296 
    11297 > select subtract #2.105
    11298 
    11299 62 models selected 
    11300 
    11301 > select add #2.117
    11302 
    11303 63 models selected 
    11304 
    11305 > select add #2.170
    11306 
    11307 64 models selected 
    11308 
    11309 > select add #2.179
    11310 
    11311 65 models selected 
    11312 
    11313 > select add #2.139
    11314 
    11315 66 models selected 
    11316 Grouped 66 regions 
    11317 
    11318 > select add #2.38
    11319 
    11320 2 models selected 
    11321 Grouped 2 regions 
    11322 
    11323 > select add #2.13
    11324 
    11325 2 models selected 
    11326 Grouped 2 regions 
    11327 
    11328 > select add #2.33
    11329 
    11330 2 models selected 
    11331 
    11332 > select add #2.34
    11333 
    11334 3 models selected 
    11335 
    11336 > select add #2.46
    11337 
    11338 4 models selected 
    11339 
    11340 > select add #2.40
    11341 
    11342 5 models selected 
    11343 Grouped 5 regions 
    11344 Opened PflA-2_imasked_imasked as #6, grid size 240,240,240, pixel 2.1, shown
    11345 at step 1, values float32 
    11346 
    11347 > save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    11348 > from_June2024/July_2024/Final-
    11349 > version_model/Flo_PflA_Local/Segment_July_26/3Xunits.mrc models #6
    11350 
    11351 Opened PflA-2_imasked_imasked as #7, grid size 240,240,240, pixel 2.1, shown
    11352 at step 1, values float32 
    11353 Segmenting PflA-2_imasked_imasked, density threshold 0.184695 
    11354 Showing 130 region surfaces 
    11355 1144 watershed regions, grouped to 130 regions 
    11356 Showing PflA-2_imasked_imasked.seg - 130 regions, 130 surfaces 
    11357 
    11358 > hide #!6 models
    11359 
    11360 > select #2.68
    11361 
    11362 1 model selected 
    11363 
    11364 > select add #2.89
    11365 
    11366 2 models selected 
    11367 
    11368 > select add #2.12
    11369 
    11370 3 models selected 
    11371 
    11372 > select add #2.24
    11373 
    11374 4 models selected 
    11375 
    11376 > select add #2.14
    11377 
    11378 5 models selected 
    11379 
    11380 > select add #2.103
    11381 
    11382 6 models selected 
    11383 
    11384 > select add #2.51
    11385 
    11386 7 models selected 
    11387 
    11388 > select add #2.15
    11389 
    11390 8 models selected 
    11391 
    11392 > select add #2.86
    11393 
    11394 9 models selected 
    11395 Grouped 9 regions 
    11396 Opened PflA-2_imasked_imasked_imasked as #8, grid size 240,240,240, pixel 2.1,
    11397 shown at step 1, values float32 
    11398 
    11399 > save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    11400 > from_June2024/July_2024/Final-
    11401 > version_model/Flo_PflA_Local/Segment_July_26/3XfliL.mrc models #8
    11402 
    11403 Opened PflA-2_imasked_imasked_imasked as #9, grid size 240,240,240, pixel 2.1,
    11404 shown at step 1, values float32 
    11405 Segmenting PflA-2_imasked_imasked_imasked, density threshold 0.184695 
    11406 Showing 121 region surfaces 
    11407 1088 watershed regions, grouped to 121 regions 
    11408 Showing PflA-2_imasked_imasked_imasked.seg - 121 regions, 121 surfaces 
    11409 
    11410 > hide #!7 models
    11411 
    11412 > hide #!8 models
    11413 
    11414 > select #2.8
    11415 
    11416 1 model selected 
    11417 
    11418 > select add #2.71
    11419 
    11420 2 models selected 
    11421 
    11422 > select add #2.44
    11423 
    11424 3 models selected 
    11425 
    11426 > select add #2.27
    11427 
    11428 4 models selected 
    11429 
    11430 > select add #2.76
    11431 
    11432 5 models selected 
    11433 
    11434 > select add #2.63
    11435 
    11436 6 models selected 
    11437 
    11438 > select add #2.92
    11439 
    11440 7 models selected 
    11441 
    11442 > select add #2.17
    11443 
    11444 8 models selected 
    11445 
    11446 > select add #2.110
    11447 
    11448 9 models selected 
    11449 
    11450 > select add #2.90
    11451 
    11452 10 models selected 
    11453 
    11454 > select add #2.117
    11455 
    11456 11 models selected 
    11457 
    11458 > select add #2.56
    11459 
    11460 12 models selected 
    11461 
    11462 > select add #2.4
    11463 
    11464 13 models selected 
    11465 
    11466 > select add #2.14
    11467 
    11468 14 models selected 
    11469 
    11470 > select add #2.55
    11471 
    11472 15 models selected 
    11473 
    11474 > select add #2.98
    11475 
    11476 16 models selected 
    11477 
    11478 > select add #2.6
    11479 
    11480 17 models selected 
    11481 
    11482 > select add #2.49
    11483 
    11484 18 models selected 
    11485 
    11486 > select add #2.79
    11487 
    11488 19 models selected 
    11489 
    11490 > select add #2.105
    11491 
    11492 20 models selected 
    11493 
    11494 > select add #2.99
    11495 
    11496 21 models selected 
    11497 
    11498 > select add #2.78
    11499 
    11500 22 models selected 
    11501 
    11502 > select add #2.41
    11503 
    11504 23 models selected 
    11505 
    11506 > select add #2.72
    11507 
    11508 24 models selected 
    11509 
    11510 > select add #2.58
    11511 
    11512 25 models selected 
    11513 
    11514 > select add #2.5
    11515 
    11516 26 models selected 
    11517 
    11518 > select add #2.33
    11519 
    11520 27 models selected 
    11521 
    11522 > select subtract #2.33
    11523 
    11524 26 models selected 
    11525 
    11526 > select add #2.33
    11527 
    11528 27 models selected 
    11529 
    11530 > select add #2.112
    11531 
    11532 28 models selected 
    11533 
    11534 > select add #2.73
    11535 
    11536 29 models selected 
    11537 
    11538 > select add #2.57
    11539 
    11540 30 models selected 
    11541 
    11542 > select add #2.10
    11543 
    11544 31 models selected 
    11545 
    11546 > select subtract #2.5
    11547 
    11548 30 models selected 
    11549 
    11550 > select add #2.5
    11551 
    11552 31 models selected 
    11553 Grouped 31 regions 
    11554 
    11555 > select add #2.106
    11556 
    11557 2 models selected 
    11558 Grouped 2 regions 
    11559 
    11560 > hide #!9 models
    11561 
    11562 > select add #2.1
    11563 
    11564 2 models selected 
    11565 
    11566 > select add #2.3
    11567 
    11568 3 models selected 
    11569 
    11570 > select add #2.2
    11571 
    11572 4 models selected 
    11573 
    11574 > select add #2.114
    11575 
    11576 5 models selected 
    11577 
    11578 > select add #2.115
    11579 
    11580 6 models selected 
    11581 
    11582 > select add #2.65
    11583 
    11584 7 models selected 
    11585 
    11586 > select add #2.28
    11587 
    11588 8 models selected 
    11589 
    11590 > select add #2.88
    11591 
    11592 9 models selected 
    11593 
    11594 > select add #2.68
    11595 
    11596 10 models selected 
    11597 
    11598 > select add #2.22
    11599 
    11600 11 models selected 
    11601 
    11602 > select add #2.43
    11603 
    11604 12 models selected 
    11605 
    11606 > select add #2.94
    11607 
    11608 13 models selected 
    11609 
    11610 > select add #2.29
    11611 
    11612 14 models selected 
    11613 
    11614 > select add #2.38
    11615 
    11616 15 models selected 
    11617 
    11618 > select add #2.64
    11619 
    11620 16 models selected 
    11621 
    11622 > select add #2.39
    11623 
    11624 17 models selected 
    11625 
    11626 > select add #2.100
    11627 
    11628 18 models selected 
    11629 
    11630 > select add #2.59
    11631 
    11632 19 models selected 
    11633 
    11634 > select add #2.12
    11635 
    11636 20 models selected 
    11637 
    11638 > select add #2.66
    11639 
    11640 21 models selected 
    11641 
    11642 > select add #2.34
    11643 
    11644 22 models selected 
    11645 Grouped 22 regions 
    11646 
    11647 > select add #2.93
    11648 
    11649 2 models selected 
    11650 
    11651 > select add #2.107
    11652 
    11653 3 models selected 
    11654 Grouped 3 regions 
    11655 
    11656 > select clear
    11657 
    11658 > select #2.1
    11659 
    11660 1 model selected 
    11661 Opened PflA-2_imasked_imasked_imasked_imasked as #10, grid size 240,240,240,
    11662 pixel 2.1, shown at step 1, values float32 
    11663 
    11664 > save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    11665 > from_June2024/July_2024/Final-
    11666 > version_model/Flo_PflA_Local/Segment_July_26/IM.mrc models #10
    11667 
    11668 Opened PflA-2_imasked_imasked_imasked_imasked as #11, grid size 240,240,240,
    11669 pixel 2.1, shown at step 1, values float32 
    11670 Segmenting 3Xunits.mrc, density threshold 0.184695 
    11671 Showing 52 region surfaces 
    11672 265 watershed regions, grouped to 52 regions 
    11673 Showing 3Xunits.seg - 52 regions, 52 surfaces 
    11674 
    11675 > hide #!10 models
    11676 
    11677 > hide #!2 models
    11678 
    11679 > hide #!11 models
    11680 
    11681 > show #!6 models
    11682 
    11683 > open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    11684 > from_June2024/July_2024/Final-version_model/Flo_PflA_Local/New_PflA.pdb
    11685 
    11686 Summary of feedback from opening /Volumes/Backup-95/Chimera-2023/PflB-PflA-
    11687 project/Start-from_June2024/July_2024/Final-
    11688 version_model/Flo_PflA_Local/New_PflA.pdb 
    11689 --- 
    11690 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 2 LEU A 78 1 77 
    11691 Start residue of secondary structure not found: HELIX 2 2 LEU A 79 ILE A 81 1
    11692 3 
    11693 Start residue of secondary structure not found: HELIX 3 3 LYS A 107 LEU A 118
    11694 1 12 
    11695 Start residue of secondary structure not found: HELIX 4 4 ASN A 119 MET A 121
    11696 1 3 
    11697 Start residue of secondary structure not found: HELIX 5 5 GLU A 154 ILE A 156
    11698 1 3 
    11699 679 messages similar to the above omitted 
    11700  
    11701 Chain information for New_PflA.pdb 
    11702 --- 
    11703 Chain | Description 
    11704 12.1/A0 12.2/A2 12.3/A4 12.4/A6 12.5/A8 12.6/At 12.7/Av 12.8/Ax 12.9/Az 12.10/BB 12.11/BD 12.12/BF 12.13/BH 12.14/BJ 12.15/BL 12.16/BN 12.17/BP 12.18/BR | No description available 
    11705 12.19/CK 12.20/CM 12.21/CO 12.22/CQ 12.23/CS 12.24/CU 12.25/CW 12.26/CY 12.27/Ca 12.28/Cc 12.29/Ce 12.30/Cg 12.31/Ci 12.32/Ck 12.33/Cm 12.34/Co 12.35/Cq 12.36/Cs | No description available 
    11706  
    11707 
    11708 > select add #12
    11709 
    11710 109872 atoms, 112014 bonds, 72 pseudobonds, 13482 residues, 55 models selected 
    11711 
    11712 > ui mousemode right "translate selected models"
    11713 
    11714 > view matrix models #12,1,0,0,-691.77,0,1,0,-586.46,0,0,1,-473.7
    11715 
    11716 > view matrix models #12,1,0,0,-747.48,0,1,0,-578.05,0,0,1,-528.69
    11717 
    11718 > view matrix models #12,1,0,0,-765.74,0,1,0,-634.57,0,0,1,-507.8
    11719 
    11720 > ui mousemode right "rotate selected models"
    11721 
    11722 > view matrix models
    11723 > #12,0.93968,-0.34172,0.015266,-557.95,0.3415,0.93976,0.015284,-792.76,-0.019569,-0.0091485,0.99977,-492.31
    11724 
    11725 > hide #!6 models
    11726 
    11727 > show #!6 models
    11728 
    11729 > view matrix models
    11730 > #12,0.93938,-0.34184,-0.02662,-536.73,0.34264,0.93876,0.036376,-803.4,0.012555,-0.043292,0.99898,-490.81
    11731 
    11732 > view matrix models
    11733 > #12,0.93488,-0.35397,-0.026433,-527.92,0.35476,0.93425,0.036495,-807.52,0.011777,-0.043496,0.99898,-490.28
    11734 
    11735 > hide #!6 models
    11736 
    11737 > show #!6 models
    11738 
    11739 > hide #!6 models
    11740 
    11741 > select clear
    11742 
    11743 > show #!6 models
    11744 
    11745 > hide #!6 models
    11746 
    11747 > show #!6 models
    11748 
    11749 > hide #!6 models
    11750 
    11751 > show #!6 models
    11752 
    11753 > hide #!6 models
    11754 
    11755 > show #!6 models
    11756 
    11757 > hide #!6 models
    11758 
    11759 Drag select of 2113 residues 
    11760 
    11761 > select add #12.20
    11762 
    11763 17231 atoms, 1136 bonds, 2113 residues, 6 models selected 
    11764 
    11765 > select add #12.19
    11766 
    11767 17231 atoms, 2272 bonds, 2113 residues, 6 models selected 
    11768 
    11769 > select add #12.18
    11770 
    11771 17231 atoms, 7359 bonds, 4 pseudobonds, 2113 residues, 7 models selected 
    11772 
    11773 > select add #12.6
    11774 
    11775 17231 atoms, 12446 bonds, 8 pseudobonds, 2113 residues, 8 models selected 
    11776 
    11777 > select add #12.4
    11778 
    11779 22198 atoms, 17533 bonds, 12 pseudobonds, 2722 residues, 9 models selected 
    11780 
    11781 > select subtract #12.4
    11782 
    11783 17203 atoms, 12446 bonds, 8 pseudobonds, 2110 residues, 7 models selected 
    11784 
    11785 > select add #12.3
    11786 
    11787 17203 atoms, 17533 bonds, 12 pseudobonds, 2110 residues, 8 models selected 
    11788 Drag select of 137 residues 
    11789 
    11790 > select add #12.21
    11791 
    11792 18312 atoms, 18669 bonds, 12 pseudobonds, 2247 residues, 9 models selected 
    11793 
    11794 > save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    11795 > from_June2024/July_2024/Final-
    11796 > version_model/Flo_PflA_Local/3XPflA_For_Figure.pdb selectedOnly true
    11797 
    11798 > select add #12
    11799 
    11800 109872 atoms, 112014 bonds, 72 pseudobonds, 13482 residues, 55 models selected 
    11801 
    11802 > select subtract #12
    11803 
    11804 Nothing selected 
    11805 
    11806 > hide #!12 models
    11807 
    11808 > show #!6 models
    11809 
    11810 > open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    11811 > from_June2024/July_2024/Final-version_model/Flo_PflA_Local/New_PflB.pdb
    11812 
    11813 Summary of feedback from opening /Volumes/Backup-95/Chimera-2023/PflB-PflA-
    11814 project/Start-from_June2024/July_2024/Final-
    11815 version_model/Flo_PflA_Local/New_PflB.pdb 
    11816 --- 
    11817 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 2 LEU A 78 1 77 
    11818 Start residue of secondary structure not found: HELIX 2 2 LEU A 79 ILE A 81 1
    11819 3 
    11820 Start residue of secondary structure not found: HELIX 3 3 LYS A 107 LEU A 118
    11821 1 12 
    11822 Start residue of secondary structure not found: HELIX 4 4 ASN A 119 MET A 121
    11823 1 3 
    11824 Start residue of secondary structure not found: HELIX 5 5 GLU A 154 ILE A 156
    11825 1 3 
    11826 337 messages similar to the above omitted 
    11827  
    11828 Chain information for New_PflB.pdb 
    11829 --- 
    11830 Chain | Description 
    11831 13.1/CJ 13.2/CL 13.3/CN 13.4/CP 13.5/CR 13.6/CT 13.7/CV 13.8/CX 13.9/CZ 13.10/Cb 13.11/Cd 13.12/Cf 13.13/Ch 13.14/Cj 13.15/Cl 13.16/Cn 13.17/Cp 13.18/Cr | No description available 
    11832  
    11833 
    11834 > select add #13
    11835 
    11836 122922 atoms, 125496 bonds, 15174 residues, 19 models selected 
    11837 
    11838 > ui mousemode right "translate selected models"
    11839 
    11840 > view matrix models #13,1,0,0,-890.52,0,1,0,-614.02,0,0,1,-0.53894
    11841 
    11842 > view matrix models #13,1,0,0,-828.91,0,1,0,-519.77,0,0,1,-541.34
    11843 
    11844 > color #6 #b2b2b27d models
    11845 
    11846 > view matrix models #13,1,0,0,-799.1,0,1,0,-520.23,0,0,1,-537.82
    11847 
    11848 > view matrix models #13,1,0,0,-798.64,0,1,0,-493.13,0,0,1,-531.94
    11849 
    11850 > view matrix models #13,1,0,0,-797.26,0,1,0,-484.01,0,0,1,-531.99
    11851 
    11852 > view matrix models #13,1,0,0,-803.83,0,1,0,-489.12,0,0,1,-536.9
    11853 
    11854 > view matrix models #13,1,0,0,-804.61,0,1,0,-487.3,0,0,1,-536.07
    11855 
    11856 > view matrix models #13,1,0,0,-805.15,0,1,0,-486.78,0,0,1,-536.22
    11857 
    11858 > view matrix models #13,1,0,0,-806.6,0,1,0,-486.23,0,0,1,-536.41
    11859 
    11860 > view matrix models #13,1,0,0,-806.63,0,1,0,-485.73,0,0,1,-536.5
    11861 
    11862 > open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    11863 > from_June2024/July_2024/Final-
    11864 > version_model/Flo_PflA_Local/3XPflA_For_Figure.pdb
    11865 
    11866 Summary of feedback from opening /Volumes/Backup-95/Chimera-2023/PflB-PflA-
    11867 project/Start-from_June2024/July_2024/Final-
    11868 version_model/Flo_PflA_Local/3XPflA_For_Figure.pdb 
    11869 --- 
    11870 warnings | Start residue of secondary structure not found: HELIX 1 1 TYRA0 183 ASPA0 196 1 14 
    11871 Start residue of secondary structure not found: HELIX 2 2 TYRA0 200 ASNA0 213
    11872 1 14 
    11873 Start residue of secondary structure not found: HELIX 3 3 LYSA0 220 LEUA0 234
    11874 1 15 
    11875 Start residue of secondary structure not found: HELIX 4 4 LYSA0 238 ASNA0 251
    11876 1 14 
    11877 Start residue of secondary structure not found: HELIX 5 5 ILEA0 258 GLUA0 271
    11878 1 14 
    11879 247 messages similar to the above omitted 
    11880  
    11881 Chain information for 3XPflA_For_Figure.pdb 
    11882 --- 
    11883 Chain | Description 
    11884 14.1/A4 14.2/At 14.3/BR | No description available 
    11885 14.4/CK 14.5/CM 14.6/CO | No description available 
    11886  
    11887 
    11888 > select subtract #13
    11889 
    11890 Nothing selected 
    11891 
    11892 > select add #13.1
    11893 
    11894 6829 atoms, 6972 bonds, 843 residues, 1 model selected 
    11895 
    11896 > select add #13.2
    11897 
    11898 13658 atoms, 13944 bonds, 1686 residues, 2 models selected 
    11899 
    11900 > select add #13.18
    11901 
    11902 20487 atoms, 20916 bonds, 2529 residues, 3 models selected 
    11903 
    11904 > hide #!14 models
    11905 
    11906 > save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    11907 > from_June2024/July_2024/Final-
    11908 > version_model/Flo_PflA_Local/3XPflB_For_Figure.pdb selectedOnly true
    11909 
    11910 > select add #13
    11911 
    11912 122922 atoms, 125496 bonds, 15174 residues, 19 models selected 
    11913 
    11914 > select subtract #13
    11915 
    11916 Nothing selected 
    11917 
    11918 > hide #!13 models
    11919 
    11920 > show #!12 models
    11921 
    11922 > select add #12
    11923 
    11924 109872 atoms, 112014 bonds, 72 pseudobonds, 13482 residues, 55 models selected 
    11925 
    11926 > ui mousemode right "rotate selected models"
    11927 
    11928 > view matrix models
    11929 > #12,0.93917,-0.3423,-0.027997,-535.69,0.34313,0.93867,0.033954,-802.39,0.014657,-0.041495,0.99903,-492.92
    11930 
    11931 > ui mousemode right "translate selected models"
    11932 
    11933 > view matrix models
    11934 > #12,0.93917,-0.3423,-0.027997,-544.48,0.34313,0.93867,0.033954,-796.05,0.014657,-0.041495,0.99903,-495.99
    11935 
    11936 > ui mousemode right "rotate selected models"
    11937 
    11938 > view matrix models
    11939 > #12,0.94942,-0.31252,-0.030531,-564.67,0.31337,0.9492,0.028622,-783.09,0.020035,-0.036742,0.99912,-501.47
    11940 
    11941 > view matrix models
    11942 > #12,0.9534,-0.30006,-0.031633,-572.93,0.3009,0.95329,0.026431,-777.51,0.022225,-0.034717,0.99915,-503.74
    11943 
    11944 > ui mousemode right "move picked models"
    11945 
    11946 > ui mousemode right "translate selected models"
    11947 
    11948 > view matrix models
    11949 > #12,0.9534,-0.30006,-0.031633,-591.15,0.3009,0.95329,0.026431,-773.38,0.022225,-0.034717,0.99915,-507.83
    11950 
    11951 > view matrix models
    11952 > #12,0.9534,-0.30006,-0.031633,-589.15,0.3009,0.95329,0.026431,-773.36,0.022225,-0.034717,0.99915,-523.8
    11953 
    11954 > show #!1 models
    11955 
    11956 > hide #!1 models
    11957 
    11958 > show #!13 models
    11959 
    11960 > view matrix models
    11961 > #12,0.9534,-0.30006,-0.031633,-571.9,0.3009,0.95329,0.026431,-763.51,0.022225,-0.034717,0.99915,-523.95
    11962 
    11963 > ui mousemode right "rotate selected models"
    11964 
    11965 > ui mousemode right "translate selected models"
    11966 
    11967 > view matrix models
    11968 > #12,0.9534,-0.30006,-0.031633,-578.46,0.3009,0.95329,0.026431,-764.81,0.022225,-0.034717,0.99915,-524.27
    11969 
    11970 > ui mousemode right "rotate selected models"
    11971 
    11972 > view matrix models
    11973 > #12,0.97201,-0.22901,-0.052453,-616.07,0.23037,0.97287,0.021462,-735.11,0.046115,-0.032945,0.99839,-537.61
    11974 
    11975 > ui mousemode right "translate selected models"
    11976 
    11977 > view matrix models
    11978 > #12,0.97201,-0.22901,-0.052453,-615.62,0.23037,0.97287,0.021462,-720.56,0.046115,-0.032945,0.99839,-542.07
    11979 
    11980 > view matrix models
    11981 > #12,0.97201,-0.22901,-0.052453,-634.23,0.23037,0.97287,0.021462,-725.26,0.046115,-0.032945,0.99839,-543.66
    11982 
    11983 > close #12-14
    11984 
    11985 > open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    11986 > from_June2024/July_2024/Final-version_model/Flo_PflA_Local/New_PflA.pdb
    11987 > /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    11988 > from_June2024/July_2024/Final-version_model/Flo_PflA_Local/New_PflB.pdb
    11989 
    11990 Summary of feedback from opening /Volumes/Backup-95/Chimera-2023/PflB-PflA-
    11991 project/Start-from_June2024/July_2024/Final-
    11992 version_model/Flo_PflA_Local/New_PflA.pdb 
    11993 --- 
    11994 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 2 LEU A 78 1 77 
    11995 Start residue of secondary structure not found: HELIX 2 2 LEU A 79 ILE A 81 1
    11996 3 
    11997 Start residue of secondary structure not found: HELIX 3 3 LYS A 107 LEU A 118
    11998 1 12 
    11999 Start residue of secondary structure not found: HELIX 4 4 ASN A 119 MET A 121
    12000 1 3 
    12001 Start residue of secondary structure not found: HELIX 5 5 GLU A 154 ILE A 156
    12002 1 3 
    12003 679 messages similar to the above omitted 
    12004  
    12005 Summary of feedback from opening /Volumes/Backup-95/Chimera-2023/PflB-PflA-
    12006 project/Start-from_June2024/July_2024/Final-
    12007 version_model/Flo_PflA_Local/New_PflB.pdb 
    12008 --- 
    12009 warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 2 LEU A 78 1 77 
    12010 Start residue of secondary structure not found: HELIX 2 2 LEU A 79 ILE A 81 1
    12011 3 
    12012 Start residue of secondary structure not found: HELIX 3 3 LYS A 107 LEU A 118
    12013 1 12 
    12014 Start residue of secondary structure not found: HELIX 4 4 ASN A 119 MET A 121
    12015 1 3 
    12016 Start residue of secondary structure not found: HELIX 5 5 GLU A 154 ILE A 156
    12017 1 3 
    12018 337 messages similar to the above omitted 
    12019  
    12020 Chain information for New_PflA.pdb 
    12021 --- 
    12022 Chain | Description 
    12023 12.1/A0 12.2/A2 12.3/A4 12.4/A6 12.5/A8 12.6/At 12.7/Av 12.8/Ax 12.9/Az 12.10/BB 12.11/BD 12.12/BF 12.13/BH 12.14/BJ 12.15/BL 12.16/BN 12.17/BP 12.18/BR | No description available 
    12024 12.19/CK 12.20/CM 12.21/CO 12.22/CQ 12.23/CS 12.24/CU 12.25/CW 12.26/CY 12.27/Ca 12.28/Cc 12.29/Ce 12.30/Cg 12.31/Ci 12.32/Ck 12.33/Cm 12.34/Co 12.35/Cq 12.36/Cs | No description available 
    12025  
    12026 Chain information for New_PflB.pdb 
    12027 --- 
    12028 Chain | Description 
    12029 13.1/CJ 13.2/CL 13.3/CN 13.4/CP 13.5/CR 13.6/CT 13.7/CV 13.8/CX 13.9/CZ 13.10/Cb 13.11/Cd 13.12/Cf 13.13/Ch 13.14/Cj 13.15/Cl 13.16/Cn 13.17/Cp 13.18/Cr | No description available 
    12030  
    12031 
    12032 > select add #12
    12033 
    12034 109872 atoms, 112014 bonds, 72 pseudobonds, 13482 residues, 55 models selected 
    12035 
    12036 > select add #13
    12037 
    12038 232794 atoms, 237510 bonds, 72 pseudobonds, 28656 residues, 74 models selected 
    12039 
    12040 > view matrix models
    12041 > #12,1,0,0,-521.29,0,1,0,-757.15,0,0,1,-99.846,#13,1,0,0,-521.29,0,1,0,-757.15,0,0,1,-99.846
    12042 
    12043 > view matrix models
    12044 > #12,1,0,0,-674.3,0,1,0,-816.73,0,0,1,-503,#13,1,0,0,-674.3,0,1,0,-816.73,0,0,1,-503
    12045 
    12046 > view matrix models
    12047 > #12,1,0,0,-818.6,0,1,0,-541.33,0,0,1,-541.51,#13,1,0,0,-818.6,0,1,0,-541.33,0,0,1,-541.51
    12048 
    12049 > view matrix models
    12050 > #12,1,0,0,-801.6,0,1,0,-547.01,0,0,1,-538.38,#13,1,0,0,-801.6,0,1,0,-547.01,0,0,1,-538.38
    12051 
    12052 > ui mousemode right "rotate selected models"
    12053 
    12054 [Repeated 1 time(s)]
    12055 
    12056 > view matrix models
    12057 > #12,0.99943,-0.0024951,0.03356,-816,0.0025771,0.99999,-0.0023996,-547.24,-0.033554,0.0024847,0.99943,-521.47,#13,0.99943,-0.0024951,0.03356,-816,0.0025771,0.99999,-0.0023996,-547.24,-0.033554,0.0024847,0.99943,-521.47
    12058 
    12059 > view matrix models
    12060 > #12,0.99918,-0.029188,0.028162,-798.99,0.030798,0.99781,-0.058541,-534.38,-0.026392,0.05936,0.99789,-555.03,#13,0.99918,-0.029188,0.028162,-798.99,0.030798,0.99781,-0.058541,-534.38,-0.026392,0.05936,0.99789,-555.03
    12061 
    12062 > ui mousemode right "translate selected models"
    12063 
    12064 > view orient
    12065 
    12066 > ui mousemode right "rotate selected models"
    12067 
    12068 > view matrix models
    12069 > #12,0.78826,0.61515,-0.015745,-1010.3,-0.61478,0.78618,-0.063026,-72.53,-0.026392,0.05936,0.99789,-555.03,#13,0.78826,0.61515,-0.015745,-1010.3,-0.61478,0.78618,-0.063026,-72.53,-0.026392,0.05936,0.99789,-555.03
    12070 
    12071 > view matrix models
    12072 > #12,-0.91285,-0.35663,-0.19881,509.75,0.30121,-0.91692,0.26179,196,-0.27565,0.17909,0.94443,-460.28,#13,-0.91285,-0.35663,-0.19881,509.75,0.30121,-0.91692,0.26179,196,-0.27565,0.17909,0.94443,-460.28
    12073 
    12074 > view matrix models
    12075 > #12,-0.91231,-0.35669,-0.20115,510.6,0.30125,-0.91733,0.26031,196.89,-0.27737,0.17689,0.94434,-458.14,#13,-0.91231,-0.35669,-0.20115,510.6,0.30125,-0.91733,0.26031,196.89,-0.27737,0.17689,0.94434,-458.14
    12076 
    12077 > view matrix models
    12078 > #12,-0.91786,-0.31644,-0.23958,510.27,0.36303,-0.91334,-0.18444,372.99,-0.16046,-0.25626,0.9532,-292.95,#13,-0.91786,-0.31644,-0.23958,510.27,0.36303,-0.91334,-0.18444,372.99,-0.16046,-0.25626,0.9532,-292.95
    12079 
    12080 > undo
    12081 
    12082 > view matrix models
    12083 > #12,-0.49013,-0.868,-0.079649,501.01,0.81728,-0.4894,0.3042,-329.87,-0.30303,0.084001,0.94927,-396.92,#13,-0.49013,-0.868,-0.079649,501.01,0.81728,-0.4894,0.3042,-329.87,-0.30303,0.084001,0.94927,-396.92
    12084 
    12085 > view matrix models
    12086 > #12,-0.49535,-0.86438,-0.086411,505.08,0.82329,-0.49887,0.27077,-312.12,-0.27716,0.062985,0.95876,-404.01,#13,-0.49535,-0.86438,-0.086411,505.08,0.82329,-0.49887,0.27077,-312.12,-0.27716,0.062985,0.95876,-404.01
    12087 
    12088 > view orient
    12089 
    12090 [Repeated 1 time(s)]
    12091 
    12092 > view matrix models
    12093 > #12,-0.18563,-0.98256,0.010887,356.46,0.94272,-0.17496,0.28402,-555.89,-0.27716,0.062985,0.95876,-404.01,#13,-0.18563,-0.98256,0.010887,356.46,0.94272,-0.17496,0.28402,-555.89,-0.27716,0.062985,0.95876,-404.01
    12094 
    12095 > view matrix models
    12096 > #12,-0.18351,-0.98301,0.0031045,359.27,0.94593,-0.17572,0.27265,-551.79,-0.26748,0.052971,0.96211,-405.41,#13,-0.18351,-0.98301,0.0031045,359.27,0.94593,-0.17572,0.27265,-551.79,-0.26748,0.052971,0.96211,-405.41
    12097 
    12098 > ui mousemode right "translate selected models"
    12099 
    12100 > view matrix models
    12101 > #12,-0.18351,-0.98301,0.0031045,359.43,0.94593,-0.17572,0.27265,-548.64,-0.26748,0.052971,0.96211,-395.12,#13,-0.18351,-0.98301,0.0031045,359.43,0.94593,-0.17572,0.27265,-548.64,-0.26748,0.052971,0.96211,-395.12
    12102 
    12103 > view matrix models
    12104 > #12,-0.18351,-0.98301,0.0031045,358.91,0.94593,-0.17572,0.27265,-549.61,-0.26748,0.052971,0.96211,-394.94,#13,-0.18351,-0.98301,0.0031045,358.91,0.94593,-0.17572,0.27265,-549.61,-0.26748,0.052971,0.96211,-394.94
    12105 
    12106 > ui mousemode right "rotate selected models"
    12107 
    12108 > view matrix models
    12109 > #12,-0.12979,-0.99153,0.0042033,334.22,0.95586,-0.12399,0.26639,-579.66,-0.26361,0.038591,0.96386,-390.13,#13,-0.12979,-0.99153,0.0042033,334.22,0.95586,-0.12399,0.26639,-579.66,-0.26361,0.038591,0.96386,-390.13
    12110 
    12111 > view matrix models
    12112 > #12,-0.19228,-0.98134,0.0028902,362.81,0.94402,-0.18417,0.27368,-544.56,-0.26804,0.055352,0.96182,-395.77,#13,-0.19228,-0.98134,0.0028902,362.81,0.94402,-0.18417,0.27368,-544.56,-0.26804,0.055352,0.96182,-395.77
    12113 
    12114 > ui mousemode right "translate selected models"
    12115 
    12116 > view matrix models
    12117 > #12,-0.19228,-0.98134,0.0028902,365.42,0.94402,-0.18417,0.27368,-554.48,-0.26804,0.055352,0.96182,-392.9,#13,-0.19228,-0.98134,0.0028902,365.42,0.94402,-0.18417,0.27368,-554.48,-0.26804,0.055352,0.96182,-392.9
    12118 
    12119 > ui mousemode right "translate selected models"
    12120 
    12121 > view matrix models
    12122 > #12,-0.19228,-0.98134,0.0028902,365.05,0.94402,-0.18417,0.27368,-553.94,-0.26804,0.055352,0.96182,-393.08,#13,-0.19228,-0.98134,0.0028902,365.05,0.94402,-0.18417,0.27368,-553.94,-0.26804,0.055352,0.96182,-393.08
    12123 
    12124 > view matrix models
    12125 > #12,-0.19228,-0.98134,0.0028902,362.37,0.94402,-0.18417,0.27368,-553.57,-0.26804,0.055352,0.96182,-393.5,#13,-0.19228,-0.98134,0.0028902,362.37,0.94402,-0.18417,0.27368,-553.57,-0.26804,0.055352,0.96182,-393.5
    12126 
    12127 > ui mousemode right "rotate selected models"
    12128 
    12129 > view matrix models
    12130 > #12,0.30432,-0.95257,-6.2098e-06,82.602,0.93025,0.29719,0.21522,-776.17,-0.20501,-0.065503,0.97656,-369.52,#13,0.30432,-0.95257,-6.2098e-06,82.602,0.93025,0.29719,0.21522,-776.17,-0.20501,-0.065503,0.97656,-369.52
    12131 
    12132 > view matrix models
    12133 > #12,-0.50993,-0.86013,-0.012205,474.59,0.81576,-0.48803,0.31041,-339.58,-0.27295,0.14833,0.95052,-435.32,#13,-0.50993,-0.86013,-0.012205,474.59,0.81576,-0.48803,0.31041,-339.58,-0.27295,0.14833,0.95052,-435.32
    12134 
    12135 > ui mousemode right "translate selected models"
    12136 
    12137 > view matrix models
    12138 > #12,-0.50993,-0.86013,-0.012205,474.98,0.81576,-0.48803,0.31041,-333.86,-0.27295,0.14833,0.95052,-421.7,#13,-0.50993,-0.86013,-0.012205,474.98,0.81576,-0.48803,0.31041,-333.86,-0.27295,0.14833,0.95052,-421.7
    12139 
    12140 > view matrix models
    12141 > #12,-0.50993,-0.86013,-0.012205,481.34,0.81576,-0.48803,0.31041,-331.89,-0.27295,0.14833,0.95052,-421.33,#13,-0.50993,-0.86013,-0.012205,481.34,0.81576,-0.48803,0.31041,-331.89,-0.27295,0.14833,0.95052,-421.33
    12142 
    12143 > select clear
    12144 
    12145 > select add #13.1
    12146 
    12147 6829 atoms, 6972 bonds, 843 residues, 1 model selected 
    12148 
    12149 > select subtract #13.1
    12150 
    12151 Nothing selected 
    12152 
    12153 > select add #13.4
    12154 
    12155 6829 atoms, 6972 bonds, 843 residues, 1 model selected 
    12156 
    12157 > select subtract #13.4
    12158 
    12159 Nothing selected 
    12160 
    12161 > select add #13.9
    12162 
    12163 6829 atoms, 6972 bonds, 843 residues, 1 model selected 
    12164 
    12165 > select subtract #13.9
    12166 
    12167 Nothing selected 
    12168 
    12169 > select add #13.13
    12170 
    12171 6829 atoms, 6972 bonds, 843 residues, 1 model selected 
    12172 
    12173 > select add #13.14
    12174 
    12175 13658 atoms, 13944 bonds, 1686 residues, 2 models selected 
    12176 
    12177 > show #!1 models
    12178 
    12179 > hide #!1 models
    12180 
    12181 > show #!3 models
    12182 
    12183 > hide #!3 models
    12184 
    12185 > show #!2 models
    12186 
    12187 > hide #!2 models
    12188 
    12189 > show #!4 models
    12190 
    12191 > hide #!4 models
    12192 
    12193 > select add #13.12
    12194 
    12195 20487 atoms, 20916 bonds, 2529 residues, 3 models selected 
    12196 
    12197 > select subtract #13.12
    12198 
    12199 13658 atoms, 13944 bonds, 1686 residues, 2 models selected 
    12200 
    12201 > select add #13.15
    12202 
    12203 20487 atoms, 20916 bonds, 2529 residues, 3 models selected 
    12204 
    12205 > select add #12.28
    12206 
    12207 21596 atoms, 22052 bonds, 2666 residues, 4 models selected 
    12208 
    12209 > select subtract #12.28
    12210 
    12211 20487 atoms, 20916 bonds, 2529 residues, 3 models selected 
    12212 
    12213 > select add #12.19
    12214 
    12215 21596 atoms, 22052 bonds, 2666 residues, 4 models selected 
    12216 
    12217 > select subtract #12.19
    12218 
    12219 20487 atoms, 20916 bonds, 2529 residues, 3 models selected 
    12220 
    12221 > select subtract #13.13
    12222 
    12223 13658 atoms, 13944 bonds, 1686 residues, 2 models selected 
    12224 
    12225 > select subtract #13.14
    12226 
    12227 6829 atoms, 6972 bonds, 843 residues, 1 model selected 
    12228 
    12229 > select subtract #13.15
    12230 
    12231 Nothing selected 
    12232 
    12233 > hide #!13 models
    12234 
    12235 > hide #!6 models
    12236 
    12237 > undo
    12238 
    12239 > show #!13 models
    12240 
    12241 > hide #!13 models
    12242 
    12243 > undo
    12244 
    12245 [Repeated 7 time(s)]
    12246 
    12247 > select add #13
    12248 
    12249 122922 atoms, 125496 bonds, 15174 residues, 19 models selected 
    12250 
    12251 > select subtract #13
    12252 
    12253 Nothing selected 
    12254 
    12255 > hide #!13 models
    12256 
    12257 > hide #!6 models
    12258 
    12259 Drag select of 1603 residues 
    12260 Drag select of 128 residues 
    12261 
    12262 > select add #12.33
    12263 
    12264 14230 atoms, 1136 bonds, 1740 residues, 6 models selected 
    12265 
    12266 > select add #12.32
    12267 
    12268 14418 atoms, 2272 bonds, 1765 residues, 6 models selected 
    12269 
    12270 > select add #12.31
    12271 
    12272 14502 atoms, 3408 bonds, 1776 residues, 6 models selected 
    12273 
    12274 > select add #12.15
    12275 
    12276 16773 atoms, 8495 bonds, 4 pseudobonds, 2056 residues, 7 models selected 
    12277 
    12278 > select add #12.14
    12279 
    12280 16773 atoms, 13582 bonds, 8 pseudobonds, 2056 residues, 8 models selected 
    12281 
    12282 > select add #12.9
    12283 
    12284 18312 atoms, 18669 bonds, 12 pseudobonds, 2247 residues, 9 models selected 
    12285 
    12286 > hide #12.36 models
    12287 
    12288 > show #12.36 models
    12289 
    12290 > show #!13 models
    12291 
    12292 > select add #13.13
    12293 
    12294 25141 atoms, 25641 bonds, 12 pseudobonds, 3090 residues, 10 models selected 
    12295 
    12296 > select add #13.14
    12297 
    12298 31970 atoms, 32613 bonds, 12 pseudobonds, 3933 residues, 11 models selected 
    12299 
    12300 > select add #13.15
    12301 
    12302 38799 atoms, 39585 bonds, 12 pseudobonds, 4776 residues, 12 models selected 
    12303 
    12304 > save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    12305 > from_June2024/July_2024/Final-version_model/Flo_PflA_Local/3XPflA-
    12306 > PflB_For_Figure.pdb selectedOnly true
    12307 
    12308 > select add #13
    12309 
    12310 141234 atoms, 144165 bonds, 12 pseudobonds, 17421 residues, 28 models selected 
    12311 
    12312 > select add #12
    12313 
    12314 232794 atoms, 237510 bonds, 72 pseudobonds, 28656 residues, 74 models selected 
    12315 
    12316 > select subtract #12
    12317 
    12318 122922 atoms, 125496 bonds, 15174 residues, 19 models selected 
    12319 
    12320 > select subtract #13
    12321 
    12322 Nothing selected 
    12323 
    12324 > hide #!13 models
    12325 
    12326 > hide #!12 models
    12327 
    12328 > open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    12329 > from_June2024/July_2024/Final-version_model/Flo_PflA_Local/3XPflA-
    12330 > PflB_For_Figure.pdb
    12331 
    12332 Summary of feedback from opening /Volumes/Backup-95/Chimera-2023/PflB-PflA-
    12333 project/Start-from_June2024/July_2024/Final-
    12334 version_model/Flo_PflA_Local/3XPflA-PflB_For_Figure.pdb 
    12335 --- 
    12336 warnings | Start residue of secondary structure not found: HELIX 1 1 TYRA0 183 ASPA0 196 1 14 
    12337 Start residue of secondary structure not found: HELIX 2 2 TYRA0 200 ASNA0 213
    12338 1 14 
    12339 Start residue of secondary structure not found: HELIX 3 3 LYSA0 220 LEUA0 234
    12340 1 15 
    12341 Start residue of secondary structure not found: HELIX 4 4 LYSA0 238 ASNA0 251
    12342 1 14 
    12343 Start residue of secondary structure not found: HELIX 5 5 ILEA0 258 GLUA0 271
    12344 1 14 
    12345 373 messages similar to the above omitted 
    12346  
    12347 Chain information for 3XPflA-PflB_For_Figure.pdb 
    12348 --- 
    12349 Chain | Description 
    12350 14.1/Az 14.2/BJ 14.3/BL | No description available 
    12351 14.7/Ch 14.8/Cj 14.9/Cl | No description available 
    12352 14.4/Ci 14.5/Ck 14.6/Cm | No description available 
    12353  
    12354 
    12355 > show #!1 models
    12356 
    12357 > show #!2 models
    12358 
    12359 > hide #!1 models
    12360 
    12361 > hide #!2 models
    12362 
    12363 > show #!6 models
    12364 
    12365 > show #!1 models
    12366 
    12367 > hide #!1 models
    12368 
    12369 > show #!1 models
    12370 
    12371 > hide #!1 models
    12372 
    12373 > show #!1 models
    12374 
    12375 > hide #!1 models
    12376 
    12377 > show #!1 models
    12378 
    12379 > hide #!1 models
    12380 
    12381 > combine #14 modelId #15 name 3XPflAB
    12382 
    12383 > hide #!14 models
    12384 
    12385 > ui tool show "Fit in Map"
    12386 
    12387 > fitmap #15 inMap #6
    12388 
    12389 Fit molecule 3XPflAB (#15) to map 3Xunits.mrc (#6) using 38799 atoms 
    12390 average map value = 2.154, steps = 168 
    12391 shifted from previous position = 9.31 
    12392 rotated from previous position = 16.8 degrees 
    12393 atoms outside contour = 17471, contour level = 0.1847 
    12394  
    12395 Position of 3XPflAB (#15) relative to 3Xunits.mrc (#6) coordinates: 
    12396 Matrix rotation and translation 
    12397 0.99462895 0.03678980 0.09674590 -6.40729211 
    12398 -0.00917946 0.96236927 -0.27158998 -9.52019787 
    12399 -0.10309702 0.26924318 0.95753805 -12.34964828 
    12400 Axis 0.93504439 0.34550766 -0.07947608 
    12401 Axis point 0.00000000 43.50384781 -30.52375104 
    12402 Rotation angle (degrees) 16.81017889 
    12403 Shift along axis -8.29890223 
    12404  
    12405 
    12406 > fitmap #15 inMap #6
    12407 
    12408 Fit molecule 3XPflAB (#15) to map 3Xunits.mrc (#6) using 38799 atoms 
    12409 average map value = 2.154, steps = 28 
    12410 shifted from previous position = 0.0497 
    12411 rotated from previous position = 0.0178 degrees 
    12412 atoms outside contour = 17462, contour level = 0.1847 
    12413  
    12414 Position of 3XPflAB (#15) relative to 3Xunits.mrc (#6) coordinates: 
    12415 Matrix rotation and translation 
    12416 0.99464111 0.03692161 0.09657053 -6.40475417 
    12417 -0.00937546 0.96242184 -0.27139696 -9.49328505 
    12418 -0.10296200 0.26903717 0.95761048 -12.38014369 
    12419 Axis 0.93508874 0.34524211 -0.08010574 
    12420 Axis point 0.00000000 43.67465586 -30.50033372 
    12421 Rotation angle (degrees) 16.79658762 
    12422 Shift along axis -8.27477473 
    12423  
    12424 
    12425 > fitmap #15 inMap #6
    12426 
    12427 Fit molecule 3XPflAB (#15) to map 3Xunits.mrc (#6) using 38799 atoms 
    12428 average map value = 2.154, steps = 28 
    12429 shifted from previous position = 0.05 
    12430 rotated from previous position = 0.0179 degrees 
    12431 atoms outside contour = 17470, contour level = 0.1847 
    12432  
    12433 Position of 3XPflAB (#15) relative to 3Xunits.mrc (#6) coordinates: 
    12434 Matrix rotation and translation 
    12435 0.99462364 0.03681644 0.09679029 -6.40747251 
    12436 -0.00919551 0.96237529 -0.27156812 -9.52193056 
    12437 -0.10314675 0.26921804 0.95753976 -12.34665377 
    12438 Axis 0.93497610 0.34567518 -0.07955098 
    12439 Axis point 0.00000000 43.49956479 -30.52433596 
    12440 Rotation angle (degrees) 16.80993871 
    12441 Shift along axis -8.30014028 
    12442  
    12443 
    12444 > save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    12445 > from_June2024/July_2024/Final-
    12446 > version_model/Flo_PflA_Local/For_Figure4_PflAB.cxs includeMaps true
    12447 
    12448 [Repeated 1 time(s)]
    12449 
    12450 ——— End of log from Fri Jul 26 15:41:13 2024 ———
    12451 
    12452 opened ChimeraX session 
    12453 Showing 3Xunits.seg - 52 regions, 52 surfaces 
    12454 
    12455 > open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    12456 > from_June2024/July_2024/Final-version_model/Flo_PflA_Local/38xcage.pdb
    12457 
    12458 Chain information for 38xcage.pdb 
    12459 --- 
    12460 Chain | Description 
    12461 16.1/A 16.2/A 16.3/A 16.4/A 16.5/A 16.6/A 16.7/A 16.8/A 16.9/A 16.10/A 16.11/A 16.12/A 16.13/A 16.14/A 16.15/A 16.16/A 16.17/A 16.18/A 16.19/A 16.20/A 16.21/A 16.22/A 16.23/A 16.24/A 16.25/A 16.26/A 16.27/A 16.28/A 16.29/A 16.30/A 16.31/A 16.32/A 16.33/A 16.34/A 16.35/A 16.36/A | No description available 
    12462 16.1/B 16.2/B 16.3/B 16.4/B 16.5/B 16.6/B 16.7/B 16.8/B 16.9/B 16.10/B 16.11/B 16.12/B 16.13/B 16.14/B 16.15/B 16.16/B 16.17/B 16.18/B 16.19/B 16.20/B 16.21/B 16.22/B 16.23/B 16.24/B 16.25/B 16.26/B 16.27/B 16.28/B 16.29/B 16.30/B 16.31/B 16.32/B 16.33/B 16.34/B 16.35/B 16.36/B | No description available 
    12463  
    12464 
    12465 > select add #16
    12466 
    12467 99648 atoms, 101772 bonds, 12096 residues, 37 models selected 
    12468 
    12469 > view matrix models #16,1,0,0,-827.48,0,1,0,-569.5,0,0,1,-43.802
    12470 
    12471 > ui mousemode right "rotate selected models"
    12472 
    12473 > view matrix models
    12474 > #16,0.99267,0.1207,-0.0060172,-885.78,-0.12075,0.99263,-0.0097829,-496.35,0.0047921,0.010438,0.99993,-51.959
    12475 
    12476 > ui mousemode right "move picked models"
    12477 
    12478 > ui mousemode right "translate selected models"
    12479 
    12480 > view matrix models
    12481 > #16,0.99267,0.1207,-0.0060172,-851.95,-0.12075,0.99263,-0.0097829,-530.26,0.0047921,0.010438,0.99993,-505.69
    12482 
    12483 > hide #!6 models
    12484 
    12485 > hide #!2 models
    12486 
    12487 > show #!6 models
    12488 
    12489 > view matrix models
    12490 > #16,0.99267,0.1207,-0.0060172,-843.71,-0.12075,0.99263,-0.0097829,-517.73,0.0047921,0.010438,0.99993,-505.14
    12491 
    12492 > view matrix models
    12493 > #16,0.99267,0.1207,-0.0060172,-833.32,-0.12075,0.99263,-0.0097829,-552.99,0.0047921,0.010438,0.99993,-547.81
    12494 
    12495 > view matrix models
    12496 > #16,0.99267,0.1207,-0.0060172,-832.55,-0.12075,0.99263,-0.0097829,-552.33,0.0047921,0.010438,0.99993,-547.97
    12497 
    12498 > view matrix models
    12499 > #16,0.99267,0.1207,-0.0060172,-830.52,-0.12075,0.99263,-0.0097829,-546.96,0.0047921,0.010438,0.99993,-548.4
    12500 
    12501 > ui mousemode right "rotate selected models"
    12502 
    12503 > view matrix models
    12504 > #16,0.98673,0.16225,-0.0065777,-849.42,-0.16226,0.98675,-0.001445,-525.19,0.0062561,0.0024931,0.99998,-544.93
    12505 
    12506 > view matrix models
    12507 > #16,0.98655,0.16312,-0.010639,-848,-0.16318,0.98658,-0.0052162,-522.94,0.0096456,0.0068822,0.99993,-549.09
    12508 
    12509 > view matrix models
    12510 > #16,0.98493,0.16616,0.047895,-874.67,-0.16542,0.98604,-0.019171,-515.27,-0.050411,0.01096,0.99867,-518.47
    12511 
    12512 > ui mousemode right "translate selected models"
    12513 
    12514 > view matrix models
    12515 > #16,0.98493,0.16616,0.047895,-885.95,-0.16542,0.98604,-0.019171,-505.9,-0.050411,0.01096,0.99867,-516.38
    12516 
    12517 > view matrix models
    12518 > #16,0.98493,0.16616,0.047895,-900.24,-0.16542,0.98604,-0.019171,-500.14,-0.050411,0.01096,0.99867,-513.67
    12519 
    12520 > select subtract #16
    12521 
    12522 Nothing selected 
    12523 
    12524 > select add #16.6
    12525 
    12526 2768 atoms, 2827 bonds, 336 residues, 1 model selected 
    12527 
    12528 > select subtract #16.6
    12529 
    12530 Nothing selected 
    12531 
    12532 > select add #16.27
    12533 
    12534 2768 atoms, 2827 bonds, 336 residues, 1 model selected 
    12535 
    12536 > select add #16.28
    12537 
    12538 5536 atoms, 5654 bonds, 672 residues, 2 models selected 
    12539 
    12540 > select add #16.29
    12541 
    12542 8304 atoms, 8481 bonds, 1008 residues, 3 models selected 
    12543 
    12544 > select add #16.9
    12545 
    12546 11072 atoms, 11308 bonds, 1344 residues, 4 models selected 
    12547 
    12548 > select add #16.10
    12549 
    12550 13840 atoms, 14135 bonds, 1680 residues, 5 models selected 
    12551 
    12552 > select add #16.11
    12553 
    12554 16608 atoms, 16962 bonds, 2016 residues, 6 models selected 
    12555 
    12556 > save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    12557 > from_June2024/July_2024/Final-version_model/Flo_PflA_Local/Cage-
    12558 > for-3units.pdb selectedOnly true
    12559 
    12560 > select add #16
    12561 
    12562 99648 atoms, 101772 bonds, 12096 residues, 37 models selected 
    12563 
    12564 > select subtract #16
    12565 
    12566 Nothing selected 
    12567 
    12568 > hide #!16 models
    12569 
    12570 > open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    12571 > from_June2024/July_2024/Final-version_model/Flo_PflA_Local/Cage-
    12572 > for-3units.pdb
    12573 
    12574 Summary of feedback from opening /Volumes/Backup-95/Chimera-2023/PflB-PflA-
    12575 project/Start-from_June2024/July_2024/Final-version_model/Flo_PflA_Local/Cage-
    12576 for-3units.pdb 
    12577 --- 
    12578 warnings | Start residue of secondary structure not found: HELIX 1 1 TYRA0 183 ASPA0 196 1 14 
    12579 Start residue of secondary structure not found: HELIX 2 2 TYRA0 200 ASNA0 213
    12580 1 14 
    12581 Start residue of secondary structure not found: HELIX 3 3 LYSA0 220 LEUA0 234
    12582 1 15 
    12583 Start residue of secondary structure not found: HELIX 4 4 LYSA0 238 ASNA0 251
    12584 1 14 
    12585 Start residue of secondary structure not found: HELIX 5 5 ILEA0 258 GLUA0 271
    12586 1 14 
    12587 247 messages similar to the above omitted 
    12588  
    12589 Chain information for Cage-for-3units.pdb 
    12590 --- 
    12591 Chain | Description 
    12592 17.1/A 17.2/A 17.3/A 17.4/A 17.5/A 17.6/A | No description available 
    12593 17.1/B 17.2/B 17.3/B 17.4/B 17.5/B 17.6/B | No description available 
    12594  
    12595 
    12596 > select add #17
    12597 
    12598 16608 atoms, 16962 bonds, 2016 residues, 7 models selected 
    12599 
    12600 > select subtract #17
    12601 
    12602 Nothing selected 
    12603 
    12604 > select add #17.1
    12605 
    12606 2768 atoms, 2827 bonds, 336 residues, 1 model selected 
    12607 
    12608 > combine #17 modelId #18 name Cage
    12609 
    12610 Remapping chain ID 'A' in Cage-for-3units.pdb #17.2 to 'C' 
    12611 Remapping chain ID 'B' in Cage-for-3units.pdb #17.2 to 'D' 
    12612 Remapping chain ID 'A' in Cage-for-3units.pdb #17.3 to 'E' 
    12613 Remapping chain ID 'B' in Cage-for-3units.pdb #17.3 to 'F' 
    12614 Remapping chain ID 'A' in Cage-for-3units.pdb #17.4 to 'G' 
    12615 Remapping chain ID 'B' in Cage-for-3units.pdb #17.4 to 'H' 
    12616 Remapping chain ID 'A' in Cage-for-3units.pdb #17.5 to 'I' 
    12617 Remapping chain ID 'B' in Cage-for-3units.pdb #17.5 to 'J' 
    12618 Remapping chain ID 'A' in Cage-for-3units.pdb #17.6 to 'K' 
    12619 Remapping chain ID 'B' in Cage-for-3units.pdb #17.6 to 'L' 
    12620 
    12621 > ui tool show "Fit in Map"
    12622 
    12623 > fitmap #18 inMap #6
    12624 
    12625 Fit molecule Cage (#18) to map 3Xunits.mrc (#6) using 16608 atoms 
    12626 average map value = 2.444, steps = 152 
    12627 shifted from previous position = 22.7 
    12628 rotated from previous position = 11.5 degrees 
    12629 atoms outside contour = 8239, contour level = 0.1847 
    12630  
    12631 Position of Cage (#18) relative to 3Xunits.mrc (#6) coordinates: 
    12632 Matrix rotation and translation 
    12633 0.98420114 0.17466936 0.02896094 15.18429004 
    12634 -0.17661022 0.98008584 0.09077766 20.68378027 
    12635 -0.01252813 -0.09445827 0.99544999 19.05066641 
    12636 Axis -0.46391541 0.10390761 -0.87976457 
    12637 Axis point 131.82850583 -17.49249647 0.00000000 
    12638 Rotation angle (degrees) 11.51614665 
    12639 Shift along axis -21.65512535 
    12640  
    12641 
    12642 > select add #17
    12643 
    12644 16608 atoms, 16962 bonds, 2016 residues, 7 models selected 
    12645 
    12646 > hide #!17 models
    12647 
    12648 > select subtract #17
    12649 
    12650 Nothing selected 
    12651 
    12652 > close #17
    12653 
    12654 > split #18
    12655 
    12656 Split Cage (#18) into 12 models 
    12657 Chain information for Cage A #18.1 
    12658 --- 
    12659 Chain | Description 
    12660 A | No description available 
    12661  
    12662 Chain information for Cage B #18.2 
    12663 --- 
    12664 Chain | Description 
    12665 B | No description available 
    12666  
    12667 Chain information for Cage C #18.3 
    12668 --- 
    12669 Chain | Description 
    12670 C | No description available 
    12671  
    12672 Chain information for Cage D #18.4 
    12673 --- 
    12674 Chain | Description 
    12675 D | No description available 
    12676  
    12677 Chain information for Cage E #18.5 
    12678 --- 
    12679 Chain | Description 
    12680 E | No description available 
    12681  
    12682 Chain information for Cage F #18.6 
    12683 --- 
    12684 Chain | Description 
    12685 F | No description available 
    12686  
    12687 Chain information for Cage G #18.7 
    12688 --- 
    12689 Chain | Description 
    12690 G | No description available 
    12691  
    12692 Chain information for Cage H #18.8 
    12693 --- 
    12694 Chain | Description 
    12695 H | No description available 
    12696  
    12697 Chain information for Cage I #18.9 
    12698 --- 
    12699 Chain | Description 
    12700 I | No description available 
    12701  
    12702 Chain information for Cage J #18.10 
    12703 --- 
    12704 Chain | Description 
    12705 J | No description available 
    12706  
    12707 Chain information for Cage K #18.11 
    12708 --- 
    12709 Chain | Description 
    12710 K | No description available 
    12711  
    12712 Chain information for Cage L #18.12 
    12713 --- 
    12714 Chain | Description 
    12715 L | No description available 
    12716  
    12717 
    12718 > split #15]
    12719 
    12720 Expected a structures specifier or a keyword 
    12721 
    12722 > split #15
    12723 
    12724 Split 3XPflAB (#15) into 9 models 
    12725 Chain information for 3XPflAB Az #15.1 
    12726 --- 
    12727 Chain | Description 
    12728 Az | No description available 
    12729  
    12730 Chain information for 3XPflAB BJ #15.2 
    12731 --- 
    12732 Chain | Description 
    12733 BJ | No description available 
    12734  
    12735 Chain information for 3XPflAB BL #15.3 
    12736 --- 
    12737 Chain | Description 
    12738 BL | No description available 
    12739  
    12740 Chain information for 3XPflAB Ch #15.4 
    12741 --- 
    12742 Chain | Description 
    12743 Ch | No description available 
    12744  
    12745 Chain information for 3XPflAB Ci #15.5 
    12746 --- 
    12747 Chain | Description 
    12748 Ci | No description available 
    12749  
    12750 Chain information for 3XPflAB Cj #15.6 
    12751 --- 
    12752 Chain | Description 
    12753 Cj | No description available 
    12754  
    12755 Chain information for 3XPflAB Ck #15.7 
    12756 --- 
    12757 Chain | Description 
    12758 Ck | No description available 
    12759  
    12760 Chain information for 3XPflAB Cl #15.8 
    12761 --- 
    12762 Chain | Description 
    12763 Cl | No description available 
    12764  
    12765 Chain information for 3XPflAB Cm #15.9 
    12766 --- 
    12767 Chain | Description 
    12768 Cm | No description available 
    12769  
    12770 
    12771 > select add #18.12
    12772 
    12773 1486 atoms, 1517 bonds, 179 residues, 1 model selected 
    12774 
    12775 > select subtract #18.12
    12776 
    12777 Nothing selected 
    12778 
    12779 > hide #18.1 models
    12780 
    12781 > show #18.1 models
    12782 
    12783 > hide #18.1 models
    12784 
    12785 > hide #18.2 models
    12786 
    12787 > hide #!6 models
    12788 
    12789 > hide #!18 models
    12790 
    12791 Drag select of 564 residues 
    12792 Drag select of 129 residues 
    12793 
    12794 > select clear
    12795 
    12796 > hide #!15 models
    12797 
    12798 > show #!16 models
    12799 
    12800 > hide #!16 models
    12801 
    12802 > show #!15 models
    12803 
    12804 Drag select of 515 residues 
    12805 
    12806 > select add #15.1
    12807 
    12808 8499 atoms, 5088 bonds, 1047 residues, 3 models selected 
    12809 
    12810 > select subtract #15.1
    12811 
    12812 3504 atoms, 435 residues, 2 models selected 
    12813 
    12814 > hide #15.1 models
    12815 
    12816 > hide #15.4 models
    12817 
    12818 > hide #15.5 models
    12819 
    12820 > select add #15.9
    12821 
    12822 4613 atoms, 1136 bonds, 572 residues, 3 models selected 
    12823 
    12824 > select subtract #15.9
    12825 
    12826 3504 atoms, 435 residues, 2 models selected 
    12827 
    12828 > select add #15.8
    12829 
    12830 10333 atoms, 6972 bonds, 1278 residues, 3 models selected 
    12831 
    12832 > select subtract #15.8
    12833 
    12834 3504 atoms, 435 residues, 2 models selected 
    12835 
    12836 > select add #15.7
    12837 
    12838 4613 atoms, 1136 bonds, 572 residues, 3 models selected 
    12839 
    12840 > select subtract #15.7
    12841 
    12842 3504 atoms, 435 residues, 2 models selected 
    12843 
    12844 > select add #15.6
    12845 
    12846 10333 atoms, 6972 bonds, 1278 residues, 3 models selected 
    12847 
    12848 > select subtract #15.6
    12849 
    12850 3504 atoms, 435 residues, 2 models selected 
    12851 
    12852 > select add #15.3
    12853 
    12854 8499 atoms, 5088 bonds, 1047 residues, 3 models selected 
    12855 
    12856 > select subtract #15.3
    12857 
    12858 3504 atoms, 435 residues, 2 models selected 
    12859 
    12860 > select add #15.2
    12861 
    12862 8499 atoms, 5088 bonds, 1047 residues, 3 models selected 
    12863 
    12864 > select subtract #15.2
    12865 
    12866 3504 atoms, 435 residues, 2 models selected 
    12867 
    12868 > show #!2 models
    12869 
    12870 > hide #!2 models
    12871 
    12872 > show #!18 models
    12873 
    12874 > show #!6 models
    12875 
    12876 > show #15.5 models
    12877 
    12878 > hide #15.5 models
    12879 
    12880 > show #15.4 models
    12881 
    12882 > select add #15.4
    12883 
    12884 7938 atoms, 6972 bonds, 980 residues, 2 models selected 
    12885 
    12886 > select subtract #15.4
    12887 
    12888 1109 atoms, 137 residues, 1 model selected 
    12889 
    12890 > hide #15.2 models
    12891 
    12892 > show #15.2 models
    12893 
    12894 > hide #15.9 models
    12895 
    12896 > show #15.9 models
    12897 
    12898 > hide #15.8 models
    12899 
    12900 > hide #15.2 models
    12901 
    12902 > show #15.2 models
    12903 
    12904 > hide #15.3 models
    12905 
    12906 > hide #15.4 models
    12907 
    12908 > show #15.4 models
    12909 
    12910 > hide #15.6 models
    12911 
    12912 > show #15.6 models
    12913 
    12914 > hide #15.7 models
    12915 
    12916 > show #15.7 models
    12917 
    12918 > select add #15.5
    12919 
    12920 1109 atoms, 1136 bonds, 137 residues, 1 model selected 
    12921 Drag select of 15 residues 
    12922 
    12923 > hide #15.9 models
    12924 
    12925 > select add #15.9
    12926 
    12927 2218 atoms, 2272 bonds, 274 residues, 2 models selected 
    12928 
    12929 > select subtract #15.9
    12930 
    12931 1109 atoms, 1136 bonds, 137 residues, 1 model selected 
    12932 
    12933 > set bgColor white
    12934 
    12935 > set bgColor #ffffff00
    12936 
    12937 > color #6 #72727233 models
    12938 
    12939 > hide #15.2 models
    12940 
    12941 > show #15.2 models
    12942 
    12943 > color #15.2 #9850ffff models
    12944 
    12945 > color #15.2 #d310c9ff
    12946 
    12947 > color #15.2 #ec701aff
    12948 
    12949 > color #15.2 #ca676980
    12950 
    12951 > color #15.2 #ca6769ff
    12952 
    12953 > color #15.2 #ca5254ff
    12954 
    12955 > color #15.2 #ca515eff
    12956 
    12957 > color #15.2 #ca4949ff
    12958 
    12959 > select subtract #15.5
    12960 
    12961 Nothing selected 
    12962 
    12963 > hide #15.6 models
    12964 
    12965 > show #15.6 models
    12966 
    12967 > hide #15.7 models
    12968 
    12969 > show #15.7 models
    12970 
    12971 > color #15.7 #9850ffff models
    12972 
    12973 > color #15.7 #ca4949ff
    12974 
    12975 > hide #15.4 models
    12976 
    12977 > show #15.4 models
    12978 
    12979 > hide #15.4 models
    12980 
    12981 > show #15.4 models
    12982 
    12983 > hide #15.6 models
    12984 
    12985 > show #15.6 models
    12986 
    12987 > color #15.6 #0067b6ff models
    12988 
    12989 > show #15.5 models
    12990 
    12991 > hide #15.5 models
    12992 
    12993 > show #15.4 models
    12994 
    12995 > color #15.4 magenta models
    12996 
    12997 > color #15.6 magenta models
    12998 
    12999 > color #15.6 #93329aff
    13000 
    13001 > color #15.4 magenta models
    13002 
    13003 [Repeated 1 time(s)]
    13004 
    13005 > color #15.6 magenta models
    13006 
    13007 > color #15.4 #b53ebdff
    13008 
    13009 > color #15.4 #8c3092ff
    13010 
    13011 > color #18 #52cdd6ff models
    13012 
    13013 > select add #6
    13014 
    13015 2 models selected 
    13016 
    13017 > select add #15
    13018 
    13019 38799 atoms, 39588 bonds, 4776 residues, 12 models selected 
    13020 
    13021 > select add #18
    13022 
    13023 55407 atoms, 56550 bonds, 6792 residues, 25 models selected 
    13024 
    13025 > show sel & #15.2,4,6-7#18.3-12 surfaces
    13026 
    13027 > hide sel & #!15.2,4,6-7#!18.3-12 atoms
    13028 
    13029 > hide sel & #!15.2,4,6-7#!18.3-12 cartoons
    13030 
    13031 > lighting soft
    13032 
    13033 > view orient
    13034 
    13035 > select subtract #15
    13036 
    13037 16608 atoms, 16962 bonds, 2016 residues, 29 models selected 
    13038 
    13039 > select clear
    13040 
    13041 > select add #15.2
    13042 
    13043 4995 atoms, 5088 bonds, 612 residues, 1 model selected 
    13044 
    13045 > select subtract #15.2
    13046 
    13047 1 model selected 
    13048 
    13049 > select add #15.2
    13050 
    13051 4995 atoms, 5088 bonds, 612 residues, 1 model selected 
    13052 
    13053 > select subtract #15.2
    13054 
    13055 1 model selected 
    13056 
    13057 > hide #!15.2 models
    13058 
    13059 > show #!15.2 models
    13060 
    13061 > select add #15.2
    13062 
    13063 4995 atoms, 5088 bonds, 612 residues, 1 model selected 
    13064 
    13065 > select subtract #15.2
    13066 
    13067 1 model selected 
    13068 
    13069 > select add #15.4
    13070 
    13071 6829 atoms, 6972 bonds, 843 residues, 1 model selected 
    13072 
    13073 > select add #15.6
    13074 
    13075 13658 atoms, 13944 bonds, 1686 residues, 3 models selected 
    13076 
    13077 > select subtract #15.6
    13078 
    13079 6829 atoms, 6972 bonds, 843 residues, 3 models selected 
    13080 
    13081 > select add #15.6
    13082 
    13083 13658 atoms, 13944 bonds, 1686 residues, 3 models selected 
    13084 
    13085 > select subtract #15.6
    13086 
    13087 6829 atoms, 6972 bonds, 843 residues, 3 models selected 
    13088 
    13089 > select add #15.7
    13090 
    13091 7938 atoms, 8108 bonds, 980 residues, 3 models selected 
    13092 
    13093 > select subtract #15.7
    13094 
    13095 6829 atoms, 6972 bonds, 843 residues, 3 models selected 
    13096 
    13097 > select add #15.6
    13098 
    13099 13658 atoms, 13944 bonds, 1686 residues, 3 models selected 
    13100 Alignment identifier is 1 
    13101 
    13102 > select #15.4/Ch:1 #15.6/Cj:1
    13103 
    13104 16 atoms, 14 bonds, 2 residues, 2 models selected 
    13105 
    13106 > select #15.4/Ch:1-142 #15.6/Cj:1-142
    13107 
    13108 2204 atoms, 2218 bonds, 282 residues, 2 models selected 
    13109 1 [ID: 1] region chains Ch,Cj [1-141] RMSD: 127.125 
    13110  
    13111 
    13112 > hide sel surfaces
    13113 
    13114 > save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    13115 > from_June2024/July_2024/Final-
    13116 > version_model/Flo_PflA_Local/For_Figure4_PflAB.cxs includeMaps true
    13117 
    13118 > view
    13119 
    13120 [Repeated 1 time(s)]
    13121 
    13122 > view name Top1
    13123 
    13124 > save /Users/shoichi/Desktop/PflAB_local.png supersample 2
    13125 > transparentBackground true
    13126 
    13127 > turn x 35
    13128 
    13129 > turn x -35
    13130 
    13131 [Repeated 2 time(s)]
    13132 
    13133 > view Top1
    13134 
    13135 > turn x 90
    13136 
    13137 [Repeated 2 time(s)]
    13138 
    13139 > turn x 10
    13140 
    13141 [Repeated 5 time(s)]
    13142 
    13143 > view Top1
    13144 
    13145 > turn x -35
    13146 
    13147 > select up
    13148 
    13149 13658 atoms, 13944 bonds, 1686 residues, 4 models selected 
    13150 
    13151 > select up
    13152 
    13153 13658 atoms, 13944 bonds, 1686 residues, 4 models selected 
    13154 
    13155 > view Top1
    13156 
    13157 > select add #15
    13158 
    13159 38799 atoms, 39588 bonds, 4776 residues, 12 models selected 
    13160 
    13161 > select subtract #15
    13162 
    13163 4 models selected 
    13164 
    13165 > save /Users/shoichi/Desktop/PflAB_local.png supersample 2
    13166 > transparentBackground true
    13167 
    13168 > turn x 90
    13169 
    13170 [Repeated 2 time(s)]
    13171 
    13172 > hide #!15 models
    13173 
    13174 > hide #!18 models
    13175 
    13176 > ui tool show "Map Eraser"
    13177 
    13178 > volume erase #6 center 28.224,-131.56,-185.36 radius 57.668
    13179 
    13180 > show #!18 models
    13181 
    13182 > close #17
    13183 
    13184 > show #!16 models
    13185 
    13186 > hide #!16 models
    13187 
    13188 > show #!15 models
    13189 
    13190 > view Top1
    13191 
    13192 > turn x 90
    13193 
    13194 [Repeated 2 time(s)]
    13195 
    13196 > view Top1
    13197 
    13198 > turn x -40
    13199 
    13200 [Repeated 1 time(s)]
    13201 
    13202 > view Top1
    13203 
    13204 > turn x -70
    13205 
    13206 > view Top1
    13207 
    13208 > turn x -50
    13209 
    13210 > save /Users/shoichi/Desktop/PflAB_local-tilt50.png supersample 2
    13211 > transparentBackground true
    13212 
    13213 > hide #!18 models
    13214 
    13215 > hide #!15 models
    13216 
    13217 > ui tool show "Segment Map"
    13218 
    13219 Segmenting 3Xunits.mrc, density threshold 0.184695 
    13220 Showing 51 region surfaces 
    13221 262 watershed regions, grouped to 51 regions 
    13222 Showing 3Xunits.seg - 51 regions, 51 surfaces 
    13223 
    13224 > show #!16 models
    13225 
    13226 > hide #!16 models
    13227 
    13228 > show #!18 models
    13229 
    13230 > hide #!18 models
    13231 
    13232 > select add #2.49
    13233 
    13234 1 model selected 
    13235 
    13236 > select add #2.5
    13237 
    13238 2 models selected 
    13239 
    13240 > select add #2.3
    13241 
    13242 3 models selected 
    13243 
    13244 > select add #2.11
    13245 
    13246 4 models selected 
    13247 
    13248 > select add #2.8
    13249 
    13250 5 models selected 
    13251 
    13252 > select add #2.33
    13253 
    13254 6 models selected 
    13255 
    13256 > select add #2.32
    13257 
    13258 7 models selected 
    13259 
    13260 > select add #2.18
    13261 
    13262 8 models selected 
    13263 
    13264 > select add #2.16
    13265 
    13266 9 models selected 
    13267 
    13268 > select add #2.17
    13269 
    13270 10 models selected 
    13271 
    13272 > select add #2.31
    13273 
    13274 11 models selected 
    13275 
    13276 > select add #2.45
    13277 
    13278 12 models selected 
    13279 
    13280 > select add #2.30
    13281 
    13282 13 models selected 
    13283 
    13284 > select add #2.25
    13285 
    13286 14 models selected 
    13287 
    13288 > select add #2.44
    13289 
    13290 15 models selected 
    13291 
    13292 > select add #2.2
    13293 
    13294 16 models selected 
    13295 
    13296 > select subtract #2.2
    13297 
    13298 15 models selected 
    13299 
    13300 > show #!16 models
    13301 
    13302 > hide #!16 models
    13303 
    13304 > show #!18 models
    13305 
    13306 > hide #!18 models
    13307 
    13308 > show #!15 models
    13309 
    13310 > hide #!15 models
    13311 
    13312 > show #!15 models
    13313 
    13314 > hide #!15 models
    13315 
    13316 > select add #2.21
    13317 
    13318 16 models selected 
    13319 
    13320 > select subtract #2.21
    13321 
    13322 15 models selected 
    13323 
    13324 > select add #2.43
    13325 
    13326 16 models selected 
    13327 
    13328 > select add #2.6
    13329 
    13330 17 models selected 
    13331 
    13332 > select add #2.7
    13333 
    13334 18 models selected 
    13335 
    13336 > select add #2.12
    13337 
    13338 19 models selected 
    13339 
    13340 > select add #2.19
    13341 
    13342 20 models selected 
    13343 
    13344 > select add #2.14
    13345 
    13346 21 models selected 
    13347 
    13348 > select add #2.35
    13349 
    13350 22 models selected 
    13351 
    13352 > select add #2.23
    13353 
    13354 23 models selected 
    13355 
    13356 > select add #2.24
    13357 
    13358 24 models selected 
    13359 
    13360 > select add #2.29
    13361 
    13362 25 models selected 
    13363 
    13364 > select add #2.40
    13365 
    13366 26 models selected 
    13367 
    13368 > select add #2.36
    13369 
    13370 27 models selected 
    13371 
    13372 > select add #2.26
    13373 
    13374 28 models selected 
    13375 
    13376 > select add #2.46
    13377 
    13378 29 models selected 
    13379 
    13380 > select add #2.38
    13381 
    13382 30 models selected 
    13383 
    13384 > show #!15 models
    13385 
    13386 > hide #!15 models
    13387 
    13388 > show #!15 models
    13389 
    13390 > hide #!15 models
    13391 
    13392 > select subtract #2.30
    13393 
    13394 29 models selected 
    13395 
    13396 > show #!15 models
    13397 
    13398 > select add #2.37
    13399 
    13400 30 models selected 
    13401 
    13402 > select add #2.9
    13403 
    13404 31 models selected 
    13405 
    13406 > select add #2.28
    13407 
    13408 32 models selected 
    13409 
    13410 > select add #2.20
    13411 
    13412 33 models selected 
    13413 
    13414 > select add #2.13
    13415 
    13416 34 models selected 
    13417 
    13418 > select add #2.15
    13419 
    13420 35 models selected 
    13421 
    13422 > select add #2.50
    13423 
    13424 36 models selected 
    13425 
    13426 > show #!18 models
    13427 
    13428 > hide #!18 models
    13429 
    13430 Opened 3Xunits_imasked as #17, grid size 240,240,240, pixel 2.1, shown at step
    13431 1, values float32 
    13432 
    13433 > save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    13434 > from_June2024/July_2024/Final-version_model/Flo_PflA_Local/1Xunit-no-
    13435 > topcage.mrc models #17
    13436 
    13437 > select add #2
    13438 
    13439 52 models selected 
    13440 
    13441 > select subtract #2
    13442 
    13443 Nothing selected 
    13444 
    13445 > hide #!2 models
    13446 
    13447 > hide #!6 models
    13448 
    13449 > show #!18 models
    13450 
    13451 > hide #!18.3 models
    13452 
    13453 > show #!18.3 models
    13454 
    13455 > hide #!18.3 models
    13456 
    13457 > show #!18.3 models
    13458 
    13459 > hide #!18.3 models
    13460 
    13461 > show #!18.3 models
    13462 
    13463 > hide #!18.4 models
    13464 
    13465 > show #!18.4 models
    13466 
    13467 > hide #!18.5 models
    13468 
    13469 > show #!18.5 models
    13470 
    13471 > hide #!18.6 models
    13472 
    13473 > show #!18.6 models
    13474 
    13475 > hide #!18.7 models
    13476 
    13477 > show #!18.7 models
    13478 
    13479 > hide #!18.7 models
    13480 
    13481 > hide #!18.8 models
    13482 
    13483 > show #!18.8 models
    13484 
    13485 > show #!18.7 models
    13486 
    13487 > hide #!18.9 models
    13488 
    13489 > show #!18.9 models
    13490 
    13491 > hide #!18.10 models
    13492 
    13493 > show #!18.10 models
    13494 
    13495 > hide #!18.11 models
    13496 
    13497 > hide #!18.12 models
    13498 
    13499 > view Top1
    13500 
    13501 > turn x -50
    13502 
    13503 > view name Tilt50
    13504 
    13505 > turn y 10
    13506 
    13507 [Repeated 3 time(s)]
    13508 
    13509 > view Tilt50
    13510 
    13511 > view Top1
    13512 
    13513 > save /Users/shoichi/Desktop/PflAB_local-mono.png supersample 2
    13514 > transparentBackground true
    13515 
    13516 > view Tilt50
    13517 
    13518 > save /Users/shoichi/Desktop/PflAB_local-mono-tilt50.png supersample 2
    13519 > transparentBackground true
    13520 
    13521 > turn x -40
    13522 
    13523 > save /Users/shoichi/Desktop/PflAB_local-mono-tilt90.png supersample 2
    13524 > transparentBackground true
    13525 
    13526 > turn y 90
    13527 
    13528 > turn y -90
    13529 
    13530 [Repeated 1 time(s)]
    13531 
    13532 > show #!6 models
    13533 
    13534 > view Top1
    13535 
    13536 > turn y -90
    13537 
    13538 [Repeated 3 time(s)]
    13539 
    13540 > view Top1
    13541 
    13542 [Repeated 1 time(s)]
    13543 
    13544 > turn z -90
    13545 
    13546 [Repeated 4 time(s)]
    13547 
    13548 > turn x -50
    13549 
    13550 > hide #!6 models
    13551 
    13552 > save /Users/shoichi/Desktop/PflAB_local-mono-fromcage.png supersample 2
    13553 > transparentBackground true
    13554 
    13555 > save /Users/shoichi/Desktop/PflAB_local-mono-fromcage-zoom.png supersample 2
    13556 > transparentBackground true
    13557 
    13558 > save /Users/shoichi/Desktop/PflAB_local-mono-fromcage.png supersample 2
    13559 > transparentBackground true
    13560 
    13561 > show #!1 models
    13562 
    13563 > save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    13564 > from_June2024/July_2024/Final-
    13565 > version_model/Flo_PflA_Local/For_Figure4_PflAB.cxs includeMaps true
    13566 
    13567 ——— End of log from Fri Jul 26 17:21:33 2024 ———
    13568 
    13569 opened ChimeraX session 
    13570 Showing 3Xunits.seg - 51 regions, 51 surfaces 
    13571 
    13572 > hide #!1 models
    13573 
    13574 > show #!1 models
    13575 
    13576 > hide #!2 models
    13577 
    13578 > hide #!1 models
    13579 
    13580 > hide #!18 models
    13581 
    13582 > show #!18 models
    13583 
    13584 > color #18 #48a9c0ff models
    13585 
    13586 > color #18 #4a9ed2ff models
    13587 
    13588 > view Top1
    13589 
    13590 > save /Users/shoichi/Desktop/Fig4D-1_08222024.png supersample 2
    13591 > transparentBackground true
    13592 
    13593 > turn x 90
    13594 
    13595 [Repeated 2 time(s)]
    13596 
    13597 > save /Users/shoichi/Desktop/Fig4D-2_08222024.png supersample 2
    13598 > transparentBackground true
    13599 
    13600 > turn -Y 90
    13601 
    13602 > turn -x 1
    13603 
    13604 > turn -x -1
    13605 
    13606 > turn -z -1
    13607 
    13608 > turn -z 1
    13609 
    13610 [Repeated 9 time(s)]
    13611 
    13612 > turn -z -0.5
    13613 
    13614 > view name Fig4E
    13615 
    13616 > turn -Y -90
    13617 
    13618 > view name Fig4D2
    13619 
    13620 > turn -x -90
    13621 
    13622 > view name Fig4D1
    13623 
    13624 > save /Users/shoichi/Desktop/Fig4D-1_08222024.png supersample 2
    13625 > transparentBackground true
    13626 
    13627 > view Fig4D2
    13628 
    13629 > save /Users/shoichi/Desktop/Fig4D-2_08222024.png supersample 2
    13630 > transparentBackground true
    13631 
    13632 > view Fig4E
    13633 
    13634 > save /Users/shoichi/Desktop/Fig4E-1_08222024.png supersample 2
    13635 > transparentBackground true
    13636 
    13637 > turn x 1
    13638 
    13639 > turn x -1
    13640 
    13641 > turn x 40
    13642 
    13643 > save /Users/shoichi/Desktop/Fig4E-2_08222024.png supersample 2
    13644 > transparentBackground true
    13645 
    13646 > view name Fig4E2
    13647 
    13648 > view Fig4D1
    13649 
    13650 > hide #!15 models
    13651 
    13652 > show #!15 models
    13653 
    13654 > show #!4 models
    13655 
    13656 > hide #!4 models
    13657 
    13658 > show #!6 models
    13659 
    13660 > hide #!17 models
    13661 
    13662 > save /Users/shoichi/Desktop/Fig4C1.png supersample 2 transparentBackground
    13663 > true
    13664 
    13665 > turn x 50
    13666 
    13667 > turn x -50
    13668 
    13669 [Repeated 1 time(s)]
    13670 
    13671 > save /Users/shoichi/Desktop/Fig4C2.png supersample 2 transparentBackground
    13672 > true
    13673 
    13674 > save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    13675 > from_June2024/July_2024/Final-
    13676 > version_model/Flo_PflA_Local/For_Figure4_PflAB.cxs includeMaps true
    13677 
    13678 ——— End of log from Thu Aug 22 11:39:22 2024 ———
    13679 
    13680 opened ChimeraX session 
    13681 Showing 3Xunits.seg - 51 regions, 51 surfaces 
    13682 
    13683 > hide #!2 models
    13684 
    13685 > hide #!6 models
    13686 
    13687 > show #!6 models
    13688 
    13689 > hide #!6 models
    13690 
    13691 > hide #!15 models
    13692 
    13693 > show #!15 models
    13694 
    13695 > show #!17 models
    13696 
    13697 > hide #!18 models
    13698 
    13699 > show #!18 models
    13700 
    13701 > hide #17.1 models
    13702 
    13703 > show #17.1 models
    13704 
    13705 > hide #!15 models
    13706 
    13707 > show #!15 models
    13708 
    13709 > hide #!18 models
    13710 
    13711 > show #!2 models
    13712 
    13713 > hide #!15 models
    13714 
    13715 > hide #!17 models
    13716 
    13717 > hide #17.1 models
    13718 
    13719 > show #!15 models
    13720 
    13721 > hide #!15 models
    13722 
    13723 > select #2.6
    13724 
    13725 1 model selected 
    13726 
    13727 > select add #2.47
    13728 
    13729 2 models selected 
    13730 
    13731 > select add #2.37
    13732 
    13733 3 models selected 
    13734 
    13735 > select clear
    13736 
    13737 > select #2.30
    13738 
    13739 1 model selected 
    13740 
    13741 > select add #2.45
    13742 
    13743 2 models selected 
    13744 
    13745 > select add #2.12
    13746 
    13747 3 models selected 
    13748 
    13749 > select add #2.33
    13750 
    13751 4 models selected 
    13752 
    13753 > select add #2.50
    13754 
    13755 5 models selected 
    13756 
    13757 > select add #2.21
    13758 
    13759 6 models selected 
    13760 
    13761 > select add #2.16
    13762 
    13763 7 models selected 
    13764 
    13765 > select add #2.15
    13766 
    13767 8 models selected 
    13768 
    13769 > select add #2.24
    13770 
    13771 9 models selected 
    13772 
    13773 > select add #2.26
    13774 
    13775 10 models selected 
    13776 
    13777 > select add #2.18
    13778 
    13779 11 models selected 
    13780 
    13781 > select add #2.19
    13782 
    13783 12 models selected 
    13784 
    13785 > select add #2.9
    13786 
    13787 13 models selected 
    13788 
    13789 > select add #2.40
    13790 
    13791 14 models selected 
    13792 
    13793 > select add #2.10
    13794 
    13795 15 models selected 
    13796 
    13797 > select add #2.8
    13798 
    13799 16 models selected 
    13800 
    13801 > select add #2.14
    13802 
    13803 17 models selected 
    13804 
    13805 > select add #2.41
    13806 
    13807 18 models selected 
    13808 
    13809 > select add #2.46
    13810 
    13811 19 models selected 
    13812 
    13813 > select add #2.3
    13814 
    13815 20 models selected 
    13816 
    13817 > select add #2.7
    13818 
    13819 21 models selected 
    13820 
    13821 > select add #2.51
    13822 
    13823 22 models selected 
    13824 
    13825 > select add #2.48
    13826 
    13827 23 models selected 
    13828 
    13829 > select add #2.20
    13830 
    13831 24 models selected 
    13832 
    13833 > select add #2.47
    13834 
    13835 25 models selected 
    13836 
    13837 > select subtract #2.47
    13838 
    13839 24 models selected 
    13840 
    13841 > select add #2.25
    13842 
    13843 25 models selected 
    13844 
    13845 > select add #2.13
    13846 
    13847 26 models selected 
    13848 
    13849 > select add #2.42
    13850 
    13851 27 models selected 
    13852 
    13853 > select add #2.38
    13854 
    13855 28 models selected 
    13856 
    13857 > select add #2.35
    13858 
    13859 29 models selected 
    13860 
    13861 > select add #2.34
    13862 
    13863 30 models selected 
    13864 
    13865 > select add #2.17
    13866 
    13867 31 models selected 
    13868 
    13869 > select add #2.29
    13870 
    13871 32 models selected 
    13872 
    13873 > show #!15 models
    13874 
    13875 > hide #!15 models
    13876 
    13877 > show #!15 models
    13878 
    13879 > hide #!15 models
    13880 
    13881 Grouped 32 regions 
    13882 
    13883 > select add #2.22
    13884 
    13885 2 models selected 
    13886 
    13887 > show #!15 models
    13888 
    13889 > hide #!15 models
    13890 
    13891 The cached device pixel ratio value was stale on window expose. Please file a
    13892 QTBUG which explains how to reproduce. 
    13893 
    13894 Opened 3Xunits_imasked as #19, grid size 240,240,240, pixel 2.1, shown at step
    13895 1, values float32 
    13896 
    13897 > hide #!19 models
    13898 
    13899 > show #!19 models
    13900 
    13901 > save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    13902 > from_June2024/July_2024/Final-version_model/Flo_PflA_Local/New-1xPflAB.cxs
    13903 > includeMaps true
    13904 
    13905 The cached device pixel ratio value was stale on window expose. Please file a
    13906 QTBUG which explains how to reproduce. 
    13907 
    13908 Segmenting 3Xunits_imasked, density threshold 0.184695 
    13909 Showing 18 region surfaces 
    13910 89 watershed regions, grouped to 18 regions 
    13911 Showing 3Xunits_imasked.seg - 18 regions, 18 surfaces 
    13912 
    13913 > select #2.14
    13914 
    13915 1 model selected 
    13916 
    13917 > select add #2.18
    13918 
    13919 2 models selected 
    13920 
    13921 > select add #2.16
    13922 
    13923 3 models selected 
    13924 Grouped 3 regions 
    13925 
    13926 > select clear
    13927 
    13928 > select #2.11
    13929 
    13930 1 model selected 
    13931 Ungrouped to 2 regions 
    13932 [Repeated 1 time(s)]Ungrouped to 0 regions 
    13933 
    13934 > select #2.19
    13935 
    13936 1 model selected 
    13937 
    13938 > select add #2.14
    13939 
    13940 2 models selected 
    13941 
    13942 > select clear
    13943 
    13944 > select #2.14
    13945 
    13946 1 model selected 
    13947 Opened 3Xunits_imasked_imasked as #20, grid size 240,240,240, pixel 2.1, shown
    13948 at step 1, values float32 
    13949 
    13950 The cached device pixel ratio value was stale on window expose. Please file a
    13951 QTBUG which explains how to reproduce. 
    13952 
    13953 > save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    13954 > from_June2024/July_2024/Final-version_model/Flo_PflA_Local/1xPflAB-New.mrc
    13955 > models #19
    13956 
    13957 The cached device pixel ratio value was stale on window expose. Please file a
    13958 QTBUG which explains how to reproduce. 
    13959 
    13960 > save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    13961 > from_June2024/July_2024/Final-version_model/Flo_PflA_Local/1xPflAB-New-no-
    13962 > cyt-cage.mrc models #20
    13963 
    13964 > hide #!19 models
    13965 
    13966 > hide #!2 models
    13967 
    13968 > select add #2
    13969 
    13970 19 models selected 
    13971 
    13972 > select subtract #2
    13973 
    13974 Nothing selected 
    13975 
    13976 > show #!15 models
    13977 
    13978 > color #20 #72727240 models
    13979 
    13980 > view orient
    13981 
    13982 [Repeated 1 time(s)]
    13983 
    13984 > view name Fig4C
    13985 
    13986 > ls
    13987 
    13988 Unknown command: ls 
    13989 
    13990 > save /Users/shoichitachiyama/Desktop/Fig4Ca_09042024.png supersample 2
    13991 > transparentBackground true
    13992 
    13993 [Repeated 1 time(s)]
    13994 
    13995 > view name Fig4C
    13996 
    13997 > turn x 50
    13998 
    13999 > turn x -50
    14000 
    14001 [Repeated 1 time(s)]
    14002 
    14003 > save /Users/shoichitachiyama/Desktop/Fig4Cb_09042024.png supersample 2
    14004 > transparentBackground true
    14005 
    14006 > show #!8 models
    14007 
    14008 > hide #!8 models
    14009 
    14010 > show #!17 models
    14011 
    14012 > hide #!17 models
    14013 
    14014 > show #17.1 models
    14015 
    14016 > hide #17.1 models
    14017 
    14018 > save /Users/shoichitachiyama/Desktop/Fig4Cb_09042024.png supersample 2
    14019 > transparentBackground true
    14020 
    14021 > hide #!20 models
    14022 
    14023 > show #!20 models
    14024 
    14025 > show #!8 models
    14026 
    14027 > hide #!8 models
    14028 
    14029 > save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    14030 > from_June2024/July_2024/Final-
    14031 > version_model/Flo_PflA_Local/For_Figure4_PflAB_Sep2024.cxs includeMaps true
    14032 
    14033 ——— End of log from Wed Sep 4 18:57:11 2024 ———
    14034 
    14035 opened ChimeraX session 
    14036 Showing 3Xunits_imasked.seg - 18 regions, 18 surfaces 
    14037 
    14038 > hide #!2 models
    14039 
    14040 > show #!8 models
    14041 
    14042 The cached device pixel ratio value was stale on window expose. Please file a
    14043 QTBUG which explains how to reproduce. 
    14044 
    14045 Segmenting 3XfliL.mrc, density threshold 0.184695 
    14046 Showing 9 region surfaces 
    14047 56 watershed regions, grouped to 9 regions 
    14048 Showing 3XfliL.seg - 9 regions, 9 surfaces 
    14049 
    14050 > select #2.1
    14051 
    14052 1 model selected 
    14053 
    14054 > select add #2.8
    14055 
    14056 2 models selected 
    14057 
    14058 > select add #2.6
    14059 
    14060 3 models selected 
    14061 
    14062 The cached device pixel ratio value was stale on window expose. Please file a
    14063 QTBUG which explains how to reproduce. 
    14064 
    14065 Opened 3XfliL_imasked as #21, grid size 240,240,240, pixel 2.1, shown at step
    14066 1, values float32 
    14067 
    14068 The cached device pixel ratio value was stale on window expose. Please file a
    14069 QTBUG which explains how to reproduce. 
    14070 
    14071 > save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    14072 > from_June2024/July_2024/Final-version_model/Flo_PflA_Local/2xFliL.mrc models
    14073 > #21
    14074 
    14075 > close #2
    14076 
    14077 > hide #!8 models
    14078 
    14079 > open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    14080 > from_June2024/July_2024/Final-version_model/Flo_PflA_Local/Stator-
    14081 > complexb.pdb
    14082 
    14083 Summary of feedback from opening /Volumes/Backup-95/Chimera-2023/PflB-PflA-
    14084 project/Start-from_June2024/July_2024/Final-
    14085 version_model/Flo_PflA_Local/Stator-complexb.pdb 
    14086 --- 
    14087 warnings | Start residue of secondary structure not found: HELIX 1 1 TYRA0 183 ASPA0 196 1 14 
    14088 Start residue of secondary structure not found: HELIX 2 2 TYRA0 200 ASNA0 213
    14089 1 14 
    14090 Start residue of secondary structure not found: HELIX 3 3 LYSA0 220 LEUA0 234
    14091 1 15 
    14092 Start residue of secondary structure not found: HELIX 4 4 LYSA0 238 ASNA0 251
    14093 1 14 
    14094 Start residue of secondary structure not found: HELIX 5 5 ILEA0 258 GLUA0 271
    14095 1 14 
    14096 919 messages similar to the above omitted 
    14097  
    14098 Chain information for Stator-complexb.pdb 
    14099 --- 
    14100 Chain | Description 
    14101 2.1/? | No description available 
    14102 2.2/C 2.3/D 2.4/E 2.5/F 2.6/G 2.7/H 2.8/I 2.9/J 2.10/K 2.11/L | No description available 
    14103 2.22/K | No description available 
    14104 2.22/L | No description available 
    14105 2.12/M 2.13/N 2.14/O 2.15/P 2.16/Q 2.17/R 2.18/S 2.19/T 2.20/U 2.21/V | No description available 
    14106  
    14107 
    14108 > open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    14109 > from_June2024/July_2024/Final-version_model/Flo_PflA_Local/Stator-
    14110 > complexb.pdb
    14111 
    14112 Summary of feedback from opening /Volumes/Backup-95/Chimera-2023/PflB-PflA-
    14113 project/Start-from_June2024/July_2024/Final-
    14114 version_model/Flo_PflA_Local/Stator-complexb.pdb 
    14115 --- 
    14116 warnings | Start residue of secondary structure not found: HELIX 1 1 TYRA0 183 ASPA0 196 1 14 
    14117 Start residue of secondary structure not found: HELIX 2 2 TYRA0 200 ASNA0 213
    14118 1 14 
    14119 Start residue of secondary structure not found: HELIX 3 3 LYSA0 220 LEUA0 234
    14120 1 15 
    14121 Start residue of secondary structure not found: HELIX 4 4 LYSA0 238 ASNA0 251
    14122 1 14 
    14123 Start residue of secondary structure not found: HELIX 5 5 ILEA0 258 GLUA0 271
    14124 1 14 
    14125 919 messages similar to the above omitted 
    14126  
    14127 Chain information for Stator-complexb.pdb 
    14128 --- 
    14129 Chain | Description 
    14130 22.1/? | No description available 
    14131 22.2/C 22.3/D 22.4/E 22.5/F 22.6/G 22.7/H 22.8/I 22.9/J 22.10/K 22.11/L | No description available 
    14132 22.22/K | No description available 
    14133 22.22/L | No description available 
    14134 22.12/M 22.13/N 22.14/O 22.15/P 22.16/Q 22.17/R 22.18/S 22.19/T 22.20/U 22.21/V | No description available 
    14135  
    14136 
    14137 > select add #21
    14138 
    14139 2 models selected 
    14140 
    14141 > show #!6 models
    14142 
    14143 > view orient
    14144 
    14145 > view matrix models #21,1,0,0,-0.48533,0,1,0,4.9028,0,0,1,0
    14146 
    14147 > undo
    14148 
    14149 > select subtract #21
    14150 
    14151 Nothing selected 
    14152 
    14153 > select add #22
    14154 
    14155 23554 atoms, 23886 bonds, 2988 residues, 23 models selected 
    14156 
    14157 > select add #2
    14158 
    14159 47108 atoms, 47772 bonds, 5976 residues, 46 models selected 
    14160 
    14161 > select subtract #2
    14162 
    14163 23554 atoms, 23886 bonds, 2988 residues, 23 models selected 
    14164 
    14165 > view matrix models #22,1,0,0,-14.173,0,1,0,103.19,0,0,1,0
    14166 
    14167 > view matrix models #22,1,0,0,-15.419,0,1,0,106.11,0,0,1,-1.9686
    14168 
    14169 > select add #2
    14170 
    14171 47108 atoms, 47772 bonds, 5976 residues, 46 models selected 
    14172 
    14173 > select subtract #2
    14174 
    14175 23554 atoms, 23886 bonds, 2988 residues, 23 models selected 
    14176 
    14177 > hide #2.11 models
    14178 
    14179 > show #2.11 models
    14180 
    14181 > hide #2.12 models
    14182 
    14183 > show #2.12 models
    14184 
    14185 > hide #2.21 models
    14186 
    14187 > show #2.21 models
    14188 
    14189 > hide #2.21 models
    14190 
    14191 > hide #2.20 models
    14192 
    14193 > hide #2.19 models
    14194 
    14195 > hide #2.18 models
    14196 
    14197 > hide #2.17 models
    14198 
    14199 > hide #2.16 models
    14200 
    14201 > hide #2.15 models
    14202 
    14203 > hide #2.14 models
    14204 
    14205 > hide #2.13 models
    14206 
    14207 > hide #2.12 models
    14208 
    14209 > close #2.12-21
    14210 
    14211 > hide #22.12 models
    14212 
    14213 > hide #22.13 models
    14214 
    14215 > hide #22.14 models
    14216 
    14217 > hide #22.15 models
    14218 
    14219 > hide #22.16 models
    14220 
    14221 > hide #22.17 models
    14222 
    14223 > hide #22.18 models
    14224 
    14225 > hide #22.19 models
    14226 
    14227 > hide #22.20 models
    14228 
    14229 > hide #22.21 models
    14230 
    14231 > close #22.12-21
    14232 
    14233 > select subtract #22
    14234 
    14235 Nothing selected 
    14236 
    14237 > select add #22
    14238 
    14239 21694 atoms, 22006 bonds, 2748 residues, 13 models selected 
    14240 
    14241 > select subtract #22
    14242 
    14243 Nothing selected 
    14244 
    14245 > select add #2
    14246 
    14247 21694 atoms, 22006 bonds, 2748 residues, 13 models selected 
    14248 
    14249 > ui mousemode right "rotate selected models"
    14250 
    14251 > view matrix models
    14252 > #2,0.99996,-0.0049032,-0.0077954,-0.63495,0.0050391,0.99983,0.017514,1.0297,0.0077082,-0.017552,0.99982,-0.63371
    14253 
    14254 > ui mousemode right "translate selected models"
    14255 
    14256 > view matrix models
    14257 > #2,0.99996,-0.0049032,-0.0077954,-0.92663,0.0050391,0.99983,0.017514,1.3841,0.0077082,-0.017552,0.99982,-1.1098
    14258 
    14259 > select subtract #2
    14260 
    14261 Nothing selected 
    14262 
    14263 > hide #!6 models
    14264 
    14265 > color #2 #b7a359ff models
    14266 
    14267 > color #22 #b7a359ff models
    14268 
    14269 > select add #22.22
    14270 
    14271 4099 atoms, 4171 bonds, 518 residues, 1 model selected 
    14272 
    14273 > select subtract #22.22
    14274 
    14275 Nothing selected 
    14276 
    14277 > hide #22.22 models
    14278 
    14279 > show #22.22 models
    14280 
    14281 > color #22.22 #905d12ff models
    14282 
    14283 > color #2.22 #905d12ff models
    14284 
    14285 > color #2.1 #a69b32ff models
    14286 
    14287 > color #22.1 #a69b32ff models
    14288 
    14289 > select add #22
    14290 
    14291 21694 atoms, 22006 bonds, 2748 residues, 13 models selected 
    14292 
    14293 > select add #2
    14294 
    14295 43388 atoms, 44012 bonds, 5496 residues, 26 models selected 
    14296 
    14297 > hide sel cartoons
    14298 
    14299 > show sel surfaces
    14300 
    14301 > select clear
    14302 
    14303 > color #21 #72727240 models
    14304 
    14305 Cell requested for row 0 is out of bounds for table with 34 rows! Resizing
    14306 table model. 
    14307 
    14308 > show #!16 models
    14309 
    14310 > hide #!16 models
    14311 
    14312 > show #!18 models
    14313 
    14314 > view orient
    14315 
    14316 > view Fig4C1
    14317 
    14318 Expected an objects specifier or a view name or a keyword 
    14319 
    14320 > view Fig4Ca
    14321 
    14322 Expected an objects specifier or a view name or a keyword 
    14323 
    14324 > view Fig4C
    14325 
    14326 > save /Users/shoichitachiyama/Desktop/Fig4CD_09042024.png supersample 2
    14327 > transparentBackground true
    14328 
    14329 > save /Users/shoichitachiyama/Desktop/Fig4D_09042024.png supersample 2
    14330 > transparentBackground true
    14331 
    14332 > view Fig5Cb
    14333 
    14334 Expected an objects specifier or a view name or a keyword 
    14335 
    14336 > view Fig5C2
    14337 
    14338 Expected an objects specifier or a view name or a keyword 
    14339 
    14340 > turn x 90
    14341 
    14342 [Repeated 3 time(s)]
    14343 
    14344 > turn x 45
    14345 
    14346 > turn x -45
    14347 
    14348 [Repeated 1 time(s)]
    14349 
    14350 > view Fig5D
    14351 
    14352 Expected an objects specifier or a view name or a keyword 
    14353 
    14354 > view Fig4C
    14355 
    14356 > turn x -90
    14357 
    14358 > view Fig4C
    14359 
    14360 > turn x -90
    14361 
    14362 > save /Users/shoichitachiyama/Desktop/Fig4Db_09042024.png supersample 2
    14363 > transparentBackground true
    14364 
    14365 > view Fig4C
    14366 
    14367 > turn x -90
    14368 
    14369 > turn y -90
    14370 
    14371 > save /Users/shoichitachiyama/Desktop/Fig4Dc_09042024.png supersample 2
    14372 > transparentBackground true
    14373 
    14374 > turn x -40
    14375 
    14376 > turn x 40
    14377 
    14378 [Repeated 1 time(s)]
    14379 
    14380 > save /Users/shoichitachiyama/Desktop/Fig4Dd_09042024.png supersample 2
    14381 > transparentBackground true
    14382 
    14383 > save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    14384 > from_June2024/July_2024/Final-
    14385 > version_model/Flo_PflA_Local/For_Figure4_PflAB_Sep2024.cxs includeMaps true
    14386 
    14387 ——— End of log from Wed Sep 4 20:03:04 2024 ———
    14388 
    14389 opened ChimeraX session 
    14390 
    14391 > hide #!2 models
    14392 
    14393 > show #!2 models
    14394 
    14395 > hide #!15 models
    14396 
    14397 > show #!15 models
    14398 
    14399 > hide #!17 models
    14400 
    14401 > hide #!18 models
    14402 
    14403 > show #!18 models
    14404 
    14405 > hide #!20 models
    14406 
    14407 > hide #!21 models
    14408 
    14409 > hide #!22 models
    14410 
    14411 > show #!22 models
    14412 
    14413 > view orient
    14414 
    14415 > save /Users/shoichi/Desktop/HP-Fig4D_09172024.png supersample 2
    14416 > transparentBackground true
    14417 
    14418 > turn x -90
    14419 
    14420 > save /Users/shoichi/Desktop/HP-Fig4D2_09172024.png supersample 2
    14421 > transparentBackground true
    14422 
    14423 > view orient
    14424 
    14425 > hide #!18 models
    14426 
    14427 > hide #!22 models
    14428 
    14429 > hide #!2 models
    14430 
    14431 > show #!20 models
    14432 
    14433 > hide #!15 models
    14434 
    14435 > show #!15 models
    14436 
    14437 > hide #!15 models
    14438 
    14439 > show #!15 models
    14440 
    14441 > show #!19 models
    14442 
    14443 > hide #!19 models
    14444 
    14445 > hide #!20 models
    14446 
    14447 > show #!19 models
    14448 
    14449 > hide #!19 models
    14450 
    14451 > show #!19 models
    14452 
    14453 > hide #!19 models
    14454 
    14455 > show #!14 models
    14456 
    14457 > hide #!14 models
    14458 
    14459 > hide #!15 models
    14460 
    14461 > show #!15 models
    14462 
    14463 > show #!6 models
    14464 
    14465 > volume #6 level 0.03792
    14466 
    14467 > hide #!6 models
    14468 
    14469 > show #!19 models
    14470 
    14471 > show #!1 models
    14472 
    14473 > hide #!1 models
    14474 
    14475 > show #!1 models
    14476 
    14477 > hide #!1 models
    14478 
    14479 > show #!1 models
    14480 
    14481 > color #1 #b2b2b283 models
    14482 
    14483 > hide #!1 models
    14484 
    14485 > show #!1 models
    14486 
    14487 > hide #!1 models
    14488 
    14489 > show #!1 models
    14490 
    14491 > hide #!1 models
    14492 
    14493 > show #!1 models
    14494 
    14495 > hide #!1 models
    14496 
    14497 > show #!1 models
    14498 
    14499 > hide #!19 models
    14500 
    14501 > show #!19 models
    14502 
    14503 > hide #!19 models
    14504 
    14505 > hide #!1 models
    14506 
    14507 > show #!20 models
    14508 
    14509 > select add #15
    14510 
    14511 38799 atoms, 39588 bonds, 4776 residues, 10 models selected 
    14512 
    14513 > hide sel & #!15.2,4,6-7 surfaces
    14514 
    14515 > show sel & #!15.2,4,6-7 cartoons
    14516 
    14517 > show sel & #!15.2,4,6-7 surfaces
    14518 
    14519 > ui mousemode right "translate selected models"
    14520 
    14521 > select subtract #15
    14522 
    14523 4 models selected 
    14524 
    14525 > show #!14 models
    14526 
    14527 > hide #!14 models
    14528 
    14529 > show #!14 models
    14530 
    14531 > hide #!14 models
    14532 
    14533 > show #!12 models
    14534 
    14535 > hide #!12 models
    14536 
    14537 > show #!13 models
    14538 
    14539 > hide #!13 models
    14540 
    14541 > show #!6 models
    14542 
    14543 > hide #!6 models
    14544 
    14545 > select add #20
    14546 
    14547 2 models selected 
    14548 
    14549 > select subtract #20
    14550 
    14551 Nothing selected 
    14552 
    14553 > select add #20
    14554 
    14555 2 models selected 
    14556 
    14557 > select subtract #20
    14558 
    14559 Nothing selected 
    14560 
    14561 > show #!6 models
    14562 
    14563 > hide #!15 models
    14564 
    14565 > ui tool show "Segment Map"
    14566 
    14567 > hide #!20 models
    14568 
    14569 The cached device pixel ratio value was stale on window expose. Please file a
    14570 QTBUG which explains how to reproduce. 
    14571 
    14572 Segmenting 3Xunits.mrc, density threshold 0.037925 
    14573 Showing 318 region surfaces 
    14574 26453 watershed regions, grouped to 318 regions 
    14575 Showing 3Xunits.seg - 318 regions, 318 surfaces 
    14576 Drag select of 31808, 15646 of 51436 triangles, 31845, 10703 of 26232
    14577 triangles, 31801, 11883 of 25260 triangles, 31805, 31816, 31757, 31835, 7743
    14578 of 20008 triangles, 31665, 1005 of 18676 triangles, 31826, 11641 of 19392
    14579 triangles, 31711, 3506 of 17600 triangles, 31789, 8007 of 16980 triangles,
    14580 31833, 9323 of 17928 triangles, 31672, 31815, 10093 of 17432 triangles, 31753,
    14581 31736, 5704 of 17348 triangles, 31828, 11195 of 17232 triangles, 31842, 8537
    14582 of 16596 triangles, 31851, 9605 of 16580 triangles, 31836, 9456 of 15488
    14583 triangles, 31745, 31661, 31817, 31790, 6439 of 13600 triangles, 31853, 288 of
    14584 12348 triangles, 31803, 4501 of 14200 triangles, 31775, 8083 of 13516
    14585 triangles, 31673, 6794 of 12616 triangles, 31806, 31618, 8406 of 10620
    14586 triangles, 31579, 7487 of 11588 triangles, 31748, 7457 of 11728 triangles,
    14587 31717, 31776, 7683 of 11900 triangles, 31715, 7583 of 11552 triangles, 31841,
    14588 6433 of 11336 triangles, 30874, 5372 of 10376 triangles, 31691, 4405 of 10484
    14589 triangles, 31694, 6562 of 9188 triangles, 31864, 6686 of 10620 triangles,
    14590 31802, 4554 of 9644 triangles, 31659, 4942 of 10672 triangles, 31539, 30901,
    14591 4075 of 8316 triangles, 31832, 4954 of 9116 triangles, 31601, 30837, 7063 of
    14592 9164 triangles, 31859, 5346 of 9508 triangles, 30843, 2361 of 7456 triangles,
    14593 31865, 5101 of 8924 triangles, 31779, 6356 of 9084 triangles, 31738, 5023 of
    14594 9760 triangles, 31587, 5689 of 8816 triangles, 31855, 5432 of 8876 triangles,
    14595 31741, 5792 of 8972 triangles, 31708, 4173 of 8704 triangles, 31696, 5317 of
    14596 8284 triangles, 31631, 4074 of 9032 triangles, 31628, 5031 of 7848 triangles,
    14597 31308, 1501 of 7300 triangles, 31720, 4394 of 7736 triangles, 31699, 5754 of
    14598 7664 triangles, 31718, 3292 of 7676 triangles, 31723, 3342 of 7700 triangles,
    14599 31866, 4720 of 7680 triangles, 31848, 4086 of 7816 triangles, 31645, 3792 of
    14600 7496 triangles, 31643, 3950 of 7200 triangles, 31862, 4364 of 6784 triangles,
    14601 31584, 4153 of 6740 triangles, 30847, 5304 of 6668 triangles, 31728, 4636 of
    14602 7048 triangles, 31846, 4388 of 7240 triangles, 31710, 4258 of 6136 triangles,
    14603 31630, 3402 of 6072 triangles, 31627, 2921 of 5568 triangles, 31821, 3963 of
    14604 6220 triangles, 31780, 3080 of 6032 triangles, 31849, 2208 of 5944 triangles,
    14605 31684, 3293 of 5500 triangles, 31649, 3028 of 6004 triangles, 31121, 3008 of
    14606 5176 triangles, 30850, 2505 of 5224 triangles, 31207, 3581 of 4728 triangles,
    14607 30939, 3720 of 5092 triangles, 31614, 3094 of 5448 triangles, 30948, 3503 of
    14608 5120 triangles, 31582, 2748 of 5156 triangles, 31639, 2544 of 4796 triangles,
    14609 31732, 3367 of 4856 triangles, 31730, 2908 of 4520 triangles, 31770, 2124 of
    14610 3700 triangles, 31844, 3162 of 3856 triangles, 31856, 1664 of 3760 triangles,
    14611 31784, 2600 of 3976 triangles, 31622, 841 of 3336 triangles, 30917, 660 of
    14612 2900 triangles, 31774, 2220 of 3028 triangles, 31424, 1624 of 2188 triangles,
    14613 31266, 308 of 2052 triangles, 30868, 1098 of 1280 triangles, 31210, 352 of
    14614 1100 triangles, 31020, 48 of 964 triangles, 30839, 851 of 888 triangles,
    14615 31011, 28692, 310 of 380 triangles, 6 3Xunits.mrc 
    14616 
    14617 > select clear
    14618 
    14619 > select #23.71
    14620 
    14621 1 model selected 
    14622 
    14623 > select add #23.310
    14624 
    14625 2 models selected 
    14626 
    14627 > select add #23.263
    14628 
    14629 3 models selected 
    14630 
    14631 > select add #23.53
    14632 
    14633 4 models selected 
    14634 
    14635 > hide #!6 models
    14636 
    14637 Drag select of 31815, 3679 of 17432 triangles, 31851, 4783 of 16580 triangles,
    14638 31775, 1474 of 13516 triangles, 31579, 1842 of 11588 triangles, 31748, 2215 of
    14639 11728 triangles, 31694, 1423 of 9188 triangles, 31864, 1344 of 10620
    14640 triangles, 31659, 141 of 10672 triangles, 30901, 3021 of 8316 triangles,
    14641 30837, 1419 of 9164 triangles, 31859, 1937 of 9508 triangles, 31738, 2701 of
    14642 9760 triangles, 31631, 3152 of 9032 triangles, 31699, 2345 of 7664 triangles,
    14643 31723, 570 of 7700 triangles, 31848, 1248 of 7816 triangles, 31645, 2741 of
    14644 7496 triangles, 31862, 81 of 6784 triangles, 31584, 958 of 6740 triangles,
    14645 31728, 140 of 7048 triangles, 31630, 622 of 6072 triangles, 31780, 107 of 6032
    14646 triangles, 31849, 125 of 5944 triangles, 31649, 1114 of 6004 triangles, 31207,
    14647 765 of 4728 triangles, 30939, 911 of 5092 triangles, 31614, 1806 of 5448
    14648 triangles, 31770, 465 of 3700 triangles, 31856, 741 of 3760 triangles, 31784,
    14649 1398 of 3976 triangles, 31774, 916 of 3028 triangles, 31210, 318 of 1100
    14650 triangles, 30839, 71 of 888 triangles 
    14651 Drag select of 31808, 81 of 51436 triangles, 31801, 553 of 25260 triangles,
    14652 31826, 1444 of 19392 triangles, 31828, 2305 of 17232 triangles, 31842, 2279 of
    14653 16596 triangles, 31836, 25 of 15488 triangles, 31790, 795 of 13600 triangles,
    14654 31673, 70 of 12616 triangles, 31776, 1479 of 11900 triangles, 31715, 768 of
    14655 11552 triangles, 31841, 1142 of 11336 triangles, 31691, 185 of 10484
    14656 triangles, 31802, 34 of 9644 triangles, 31779, 801 of 9084 triangles, 31587,
    14657 209 of 8816 triangles, 31855, 718 of 8876 triangles, 31741, 1429 of 8972
    14658 triangles, 31708, 1140 of 8704 triangles, 31696, 1323 of 8284 triangles,
    14659 31720, 107 of 7736 triangles, 31718, 535 of 7676 triangles, 31643, 267 of 7200
    14660 triangles, 30847, 380 of 6668 triangles, 31846, 884 of 7240 triangles, 31710,
    14661 109 of 6136 triangles, 31627, 13 of 5568 triangles, 31821, 529 of 6220
    14662 triangles, 31684, 328 of 5500 triangles, 31121, 731 of 5176 triangles, 30850,
    14663 349 of 5224 triangles, 31732, 225 of 4856 triangles, 31730, 640 of 4520
    14664 triangles, 31844, 847 of 3856 triangles, 31266, 59 of 2052 triangles, 31011,
    14665 54 of 620 triangles 
    14666 Drag select of 31845, 7035 of 26232 triangles, 31805, 31816, 31757, 20325 of
    14667 21016 triangles, 31835, 4532 of 20008 triangles, 31665, 68 of 18676 triangles,
    14668 31711, 1002 of 17600 triangles, 31789, 6633 of 16980 triangles, 31833, 7775 of
    14669 17928 triangles, 31753, 14962 of 14964 triangles, 31736, 3588 of 17348
    14670 triangles, 31745, 10624 of 13572 triangles, 31661, 31817, 31803, 2607 of 14200
    14671 triangles, 31806, 31618, 6795 of 10620 triangles, 31717, 30874, 3861 of 10376
    14672 triangles, 31539, 31832, 3444 of 9116 triangles, 31601, 9680 of 9764
    14673 triangles, 30843, 523 of 7456 triangles, 31865, 3029 of 8924 triangles, 31628,
    14674 4586 of 7848 triangles, 31308, 142 of 7300 triangles, 31866, 4612 of 7680
    14675 triangles, 30948, 3160 of 5120 triangles, 31639, 2358 of 4796 triangles,
    14676 31622, 192 of 3336 triangles, 31424, 1566 of 2188 triangles, 31020, 44 of 964
    14677 triangles, 28692, 206 of 380 triangles 
    14678 
    14679 > select add #23.101
    14680 
    14681 106 models selected 
    14682 
    14683 > select add #23.74
    14684 
    14685 107 models selected 
    14686 
    14687 > select add #23.201
    14688 
    14689 108 models selected 
    14690 
    14691 > select add #23.96
    14692 
    14693 109 models selected 
    14694 
    14695 > select add #23.88
    14696 
    14697 110 models selected 
    14698 
    14699 > select add #23.115
    14700 
    14701 111 models selected 
    14702 
    14703 > select add #23.57
    14704 
    14705 112 models selected 
    14706 
    14707 > select add #23.58
    14708 
    14709 113 models selected 
    14710 
    14711 > select add #23.77
    14712 
    14713 114 models selected 
    14714 
    14715 > select add #23.130
    14716 
    14717 115 models selected 
    14718 
    14719 > select add #23.138
    14720 
    14721 116 models selected 
    14722 
    14723 > select subtract #23.138
    14724 
    14725 115 models selected 
    14726 
    14727 > select add #23.138
    14728 
    14729 116 models selected 
    14730 
    14731 > select add #23.122
    14732 
    14733 117 models selected 
    14734 
    14735 > select add #23.205
    14736 
    14737 118 models selected 
    14738 
    14739 > select add #23.64
    14740 
    14741 119 models selected 
    14742 Drag select of 30917, 939 of 2900 triangles 
    14743 
    14744 > select add #23.170
    14745 
    14746 121 models selected 
    14747 
    14748 > select add #23.145
    14749 
    14750 122 models selected 
    14751 
    14752 > select add #23.105
    14753 
    14754 123 models selected 
    14755 
    14756 > select add #23.79
    14757 
    14758 124 models selected 
    14759 
    14760 > select add #23.183
    14761 
    14762 125 models selected 
    14763 
    14764 > select add #23.118
    14765 
    14766 126 models selected 
    14767 
    14768 > select subtract #23.118
    14769 
    14770 125 models selected 
    14771 
    14772 > select add #23.139
    14773 
    14774 126 models selected 
    14775 
    14776 > select add #23.118
    14777 
    14778 127 models selected 
    14779 
    14780 > select add #23.200
    14781 
    14782 128 models selected 
    14783 
    14784 > select add #23.104
    14785 
    14786 129 models selected 
    14787 
    14788 > select subtract #23.104
    14789 
    14790 128 models selected 
    14791 
    14792 > select add #23.110
    14793 
    14794 129 models selected 
    14795 
    14796 > select add #23.269
    14797 
    14798 130 models selected 
    14799 
    14800 > select add #23.104
    14801 
    14802 131 models selected 
    14803 
    14804 > select add #23.192
    14805 
    14806 132 models selected 
    14807 
    14808 > select add #23.135
    14809 
    14810 133 models selected 
    14811 
    14812 > select add #23.127
    14813 
    14814 134 models selected 
    14815 
    14816 > select add #23.169
    14817 
    14818 135 models selected 
    14819 
    14820 > select add #23.153
    14821 
    14822 136 models selected 
    14823 
    14824 > select add #23.266
    14825 
    14826 137 models selected 
    14827 
    14828 > select add #23.95
    14829 
    14830 138 models selected 
    14831 
    14832 > select add #23.124
    14833 
    14834 139 models selected 
    14835 
    14836 > select add #23.176
    14837 
    14838 140 models selected 
    14839 
    14840 > select add #23.91
    14841 
    14842 141 models selected 
    14843 
    14844 > select add #23.83
    14845 
    14846 142 models selected 
    14847 
    14848 > select add #23.154
    14849 
    14850 143 models selected 
    14851 
    14852 > select add #23.166
    14853 
    14854 144 models selected 
    14855 
    14856 > select add #23.186
    14857 
    14858 145 models selected 
    14859 
    14860 > select add #23.222
    14861 
    14862 146 models selected 
    14863 
    14864 > select add #23.188
    14865 
    14866 147 models selected 
    14867 
    14868 > select add #23.117
    14869 
    14870 148 models selected 
    14871 
    14872 > select add #23.34
    14873 
    14874 149 models selected 
    14875 
    14876 > select add #23.66
    14877 
    14878 150 models selected 
    14879 
    14880 > select add #23.235
    14881 
    14882 151 models selected 
    14883 
    14884 > select add #23.81
    14885 
    14886 152 models selected 
    14887 
    14888 > select add #23.234
    14889 
    14890 153 models selected 
    14891 
    14892 > select add #23.46
    14893 
    14894 154 models selected 
    14895 
    14896 > select add #23.76
    14897 
    14898 155 models selected 
    14899 
    14900 > select add #23.99
    14901 
    14902 156 models selected 
    14903 
    14904 > select add #23.82
    14905 
    14906 157 models selected 
    14907 
    14908 > select subtract #23.117
    14909 
    14910 156 models selected 
    14911 
    14912 > select add #23.132
    14913 
    14914 157 models selected 
    14915 
    14916 > select add #23.117
    14917 
    14918 158 models selected 
    14919 Drag select of 31813, 7756 of 36304 triangles, 31703, 13 of 14596 triangles,
    14920 31768, 31793, 1968 of 12160 triangles, 31704, 6782 of 10356 triangles, 31662,
    14921 749 of 8176 triangles, 31829, 4006 of 7124 triangles 
    14922 Drag select of 1769, 31771, 31840, 7329 of 16068 triangles, 31818, 6770 of
    14923 16040 triangles, 31762, 31800, 2967 of 11620 triangles, 31838, 3746 of 10984
    14924 triangles, 31794, 5854 of 10336 triangles, 31706, 5479 of 9924 triangles,
    14925 31823, 5043 of 9616 triangles, 31132, 31824, 4295 of 7836 triangles, 31687,
    14926 3465 of 8048 triangles, 30861, 3431 of 7340 triangles, 31820, 3503 of 7556
    14927 triangles, 30909, 2558 of 5784 triangles, 30954, 2789 of 5640 triangles,
    14928 31577, 2918 of 4476 triangles, 31097, 31573, 1840 of 4408 triangles, 30869,
    14929 1248 of 2960 triangles, 31139, 558 of 2520 triangles, 31152, 523 of 2232
    14930 triangles 
    14931 
    14932 > select add #23.246
    14933 
    14934 189 models selected 
    14935 
    14936 > select add #23.298
    14937 
    14938 190 models selected 
    14939 
    14940 > select add #23.219
    14941 
    14942 191 models selected 
    14943 
    14944 > select add #23.216
    14945 
    14946 192 models selected 
    14947 
    14948 > select add #23.252
    14949 
    14950 193 models selected 
    14951 
    14952 > select add #23.126
    14953 
    14954 194 models selected 
    14955 
    14956 > select add #23.202
    14957 
    14958 195 models selected 
    14959 
    14960 > select add #23.241
    14961 
    14962 196 models selected 
    14963 
    14964 > select add #23.111
    14965 
    14966 197 models selected 
    14967 
    14968 > select add #23.155
    14969 
    14970 198 models selected 
    14971 
    14972 > select add #23.173
    14973 
    14974 199 models selected 
    14975 
    14976 > select add #23.260
    14977 
    14978 200 models selected 
    14979 
    14980 > select add #23.302
    14981 
    14982 201 models selected 
    14983 
    14984 > select add #23.167
    14985 
    14986 202 models selected 
    14987 
    14988 > select add #23.10
    14989 
    14990 203 models selected 
    14991 
    14992 > select subtract #23.10
    14993 
    14994 202 models selected 
    14995 
    14996 > select add #23.295
    14997 
    14998 203 models selected 
    14999 
    15000 > select add #23.276
    15001 
    15002 204 models selected 
    15003 
    15004 > select add #23.210
    15005 
    15006 205 models selected 
    15007 
    15008 > select add #23.265
    15009 
    15010 206 models selected 
    15011 
    15012 > select add #23.134
    15013 
    15014 207 models selected 
    15015 
    15016 > select add #23.119
    15017 
    15018 208 models selected 
    15019 
    15020 > select add #23.75
    15021 
    15022 209 models selected 
    15023 
    15024 > select add #23.211
    15025 
    15026 210 models selected 
    15027 
    15028 > select add #23.113
    15029 
    15030 211 models selected 
    15031 
    15032 > select add #23.177
    15033 
    15034 212 models selected 
    15035 
    15036 > select add #23.128
    15037 
    15038 213 models selected 
    15039 
    15040 > select add #23.226
    15041 
    15042 214 models selected 
    15043 
    15044 > select add #23.259
    15045 
    15046 215 models selected 
    15047 
    15048 > select add #23.236
    15049 
    15050 216 models selected 
    15051 
    15052 > select add #23.247
    15053 
    15054 217 models selected 
    15055 
    15056 > select add #23.294
    15057 
    15058 218 models selected 
    15059 
    15060 > select add #23.315
    15061 
    15062 219 models selected 
    15063 
    15064 > select add #23.291
    15065 
    15066 220 models selected 
    15067 
    15068 > select add #23.233
    15069 
    15070 221 models selected 
    15071 
    15072 > select add #23.254
    15073 
    15074 222 models selected 
    15075 
    15076 > select add #23.151
    15077 
    15078 223 models selected 
    15079 
    15080 > select add #23.237
    15081 
    15082 224 models selected 
    15083 
    15084 > select add #23.171
    15085 
    15086 225 models selected 
    15087 
    15088 > select add #23.225
    15089 
    15090 226 models selected 
    15091 
    15092 > select subtract #23.225
    15093 
    15094 225 models selected 
    15095 
    15096 > select add #23.8
    15097 
    15098 226 models selected 
    15099 
    15100 > select add #23.17
    15101 
    15102 227 models selected 
    15103 
    15104 > select subtract #23.8
    15105 
    15106 226 models selected 
    15107 
    15108 > select subtract #23.17
    15109 
    15110 225 models selected 
    15111 
    15112 > select add #23.225
    15113 
    15114 226 models selected 
    15115 
    15116 > select add #23.42
    15117 
    15118 227 models selected 
    15119 
    15120 > select subtract #23.42
    15121 
    15122 226 models selected 
    15123 Drag select of 31607, 1565 of 6884 triangles, 31680, 1071 of 5808 triangles 
    15124 
    15125 > select add #23.273
    15126 
    15127 229 models selected 
    15128 
    15129 > select add #23.284
    15130 
    15131 230 models selected 
    15132 
    15133 > select add #23.288
    15134 
    15135 231 models selected 
    15136 
    15137 > select add #23.308
    15138 
    15139 232 models selected 
    15140 
    15141 > select add #23.313
    15142 
    15143 233 models selected 
    15144 
    15145 > select add #23.244
    15146 
    15147 234 models selected 
    15148 
    15149 > select add #23.108
    15150 
    15151 235 models selected 
    15152 
    15153 > select add #23.114
    15154 
    15155 236 models selected 
    15156 
    15157 > select add #23.274
    15158 
    15159 237 models selected 
    15160 Drag select of 30947, 31289, 1390 of 3768 triangles, 31321, 2312 of 2832
    15161 triangles, 31328, 27021, 148 of 352 triangles 
    15162 Drag select of 31867, 2101 of 19448 triangles, 31588, 1801 of 9000 triangles,
    15163 31273, 3306 of 9504 triangles, 31481, 1474 of 8272 triangles, 31275, 1366 of
    15164 4792 triangles, 31482, 3114 of 7212 triangles, 30973, 2628 of 6800 triangles,
    15165 30977, 4416 of 6628 triangles, 31571, 3425 of 7012 triangles, 31000, 3303 of
    15166 6396 triangles, 31791, 1098 of 5672 triangles, 31619, 6 of 4736 triangles 
    15167 Drag select of 31295, 4490 of 8232 triangles, 31758, 4678 of 6880 triangles,
    15168 31381, 657 of 4136 triangles, 31620, 1376 of 4012 triangles 
    15169 
    15170 > select add #23.261
    15171 
    15172 259 models selected 
    15173 
    15174 > select add #23.214
    15175 
    15176 260 models selected 
    15177 
    15178 > select add #23.290
    15179 
    15180 261 models selected 
    15181 
    15182 > select add #23.27
    15183 
    15184 262 models selected 
    15185 
    15186 > select subtract #23.27
    15187 
    15188 261 models selected 
    15189 
    15190 > select add #23.301
    15191 
    15192 262 models selected 
    15193 
    15194 > select add #23.272
    15195 
    15196 263 models selected 
    15197 
    15198 > select add #23.204
    15199 
    15200 264 models selected 
    15201 
    15202 > select add #23.293
    15203 
    15204 265 models selected 
    15205 
    15206 > select add #23.7
    15207 
    15208 266 models selected 
    15209 
    15210 > select subtract #23.7
    15211 
    15212 265 models selected 
    15213 
    15214 The cached device pixel ratio value was stale on window expose. Please file a
    15215 QTBUG which explains how to reproduce. 
    15216 
    15217 Opened 3Xunits_imasked as #24, grid size 240,240,240, pixel 2.1, shown at step
    15218 1, values float32 
    15219 Segmenting 3Xunits_imasked, density threshold 0.037925 
    15220 Showing 53 region surfaces 
    15221 1349 watershed regions, grouped to 53 regions 
    15222 Showing 3Xunits_imasked.seg - 53 regions, 53 surfaces 
    15223 
    15224 > select add #23.40
    15225 
    15226 1 model selected 
    15227 
    15228 > select add #23.31
    15229 
    15230 2 models selected 
    15231 
    15232 > select add #23.33
    15233 
    15234 3 models selected 
    15235 
    15236 > select add #23.28
    15237 
    15238 4 models selected 
    15239 
    15240 > select add #23.36
    15241 
    15242 5 models selected 
    15243 
    15244 > select add #23.23
    15245 
    15246 6 models selected 
    15247 
    15248 > select add #23
    15249 
    15250 54 models selected 
    15251 
    15252 > select subtract #23
    15253 
    15254 Nothing selected 
    15255 
    15256 > hide #!23 models
    15257 
    15258 > show #!23 models
    15259 
    15260 > hide #!24 models
    15261 
    15262 > select add #23.9
    15263 
    15264 1 model selected 
    15265 
    15266 > select add #23.11
    15267 
    15268 2 models selected 
    15269 
    15270 > select add #23.12
    15271 
    15272 3 models selected 
    15273 
    15274 > show #!15 models
    15275 
    15276 > select add #23.18
    15277 
    15278 4 models selected 
    15279 
    15280 > select add #23.16
    15281 
    15282 5 models selected 
    15283 
    15284 > select add #23.17
    15285 
    15286 6 models selected 
    15287 
    15288 > select subtract #23.16
    15289 
    15290 5 models selected 
    15291 
    15292 > select subtract #23.17
    15293 
    15294 4 models selected 
    15295 
    15296 > select add #23.17
    15297 
    15298 5 models selected 
    15299 
    15300 > select add #23.32
    15301 
    15302 6 models selected 
    15303 
    15304 > select add #23.41
    15305 
    15306 7 models selected 
    15307 
    15308 > select add #23.8
    15309 
    15310 8 models selected 
    15311 
    15312 > select subtract #23.8
    15313 
    15314 7 models selected 
    15315 
    15316 > select add #23.15
    15317 
    15318 8 models selected 
    15319 
    15320 > select add #23.19
    15321 
    15322 9 models selected 
    15323 Grouped 9 regions 
    15324 
    15325 > select clear
    15326 
    15327 > select #23.9
    15328 
    15329 1 model selected 
    15330 
    15331 > select clear
    15332 
    15333 > select #23.13
    15334 
    15335 1 model selected 
    15336 
    15337 > select add #23.14
    15338 
    15339 2 models selected 
    15340 
    15341 > select add #23.16
    15342 
    15343 3 models selected 
    15344 Ungrouped to 8 regions 
    15345 Ungrouped to 15 regions 
    15346 Ungrouped to 6 regions 
    15347 Ungrouped to 0 regions 
    15348 
    15349 > select #23.32
    15350 
    15351 1 model selected 
    15352 
    15353 > select add #23.41
    15354 
    15355 2 models selected 
    15356 
    15357 > select add #23.11
    15358 
    15359 3 models selected 
    15360 
    15361 > select add #23.54
    15362 
    15363 4 models selected 
    15364 
    15365 > select add #23.19
    15366 
    15367 5 models selected 
    15368 
    15369 > select add #23.18
    15370 
    15371 6 models selected 
    15372 
    15373 > select add #23.20
    15374 
    15375 7 models selected 
    15376 
    15377 > select subtract #23.20
    15378 
    15379 6 models selected 
    15380 Grouped 6 regions 
    15381 
    15382 > select add #23.59
    15383 
    15384 2 models selected 
    15385 
    15386 > select add #23.58
    15387 
    15388 3 models selected 
    15389 
    15390 > select add #23.63
    15391 
    15392 4 models selected 
    15393 
    15394 > select add #23.62
    15395 
    15396 5 models selected 
    15397 Grouped 5 regions 
    15398 
    15399 > select #23.17
    15400 
    15401 1 model selected 
    15402 
    15403 > select add #23.15
    15404 
    15405 2 models selected 
    15406 
    15407 > select add #23.13
    15408 
    15409 3 models selected 
    15410 
    15411 > select add #23.57
    15412 
    15413 4 models selected 
    15414 
    15415 > select add #23.56
    15416 
    15417 5 models selected 
    15418 Grouped 5 regions 
    15419 
    15420 > select add #23.11
    15421 
    15422 2 models selected 
    15423 Grouped 2 regions 
    15424 Showing 48 region surfaces 
    15425 
    15426 > select add #23.9
    15427 
    15428 2 models selected 
    15429 Grouped 2 regions 
    15430 
    15431 > select add #23.23
    15432 
    15433 2 models selected 
    15434 
    15435 > select add #23.36
    15436 
    15437 3 models selected 
    15438 
    15439 > select add #23.28
    15440 
    15441 4 models selected 
    15442 
    15443 > select add #23.40
    15444 
    15445 5 models selected 
    15446 
    15447 > select add #23.33
    15448 
    15449 6 models selected 
    15450 
    15451 > select add #23.31
    15452 
    15453 7 models selected 
    15454 Grouped 7 regions 
    15455 
    15456 > select add #23.20
    15457 
    15458 2 models selected 
    15459 
    15460 > select clear
    15461 
    15462 > select #23.20
    15463 
    15464 1 model selected 
    15465 Ungrouped to 2 regions 
    15466 Ungrouped to 5 regions 
    15467 Ungrouped to 0 regions 
    15468 
    15469 > select #23.9
    15470 
    15471 1 model selected 
    15472 
    15473 > select add #23.15
    15474 
    15475 2 models selected 
    15476 
    15477 > select add #23.18
    15478 
    15479 3 models selected 
    15480 
    15481 > select add #23.19
    15482 
    15483 4 models selected 
    15484 
    15485 > select add #23.20
    15486 
    15487 5 models selected 
    15488 
    15489 > select add #23.29
    15490 
    15491 6 models selected 
    15492 Grouped 6 regions 
    15493 
    15494 > select #23.1
    15495 
    15496 1 model selected 
    15497 Grouped 1 regions 
    15498 Showing 40 region surfaces 
    15499 
    15500 > select clear
    15501 
    15502 > select #23.9
    15503 
    15504 1 model selected 
    15505 
    15506 > select add #23.22
    15507 
    15508 2 models selected 
    15509 
    15510 > select add #23.39
    15511 
    15512 3 models selected 
    15513 
    15514 > select add #23.38
    15515 
    15516 4 models selected 
    15517 
    15518 > select add #23.37
    15519 
    15520 5 models selected 
    15521 
    15522 > select add #23.25
    15523 
    15524 6 models selected 
    15525 
    15526 > select add #23.43
    15527 
    15528 7 models selected 
    15529 
    15530 > select add #23.49
    15531 
    15532 8 models selected 
    15533 
    15534 > select add #23.42
    15535 
    15536 9 models selected 
    15537 
    15538 > select add #23.34
    15539 
    15540 10 models selected 
    15541 
    15542 > select add #23.24
    15543 
    15544 11 models selected 
    15545 
    15546 > select add #23.35
    15547 
    15548 12 models selected 
    15549 Grouped 12 regions 
    15550 
    15551 > select clear
    15552 
    15553 > select #23.9
    15554 
    15555 1 model selected 
    15556 Opened 3Xunits_imasked_imasked as #25, grid size 240,240,240, pixel 2.1, shown
    15557 at step 1, values float32 
    15558 Segmenting 3Xunits_imasked_imasked, density threshold 0.037925 
    15559 Showing 22 region surfaces 
    15560 491 watershed regions, grouped to 22 regions 
    15561 Showing 3Xunits_imasked_imasked.seg - 22 regions, 22 surfaces 
    15562 
    15563 The cached device pixel ratio value was stale on window expose. Please file a
    15564 QTBUG which explains how to reproduce. 
    15565 
    15566 > save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    15567 > from_June2024/July_2024/Final-version_model/Flo_PflA_Local/3xOnly-PflAB.mrc
    15568 > models #25
    15569 
    15570 > select #23.8
    15571 
    15572 1 model selected 
    15573 
    15574 > select add #23.3
    15575 
    15576 2 models selected 
    15577 
    15578 > select add #23.5
    15579 
    15580 3 models selected 
    15581 
    15582 > select add #23.17
    15583 
    15584 4 models selected 
    15585 
    15586 > select clear
    15587 
    15588 > select #23.3
    15589 
    15590 1 model selected 
    15591 Ungrouped to 2 regions 
    15592 
    15593 > select clear
    15594 
    15595 > select #23.24
    15596 
    15597 1 model selected 
    15598 
    15599 > select add #23.8
    15600 
    15601 2 models selected 
    15602 
    15603 > select add #23.23
    15604 
    15605 3 models selected 
    15606 
    15607 > select add #23.5
    15608 
    15609 4 models selected 
    15610 
    15611 > select add #23.17
    15612 
    15613 5 models selected 
    15614 
    15615 > select add #23.18
    15616 
    15617 6 models selected 
    15618 
    15619 > select add #23.14
    15620 
    15621 7 models selected 
    15622 
    15623 > select add #23.6
    15624 
    15625 8 models selected 
    15626 
    15627 > select add #23.7
    15628 
    15629 9 models selected 
    15630 
    15631 > hide #!25 models
    15632 
    15633 > select add #23.13
    15634 
    15635 10 models selected 
    15636 
    15637 > select add #23.12
    15638 
    15639 11 models selected 
    15640 
    15641 > select add #23.15
    15642 
    15643 12 models selected 
    15644 Grouped 12 regions 
    15645 
    15646 > select clear
    15647 
    15648 > select #23.3
    15649 
    15650 1 model selected 
    15651 
    15652 > select clear
    15653 
    15654 > select #23.2
    15655 
    15656 1 model selected 
    15657 
    15658 > select clear
    15659 
    15660 > select #23.2
    15661 
    15662 1 model selected 
    15663 Ungrouped to 3 regions 
    15664 Ungrouped to 8 regions 
    15665 Ungrouped to 3 regions 
    15666 Ungrouped to 0 regions 
    15667 
    15668 > select #23.8
    15669 
    15670 1 model selected 
    15671 
    15672 > select add #23.2
    15673 
    15674 2 models selected 
    15675 
    15676 > select add #23.5
    15677 
    15678 3 models selected 
    15679 Grouped 3 regions 
    15680 Showing 19 region surfaces 
    15681 
    15682 > select clear
    15683 
    15684 > select #23.2
    15685 
    15686 1 model selected 
    15687 
    15688 > select clear
    15689 
    15690 > select #23.2
    15691 
    15692 1 model selected 
    15693 Opened 3xOnly-PflAB_imasked as #26, grid size 240,240,240, pixel 2.1, shown at
    15694 step 1, values float32 
    15695 
    15696 > hide #!23 models
    15697 
    15698 > select add #23
    15699 
    15700 20 models selected 
    15701 
    15702 > select subtract #23
    15703 
    15704 Nothing selected 
    15705 
    15706 > hide #!26 models
    15707 
    15708 > show #!26 models
    15709 
    15710 The cached device pixel ratio value was stale on window expose. Please file a
    15711 QTBUG which explains how to reproduce. 
    15712 
    15713 > save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    15714 > from_June2024/July_2024/Final-version_model/Flo_PflA_Local/3xOnly-PflAB.mrc
    15715 > models #26
    15716 
    15717 Segmenting 3xOnly-PflAB.mrc, density threshold 0.037925 
    15718 Showing 22 region surfaces 
    15719 488 watershed regions, grouped to 22 regions 
    15720 Showing 3xOnly-PflAB.seg - 22 regions, 22 surfaces 
    15721 
    15722 > select #23.8
    15723 
    15724 1 model selected 
    15725 
    15726 > select add #23.2
    15727 
    15728 2 models selected 
    15729 
    15730 > select add #23.4
    15731 
    15732 3 models selected 
    15733 
    15734 > select add #23.17
    15735 
    15736 4 models selected 
    15737 
    15738 > select add #23.18
    15739 
    15740 5 models selected 
    15741 
    15742 > select add #23.14
    15743 
    15744 6 models selected 
    15745 
    15746 > select add #23.6
    15747 
    15748 7 models selected 
    15749 
    15750 > select add #23.13
    15751 
    15752 8 models selected 
    15753 
    15754 > select add #23.7
    15755 
    15756 9 models selected 
    15757 
    15758 > select add #23.15
    15759 
    15760 10 models selected 
    15761 
    15762 > select add #23.12
    15763 
    15764 11 models selected 
    15765 
    15766 > hide #!26 models
    15767 
    15768 Grouped 11 regions 
    15769 
    15770 > select clear
    15771 
    15772 > select #23.20
    15773 
    15774 1 model selected 
    15775 
    15776 > select add #23.2
    15777 
    15778 2 models selected 
    15779 Grouped 2 regions 
    15780 
    15781 > select clear
    15782 
    15783 > select add #23.21
    15784 
    15785 1 model selected 
    15786 
    15787 > select add #23.22
    15788 
    15789 2 models selected 
    15790 
    15791 > select add #15.2/BJ:459@CD
    15792 
    15793 1 atom, 1 residue, 3 models selected 
    15794 
    15795 > select clear
    15796 
    15797 > select #23.21
    15798 
    15799 1 model selected 
    15800 
    15801 > select add #23.22
    15802 
    15803 2 models selected 
    15804 
    15805 > select add #23.2
    15806 
    15807 3 models selected 
    15808 
    15809 > hide #!15 models
    15810 
    15811 Grouped 3 regions 
    15812 
    15813 > select clear
    15814 
    15815 > select #23.11
    15816 
    15817 1 model selected 
    15818 
    15819 > select add #23.10
    15820 
    15821 2 models selected 
    15822 Ungrouped to 4 regions 
    15823 Ungrouped to 11 regions 
    15824 Ungrouped to 68 regions 
    15825 Ungrouped to 29 regions 
    15826 
    15827 > select clear
    15828 
    15829 [Repeated 1 time(s)]Drag select of 608, 23 of 125476 triangles, 211, 15 of 56
    15830 triangles, 79, 140 of 148 triangles, 77, 104, 72, 58 of 80 triangles, 163, 69
    15831 of 132 triangles, 80, 13 of 56 triangles, 78, 105, 81, 26 of 56 triangles,
    15832 103, 191, 147, 10 of 56 triangles, 227, 48 of 56 triangles, 128, 179, 138 of
    15833 156 triangles, 193, 212, 28 of 56 triangles, 226, 18 of 120 triangles 
    15834 
    15835 > select add #23.103
    15836 
    15837 21 models selected 
    15838 
    15839 > select clear
    15840 
    15841 > select add #23.92
    15842 
    15843 1 model selected 
    15844 
    15845 > select add #23.93
    15846 
    15847 2 models selected 
    15848 
    15849 > select add #23.42
    15850 
    15851 3 models selected 
    15852 
    15853 > select add #23.44
    15854 
    15855 4 models selected 
    15856 
    15857 > select add #23.88
    15858 
    15859 5 models selected 
    15860 
    15861 > select add #23.40
    15862 
    15863 6 models selected 
    15864 
    15865 > select add #23.21
    15866 
    15867 7 models selected 
    15868 
    15869 > select add #23.91
    15870 
    15871 8 models selected 
    15872 
    15873 > select add #23.22
    15874 
    15875 9 models selected 
    15876 
    15877 > select add #23.87
    15878 
    15879 10 models selected 
    15880 
    15881 > select add #23.100
    15882 
    15883 11 models selected 
    15884 
    15885 > select add #23.9
    15886 
    15887 12 models selected 
    15888 
    15889 > select subtract #23.9
    15890 
    15891 11 models selected 
    15892 
    15893 > select add #23.101
    15894 
    15895 12 models selected 
    15896 
    15897 > select add #23.54
    15898 
    15899 13 models selected 
    15900 
    15901 > select add #23.62
    15902 
    15903 14 models selected 
    15904 
    15905 > select add #23.68
    15906 
    15907 15 models selected 
    15908 
    15909 > select add #23.96
    15910 
    15911 16 models selected 
    15912 
    15913 > select add #23.107
    15914 
    15915 17 models selected 
    15916 
    15917 > select add #23.67
    15918 
    15919 18 models selected 
    15920 
    15921 > select add #23.66
    15922 
    15923 19 models selected 
    15924 
    15925 > select add #23.108
    15926 
    15927 20 models selected 
    15928 
    15929 > select add #23.99
    15930 
    15931 21 models selected 
    15932 
    15933 > select add #23.104
    15934 
    15935 22 models selected 
    15936 
    15937 > select add #23.97
    15938 
    15939 23 models selected 
    15940 
    15941 > select add #23.60
    15942 
    15943 24 models selected 
    15944 
    15945 > select add #23.78
    15946 
    15947 25 models selected 
    15948 
    15949 > select add #23.49
    15950 
    15951 26 models selected 
    15952 
    15953 > select add #23.79
    15954 
    15955 27 models selected 
    15956 
    15957 > select add #23.105
    15958 
    15959 28 models selected 
    15960 
    15961 > select add #23.109
    15962 
    15963 29 models selected 
    15964 
    15965 > select add #23.89
    15966 
    15967 30 models selected 
    15968 
    15969 > select add #23.20
    15970 
    15971 31 models selected 
    15972 
    15973 > select add #23.58
    15974 
    15975 32 models selected 
    15976 
    15977 > select add #23.102
    15978 
    15979 33 models selected 
    15980 
    15981 > select add #23.51
    15982 
    15983 34 models selected 
    15984 
    15985 > select subtract #23.42
    15986 
    15987 33 models selected 
    15988 
    15989 > select add #23.19
    15990 
    15991 34 models selected 
    15992 Grouped 34 regions 
    15993 
    15994 > select add #23.2
    15995 
    15996 2 models selected 
    15997 Grouped 2 regions 
    15998 Drag select of 244, 44 of 56 triangles, 84, 131 of 160 triangles, 195, 108,
    15999 243, 17 of 56 triangles, 192, 148, 228, 11 of 56 triangles, 229, 194, 19 of 56
    16000 triangles, 129, 164, 22 of 56 triangles, 151, 88 of 112 triangles, 211, 32 of
    16001 56 triangles, 106, 130, 196, 150, 133, 162, 41 of 56 triangles, 181, 107, 109
    16002 of 172 triangles, 80, 54 of 56 triangles, 103, 147 
    16003 Grouped 26 regions 
    16004 Drag select of 201, 134, 156, 37 of 56 triangles, 169 
    16005 
    16006 > select add #23.1
    16007 
    16008 6 models selected 
    16009 
    16010 > select subtract #23.1
    16011 
    16012 5 models selected 
    16013 
    16014 > select add #23.59
    16015 
    16016 6 models selected 
    16017 
    16018 > select add #23.61
    16019 
    16020 7 models selected 
    16021 
    16022 > select add #23.63
    16023 
    16024 8 models selected 
    16025 
    16026 > select add #23.64
    16027 
    16028 9 models selected 
    16029 
    16030 > select add #23.106
    16031 
    16032 10 models selected 
    16033 
    16034 > select add #23.95
    16035 
    16036 11 models selected 
    16037 
    16038 > select add #23.32
    16039 
    16040 12 models selected 
    16041 
    16042 > select add #23.39
    16043 
    16044 13 models selected 
    16045 
    16046 > select add #23.33
    16047 
    16048 14 models selected 
    16049 
    16050 > select add #23.27
    16051 
    16052 15 models selected 
    16053 
    16054 > select add #23.31
    16055 
    16056 16 models selected 
    16057 Grouped 16 regions 
    16058 
    16059 > select add #23.82
    16060 
    16061 2 models selected 
    16062 
    16063 > select add #23.29
    16064 
    16065 3 models selected 
    16066 
    16067 > select add #23.30
    16068 
    16069 4 models selected 
    16070 
    16071 > select add #23.34
    16072 
    16073 5 models selected 
    16074 
    16075 > select add #23.23
    16076 
    16077 6 models selected 
    16078 
    16079 > select add #23.8
    16080 
    16081 7 models selected 
    16082 
    16083 > select add #23.28
    16084 
    16085 8 models selected 
    16086 
    16087 > select add #23.7
    16088 
    16089 9 models selected 
    16090 
    16091 > select add #23.4
    16092 
    16093 10 models selected 
    16094 
    16095 > select add #23.35
    16096 
    16097 11 models selected 
    16098 
    16099 > select add #23.81
    16100 
    16101 12 models selected 
    16102 Grouped 12 regions 
    16103 
    16104 > select add #23.25
    16105 
    16106 2 models selected 
    16107 Grouped 2 regions 
    16108 Opened 3xOnly-PflAB_imasked as #27, grid size 240,240,240, pixel 2.1, shown at
    16109 step 1, values float32 
    16110 
    16111 The cached device pixel ratio value was stale on window expose. Please file a
    16112 QTBUG which explains how to reproduce. 
    16113 
    16114 > save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    16115 > from_June2024/July_2024/Final-version_model/Flo_PflA_Local/1xOnly-PflAB.mrc
    16116 > models #27
    16117 
    16118 > close #23
    16119 
    16120 > show #!26 models
    16121 
    16122 > hide #!27 models
    16123 
    16124 > hide #!26 models
    16125 
    16126 > show #!27 models
    16127 
    16128 > show #!17 models
    16129 
    16130 > hide #!17 models
    16131 
    16132 > show #!15 models
    16133 
    16134 > select add #15
    16135 
    16136 38799 atoms, 39588 bonds, 4776 residues, 10 models selected 
    16137 Alignment identifier is 1 
    16138 Alignment identifier is 2 
    16139 Alignment identifier is 3 
    16140 
    16141 > select #15.4/Ch:1-2 #15.6/Cj:1-2 #15.8/Cl:1-2
    16142 
    16143 48 atoms, 45 bonds, 6 residues, 3 models selected 
    16144 
    16145 > select #15.4/Ch:1-107 #15.6/Cj:1-107 #15.8/Cl:1-107
    16146 
    16147 2523 atoms, 2544 bonds, 321 residues, 3 models selected 
    16148 2 [ID: 2] region chains Ch,Cj,Cl [1-107] RMSD: 183.500 
    16149  
    16150 
    16151 > select #15.4/Ch:121-122 #15.6/Cj:121-122 #15.8/Cl:121-122
    16152 
    16153 51 atoms, 48 bonds, 6 residues, 3 models selected 
    16154 
    16155 > select #15.4/Ch:1-122 #15.6/Cj:1-122 #15.8/Cl:1-122
    16156 
    16157 2859 atoms, 2880 bonds, 366 residues, 3 models selected 
    16158 2 [ID: 2] region chains Ch,Cj,Cl [1-122] RMSD: 179.940 
    16159  
    16160 
    16161 > select #15.4/Ch:135 #15.6/Cj:135 #15.8/Cl:135
    16162 
    16163 24 atoms, 21 bonds, 3 residues, 3 models selected 
    16164 
    16165 > select #15.4/Ch:1-135 #15.6/Cj:1-135 #15.8/Cl:1-135
    16166 
    16167 3153 atoms, 3177 bonds, 405 residues, 3 models selected 
    16168 2 [ID: 2] region chains Ch,Cj,Cl [1-135] RMSD: 178.301 
    16169  
    16170 
    16171 > hide sel & #!15.4,6 surfaces
    16172 
    16173 > hide sel & #!15.4,6 cartoons
    16174 
    16175 > view orient
    16176 
    16177 > save /Users/shoichi/Desktop/HP-Fig4C2_09172024.png supersample 2
    16178 > transparentBackground true
    16179 
    16180 > show #15.1 models
    16181 
    16182 > show #15.3 models
    16183 
    16184 > show #15.5 models
    16185 
    16186 > show #15.8 models
    16187 
    16188 > show #15.9 models
    16189 
    16190 > show #!26 models
    16191 
    16192 > combine #15 modelId #28 name 3xPflAB
    16193 
    16194 > select add #15
    16195 
    16196 38799 atoms, 39588 bonds, 4776 residues, 12 models selected 
    16197 
    16198 > select subtract #15
    16199 
    16200 4 models selected 
    16201 
    16202 > hide #!15 models
    16203 
    16204 > ui tool show "Fit in Map"
    16205 
    16206 The cached device pixel ratio value was stale on window expose. Please file a
    16207 QTBUG which explains how to reproduce. 
    16208 
    16209 [Repeated 1 time(s)]
    16210 
    16211 > fitmap #28 inMap #26
    16212 
    16213 Fit molecule 3xPflAB (#28) to map 3xOnly-PflAB.mrc (#26) using 38799 atoms 
    16214 average map value = 1.878, steps = 48 
    16215 shifted from previous position = 1.88 
    16216 rotated from previous position = 1.35 degrees 
    16217 atoms outside contour = 18849, contour level = 0.037925 
    16218  
    16219 Position of 3xPflAB (#28) relative to 3xOnly-PflAB.mrc (#26) coordinates: 
    16220 Matrix rotation and translation 
    16221 0.99197492 0.04194380 0.11927478 -7.25388896 
    16222 -0.00861248 0.96359505 -0.26722724 -10.03562167 
    16223 -0.12614112 0.26405547 0.95622337 -12.21729786 
    16224 Axis 0.90445517 0.41779579 -0.08606696 
    16225 Axis point 0.00000000 44.70924253 -28.47666633 
    16226 Rotation angle (degrees) 17.07979035 
    16227 Shift along axis -9.70215212 
    16228  
    16229 
    16230 > fitmap #28 inMap #26
    16231 
    16232 Fit molecule 3xPflAB (#28) to map 3xOnly-PflAB.mrc (#26) using 38799 atoms 
    16233 average map value = 1.878, steps = 60 
    16234 shifted from previous position = 0.0218 
    16235 rotated from previous position = 0.00175 degrees 
    16236 atoms outside contour = 18848, contour level = 0.037925 
    16237  
    16238 Position of 3xPflAB (#28) relative to 3xOnly-PflAB.mrc (#26) coordinates: 
    16239 Matrix rotation and translation 
    16240 0.99197770 0.04194422 0.11925151 -7.27068129 
    16241 -0.00862150 0.96359995 -0.26720930 -10.02121140 
    16242 -0.12611863 0.26403754 0.95623129 -12.21052200 
    16243 Axis 0.90447225 0.41775398 -0.08609046 
    16244 Axis point 0.00000000 44.70236205 -28.41007722 
    16245 Rotation angle (degrees) 17.07826916 
    16246 Shift along axis -9.71132087 
    16247  
    16248 
    16249 > fitmap #28 inMap #26
    16250 
    16251 Fit molecule 3xPflAB (#28) to map 3xOnly-PflAB.mrc (#26) using 38799 atoms 
    16252 average map value = 1.878, steps = 40 
    16253 shifted from previous position = 0.00987 
    16254 rotated from previous position = 0.00587 degrees 
    16255 atoms outside contour = 18849, contour level = 0.037925 
    16256  
    16257 Position of 3xPflAB (#28) relative to 3xOnly-PflAB.mrc (#26) coordinates: 
    16258 Matrix rotation and translation 
    16259 0.99196661 0.04194146 0.11934472 -7.27163799 
    16260 -0.00858908 0.96359028 -0.26724522 -10.02508686 
    16261 -0.12620806 0.26407327 0.95620962 -12.20228003 
    16262 Axis 0.90438160 0.41796667 -0.08601034 
    16263 Axis point 0.00000000 44.66325190 -28.40049253 
    16264 Rotation angle (degrees) 17.08240812 
    16265 Shift along axis -9.71696549 
    16266  
    16267 
    16268 > split #28
    16269 
    16270 Split 3xPflAB (#28) into 9 models 
    16271 Chain information for 3xPflAB Az #28.1 
    16272 --- 
    16273 Chain | Description 
    16274 Az | No description available 
    16275  
    16276 Chain information for 3xPflAB BJ #28.2 
    16277 --- 
    16278 Chain | Description 
    16279 BJ | No description available 
    16280  
    16281 Chain information for 3xPflAB BL #28.3 
    16282 --- 
    16283 Chain | Description 
    16284 BL | No description available 
    16285  
    16286 Chain information for 3xPflAB Ch #28.4 
    16287 --- 
    16288 Chain | Description 
    16289 Ch | No description available 
    16290  
    16291 Chain information for 3xPflAB Ci #28.5 
    16292 --- 
    16293 Chain | Description 
    16294 Ci | No description available 
    16295  
    16296 Chain information for 3xPflAB Cj #28.6 
    16297 --- 
    16298 Chain | Description 
    16299 Cj | No description available 
    16300  
    16301 Chain information for 3xPflAB Ck #28.7 
    16302 --- 
    16303 Chain | Description 
    16304 Ck | No description available 
    16305  
    16306 Chain information for 3xPflAB Cl #28.8 
    16307 --- 
    16308 Chain | Description 
    16309 Cl | No description available 
    16310  
    16311 Chain information for 3xPflAB Cm #28.9 
    16312 --- 
    16313 Chain | Description 
    16314 Cm | No description available 
    16315  
    16316 
    16317 > hide #28.1 models
    16318 
    16319 > hide #28.2 models
    16320 
    16321 > show #28.2 models
    16322 
    16323 > hide #28.3 models
    16324 
    16325 > hide #28.5 models
    16326 
    16327 > hide #28.8 models
    16328 
    16329 > hide #28.9 models
    16330 
    16331 > select add #28
    16332 
    16333 38799 atoms, 39588 bonds, 4776 residues, 10 models selected 
    16334 
    16335 > select subtract #28
    16336 
    16337 Nothing selected 
    16338 
    16339 > select add #28.2
    16340 
    16341 4995 atoms, 5088 bonds, 612 residues, 1 model selected 
    16342 
    16343 > select add #28.4
    16344 
    16345 11824 atoms, 12060 bonds, 1455 residues, 2 models selected 
    16346 
    16347 > select add #28.6
    16348 
    16349 18653 atoms, 19032 bonds, 2298 residues, 3 models selected 
    16350 
    16351 > select add #28.7
    16352 
    16353 19762 atoms, 20168 bonds, 2435 residues, 4 models selected 
    16354 
    16355 > hide sel cartoons
    16356 
    16357 > show sel surfaces
    16358 
    16359 > select add #27
    16360 
    16361 19762 atoms, 20168 bonds, 2435 residues, 10 models selected 
    16362 
    16363 > select add #28
    16364 
    16365 38799 atoms, 39588 bonds, 4776 residues, 16 models selected 
    16366 
    16367 > select subtract #27
    16368 
    16369 38799 atoms, 39588 bonds, 4776 residues, 14 models selected 
    16370 Alignment identifier is 1 
    16371 Alignment identifier is 2 
    16372 Alignment identifier is 3 
    16373 
    16374 > select #28.4/Ch:1-2 #28.6/Cj:1-2 #28.8/Cl:1-2
    16375 
    16376 48 atoms, 45 bonds, 6 residues, 3 models selected 
    16377 
    16378 > select #28.4/Ch:1-135 #28.6/Cj:1-135 #28.8/Cl:1-135
    16379 
    16380 3153 atoms, 3177 bonds, 405 residues, 3 models selected 
    16381 2 [ID: 2] region chains Ch,Cj,Cl [1-135] RMSD: 178.301 
    16382  
    16383 
    16384 > hide sel & #!28.4,6 surfaces
    16385 
    16386 > hide #!26 models
    16387 
    16388 > view orient
    16389 
    16390 > save /Users/shoichi/Desktop/HP-Fig4C2_09172024.png supersample 2
    16391 > transparentBackground true
    16392 
    16393 > select add #28.4
    16394 
    16395 8931 atoms, 9090 bonds, 1113 residues, 5 models selected 
    16396 
    16397 > select add #28.6
    16398 
    16399 14709 atoms, 15003 bonds, 1821 residues, 5 models selected 
    16400 
    16401 > select add #28.8
    16402 
    16403 20487 atoms, 20916 bonds, 2529 residues, 5 models selected 
    16404 
    16405 > select subtract #28.8
    16406 
    16407 13658 atoms, 13944 bonds, 1686 residues, 4 models selected 
    16408 
    16409 > select add #28.7
    16410 
    16411 14767 atoms, 15080 bonds, 1823 residues, 5 models selected 
    16412 
    16413 > select add #28.2
    16414 
    16415 19762 atoms, 20168 bonds, 2435 residues, 7 models selected 
    16416 
    16417 > hide sel surfaces
    16418 
    16419 > show sel cartoons
    16420 
    16421 > select add #28
    16422 
    16423 38799 atoms, 39588 bonds, 4776 residues, 14 models selected 
    16424 
    16425 > select subtract #28
    16426 
    16427 4 models selected 
    16428 
    16429 > select add #28.2
    16430 
    16431 4995 atoms, 5088 bonds, 612 residues, 1 model selected 
    16432 
    16433 > select add #28.4
    16434 
    16435 11824 atoms, 12060 bonds, 1455 residues, 3 models selected 
    16436 
    16437 > select add #28.6
    16438 
    16439 18653 atoms, 19032 bonds, 2298 residues, 5 models selected 
    16440 
    16441 > select add #28.7
    16442 
    16443 19762 atoms, 20168 bonds, 2435 residues, 7 models selected 
    16444 
    16445 The cached device pixel ratio value was stale on window expose. Please file a
    16446 QTBUG which explains how to reproduce. 
    16447 
    16448 > save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    16449 > from_June2024/July_2024/Final-version_model/Flo_PflA_Local/1X_PflAB-
    16450 > Sep18-2024.pdb selectedOnly true
    16451 
    16452 > select add #28
    16453 
    16454 38799 atoms, 39588 bonds, 4776 residues, 14 models selected 
    16455 
    16456 > select subtract #28
    16457 
    16458 4 models selected 
    16459 
    16460 > hide #!28 models
    16461 
    16462 > open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    16463 > from_June2024/July_2024/Final-version_model/Flo_PflA_Local/1X_PflAB-
    16464 > Sep18-2024.pdb
    16465 
    16466 Chain information for 1X_PflAB-Sep18-2024.pdb 
    16467 --- 
    16468 Chain | Description 
    16469 23.1/BJ | No description available 
    16470 23.2/Ch 23.3/Cj | No description available 
    16471 23.4/Ck | No description available 
    16472  
    16473 
    16474 > combine #23 modelId #29 name 1xPflAB-Sep18-2024
    16475 
    16476 > show #!28 models
    16477 
    16478 > hide #!28 models
    16479 
    16480 > show #!26 models
    16481 
    16482 > view orient
    16483 
    16484 > sym #29 C18 copies true center #29
    16485 
    16486 Made 18 copies for 1xPflAB-Sep18-2024 symmetry C18 
    16487 
    16488 > close #30
    16489 
    16490 > show #!3 models
    16491 
    16492 > hide #!3 models
    16493 
    16494 > show #!2 models
    16495 
    16496 > hide #!2 models
    16497 
    16498 > show #!1 models
    16499 
    16500 > ui tool show "Segment Map"
    16501 
    16502 Segmenting PflA-2.1A-230911.mrc, density threshold 0.184695 
    16503 Showing 295 region surfaces 
    16504 3349 watershed regions, grouped to 295 regions 
    16505 Showing PflA-2.1A-230911.seg - 295 regions, 295 surfaces 
    16506 
    16507 > hide #!1 models
    16508 
    16509 > select #30.16
    16510 
    16511 1 model selected 
    16512 
    16513 > select add #30.145
    16514 
    16515 2 models selected 
    16516 
    16517 > select add #30.256
    16518 
    16519 3 models selected 
    16520 Grouped 3 regions 
    16521 Opened PflA-2.1A-230911_imasked as #31, grid size 240,240,240, pixel 2.1,
    16522 shown at step 1, values float32 
    16523 
    16524 The cached device pixel ratio value was stale on window expose. Please file a
    16525 QTBUG which explains how to reproduce. 
    16526 
    16527 > save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    16528 > from_June2024/July_2024/Final-version_model/Flo_PflA_Local/Rod.mrc models
    16529 > #31
    16530 
    16531 > close #30
    16532 
    16533 > view orient
    16534 
    16535 > sym #29 C18 copies true center #31
    16536 
    16537 Made 18 copies for 1xPflAB-Sep18-2024 symmetry C18 
    16538 
    16539 > show #29 models
    16540 
    16541 > hide #!30 models
    16542 
    16543 > show #!30 models
    16544 
    16545 > hide #30.2 models
    16546 
    16547 > show #30.2 models
    16548 
    16549 > hide #30.1 models
    16550 
    16551 > hide #30.3 models
    16552 
    16553 > hide #30.4 models
    16554 
    16555 > hide #30.5 models
    16556 
    16557 > hide #30.6 models
    16558 
    16559 > hide #30.7 models
    16560 
    16561 > hide #30.8 models
    16562 
    16563 > hide #30.9 models
    16564 
    16565 > hide #30.10 models
    16566 
    16567 > hide #30.11 models
    16568 
    16569 > hide #30.12 models
    16570 
    16571 > hide #30.13 models
    16572 
    16573 > hide #30.14 models
    16574 
    16575 > hide #30.15 models
    16576 
    16577 > hide #30.16 models
    16578 
    16579 > hide #30.17 models
    16580 
    16581 > select add #30.2
    16582 
    16583 19762 atoms, 20168 bonds, 2435 residues, 1 model selected 
    16584 
    16585 > ui mousemode right "rotate selected models"
    16586 
    16587 > view matrix models
    16588 > #30.2,0.90121,-0.43338,0,-9.7896,0.43338,0.90121,0,76.344,0,0,1,0
    16589 
    16590 > ui mousemode right "translate selected models"
    16591 
    16592 > view matrix models
    16593 > #30.2,0.90121,-0.43338,0,-8.5295,0.43338,0.90121,0,88.133,0,0,1,0
    16594 
    16595 > select subtract #30.2
    16596 
    16597 Nothing selected 
    16598 
    16599 > hide #30.2 models
    16600 
    16601 > show #30.2 models
    16602 
    16603 > hide #30.2 models
    16604 
    16605 > show #30.2 models
    16606 
    16607 > select add #30.2
    16608 
    16609 19762 atoms, 20168 bonds, 2435 residues, 1 model selected 
    16610 
    16611 > save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    16612 > from_June2024/July_2024/Final-version_model/Flo_PflA_Local/1xPflAB-P2.pdb
    16613 > selectedOnly true
    16614 
    16615 > hide #!31 models
    16616 
    16617 > select subtract #30.2
    16618 
    16619 Nothing selected 
    16620 
    16621 > hide #30.2 models
    16622 
    16623 > select add #30.18
    16624 
    16625 19762 atoms, 20168 bonds, 2435 residues, 1 model selected 
    16626 
    16627 > save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    16628 > from_June2024/July_2024/Final-version_model/Flo_PflA_Local/1xPflAB-P3.pdb
    16629 > selectedOnly true
    16630 
    16631 > open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    16632 > from_June2024/July_2024/Final-version_model/Flo_PflA_Local/1xPflAB-P2.pdb
    16633 
    16634 Summary of feedback from opening /Volumes/Backup-95/Chimera-2023/PflB-PflA-
    16635 project/Start-from_June2024/July_2024/Final-
    16636 version_model/Flo_PflA_Local/1xPflAB-P2.pdb 
    16637 --- 
    16638 warnings | Start residue of secondary structure not found: HELIX 1 1 TYRA0 183 ASPA0 196 1 14 
    16639 Start residue of secondary structure not found: HELIX 2 2 TYRA0 200 ASNA0 213
    16640 1 14 
    16641 Start residue of secondary structure not found: HELIX 3 3 LYSA0 220 LEUA0 234
    16642 1 15 
    16643 Start residue of secondary structure not found: HELIX 4 4 LYSA0 238 ASNA0 251
    16644 1 14 
    16645 Start residue of secondary structure not found: HELIX 5 5 ILEA0 258 GLUA0 271
    16646 1 14 
    16647 37 messages similar to the above omitted 
    16648  
    16649 Chain information for 1xPflAB-P2.pdb #32 
    16650 --- 
    16651 Chain | Description 
    16652 BJ | No description available 
    16653 Ch Cj | No description available 
    16654 Ck | No description available 
    16655  
    16656 
    16657 > open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    16658 > from_June2024/July_2024/Final-version_model/Flo_PflA_Local/1xPflAB-P3.pdb
    16659 
    16660 Summary of feedback from opening /Volumes/Backup-95/Chimera-2023/PflB-PflA-
    16661 project/Start-from_June2024/July_2024/Final-
    16662 version_model/Flo_PflA_Local/1xPflAB-P3.pdb 
    16663 --- 
    16664 warnings | Start residue of secondary structure not found: HELIX 1 1 TYRA0 183 ASPA0 196 1 14 
    16665 Start residue of secondary structure not found: HELIX 2 2 TYRA0 200 ASNA0 213
    16666 1 14 
    16667 Start residue of secondary structure not found: HELIX 3 3 LYSA0 220 LEUA0 234
    16668 1 15 
    16669 Start residue of secondary structure not found: HELIX 4 4 LYSA0 238 ASNA0 251
    16670 1 14 
    16671 Start residue of secondary structure not found: HELIX 5 5 ILEA0 258 GLUA0 271
    16672 1 14 
    16673 37 messages similar to the above omitted 
    16674  
    16675 Chain information for 1xPflAB-P3.pdb #33 
    16676 --- 
    16677 Chain | Description 
    16678 BJ | No description available 
    16679 Ch Cj | No description available 
    16680 Ck | No description available 
    16681  
    16682 
    16683 > select add #30
    16684 
    16685 355716 atoms, 363024 bonds, 43830 residues, 19 models selected 
    16686 
    16687 > select subtract #30
    16688 
    16689 Nothing selected 
    16690 
    16691 > hide #!30 models
    16692 
    16693 > hide #!23 models
    16694 
    16695 > hide #!27 models
    16696 
    16697 > fitmap #32 inMap #26
    16698 
    16699 Fit molecule 1xPflAB-P2.pdb (#32) to map 3xOnly-PflAB.mrc (#26) using 19762
    16700 atoms 
    16701 average map value = 1.609, steps = 76 
    16702 shifted from previous position = 4.75 
    16703 rotated from previous position = 5.97 degrees 
    16704 atoms outside contour = 10293, contour level = 0.037925 
    16705  
    16706 Position of 1xPflAB-P2.pdb (#32) relative to 3xOnly-PflAB.mrc (#26)
    16707 coordinates: 
    16708 Matrix rotation and translation 
    16709 0.99473557 0.10193329 0.01052391 -18.34266851 
    16710 -0.10172536 0.99463679 -0.01869760 -0.21008206 
    16711 -0.01237338 0.01752862 0.99976980 -2.55026439 
    16712 Axis 0.17406499 0.11002022 -0.97856882 
    16713 Axis point -10.67948235 178.16616913 0.00000000 
    16714 Rotation angle (degrees) 5.97297980 
    16715 Shift along axis -0.72032053 
    16716  
    16717 
    16718 > fitmap #32 inMap #26
    16719 
    16720 Fit molecule 1xPflAB-P2.pdb (#32) to map 3xOnly-PflAB.mrc (#26) using 19762
    16721 atoms 
    16722 average map value = 1.609, steps = 48 
    16723 shifted from previous position = 0.0247 
    16724 rotated from previous position = 0.0292 degrees 
    16725 atoms outside contour = 10296, contour level = 0.037925 
    16726  
    16727 Position of 1xPflAB-P2.pdb (#32) relative to 3xOnly-PflAB.mrc (#26)
    16728 coordinates: 
    16729 Matrix rotation and translation 
    16730 0.99470505 0.10225763 0.01025897 -18.39976411 
    16731 -0.10205776 0.99460805 -0.01841292 -0.16726036 
    16732 -0.01208652 0.01726842 0.99977783 -2.53376431 
    16733 Axis 0.17104502 0.10711715 -0.97942305 
    16734 Axis point -10.33923583 178.25674648 0.00000000 
    16735 Rotation angle (degrees) 5.98706579 
    16736 Shift along axis -0.68347725 
    16737  
    16738 
    16739 > fitmap #32 inMap #26
    16740 
    16741 Fit molecule 1xPflAB-P2.pdb (#32) to map 3xOnly-PflAB.mrc (#26) using 19762
    16742 atoms 
    16743 average map value = 1.609, steps = 44 
    16744 shifted from previous position = 0.0147 
    16745 rotated from previous position = 0.0133 degrees 
    16746 atoms outside contour = 10294, contour level = 0.037925 
    16747  
    16748 Position of 1xPflAB-P2.pdb (#32) relative to 3xOnly-PflAB.mrc (#26)
    16749 coordinates: 
    16750 Matrix rotation and translation 
    16751 0.99471763 0.10212357 0.01037345 -18.37068452 
    16752 -0.10191993 0.99461944 -0.01856086 -0.19105890 
    16753 -0.01221314 0.01740555 0.99977392 -2.54759165 
    16754 Axis 0.17256978 0.10837229 -0.97901742 
    16755 Axis point -10.53934899 178.16422167 0.00000000 
    16756 Rotation angle (degrees) 5.98155561 
    16757 Shift along axis -0.69679389 
    16758  
    16759 
    16760 > select add #32
    16761 
    16762 19762 atoms, 20168 bonds, 2435 residues, 1 model selected 
    16763 
    16764 > view matrix models
    16765 > #32,0.99472,0.10212,0.010373,-17.328,-0.10192,0.99462,-0.018561,-1.3395,-0.012213,0.017406,0.99977,-2.5476
    16766 
    16767 > fitmap #32 inMap #26
    16768 
    16769 Fit molecule 1xPflAB-P2.pdb (#32) to map 3xOnly-PflAB.mrc (#26) using 19762
    16770 atoms 
    16771 average map value = 1.609, steps = 72 
    16772 shifted from previous position = 1.53 
    16773 rotated from previous position = 0.00799 degrees 
    16774 atoms outside contour = 10291, contour level = 0.037925 
    16775  
    16776 Position of 1xPflAB-P2.pdb (#32) relative to 3xOnly-PflAB.mrc (#26)
    16777 coordinates: 
    16778 Matrix rotation and translation 
    16779 0.99472682 0.10202677 0.01044519 -18.35075180 
    16780 -0.10182104 0.99462828 -0.01862955 -0.21776303 
    16781 -0.01228980 0.01746777 0.99977189 -2.52370286 
    16782 Axis 0.17332496 0.10916437 -0.97879599 
    16783 Axis point -10.74529701 178.05945517 0.00000000 
    16784 Rotation angle (degrees) 5.97715484 
    16785 Shift along axis -0.73422497 
    16786  
    16787 
    16788 > view matrix models
    16789 > #32,0.99473,0.10203,0.010445,-15.954,-0.10182,0.99463,-0.01863,0.054505,-0.01229,0.017468,0.99977,-2.5237
    16790 
    16791 > fitmap #32 inMap #26
    16792 
    16793 Fit molecule 1xPflAB-P2.pdb (#32) to map 3xOnly-PflAB.mrc (#26) using 19762
    16794 atoms 
    16795 average map value = 1.609, steps = 52 
    16796 shifted from previous position = 2.43 
    16797 rotated from previous position = 0.016 degrees 
    16798 atoms outside contour = 10292, contour level = 0.037925 
    16799  
    16800 Position of 1xPflAB-P2.pdb (#32) relative to 3xOnly-PflAB.mrc (#26)
    16801 coordinates: 
    16802 Matrix rotation and translation 
    16803 0.99473661 0.10191776 0.01057617 -18.35162729 
    16804 -0.10170703 0.99463581 -0.01884877 -0.20848970 
    16805 -0.01244046 0.01767389 0.99976641 -2.57228974 
    16806 Axis 0.17546256 0.11057672 -0.97825645 
    16807 Axis point -10.66158881 178.26136266 0.00000000 
    16808 Rotation angle (degrees) 5.97389706 
    16809 Shift along axis -0.72671868 
    16810  
    16811 
    16812 > view matrix models
    16813 > #32,0.99474,0.10192,0.010576,-16.201,-0.10171,0.99464,-0.018849,-2.3657,-0.01244,0.017674,0.99977,-2.5723
    16814 
    16815 > select subtract #32
    16816 
    16817 Nothing selected 
    16818 
    16819 > fitmap #33 inMap #26
    16820 
    16821 Fit molecule 1xPflAB-P3.pdb (#33) to map 3xOnly-PflAB.mrc (#26) using 19762
    16822 atoms 
    16823 average map value = 2.097, steps = 64 
    16824 shifted from previous position = 9.88 
    16825 rotated from previous position = 1.13 degrees 
    16826 atoms outside contour = 9345, contour level = 0.037925 
    16827  
    16828 Position of 1xPflAB-P3.pdb (#33) relative to 3xOnly-PflAB.mrc (#26)
    16829 coordinates: 
    16830 Matrix rotation and translation 
    16831 0.99984804 -0.01417461 0.01014753 -3.52645977 
    16832 0.01408196 0.99985903 0.00914379 -9.84630785 
    16833 -0.01027571 -0.00899950 0.99990670 0.34137374 
    16834 Axis -0.46162681 0.51963656 0.71894265 
    16835 Axis point 575.92914554 -360.58206793 0.00000000 
    16836 Rotation angle (degrees) 1.12601899 
    16837 Shift along axis -3.24316504 
    16838  
    16839 
    16840 > fitmap #33 inMap #26
    16841 
    16842 Fit molecule 1xPflAB-P3.pdb (#33) to map 3xOnly-PflAB.mrc (#26) using 19762
    16843 atoms 
    16844 average map value = 2.097, steps = 24 
    16845 shifted from previous position = 0.00676 
    16846 rotated from previous position = 0.00417 degrees 
    16847 atoms outside contour = 9345, contour level = 0.037925 
    16848  
    16849 Position of 1xPflAB-P3.pdb (#33) relative to 3xOnly-PflAB.mrc (#26)
    16850 coordinates: 
    16851 Matrix rotation and translation 
    16852 0.99984849 -0.01418178 0.01009336 -3.52415361 
    16853 0.01409012 0.99985936 0.00909589 -9.84776388 
    16854 -0.01022093 -0.00895230 0.99990769 0.33633104 
    16855 Axis -0.46025304 0.51804168 0.72097154 
    16856 Axis point 576.30743341 -359.71068987 0.00000000 
    16857 Rotation angle (degrees) 1.12345930 
    16858 Shift along axis -3.23706458 
    16859  
    16860 
    16861 > fitmap #33 inMap #26
    16862 
    16863 Fit molecule 1xPflAB-P3.pdb (#33) to map 3xOnly-PflAB.mrc (#26) using 19762
    16864 atoms 
    16865 average map value = 2.097, steps = 28 
    16866 shifted from previous position = 0.00519 
    16867 rotated from previous position = 0.00508 degrees 
    16868 atoms outside contour = 9343, contour level = 0.037925 
    16869  
    16870 Position of 1xPflAB-P3.pdb (#33) relative to 3xOnly-PflAB.mrc (#26)
    16871 coordinates: 
    16872 Matrix rotation and translation 
    16873 0.99984932 -0.01418343 0.01000828 -3.52396480 
    16874 0.01409227 0.99985910 0.00912103 -9.84536330 
    16875 -0.01013624 -0.00897861 0.99990832 0.32653865 
    16876 Axis -0.46228627 0.51451490 0.72219514 
    16877 Axis point 578.18872638 -358.91993357 0.00000000 
    16878 Rotation angle (degrees) 1.12170651 
    16879 Shift along axis -3.20068097 
    16880  
    16881 
    16882 > select add #33
    16883 
    16884 19762 atoms, 20168 bonds, 2435 residues, 1 model selected 
    16885 
    16886 > ui mousemode right "rotate selected models"
    16887 
    16888 > view matrix models
    16889 > #33,0.99973,0.020993,0.010323,-1.3467,-0.021084,0.99974,0.0087634,-9.5356,-0.010136,-0.0089786,0.99991,0.32654
    16890 
    16891 > ui mousemode right "translate selected models"
    16892 
    16893 > view matrix models
    16894 > #33,0.99973,0.020993,0.010323,0.99315,-0.021084,0.99974,0.0087634,-13.601,-0.010136,-0.0089786,0.99991,0.32654
    16895 
    16896 > view matrix models
    16897 > #33,0.99973,0.020993,0.010323,4.8889,-0.021084,0.99974,0.0087634,-14.985,-0.010136,-0.0089786,0.99991,0.32394
    16898 
    16899 > fitmap #33 inMap #26
    16900 
    16901 Fit molecule 1xPflAB-P3.pdb (#33) to map 3xOnly-PflAB.mrc (#26) using 19762
    16902 atoms 
    16903 average map value = 2.097, steps = 72 
    16904 shifted from previous position = 9.49 
    16905 rotated from previous position = 2.01 degrees 
    16906 atoms outside contour = 9338, contour level = 0.037925 
    16907  
    16908 Position of 1xPflAB-P3.pdb (#33) relative to 3xOnly-PflAB.mrc (#26)
    16909 coordinates: 
    16910 Matrix rotation and translation 
    16911 0.99984739 -0.01410746 0.01030409 -3.54810052 
    16912 0.01401132 0.99985818 0.00934308 -9.84531491 
    16913 -0.01043444 -0.00919728 0.99990326 0.37354334 
    16914 Axis -0.46873867 0.52431284 0.71090091 
    16915 Axis point 577.97851061 -365.18963893 0.00000000 
    16916 Rotation angle (degrees) 1.13320465 
    16917 Shift along axis -3.23334081 
    16918  
    16919 
    16920 > select add #32
    16921 
    16922 39524 atoms, 40336 bonds, 4870 residues, 2 models selected 
    16923 
    16924 > split #32
    16925 
    16926 Split 1xPflAB-P2.pdb (#32) into 4 models 
    16927 Chain information for 1xPflAB-P2.pdb BJ #32.1 
    16928 --- 
    16929 Chain | Description 
    16930 BJ | No description available 
    16931  
    16932 Chain information for 1xPflAB-P2.pdb Ch #32.2 
    16933 --- 
    16934 Chain | Description 
    16935 Ch | No description available 
    16936  
    16937 Chain information for 1xPflAB-P2.pdb Cj #32.3 
    16938 --- 
    16939 Chain | Description 
    16940 Cj | No description available 
    16941  
    16942 Chain information for 1xPflAB-P2.pdb Ck #32.4 
    16943 --- 
    16944 Chain | Description 
    16945 Ck | No description available 
    16946  
    16947 
    16948 > split #33
    16949 
    16950 Split 1xPflAB-P3.pdb (#33) into 4 models 
    16951 Chain information for 1xPflAB-P3.pdb BJ #33.1 
    16952 --- 
    16953 Chain | Description 
    16954 BJ | No description available 
    16955  
    16956 Chain information for 1xPflAB-P3.pdb Ch #33.2 
    16957 --- 
    16958 Chain | Description 
    16959 Ch | No description available 
    16960  
    16961 Chain information for 1xPflAB-P3.pdb Cj #33.3 
    16962 --- 
    16963 Chain | Description 
    16964 Cj | No description available 
    16965  
    16966 Chain information for 1xPflAB-P3.pdb Ck #33.4 
    16967 --- 
    16968 Chain | Description 
    16969 Ck | No description available 
    16970  
    16971 
    16972 > hide #32.1 models
    16973 
    16974 > show #32.1 models
    16975 
    16976 > hide #32.2 models
    16977 
    16978 > show #32.2 models
    16979 
    16980 > hide #32.2 models
    16981 
    16982 > hide #32.3 models
    16983 
    16984 > show #32.3 models
    16985 
    16986 > hide #32.3 models
    16987 
    16988 > show #32.3 models
    16989 
    16990 > hide #33.1 models
    16991 
    16992 > show #33.1 models
    16993 
    16994 > hide #33.2 models
    16995 
    16996 > show #33.2 models
    16997 
    16998 > hide #33.3 models
    16999 
    17000 > select add #33.4
    17001 
    17002 1109 atoms, 1136 bonds, 137 residues, 1 model selected 
    17003 
    17004 > select subtract #33.4
    17005 
    17006 Nothing selected 
    17007 
    17008 > select add #33.2
    17009 
    17010 6829 atoms, 6972 bonds, 843 residues, 1 model selected 
    17011 Alignment identifier is 33.2/Ch 
    17012 
    17013 > select #33.2/Ch:1-2
    17014 
    17015 16 atoms, 15 bonds, 2 residues, 1 model selected 
    17016 
    17017 > select #33.2/Ch:1-135
    17018 
    17019 1051 atoms, 1059 bonds, 135 residues, 1 model selected 
    17020 
    17021 > hide sel cartoons
    17022 
    17023 Drag select of 26 3xOnly-PflAB.mrc , 191 residues 
    17024 
    17025 > hide sel cartoons
    17026 
    17027 > hide sel surfaces
    17028 
    17029 > select #33.2/Ch:315
    17030 
    17031 4 atoms, 3 bonds, 1 residue, 1 model selected 
    17032 
    17033 > select #33.2/Ch:315-841
    17034 
    17035 4318 atoms, 4420 bonds, 527 residues, 1 model selected 
    17036 
    17037 > show sel surfaces
    17038 
    17039 > select #33.2/Ch:841-842
    17040 
    17041 20 atoms, 20 bonds, 2 residues, 1 model selected 
    17042 
    17043 > select #33.2/Ch:838-842
    17044 
    17045 42 atoms, 42 bonds, 5 residues, 1 model selected 
    17046 
    17047 > hide sel surfaces
    17048 
    17049 > select add #33.2
    17050 
    17051 6829 atoms, 6972 bonds, 843 residues, 2 models selected 
    17052 
    17053 > show sel surfaces
    17054 
    17055 > select #33.2/Ch:1-2
    17056 
    17057 16 atoms, 15 bonds, 2 residues, 1 model selected 
    17058 
    17059 > select #33.2/Ch:1-135
    17060 
    17061 1051 atoms, 1059 bonds, 135 residues, 1 model selected 
    17062 
    17063 > hide sel surfaces
    17064 
    17065 > select add #33.2
    17066 
    17067 6829 atoms, 6972 bonds, 843 residues, 2 models selected 
    17068 
    17069 > select add #33
    17070 
    17071 19762 atoms, 20168 bonds, 2435 residues, 6 models selected 
    17072 
    17073 > select subtract #33
    17074 
    17075 1 model selected 
    17076 
    17077 > select add #33
    17078 
    17079 19762 atoms, 20168 bonds, 2435 residues, 5 models selected 
    17080 
    17081 > select subtract #33
    17082 
    17083 1 model selected 
    17084 
    17085 > close #30
    17086 
    17087 > close #29
    17088 
    17089 > select add #28.2
    17090 
    17091 4995 atoms, 5088 bonds, 612 residues, 1 model selected 
    17092 
    17093 > select subtract #28.2
    17094 
    17095 1 model selected 
    17096 
    17097 > show #!28 models
    17098 
    17099 > hide #32.3 models
    17100 
    17101 > show #32.3 models
    17102 
    17103 > hide #32.1 models
    17104 
    17105 > show #32.1 models
    17106 
    17107 > color #32.1 #ca4949ff
    17108 
    17109 > color #33.1 #ca4949ff
    17110 
    17111 > hide #!28.4 models
    17112 
    17113 > show #!28.4 models
    17114 
    17115 > hide #32.4 models
    17116 
    17117 > show #32.4 models
    17118 
    17119 > hide #32.3 models
    17120 
    17121 > show #32.3 models
    17122 
    17123 > color #32.3 #8c3092ff
    17124 
    17125 > hide #33.4 models
    17126 
    17127 > show #33.4 models
    17128 
    17129 > hide #!33.2 models
    17130 
    17131 > show #!33.2 models
    17132 
    17133 > color #33.2 magenta
    17134 
    17135 > show #!1 models
    17136 
    17137 > hide #!1 models
    17138 
    17139 > hide #32.4 models
    17140 
    17141 > show #32.4 models
    17142 
    17143 > color #32.4 #ca4949ff
    17144 
    17145 > color #33.4 #ca4949ff
    17146 
    17147 > hide #!28 models
    17148 
    17149 > hide #!32 models
    17150 
    17151 > hide #!33 models
    17152 
    17153 > ui tool show "Segment Map"
    17154 
    17155 Segmenting PflA-2.1A-230911.mrc, density threshold 0.184695 
    17156 Showing 295 region surfaces 
    17157 3349 watershed regions, grouped to 295 regions 
    17158 Showing PflA-2.1A-230911.seg - 295 regions, 295 surfaces 
    17159 
    17160 > select add #29.3
    17161 
    17162 1 model selected 
    17163 
    17164 > select add #29.256
    17165 
    17166 2 models selected 
    17167 
    17168 > select add #29.4
    17169 
    17170 3 models selected 
    17171 
    17172 > select add #29.145
    17173 
    17174 4 models selected 
    17175 
    17176 > select add #29.16
    17177 
    17178 5 models selected 
    17179 
    17180 > select add #29.250
    17181 
    17182 6 models selected 
    17183 Drag select of 4700, 489 of 20620 triangles, 4887, 3576 of 19436 triangles,
    17184 4964, 26 of 13104 triangles, 4763, 4895, 4696, 550 of 9412 triangles, 4866 
    17185 Drag select of 4899, 615 of 27220 triangles, 4902, 5446 of 23188 triangles,
    17186 4949, 15956 of 19796 triangles, 4692, 3867 of 20372 triangles, 4932, 13845 of
    17187 19788 triangles, 4915, 16250 of 18084 triangles, 4897, 751 of 19224 triangles,
    17188 4704, 8950 of 17972 triangles, 4922, 44 of 17548 triangles, 4886, 3440 of
    17189 16072 triangles, 4943, 14122 of 15236 triangles, 4708, 639 of 14432 triangles,
    17190 4909, 12696 of 14460 triangles, 4691, 8890 of 14140 triangles, 4918, 10905 of
    17191 15304 triangles, 4675, 5509 of 12864 triangles, 4850, 7532 of 14224 triangles,
    17192 4910, 3199 of 13064 triangles, 4952, 3122 of 13532 triangles, 4756, 9030 of
    17193 12092 triangles, 4959, 2165 of 11244 triangles, 4916, 1297 of 12440 triangles,
    17194 4742, 2132 of 11168 triangles, 4721, 609 of 11256 triangles, 4728, 277 of
    17195 11200 triangles, 4926, 5930 of 12096 triangles, 4942, 2162 of 9944 triangles,
    17196 4904, 6909 of 9736 triangles, 4913, 4703, 2359 of 10328 triangles, 4712, 3174
    17197 of 9008 triangles, 4805, 3653 of 9596 triangles, 4758, 7801 of 7876 triangles,
    17198 4762, 7903 of 8936 triangles, 4294, 6972 of 7764 triangles, 4282, 1463 of 6712
    17199 triangles, 4321, 4605, 6426 of 6700 triangles, 4573, 5123 of 6248 triangles,
    17200 4342, 2525 of 4648 triangles, 4340, 1758 of 4632 triangles 
    17201 Drag select of 4668, 14222 of 14912 triangles, 4896, 2950 of 15160 triangles,
    17202 4663, 12051 of 14720 triangles, 4761, 3120 of 15236 triangles, 4891, 971 of
    17203 14104 triangles, 4888, 6670 of 11360 triangles, 4726, 9406 of 10748 triangles,
    17204 4713, 3094 of 10880 triangles, 4380, 1387 of 4444 triangles, 3860, 866 of 4348
    17205 triangles 
    17206 
    17207 > select add #29.239
    17208 
    17209 65 models selected 
    17210 Drag select of 4689, 1369 of 19220 triangles, 4889, 7346 of 19404 triangles,
    17211 4738, 8412 of 18596 triangles, 4885, 6608 of 18508 triangles, 4954, 3180 of
    17212 16240 triangles, 4938, 10669 of 19236 triangles, 4951, 9496 of 18276
    17213 triangles, 4914, 8181 of 16520 triangles, 4735, 3535 of 16136 triangles, 4934,
    17214 5144 of 15096 triangles, 4944, 7567 of 15396 triangles, 4940, 10304 of 16352
    17215 triangles, 4900, 9260 of 14060 triangles, 4892, 11398 of 13456 triangles,
    17216 4857, 4266 of 12868 triangles, 4923, 10595 of 13012 triangles, 4946, 7135 of
    17217 12704 triangles, 4905, 4951 of 12716 triangles, 4734, 6050 of 13180 triangles,
    17218 4719, 7639 of 13024 triangles, 4903, 4366 of 12188 triangles, 4694, 4063 of
    17219 12536 triangles, 4784, 4118 of 12580 triangles, 4746, 4022 of 12820 triangles,
    17220 4671, 360 of 11748 triangles, 4676, 7112 of 10476 triangles, 4941, 3032 of
    17221 10760 triangles, 4269, 5558 of 9676 triangles, 4890, 11050 of 11756 triangles,
    17222 4782, 6972 of 9776 triangles, 4879, 2916 of 8508 triangles, 4698, 2987 of 9220
    17223 triangles, 4877, 6702 of 9200 triangles, 4724, 6962 of 8944 triangles, 4091,
    17224 1619 of 8108 triangles, 4774, 2105 of 8116 triangles, 4711, 7128 of 7880
    17225 triangles, 4800, 5186 of 8140 triangles, 4715, 1608 of 6440 triangles, 4874,
    17226 5216 of 7408 triangles, 4853, 5165 of 7556 triangles, 4741, 3827 of 7216
    17227 triangles 
    17228 Drag select of 4927, 13477 of 15704 triangles, 4878, 9453 of 9600 triangles,
    17229 4309, 7829 of 8912 triangles, 4534, 6567 of 6700 triangles, 4670, 5829 of 6004
    17230 triangles 
    17231 Drag select of 4750, 6730 of 11416 triangles, 4906, 12393 of 12516 triangles,
    17232 4930, 4834, 7953 of 10404 triangles, 4865, 4183 of 10016 triangles, 4815,
    17233 4928, 4577, 8835 of 9196 triangles, 4172, 4688, 4804, 4965, 8439 of 8488
    17234 triangles, 4795, 3745 of 8332 triangles, 4214, 2221 of 7504 triangles, 4788,
    17235 4880, 4789, 3398, 2931 of 5904 triangles, 4359, 4420, 5129 of 5492 triangles,
    17236 3375, 4992 of 5048 triangles, 3388, 4562, 59 of 4036 triangles, 160, 895 of
    17237 2876 triangles 
    17238 
    17239 > select add #29.179
    17240 
    17241 137 models selected 
    17242 
    17243 > select add #29.224
    17244 
    17245 138 models selected 
    17246 
    17247 > select add #29.213
    17248 
    17249 139 models selected 
    17250 
    17251 > show #!33 models
    17252 
    17253 > hide #!33 models
    17254 
    17255 > select add #33
    17256 
    17257 19762 atoms, 20168 bonds, 2435 residues, 144 models selected 
    17258 
    17259 > select add #32
    17260 
    17261 39524 atoms, 40336 bonds, 4870 residues, 150 models selected 
    17262 
    17263 > show #!32 models
    17264 
    17265 > show #!33 models
    17266 
    17267 > select add #29
    17268 
    17269 39524 atoms, 40336 bonds, 4870 residues, 307 models selected 
    17270 
    17271 > select subtract #29
    17272 
    17273 39524 atoms, 40336 bonds, 4870 residues, 11 models selected 
    17274 
    17275 > hide sel & #32.1,3-4#33.1,4#!33.2 cartoons
    17276 
    17277 > show sel & #32.1,3-4#33.1,4#!33.2 surfaces
    17278 
    17279 > select subtract #32
    17280 
    17281 19762 atoms, 20168 bonds, 2435 residues, 11 models selected 
    17282 
    17283 > select subtract #33
    17284 
    17285 3 models selected 
    17286 
    17287 > hide #!32 models
    17288 
    17289 > show #!32 models
    17290 
    17291 > hide #!33 models
    17292 
    17293 > hide #!32 models
    17294 
    17295 > select clear
    17296 
    17297 Drag select of 4911, 4939, 4937, 4947, 4901, 4933, 4812, 4908, 4864, 4907,
    17298 4779, 4935, 4953, 4958, 13741 of 14800 triangles, 4966, 4948, 4936, 4217,
    17299 4917, 4793, 4748, 4919, 4894, 4845, 4772, 4669, 4679, 4855, 4818, 4823, 4539,
    17300 4781, 4957, 4797, 4119, 4072, 4174, 4524, 4452, 4611, 4754, 4570, 4962, 4559,
    17301 4961, 4912, 4209, 4553, 4955, 4727, 4771, 4821, 4808, 4137, 4893, 4876, 4664,
    17302 4262, 3475, 4783, 4235, 4929, 4852, 4199, 4707, 4505, 4861, 4920, 4817, 4830,
    17303 4921, 4405, 4856, 4162, 4950, 4460, 4595, 3405, 4149, 4747, 4567, 1073, 4422,
    17304 4446, 4841, 4931, 4835, 4963, 4682, 4787, 4924, 4148, 3917, 8386 of 8404
    17305 triangles, 4413, 4945, 4110, 4538, 4208, 4956, 4336, 3440, 4868, 4138, 4454,
    17306 4838, 4725, 4705, 4858, 4833, 4813, 855, 4960, 4204, 4544, 3450, 4461, 4171,
    17307 4839, 4099, 4677, 4201, 4822, 3446, 4547, 4898, 4502, 3410, 4518, 4860, 4200,
    17308 4731, 3411, 3453, 4872, 4732, 4831, 4825, 4525, 4477, 4632, 4437, 4847, 4596,
    17309 4205, 4187, 4491, 4807, 4770, 4472, 712, 4001, 3470, 3517, 858, 696, 4470,
    17310 4656, 4315, 1461, 26 3xOnly-PflAB.mrc 
    17311 Grouped 159 regions 
    17312 Showing 137 region surfaces 
    17313 
    17314 > select #29.1
    17315 
    17316 1 model selected 
    17317 Opened PflA-2.1A-230911_imasked as #30, grid size 240,240,240, pixel 2.1,
    17318 shown at step 1, values float32 
    17319 Segmenting PflA-2.1A-230911_imasked, density threshold 0.184695 
    17320 Showing 159 region surfaces 
    17321 1246 watershed regions, grouped to 159 regions 
    17322 Showing PflA-2.seg - 159 regions, 159 surfaces 
    17323 
    17324 > select add #29.7
    17325 
    17326 1 model selected 
    17327 
    17328 > select add #29.81
    17329 
    17330 2 models selected 
    17331 
    17332 > select add #29.134
    17333 
    17334 3 models selected 
    17335 
    17336 > select add #29.60
    17337 
    17338 4 models selected 
    17339 
    17340 > select add #29.106
    17341 
    17342 5 models selected 
    17343 
    17344 > select add #29.16
    17345 
    17346 6 models selected 
    17347 
    17348 > select add #29.13
    17349 
    17350 7 models selected 
    17351 
    17352 > select add #29.31
    17353 
    17354 8 models selected 
    17355 
    17356 > select add #29.84
    17357 
    17358 9 models selected 
    17359 
    17360 > select add #29.39
    17361 
    17362 10 models selected 
    17363 
    17364 > select add #29.40
    17365 
    17366 11 models selected 
    17367 
    17368 > select add #29.28
    17369 
    17370 12 models selected 
    17371 
    17372 > select add #29.97
    17373 
    17374 13 models selected 
    17375 
    17376 > select add #29.72
    17377 
    17378 14 models selected 
    17379 
    17380 > select add #29.51
    17381 
    17382 15 models selected 
    17383 
    17384 > select add #29.33
    17385 
    17386 16 models selected 
    17387 
    17388 > select add #29.56
    17389 
    17390 17 models selected 
    17391 
    17392 > select add #29.93
    17393 
    17394 18 models selected 
    17395 
    17396 > select add #29.32
    17397 
    17398 19 models selected 
    17399 
    17400 > select add #29.38
    17401 
    17402 20 models selected 
    17403 
    17404 > select add #29.30
    17405 
    17406 21 models selected 
    17407 Grouped 21 regions 
    17408 
    17409 > select add #29.15
    17410 
    17411 2 models selected 
    17412 
    17413 > select add #29.133
    17414 
    17415 3 models selected 
    17416 
    17417 > select add #29.141
    17418 
    17419 4 models selected 
    17420 
    17421 > select add #29.54
    17422 
    17423 5 models selected 
    17424 
    17425 > select add #29.109
    17426 
    17427 6 models selected 
    17428 
    17429 > select add #29.149
    17430 
    17431 7 models selected 
    17432 
    17433 > select add #29.26
    17434 
    17435 8 models selected 
    17436 
    17437 > select add #29.44
    17438 
    17439 9 models selected 
    17440 
    17441 > select add #29.34
    17442 
    17443 10 models selected 
    17444 
    17445 > select add #29.59
    17446 
    17447 11 models selected 
    17448 
    17449 > select add #29.14
    17450 
    17451 12 models selected 
    17452 
    17453 > select add #29.78
    17454 
    17455 13 models selected 
    17456 
    17457 > select add #29.53
    17458 
    17459 14 models selected 
    17460 
    17461 > select add #29.36
    17462 
    17463 15 models selected 
    17464 
    17465 > select add #29.11
    17466 
    17467 16 models selected 
    17468 
    17469 > select add #29.37
    17470 
    17471 17 models selected 
    17472 
    17473 > select add #29.24
    17474 
    17475 18 models selected 
    17476 
    17477 > select add #29.120
    17478 
    17479 19 models selected 
    17480 
    17481 > select add #29.90
    17482 
    17483 20 models selected 
    17484 
    17485 > select add #29.94
    17486 
    17487 21 models selected 
    17488 Grouped 21 regions 
    17489 
    17490 > select subtract #29.7
    17491 
    17492 Nothing selected 
    17493 
    17494 > select add #29.7
    17495 
    17496 1 model selected 
    17497 
    17498 > select add #29.83
    17499 
    17500 2 models selected 
    17501 
    17502 > select add #29.42
    17503 
    17504 3 models selected 
    17505 
    17506 > select add #29.82
    17507 
    17508 4 models selected 
    17509 
    17510 > select add #29.115
    17511 
    17512 5 models selected 
    17513 
    17514 > select add #29.61
    17515 
    17516 6 models selected 
    17517 
    17518 > select add #29.111
    17519 
    17520 7 models selected 
    17521 
    17522 > select add #29.92
    17523 
    17524 8 models selected 
    17525 
    17526 > select add #29.100
    17527 
    17528 9 models selected 
    17529 
    17530 > select add #29.10
    17531 
    17532 10 models selected 
    17533 
    17534 > select subtract #29.7
    17535 
    17536 9 models selected 
    17537 
    17538 > select add #29.7
    17539 
    17540 10 models selected 
    17541 
    17542 > select add #29.103
    17543 
    17544 11 models selected 
    17545 
    17546 > select add #29.96
    17547 
    17548 12 models selected 
    17549 
    17550 > select add #29.101
    17551 
    17552 13 models selected 
    17553 
    17554 > select add #29.9
    17555 
    17556 14 models selected 
    17557 
    17558 > select add #29.77
    17559 
    17560 15 models selected 
    17561 
    17562 > select add #29.98
    17563 
    17564 16 models selected 
    17565 
    17566 > select add #29.124
    17567 
    17568 17 models selected 
    17569 
    17570 > select add #29.25
    17571 
    17572 18 models selected 
    17573 Grouped 18 regions 
    17574 
    17575 > select add #29.18
    17576 
    17577 2 models selected 
    17578 
    17579 > select add #29.65
    17580 
    17581 3 models selected 
    17582 
    17583 > select add #29.67
    17584 
    17585 4 models selected 
    17586 
    17587 > select add #29.79
    17588 
    17589 5 models selected 
    17590 
    17591 > select add #29.27
    17592 
    17593 6 models selected 
    17594 
    17595 > select add #29.47
    17596 
    17597 7 models selected 
    17598 
    17599 > select add #29.64
    17600 
    17601 8 models selected 
    17602 
    17603 > select add #29.146
    17604 
    17605 9 models selected 
    17606 
    17607 > select add #29.122
    17608 
    17609 10 models selected 
    17610 Grouped 10 regions 
    17611 
    17612 > select add #29.123
    17613 
    17614 2 models selected 
    17615 Grouped 2 regions 
    17616 
    17617 > select clear
    17618 
    17619 > select #29.58
    17620 
    17621 1 model selected 
    17622 
    17623 > select add #29.7
    17624 
    17625 2 models selected 
    17626 Grouped 2 regions 
    17627 
    17628 > select clear
    17629 
    17630 > select #29.7
    17631 
    17632 1 model selected 
    17633 
    17634 > select add #29.127
    17635 
    17636 2 models selected 
    17637 Grouped 2 regions 
    17638 Opened PflA-2_imasked as #34, grid size 240,240,240, pixel 2.1, shown at step
    17639 1, values float32 
    17640 
    17641 > select add #32
    17642 
    17643 19762 atoms, 20168 bonds, 2435 residues, 94 models selected 
    17644 
    17645 > select subtract #32
    17646 
    17647 92 models selected 
    17648 
    17649 > show #!32 models
    17650 
    17651 > show #!33 models
    17652 
    17653 > hide #!33 models
    17654 
    17655 Opened PflA-2_imasked as #35, grid size 240,240,240, pixel 2.1, shown at step
    17656 1, values float32 
    17657 Segmenting PflA-2_imasked, density threshold 0.184695 
    17658 Showing 69 region surfaces 
    17659 415 watershed regions, grouped to 69 regions 
    17660 Showing PflA-2_imasked.seg - 69 regions, 69 surfaces 
    17661 
    17662 > hide #!32 models
    17663 
    17664 > close #35
    17665 
    17666 > show #!32 models
    17667 
    17668 > show #!33 models
    17669 
    17670 > select #29.57
    17671 
    17672 1 model selected 
    17673 
    17674 > select add #29.65
    17675 
    17676 2 models selected 
    17677 
    17678 > select add #29.10
    17679 
    17680 3 models selected 
    17681 
    17682 > select add #29.43
    17683 
    17684 4 models selected 
    17685 
    17686 > select add #29.1
    17687 
    17688 5 models selected 
    17689 
    17690 > select add #29.46
    17691 
    17692 6 models selected 
    17693 
    17694 > select add #29.17
    17695 
    17696 7 models selected 
    17697 
    17698 > select add #29.45
    17699 
    17700 8 models selected 
    17701 
    17702 > select add #29.26
    17703 
    17704 9 models selected 
    17705 
    17706 > select subtract #29.26
    17707 
    17708 8 models selected 
    17709 
    17710 > select add #29.26
    17711 
    17712 9 models selected 
    17713 
    17714 > select subtract #29.26
    17715 
    17716 8 models selected 
    17717 
    17718 > select add #29.24
    17719 
    17720 9 models selected 
    17721 
    17722 > select add #29.25
    17723 
    17724 10 models selected 
    17725 
    17726 > show #!28 models
    17727 
    17728 > select add #29.52
    17729 
    17730 11 models selected 
    17731 
    17732 > select add #29.15
    17733 
    17734 12 models selected 
    17735 
    17736 > select add #29.39
    17737 
    17738 13 models selected 
    17739 
    17740 > select add #29.29
    17741 
    17742 14 models selected 
    17743 
    17744 > select add #28.2
    17745 
    17746 4995 atoms, 5088 bonds, 612 residues, 15 models selected 
    17747 
    17748 > select subtract #28.2
    17749 
    17750 15 models selected 
    17751 Grouped 14 regions 
    17752 
    17753 > select clear
    17754 
    17755 > select #29.1
    17756 
    17757 1 model selected 
    17758 
    17759 > select clear
    17760 
    17761 > select add #28.2
    17762 
    17763 4995 atoms, 5088 bonds, 612 residues, 1 model selected 
    17764 
    17765 > select add #28.4
    17766 
    17767 11824 atoms, 12060 bonds, 1455 residues, 3 models selected 
    17768 
    17769 > select add #28.6
    17770 
    17771 18653 atoms, 19032 bonds, 2298 residues, 5 models selected 
    17772 
    17773 > select add #28.7
    17774 
    17775 19762 atoms, 20168 bonds, 2435 residues, 7 models selected 
    17776 
    17777 > show sel surfaces
    17778 
    17779 > select add #28
    17780 
    17781 38799 atoms, 39588 bonds, 4776 residues, 14 models selected 
    17782 
    17783 > select subtract #28
    17784 
    17785 4 models selected 
    17786 Showing 56 region surfaces 
    17787 
    17788 > select #29.1
    17789 
    17790 1 model selected 
    17791 
    17792 > select add #29.19
    17793 
    17794 2 models selected 
    17795 
    17796 > select add #29.23
    17797 
    17798 3 models selected 
    17799 
    17800 > select add #29.49
    17801 
    17802 4 models selected 
    17803 
    17804 > select add #29.18
    17805 
    17806 5 models selected 
    17807 
    17808 > select add #29.33
    17809 
    17810 6 models selected 
    17811 
    17812 > select add #29.20
    17813 
    17814 7 models selected 
    17815 
    17816 > select add #29.27
    17817 
    17818 8 models selected 
    17819 
    17820 > select add #29.6
    17821 
    17822 9 models selected 
    17823 
    17824 > select add #29.21
    17825 
    17826 10 models selected 
    17827 
    17828 > select add #29.4
    17829 
    17830 11 models selected 
    17831 
    17832 > select add #29.30
    17833 
    17834 12 models selected 
    17835 
    17836 > select add #29.50
    17837 
    17838 13 models selected 
    17839 
    17840 > select add #29.62
    17841 
    17842 14 models selected 
    17843 
    17844 > select add #29.36
    17845 
    17846 15 models selected 
    17847 
    17848 > select add #29.22
    17849 
    17850 16 models selected 
    17851 
    17852 > select add #29.11
    17853 
    17854 17 models selected 
    17855 
    17856 > select add #29.47
    17857 
    17858 18 models selected 
    17859 
    17860 > select add #29.61
    17861 
    17862 19 models selected 
    17863 
    17864 > select add #29.12
    17865 
    17866 20 models selected 
    17867 
    17868 > select add #29.41
    17869 
    17870 21 models selected 
    17871 
    17872 > select add #29.64
    17873 
    17874 22 models selected 
    17875 
    17876 > select add #29.34
    17877 
    17878 23 models selected 
    17879 
    17880 > select add #29.53
    17881 
    17882 24 models selected 
    17883 
    17884 > select add #29.40
    17885 
    17886 25 models selected 
    17887 
    17888 > select add #29.55
    17889 
    17890 26 models selected 
    17891 
    17892 > select add #29.51
    17893 
    17894 27 models selected 
    17895 
    17896 > select add #29.32
    17897 
    17898 28 models selected 
    17899 
    17900 > select add #29.56
    17901 
    17902 29 models selected 
    17903 
    17904 > select subtract #29.32
    17905 
    17906 28 models selected 
    17907 
    17908 > select subtract #29.56
    17909 
    17910 27 models selected 
    17911 Grouped 27 regions 
    17912 
    17913 > select #29.32
    17914 
    17915 1 model selected 
    17916 
    17917 > select add #29.56
    17918 
    17919 2 models selected 
    17920 
    17921 > select add #29.48
    17922 
    17923 3 models selected 
    17924 
    17925 > select add #29.54
    17926 
    17927 4 models selected 
    17928 
    17929 > select add #29.35
    17930 
    17931 5 models selected 
    17932 
    17933 > select add #29.59
    17934 
    17935 6 models selected 
    17936 
    17937 > select add #29.44
    17938 
    17939 7 models selected 
    17940 
    17941 > select add #29.60
    17942 
    17943 8 models selected 
    17944 
    17945 > select add #29.28
    17946 
    17947 9 models selected 
    17948 
    17949 > select add #29.1
    17950 
    17951 10 models selected 
    17952 
    17953 > select add #32
    17954 
    17955 19762 atoms, 20168 bonds, 2435 residues, 15 models selected 
    17956 
    17957 > select subtract #32
    17958 
    17959 13 models selected 
    17960 
    17961 > select add #30
    17962 
    17963 12 models selected 
    17964 
    17965 > select subtract #30
    17966 
    17967 10 models selected 
    17968 
    17969 > select add #30
    17970 
    17971 12 models selected 
    17972 
    17973 > select subtract #30
    17974 
    17975 10 models selected 
    17976 
    17977 > select clear
    17978 
    17979 > hide #!30 models
    17980 
    17981 > hide #!29 models
    17982 
    17983 > show #!11 models
    17984 
    17985 > hide #!34 models
    17986 
    17987 > show #!34 models
    17988 
    17989 > hide #!34 models
    17990 
    17991 > hide #!11 models
    17992 
    17993 > show #!11 models
    17994 
    17995 > close #11
    17996 
    17997 > close #34
    17998 
    17999 Segmenting PflA-2.1A-230911.mrc, density threshold 0.184695 
    18000 Showing 295 region surfaces 
    18001 3349 watershed regions, grouped to 295 regions 
    18002 Showing PflA-2.1A-230911.seg - 295 regions, 295 surfaces 
    18003 Drag select of 4907, 27032 of 27220 triangles, 4951, 22300 of 23188 triangles,
    18004 4720, 4945, 4668, 15469 of 19220 triangles, 4957, 4679, 20000 of 20372
    18005 triangles, 4765, 2043 of 18048 triangles, 4933, 4931, 15275 of 19404
    18006 triangles, 4666, 18478 of 18596 triangles, 4903, 17730 of 18084 triangles,
    18007 4921, 13998 of 18508 triangles, 4922, 15563 of 16240 triangles, 4902, 4721,
    18008 4913, 11549 of 15704 triangles, 4896, 4956, 4898, 4958, 13764 of 18276
    18009 triangles, 4919, 4784, 3146 of 14912 triangles, 4946, 4719, 13132 of 16136
    18010 triangles, 4763, 3540 of 14720 triangles, 4953, 4938, 4891, 15577 of 16352
    18011 triangles, 4966, 4673, 4892, 4795, 4793, 4914, 4889, 4928, 4776, 9889 of 12868
    18012 triangles, 4909, 4916, 12248 of 13012 triangles, 4759, 12515 of 12864
    18013 triangles, 4860, 4934, 4965, 4963, 4739, 10306 of 13180 triangles, 4814, 4927,
    18014 4948, 4830, 12374 of 12536 triangles, 4875, 10999 of 12580 triangles, 4910,
    18015 4778, 11924 of 12092 triangles, 4835, 12818 of 12820 triangles, 4943, 4761,
    18016 4941, 4917, 4936, 4783, 774 of 10748 triangles, 4856, 9392 of 11748 triangles,
    18017 4838, 4662, 4695, 4920, 4833, 4901, 9358 of 10760 triangles, 4935, 4753, 4952,
    18018 4096, 9615 of 9676 triangles, 4961, 4742, 4722, 4915, 4710, 8928 of 9776
    18019 triangles, 4817, 6437 of 8508 triangles, 4735, 4746, 4877, 4791, 9178 of 9200
    18020 triangles, 4754, 4713, 8651 of 8944 triangles, 4467, 6529 of 8108 triangles,
    18021 4699, 7813 of 7876 triangles, 4857, 6662 of 9600 triangles, 4714, 4749, 4809,
    18022 7878 of 7880 triangles, 4290, 7135 of 8912 triangles, 4700, 4319, 4874, 4282,
    18023 4832, 6638 of 7408 triangles, 4866, 4845, 7538 of 7556 triangles, 4522, 7676
    18024 of 7912 triangles, 4844, 7211 of 7216 triangles, 4750, 1129 of 5968 triangles,
    18025 4546, 4885 of 6700 triangles, 4327, 4140, 4876, 4769 of 6004 triangles, 4634,
    18026 3407, 4459, 4627 
    18027 
    18028 > select add #11.145
    18029 
    18030 109 models selected 
    18031 
    18032 > select add #11.4
    18033 
    18034 110 models selected 
    18035 
    18036 > select add #11.3
    18037 
    18038 111 models selected 
    18039 
    18040 > select add #11.139
    18041 
    18042 112 models selected 
    18043 
    18044 > select add #11.256
    18045 
    18046 113 models selected 
    18047 
    18048 > select add #11.179
    18049 
    18050 114 models selected 
    18051 
    18052 > select add #11.224
    18053 
    18054 115 models selected 
    18055 
    18056 > select add #11.232
    18057 
    18058 116 models selected 
    18059 
    18060 > select add #11.147
    18061 
    18062 117 models selected 
    18063 
    18064 > select add #11.198
    18065 
    18066 118 models selected 
    18067 
    18068 > select add #11.230
    18069 
    18070 119 models selected 
    18071 
    18072 > select add #11.233
    18073 
    18074 120 models selected 
    18075 
    18076 > select add #11.158
    18077 
    18078 121 models selected 
    18079 
    18080 > select add #11.114
    18081 
    18082 122 models selected 
    18083 
    18084 > select add #11.201
    18085 
    18086 123 models selected 
    18087 
    18088 > select add #11.97
    18089 
    18090 124 models selected 
    18091 
    18092 > select add #11.281
    18093 
    18094 125 models selected 
    18095 
    18096 > select add #11.289
    18097 
    18098 126 models selected 
    18099 Drag select of 4767, 9531 of 11416 triangles, 4829, 10271 of 10404 triangles,
    18100 4855, 6857 of 10016 triangles, 4824, 4501, 4316, 4799, 5684 of 8332 triangles,
    18101 4110, 4486 of 7504 triangles, 3420, 4692 of 5904 triangles, 4519, 4404, 791 of
    18102 6452 triangles, 4139, 3370, 4294, 1508 of 4868 triangles, 4159, 1394 of 4036
    18103 triangles, 160, 2191 of 2876 triangles 
    18104 
    18105 > select add #11.1
    18106 
    18107 143 models selected 
    18108 
    18109 > select add #11.113
    18110 
    18111 144 models selected 
    18112 
    18113 > select add #11.100
    18114 
    18115 145 models selected 
    18116 
    18117 > select add #11.130
    18118 
    18119 146 models selected 
    18120 
    18121 > select add #11.191
    18122 
    18123 147 models selected 
    18124 
    18125 > select add #11.129
    18126 
    18127 148 models selected 
    18128 
    18129 > select add #11.106
    18130 
    18131 149 models selected 
    18132 
    18133 > select add #11.119
    18134 
    18135 150 models selected 
    18136 
    18137 > select add #11.254
    18138 
    18139 151 models selected 
    18140 
    18141 > select add #11.140
    18142 
    18143 152 models selected 
    18144 
    18145 > select add #11.6
    18146 
    18147 153 models selected 
    18148 
    18149 > select add #11.105
    18150 
    18151 154 models selected 
    18152 
    18153 > select add #11.287
    18154 
    18155 155 models selected 
    18156 
    18157 > select add #11.2
    18158 
    18159 156 models selected 
    18160 
    18161 > select add #11.195
    18162 
    18163 157 models selected 
    18164 
    18165 > select add #11.101
    18166 
    18167 158 models selected 
    18168 
    18169 > select add #11.213
    18170 
    18171 159 models selected 
    18172 
    18173 > select add #11.286
    18174 
    18175 160 models selected 
    18176 
    18177 > select add #11.150
    18178 
    18179 161 models selected 
    18180 
    18181 > select add #11.243
    18182 
    18183 162 models selected 
    18184 
    18185 > select add #11.199
    18186 
    18187 163 models selected 
    18188 
    18189 > select add #11.95
    18190 
    18191 164 models selected 
    18192 
    18193 > select add #11.197
    18194 
    18195 165 models selected 
    18196 
    18197 > select add #11.48
    18198 
    18199 166 models selected 
    18200 
    18201 > select add #11.177
    18202 
    18203 167 models selected 
    18204 
    18205 > select add #11.265
    18206 
    18207 168 models selected 
    18208 
    18209 > select add #11.54
    18210 
    18211 169 models selected 
    18212 
    18213 > select add #11.20
    18214 
    18215 170 models selected 
    18216 
    18217 > select add #11.8
    18218 
    18219 171 models selected 
    18220 
    18221 > select add #11.53
    18222 
    18223 172 models selected 
    18224 
    18225 > select add #11.10
    18226 
    18227 173 models selected 
    18228 
    18229 > select add #11.27
    18230 
    18231 174 models selected 
    18232 
    18233 > select add #11.117
    18234 
    18235 175 models selected 
    18236 
    18237 > select add #11.205
    18238 
    18239 176 models selected 
    18240 
    18241 > select add #11.173
    18242 
    18243 177 models selected 
    18244 
    18245 > select add #11.168
    18246 
    18247 178 models selected 
    18248 
    18249 > select add #11.262
    18250 
    18251 179 models selected 
    18252 
    18253 > select add #11.169
    18254 
    18255 180 models selected 
    18256 
    18257 > select add #11.141
    18258 
    18259 181 models selected 
    18260 
    18261 > select add #11.204
    18262 
    18263 182 models selected 
    18264 
    18265 > select add #11.273
    18266 
    18267 183 models selected 
    18268 
    18269 > select add #11.103
    18270 
    18271 184 models selected 
    18272 
    18273 > select add #11.186
    18274 
    18275 185 models selected 
    18276 
    18277 > select add #11.290
    18278 
    18279 186 models selected 
    18280 
    18281 > select add #11.245
    18282 
    18283 187 models selected 
    18284 
    18285 > select add #11.151
    18286 
    18287 188 models selected 
    18288 
    18289 > select add #11.11
    18290 
    18291 189 models selected 
    18292 
    18293 > select add #11.133
    18294 
    18295 190 models selected 
    18296 
    18297 > select add #11.284
    18298 
    18299 191 models selected 
    18300 
    18301 > select add #11.208
    18302 
    18303 192 models selected 
    18304 
    18305 > select add #11.170
    18306 
    18307 193 models selected 
    18308 
    18309 > select add #11.217
    18310 
    18311 194 models selected 
    18312 
    18313 > select add #11.268
    18314 
    18315 195 models selected 
    18316 
    18317 > select add #11.43
    18318 
    18319 196 models selected 
    18320 
    18321 > select add #11.248
    18322 
    18323 197 models selected 
    18324 
    18325 > select add #11.162
    18326 
    18327 198 models selected 
    18328 
    18329 > select add #11.138
    18330 
    18331 199 models selected 
    18332 
    18333 > select add #11.266
    18334 
    18335 200 models selected 
    18336 
    18337 > select add #11.291
    18338 
    18339 201 models selected 
    18340 
    18341 > select add #11.50
    18342 
    18343 202 models selected 
    18344 
    18345 > select add #11.90
    18346 
    18347 203 models selected 
    18348 
    18349 > select add #11.255
    18350 
    18351 204 models selected 
    18352 
    18353 > select add #11.148
    18354 
    18355 205 models selected 
    18356 
    18357 > select add #11.52
    18358 
    18359 206 models selected 
    18360 
    18361 > select add #11.222
    18362 
    18363 207 models selected 
    18364 
    18365 > select add #11.267
    18366 
    18367 208 models selected 
    18368 
    18369 > select add #11.74
    18370 
    18371 209 models selected 
    18372 
    18373 > select add #11.270
    18374 
    18375 210 models selected 
    18376 
    18377 > select add #11.178
    18378 
    18379 211 models selected 
    18380 
    18381 > select add #11.278
    18382 
    18383 212 models selected 
    18384 
    18385 > select add #11.57
    18386 
    18387 213 models selected 
    18388 Grouped 213 regions 
    18389 
    18390 > select #11.1
    18391 
    18392 1 model selected 
    18393 
    18394 > hide #!26 models
    18395 
    18396 > select clear
    18397 
    18398 > select #11.1
    18399 
    18400 1 model selected 
    18401 Opened PflA-2.1A-230911_imasked as #29, grid size 240,240,240, pixel 2.1,
    18402 shown at step 1, values float32 
    18403 Segmenting PflA-2.1A-230911_imasked, density threshold 0.184695 
    18404 Showing 81 region surfaces 
    18405 463 watershed regions, grouped to 81 regions 
    18406 Showing PflA-2.seg - 81 regions, 81 surfaces 
    18407 
    18408 > hide #!29 models
    18409 
    18410 > select add #11.64
    18411 
    18412 1 model selected 
    18413 
    18414 > select add #11.79
    18415 
    18416 2 models selected 
    18417 
    18418 > select add #11.50
    18419 
    18420 3 models selected 
    18421 
    18422 > select add #11.4
    18423 
    18424 4 models selected 
    18425 
    18426 > select add #11.29
    18427 
    18428 5 models selected 
    18429 
    18430 > select add #11.20
    18431 
    18432 6 models selected 
    18433 
    18434 > select add #11.6
    18435 
    18436 7 models selected 
    18437 
    18438 > select add #11.21
    18439 
    18440 8 models selected 
    18441 
    18442 > select add #11.36
    18443 
    18444 9 models selected 
    18445 
    18446 > select add #11.11
    18447 
    18448 10 models selected 
    18449 
    18450 > select add #11.66
    18451 
    18452 11 models selected 
    18453 
    18454 > select add #11.76
    18455 
    18456 12 models selected 
    18457 
    18458 > select add #11.80
    18459 
    18460 13 models selected 
    18461 
    18462 > select add #11.81
    18463 
    18464 14 models selected 
    18465 
    18466 > select add #11.49
    18467 
    18468 15 models selected 
    18469 
    18470 > select add #11.17
    18471 
    18472 16 models selected 
    18473 
    18474 > select add #11.32
    18475 
    18476 17 models selected 
    18477 
    18478 > select add #11.26
    18479 
    18480 18 models selected 
    18481 
    18482 > select add #11.19
    18483 
    18484 19 models selected 
    18485 
    18486 > select add #11.41
    18487 
    18488 20 models selected 
    18489 
    18490 > select add #11.18
    18491 
    18492 21 models selected 
    18493 
    18494 > select add #11.22
    18495 
    18496 22 models selected 
    18497 
    18498 > select add #11.52
    18499 
    18500 23 models selected 
    18501 
    18502 > select add #11.14
    18503 
    18504 24 models selected 
    18505 
    18506 > select add #11.39
    18507 
    18508 25 models selected 
    18509 
    18510 > select add #11.28
    18511 
    18512 26 models selected 
    18513 
    18514 > select add #11.47
    18515 
    18516 27 models selected 
    18517 
    18518 > select add #11.46
    18519 
    18520 28 models selected 
    18521 
    18522 > select add #11.25
    18523 
    18524 29 models selected 
    18525 
    18526 > select add #11.23
    18527 
    18528 30 models selected 
    18529 
    18530 > select add #11.24
    18531 
    18532 31 models selected 
    18533 
    18534 > select add #11.16
    18535 
    18536 32 models selected 
    18537 
    18538 > select add #11.1
    18539 
    18540 33 models selected 
    18541 
    18542 > select add #11.44
    18543 
    18544 34 models selected 
    18545 
    18546 > select add #11.34
    18547 
    18548 35 models selected 
    18549 
    18550 > select add #11.57
    18551 
    18552 36 models selected 
    18553 
    18554 > select add #11.69
    18555 
    18556 37 models selected 
    18557 
    18558 > select add #11.72
    18559 
    18560 38 models selected 
    18561 Grouped 38 regions 
    18562 
    18563 > select #11.42
    18564 
    18565 1 model selected 
    18566 
    18567 > select add #11.68
    18568 
    18569 2 models selected 
    18570 
    18571 > select add #11.70
    18572 
    18573 3 models selected 
    18574 
    18575 > select add #11.33
    18576 
    18577 4 models selected 
    18578 
    18579 > select add #11.53
    18580 
    18581 5 models selected 
    18582 
    18583 > select add #11.60
    18584 
    18585 6 models selected 
    18586 
    18587 > select add #11.9
    18588 
    18589 7 models selected 
    18590 
    18591 > select add #11.51
    18592 
    18593 8 models selected 
    18594 
    18595 > select add #11.55
    18596 
    18597 9 models selected 
    18598 
    18599 > select add #11.31
    18600 
    18601 10 models selected 
    18602 
    18603 > select add #11.56
    18604 
    18605 11 models selected 
    18606 
    18607 > select add #11.75
    18608 
    18609 12 models selected 
    18610 
    18611 > select add #11.48
    18612 
    18613 13 models selected 
    18614 
    18615 > select add #11.54
    18616 
    18617 14 models selected 
    18618 
    18619 > select add #11.78
    18620 
    18621 15 models selected 
    18622 
    18623 > select add #11.35
    18624 
    18625 16 models selected 
    18626 
    18627 > select add #11.59
    18628 
    18629 17 models selected 
    18630 
    18631 > select add #11.62
    18632 
    18633 18 models selected 
    18634 
    18635 > select add #11.73
    18636 
    18637 19 models selected 
    18638 
    18639 > select add #11.45
    18640 
    18641 20 models selected 
    18642 
    18643 > select add #11.61
    18644 
    18645 21 models selected 
    18646 
    18647 > select add #11.63
    18648 
    18649 22 models selected 
    18650 
    18651 > select add #11.27
    18652 
    18653 23 models selected 
    18654 
    18655 > select add #11.65
    18656 
    18657 24 models selected 
    18658 
    18659 > select subtract #11.27
    18660 
    18661 23 models selected 
    18662 Grouped 23 regions 
    18663 
    18664 > select clear
    18665 
    18666 > select #11.27
    18667 
    18668 1 model selected 
    18669 Ungrouped to 6 regions 
    18670 Ungrouped to 9 regions 
    18671 Ungrouped to 0 regions 
    18672 
    18673 > select #11.4
    18674 
    18675 1 model selected 
    18676 
    18677 > select add #11.20
    18678 
    18679 2 models selected 
    18680 
    18681 > select add #11.19
    18682 
    18683 3 models selected 
    18684 
    18685 > select add #11.16
    18686 
    18687 4 models selected 
    18688 
    18689 > select add #11.26
    18690 
    18691 5 models selected 
    18692 
    18693 > select add #11.25
    18694 
    18695 6 models selected 
    18696 Grouped 6 regions 
    18697 
    18698 > select add #11.1
    18699 
    18700 2 models selected 
    18701 Opened PflA-2_imasked as #34, grid size 240,240,240, pixel 2.1, shown at step
    18702 1, values float32 
    18703 
    18704 > hide #!11 models
    18705 
    18706 The cached device pixel ratio value was stale on window expose. Please file a
    18707 QTBUG which explains how to reproduce. 
    18708 
    18709 > save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    18710 > from_June2024/July_2024/Final-version_model/Flo_PflA_Local/3xOnly-PflAB.mrc
    18711 > models #34
    18712 
    18713 > view orient
    18714 
    18715 > select add #11
    18716 
    18717 28 models selected 
    18718 
    18719 > select subtract #11
    18720 
    18721 Nothing selected 
    18722 
    18723 > select add #28
    18724 
    18725 38799 atoms, 39588 bonds, 4776 residues, 10 models selected 
    18726 Alignment identifier is 1 
    18727 Alignment identifier is 2 
    18728 Alignment identifier is 3 
    18729 
    18730 > select #28.4/Ch:1-3 #28.6/Cj:1-3 #28.8/Cl:1-3
    18731 
    18732 72 atoms, 69 bonds, 9 residues, 3 models selected 
    18733 
    18734 > select #28.4/Ch:1-135 #28.6/Cj:1-135 #28.8/Cl:1-135
    18735 
    18736 3153 atoms, 3177 bonds, 405 residues, 3 models selected 
    18737 2 [ID: 2] region chains Ch,Cj,Cl [1-135] RMSD: 178.301 
    18738  
    18739 
    18740 > hide sel & #!28.4,6 surfaces
    18741 
    18742 > hide sel & #!28.4,6 cartoons
    18743 
    18744 > select add #28
    18745 
    18746 38799 atoms, 39588 bonds, 4776 residues, 12 models selected 
    18747 
    18748 > select subtract #28
    18749 
    18750 4 models selected 
    18751 
    18752 > select add #32
    18753 
    18754 19762 atoms, 20168 bonds, 2435 residues, 5 models selected 
    18755 Alignment identifier is 32.1/BJ 
    18756 Alignment identifier is 1 
    18757 Alignment identifier is 32.4/Ck 
    18758 
    18759 > select #32.2/Ch:1-2 #32.3/Cj:1-2
    18760 
    18761 32 atoms, 30 bonds, 4 residues, 2 models selected 
    18762 
    18763 > select #32.2/Ch:1-135 #32.3/Cj:1-135
    18764 
    18765 2102 atoms, 2118 bonds, 270 residues, 2 models selected 
    18766 1 [ID: 1] region chains Ch,Cj [1-135] RMSD: 127.364 
    18767  
    18768 
    18769 > hide sel & #!32.3 surfaces
    18770 
    18771 > hide sel & #!32.3 cartoons
    18772 
    18773 > select add #32
    18774 
    18775 19762 atoms, 20168 bonds, 2435 residues, 6 models selected 
    18776 
    18777 > select subtract #32
    18778 
    18779 3 models selected 
    18780 
    18781 > select add #33
    18782 
    18783 19762 atoms, 20168 bonds, 2435 residues, 5 models selected 
    18784 Alignment identifier is 33.1/BJ 
    18785 Alignment identifier is 1 
    18786 Alignment identifier is 33.4/Ck 
    18787 
    18788 > select #33.2/Ch:1-4 #33.3/Cj:1-4
    18789 
    18790 66 atoms, 64 bonds, 8 residues, 2 models selected 
    18791 
    18792 > select #33.2/Ch:1-135 #33.3/Cj:1-135
    18793 
    18794 2102 atoms, 2118 bonds, 270 residues, 2 models selected 
    18795 1 [ID: 1] region chains Ch,Cj [1-135] RMSD: 127.364 
    18796  
    18797 
    18798 > hide sel & #!33.2 surfaces
    18799 
    18800 > hide sel & #!33.2 cartoons
    18801 
    18802 > select add #33
    18803 
    18804 19762 atoms, 20168 bonds, 2435 residues, 6 models selected 
    18805 
    18806 > select subtract #33
    18807 
    18808 3 models selected 
    18809 
    18810 > show #!19 models
    18811 
    18812 > hide #!19 models
    18813 
    18814 > color #34 #72727233 models
    18815 
    18816 > save /Users/shoichi/Desktop/HP-Fig4C1_09172024.png supersample 2
    18817 > transparentBackground true
    18818 
    18819 > save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
    18820 > from_June2024/July_2024/Final-
    18821 > version_model/Flo_PflA_Local/Sep18-2024_Figure4_PflAB.cxs includeMaps true
    18822 
    18823 ——— End of log from Wed Sep 18 14:12:12 2024 ———
    18824 
    18825 opened ChimeraX session 
    18826 Showing PflA-2.seg - 27 regions, 27 surfaces 
    18827 
    18828 > open /Users/shoichitachiyama/Desktop/PflAB-working/PilNO_BasedonJack.pdb
    18829 
    18830 Summary of feedback from opening /Users/shoichitachiyama/Desktop/PflAB-
    18831 working/PilNO_BasedonJack.pdb 
    18832 --- 
    18833 warnings | End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10 
    18834 End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5 
    18835 Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
    18836 1 9 
    18837 Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
    18838 1 7 
    18839 Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
    18840 1 3 
    18841 Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
    18842 1 4 
    18843 Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
    18844 1 3 
    18845 2 messages similar to the above omitted 
    18846 End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0 
    18847 Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
    18848 0 
    18849 Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
    18850 0 
    18851 Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
    18852 107 0 
    18853 Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
    18854 133 0 
    18855 Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
    18856 145 0 
    18857 9 messages similar to the above omitted 
    18858 End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10 
    18859 End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5 
    18860 Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
    18861 1 9 
    18862 Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
    18863 1 7 
    18864 Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
    18865 1 3 
    18866 Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
    18867 1 4 
    18868 Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
    18869 1 3 
    18870 2 messages similar to the above omitted 
    18871 End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0 
    18872 Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
    18873 0 
    18874 Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
    18875 0 
    18876 Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
    18877 107 0 
    18878 Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
    18879 133 0 
    18880 Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
    18881 145 0 
    18882 9 messages similar to the above omitted 
    18883 End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10 
    18884 End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5 
    18885 Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
    18886 1 9 
    18887 Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
    18888 1 7 
    18889 Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
    18890 1 3 
    18891 Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
    18892 1 4 
    18893 Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
    18894 1 3 
    18895 2 messages similar to the above omitted 
    18896 End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0 
    18897 Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
    18898 0 
    18899 Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
    18900 0 
    18901 Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
    18902 107 0 
    18903 Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
    18904 133 0 
    18905 Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
    18906 145 0 
    18907 9 messages similar to the above omitted 
    18908 End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10 
    18909 End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5 
    18910 Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
    18911 1 9 
    18912 Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
    18913 1 7 
    18914 Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
    18915 1 3 
    18916 Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
    18917 1 4 
    18918 Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
    18919 1 3 
    18920 2 messages similar to the above omitted 
    18921 End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0 
    18922 Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
    18923 0 
    18924 Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
    18925 0 
    18926 Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
    18927 107 0 
    18928 Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
    18929 133 0 
    18930 Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
    18931 145 0 
    18932 9 messages similar to the above omitted 
    18933 End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10 
    18934 End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5 
    18935 Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
    18936 1 9 
    18937 Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
    18938 1 7 
    18939 Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
    18940 1 3 
    18941 Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
    18942 1 4 
    18943 Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
    18944 1 3 
    18945 2 messages similar to the above omitted 
    18946 End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0 
    18947 Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
    18948 0 
    18949 Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
    18950 0 
    18951 Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
    18952 107 0 
    18953 Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
    18954 133 0 
    18955 Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
    18956 145 0 
    18957 9 messages similar to the above omitted 
    18958 End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10 
    18959 End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5 
    18960 Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
    18961 1 9 
    18962 Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
    18963 1 7 
    18964 Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
    18965 1 3 
    18966 Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
    18967 1 4 
    18968 Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
    18969 1 3 
    18970 2 messages similar to the above omitted 
    18971 End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0 
    18972 Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
    18973 0 
    18974 Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
    18975 0 
    18976 Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
    18977 107 0 
    18978 Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
    18979 133 0 
    18980 Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
    18981 145 0 
    18982 9 messages similar to the above omitted 
    18983 End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10 
    18984 End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5 
    18985 Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
    18986 1 9 
    18987 Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
    18988 1 7 
    18989 Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
    18990 1 3 
    18991 Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
    18992 1 4 
    18993 Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
    18994 1 3 
    18995 2 messages similar to the above omitted 
    18996 End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0 
    18997 Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
    18998 0 
    18999 Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
    19000 0 
    19001 Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
    19002 107 0 
    19003 Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
    19004 133 0 
    19005 Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
    19006 145 0 
    19007 9 messages similar to the above omitted 
    19008 End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10 
    19009 End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5 
    19010 Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
    19011 1 9 
    19012 Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
    19013 1 7 
    19014 Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
    19015 1 3 
    19016 Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
    19017 1 4 
    19018 Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
    19019 1 3 
    19020 2 messages similar to the above omitted 
    19021 End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0 
    19022 Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
    19023 0 
    19024 Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
    19025 0 
    19026 Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
    19027 107 0 
    19028 Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
    19029 133 0 
    19030 Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
    19031 145 0 
    19032 9 messages similar to the above omitted 
    19033 End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10 
    19034 End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5 
    19035 Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
    19036 1 9 
    19037 Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
    19038 1 7 
    19039 Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
    19040 1 3 
    19041 Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
    19042 1 4 
    19043 Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
    19044 1 3 
    19045 2 messages similar to the above omitted 
    19046 End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0 
    19047 Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
    19048 0 
    19049 Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
    19050 0 
    19051 Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
    19052 107 0 
    19053 Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
    19054 133 0 
    19055 Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
    19056 145 0 
    19057 9 messages similar to the above omitted 
    19058 End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10 
    19059 End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5 
    19060 Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
    19061 1 9 
    19062 Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
    19063 1 7 
    19064 Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
    19065 1 3 
    19066 Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
    19067 1 4 
    19068 Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
    19069 1 3 
    19070 2 messages similar to the above omitted 
    19071 End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0 
    19072 Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
    19073 0 
    19074 Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
    19075 0 
    19076 Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
    19077 107 0 
    19078 Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
    19079 133 0 
    19080 Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
    19081 145 0 
    19082 9 messages similar to the above omitted 
    19083 End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10 
    19084 End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5 
    19085 Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
    19086 1 9 
    19087 Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
    19088 1 7 
    19089 Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
    19090 1 3 
    19091 Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
    19092 1 4 
    19093 Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
    19094 1 3 
    19095 2 messages similar to the above omitted 
    19096 End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0 
    19097 Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
    19098 0 
    19099 Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
    19100 0 
    19101 Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
    19102 107 0 
    19103 Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
    19104 133 0 
    19105 Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
    19106 145 0 
    19107 9 messages similar to the above omitted 
    19108 End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10 
    19109 End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5 
    19110 Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
    19111 1 9 
    19112 Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
    19113 1 7 
    19114 Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
    19115 1 3 
    19116 Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
    19117 1 4 
    19118 Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
    19119 1 3 
    19120 2 messages similar to the above omitted 
    19121 End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0 
    19122 Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
    19123 0 
    19124 Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
    19125 0 
    19126 Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
    19127 107 0 
    19128 Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
    19129 133 0 
    19130 Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
    19131 145 0 
    19132 9 messages similar to the above omitted 
    19133 End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10 
    19134 End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5 
    19135 Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
    19136 1 9 
    19137 Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
    19138 1 7 
    19139 Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
    19140 1 3 
    19141 Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
    19142 1 4 
    19143 Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
    19144 1 3 
    19145 2 messages similar to the above omitted 
    19146 End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0 
    19147 Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
    19148 0 
    19149 Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
    19150 0 
    19151 Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
    19152 107 0 
    19153 Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
    19154 133 0 
    19155 Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
    19156 145 0 
    19157 9 messages similar to the above omitted 
    19158 End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10 
    19159 End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5 
    19160 Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
    19161 1 9 
    19162 Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
    19163 1 7 
    19164 Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
    19165 1 3 
    19166 Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
    19167 1 4 
    19168 Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
    19169 1 3 
    19170 2 messages similar to the above omitted 
    19171 End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0 
    19172 Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
    19173 0 
    19174 Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
    19175 0 
    19176 Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
    19177 107 0 
    19178 Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
    19179 133 0 
    19180 Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
    19181 145 0 
    19182 9 messages similar to the above omitted 
    19183 End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10 
    19184 End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5 
    19185 Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
    19186 1 9 
    19187 Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
    19188 1 7 
    19189 Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
    19190 1 3 
    19191 Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
    19192 1 4 
    19193 Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
    19194 1 3 
    19195 2 messages similar to the above omitted 
    19196 End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0 
    19197 Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
    19198 0 
    19199 Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
    19200 0 
    19201 Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
    19202 107 0 
    19203 Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
    19204 133 0 
    19205 Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
    19206 145 0 
    19207 9 messages similar to the above omitted 
    19208 End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10 
    19209 End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5 
    19210 Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
    19211 1 9 
    19212 Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
    19213 1 7 
    19214 Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
    19215 1 3 
    19216 Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
    19217 1 4 
    19218 Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
    19219 1 3 
    19220 2 messages similar to the above omitted 
    19221 End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0 
    19222 Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
    19223 0 
    19224 Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
    19225 0 
    19226 Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
    19227 107 0 
    19228 Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
    19229 133 0 
    19230 Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
    19231 145 0 
    19232 9 messages similar to the above omitted 
    19233 End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10 
    19234 End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5 
    19235 Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
    19236 1 9 
    19237 Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
    19238 1 7 
    19239 Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
    19240 1 3 
    19241 Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
    19242 1 4 
    19243 Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
    19244 1 3 
    19245 2 messages similar to the above omitted 
    19246 End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0 
    19247 Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
    19248 0 
    19249 Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
    19250 0 
    19251 Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
    19252 107 0 
    19253 Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
    19254 133 0 
    19255 Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
    19256 145 0 
    19257 9 messages similar to the above omitted 
    19258 End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10 
    19259 End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5 
    19260 Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
    19261 1 9 
    19262 Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
    19263 1 7 
    19264 Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
    19265 1 3 
    19266 Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
    19267 1 4 
    19268 Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
    19269 1 3 
    19270 2 messages similar to the above omitted 
    19271 End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0 
    19272 Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
    19273 0 
    19274 Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
    19275 0 
    19276 Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
    19277 107 0 
    19278 Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
    19279 133 0 
    19280 Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
    19281 145 0 
    19282 9 messages similar to the above omitted 
    19283 End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10 
    19284 End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5 
    19285 Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
    19286 1 9 
    19287 Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
    19288 1 7 
    19289 Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
    19290 1 3 
    19291 Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
    19292 1 4 
    19293 Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
    19294 1 3 
    19295 2 messages similar to the above omitted 
    19296 End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0 
    19297 Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
    19298 0 
    19299 Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
    19300 0 
    19301 Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
    19302 107 0 
    19303 Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
    19304 133 0 
    19305 Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
    19306 145 0 
    19307 9 messages similar to the above omitted 
    19308 End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10 
    19309 End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5 
    19310 Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
    19311 1 9 
    19312 Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
    19313 1 7 
    19314 Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
    19315 1 3 
    19316 Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
    19317 1 4 
    19318 Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
    19319 1 3 
    19320 2 messages similar to the above omitted 
    19321 End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0 
    19322 Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
    19323 0 
    19324 Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
    19325 0 
    19326 Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
    19327 107 0 
    19328 Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
    19329 133 0 
    19330 Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
    19331 145 0 
    19332 9 messages similar to the above omitted 
    19333 End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10 
    19334 End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5 
    19335 Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
    19336 1 9 
    19337 Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
    19338 1 7 
    19339 Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
    19340 1 3 
    19341 Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
    19342 1 4 
    19343 Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
    19344 1 3 
    19345 2 messages similar to the above omitted 
    19346 End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0 
    19347 Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
    19348 0 
    19349 Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
    19350 0 
    19351 Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
    19352 107 0 
    19353 Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
    19354 133 0 
    19355 Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
    19356 145 0 
    19357 9 messages similar to the above omitted 
    19358 End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10 
    19359 End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5 
    19360 Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
    19361 1 9 
    19362 Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
    19363 1 7 
    19364 Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
    19365 1 3 
    19366 Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
    19367 1 4 
    19368 Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
    19369 1 3 
    19370 2 messages similar to the above omitted 
    19371 End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0 
    19372 Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
    19373 0 
    19374 Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
    19375 0 
    19376 Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
    19377 107 0 
    19378 Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
    19379 133 0 
    19380 Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
    19381 145 0 
    19382 9 messages similar to the above omitted 
    19383 End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10 
    19384 End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5 
    19385 Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
    19386 1 9 
    19387 Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
    19388 1 7 
    19389 Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
    19390 1 3 
    19391 Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
    19392 1 4 
    19393 Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
    19394 1 3 
    19395 2 messages similar to the above omitted 
    19396 End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0 
    19397 Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
    19398 0 
    19399 Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
    19400 0 
    19401 Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
    19402 107 0 
    19403 Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
    19404 133 0 
    19405 Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
    19406 145 0 
    19407 9 messages similar to the above omitted 
    19408 End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10 
    19409 End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5 
    19410 Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
    19411 1 9 
    19412 Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
    19413 1 7 
    19414 Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
    19415 1 3 
    19416 Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
    19417 1 4 
    19418 Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
    19419 1 3 
    19420 2 messages similar to the above omitted 
    19421 End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0 
    19422 Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
    19423 0 
    19424 Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
    19425 0 
    19426 Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
    19427 107 0 
    19428 Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
    19429 133 0 
    19430 Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
    19431 145 0 
    19432 9 messages similar to the above omitted 
    19433 End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10 
    19434 End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5 
    19435 Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
    19436 1 9 
    19437 Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
    19438 1 7 
    19439 Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
    19440 1 3 
    19441 Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
    19442 1 4 
    19443 Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
    19444 1 3 
    19445 2 messages similar to the above omitted 
    19446 End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0 
    19447 Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
    19448 0 
    19449 Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
    19450 0 
    19451 Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
    19452 107 0 
    19453 Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
    19454 133 0 
    19455 Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
    19456 145 0 
    19457 9 messages similar to the above omitted 
    19458 End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10 
    19459 End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5 
    19460 Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
    19461 1 9 
    19462 Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
    19463 1 7 
    19464 Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
    19465 1 3 
    19466 Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
    19467 1 4 
    19468 Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
    19469 1 3 
    19470 2 messages similar to the above omitted 
    19471 End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0 
    19472 Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
    19473 0 
    19474 Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
    19475 0 
    19476 Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
    19477 107 0 
    19478 Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
    19479 133 0 
    19480 Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
    19481 145 0 
    19482 9 messages similar to the above omitted 
    19483 End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10 
    19484 End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5 
    19485 Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
    19486 1 9 
    19487 Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
    19488 1 7 
    19489 Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
    19490 1 3 
    19491 Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
    19492 1 4 
    19493 Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
    19494 1 3 
    19495 2 messages similar to the above omitted 
    19496 End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0 
    19497 Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
    19498 0 
    19499 Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
    19500 0 
    19501 Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
    19502 107 0 
    19503 Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
    19504 133 0 
    19505 Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
    19506 145 0 
    19507 9 messages similar to the above omitted 
    19508 End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10 
    19509 End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5 
    19510 Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
    19511 1 9 
    19512 Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
    19513 1 7 
    19514 Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
    19515 1 3 
    19516 Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
    19517 1 4 
    19518 Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
    19519 1 3 
    19520 2 messages similar to the above omitted 
    19521 End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0 
    19522 Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
    19523 0 
    19524 Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
    19525 0 
    19526 Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
    19527 107 0 
    19528 Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
    19529 133 0 
    19530 Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
    19531 145 0 
    19532 9 messages similar to the above omitted 
    19533 End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10 
    19534 End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5 
    19535 Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
    19536 1 9 
    19537 Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
    19538 1 7 
    19539 Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
    19540 1 3 
    19541 Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
    19542 1 4 
    19543 Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
    19544 1 3 
    19545 2 messages similar to the above omitted 
    19546 End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0 
    19547 Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
    19548 0 
    19549 Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
    19550 0 
    19551 Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
    19552 107 0 
    19553 Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
    19554 133 0 
    19555 Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
    19556 145 0 
    19557 9 messages similar to the above omitted 
    19558 End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10 
    19559 End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5 
    19560 Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
    19561 1 9 
    19562 Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
    19563 1 7 
    19564 Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
    19565 1 3 
    19566 Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
    19567 1 4 
    19568 Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
    19569 1 3 
    19570 2 messages similar to the above omitted 
    19571 End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0 
    19572 Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
    19573 0 
    19574 Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
    19575 0 
    19576 Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
    19577 107 0 
    19578 Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
    19579 133 0 
    19580 Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
    19581 145 0 
    19582 9 messages similar to the above omitted 
    19583 End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10 
    19584 End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5 
    19585 Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
    19586 1 9 
    19587 Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
    19588 1 7 
    19589 Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
    19590 1 3 
    19591 Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
    19592 1 4 
    19593 Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
    19594 1 3 
    19595 2 messages similar to the above omitted 
    19596 End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0 
    19597 Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
    19598 0 
    19599 Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
    19600 0 
    19601 Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
    19602 107 0 
    19603 Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
    19604 133 0 
    19605 Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
    19606 145 0 
    19607 9 messages similar to the above omitted 
    19608 End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10 
    19609 End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5 
    19610 Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
    19611 1 9 
    19612 Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
    19613 1 7 
    19614 Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
    19615 1 3 
    19616 Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
    19617 1 4 
    19618 Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
    19619 1 3 
    19620 2 messages similar to the above omitted 
    19621 End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0 
    19622 Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
    19623 0 
    19624 Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
    19625 0 
    19626 Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
    19627 107 0 
    19628 Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
    19629 133 0 
    19630 Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
    19631 145 0 
    19632 9 messages similar to the above omitted 
    19633 End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10 
    19634 End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5 
    19635 Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
    19636 1 9 
    19637 Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
    19638 1 7 
    19639 Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
    19640 1 3 
    19641 Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
    19642 1 4 
    19643 Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
    19644 1 3 
    19645 2 messages similar to the above omitted 
    19646 End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0 
    19647 Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
    19648 0 
    19649 Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
    19650 0 
    19651 Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
    19652 107 0 
    19653 Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
    19654 133 0 
    19655 Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
    19656 145 0 
    19657 9 messages similar to the above omitted 
    19658 End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10 
    19659 End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5 
    19660 Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
    19661 1 9 
    19662 Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
    19663 1 7 
    19664 Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
    19665 1 3 
    19666 Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
    19667 1 4 
    19668 Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
    19669 1 3 
    19670 2 messages similar to the above omitted 
    19671 End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0 
    19672 Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
    19673 0 
    19674 Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
    19675 0 
    19676 Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
    19677 107 0 
    19678 Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
    19679 133 0 
    19680 Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
    19681 145 0 
    19682 9 messages similar to the above omitted 
    19683 End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10 
    19684 End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5 
    19685 Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
    19686 1 9 
    19687 Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
    19688 1 7 
    19689 Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
    19690 1 3 
    19691 Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
    19692 1 4 
    19693 Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
    19694 1 3 
    19695 2 messages similar to the above omitted 
    19696 End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0 
    19697 Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
    19698 0 
    19699 Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
    19700 0 
    19701 Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
    19702 107 0 
    19703 Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
    19704 133 0 
    19705 Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
    19706 145 0 
    19707 9 messages similar to the above omitted 
    19708 End residue of secondary structure not found: HELIX 1 1 LYS A 22 ALA A 31 1 10 
    19709 End residue of secondary structure not found: HELIX 2 2 LYS A 89 ILE A 93 1 5 
    19710 Start residue of secondary structure not found: HELIX 3 3 THR A 152 ASN A 160
    19711 1 9 
    19712 Start residue of secondary structure not found: HELIX 4 4 LEU A 211 VAL A 217
    19713 1 7 
    19714 Start residue of secondary structure not found: HELIX 5 5 VAL A 218 ASN A 220
    19715 1 3 
    19716 Start residue of secondary structure not found: HELIX 6 6 LEU A 258 TYR A 261
    19717 1 4 
    19718 Start residue of secondary structure not found: HELIX 7 7 LEU A 282 PHE A 284
    19719 1 3 
    19720 2 messages similar to the above omitted 
    19721 End residue of secondary structure not found: SHEET 2 2 1 LYS A 60 ASP A 65 0 
    19722 Start residue of secondary structure not found: SHEET 3 3 1 LEU A 70 GLN A 74
    19723 0 
    19724 Start residue of secondary structure not found: SHEET 4 4 1 MET A 96 VAL A 99
    19725 0 
    19726 Start residue of secondary structure not found: SHEET 5 5 1 ALA A 104 ALA A
    19727 107 0 
    19728 Start residue of secondary structure not found: SHEET 6 6 1 VAL A 131 SER A
    19729 133 0 
    19730 Start residue of secondary structure not found: SHEET 7 7 1 GLY A 141 GLY A
    19731 145 0 
    19732 9 messages similar to the above omitted 
    19733  
    19734 Chain information for PilNO_BasedonJack.pdb 
    19735 --- 
    19736 Chain | Description 
    19737 35.1/A 35.2/A 35.3/A 35.4/A 35.5/A 35.6/A 35.7/A 35.8/A 35.9/A 35.10/A 35.11/A 35.12/A 35.13/A 35.14/A 35.15/A 35.16/A 35.17/A 35.18/A 35.19/A 35.20/A 35.21/A 35.22/A 35.23/A 35.24/A 35.25/A 35.26/A 35.27/A 35.28/A 35.29/A 35.30/A 35.31/A 35.32/A 35.33/A 35.34/A 35.35/A 35.36/A | No description available 
    19738 35.1/B 35.2/B 35.3/B 35.4/B 35.5/B 35.6/B 35.7/B 35.8/B 35.9/B 35.10/B 35.11/B 35.12/B 35.13/B 35.14/B 35.15/B 35.16/B 35.17/B 35.18/B 35.19/B 35.20/B 35.21/B 35.22/B 35.23/B 35.24/B 35.25/B 35.26/B 35.27/B 35.28/B 35.29/B 35.30/B 35.31/B 35.32/B 35.33/B 35.34/B 35.35/B 35.36/B | No description available 
    19739  
     3251[deleted to fit within ticket size limits]
    197403252
    197413253> hide #!11 models