Changes between Initial Version and Version 1 of Ticket #8823


Ignore:
Timestamp:
Apr 12, 2023, 9:04:47 AM (3 years ago)
Author:
Eric Pettersen
Comment:

Reported by Leonardo Lima

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #8823

    • Property Cc Eric Pettersen Tom Goddard added
    • Property Component Unassigned → Third Party
    • Property Owner set to Tristan Croll
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → assigned
    • Property Summary ChimeraX bug report submission → Crash deleting atomic symmetry model(?)

  • Ticket #8823 – Description

    initial v1  
    29842984Changed 53 atom styles 
    29852985
    2986 > select clear
    2987 
    2988 > style #1/r:116|/r:112|/r:113 stick
    2989 
    2990 Changed 53 atom styles 
    2991 
    2992 > select clear
    2993 
    2994 [Repeated 1 time(s)]
    2995 
    2996 > ui tool show "Ramachandran Plot"
    2997 
    2998 > isolde pepflip sel
    2999 
    3000 Flipping the peptide bond for 1 residues 
    3001 
    3002 > select clear
    3003 
    3004 > isolde pepflip sel
    3005 
    3006 Flipping the peptide bond for 1 residues 
    3007 
    3008 > select clear
    3009 
    3010 > ui tool show "Ramachandran Plot"
    3011 
    3012 [Repeated 1 time(s)]
    3013 
    3014 > isolde pepflip sel
    3015 
    3016 Flipping the peptide bond for 1 residues 
    3017 
    3018 > select clear
    3019 
    3020 > isolde pepflip sel
    3021 
    3022 Flipping the peptide bond for 1 residues 
    3023 
    3024 > select clear
    3025 
    3026 > ui tool show "Ramachandran Plot"
    3027 
    3028 > select clear
    3029 
    3030 > ui tool show "Ramachandran Plot"
    3031 
    3032 [Repeated 1 time(s)]
    3033 
    3034 > select clear
    3035 
    3036 > isolde sim stop
    3037 
    3038 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3039 chains... 
    3040 ISOLDE: stopped sim 
    3041 
    3042 > isolde sim start sel
    3043 
    3044 ISOLDE: started sim 
    3045 
    3046 > isolde sim stop
    3047 
    3048 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3049 chains... 
    3050 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    3051 standards. 
    3052 ISOLDE: stopped sim 
    3053 
    3054 > view #1/r:121
    3055 
    3056 > select #1/r:121
    3057 
    3058 21 atoms, 21 bonds, 1 residue, 1 model selected 
    3059 
    3060 > isolde sim start sel
    3061 
    3062 ISOLDE: started sim 
    3063 
    3064 > select clear
    3065 
    3066 [Repeated 3 time(s)]
    3067 
    3068 > isolde pepflip sel
    3069 
    3070 Flipping the peptide bond for 1 residues 
    3071 
    3072 > isolde pepflip sel
    3073 
    3074 Flipping the peptide bond for 1 residues 
    3075 
    3076 > select clear
    3077 
    3078 Unable to flip peptide bond after 50 rounds. Giving up. 
    3079 
    3080 > isolde pepflip sel
    3081 
    3082 Flipping the peptide bond for 1 residues 
    3083 
    3084 > isolde pepflip sel
    3085 
    3086 Flipping the peptide bond for 1 residues 
    3087 
    3088 > select clear
    3089 
    3090 > isolde pepflip sel
    3091 
    3092 Flipping the peptide bond for 1 residues 
    3093 
    3094 > isolde pepflip sel
    3095 
    3096 Flipping the peptide bond for 1 residues 
    3097 
    3098 > select clear
    3099 
    3100 [Repeated 2 time(s)]
    3101 
    3102 > ui tool show "Ramachandran Plot"
    3103 
    3104 > isolde pepflip sel
    3105 
    3106 Flipping the peptide bond for 1 residues 
    3107 
    3108 > select clear
    3109 
    3110 [Repeated 2 time(s)]
    3111 
    3112 > isolde pepflip sel
    3113 
    3114 Flipping the peptide bond for 1 residues 
    3115 
    3116 > select clear
    3117 
    3118 > isolde pepflip sel
    3119 
    3120 Flipping the peptide bond for 1 residues 
    3121 
    3122 > isolde pepflip sel
    3123 
    3124 Flipping the peptide bond for 1 residues 
    3125 
    3126 > select clear
    3127 
    3128 > ui tool show "Ramachandran Plot"
    3129 
    3130 [Repeated 2 time(s)]
    3131 
    3132 > isolde sim stop
    3133 
    3134 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3135 chains... 
    3136 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    3137 standards. 
    3138 ISOLDE: stopped sim 
    3139 
    3140 > isolde sim start sel
    3141 
    3142 ISOLDE: started sim 
    3143 
    3144 > select clear
    3145 
    3146 > isolde pepflip sel
    3147 
    3148 Flipping the peptide bond for 1 residues 
    3149 
    3150 > select clear
    3151 
    3152 > isolde sim stop
    3153 
    3154 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3155 chains... 
    3156 ISOLDE: stopped sim 
    3157 
    3158 > view #1/r:121
    3159 
    3160 > select #1/r:121
    3161 
    3162 21 atoms, 21 bonds, 1 residue, 1 model selected 
    3163 
    3164 > isolde sim start sel
    3165 
    3166 ISOLDE: started sim 
    3167 
    3168 > ui tool show "Ramachandran Plot"
    3169 
    3170 > isolde sim stop
    3171 
    3172 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3173 chains... 
    3174 ISOLDE: stopped sim 
    3175 
    3176 > isolde sim start sel
    3177 
    3178 ISOLDE: started sim 
    3179 
    3180 > isolde sim stop
    3181 
    3182 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3183 chains... 
    3184 ISOLDE: stopped sim 
    3185 
    3186 > isolde pepflip sel
    3187 
    3188 Flipping the peptide bond for 1 residues 
    3189 ISOLDE: started sim 
    3190 
    3191 > isolde pepflip sel
    3192 
    3193 Flipping the peptide bond for 1 residues 
    3194 
    3195 > isolde pepflip sel
    3196 
    3197 Flipping the peptide bond for 1 residues 
    3198 
    3199 > isolde pepflip sel
    3200 
    3201 Flipping the peptide bond for 1 residues 
    3202 
    3203 > isolde pepflip sel
    3204 
    3205 Flipping the peptide bond for 1 residues 
    3206 
    3207 > isolde pepflip sel
    3208 
    3209 Flipping the peptide bond for 1 residues 
    3210 
    3211 > isolde pepflip sel
    3212 
    3213 Flipping the peptide bond for 1 residues 
    3214 
    3215 > select clear
    3216 
    3217 > ui tool show "Ramachandran Plot"
    3218 
    3219 > select #1/O:9
    3220 
    3221 20 atoms, 20 bonds, 1 residue, 1 model selected 
    3222 
    3223 > ui tool show "Ramachandran Plot"
    3224 
    3225 > select clear
    3226 
    3227 [Repeated 2 time(s)]
    3228 
    3229 > isolde pepflip sel
    3230 
    3231 Flipping the peptide bond for 1 residues 
    3232 
    3233 > select clear
    3234 
    3235 > isolde pepflip sel
    3236 
    3237 Flipping the peptide bond for 1 residues 
    3238 
    3239 > isolde pepflip sel
    3240 
    3241 Flipping the peptide bond for 1 residues 
    3242 
    3243 > select clear
    3244 
    3245 [Repeated 3 time(s)]
    3246 
    3247 > isolde pepflip sel
    3248 
    3249 Flipping the peptide bond for 1 residues 
    3250 
    3251 > select clear
    3252 
    3253 > ui tool show "Ramachandran Plot"
    3254 
    3255 [Repeated 1 time(s)]
    3256 
    3257 > select clear
    3258 
    3259 [Repeated 1 time(s)]
    3260 
    3261 > isolde pepflip sel
    3262 
    3263 Flipping the peptide bond for 1 residues 
    3264 
    3265 > select clear
    3266 
    3267 > ui tool show "Ramachandran Plot"
    3268 
    3269 > isolde pepflip sel
    3270 
    3271 Flipping the peptide bond for 1 residues 
    3272 
    3273 > isolde pepflip sel
    3274 
    3275 Flipping the peptide bond for 1 residues 
    3276 
    3277 > isolde pepflip sel
    3278 
    3279 Flipping the peptide bond for 1 residues 
    3280 
    3281 > isolde pepflip sel
    3282 
    3283 Flipping the peptide bond for 1 residues 
    3284 
    3285 > select clear
    3286 
    3287 > isolde pepflip sel
    3288 
    3289 Flipping the peptide bond for 1 residues 
    3290 
    3291 > isolde pepflip sel
    3292 
    3293 Flipping the peptide bond for 1 residues 
    3294 
    3295 > select clear
    3296 
    3297 > isolde pepflip sel
    3298 
    3299 Flipping the peptide bond for 1 residues 
    3300 
    3301 > isolde pepflip sel
    3302 
    3303 Flipping the peptide bond for 1 residues 
    3304 
    3305 > select clear
    3306 
    3307 [Repeated 1 time(s)]
    3308 
    3309 > isolde pepflip sel
    3310 
    3311 Flipping the peptide bond for 1 residues 
    3312 
    3313 > isolde pepflip sel
    3314 
    3315 Flipping the peptide bond for 1 residues 
    3316 
    3317 > isolde pepflip sel
    3318 
    3319 Flipping the peptide bond for 1 residues 
    3320 
    3321 > isolde pepflip sel
    3322 
    3323 Flipping the peptide bond for 1 residues 
    3324 
    3325 > isolde pepflip sel
    3326 
    3327 Flipping the peptide bond for 1 residues 
    3328 
    3329 > isolde pepflip sel
    3330 
    3331 Flipping the peptide bond for 1 residues 
    3332 
    3333 > isolde pepflip sel
    3334 
    3335 Flipping the peptide bond for 1 residues 
    3336 
    3337 > isolde sim stop
    3338 
    3339 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3340 chains... 
    3341 ISOLDE: stopped sim 
    3342 
    3343 > select #1
    3344 
    3345 144428 atoms, 150209 bonds, 5 pseudobonds, 6905 residues, 22 models selected 
    3346 
    3347 > select #1>O8-13
    3348 
    3349 Expected an objects specifier or a keyword 
    3350 
    3351 > select #1/O:8-13
    3352 
    3353 110 atoms, 112 bonds, 6 residues, 1 model selected 
    3354 
    3355 > select #1/O:10-11
    3356 
    3357 36 atoms, 35 bonds, 2 residues, 1 model selected 
    3358 
    3359 > isolde sim start sel
    3360 
    3361 ISOLDE: started sim 
    3362 
    3363 > isolde pepflip sel
    3364 
    3365 Flipping the peptide bond for 1 residues 
    3366 
    3367 > isolde pepflip sel
    3368 
    3369 Flipping the peptide bond for 1 residues 
    3370 
    3371 > isolde pepflip sel
    3372 
    3373 Flipping the peptide bond for 1 residues 
    3374 
    3375 > isolde pepflip sel
    3376 
    3377 Flipping the peptide bond for 1 residues 
    3378 
    3379 > select clear
    3380 
    3381 > isolde pepflip sel
    3382 
    3383 Flipping the peptide bond for 1 residues 
    3384 
    3385 > isolde pepflip sel
    3386 
    3387 Flipping the peptide bond for 1 residues 
    3388 
    3389 > isolde sim stop
    3390 
    3391 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3392 chains... 
    3393 ISOLDE: stopped sim 
    3394 
    3395 > select #1
    3396 
    3397 144428 atoms, 150209 bonds, 5 pseudobonds, 6905 residues, 22 models selected 
    3398 
    3399 > select #1/r:58-64|/O:1-15
    3400 
    3401 358 atoms, 361 bonds, 22 residues, 1 model selected 
    3402 
    3403 > isolde sim start sel
    3404 
    3405 ISOLDE: started sim 
    3406 
    3407 > select clear
    3408 
    3409 > isolde pepflip sel
    3410 
    3411 Flipping the peptide bond for 1 residues 
    3412 
    3413 > isolde pepflip sel
    3414 
    3415 Flipping the peptide bond for 1 residues 
    3416 
    3417 > isolde pepflip sel
    3418 
    3419 Flipping the peptide bond for 1 residues 
    3420 
    3421 > isolde pepflip sel
    3422 
    3423 Flipping the peptide bond for 1 residues 
    3424 
    3425 > isolde pepflip sel
    3426 
    3427 Flipping the peptide bond for 1 residues 
    3428 
    3429 > isolde pepflip sel
    3430 
    3431 Flipping the peptide bond for 1 residues 
    3432 
    3433 > select clear
    3434 
    3435 > isolde pepflip sel
    3436 
    3437 Flipping the peptide bond for 1 residues 
    3438 
    3439 > isolde pepflip sel
    3440 
    3441 Flipping the peptide bond for 1 residues 
    3442 
    3443 > select clear
    3444 
    3445 Unable to flip peptide bond after 50 rounds. Giving up. 
    3446 
    3447 > ui tool show "Ramachandran Plot"
    3448 
    3449 > select clear
    3450 
    3451 > isolde pepflip sel
    3452 
    3453 Flipping the peptide bond for 1 residues 
    3454 
    3455 > select clear
    3456 
    3457 [Repeated 1 time(s)]
    3458 
    3459 > ui tool show "Ramachandran Plot"
    3460 
    3461 > view sel
    3462 
    3463 > isolde sim stop
    3464 
    3465 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3466 chains... 
    3467 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    3468 standards. 
    3469 ISOLDE: stopped sim 
    3470 
    3471 > isolde sim start sel
    3472 
    3473 ISOLDE: started sim 
    3474 
    3475 > select clear
    3476 
    3477 > isolde pepflip sel
    3478 
    3479 Flipping the peptide bond for 1 residues 
    3480 
    3481 > isolde pepflip sel
    3482 
    3483 Flipping the peptide bond for 1 residues 
    3484 
    3485 > isolde pepflip sel
    3486 
    3487 Flipping the peptide bond for 1 residues 
    3488 
    3489 > isolde pepflip sel
    3490 
    3491 Flipping the peptide bond for 1 residues 
    3492 
    3493 > select clear
    3494 
    3495 > isolde pepflip sel
    3496 
    3497 Flipping the peptide bond for 1 residues 
    3498 
    3499 > isolde pepflip sel
    3500 
    3501 Flipping the peptide bond for 1 residues 
    3502 
    3503 > isolde pepflip sel
    3504 
    3505 Flipping the peptide bond for 1 residues 
    3506 
    3507 > isolde sim stop
    3508 
    3509 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3510 chains... 
    3511 ISOLDE: stopped sim 
    3512 
    3513 > isolde sim start sel
    3514 
    3515 ISOLDE: started sim 
    3516 
    3517 > select clear
    3518 
    3519 > isolde pepflip sel
    3520 
    3521 Flipping the peptide bond for 1 residues 
    3522 
    3523 > isolde pepflip sel
    3524 
    3525 Flipping the peptide bond for 1 residues 
    3526 
    3527 > select clear
    3528 
    3529 > select #1/r:58-64|/O:1-15
    3530 
    3531 358 atoms, 361 bonds, 22 residues, 1 model selected 
    3532 
    3533 > select #1/r:42
    3534 
    3535 16 atoms, 15 bonds, 1 residue, 1 model selected 
    3536 
    3537 > ui tool show "Ramachandran Plot"
    3538 
    3539 > isolde sim stop
    3540 
    3541 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3542 chains... 
    3543 ISOLDE: stopped sim 
    3544 
    3545 > view #1/r:42
    3546 
    3547 > select #1/r:42
    3548 
    3549 16 atoms, 15 bonds, 1 residue, 1 model selected 
    3550 
    3551 > isolde sim start sel
    3552 
    3553 ISOLDE: started sim 
    3554 
    3555 > ui tool show "Ramachandran Plot"
    3556 
    3557 > isolde sim stop
    3558 
    3559 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3560 chains... 
    3561 ISOLDE: stopped sim 
    3562 
    3563 > view #1/r:58-64|/O:1-15
    3564 
    3565 > select #1/r:58-64|/O:1-15
    3566 
    3567 358 atoms, 361 bonds, 22 residues, 1 model selected 
    3568 
    3569 > isolde sim start sel
    3570 
    3571 ISOLDE: started sim 
    3572 
    3573 > ui tool show "Ramachandran Plot"
    3574 
    3575 > select clear
    3576 
    3577 > isolde sim stop
    3578 
    3579 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3580 chains... 
    3581 ISOLDE: stopped sim 
    3582 
    3583 > view #1/O:10
    3584 
    3585 > select#1/O:10
    3586 
    3587 Unknown command: select#1/O:10 
    3588 
    3589 > select #1/O:10
    3590 
    3591 14 atoms, 13 bonds, 1 residue, 1 model selected 
    3592 
    3593 > select #1/O:10
    3594 
    3595 14 atoms, 13 bonds, 1 residue, 1 model selected 
    3596 
    3597 > isolde sim start sel
    3598 
    3599 ISOLDE: started sim 
    3600 
    3601 > ui tool show "Ramachandran Plot"
    3602 
    3603 > select clear
    3604 
    3605 > isolde sim stop
    3606 
    3607 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3608 chains... 
    3609 ISOLDE: stopped sim 
    3610 
    3611 > select #1/O:10
    3612 
    3613 14 atoms, 13 bonds, 1 residue, 1 model selected 
    3614 
    3615 > isolde sim start sel
    3616 
    3617 ISOLDE: started sim 
    3618 
    3619 > isolde sim stop
    3620 
    3621 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3622 chains... 
    3623 ISOLDE: stopped sim 
    3624 
    3625 > isolde sim start sel
    3626 
    3627 ISOLDE: started sim 
    3628 
    3629 > select clear
    3630 
    3631 > ui tool show "Ramachandran Plot"
    3632 
    3633 [Repeated 1 time(s)]
    3634 
    3635 > select clear
    3636 
    3637 [Repeated 6 time(s)]
    3638 
    3639 > ui tool show "Ramachandran Plot"
    3640 
    3641 > isolde sim stop
    3642 
    3643 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3644 chains... 
    3645 ISOLDE: stopped sim 
    3646 
    3647 > isolde sim start sel
    3648 
    3649 ISOLDE: started sim 
    3650 
    3651 > isolde pepflip sel
    3652 
    3653 Flipping the peptide bond for 1 residues 
    3654 
    3655 > select clear
    3656 
    3657 > isolde pepflip sel
    3658 
    3659 Flipping the peptide bond for 1 residues 
    3660 
    3661 > isolde pepflip sel
    3662 
    3663 Flipping the peptide bond for 1 residues 
    3664 
    3665 > select clear
    3666 
    3667 [Repeated 1 time(s)]
    3668 
    3669 > ui tool show "Ramachandran Plot"
    3670 
    3671 [Repeated 1 time(s)]
    3672 
    3673 > select clear
    3674 
    3675 [Repeated 1 time(s)]
    3676 
    3677 > isolde pepflip sel
    3678 
    3679 Flipping the peptide bond for 1 residues 
    3680 
    3681 > isolde pepflip sel
    3682 
    3683 Flipping the peptide bond for 1 residues 
    3684 
    3685 > select clear
    3686 
    3687 > isolde sim pause
    3688 
    3689 > select #1
    3690 
    3691 144428 atoms, 150209 bonds, 5 pseudobonds, 6905 residues, 22 models selected 
    3692 
    3693 > select #1/u:8-9
    3694 
    3695 34 atoms, 33 bonds, 2 residues, 1 model selected 
    3696 
    3697 > isolde sim resume
    3698 
    3699 > isolde pepflip sel
    3700 
    3701 Flipping the peptide bond for 1 residues 
    3702 
    3703 > select clear
    3704 
    3705 > select #1
    3706 
    3707 144428 atoms, 150209 bonds, 5 pseudobonds, 6905 residues, 22 models selected 
    3708 
    3709 > isolde sim stop
    3710 
    3711 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3712 chains... 
    3713 ISOLDE: stopped sim 
    3714 
    3715 > select #1/u:60-65|/u:8-12
    3716 
    3717 180 atoms, 180 bonds, 11 residues, 1 model selected 
    3718 
    3719 > isolde sim start sel
    3720 
    3721 ISOLDE: started sim 
    3722 
    3723 > isolde pepflip sel
    3724 
    3725 Flipping the peptide bond for 1 residues 
    3726 
    3727 > isolde pepflip sel
    3728 
    3729 Flipping the peptide bond for 1 residues 
    3730 
    3731 > isolde pepflip sel
    3732 
    3733 Flipping the peptide bond for 1 residues 
    3734 
    3735 > isolde pepflip sel
    3736 
    3737 Flipping the peptide bond for 1 residues 
    3738 
    3739 > isolde pepflip sel
    3740 
    3741 Flipping the peptide bond for 1 residues 
    3742 
    3743 > select clear
    3744 
    3745 [Repeated 1 time(s)]
    3746 
    3747 > isolde pepflip sel
    3748 
    3749 Flipping the peptide bond for 1 residues 
    3750 
    3751 > isolde pepflip sel
    3752 
    3753 Flipping the peptide bond for 1 residues 
    3754 Unable to flip peptide bond after 50 rounds. Giving up. 
    3755 
    3756 > isolde pepflip sel
    3757 
    3758 Flipping the peptide bond for 1 residues 
    3759 
    3760 > isolde pepflip sel
    3761 
    3762 Flipping the peptide bond for 1 residues 
    3763 
    3764 > select clear
    3765 
    3766 [Repeated 1 time(s)]
    3767 
    3768 > isolde sim stop
    3769 
    3770 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3771 chains... 
    3772 ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
    3773 standards. 
    3774 ISOLDE: stopped sim 
    3775 
    3776 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    3777 > mut8-no-C-ter/10-KSRP-no-C-ter-Step1-tenthSubsteps.cxs
    3778 
    3779 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    3780 
    3781 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    3782 > mut8-no-C-ter/10-KSRP-no-C-ter-Step1-tenthSubsteps.pdb
    3783 
    3784 > select #1/u:47-54
    3785 
    3786 123 atoms, 122 bonds, 8 residues, 1 model selected 
    3787 
    3788 > select clear
    3789 
    3790 > select #1/u:57-67
    3791 
    3792 162 atoms, 161 bonds, 11 residues, 1 model selected 
    3793 
    3794 > isolde sim start sel
    3795 
    3796 ISOLDE: started sim 
    3797 
    3798 > select #1/u:57-67
    3799 
    3800 162 atoms, 161 bonds, 11 residues, 1 model selected 
    3801 
    3802 > hide #!1.2 models
    3803 
    3804 > show #!1.2 models
    3805 
    3806 > hide #!1.2 models
    3807 
    3808 > show #!1.2 models
    3809 
    3810 > hide #!1.2 models
    3811 
    3812 > show #!1.2 models
    3813 
    3814 > isolde sim stop
    3815 
    3816 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3817 chains... 
    3818 ISOLDE: Corrected atom nomenclature of 6 residues in model #1.2 to IUPAC-IUB
    3819 standards. 
    3820 ISOLDE: stopped sim 
    3821 
    3822 > select #1/u:57-67
    3823 
    3824 162 atoms, 161 bonds, 11 residues, 1 model selected 
    3825 
    3826 > select #1/u:57-71
    3827 
    3828 223 atoms, 222 bonds, 15 residues, 1 model selected 
    3829 
    3830 > isolde sim start sel
    3831 
    3832 ISOLDE: started sim 
    3833 
    3834 > isolde pepflip sel
    3835 
    3836 Flipping the peptide bond for 1 residues 
    3837 
    3838 > isolde pepflip sel
    3839 
    3840 Flipping the peptide bond for 1 residues 
    3841 
    3842 > isolde pepflip sel
    3843 
    3844 Flipping the peptide bond for 1 residues 
    3845 
    3846 > isolde pepflip sel
    3847 
    3848 Flipping the peptide bond for 1 residues 
    3849 
    3850 > isolde pepflip sel
    3851 
    3852 Flipping the peptide bond for 1 residues 
    3853 
    3854 > isolde pepflip sel
    3855 
    3856 Flipping the peptide bond for 1 residues 
    3857 
    3858 > isolde pepflip sel
    3859 
    3860 Flipping the peptide bond for 1 residues 
    3861 
    3862 > isolde pepflip sel
    3863 
    3864 Flipping the peptide bond for 1 residues 
    3865 
    3866 > isolde pepflip sel
    3867 
    3868 Flipping the peptide bond for 1 residues 
    3869 
    3870 > isolde pepflip sel
    3871 
    3872 Flipping the peptide bond for 1 residues 
    3873 
    3874 > isolde sim start sel
    3875 
    3876 Simulation already running! 
    3877 
    3878 > isolde sim stop
    3879 
    3880 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3881 chains... 
    3882 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    3883 standards. 
    3884 ISOLDE: stopped sim 
    3885 
    3886 > isolde sim start sel
    3887 
    3888 ISOLDE: started sim 
    3889 
    3890 > isolde sim stop discardTo start
    3891 
    3892 reverting to start 
    3893 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3894 chains... 
    3895 ISOLDE: stopped sim 
    3896 
    3897 > isolde sim start sel
    3898 
    3899 ISOLDE: started sim 
    3900 
    3901 > isolde pepflip sel
    3902 
    3903 Flipping the peptide bond for 1 residues 
    3904 
    3905 > isolde pepflip sel
    3906 
    3907 Flipping the peptide bond for 1 residues 
    3908 
    3909 > isolde sim pause
    3910 
    3911 > isolde sim resume
    3912 
    3913 > isolde pepflip sel
    3914 
    3915 Flipping the peptide bond for 1 residues 
    3916 
    3917 > select clear
    3918 
    3919 [Repeated 2 time(s)]
    3920 
    3921 > isolde pepflip sel
    3922 
    3923 Flipping the peptide bond for 1 residues 
    3924 
    3925 > isolde sim stop
    3926 
    3927 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3928 chains... 
    3929 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    3930 standards. 
    3931 ISOLDE: stopped sim 
    3932 
    3933 > isolde sim start sel
    3934 
    3935 ISOLDE: started sim 
    3936 
    3937 > select clear
    3938 
    3939 [Repeated 5 time(s)]
    3940 
    3941 > isolde sim stop
    3942 
    3943 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3944 chains... 
    3945 ISOLDE: stopped sim 
    3946 
    3947 > select clear
    3948 
    3949 [Repeated 1 time(s)]
    3950 
    3951 > isolde sim start sel
    3952 
    3953 ISOLDE: started sim 
    3954 
    3955 > isolde sim stop
    3956 
    3957 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3958 chains... 
    3959 ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
    3960 standards. 
    3961 ISOLDE: stopped sim 
    3962 
    3963 > isolde sim start sel
    3964 
    3965 ISOLDE: started sim 
    3966 
    3967 > isolde pepflip sel
    3968 
    3969 Flipping the peptide bond for 1 residues 
    3970 
    3971 > isolde pepflip sel
    3972 
    3973 Flipping the peptide bond for 1 residues 
    3974 Unable to flip peptide bond after 50 rounds. Giving up. 
    3975 
    3976 > select clear
    3977 
    3978 [Repeated 2 time(s)]
    3979 
    3980 > isolde pepflip sel
    3981 
    3982 Flipping the peptide bond for 1 residues 
    3983 Peptide bond must be mobile in the simulation! 
    3984 
    3985 > select clear
    3986 
    3987 > isolde pepflip sel
    3988 
    3989 Flipping the peptide bond for 1 residues 
    3990 
    3991 > isolde pepflip sel
    3992 
    3993 Flipping the peptide bond for 1 residues 
    3994 
    3995 > select clear
    3996 
    3997 [Repeated 1 time(s)]
    3998 
    3999 > isolde pepflip sel
    4000 
    4001 Flipping the peptide bond for 1 residues 
    4002 
    4003 > isolde pepflip sel
    4004 
    4005 Flipping the peptide bond for 1 residues 
    4006 
    4007 > select clear
    4008 
    4009 [Repeated 1 time(s)]
    4010 
    4011 > isolde pepflip sel
    4012 
    4013 Flipping the peptide bond for 1 residues 
    4014 
    4015 > isolde pepflip sel
    4016 
    4017 Flipping the peptide bond for 1 residues 
    4018 
    4019 > isolde pepflip sel
    4020 
    4021 Flipping the peptide bond for 1 residues 
    4022 
    4023 > isolde pepflip sel
    4024 
    4025 Flipping the peptide bond for 1 residues 
    4026 
    4027 > select clear
    4028 
    4029 [Repeated 2 time(s)]
    4030 
    4031 > isolde pepflip sel
    4032 
    4033 Flipping the peptide bond for 1 residues 
    4034 
    4035 > isolde pepflip sel
    4036 
    4037 Flipping the peptide bond for 1 residues 
    4038 
    4039 > isolde pepflip sel
    4040 
    4041 Flipping the peptide bond for 1 residues 
    4042 
    4043 > select clear
    4044 
    4045 > ui tool show "Ramachandran Plot"
    4046 
    4047 > select clear
    4048 
    4049 > isolde pepflip sel
    4050 
    4051 Flipping the peptide bond for 1 residues 
    4052 
    4053 > ui tool show "Ramachandran Plot"
    4054 
    4055 > isolde pepflip sel
    4056 
    4057 Flipping the peptide bond for 1 residues 
    4058 
    4059 > select clear
    4060 
    4061 > isolde sim start sel
    4062 
    4063 No atoms selected! 
    4064 
    4065 > ui tool show "Ramachandran Plot"
    4066 
    4067 > isolde pepflip sel
    4068 
    4069 Flipping the peptide bond for 1 residues 
    4070 
    4071 > ui tool show "Ramachandran Plot"
    4072 
    4073 Traceback (most recent call last): 
    4074 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    4075 packages/matplotlib/cbook/__init__.py", line 287, in process 
    4076 func(*args, **kwargs) 
    4077 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    4078 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    4079 on_resize 
    4080 c.draw() 
    4081 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    4082 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    4083 self.figure.draw(self.renderer) 
    4084 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    4085 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    4086 result = draw(artist, renderer, *args, **kwargs) 
    4087 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    4088 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    4089 return draw(artist, renderer) 
    4090 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    4091 packages/matplotlib/figure.py", line 2796, in draw 
    4092 artists = self._get_draw_artists(renderer) 
    4093 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    4094 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    4095 ax.apply_aspect() 
    4096 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    4097 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    4098 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    4099 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    4100 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    4101 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    4102 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    4103 
    4104 > select clear
    4105 
    4106 [Repeated 1 time(s)]
    4107 
    4108 > isolde pepflip sel
    4109 
    4110 Flipping the peptide bond for 1 residues 
    4111 
    4112 > isolde pepflip sel
    4113 
    4114 Flipping the peptide bond for 1 residues 
    4115 
    4116 > select clear
    4117 
    4118 [Repeated 1 time(s)]
    4119 
    4120 > isolde pepflip sel
    4121 
    4122 Flipping the peptide bond for 1 residues 
    4123 
    4124 > isolde pepflip sel
    4125 
    4126 Flipping the peptide bond for 1 residues 
    4127 
    4128 > select clear
    4129 
    4130 [Repeated 3 time(s)]
    4131 
    4132 > isolde pepflip sel
    4133 
    4134 Flipping the peptide bond for 1 residues 
    4135 
    4136 > isolde pepflip sel
    4137 
    4138 Flipping the peptide bond for 1 residues 
    4139 
    4140 > isolde pepflip sel
    4141 
    4142 Flipping the peptide bond for 1 residues 
    4143 
    4144 > isolde pepflip sel
    4145 
    4146 Flipping the peptide bond for 1 residues 
    4147 
    4148 > isolde pepflip sel
    4149 
    4150 Flipping the peptide bond for 1 residues 
    4151 
    4152 > select clear
    4153 
    4154 [Repeated 2 time(s)]
    4155 
    4156 > select #1/u:57-71
    4157 
    4158 223 atoms, 222 bonds, 15 residues, 1 model selected 
    4159 
    4160 > select #1/u:57-71
    4161 
    4162 223 atoms, 222 bonds, 15 residues, 1 model selected 
    4163 
    4164 > select #1/u:57-67
    4165 
    4166 162 atoms, 161 bonds, 11 residues, 1 model selected 
    4167 
    4168 > select clear
    4169 
    4170 > select #1/u:25
    4171 
    4172 24 atoms, 23 bonds, 1 residue, 1 model selected 
    4173 
    4174 > view #1/u:25
    4175 
    4176 > select clear
    4177 
    4178 [Repeated 1 time(s)]
    4179 
    4180 > ui tool show "Ramachandran Plot"
    4181 
    4182 > isolde sim stop
    4183 
    4184 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4185 chains... 
    4186 ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
    4187 standards. 
    4188 ISOLDE: stopped sim 
    4189 
    4190 > isolde sim start sel
    4191 
    4192 ISOLDE: started sim 
    4193 
    4194 > isolde pepflip sel
    4195 
    4196 Flipping the peptide bond for 1 residues 
    4197 
    4198 > isolde pepflip sel
    4199 
    4200 Flipping the peptide bond for 1 residues 
    4201 
    4202 > select clear
    4203 
    4204 [Repeated 4 time(s)]
    4205 
    4206 > isolde pepflip sel
    4207 
    4208 Flipping the peptide bond for 1 residues 
    4209 
    4210 > isolde pepflip sel
    4211 
    4212 Flipping the peptide bond for 1 residues 
    4213 
    4214 > select clear
    4215 
    4216 [Repeated 1 time(s)]
    4217 
    4218 > select #1/u:57-67
    4219 
    4220 162 atoms, 161 bonds, 11 residues, 1 model selected 
    4221 
    4222 > select #1/u:28-42
    4223 
    4224 245 atoms, 247 bonds, 15 residues, 1 model selected 
    4225 
    4226 > isolde sim stop
    4227 
    4228 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4229 chains... 
    4230 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    4231 standards. 
    4232 ISOLDE: stopped sim 
    4233 
    4234 > style #1 ribbon
    4235 
    4236 Expected a keyword 
    4237 
    4238 > select #1/u:57-67
    4239 
    4240 162 atoms, 161 bonds, 11 residues, 1 model selected 
    4241 
    4242 > select #1/u:28-42
    4243 
    4244 245 atoms, 247 bonds, 15 residues, 1 model selected 
    4245 
    4246 > isolde sim start sel
    4247 
    4248 ISOLDE: started sim 
    4249 
    4250 > select #1/u:28-42
    4251 
    4252 245 atoms, 247 bonds, 15 residues, 1 model selected 
    4253 
    4254 > select #1/o:53-56
    4255 
    4256 68 atoms, 67 bonds, 4 residues, 1 model selected 
    4257 
    4258 > isolde sim stop
    4259 
    4260 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4261 chains... 
    4262 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    4263 standards. 
    4264 ISOLDE: stopped sim 
    4265 
    4266 > select #1/u:28-42|/o:53-56|/u:43-47
    4267 
    4268 400 atoms, 402 bonds, 24 residues, 1 model selected 
    4269 
    4270 > select #1/u:28-42|/o:53-56|/u:43-47
    4271 
    4272 400 atoms, 402 bonds, 24 residues, 1 model selected 
    4273 
    4274 > isolde sim start sel
    4275 
    4276 ISOLDE: started sim 
    4277 
    4278 > select clear
    4279 
    4280 > isolde pepflip sel
    4281 
    4282 Flipping the peptide bond for 1 residues 
    4283 
    4284 > isolde pepflip sel
    4285 
    4286 Flipping the peptide bond for 1 residues 
    4287 
    4288 > isolde pepflip sel
    4289 
    4290 Flipping the peptide bond for 1 residues 
    4291 
    4292 > select clear
    4293 
    4294 > isolde pepflip sel
    4295 
    4296 Flipping the peptide bond for 1 residues 
    4297 
    4298 > select clear
    4299 
    4300 > isolde pepflip sel
    4301 
    4302 Flipping the peptide bond for 1 residues 
    4303 
    4304 > isolde pepflip sel
    4305 
    4306 Flipping the peptide bond for 1 residues 
    4307 
    4308 > select clear
    4309 
    4310 Unable to flip peptide bond after 50 rounds. Giving up. 
    4311 
    4312 > select clear
    4313 
    4314 > isolde pepflip sel
    4315 
    4316 Flipping the peptide bond for 1 residues 
    4317 
    4318 > isolde pepflip sel
    4319 
    4320 Flipping the peptide bond for 1 residues 
    4321 
    4322 > select clear
    4323 
    4324 Unable to flip peptide bond after 50 rounds. Giving up. 
    4325 
    4326 > isolde pepflip sel
    4327 
    4328 Flipping the peptide bond for 1 residues 
    4329 
    4330 > select clear
    4331 
    4332 > hide #!1.2 models
    4333 
    4334 > show #!1.2 models
    4335 
    4336 > hide #!1.2 models
    4337 
    4338 > show #!1.2 models
    4339 
    4340 > hide #!1.2 models
    4341 
    4342 > show #!1.2 models
    4343 
    4344 > isolde pepflip sel
    4345 
    4346 Flipping the peptide bond for 1 residues 
    4347 
    4348 > isolde pepflip sel
    4349 
    4350 Flipping the peptide bond for 1 residues 
    4351 
    4352 > isolde sim stop discardTo start
    4353 
    4354 [Repeated 1 time(s)]reverting to start 
    4355 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4356 chains... 
    4357 ISOLDE: stopped sim 
    4358 
    4359 > select #1
    4360 
    4361 144428 atoms, 150209 bonds, 5 pseudobonds, 6905 residues, 22 models selected 
    4362 
    4363 > select clear
    4364 
    4365 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    4366 > mut8-no-C-ter/11-KSRP-no-C-ter-Step1-EleventhSubsteps.cxs
    4367 
    4368 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    4369 
    4370 ——— End of log from Thu Mar 9 08:50:34 2023 ———
    4371 
    4372 opened ChimeraX session 
    4373 
    4374 > select #1/u:28-42|/o:53-56|/u:43-47
    4375 
    4376 400 atoms, 402 bonds, 24 residues, 1 model selected 
    4377 
    4378 > isolde sim start sel
    4379 
    4380 Launching using CUDA failed with the below message. Falling back to using
    4381 OpenCL. 
    4382  
    4383 Error compiling program: nvrtc: error: invalid value for --gpu-architecture
    4384 (-arch) 
    4385  
    4386 
    4387 ISOLDE: started sim 
    4388 ISOLDE: created disulfide bonds between the following residues: 
    4389 T78-T81 
    4390 
    4391 > isolde sim stop discardTo start
    4392 
    4393 reverting to start 
    4394 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4395 chains... 
    4396 ISOLDE: stopped sim 
    4397 
    4398 > select #1/u:28-42|/o:53-56|/u:43-47
    4399 
    4400 400 atoms, 402 bonds, 24 residues, 1 model selected 
    4401 
    4402 > isolde sim start sel
    4403 
    4404 ISOLDE: started sim 
    4405 
    4406 > select #1/u:36-50
    4407 
    4408 229 atoms, 230 bonds, 15 residues, 1 model selected 
    4409 
    4410 > isolde sim stop
    4411 
    4412 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4413 chains... 
    4414 ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
    4415 standards. 
    4416 ISOLDE: stopped sim 
    4417 
    4418 > select #1/u:12
    4419 
    4420 17 atoms, 17 bonds, 1 residue, 1 model selected 
    4421 
    4422 > view #1/u:12
    4423 
    4424 > select #1/u:12
    4425 
    4426 17 atoms, 17 bonds, 1 residue, 1 model selected 
    4427 
    4428 > isolde sim start sel
    4429 
    4430 ISOLDE: started sim 
    4431 
    4432 > isolde sim stop
    4433 
    4434 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4435 chains... 
    4436 ISOLDE: stopped sim 
    4437 
    4438 > isolde sim start sel
    4439 
    4440 ISOLDE: started sim 
    4441 
    4442 > isolde pepflip sel
    4443 
    4444 Flipping the peptide bond for 1 residues 
    4445 
    4446 > isolde pepflip sel
    4447 
    4448 Flipping the peptide bond for 1 residues 
    4449 
    4450 > select clear
    4451 
    4452 > ui tool show "Ramachandran Plot"
    4453 
    4454 > isolde sim stop
    4455 
    4456 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4457 chains... 
    4458 ISOLDE: stopped sim 
    4459 
    4460 > isolde sim start sel
    4461 
    4462 ISOLDE: started sim 
    4463 
    4464 > isolde pepflip sel
    4465 
    4466 Flipping the peptide bond for 1 residues 
    4467 
    4468 > select clear
    4469 
    4470 > isolde pepflip sel
    4471 
    4472 Flipping the peptide bond for 1 residues 
    4473 
    4474 > isolde pepflip sel
    4475 
    4476 Flipping the peptide bond for 1 residues 
    4477 
    4478 > select clear
    4479 
    4480 > isolde pepflip sel
    4481 
    4482 Flipping the peptide bond for 1 residues 
    4483 
    4484 > isolde pepflip sel
    4485 
    4486 Flipping the peptide bond for 1 residues 
    4487 
    4488 > isolde pepflip sel
    4489 
    4490 Flipping the peptide bond for 1 residues 
    4491 
    4492 > select clear
    4493 
    4494 > isolde pepflip sel
    4495 
    4496 Flipping the peptide bond for 1 residues 
    4497 
    4498 > select clear
    4499 
    4500 > ui tool show "Ramachandran Plot"
    4501 
    4502 [Repeated 1 time(s)]
    4503 
    4504 > isolde sim stop
    4505 
    4506 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4507 chains... 
    4508 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    4509 standards. 
    4510 ISOLDE: stopped sim 
    4511 
    4512 > select #1/o:55
    4513 
    4514 22 atoms, 21 bonds, 1 residue, 1 model selected 
    4515 
    4516 > isolde sim start sel
    4517 
    4518 ISOLDE: started sim 
    4519 
    4520 > select clear
    4521 
    4522 [Repeated 5 time(s)]
    4523 
    4524 > isolde pepflip sel
    4525 
    4526 Flipping the peptide bond for 1 residues 
    4527 
    4528 > isolde pepflip sel
    4529 
    4530 Flipping the peptide bond for 1 residues 
    4531 
    4532 > isolde pepflip sel
    4533 
    4534 Flipping the peptide bond for 1 residues 
    4535 
    4536 > isolde pepflip sel
    4537 
    4538 Flipping the peptide bond for 1 residues 
    4539 
    4540 > isolde pepflip sel
    4541 
    4542 Flipping the peptide bond for 1 residues 
    4543 
    4544 > isolde pepflip sel
    4545 
    4546 Flipping the peptide bond for 1 residues 
    4547 
    4548 > select clear
    4549 
    4550 [Repeated 3 time(s)]
    4551 
    4552 > isolde pepflip sel
    4553 
    4554 Flipping the peptide bond for 1 residues 
    4555 
    4556 > isolde pepflip sel
    4557 
    4558 Flipping the peptide bond for 1 residues 
    4559 
    4560 > isolde pepflip sel
    4561 
    4562 Flipping the peptide bond for 1 residues 
    4563 
    4564 > select clear
    4565 
    4566 > isolde pepflip sel
    4567 
    4568 Flipping the peptide bond for 1 residues 
    4569 
    4570 > isolde pepflip sel
    4571 
    4572 Flipping the peptide bond for 1 residues 
    4573 
    4574 > select clear
    4575 
    4576 > isolde pepflip sel
    4577 
    4578 Flipping the peptide bond for 1 residues 
    4579 
    4580 > select clear
    4581 
    4582 > ui tool show "Ramachandran Plot"
    4583 
    4584 [Repeated 1 time(s)]
    4585 
    4586 > isolde pepflip sel
    4587 
    4588 Flipping the peptide bond for 1 residues 
    4589 
    4590 > isolde pepflip sel
    4591 
    4592 Flipping the peptide bond for 1 residues 
    4593 
    4594 > select clear
    4595 
    4596 > view #1/o:55
    4597 
    4598 > isolde pepflip sel
    4599 
    4600 Flipping the peptide bond for 1 residues 
    4601 
    4602 > isolde pepflip sel
    4603 
    4604 Flipping the peptide bond for 1 residues 
    4605 
    4606 > select clear
    4607 
    4608 > isolde pepflip sel
    4609 
    4610 Flipping the peptide bond for 1 residues 
    4611 
    4612 > isolde pepflip sel
    4613 
    4614 Flipping the peptide bond for 1 residues 
    4615 
    4616 > select clear
    4617 
    4618 > isolde pepflip sel
    4619 
    4620 Flipping the peptide bond for 1 residues 
    4621 
    4622 > isolde pepflip sel
    4623 
    4624 Flipping the peptide bond for 1 residues 
    4625 
    4626 > isolde pepflip sel
    4627 
    4628 Flipping the peptide bond for 1 residues 
    4629 
    4630 > isolde pepflip sel
    4631 
    4632 Flipping the peptide bond for 1 residues 
    4633 
    4634 > isolde pepflip sel
    4635 
    4636 Flipping the peptide bond for 1 residues 
    4637 
    4638 > isolde pepflip sel
    4639 
    4640 Flipping the peptide bond for 1 residues 
    4641 
    4642 > isolde sim stop
    4643 
    4644 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4645 chains... 
    4646 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    4647 standards. 
    4648 ISOLDE: stopped sim 
    4649 
    4650 > select #1/o:55|/o:37
    4651 
    4652 39 atoms, 37 bonds, 2 residues, 1 model selected 
    4653 
    4654 > select #1/o:55|/o:37
    4655 
    4656 39 atoms, 37 bonds, 2 residues, 1 model selected 
    4657 
    4658 > select #1/o:37
    4659 
    4660 17 atoms, 16 bonds, 1 residue, 1 model selected 
    4661 
    4662 > select #1/u:37A/o:55
    4663 
    4664 22 atoms, 21 bonds, 1 residue, 1 model selected 
    4665 
    4666 > select #1/u:37/o:55
    4667 
    4668 38 atoms, 36 bonds, 2 residues, 1 model selected 
    4669 
    4670 > isolde sim start sel
    4671 
    4672 ISOLDE: started sim 
    4673 
    4674 > select clear
    4675 
    4676 > isolde pepflip sel
    4677 
    4678 Flipping the peptide bond for 1 residues 
    4679 
    4680 > select clear
    4681 
    4682 [Repeated 2 time(s)]
    4683 
    4684 > isolde pepflip sel
    4685 
    4686 Flipping the peptide bond for 1 residues 
    4687 
    4688 > isolde pepflip sel
    4689 
    4690 Flipping the peptide bond for 1 residues 
    4691 
    4692 > isolde pepflip sel
    4693 
    4694 Flipping the peptide bond for 1 residues 
    4695 
    4696 > select clear
    4697 
    4698 [Repeated 3 time(s)]
    4699 
    4700 > isolde pepflip sel
    4701 
    4702 Flipping the peptide bond for 1 residues 
    4703 
    4704 > select clear
    4705 
    4706 [Repeated 1 time(s)]
    4707 
    4708 > isolde pepflip sel
    4709 
    4710 Flipping the peptide bond for 1 residues 
    4711 
    4712 > isolde pepflip sel
    4713 
    4714 Flipping the peptide bond for 1 residues 
    4715 
    4716 > isolde pepflip sel
    4717 
    4718 Flipping the peptide bond for 1 residues 
    4719 
    4720 > select clear
    4721 
    4722 [Repeated 1 time(s)]
    4723 
    4724 > isolde pepflip sel
    4725 
    4726 Flipping the peptide bond for 1 residues 
    4727 
    4728 > isolde pepflip sel
    4729 
    4730 Flipping the peptide bond for 1 residues 
    4731 
    4732 > isolde cisflip sel
    4733 
    4734 Performing cistrans flip for 1 residues 
    4735 
    4736 > isolde cisflip sel
    4737 
    4738 Performing cistrans flip for 1 residues 
    4739 
    4740 > isolde cisflip sel
    4741 
    4742 Performing cistrans flip for 1 residues 
    4743 
    4744 > isolde pepflip sel
    4745 
    4746 Flipping the peptide bond for 1 residues 
    4747 
    4748 > isolde pepflip sel
    4749 
    4750 Flipping the peptide bond for 1 residues 
    4751 
    4752 > isolde pepflip sel
    4753 
    4754 Flipping the peptide bond for 1 residues 
    4755 
    4756 > isolde pepflip sel
    4757 
    4758 Flipping the peptide bond for 1 residues 
    4759 
    4760 > isolde pepflip sel
    4761 
    4762 Flipping the peptide bond for 1 residues 
    4763 
    4764 > isolde pepflip sel
    4765 
    4766 Flipping the peptide bond for 1 residues 
    4767 
    4768 > isolde pepflip sel
    4769 
    4770 Flipping the peptide bond for 1 residues 
    4771 
    4772 > isolde pepflip sel
    4773 
    4774 Flipping the peptide bond for 1 residues 
    4775 
    4776 > select clear
    4777 
    4778 > isolde pepflip sel
    4779 
    4780 Flipping the peptide bond for 1 residues 
    4781 
    4782 > isolde pepflip sel
    4783 
    4784 Flipping the peptide bond for 1 residues 
    4785 Unable to flip peptide bond after 50 rounds. Giving up. 
    4786 
    4787 > isolde sim pause
    4788 
    4789 > select #1
    4790 
    4791 144426 atoms, 150208 bonds, 5 pseudobonds, 6905 residues, 22 models selected 
    4792 
    4793 > select clear
    4794 
    4795 [Repeated 2 time(s)]
    4796 
    4797 > isolde sim resume
    4798 
    4799 > select clear
    4800 
    4801 > isolde pepflip sel
    4802 
    4803 Flipping the peptide bond for 1 residues 
    4804 
    4805 > select clear
    4806 
    4807 > isolde pepflip sel
    4808 
    4809 Flipping the peptide bond for 1 residues 
    4810 
    4811 > select clear
    4812 
    4813 > isolde pepflip sel
    4814 
    4815 Flipping the peptide bond for 1 residues 
    4816 
    4817 > isolde pepflip sel
    4818 
    4819 Flipping the peptide bond for 1 residues 
    4820 
    4821 > isolde pepflip sel
    4822 
    4823 Flipping the peptide bond for 1 residues 
    4824 
    4825 > isolde pepflip sel
    4826 
    4827 Flipping the peptide bond for 1 residues 
    4828 
    4829 > isolde pepflip sel
    4830 
    4831 Flipping the peptide bond for 1 residues 
    4832 
    4833 > isolde pepflip sel
    4834 
    4835 Flipping the peptide bond for 1 residues 
    4836 
    4837 > isolde sim pause
    4838 
    4839 > isolde sim resume
    4840 
    4841 > isolde pepflip sel
    4842 
    4843 Flipping the peptide bond for 1 residues 
    4844 
    4845 > select clear
    4846 
    4847 [Repeated 1 time(s)]
    4848 
    4849 > isolde pepflip sel
    4850 
    4851 Flipping the peptide bond for 1 residues 
    4852 
    4853 > isolde pepflip sel
    4854 
    4855 Flipping the peptide bond for 1 residues 
    4856 
    4857 > isolde sim pause
    4858 
    4859 > select #1
    4860 
    4861 144426 atoms, 150208 bonds, 5 pseudobonds, 6905 residues, 22 models selected 
    4862 
    4863 > isolde sim resume
    4864 
    4865 > select clear
    4866 
    4867 > isolde pepflip sel
    4868 
    4869 Flipping the peptide bond for 1 residues 
    4870 
    4871 > isolde pepflip sel
    4872 
    4873 Flipping the peptide bond for 1 residues 
    4874 
    4875 > select clear
    4876 
    4877 [Repeated 3 time(s)]
    4878 
    4879 > isolde pepflip sel
    4880 
    4881 Flipping the peptide bond for 1 residues 
    4882 
    4883 > isolde pepflip sel
    4884 
    4885 Flipping the peptide bond for 1 residues 
    4886 
    4887 > select clear
    4888 
    4889 Unable to flip peptide bond after 50 rounds. Giving up. 
    4890 
    4891 > isolde pepflip sel
    4892 
    4893 Flipping the peptide bond for 1 residues 
    4894 
    4895 > select clear
    4896 
    4897 > isolde pepflip sel
    4898 
    4899 Flipping the peptide bond for 1 residues 
    4900 
    4901 > isolde pepflip sel
    4902 
    4903 Flipping the peptide bond for 1 residues 
    4904 
    4905 > isolde pepflip sel
    4906 
    4907 Flipping the peptide bond for 1 residues 
    4908 
    4909 > select clear
    4910 
    4911 [Repeated 1 time(s)]
    4912 
    4913 > ui tool show "Ramachandran Plot"
    4914 
    4915 > isolde pepflip sel
    4916 
    4917 Flipping the peptide bond for 1 residues 
    4918 
    4919 > isolde pepflip sel
    4920 
    4921 Flipping the peptide bond for 1 residues 
    4922 
    4923 > select clear
    4924 
    4925 > isolde pepflip sel
    4926 
    4927 Flipping the peptide bond for 1 residues 
    4928 
    4929 > select clear
    4930 
    4931 > isolde pepflip sel
    4932 
    4933 Flipping the peptide bond for 1 residues 
    4934 
    4935 > isolde pepflip sel
    4936 
    4937 Flipping the peptide bond for 1 residues 
    4938 
    4939 > select clear
    4940 
    4941 > isolde pepflip sel
    4942 
    4943 Flipping the peptide bond for 1 residues 
    4944 
    4945 > select clear
    4946 
    4947 > ui tool show "Ramachandran Plot"
    4948 
    4949 > isolde pepflip sel
    4950 
    4951 Flipping the peptide bond for 1 residues 
    4952 
    4953 > select clear
    4954 
    4955 > isolde pepflip sel
    4956 
    4957 Flipping the peptide bond for 1 residues 
    4958 
    4959 > isolde pepflip sel
    4960 
    4961 Flipping the peptide bond for 1 residues 
    4962 
    4963 > select clear
    4964 
    4965 [Repeated 4 time(s)]
    4966 
    4967 > ui tool show "Ramachandran Plot"
    4968 
    4969 > isolde pepflip sel
    4970 
    4971 Flipping the peptide bond for 1 residues 
    4972 
    4973 > select clear
    4974 
    4975 > isolde pepflip sel
    4976 
    4977 Flipping the peptide bond for 1 residues 
    4978 
    4979 > ui tool show "Ramachandran Plot"
    4980 
    4981 > isolde pepflip sel
    4982 
    4983 Flipping the peptide bond for 1 residues 
    4984 
    4985 > isolde pepflip sel
    4986 
    4987 Flipping the peptide bond for 1 residues 
    4988 
    4989 > isolde pepflip sel
    4990 
    4991 Flipping the peptide bond for 1 residues 
    4992 
    4993 > ui tool show "Ramachandran Plot"
    4994 
    4995 > isolde pepflip sel
    4996 
    4997 Flipping the peptide bond for 1 residues 
    4998 
    4999 > isolde pepflip sel
    5000 
    5001 Flipping the peptide bond for 1 residues 
    5002 
    5003 > select clear
    5004 
    5005 [Repeated 1 time(s)]Unable to flip peptide bond after 50 rounds. Giving up. 
    5006 
    5007 > ui tool show "Ramachandran Plot"
    5008 
    5009 Traceback (most recent call last): 
    5010 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    5011 packages/matplotlib/cbook/__init__.py", line 287, in process 
    5012 func(*args, **kwargs) 
    5013 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    5014 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    5015 on_resize 
    5016 c.draw() 
    5017 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    5018 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    5019 self.figure.draw(self.renderer) 
    5020 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    5021 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    5022 result = draw(artist, renderer, *args, **kwargs) 
    5023 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    5024 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    5025 return draw(artist, renderer) 
    5026 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    5027 packages/matplotlib/figure.py", line 2796, in draw 
    5028 artists = self._get_draw_artists(renderer) 
    5029 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    5030 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    5031 ax.apply_aspect() 
    5032 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    5033 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    5034 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    5035 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    5036 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    5037 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    5038 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    5039 
    5040 > isolde pepflip sel
    5041 
    5042 Flipping the peptide bond for 1 residues 
    5043 
    5044 > isolde pepflip sel
    5045 
    5046 Flipping the peptide bond for 1 residues 
    5047 
    5048 > isolde pepflip sel
    5049 
    5050 Flipping the peptide bond for 1 residues 
    5051 
    5052 > select clear
    5053 
    5054 > ui tool show "Ramachandran Plot"
    5055 
    5056 > isolde pepflip sel
    5057 
    5058 Flipping the peptide bond for 1 residues 
    5059 
    5060 > select clear
    5061 
    5062 [Repeated 1 time(s)]
    5063 
    5064 > ui tool show "Ramachandran Plot"
    5065 
    5066 > view #1/u:37
    5067 
    5068 > ui tool show "Ramachandran Plot"
    5069 
    5070 > isolde pepflip sel
    5071 
    5072 Flipping the peptide bond for 1 residues 
    5073 
    5074 > select clear
    5075 
    5076 > ui tool show "Ramachandran Plot"
    5077 
    5078 > isolde pepflip sel
    5079 
    5080 Flipping the peptide bond for 1 residues 
    5081 
    5082 > isolde pepflip sel
    5083 
    5084 Flipping the peptide bond for 1 residues 
    5085 
    5086 > ui tool show "Ramachandran Plot"
    5087 
    5088 > select clear
    5089 
    5090 > ui tool show "Ramachandran Plot"
    5091 
    5092 [Repeated 1 time(s)]
    5093 
    5094 > isolde pepflip sel
    5095 
    5096 Flipping the peptide bond for 1 residues 
    5097 
    5098 > select clear
    5099 
    5100 > ui tool show "Ramachandran Plot"
    5101 
    5102 > ui tool show ISOLDE
    5103 
    5104 > ui tool show "Ramachandran Plot"
    5105 
    5106 > isolde pepflip sel
    5107 
    5108 Flipping the peptide bond for 1 residues 
    5109 
    5110 > isolde pepflip sel
    5111 
    5112 Flipping the peptide bond for 1 residues 
    5113 
    5114 > select clear
    5115 
    5116 > ui tool show "Ramachandran Plot"
    5117 
    5118 [Repeated 2 time(s)]
    5119 
    5120 > isolde pepflip sel
    5121 
    5122 Flipping the peptide bond for 1 residues 
    5123 
    5124 > ui tool show "Ramachandran Plot"
    5125 
    5126 > select clear
    5127 
    5128 > ui tool show "Ramachandran Plot"
    5129 
    5130 > isolde pepflip sel
    5131 
    5132 Flipping the peptide bond for 1 residues 
    5133 
    5134 > select clear
    5135 
    5136 > isolde pepflip sel
    5137 
    5138 Flipping the peptide bond for 1 residues 
    5139 
    5140 > isolde pepflip sel
    5141 
    5142 Flipping the peptide bond for 1 residues 
    5143 
    5144 > ui tool show "Ramachandran Plot"
    5145 
    5146 > isolde pepflip sel
    5147 
    5148 Flipping the peptide bond for 1 residues 
    5149 
    5150 > isolde pepflip sel
    5151 
    5152 Flipping the peptide bond for 1 residues 
    5153 
    5154 > select clear
    5155 
    5156 [Repeated 1 time(s)]
    5157 
    5158 > isolde pepflip sel
    5159 
    5160 Flipping the peptide bond for 1 residues 
    5161 
    5162 > isolde pepflip sel
    5163 
    5164 Flipping the peptide bond for 1 residues 
    5165 
    5166 > select clear
    5167 
    5168 > isolde pepflip sel
    5169 
    5170 Flipping the peptide bond for 1 residues 
    5171 
    5172 > isolde pepflip sel
    5173 
    5174 Flipping the peptide bond for 1 residues 
    5175 
    5176 > ui tool show "Ramachandran Plot"
    5177 
    5178 > isolde pepflip sel
    5179 
    5180 Flipping the peptide bond for 1 residues 
    5181 
    5182 > select clear
    5183 
    5184 [Repeated 1 time(s)]
    5185 
    5186 > ui tool show "Ramachandran Plot"
    5187 
    5188 [Repeated 1 time(s)]
    5189 
    5190 > select clear
    5191 
    5192 [Repeated 3 time(s)]
    5193 
    5194 > ui tool show "Ramachandran Plot"
    5195 
    5196 [Repeated 2 time(s)]
    5197 
    5198 > isolde pepflip sel
    5199 
    5200 Flipping the peptide bond for 1 residues 
    5201 
    5202 > isolde pepflip sel
    5203 
    5204 Flipping the peptide bond for 1 residues 
    5205 
    5206 > isolde pepflip sel
    5207 
    5208 Flipping the peptide bond for 1 residues 
    5209 
    5210 > isolde pepflip sel
    5211 
    5212 Flipping the peptide bond for 1 residues 
    5213 
    5214 > select clear
    5215 
    5216 Unable to flip peptide bond after 50 rounds. Giving up. 
    5217 
    5218 > ui tool show "Ramachandran Plot"
    5219 
    5220 > select clear
    5221 
    5222 > ui tool show "Ramachandran Plot"
    5223 
    5224 > isolde pepflip sel
    5225 
    5226 Flipping the peptide bond for 1 residues 
    5227 
    5228 > isolde pepflip sel
    5229 
    5230 Flipping the peptide bond for 1 residues 
    5231 
    5232 > select clear
    5233 
    5234 [Repeated 1 time(s)]
    5235 
    5236 > ui tool show "Ramachandran Plot"
    5237 
    5238 > hide #!1.2 models
    5239 
    5240 > show #!1.2 models
    5241 
    5242 > ui tool show "Ramachandran Plot"
    5243 
    5244 > select clear
    5245 
    5246 [Repeated 3 time(s)]
    5247 
    5248 > ui tool show "Ramachandran Plot"
    5249 
    5250 > isolde pepflip sel
    5251 
    5252 Flipping the peptide bond for 1 residues 
    5253 
    5254 > isolde pepflip sel
    5255 
    5256 Flipping the peptide bond for 1 residues 
    5257 
    5258 > isolde pepflip sel
    5259 
    5260 Flipping the peptide bond for 1 residues 
    5261 
    5262 > isolde pepflip sel
    5263 
    5264 Flipping the peptide bond for 1 residues 
    5265 
    5266 > isolde pepflip sel
    5267 
    5268 Flipping the peptide bond for 1 residues 
    5269 
    5270 > isolde pepflip sel
    5271 
    5272 Flipping the peptide bond for 1 residues 
    5273 
    5274 > isolde pepflip sel
    5275 
    5276 Flipping the peptide bond for 1 residues 
    5277 
    5278 > isolde pepflip sel
    5279 
    5280 Flipping the peptide bond for 1 residues 
    5281 
    5282 > select clear
    5283 
    5284 > isolde pepflip sel
    5285 
    5286 Flipping the peptide bond for 1 residues 
    5287 
    5288 > isolde pepflip sel
    5289 
    5290 Flipping the peptide bond for 1 residues 
    5291 
    5292 > isolde pepflip sel
    5293 
    5294 Flipping the peptide bond for 1 residues 
    5295 
    5296 > ui tool show "Ramachandran Plot"
    5297 
    5298 > select clear
    5299 
    5300 > isolde pepflip sel
    5301 
    5302 Flipping the peptide bond for 1 residues 
    5303 
    5304 > isolde pepflip sel
    5305 
    5306 Flipping the peptide bond for 1 residues 
    5307 
    5308 > select clear
    5309 
    5310 [Repeated 1 time(s)]
    5311 
    5312 > isolde pepflip sel
    5313 
    5314 Flipping the peptide bond for 1 residues 
    5315 
    5316 > isolde pepflip sel
    5317 
    5318 Flipping the peptide bond for 1 residues 
    5319 
    5320 > select clear
    5321 
    5322 > isolde pepflip sel
    5323 
    5324 Flipping the peptide bond for 1 residues 
    5325 
    5326 > isolde pepflip sel
    5327 
    5328 Flipping the peptide bond for 1 residues 
    5329 
    5330 > isolde pepflip sel
    5331 
    5332 Flipping the peptide bond for 1 residues 
    5333 
    5334 > isolde pepflip sel
    5335 
    5336 Flipping the peptide bond for 1 residues 
    5337 
    5338 > select clear
    5339 
    5340 > isolde pepflip sel
    5341 
    5342 Flipping the peptide bond for 1 residues 
    5343 
    5344 > select clear
    5345 
    5346 > ui tool show "Ramachandran Plot"
    5347 
    5348 > isolde pepflip sel
    5349 
    5350 Flipping the peptide bond for 1 residues 
    5351 
    5352 > select clear
    5353 
    5354 [Repeated 1 time(s)]
    5355 
    5356 > isolde pepflip sel
    5357 
    5358 Flipping the peptide bond for 1 residues 
    5359 
    5360 > isolde pepflip sel
    5361 
    5362 Flipping the peptide bond for 1 residues 
    5363 
    5364 > isolde pepflip sel
    5365 
    5366 Flipping the peptide bond for 1 residues 
    5367 
    5368 > isolde pepflip sel
    5369 
    5370 Flipping the peptide bond for 1 residues 
    5371 
    5372 > isolde pepflip sel
    5373 
    5374 Flipping the peptide bond for 1 residues 
    5375 
    5376 > select clear
    5377 
    5378 > ui tool show "Ramachandran Plot"
    5379 
    5380 > isolde pepflip sel
    5381 
    5382 Flipping the peptide bond for 1 residues 
    5383 
    5384 > select clear
    5385 
    5386 > ui tool show "Ramachandran Plot"
    5387 
    5388 > isolde pepflip sel
    5389 
    5390 Flipping the peptide bond for 1 residues 
    5391 Unable to flip peptide bond after 50 rounds. Giving up. 
    5392 
    5393 > select clear
    5394 
    5395 > isolde pepflip sel
    5396 
    5397 Flipping the peptide bond for 1 residues 
    5398 
    5399 > isolde pepflip sel
    5400 
    5401 Flipping the peptide bond for 1 residues 
    5402 
    5403 > ui tool show "Ramachandran Plot"
    5404 
    5405 > isolde sim pause
    5406 
    5407 > ui tool show "Ramachandran Plot"
    5408 
    5409 > isolde sim resume
    5410 
    5411 > ui tool show "Ramachandran Plot"
    5412 
    5413 > isolde sim pause
    5414 
    5415 > isolde sim stop
    5416 
    5417 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5418 chains... 
    5419 ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
    5420 standards. 
    5421 ISOLDE: stopped sim 
    5422 
    5423 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    5424 > mut8-no-C-ter/12-KSRP-no-C-ter-Step1-twelventhSubsteps-
    5425 > simulatedAnnealingIn-u37-o55-region.csx.cxs
    5426 
    5427 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    5428 
    5429 ——— End of log from Fri Mar 17 17:24:40 2023 ———
    5430 
    5431 opened ChimeraX session 
    5432 
    5433 > isolde start
    5434 
    5435 > set selectionWidth 4
    5436 
    5437 > select clear
    5438 
    5439 > view #1/o:55
    5440 
    5441 > select #1/o:55
    5442 
    5443 22 atoms, 21 bonds, 1 residue, 1 model selected 
    5444 
    5445 > isolde sim start sel
    5446 
    5447 Launching using CUDA failed with the below message. Falling back to using
    5448 OpenCL. 
    5449  
    5450 Error compiling program: nvrtc: error: invalid value for --gpu-architecture
    5451 (-arch) 
    5452  
    5453 
    5454 ISOLDE: started sim 
    5455 
    5456 > isolde sim stop discardTo start
    5457 
    5458 reverting to start 
    5459 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5460 chains... 
    5461 ISOLDE: stopped sim 
    5462 
    5463 > select #1/o:55
    5464 
    5465 22 atoms, 21 bonds, 1 residue, 1 model selected 
    5466 
    5467 > isolde sim start sel
    5468 
    5469 ISOLDE: started sim 
    5470 
    5471 > ui tool show "Ramachandran Plot"
    5472 
    5473 > select clear
    5474 
    5475 > isolde sim stop
    5476 
    5477 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5478 chains... 
    5479 ISOLDE: stopped sim 
    5480 
    5481 > view #1/u:49
    5482 
    5483 > select #1/u:49
    5484 
    5485 10 atoms, 9 bonds, 1 residue, 1 model selected 
    5486 
    5487 > isolde sim start sel
    5488 
    5489 ISOLDE: started sim 
    5490 
    5491 > isolde sim stop discardTo start
    5492 
    5493 reverting to start 
    5494 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5495 chains... 
    5496 ISOLDE: stopped sim 
    5497 
    5498 > select #1/u:49
    5499 
    5500 10 atoms, 9 bonds, 1 residue, 1 model selected 
    5501 
    5502 > isolde sim start sel
    5503 
    5504 ISOLDE: started sim 
    5505 
    5506 > ui tool show "Ramachandran Plot"
    5507 
    5508 > select clear
    5509 
    5510 > isolde pepflip sel
    5511 
    5512 Flipping the peptide bond for 1 residues 
    5513 
    5514 > select clear
    5515 
    5516 > ui tool show "Ramachandran Plot"
    5517 
    5518 > isolde sim pause
    5519 
    5520 > isolde sim resume
    5521 
    5522 > isolde sim pause
    5523 
    5524 3 models selected 
    5525 [Repeated 1 time(s)]
    5526 
    5527 > view #1
    5528 
    5529 > view #1/u:49
    5530 
    5531 > view #1/P
    5532 
    5533 > ui tool show "Ramachandran Plot"
    5534 
    5535 > view #1/u:49
    5536 
    5537 > isolde sim resume
    5538 
    5539 > ui tool show "Ramachandran Plot"
    5540 
    5541 [Repeated 2 time(s)]
    5542 
    5543 > isolde sim stop
    5544 
    5545 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5546 chains... 
    5547 ISOLDE: stopped sim 
    5548 
    5549 > view #1/u:63
    5550 
    5551 > select #1/u:63
    5552 
    5553 15 atoms, 14 bonds, 1 residue, 1 model selected 
    5554 
    5555 > isolde sim start sel
    5556 
    5557 ISOLDE: started sim 
    5558 
    5559 > ui tool show "Ramachandran Plot"
    5560 
    5561 > isolde pepflip sel
    5562 
    5563 Flipping the peptide bond for 1 residues 
    5564 
    5565 > isolde pepflip sel
    5566 
    5567 Flipping the peptide bond for 1 residues 
    5568 
    5569 > isolde pepflip sel
    5570 
    5571 Flipping the peptide bond for 1 residues 
    5572 
    5573 > ui tool show "Ramachandran Plot"
    5574 
    5575 [Repeated 1 time(s)]
    5576 
    5577 > select clear
    5578 
    5579 [Repeated 1 time(s)]
    5580 
    5581 > isolde pepflip sel
    5582 
    5583 Flipping the peptide bond for 1 residues 
    5584 
    5585 > isolde pepflip sel
    5586 
    5587 Flipping the peptide bond for 1 residues 
    5588 
    5589 > isolde pepflip sel
    5590 
    5591 Flipping the peptide bond for 1 residues 
    5592 
    5593 > ui tool show "Ramachandran Plot"
    5594 
    5595 > select clear
    5596 
    5597 > ui tool show "Ramachandran Plot"
    5598 
    5599 > select clear
    5600 
    5601 > isolde sim stop
    5602 
    5603 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5604 chains... 
    5605 ISOLDE: stopped sim 
    5606 
    5607 > view #1/u:49
    5608 
    5609 > select #1/u:49
    5610 
    5611 10 atoms, 9 bonds, 1 residue, 1 model selected 
    5612 
    5613 > isolde sim start sel
    5614 
    5615 ISOLDE: started sim 
    5616 
    5617 > ui tool show "Ramachandran Plot"
    5618 
    5619 > isolde sim stop
    5620 
    5621 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5622 chains... 
    5623 ISOLDE: stopped sim 
    5624 
    5625 > view #1/u:43
    5626 
    5627 > select #1/u:43
    5628 
    5629 21 atoms, 21 bonds, 1 residue, 1 model selected 
    5630 
    5631 > isolde sim start sel
    5632 
    5633 ISOLDE: started sim 
    5634 
    5635 > ui tool show "Ramachandran Plot"
    5636 
    5637 > select clear
    5638 
    5639 > isolde pepflip sel
    5640 
    5641 Flipping the peptide bond for 1 residues 
    5642 
    5643 > select clear
    5644 
    5645 > ui tool show "Ramachandran Plot"
    5646 
    5647 > view #1/u:43
    5648 
    5649 > ui tool show "Ramachandran Plot"
    5650 
    5651 > select clear
    5652 
    5653 > ui tool show "Ramachandran Plot"
    5654 
    5655 > select clear
    5656 
    5657 [Repeated 1 time(s)]
    5658 
    5659 > isolde pepflip sel
    5660 
    5661 Flipping the peptide bond for 1 residues 
    5662 
    5663 > select clear
    5664 
    5665 > isolde pepflip sel
    5666 
    5667 Flipping the peptide bond for 1 residues 
    5668 
    5669 > select clear
    5670 
    5671 [Repeated 1 time(s)]
    5672 
    5673 > isolde pepflip sel
    5674 
    5675 Flipping the peptide bond for 1 residues 
    5676 
    5677 > select clear
    5678 
    5679 [Repeated 1 time(s)]
    5680 
    5681 > hide #!1.1 models
    5682 
    5683 > show #!1.1 models
    5684 
    5685 > hide #!1.2 models
    5686 
    5687 > show #!1.2 models
    5688 
    5689 > hide #!1.2 models
    5690 
    5691 > show #!1.2 models
    5692 
    5693 > hide #!1.2 models
    5694 
    5695 > show #!1.2 models
    5696 
    5697 > hide #!1.2 models
    5698 
    5699 > show #!1.2 models
    5700 
    5701 > ui tool show "Ramachandran Plot"
    5702 
    5703 > select clear
    5704 
    5705 > view #1/u:43
    5706 
    5707 > isolde sim stop
    5708 
    5709 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5710 chains... 
    5711 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    5712 standards. 
    5713 ISOLDE: stopped sim 
    5714 
    5715 > isolde sim start sel
    5716 
    5717 ISOLDE: started sim 
    5718 
    5719 > select clear
    5720 
    5721 [Repeated 1 time(s)]
    5722 
    5723 > isolde sim stop
    5724 
    5725 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5726 chains... 
    5727 ISOLDE: stopped sim 
    5728 
    5729 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    5730 > mut8-no-C-ter/13-KSRP-no-C-ter-Step1-thirtenthSubsteps.pdb
    5731 
    5732 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    5733 > mut8-no-C-ter/13-KSRP-no-C-ter-Step1-thirtenthSubsteps.cxs
    5734 
    5735 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    5736 
    5737 > view #1/u:42|u:55
    5738 
    5739 Expected an objects specifier or a view name or a keyword 
    5740 
    5741 > view #1/u:42|/u:55
    5742 
    5743 > select #1/u:42|/u:55
    5744 
    5745 34 atoms, 32 bonds, 2 residues, 1 model selected 
    5746 
    5747 > isolde sim start sel
    5748 
    5749 ISOLDE: started sim 
    5750 
    5751 > isolde sim stop discardTo start
    5752 
    5753 reverting to start 
    5754 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5755 chains... 
    5756 ISOLDE: stopped sim 
    5757 
    5758 > select #1/u:42|/u:55
    5759 
    5760 34 atoms, 32 bonds, 2 residues, 1 model selected 
    5761 
    5762 > isolde sim start sel
    5763 
    5764 ISOLDE: started sim 
    5765 
    5766 > ui tool show "Ramachandran Plot"
    5767 
    5768 > select clear
    5769 
    5770 [Repeated 2 time(s)]
    5771 
    5772 > isolde pepflip sel
    5773 
    5774 Flipping the peptide bond for 1 residues 
    5775 
    5776 > isolde pepflip sel
    5777 
    5778 Flipping the peptide bond for 1 residues 
    5779 
    5780 > select clear
    5781 
    5782 > ui tool show "Ramachandran Plot"
    5783 
    5784 Unable to flip peptide bond after 50 rounds. Giving up. 
    5785 
    5786 > ui tool show "Ramachandran Plot"
    5787 
    5788 > isolde sim stop
    5789 
    5790 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5791 chains... 
    5792 ISOLDE: stopped sim 
    5793 
    5794 > view #1/u:43
    5795 
    5796 > select #1/u:43
    5797 
    5798 21 atoms, 21 bonds, 1 residue, 1 model selected 
    5799 
    5800 > isolde sim start sel
    5801 
    5802 ISOLDE: started sim 
    5803 
    5804 > ui tool show "Ramachandran Plot"
    5805 
    5806 > select clear
    5807 
    5808 > isolde sim stop
    5809 
    5810 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5811 chains... 
    5812 ISOLDE: stopped sim 
    5813 
    5814 > view #1/u:63
    5815 
    5816 > select #1/u:63
    5817 
    5818 15 atoms, 14 bonds, 1 residue, 1 model selected 
    5819 
    5820 > select #1/u:63
    5821 
    5822 15 atoms, 14 bonds, 1 residue, 1 model selected 
    5823 
    5824 > isolde sim start sel
    5825 
    5826 ISOLDE: started sim 
    5827 
    5828 > ui tool show "Ramachandran Plot"
    5829 
    5830 > isolde sim stop
    5831 
    5832 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5833 chains... 
    5834 ISOLDE: stopped sim 
    5835 
    5836 > ui tool show "Ramachandran Plot"
    5837 
    5838 > select #1/u:49
    5839 
    5840 10 atoms, 9 bonds, 1 residue, 1 model selected 
    5841 
    5842 > view #1/u:49
    5843 
    5844 > select #1/u:49
    5845 
    5846 10 atoms, 9 bonds, 1 residue, 1 model selected 
    5847 
    5848 > isolde sim start sel
    5849 
    5850 ISOLDE: started sim 
    5851 
    5852 > ui tool show "Ramachandran Plot"
    5853 
    5854 [Repeated 1 time(s)]
    5855 
    5856 > isolde sim stop
    5857 
    5858 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5859 chains... 
    5860 ISOLDE: stopped sim 
    5861 
    5862 > view #1/o:55
    5863 
    5864 > select #1/o:55
    5865 
    5866 22 atoms, 21 bonds, 1 residue, 1 model selected 
    5867 
    5868 > isolde sim start sel
    5869 
    5870 ISOLDE: started sim 
    5871 
    5872 > ui tool show "Ramachandran Plot"
    5873 
    5874 > isolde sim stop
    5875 
    5876 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5877 chains... 
    5878 ISOLDE: stopped sim 
    5879 
    5880 > view #1/u:12
    5881 
    5882 > select #1/u:12
    5883 
    5884 17 atoms, 17 bonds, 1 residue, 1 model selected 
    5885 
    5886 > isolde sim start sel
    5887 
    5888 ISOLDE: started sim 
    5889 
    5890 > ui tool show "Ramachandran Plot"
    5891 
    5892 > select clear
    5893 
    5894 > isolde sim stop
    5895 
    5896 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5897 chains... 
    5898 ISOLDE: stopped sim 
    5899 
    5900 > view #1/u:28-42|/o:53-56|/u:43-47
    5901 
    5902 > select #1/u:28-42|/o:53-56|/u:43-47
    5903 
    5904 400 atoms, 402 bonds, 24 residues, 1 model selected 
    5905 
    5906 > isolde sim start sel
    5907 
    5908 ISOLDE: started sim 
    5909 
    5910 > ui tool show "Ramachandran Plot"
    5911 
    5912 > isolde sim pause
    5913 
    5914 > ui tool show "Ramachandran Plot"
    5915 
    5916 [Repeated 2 time(s)]
    5917 
    5918 > isolde sim resume
    5919 
    5920 > isolde sim stop
    5921 
    5922 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5923 chains... 
    5924 ISOLDE: stopped sim 
    5925 
    5926 > select #1/u:35
    5927 
    5928 22 atoms, 21 bonds, 1 residue, 1 model selected 
    5929 
    5930 > view #1/u:35
    5931 
    5932 > select #1/u:35
    5933 
    5934 22 atoms, 21 bonds, 1 residue, 1 model selected 
    5935 
    5936 > select #1/u:35
    5937 
    5938 22 atoms, 21 bonds, 1 residue, 1 model selected 
    5939 
    5940 > isolde sim start sel
    5941 
    5942 ISOLDE: started sim 
    5943 
    5944 > ui tool show "Ramachandran Plot"
    5945 
    5946 > isolde sim stop
    5947 
    5948 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5949 chains... 
    5950 ISOLDE: stopped sim 
    5951 
    5952 > view #1/u:25
    5953 
    5954 > select #1/u:25
    5955 
    5956 24 atoms, 23 bonds, 1 residue, 1 model selected 
    5957 
    5958 > isolde sim start sel
    5959 
    5960 ISOLDE: started sim 
    5961 
    5962 > ui tool show "Ramachandran Plot"
    5963 
    5964 > select clear
    5965 
    5966 > isolde sim stop
    5967 
    5968 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5969 chains... 
    5970 ISOLDE: stopped sim 
    5971 
    5972 > view #1/u:60-65|/u:8-12
    5973 
    5974 > select #1/u:60-65|/u:8-12
    5975 
    5976 180 atoms, 180 bonds, 11 residues, 1 model selected 
    5977 
    5978 > isolde sim start sel
    5979 
    5980 ISOLDE: started sim 
    5981 
    5982 > ui tool show "Ramachandran Plot"
    5983 
    5984 > isolde sim stop
    5985 
    5986 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5987 chains... 
    5988 ISOLDE: stopped sim 
    5989 
    5990 > view #1/u:12
    5991 
    5992 > select sim start sel
    5993 
    5994 Expected an objects specifier or a keyword 
    5995 
    5996 > view #1/u:12
    5997 
    5998 > select #1/u:12
    5999 
    6000 17 atoms, 17 bonds, 1 residue, 1 model selected 
    6001 
    6002 > isolde sim start sel
    6003 
    6004 ISOLDE: started sim 
    6005 
    6006 > ui tool show "Ramachandran Plot"
    6007 
    6008 > isolde sim stop
    6009 
    6010 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6011 chains... 
    6012 ISOLDE: stopped sim 
    6013 
    6014 > isolde sim start sel
    6015 
    6016 ISOLDE: started sim 
    6017 
    6018 > ui tool show "Ramachandran Plot"
    6019 
    6020 [Repeated 1 time(s)]
    6021 
    6022 > select clear
    6023 
    6024 > isolde sim stop
    6025 
    6026 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6027 chains... 
    6028 ISOLDE: stopped sim 
    6029 
    6030 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    6031 > mut8-no-C-ter/4-KSRP-no-C-ter-Step1-FourtenthSubsteps-End1d1db.cxs
    6032 
    6033 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    6034 
    6035 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    6036 > mut8-no-C-ter/14-KSRP-no-C-ter-Step1-FourtenthSubsteps-End1d1db.pdb
    6037 
    6038 > isolde cisflip #1.2/Q:137
    6039 
    6040 Performing cistrans flip for 1 residues 
    6041 ISOLDE: started sim 
    6042 
    6043 > isolde sim stop discardTo start
    6044 
    6045 reverting to start 
    6046 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6047 chains... 
    6048 ISOLDE: stopped sim 
    6049 
    6050 > isolde sim start sel
    6051 
    6052 ISOLDE: started sim 
    6053 
    6054 > isolde sim stop discardTo start
    6055 
    6056 reverting to start 
    6057 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6058 chains... 
    6059 ISOLDE: stopped sim 
    6060 
    6061 > isolde sim start sel
    6062 
    6063 ISOLDE: started sim 
    6064 
    6065 > isolde cisflip sel
    6066 
    6067 Performing cistrans flip for 1 residues 
    6068 
    6069 > isolde cisflip #1.2/Q:137
    6070 
    6071 Performing cistrans flip for 1 residues 
    6072 
    6073 > isolde pepflip sel
    6074 
    6075 Flipping the peptide bond for 1 residues 
    6076 
    6077 > select clear
    6078 
    6079 [Repeated 2 time(s)]
    6080 
    6081 > ui tool show "Ramachandran Plot"
    6082 
    6083 > select clear
    6084 
    6085 > ui tool show "Ramachandran Plot"
    6086 
    6087 > view #1/Q:137
    6088 
    6089 > isolde sim pause
    6090 
    6091 > isolde sim stop
    6092 
    6093 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6094 chains... 
    6095 ISOLDE: stopped sim 
    6096 
    6097 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    6098 > mut8-no-C-ter/15-KSRP-no-C-ter-Step1-FifttenthSubsteps.pdb
    6099 
    6100 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    6101 > mut8-no-C-ter/15-KSRP-no-C-ter-Step1-FifttenthSubsteps.cxs
    6102 
    6103 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    6104 
    6105 > view #1/Q:137
    6106 
    6107 > select #1/Q:137
    6108 
    6109 14 atoms, 14 bonds, 1 residue, 1 model selected 
    6110 
    6111 > isolde sim start sel
    6112 
    6113 ISOLDE: started sim 
    6114 
    6115 > ui tool show "Ramachandran Plot"
    6116 
    6117 > isolde pepflip sel
    6118 
    6119 Flipping the peptide bond for 1 residues 
    6120 
    6121 > ui tool show "Ramachandran Plot"
    6122 
    6123 > isolde pepflip sel
    6124 
    6125 Flipping the peptide bond for 1 residues 
    6126 
    6127 > select clear
    6128 
    6129 > isolde pepflip sel
    6130 
    6131 Flipping the peptide bond for 1 residues 
    6132 
    6133 > select clear
    6134 
    6135 [Repeated 1 time(s)]
    6136 
    6137 > ui tool show "Ramachandran Plot"
    6138 
    6139 [Repeated 1 time(s)]
    6140 
    6141 > isolde sim stop
    6142 
    6143 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6144 chains... 
    6145 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    6146 standards. 
    6147 ISOLDE: stopped sim 
    6148 
    6149 > isolde sim start sel
    6150 
    6151 ISOLDE: started sim 
    6152 
    6153 > isolde sim stop discardTo start
    6154 
    6155 reverting to start 
    6156 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6157 chains... 
    6158 ISOLDE: stopped sim 
    6159 
    6160 > select #1/Q:181
    6161 
    6162 19 atoms, 18 bonds, 1 residue, 1 model selected 
    6163 
    6164 > isolde sim start sel
    6165 
    6166 ISOLDE: started sim 
    6167 
    6168 > ui tool show "Ramachandran Plot"
    6169 
    6170 > isolde sim stop
    6171 
    6172 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6173 chains... 
    6174 ISOLDE: stopped sim 
    6175 
    6176 > view #1/Q:137
    6177 
    6178 > select #1/Q:137
    6179 
    6180 14 atoms, 14 bonds, 1 residue, 1 model selected 
    6181 
    6182 > isolde sim start sel
    6183 
    6184 ISOLDE: started sim 
    6185 
    6186 > ui tool show "Ramachandran Plot"
    6187 
    6188 > select clear
    6189 
    6190 > isolde sim stop
    6191 
    6192 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6193 chains... 
    6194 ISOLDE: stopped sim 
    6195 
    6196 > isolde sim start sel
    6197 
    6198 ISOLDE: started sim 
    6199 
    6200 > isolde cisflip #1.2/O:156
    6201 
    6202 Performing cistrans flip for 1 residues 
    6203 
    6204 > isolde pepflip sel
    6205 
    6206 Flipping the peptide bond for 1 residues 
    6207 
    6208 > isolde pepflip sel
    6209 
    6210 Flipping the peptide bond for 1 residues 
    6211 
    6212 > select clear
    6213 
    6214 > isolde pepflip sel
    6215 
    6216 Flipping the peptide bond for 1 residues 
    6217 
    6218 > isolde pepflip sel
    6219 
    6220 Flipping the peptide bond for 1 residues 
    6221 
    6222 > isolde sim stop discardTo start
    6223 
    6224 reverting to start 
    6225 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6226 chains... 
    6227 ISOLDE: stopped sim 
    6228 
    6229 > view #1/Q:137
    6230 
    6231 [Repeated 1 time(s)]
    6232 
    6233 > view #1/Q:156
    6234 
    6235 > select #1/Q:156
    6236 
    6237 22 atoms, 21 bonds, 1 residue, 1 model selected 
    6238 
    6239 > select #1/O:156
    6240 
    6241 14 atoms, 14 bonds, 1 residue, 1 model selected 
    6242 
    6243 > view #1/O:156
    6244 
    6245 > select clear
    6246 
    6247 > isolde sim start sel
    6248 
    6249 ISOLDE: started sim 
    6250 
    6251 > isolde cisflip #1.2/Q:44
    6252 
    6253 Performing cistrans flip for 1 residues 
    6254 
    6255 > isolde pepflip sel
    6256 
    6257 Flipping the peptide bond for 1 residues 
    6258 
    6259 > isolde pepflip sel
    6260 
    6261 Flipping the peptide bond for 1 residues 
    6262 
    6263 > isolde pepflip sel
    6264 
    6265 Flipping the peptide bond for 1 residues 
    6266 
    6267 > isolde pepflip sel
    6268 
    6269 Flipping the peptide bond for 1 residues 
    6270 
    6271 > select clear
    6272 
    6273 > isolde pepflip sel
    6274 
    6275 Flipping the peptide bond for 1 residues 
    6276 
    6277 > isolde pepflip sel
    6278 
    6279 Flipping the peptide bond for 1 residues 
    6280 
    6281 > ui tool show "Ramachandran Plot"
    6282 
    6283 > isolde sim stop discardTo start
    6284 
    6285 reverting to start 
    6286 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6287 chains... 
    6288 ISOLDE: stopped sim 
    6289 
    6290 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    6291 > mut8-no-C-ter/15-KSRP-no-C-ter-Step1-FivetenthSubsteps-Final-of-PART-1d1.cxs
    6292 
    6293 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    6294 
    6295 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    6296 > mut8-no-C-ter/16-KSRP-no-C-ter-Step1-FivetenthSubsteps-Final-of-PART-1d1.pdb
    6297 
    6298 > ui tool show "Ramachandran Plot"
    6299 
    6300 [Repeated 1 time(s)]
    6301 
    6302 > isolde sim start sel
    6303 
    6304 ISOLDE: started sim 
    6305 
    6306 > ui tool show "Ramachandran Plot"
    6307 
    6308 > select clear
    6309 
    6310 > isolde pepflip sel
    6311 
    6312 Flipping the peptide bond for 1 residues 
    6313 
    6314 > isolde pepflip sel
    6315 
    6316 Flipping the peptide bond for 1 residues 
    6317 
    6318 > select clear
    6319 
    6320 [Repeated 1 time(s)]
    6321 
    6322 > isolde sim pause
    6323 
    6324 > isolde sim resume
    6325 
    6326 > isolde pepflip sel
    6327 
    6328 Flipping the peptide bond for 1 residues 
    6329 
    6330 > isolde pepflip sel
    6331 
    6332 Flipping the peptide bond for 1 residues 
    6333 
    6334 > select clear
    6335 
    6336 3 models selected 
    6337 
    6338 > select clear
    6339 
    6340 > ui tool show "Ramachandran Plot"
    6341 
    6342 > isolde sim pause
    6343 
    6344 > ui tool show "Ramachandran Plot"
    6345 
    6346 > view #1/h:163
    6347 
    6348 > ui tool show "Ramachandran Plot"
    6349 
    6350 > isolde sim stop
    6351 
    6352 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6353 chains... 
    6354 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    6355 standards. 
    6356 ISOLDE: stopped sim 
    6357 
    6358 > ui tool show "Ramachandran Plot"
    6359 
    6360 > view #1/h:163
    6361 
    6362 > isolde sim start sel
    6363 
    6364 ISOLDE: started sim 
    6365 
    6366 > ui tool show "Ramachandran Plot"
    6367 
    6368 Traceback (most recent call last): 
    6369 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6370 packages/matplotlib/cbook/__init__.py", line 287, in process 
    6371 func(*args, **kwargs) 
    6372 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    6373 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    6374 on_resize 
    6375 c.draw() 
    6376 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6377 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    6378 self.figure.draw(self.renderer) 
    6379 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6380 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    6381 result = draw(artist, renderer, *args, **kwargs) 
    6382 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6383 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    6384 return draw(artist, renderer) 
    6385 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6386 packages/matplotlib/figure.py", line 2796, in draw 
    6387 artists = self._get_draw_artists(renderer) 
    6388 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6389 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    6390 ax.apply_aspect() 
    6391 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6392 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    6393 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    6394 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6395 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    6396 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    6397 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    6398 
    6399 > select clear
    6400 
    6401 [Repeated 3 time(s)]
    6402 
    6403 > isolde pepflip sel
    6404 
    6405 Flipping the peptide bond for 1 residues 
    6406 
    6407 > isolde pepflip sel
    6408 
    6409 Flipping the peptide bond for 1 residues 
    6410 
    6411 > isolde pepflip sel
    6412 
    6413 Flipping the peptide bond for 1 residues 
    6414 
    6415 > select clear
    6416 
    6417 > isolde pepflip sel
    6418 
    6419 Flipping the peptide bond for 1 residues 
    6420 
    6421 > isolde pepflip sel
    6422 
    6423 Flipping the peptide bond for 1 residues 
    6424 
    6425 > select clear
    6426 
    6427 > ui tool show "Ramachandran Plot"
    6428 
    6429 Unable to flip peptide bond after 50 rounds. Giving up. 
    6430 
    6431 > isolde pepflip sel
    6432 
    6433 Flipping the peptide bond for 1 residues 
    6434 
    6435 > isolde pepflip sel
    6436 
    6437 Flipping the peptide bond for 1 residues 
    6438 
    6439 > select clear
    6440 
    6441 Unable to flip peptide bond after 50 rounds. Giving up. 
    6442 
    6443 > isolde sim pause
    6444 
    6445 > select #1/h:180|/h:184
    6446 
    6447 28 atoms, 26 bonds, 2 residues, 1 model selected 
    6448 
    6449 > isolde sim start sel
    6450 
    6451 Simulation already running! 
    6452 
    6453 > isolde sim stop
    6454 
    6455 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6456 chains... 
    6457 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    6458 standards. 
    6459 ISOLDE: stopped sim 
    6460 
    6461 > isolde sim start sel
    6462 
    6463 ISOLDE: started sim 
    6464 
    6465 > select clear
    6466 
    6467 > isolde pepflip sel
    6468 
    6469 Flipping the peptide bond for 1 residues 
    6470 
    6471 > isolde pepflip sel
    6472 
    6473 Flipping the peptide bond for 1 residues 
    6474 
    6475 > isolde pepflip sel
    6476 
    6477 Flipping the peptide bond for 1 residues 
    6478 
    6479 > select clear
    6480 
    6481 [Repeated 1 time(s)]
    6482 
    6483 > isolde pepflip sel
    6484 
    6485 Flipping the peptide bond for 1 residues 
    6486 
    6487 > select clear
    6488 
    6489 > isolde pepflip sel
    6490 
    6491 Flipping the peptide bond for 1 residues 
    6492 
    6493 > select clear
    6494 
    6495 > isolde sim pause
    6496 
    6497 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    6498 > mut8-no-C-ter/17-KSRP-no-C-ter-Step1-SevententhSubstep.pdb
    6499 
    6500 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    6501 > mut8-no-C-ter/17-KSRP-no-C-ter-Step1-SevententhSubstep.cxs
    6502 
    6503 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    6504 
    6505 > isolde sim start sel
    6506 
    6507 Simulation already running! 
    6508 
    6509 > isolde sim resume
    6510 
    6511 > select clear
    6512 
    6513 [Repeated 4 time(s)]
    6514 
    6515 > isolde pepflip sel
    6516 
    6517 Flipping the peptide bond for 1 residues 
    6518 
    6519 > isolde pepflip sel
    6520 
    6521 Flipping the peptide bond for 1 residues 
    6522 
    6523 > select clear
    6524 
    6525 > isolde pepflip sel
    6526 
    6527 Flipping the peptide bond for 1 residues 
    6528 
    6529 > select #1/h
    6530 
    6531 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    6532 
    6533 > select clear
    6534 
    6535 > ui tool show "Ramachandran Plot"
    6536 
    6537 > view #1/h:N183
    6538 
    6539 No objects specified. 
    6540 
    6541 > view #1/h:183
    6542 
    6543 > isolde sim pause
    6544 
    6545 > isolde sim resume
    6546 
    6547 > select clear
    6548 
    6549 [Repeated 2 time(s)]
    6550 
    6551 > isolde pepflip sel
    6552 
    6553 Flipping the peptide bond for 1 residues 
    6554 
    6555 > isolde pepflip sel
    6556 
    6557 Flipping the peptide bond for 1 residues 
    6558 
    6559 > isolde pepflip sel
    6560 
    6561 Flipping the peptide bond for 1 residues 
    6562 Unable to flip peptide bond after 50 rounds. Giving up. 
    6563 [Repeated 1 time(s)]
    6564 
    6565 > select clear
    6566 
    6567 > isolde sim stop
    6568 
    6569 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6570 chains... 
    6571 ISOLDE: stopped sim 
    6572 
    6573 > view #1/h
    6574 
    6575 > select #1/h
    6576 
    6577 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    6578 
    6579 > isolde sim start sel
    6580 
    6581 ISOLDE: started sim 
    6582 
    6583 > ui tool show "Ramachandran Plot"
    6584 
    6585 > isolde pepflip sel
    6586 
    6587 Flipping the peptide bond for 1 residues 
    6588 
    6589 > select clear
    6590 
    6591 > isolde sim pause
    6592 
    6593 > isolde sim resume
    6594 
    6595 > select clear
    6596 
    6597 > isolde pepflip sel
    6598 
    6599 Flipping the peptide bond for 1 residues 
    6600 
    6601 > select clear
    6602 
    6603 > isolde sim stop
    6604 
    6605 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6606 chains... 
    6607 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    6608 standards. 
    6609 ISOLDE: stopped sim 
    6610 
    6611 > select #1/h
    6612 
    6613 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    6614 
    6615 > isolde sim start sel
    6616 
    6617 ISOLDE: started sim 
    6618 
    6619 > select clear
    6620 
    6621 > isolde pepflip sel
    6622 
    6623 Flipping the peptide bond for 1 residues 
    6624 
    6625 > isolde pepflip sel
    6626 
    6627 Flipping the peptide bond for 1 residues 
    6628 
    6629 > isolde sim pause
    6630 
    6631 > ui tool show "Ramachandran Plot"
    6632 
    6633 > isolde sim resume
    6634 
    6635 > isolde pepflip sel
    6636 
    6637 Flipping the peptide bond for 1 residues 
    6638 
    6639 > isolde pepflip sel
    6640 
    6641 Flipping the peptide bond for 1 residues 
    6642 
    6643 > select #1/h:115-119
    6644 
    6645 85 atoms, 84 bonds, 5 residues, 1 model selected 
    6646 
    6647 > select clear
    6648 
    6649 > select #1/h:215-219
    6650 
    6651 70 atoms, 69 bonds, 5 residues, 1 model selected 
    6652 
    6653 > select #1/h:152-155
    6654 
    6655 61 atoms, 62 bonds, 4 residues, 1 model selected 
    6656 
    6657 > select #1/h:152-156
    6658 
    6659 80 atoms, 81 bonds, 5 residues, 1 model selected 
    6660 
    6661 > select #1/h
    6662 
    6663 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    6664 
    6665 > select clear
    6666 
    6667 [Repeated 1 time(s)]
    6668 
    6669 > isolde pepflip sel
    6670 
    6671 Flipping the peptide bond for 1 residues 
    6672 
    6673 > select clear
    6674 
    6675 > isolde pepflip sel
    6676 
    6677 Flipping the peptide bond for 1 residues 
    6678 
    6679 > isolde pepflip sel
    6680 
    6681 Flipping the peptide bond for 1 residues 
    6682 Unable to flip peptide bond after 50 rounds. Giving up. 
    6683 
    6684 > select clear
    6685 
    6686 [Repeated 1 time(s)]
    6687 
    6688 > isolde pepflip sel
    6689 
    6690 Flipping the peptide bond for 1 residues 
    6691 
    6692 > select clear
    6693 
    6694 > isolde sim pause
    6695 
    6696 > isolde sim resume
    6697 
    6698 > ui tool show "Ramachandran Plot"
    6699 
    6700 > isolde sim pause
    6701 
    6702 > isolde sim resume
    6703 
    6704 > view #1/P:244
    6705 
    6706 > view #1/h
    6707 
    6708 > ui tool show "Ramachandran Plot"
    6709 
    6710 3 models selected 
    6711 [Repeated 2 time(s)]
    6712 
    6713 > isolde sim pause
    6714 
    6715 > isolde sim resume
    6716 
    6717 > isolde sim pause
    6718 
    6719 > isolde sim resume
    6720 
    6721 > select clear
    6722 
    6723 3 models selected 
    6724 
    6725 > select clear
    6726 
    6727 > ui tool show "Ramachandran Plot"
    6728 
    6729 [Repeated 1 time(s)]
    6730 
    6731 > isolde sim pause
    6732 
    6733 > isolde sim resume
    6734 
    6735 > isolde sim pause
    6736 
    6737 > ui tool show "Ramachandran Plot"
    6738 
    6739 > isolde sim resume
    6740 
    6741 > select clear
    6742 
    6743 > isolde pepflip sel
    6744 
    6745 Flipping the peptide bond for 1 residues 
    6746 
    6747 > select clear
    6748 
    6749 > isolde pepflip sel
    6750 
    6751 Flipping the peptide bond for 1 residues 
    6752 
    6753 > select clear
    6754 
    6755 Unable to flip peptide bond after 50 rounds. Giving up. 
    6756 
    6757 > ui tool show "Ramachandran Plot"
    6758 
    6759 > isolde sim pause
    6760 
    6761 > isolde sim resume
    6762 
    6763 > select clear
    6764 
    6765 [Repeated 2 time(s)]
    6766 
    6767 > isolde pepflip sel
    6768 
    6769 Flipping the peptide bond for 1 residues 
    6770 
    6771 > select clear
    6772 
    6773 > isolde pepflip sel
    6774 
    6775 Flipping the peptide bond for 1 residues 
    6776 Unable to flip peptide bond after 50 rounds. Giving up. 
    6777 
    6778 > select clear
    6779 
    6780 > ui tool show "Ramachandran Plot"
    6781 
    6782 > isolde pepflip sel
    6783 
    6784 Flipping the peptide bond for 1 residues 
    6785 
    6786 > select clear
    6787 
    6788 > isolde pepflip sel
    6789 
    6790 Flipping the peptide bond for 1 residues 
    6791 
    6792 > select clear
    6793 
    6794 > ui tool show "Ramachandran Plot"
    6795 
    6796 > select clear
    6797 
    6798 [Repeated 3 time(s)]
    6799 
    6800 > ui tool show "Ramachandran Plot"
    6801 
    6802 > isolde sim pause
    6803 
    6804 > isolde sim resume
    6805 
    6806 > ui tool show "Ramachandran Plot"
    6807 
    6808 > select clear
    6809 
    6810 [Repeated 1 time(s)]
    6811 
    6812 > ui tool show "Ramachandran Plot"
    6813 
    6814 [Repeated 5 time(s)]
    6815 
    6816 > isolde pepflip sel
    6817 
    6818 Flipping the peptide bond for 1 residues 
    6819 
    6820 > select clear
    6821 
    6822 > isolde pepflip sel
    6823 
    6824 Flipping the peptide bond for 1 residues 
    6825 
    6826 > select clear
    6827 
    6828 > isolde pepflip sel
    6829 
    6830 Flipping the peptide bond for 1 residues 
    6831 
    6832 > select clear
    6833 
    6834 > isolde pepflip sel
    6835 
    6836 Flipping the peptide bond for 1 residues 
    6837 
    6838 > isolde pepflip sel
    6839 
    6840 Flipping the peptide bond for 1 residues 
    6841 
    6842 > ui tool show "Ramachandran Plot"
    6843 
    6844 > select clear
    6845 
    6846 > isolde pepflip sel
    6847 
    6848 Flipping the peptide bond for 1 residues 
    6849 
    6850 > isolde pepflip sel
    6851 
    6852 Flipping the peptide bond for 1 residues 
    6853 
    6854 > ui tool show "Ramachandran Plot"
    6855 
    6856 [Repeated 1 time(s)]Traceback (most recent call last): 
    6857 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6858 packages/matplotlib/cbook/__init__.py", line 287, in process 
    6859 func(*args, **kwargs) 
    6860 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    6861 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    6862 on_resize 
    6863 c.draw() 
    6864 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6865 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    6866 self.figure.draw(self.renderer) 
    6867 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6868 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    6869 result = draw(artist, renderer, *args, **kwargs) 
    6870 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6871 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    6872 return draw(artist, renderer) 
    6873 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6874 packages/matplotlib/figure.py", line 2796, in draw 
    6875 artists = self._get_draw_artists(renderer) 
    6876 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6877 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    6878 ax.apply_aspect() 
    6879 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6880 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    6881 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    6882 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6883 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    6884 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    6885 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    6886 
    6887 > select clear
    6888 
    6889 > ui tool show "Ramachandran Plot"
    6890 
    6891 > isolde pepflip sel
    6892 
    6893 Flipping the peptide bond for 1 residues 
    6894 
    6895 > select clear
    6896 
    6897 > isolde pepflip sel
    6898 
    6899 Flipping the peptide bond for 1 residues 
    6900 
    6901 > isolde pepflip sel
    6902 
    6903 Flipping the peptide bond for 1 residues 
    6904 Unable to flip peptide bond after 50 rounds. Giving up. 
    6905 Traceback (most recent call last): 
    6906 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6907 packages/matplotlib/cbook/__init__.py", line 287, in process 
    6908 func(*args, **kwargs) 
    6909 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    6910 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    6911 on_resize 
    6912 c.draw() 
    6913 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6914 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    6915 self.figure.draw(self.renderer) 
    6916 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6917 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    6918 result = draw(artist, renderer, *args, **kwargs) 
    6919 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6920 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    6921 return draw(artist, renderer) 
    6922 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6923 packages/matplotlib/figure.py", line 2796, in draw 
    6924 artists = self._get_draw_artists(renderer) 
    6925 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6926 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    6927 ax.apply_aspect() 
    6928 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6929 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    6930 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    6931 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6932 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    6933 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    6934 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    6935 
    6936 > isolde pepflip sel
    6937 
    6938 Flipping the peptide bond for 1 residues 
    6939 
    6940 > select #1/h
    6941 
    6942 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    6943 
    6944 > select clear
    6945 
    6946 [Repeated 1 time(s)]
    6947 
    6948 > ui tool show "Ramachandran Plot"
    6949 
    6950 Traceback (most recent call last): 
    6951 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6952 packages/matplotlib/cbook/__init__.py", line 287, in process 
    6953 func(*args, **kwargs) 
    6954 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    6955 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    6956 on_resize 
    6957 c.draw() 
    6958 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6959 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    6960 self.figure.draw(self.renderer) 
    6961 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6962 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    6963 result = draw(artist, renderer, *args, **kwargs) 
    6964 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6965 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    6966 return draw(artist, renderer) 
    6967 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6968 packages/matplotlib/figure.py", line 2796, in draw 
    6969 artists = self._get_draw_artists(renderer) 
    6970 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6971 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    6972 ax.apply_aspect() 
    6973 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6974 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    6975 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    6976 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6977 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    6978 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    6979 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    6980 Traceback (most recent call last): 
    6981 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6982 packages/matplotlib/cbook/__init__.py", line 287, in process 
    6983 func(*args, **kwargs) 
    6984 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    6985 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    6986 on_resize 
    6987 c.draw() 
    6988 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6989 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    6990 self.figure.draw(self.renderer) 
    6991 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6992 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    6993 result = draw(artist, renderer, *args, **kwargs) 
    6994 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6995 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    6996 return draw(artist, renderer) 
    6997 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    6998 packages/matplotlib/figure.py", line 2796, in draw 
    6999 artists = self._get_draw_artists(renderer) 
    7000 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7001 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    7002 ax.apply_aspect() 
    7003 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7004 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    7005 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    7006 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7007 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    7008 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    7009 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    7010 
    7011 > isolde pepflip sel
    7012 
    7013 Flipping the peptide bond for 1 residues 
    7014 
    7015 > select clear
    7016 
    7017 > isolde pepflip sel
    7018 
    7019 Flipping the peptide bond for 1 residues 
    7020 
    7021 > select clear
    7022 
    7023 [Repeated 2 time(s)]
    7024 
    7025 > isolde pepflip sel
    7026 
    7027 Flipping the peptide bond for 1 residues 
    7028 
    7029 > ui tool show "Ramachandran Plot"
    7030 
    7031 [Repeated 1 time(s)]
    7032 
    7033 > select clear
    7034 
    7035 > isolde pepflip sel
    7036 
    7037 Flipping the peptide bond for 1 residues 
    7038 
    7039 > isolde pepflip sel
    7040 
    7041 Flipping the peptide bond for 1 residues 
    7042 
    7043 > ui tool show "Ramachandran Plot"
    7044 
    7045 > select clear
    7046 
    7047 [Repeated 1 time(s)]
    7048 
    7049 > isolde pepflip sel
    7050 
    7051 Flipping the peptide bond for 1 residues 
    7052 
    7053 > select clear
    7054 
    7055 > isolde pepflip sel
    7056 
    7057 Flipping the peptide bond for 1 residues 
    7058 
    7059 > isolde pepflip sel
    7060 
    7061 Flipping the peptide bond for 1 residues 
    7062 
    7063 > select clear
    7064 
    7065 > isolde pepflip sel
    7066 
    7067 Flipping the peptide bond for 1 residues 
    7068 
    7069 > select clear
    7070 
    7071 [Repeated 1 time(s)]
    7072 
    7073 > select #1/h
    7074 
    7075 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    7076 
    7077 > select #1/h
    7078 
    7079 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    7080 
    7081 > ui tool show "Ramachandran Plot"
    7082 
    7083 > select clear
    7084 
    7085 Traceback (most recent call last): 
    7086 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7087 packages/matplotlib/cbook/__init__.py", line 287, in process 
    7088 func(*args, **kwargs) 
    7089 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    7090 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    7091 on_resize 
    7092 c.draw() 
    7093 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7094 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    7095 self.figure.draw(self.renderer) 
    7096 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7097 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    7098 result = draw(artist, renderer, *args, **kwargs) 
    7099 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7100 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    7101 return draw(artist, renderer) 
    7102 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7103 packages/matplotlib/figure.py", line 2796, in draw 
    7104 artists = self._get_draw_artists(renderer) 
    7105 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7106 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    7107 ax.apply_aspect() 
    7108 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7109 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    7110 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    7111 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7112 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    7113 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    7114 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    7115 Traceback (most recent call last): 
    7116 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7117 packages/matplotlib/cbook/__init__.py", line 287, in process 
    7118 func(*args, **kwargs) 
    7119 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    7120 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    7121 on_resize 
    7122 c.draw() 
    7123 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7124 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    7125 self.figure.draw(self.renderer) 
    7126 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7127 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    7128 result = draw(artist, renderer, *args, **kwargs) 
    7129 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7130 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    7131 return draw(artist, renderer) 
    7132 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7133 packages/matplotlib/figure.py", line 2796, in draw 
    7134 artists = self._get_draw_artists(renderer) 
    7135 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7136 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    7137 ax.apply_aspect() 
    7138 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7139 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    7140 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    7141 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7142 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    7143 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    7144 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    7145 
    7146 > isolde pepflip sel
    7147 
    7148 Flipping the peptide bond for 1 residues 
    7149 
    7150 > isolde pepflip sel
    7151 
    7152 Flipping the peptide bond for 1 residues 
    7153 Traceback (most recent call last): 
    7154 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7155 packages/matplotlib/cbook/__init__.py", line 287, in process 
    7156 func(*args, **kwargs) 
    7157 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    7158 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    7159 on_resize 
    7160 c.draw() 
    7161 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7162 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    7163 self.figure.draw(self.renderer) 
    7164 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7165 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    7166 result = draw(artist, renderer, *args, **kwargs) 
    7167 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7168 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    7169 return draw(artist, renderer) 
    7170 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7171 packages/matplotlib/figure.py", line 2796, in draw 
    7172 artists = self._get_draw_artists(renderer) 
    7173 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7174 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    7175 ax.apply_aspect() 
    7176 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7177 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    7178 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    7179 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7180 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    7181 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    7182 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    7183 
    7184 > ui tool show "Ramachandran Plot"
    7185 
    7186 > select #1/h
    7187 
    7188 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    7189 
    7190 > select clear
    7191 
    7192 > ui tool show "Ramachandran Plot"
    7193 
    7194 [Repeated 1 time(s)]
    7195 
    7196 > select clear
    7197 
    7198 > ui tool show "Ramachandran Plot"
    7199 
    7200 Traceback (most recent call last): 
    7201 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7202 packages/matplotlib/cbook/__init__.py", line 287, in process 
    7203 func(*args, **kwargs) 
    7204 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    7205 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    7206 on_resize 
    7207 c.draw() 
    7208 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7209 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    7210 self.figure.draw(self.renderer) 
    7211 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7212 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    7213 result = draw(artist, renderer, *args, **kwargs) 
    7214 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7215 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    7216 return draw(artist, renderer) 
    7217 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7218 packages/matplotlib/figure.py", line 2796, in draw 
    7219 artists = self._get_draw_artists(renderer) 
    7220 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7221 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    7222 ax.apply_aspect() 
    7223 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7224 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    7225 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    7226 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7227 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    7228 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    7229 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    7230 
    7231 > ui tool show "Ramachandran Plot"
    7232 
    7233 [Repeated 1 time(s)]
    7234 
    7235 > select clear
    7236 
    7237 > ui tool show "Ramachandran Plot"
    7238 
    7239 > isolde pepflip sel
    7240 
    7241 Flipping the peptide bond for 1 residues 
    7242 
    7243 > select clear
    7244 
    7245 [Repeated 1 time(s)]
    7246 
    7247 > ui tool show "Ramachandran Plot"
    7248 
    7249 > select #1/h
    7250 
    7251 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    7252 
    7253 > select #1/h
    7254 
    7255 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    7256 
    7257 > select clear
    7258 
    7259 [Repeated 1 time(s)]
    7260 
    7261 > ui tool show "Ramachandran Plot"
    7262 
    7263 > select clear
    7264 
    7265 > isolde pepflip sel
    7266 
    7267 Flipping the peptide bond for 1 residues 
    7268 
    7269 > isolde pepflip sel
    7270 
    7271 Flipping the peptide bond for 1 residues 
    7272 
    7273 > select clear
    7274 
    7275 > isolde pepflip sel
    7276 
    7277 Flipping the peptide bond for 1 residues 
    7278 
    7279 > select clear
    7280 
    7281 > isolde pepflip sel
    7282 
    7283 Flipping the peptide bond for 1 residues 
    7284 
    7285 > select clear
    7286 
    7287 Traceback (most recent call last): 
    7288 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7289 packages/matplotlib/cbook/__init__.py", line 287, in process 
    7290 func(*args, **kwargs) 
    7291 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    7292 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    7293 on_resize 
    7294 c.draw() 
    7295 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7296 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    7297 self.figure.draw(self.renderer) 
    7298 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7299 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    7300 result = draw(artist, renderer, *args, **kwargs) 
    7301 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7302 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    7303 return draw(artist, renderer) 
    7304 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7305 packages/matplotlib/figure.py", line 2796, in draw 
    7306 artists = self._get_draw_artists(renderer) 
    7307 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7308 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    7309 ax.apply_aspect() 
    7310 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7311 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    7312 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    7313 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7314 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    7315 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    7316 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    7317 
    7318 > isolde pepflip sel
    7319 
    7320 Flipping the peptide bond for 1 residues 
    7321 
    7322 > ui tool show "Ramachandran Plot"
    7323 
    7324 > select clear
    7325 
    7326 [Repeated 1 time(s)]
    7327 
    7328 > ui tool show "Ramachandran Plot"
    7329 
    7330 > isolde pepflip sel
    7331 
    7332 Flipping the peptide bond for 1 residues 
    7333 
    7334 > ui tool show "Ramachandran Plot"
    7335 
    7336 > isolde pepflip sel
    7337 
    7338 Flipping the peptide bond for 1 residues 
    7339 
    7340 > isolde pepflip sel
    7341 
    7342 Flipping the peptide bond for 1 residues 
    7343 
    7344 > select clear
    7345 
    7346 [Repeated 3 time(s)]
    7347 
    7348 > ui tool show "Ramachandran Plot"
    7349 
    7350 > isolde pepflip sel
    7351 
    7352 Flipping the peptide bond for 1 residues 
    7353 
    7354 > select clear
    7355 
    7356 > ui tool show "Ramachandran Plot"
    7357 
    7358 > select #1/h
    7359 
    7360 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    7361 
    7362 > select clear
    7363 
    7364 Traceback (most recent call last): 
    7365 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7366 packages/matplotlib/cbook/__init__.py", line 287, in process 
    7367 func(*args, **kwargs) 
    7368 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    7369 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    7370 on_resize 
    7371 c.draw() 
    7372 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7373 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    7374 self.figure.draw(self.renderer) 
    7375 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7376 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    7377 result = draw(artist, renderer, *args, **kwargs) 
    7378 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7379 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    7380 return draw(artist, renderer) 
    7381 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7382 packages/matplotlib/figure.py", line 2796, in draw 
    7383 artists = self._get_draw_artists(renderer) 
    7384 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7385 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    7386 ax.apply_aspect() 
    7387 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7388 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    7389 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    7390 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7391 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    7392 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    7393 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    7394 
    7395 > select #1/h
    7396 
    7397 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    7398 
    7399 > select #1/h
    7400 
    7401 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    7402 
    7403 > ui tool show "Ramachandran Plot"
    7404 
    7405 > select clear
    7406 
    7407 [Repeated 1 time(s)]
    7408 
    7409 > ui tool show "Ramachandran Plot"
    7410 
    7411 Traceback (most recent call last): 
    7412 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7413 packages/matplotlib/cbook/__init__.py", line 287, in process 
    7414 func(*args, **kwargs) 
    7415 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    7416 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    7417 on_resize 
    7418 c.draw() 
    7419 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7420 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    7421 self.figure.draw(self.renderer) 
    7422 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7423 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    7424 result = draw(artist, renderer, *args, **kwargs) 
    7425 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7426 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    7427 return draw(artist, renderer) 
    7428 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7429 packages/matplotlib/figure.py", line 2796, in draw 
    7430 artists = self._get_draw_artists(renderer) 
    7431 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7432 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    7433 ax.apply_aspect() 
    7434 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7435 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    7436 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    7437 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7438 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    7439 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    7440 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    7441 
    7442 > isolde pepflip sel
    7443 
    7444 Flipping the peptide bond for 1 residues 
    7445 
    7446 > select clear
    7447 
    7448 > ui tool show "Ramachandran Plot"
    7449 
    7450 [Repeated 1 time(s)]
    7451 
    7452 > isolde pepflip sel
    7453 
    7454 Flipping the peptide bond for 1 residues 
    7455 
    7456 > ui tool show "Ramachandran Plot"
    7457 
    7458 > select clear
    7459 
    7460 > ui tool show "Ramachandran Plot"
    7461 
    7462 > select clear
    7463 
    7464 [Repeated 1 time(s)]
    7465 
    7466 > ui tool show "Ramachandran Plot"
    7467 
    7468 [Repeated 2 time(s)]Traceback (most recent call last): 
    7469 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7470 packages/matplotlib/cbook/__init__.py", line 287, in process 
    7471 func(*args, **kwargs) 
    7472 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    7473 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    7474 on_resize 
    7475 c.draw() 
    7476 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7477 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    7478 self.figure.draw(self.renderer) 
    7479 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7480 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    7481 result = draw(artist, renderer, *args, **kwargs) 
    7482 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7483 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    7484 return draw(artist, renderer) 
    7485 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7486 packages/matplotlib/figure.py", line 2796, in draw 
    7487 artists = self._get_draw_artists(renderer) 
    7488 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7489 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    7490 ax.apply_aspect() 
    7491 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7492 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    7493 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    7494 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7495 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    7496 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    7497 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    7498 
    7499 > isolde pepflip sel
    7500 
    7501 Flipping the peptide bond for 1 residues 
    7502 Traceback (most recent call last): 
    7503 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7504 packages/matplotlib/cbook/__init__.py", line 287, in process 
    7505 func(*args, **kwargs) 
    7506 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    7507 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    7508 on_resize 
    7509 c.draw() 
    7510 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7511 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    7512 self.figure.draw(self.renderer) 
    7513 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7514 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    7515 result = draw(artist, renderer, *args, **kwargs) 
    7516 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7517 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    7518 return draw(artist, renderer) 
    7519 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7520 packages/matplotlib/figure.py", line 2796, in draw 
    7521 artists = self._get_draw_artists(renderer) 
    7522 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7523 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    7524 ax.apply_aspect() 
    7525 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7526 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    7527 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    7528 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7529 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    7530 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    7531 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    7532 
    7533 > isolde pepflip sel
    7534 
    7535 Flipping the peptide bond for 1 residues 
    7536 
    7537 > isolde sim stop
    7538 
    7539 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7540 chains... 
    7541 ISOLDE: Corrected atom nomenclature of 13 residues in model #1.2 to IUPAC-IUB
    7542 standards. 
    7543 ISOLDE: stopped sim 
    7544 
    7545 > select #1/h
    7546 
    7547 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    7548 
    7549 > isolde sim start sel
    7550 
    7551 ISOLDE: started sim 
    7552 
    7553 > ui tool show "Ramachandran Plot"
    7554 
    7555 [Repeated 1 time(s)]
    7556 
    7557 > isolde sim pause
    7558 
    7559 > isolde sim resume
    7560 
    7561 > ui tool show "Ramachandran Plot"
    7562 
    7563 > select clear
    7564 
    7565 > isolde pepflip sel
    7566 
    7567 Flipping the peptide bond for 1 residues 
    7568 
    7569 > isolde pepflip sel
    7570 
    7571 Flipping the peptide bond for 1 residues 
    7572 
    7573 > isolde pepflip sel
    7574 
    7575 Flipping the peptide bond for 1 residues 
    7576 
    7577 > isolde pepflip sel
    7578 
    7579 Flipping the peptide bond for 1 residues 
    7580 
    7581 > isolde pepflip sel
    7582 
    7583 Flipping the peptide bond for 1 residues 
    7584 
    7585 > isolde pepflip sel
    7586 
    7587 Flipping the peptide bond for 1 residues 
    7588 Unable to flip peptide bond after 50 rounds. Giving up. 
    7589 
    7590 > select clear
    7591 
    7592 [Repeated 1 time(s)]Unable to flip peptide bond after 50 rounds. Giving up. 
    7593 
    7594 > isolde pepflip sel
    7595 
    7596 Flipping the peptide bond for 1 residues 
    7597 
    7598 > select #1/h
    7599 
    7600 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    7601 
    7602 > select clear
    7603 
    7604 > isolde sim pause
    7605 
    7606 > isolde sim resume
    7607 
    7608 > ui tool show "Ramachandran Plot"
    7609 
    7610 > isolde pepflip sel
    7611 
    7612 Flipping the peptide bond for 1 residues 
    7613 
    7614 > isolde pepflip sel
    7615 
    7616 Flipping the peptide bond for 1 residues 
    7617 
    7618 > isolde pepflip sel
    7619 
    7620 Flipping the peptide bond for 1 residues 
    7621 
    7622 > select clear
    7623 
    7624 Unable to flip peptide bond after 50 rounds. Giving up. 
    7625 
    7626 > isolde pepflip sel
    7627 
    7628 Flipping the peptide bond for 1 residues 
    7629 
    7630 > isolde pepflip sel
    7631 
    7632 Flipping the peptide bond for 1 residues 
    7633 
    7634 > isolde pepflip sel
    7635 
    7636 Flipping the peptide bond for 1 residues 
    7637 
    7638 > select clear
    7639 
    7640 > select #1/h
    7641 
    7642 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    7643 
    7644 > ui tool show "Ramachandran Plot"
    7645 
    7646 > select clear
    7647 
    7648 > ui tool show "Ramachandran Plot"
    7649 
    7650 > select clear
    7651 
    7652 > ui tool show "Ramachandran Plot"
    7653 
    7654 > select clear
    7655 
    7656 > ui tool show "Ramachandran Plot"
    7657 
    7658 > isolde pepflip sel
    7659 
    7660 Flipping the peptide bond for 1 residues 
    7661 
    7662 > isolde pepflip sel
    7663 
    7664 Flipping the peptide bond for 1 residues 
    7665 
    7666 > isolde pepflip sel
    7667 
    7668 Flipping the peptide bond for 1 residues 
    7669 Unable to flip peptide bond after 50 rounds. Giving up. 
    7670 
    7671 > select clear
    7672 
    7673 > ui tool show "Ramachandran Plot"
    7674 
    7675 > isolde pepflip sel
    7676 
    7677 Flipping the peptide bond for 1 residues 
    7678 
    7679 > isolde pepflip sel
    7680 
    7681 Flipping the peptide bond for 1 residues 
    7682 
    7683 > select clear
    7684 
    7685 > ui tool show "Ramachandran Plot"
    7686 
    7687 > isolde pepflip sel
    7688 
    7689 Flipping the peptide bond for 1 residues 
    7690 
    7691 > isolde pepflip sel
    7692 
    7693 Flipping the peptide bond for 1 residues 
    7694 
    7695 > isolde pepflip sel
    7696 
    7697 Flipping the peptide bond for 1 residues 
    7698 
    7699 > isolde pepflip sel
    7700 
    7701 Flipping the peptide bond for 1 residues 
    7702 Unable to flip peptide bond after 50 rounds. Giving up. 
    7703 
    7704 > isolde pepflip sel
    7705 
    7706 Flipping the peptide bond for 1 residues 
    7707 Traceback (most recent call last): 
    7708 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7709 packages/matplotlib/cbook/__init__.py", line 287, in process 
    7710 func(*args, **kwargs) 
    7711 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    7712 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    7713 on_resize 
    7714 c.draw() 
    7715 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7716 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    7717 self.figure.draw(self.renderer) 
    7718 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7719 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    7720 result = draw(artist, renderer, *args, **kwargs) 
    7721 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7722 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    7723 return draw(artist, renderer) 
    7724 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7725 packages/matplotlib/figure.py", line 2796, in draw 
    7726 artists = self._get_draw_artists(renderer) 
    7727 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7728 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    7729 ax.apply_aspect() 
    7730 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7731 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    7732 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    7733 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7734 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    7735 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    7736 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    7737 Unable to flip peptide bond after 50 rounds. Giving up. 
    7738 
    7739 > isolde sim pause
    7740 
    7741 > isolde sim resume
    7742 
    7743 > ui tool show "Ramachandran Plot"
    7744 
    7745 Traceback (most recent call last): 
    7746 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7747 packages/matplotlib/cbook/__init__.py", line 287, in process 
    7748 func(*args, **kwargs) 
    7749 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    7750 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    7751 on_resize 
    7752 c.draw() 
    7753 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7754 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    7755 self.figure.draw(self.renderer) 
    7756 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7757 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    7758 result = draw(artist, renderer, *args, **kwargs) 
    7759 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7760 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    7761 return draw(artist, renderer) 
    7762 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7763 packages/matplotlib/figure.py", line 2796, in draw 
    7764 artists = self._get_draw_artists(renderer) 
    7765 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7766 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    7767 ax.apply_aspect() 
    7768 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7769 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    7770 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    7771 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    7772 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    7773 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    7774 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    7775 
    7776 > select clear
    7777 
    7778 > ui tool show "Ramachandran Plot"
    7779 
    7780 > select clear
    7781 
    7782 > style #1/h:84|/h:125 sphere
    7783 
    7784 Changed 39 atom styles 
    7785 
    7786 > style #1/h:84|/h:125 stick
    7787 
    7788 Changed 39 atom styles 
    7789 
    7790 > ui tool show "Ramachandran Plot"
    7791 
    7792 [Repeated 1 time(s)]
    7793 
    7794 > isolde sim stop
    7795 
    7796 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7797 chains... 
    7798 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    7799 standards. 
    7800 ISOLDE: stopped sim 
    7801 
    7802 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    7803 > mut8-no-C-ter/18-KSRP-no-C-ter-Step1-SevententhSubsteps-POST-FIRST-SIM-ANN-
    7804 > KSRP.cxs
    7805 
    7806 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    7807 
    7808 ——— End of log from Fri Mar 24 14:43:56 2023 ———
    7809 
    7810 opened ChimeraX session 
    7811 
    7812 > isolde start
    7813 
    7814 > set selectionWidth 4
    7815 
    7816 > isolde restrain ligands #1
    7817 
    7818 > select clear
    7819 
    7820 > select #1/h
    7821 
    7822 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    7823 
    7824 > isolde sim start sel
    7825 
    7826 Launching using CUDA failed with the below message. Falling back to using
    7827 OpenCL. 
    7828  
    7829 Error compiling program: nvrtc: error: invalid value for --gpu-architecture
    7830 (-arch) 
    7831  
    7832 
    7833 ISOLDE: started sim 
    7834 
    7835 > isolde sim stop discardTo start
    7836 
    7837 reverting to start 
    7838 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7839 chains... 
    7840 ISOLDE: stopped sim 
    7841 
    7842 > select #1/h
    7843 
    7844 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    7845 
    7846 > isolde sim start sel
    7847 
    7848 ISOLDE: started sim 
    7849 
    7850 > isolde sim stop discardTo start
    7851 
    7852 reverting to start 
    7853 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7854 chains... 
    7855 ISOLDE: stopped sim 
    7856 
    7857 > select #1/h
    7858 
    7859 2451 atoms, 2474 bonds, 153 residues, 1 model selected 
    7860 
    7861 > isolde sim start sel
    7862 
    7863 ISOLDE: started sim 
    7864 
    7865 > ui tool show "Ramachandran Plot"
    7866 
    7867 > select clear
    7868 
    7869 > ui tool show "Ramachandran Plot"
    7870 
    7871 [Repeated 2 time(s)]
    7872 
    7873 > isolde sim pause
    7874 
    7875 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    7876 > mut8-no-C-ter/19a-Test-KSRP-Env-System-on-the-middle-of-
    7877 > overFittingTo-6Times-densityField.pdb
    7878 
    7879 > isolde sim resume
    7880 
    7881 > ui tool show "Ramachandran Plot"
    7882 
    7883 [Repeated 1 time(s)]
    7884 
    7885 > isolde sim pause
    7886 
    7887 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    7888 > mut8-no-C-ter/19b-Test-KSRP-Env-System-on-the-overFittingTo-6Times-
    7889 > densityFieldSmoth-NoSmoth.pdb
    7890 
    7891 > isolde sim resume
    7892 
    7893 > ui tool show "Ramachandran Plot"
    7894 
    7895 [Repeated 4 time(s)]
    7896 
    7897 > isolde sim pause
    7898 
    7899 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    7900 > mut8-no-C-ter/19c-Test-KSRP-Env-System-After-the-overFittingTo-6Times-And-
    7901 > ComeBack-to-Default.pdb
    7902 
    7903 > isolde sim resume
    7904 
    7905 > ui tool show "Ramachandran Plot"
    7906 
    7907 [Repeated 3 time(s)]
    7908 
    7909 > select clear
    7910 
    7911 [Repeated 3 time(s)]
    7912 
    7913 > ui tool show "Ramachandran Plot"
    7914 
    7915 > isolde pepflip sel
    7916 
    7917 Flipping the peptide bond for 1 residues 
    7918 
    7919 > ui tool show "Ramachandran Plot"
    7920 
    7921 > select clear
    7922 
    7923 > isolde pepflip sel
    7924 
    7925 Flipping the peptide bond for 1 residues 
    7926 
    7927 > ui tool show "Ramachandran Plot"
    7928 
    7929 > select clear
    7930 
    7931 > isolde pepflip sel
    7932 
    7933 Flipping the peptide bond for 1 residues 
    7934 
    7935 > ui tool show "Ramachandran Plot"
    7936 
    7937 > select clear
    7938 
    7939 > isolde pepflip sel
    7940 
    7941 Flipping the peptide bond for 1 residues 
    7942 
    7943 > isolde pepflip sel
    7944 
    7945 Flipping the peptide bond for 1 residues 
    7946 
    7947 > select clear
    7948 
    7949 > ui tool show "Ramachandran Plot"
    7950 
    7951 [Repeated 3 time(s)]
    7952 
    7953 > isolde pepflip sel
    7954 
    7955 Flipping the peptide bond for 1 residues 
    7956 
    7957 > ui tool show "Ramachandran Plot"
    7958 
    7959 > select clear
    7960 
    7961 > ui tool show "Ramachandran Plot"
    7962 
    7963 > select clear
    7964 
    7965 > isolde pepflip sel
    7966 
    7967 Flipping the peptide bond for 1 residues 
    7968 
    7969 > select clear
    7970 
    7971 > isolde pepflip sel
    7972 
    7973 Flipping the peptide bond for 1 residues 
    7974 
    7975 > ui tool show "Ramachandran Plot"
    7976 
    7977 > select clear
    7978 
    7979 [Repeated 1 time(s)]
    7980 
    7981 > ui tool show "Ramachandran Plot"
    7982 
    7983 > isolde pepflip sel
    7984 
    7985 Flipping the peptide bond for 1 residues 
    7986 
    7987 > isolde pepflip sel
    7988 
    7989 Flipping the peptide bond for 1 residues 
    7990 
    7991 > select clear
    7992 
    7993 > ui tool show "Ramachandran Plot"
    7994 
    7995 [Repeated 1 time(s)]
    7996 
    7997 > select clear
    7998 
    7999 > ui tool show "Ramachandran Plot"
    8000 
    8001 > select clear
    8002 
    8003 > isolde pepflip sel
    8004 
    8005 Flipping the peptide bond for 1 residues 
    8006 
    8007 > select clear
    8008 
    8009 > ui tool show "Ramachandran Plot"
    8010 
    8011 [Repeated 1 time(s)]
    8012 
    8013 > isolde pepflip sel
    8014 
    8015 Flipping the peptide bond for 1 residues 
    8016 
    8017 > select clear
    8018 
    8019 > ui tool show "Ramachandran Plot"
    8020 
    8021 > select clear
    8022 
    8023 [Repeated 3 time(s)]
    8024 
    8025 > isolde pepflip sel
    8026 
    8027 Flipping the peptide bond for 1 residues 
    8028 
    8029 > isolde pepflip sel
    8030 
    8031 Flipping the peptide bond for 1 residues 
    8032 
    8033 > ui tool show "Ramachandran Plot"
    8034 
    8035 [Repeated 1 time(s)]
    8036 
    8037 > isolde pepflip sel
    8038 
    8039 Flipping the peptide bond for 1 residues 
    8040 
    8041 > select clear
    8042 
    8043 > ui tool show "Ramachandran Plot"
    8044 
    8045 [Repeated 2 time(s)]
    8046 
    8047 > select clear
    8048 
    8049 > ui tool show "Ramachandran Plot"
    8050 
    8051 [Repeated 1 time(s)]
    8052 
    8053 > isolde pepflip sel
    8054 
    8055 Flipping the peptide bond for 1 residues 
    8056 
    8057 > select clear
    8058 
    8059 [Repeated 1 time(s)]
    8060 
    8061 > isolde pepflip sel
    8062 
    8063 Flipping the peptide bond for 1 residues 
    8064 
    8065 > select clear
    8066 
    8067 > isolde pepflip sel
    8068 
    8069 Flipping the peptide bond for 1 residues 
    8070 
    8071 > ui tool show "Ramachandran Plot"
    8072 
    8073 [Repeated 1 time(s)]Traceback (most recent call last): 
    8074 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8075 packages/matplotlib/cbook/__init__.py", line 287, in process 
    8076 func(*args, **kwargs) 
    8077 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    8078 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    8079 on_resize 
    8080 c.draw() 
    8081 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8082 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    8083 self.figure.draw(self.renderer) 
    8084 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8085 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    8086 result = draw(artist, renderer, *args, **kwargs) 
    8087 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8088 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    8089 return draw(artist, renderer) 
    8090 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8091 packages/matplotlib/figure.py", line 2796, in draw 
    8092 artists = self._get_draw_artists(renderer) 
    8093 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8094 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    8095 ax.apply_aspect() 
    8096 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8097 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    8098 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    8099 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    8100 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    8101 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    8102 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    8103 
    8104 > select clear
    8105 
    8106 [Repeated 2 time(s)]
    8107 
    8108 > ui tool show "Ramachandran Plot"
    8109 
    8110 [Repeated 2 time(s)]
    8111 
    8112 > select clear
    8113 
    8114 > ui tool show "Ramachandran Plot"
    8115 
    8116 > select clear
    8117 
    8118 [Repeated 1 time(s)]
    8119 
    8120 > ui tool show "Ramachandran Plot"
    8121 
    8122 > select clear
    8123 
    8124 > ui tool show "Ramachandran Plot"
    8125 
    8126 > isolde sim stop
    8127 
    8128 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8129 chains... 
    8130 ISOLDE: Corrected atom nomenclature of 4 residues in model #1.2 to IUPAC-IUB
    8131 standards. 
    8132 ISOLDE: stopped sim 
    8133 
    8134 > ui tool show "Ramachandran Plot"
    8135 
    8136 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    8137 > mut8-no-C-ter/20-KSRP-no-C-ter-Step1-After-OverFitting_Yes-not_Refining-
    8138 > KSRP.pdb
    8139 
    8140 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    8141 > mut8-no-C-ter/20-KSRP-no-C-ter-Step1-After-OverFitting_Yes-not_Refining-
    8142 > KSRP.cxs
    8143 
    8144 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    8145 
    8146 ——— End of log from Mon Mar 27 09:38:45 2023 ———
    8147 
    8148 opened ChimeraX session 
    8149 
    8150 > isolde start
    8151 
    8152 > set selectionWidth 4
    8153 
    8154 > select clear
    8155 
    8156 > view #1/P:240-249
    8157 
    8158 > select #1/P:240-249
    8159 
    8160 168 atoms, 168 bonds, 10 residues, 1 model selected 
    8161 
    8162 > isolde sim start sel
    8163 
    8164 Launching using CUDA failed with the below message. Falling back to using
    8165 OpenCL. 
    8166  
    8167 Error compiling program: nvrtc: error: invalid value for --gpu-architecture
    8168 (-arch) 
    8169  
    8170 
    8171 ISOLDE: started sim 
    8172 
    8173 > isolde sim stop discardTo start
    8174 
    8175 reverting to start 
    8176 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8177 chains... 
    8178 ISOLDE: stopped sim 
    8179 
    8180 > select #1/P:240-249
    8181 
    8182 168 atoms, 168 bonds, 10 residues, 1 model selected 
    8183 
    8184 > isolde sim start sel
    8185 
    8186 ISOLDE: started sim 
    8187 
    8188 > isolde sim stop discardTo start
    8189 
    8190 reverting to start 
    8191 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8192 chains... 
    8193 ISOLDE: stopped sim 
    8194 
    8195 > select #1/P:240-249
    8196 
    8197 168 atoms, 168 bonds, 10 residues, 1 model selected 
    8198 
    8199 > isolde sim start sel
    8200 
    8201 ISOLDE: started sim 
    8202 
    8203 > select clear
    8204 
    8205 > isolde sim stop
    8206 
    8207 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8208 chains... 
    8209 ISOLDE: stopped sim 
    8210 
    8211 > select #1/
    8212 
    8213 Expected an objects specifier or a keyword 
    8214 
    8215 > select #1
    8216 
    8217 144426 atoms, 150208 bonds, 5 pseudobonds, 6905 residues, 22 models selected 
    8218 
    8219 > select #1/P:220-249
    8220 
    8221 503 atoms, 505 bonds, 30 residues, 1 model selected 
    8222 
    8223 > select #1/P:220-249
    8224 
    8225 503 atoms, 505 bonds, 30 residues, 1 model selected 
    8226 
    8227 > select #1/P:240-249
    8228 
    8229 168 atoms, 168 bonds, 10 residues, 1 model selected 
    8230 
    8231 > isolde sim start sel
    8232 
    8233 ISOLDE: started sim 
    8234 
    8235 > isolde sim stop discardTo start
    8236 
    8237 reverting to start 
    8238 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8239 chains... 
    8240 ISOLDE: stopped sim 
    8241 
    8242 > select #1/P:240-249
    8243 
    8244 168 atoms, 168 bonds, 10 residues, 1 model selected 
    8245 
    8246 > isolde sim start sel
    8247 
    8248 ISOLDE: started sim 
    8249 
    8250 > isolde sim pause
    8251 
    8252 > select #1/P
    8253 
    8254 4114 atoms, 4139 bonds, 249 residues, 1 model selected 
    8255 
    8256 > isolde sim resume
    8257 
    8258 > isolde sim pause
    8259 
    8260 > isolde sim resume
    8261 
    8262 > isolde sim pause
    8263 
    8264 > select #1/P:240-249
    8265 
    8266 168 atoms, 168 bonds, 10 residues, 1 model selected 
    8267 
    8268 > isolde sim resume
    8269 
    8270 > isolde sim pause
    8271 
    8272 > isolde sim resume
    8273 
    8274 > isolde sim pause
    8275 
    8276 > select #1/P:236-249
    8277 
    8278 221 atoms, 221 bonds, 14 residues, 1 model selected 
    8279 
    8280 > isolde sim resume
    8281 
    8282 > isolde sim pause
    8283 
    8284 > select #1/P:220-249
    8285 
    8286 503 atoms, 505 bonds, 30 residues, 1 model selected 
    8287 
    8288 > isolde sim resume
    8289 
    8290 > isolde sim pause
    8291 
    8292 > isolde sim resume
    8293 
    8294 > isolde sim pause
    8295 
    8296 > isolde sim resume
    8297 
    8298 > select clear
    8299 
    8300 > select #1/P
    8301 
    8302 4114 atoms, 4139 bonds, 249 residues, 1 model selected 
    8303 
    8304 > select #1
    8305 
    8306 144426 atoms, 150208 bonds, 5 pseudobonds, 6905 residues, 22 models selected 
    8307 
    8308 > select clear
    8309 
    8310 > ui tool show "Ramachandran Plot"
    8311 
    8312 > isolde pepflip sel
    8313 
    8314 Flipping the peptide bond for 1 residues 
    8315 
    8316 > isolde pepflip sel
    8317 
    8318 Flipping the peptide bond for 1 residues 
    8319 
    8320 > isolde pepflip sel
    8321 
    8322 Flipping the peptide bond for 1 residues 
    8323 
    8324 > ui tool show "Ramachandran Plot"
    8325 
    8326 > isolde pepflip sel
    8327 
    8328 Flipping the peptide bond for 1 residues 
    8329 
    8330 > select clear
    8331 
    8332 > ui tool show "Ramachandran Plot"
    8333 
    8334 > isolde pepflip sel
    8335 
    8336 Flipping the peptide bond for 1 residues 
    8337 
    8338 > isolde pepflip sel
    8339 
    8340 Flipping the peptide bond for 1 residues 
    8341 
    8342 > select clear
    8343 
    8344 > ui tool show "Ramachandran Plot"
    8345 
    8346 > select clear
    8347 
    8348 > ui tool show "Ramachandran Plot"
    8349 
    8350 > isolde sim stop
    8351 
    8352 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8353 chains... 
    8354 ISOLDE: stopped sim 
    8355 
    8356 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    8357 > mut8-no-C-ter/22b-Second-Point-Previous-Sim-Ann-C-ter-ChainP.cxs
    8358 
    8359 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    8360 
    8361 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    8362 > mut8-no-C-ter/22b-Second-Point-Previous-Sim-Ann-C-ter-ChainP.pdb
    8363 
    8364 > close
    8365 
    8366 > open /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    8367 > mut8-no-C-ter/20-KSRP-no-C-ter-Step1-After-OverFitting_Yes-not_Refining-
    8368 > KSRP.cxs
    8369 
    8370 Opened KSRP-Mut8_40S-concatenated-5opt.mrc as #1.1.1.1, grid size 400,400,400,
    8371 pixel 1.16, shown at level 0.264, step 1, values float32 
    8372 Opened KSRP-Mut8_40S-concatenated-5opt.mrc gaussian as #1.1.1.2, grid size
    8373 400,400,400, pixel 1.16, shown at level 0.0965, step 1, values float32 
    8374 Restoring stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    8375 opened ChimeraX session 
    8376 
    8377 > isolde start
    8378 
    8379 > view #1/P:240-249
    8380 
    8381 > select #1/P:240-249
    8382 
    8383 168 atoms, 168 bonds, 10 residues, 1 model selected 
    8384 
    8385 > isolde sim start sel
    8386 
    8387 ISOLDE: started sim 
    8388 
    8389 > isolde sim stop discardTo start
    8390 
    8391 reverting to start 
    8392 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8393 chains... 
    8394 ISOLDE: stopped sim 
    8395 
    8396 > select #1/P:240-249
    8397 
    8398 168 atoms, 168 bonds, 10 residues, 1 model selected 
    8399 
    8400 > isolde sim start sel
    8401 
    8402 ISOLDE: started sim 
    8403 
    8404 > isolde sim stop discardTo start
    8405 
    8406 reverting to start 
    8407 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8408 chains... 
    8409 ISOLDE: stopped sim 
    8410 
    8411 > select #1/P:240-249
    8412 
    8413 168 atoms, 168 bonds, 10 residues, 1 model selected 
    8414 
    8415 > isolde sim start sel
    8416 
    8417 ISOLDE: started sim 
    8418 
    8419 > isolde sim pause
    8420 
    8421 > isolde sim resume
    8422 
    8423 > isolde sim pause
    8424 
    8425 > isolde sim resume
    8426 
    8427 > isolde sim pause
    8428 
    8429 > isolde sim resume
    8430 
    8431 > isolde sim pause
    8432 
    8433 > isolde sim resume
    8434 
    8435 > isolde sim pause
    8436 
    8437 > isolde sim resume
    8438 
    8439 > isolde sim pause
    8440 
    8441 > isolde sim resume
    8442 
    8443 > isolde sim pause
    8444 
    8445 > isolde sim resume
    8446 
    8447 > isolde sim pause
    8448 
    8449 > isolde sim resume
    8450 
    8451 > isolde sim pause
    8452 
    8453 > isolde sim resume
    8454 
    8455 > isolde sim pause
    8456 
    8457 > isolde sim resume
    8458 
    8459 > isolde sim pause
    8460 
    8461 > select clear
    8462 
    8463 > isolde sim resume
    8464 
    8465 > isolde sim pause
    8466 
    8467 > isolde sim resume
    8468 
    8469 > isolde sim pause
    8470 
    8471 > isolde sim resume
    8472 
    8473 > ui tool show "Ramachandran Plot"
    8474 
    8475 > isolde sim stop
    8476 
    8477 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8478 chains... 
    8479 ISOLDE: stopped sim 
    8480 
    8481 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    8482 > mut8-no-C-ter/22c-third-Point-Previous-Sim-Ann-C-ter-ChainP.pdb
    8483 
    8484 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    8485 > mut8-no-C-ter/22c-third-Point-Previous-Sim-Ann-C-ter-ChainP.cxs
    8486 
    8487 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    8488 
    8489 > close
    8490 
    8491 > open /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    8492 > mut8-no-C-ter/20-KSRP-no-C-ter-Step1-After-OverFitting_Yes-not_Refining-
    8493 > KSRP.cxs
    8494 
    8495 Opened KSRP-Mut8_40S-concatenated-5opt.mrc as #1.1.1.1, grid size 400,400,400,
    8496 pixel 1.16, shown at level 0.264, step 1, values float32 
    8497 Opened KSRP-Mut8_40S-concatenated-5opt.mrc gaussian as #1.1.1.2, grid size
    8498 400,400,400, pixel 1.16, shown at level 0.0965, step 1, values float32 
    8499 Restoring stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    8500 opened ChimeraX session 
    8501 
    8502 > isolde start
    8503 
    8504 > ui tool show "Ramachandran Plot"
    8505 
    8506 > view #1/P:240-249
    8507 
    8508 > select #1/P:240-249
    8509 
    8510 168 atoms, 168 bonds, 10 residues, 1 model selected 
    8511 
    8512 > isolde sim start sel
    8513 
    8514 ISOLDE: started sim 
    8515 
    8516 > isolde sim stop discardTo start
    8517 
    8518 reverting to start 
    8519 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8520 chains... 
    8521 ISOLDE: stopped sim 
    8522 
    8523 > select #1/P:240-249
    8524 
    8525 168 atoms, 168 bonds, 10 residues, 1 model selected 
    8526 
    8527 > isolde sim start sel
    8528 
    8529 ISOLDE: started sim 
    8530 
    8531 > isolde sim stop discardTo start
    8532 
    8533 reverting to start 
    8534 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8535 chains... 
    8536 ISOLDE: stopped sim 
    8537 
    8538 > select #1/P:240-249
    8539 
    8540 168 atoms, 168 bonds, 10 residues, 1 model selected 
    8541 
    8542 > isolde sim start sel
    8543 
    8544 ISOLDE: started sim 
    8545 
    8546 > isolde sim stop discardTo start
    8547 
    8548 reverting to start 
    8549 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8550 chains... 
    8551 ISOLDE: stopped sim 
    8552 
    8553 > ui tool show "Ramachandran Plot"
    8554 
    8555 > select clear
    8556 
    8557 > isolde sim start sel
    8558 
    8559 ISOLDE: started sim 
    8560 
    8561 > isolde sim stop discardTo start
    8562 
    8563 reverting to start 
    8564 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8565 chains... 
    8566 ISOLDE: stopped sim 
    8567 
    8568 > select #1/V:92
    8569 
    8570 10 atoms, 9 bonds, 1 residue, 1 model selected 
    8571 
    8572 > isolde sim start sel
    8573 
    8574 ISOLDE: started sim 
    8575 
    8576 > isolde pepflip sel
    8577 
    8578 Flipping the peptide bond for 1 residues 
    8579 
    8580 > select clear
    8581 
    8582 > isolde pepflip sel
    8583 
    8584 Flipping the peptide bond for 1 residues 
    8585 
    8586 > select clear
    8587 
    8588 > ui tool show "Ramachandran Plot"
    8589 
    8590 > isolde sim stop
    8591 
    8592 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8593 chains... 
    8594 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    8595 standards. 
    8596 ISOLDE: stopped sim 
    8597 
    8598 > isolde sim start sel
    8599 
    8600 ISOLDE: started sim 
    8601 
    8602 > ui tool show "Ramachandran Plot"
    8603 
    8604 > isolde pepflip sel
    8605 
    8606 Flipping the peptide bond for 1 residues 
    8607 
    8608 > select clear
    8609 
    8610 > ui tool show "Ramachandran Plot"
    8611 
    8612 > isolde sim stop
    8613 
    8614 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8615 chains... 
    8616 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    8617 standards. 
    8618 ISOLDE: stopped sim 
    8619 
    8620 > isolde sim start sel
    8621 
    8622 ISOLDE: started sim 
    8623 
    8624 > select clear
    8625 
    8626 > isolde pepflip sel
    8627 
    8628 Flipping the peptide bond for 1 residues 
    8629 
    8630 > ui tool show "Ramachandran Plot"
    8631 
    8632 > isolde sim stop
    8633 
    8634 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8635 chains... 
    8636 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    8637 standards. 
    8638 ISOLDE: stopped sim 
    8639 
    8640 > view #1/V:92
    8641 
    8642 > select #1/V:92
    8643 
    8644 10 atoms, 9 bonds, 1 residue, 1 model selected 
    8645 
    8646 > isolde sim start sel
    8647 
    8648 ISOLDE: started sim 
    8649 
    8650 > ui tool show "Ramachandran Plot"
    8651 
    8652 > isolde pepflip sel
    8653 
    8654 Flipping the peptide bond for 1 residues 
    8655 
    8656 > isolde pepflip sel
    8657 
    8658 Flipping the peptide bond for 1 residues 
    8659 
    8660 > select clear
    8661 
    8662 > isolde pepflip sel
    8663 
    8664 Flipping the peptide bond for 1 residues 
    8665 
    8666 > select clear
    8667 
    8668 > ui tool show "Ramachandran Plot"
    8669 
    8670 > isolde sim stop
    8671 
    8672 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8673 chains... 
    8674 ISOLDE: stopped sim 
    8675 
    8676 > ui tool show "Ramachandran Plot"
    8677 
    8678 > isolde sim start sel
    8679 
    8680 ISOLDE: started sim 
    8681 
    8682 > ui tool show "Ramachandran Plot"
    8683 
    8684 > select clear
    8685 
    8686 > ui tool show "Ramachandran Plot"
    8687 
    8688 > isolde pepflip sel
    8689 
    8690 Flipping the peptide bond for 1 residues 
    8691 
    8692 > select clear
    8693 
    8694 > isolde pepflip sel
    8695 
    8696 Flipping the peptide bond for 1 residues 
    8697 
    8698 > isolde pepflip sel
    8699 
    8700 Flipping the peptide bond for 1 residues 
    8701 
    8702 > ui tool show "Ramachandran Plot"
    8703 
    8704 > select clear
    8705 
    8706 > isolde pepflip sel
    8707 
    8708 Flipping the peptide bond for 1 residues 
    8709 
    8710 > isolde pepflip sel
    8711 
    8712 Flipping the peptide bond for 1 residues 
    8713 
    8714 > select clear
    8715 
    8716 > ui tool show "Ramachandran Plot"
    8717 
    8718 > isolde pepflip sel
    8719 
    8720 Flipping the peptide bond for 1 residues 
    8721 
    8722 > select clear
    8723 
    8724 > ui tool show "Ramachandran Plot"
    8725 
    8726 > style #1/i:72|/i:75 sphere
    8727 
    8728 Changed 37 atom styles 
    8729 
    8730 > style #1/i:72|/i:75 stick
    8731 
    8732 Changed 37 atom styles 
    8733 
    8734 > select clear
    8735 
    8736 > ui tool show "Ramachandran Plot"
    8737 
    8738 > isolde sim stop
    8739 
    8740 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8741 chains... 
    8742 ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
    8743 standards. 
    8744 ISOLDE: stopped sim 
    8745 
    8746 > ui tool show "Ramachandran Plot"
    8747 
    8748 > isolde sim start sel
    8749 
    8750 ISOLDE: started sim 
    8751 
    8752 > isolde pepflip sel
    8753 
    8754 Flipping the peptide bond for 1 residues 
    8755 
    8756 > select clear
    8757 
    8758 > isolde pepflip sel
    8759 
    8760 Flipping the peptide bond for 1 residues 
    8761 
    8762 > isolde pepflip sel
    8763 
    8764 Flipping the peptide bond for 1 residues 
    8765 
    8766 > isolde pepflip sel
    8767 
    8768 Flipping the peptide bond for 1 residues 
    8769 
    8770 > select clear
    8771 
    8772 > isolde pepflip sel
    8773 
    8774 Flipping the peptide bond for 1 residues 
    8775 
    8776 > isolde pepflip sel
    8777 
    8778 Flipping the peptide bond for 1 residues 
    8779 
    8780 > isolde pepflip sel
    8781 
    8782 Flipping the peptide bond for 1 residues 
    8783 
    8784 > isolde pepflip sel
    8785 
    8786 Flipping the peptide bond for 1 residues 
    8787 
    8788 > isolde pepflip sel
    8789 
    8790 Flipping the peptide bond for 1 residues 
    8791 
    8792 > isolde pepflip sel
    8793 
    8794 Flipping the peptide bond for 1 residues 
    8795 
    8796 > select clear
    8797 
    8798 > ui tool show "Ramachandran Plot"
    8799 
    8800 > select clear
    8801 
    8802 > ui tool show "Ramachandran Plot"
    8803 
    8804 > isolde sim stop
    8805 
    8806 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8807 chains... 
    8808 ISOLDE: stopped sim 
    8809 
    8810 > ui tool show "Ramachandran Plot"
    8811 
    8812 > isolde sim start sel
    8813 
    8814 ISOLDE: started sim 
    8815 
    8816 > isolde pepflip sel
    8817 
    8818 Flipping the peptide bond for 1 residues 
    8819 
    8820 > isolde pepflip sel
    8821 
    8822 Flipping the peptide bond for 1 residues 
    8823 
    8824 > isolde pepflip sel
    8825 
    8826 Flipping the peptide bond for 1 residues 
    8827 
    8828 > select clear
    8829 
    8830 > ui tool show "Ramachandran Plot"
    8831 
    8832 > isolde pepflip sel
    8833 
    8834 Flipping the peptide bond for 1 residues 
    8835 
    8836 > select clear
    8837 
    8838 > ui tool show "Ramachandran Plot"
    8839 
    8840 > isolde sim stop
    8841 
    8842 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8843 chains... 
    8844 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    8845 standards. 
    8846 ISOLDE: stopped sim 
    8847 
    8848 > ui tool show "Ramachandran Plot"
    8849 
    8850 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    8851 > mut8-no-C-ter/20-continuingNew-FirstSteps-RefiningBEFORE-Annealing.cxs
    8852 
    8853 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    8854 
    8855 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    8856 > mut8-no-C-ter/20-KSRP-no-C-ter-Step1-After-OverFitting_Yes-not_Refining-
    8857 > KSRP.pdb
    8858 
    8859 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    8860 > mut8-no-C-ter/20-continuingNew-FirstSteps-RefiningBEFORE-Annealing.pdb
    8861 
    8862 > isolde sim start sel
    8863 
    8864 ISOLDE: started sim 
    8865 
    8866 > isolde sim stop discardTo start
    8867 
    8868 reverting to start 
    8869 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8870 chains... 
    8871 ISOLDE: stopped sim 
    8872 
    8873 > isolde sim start sel
    8874 
    8875 ISOLDE: started sim 
    8876 
    8877 > isolde pepflip sel
    8878 
    8879 Flipping the peptide bond for 1 residues 
    8880 
    8881 > isolde pepflip sel
    8882 
    8883 Flipping the peptide bond for 1 residues 
    8884 
    8885 > select clear
    8886 
    8887 > ui tool show "Ramachandran Plot"
    8888 
    8889 > isolde sim pause
    8890 
    8891 > ui tool show "Ramachandran Plot"
    8892 
    8893 > isolde sim resume
    8894 
    8895 > ui tool show "Ramachandran Plot"
    8896 
    8897 > isolde pepflip sel
    8898 
    8899 Flipping the peptide bond for 1 residues 
    8900 
    8901 > isolde pepflip sel
    8902 
    8903 Flipping the peptide bond for 1 residues 
    8904 
    8905 > select clear
    8906 
    8907 > isolde pepflip sel
    8908 
    8909 Flipping the peptide bond for 1 residues 
    8910 
    8911 > isolde pepflip sel
    8912 
    8913 Flipping the peptide bond for 1 residues 
    8914 
    8915 > isolde sim stop
    8916 
    8917 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8918 chains... 
    8919 ISOLDE: stopped sim 
    8920 
    8921 > isolde sim start sel
    8922 
    8923 ISOLDE: started sim 
    8924 
    8925 > select clear
    8926 
    8927 > ui tool show "Ramachandran Plot"
    8928 
    8929 > isolde pepflip sel
    8930 
    8931 Flipping the peptide bond for 1 residues 
    8932 
    8933 > ui tool show "Ramachandran Plot"
    8934 
    8935 > select clear
    8936 
    8937 > ui tool show "Ramachandran Plot"
    8938 
    8939 > isolde sim stop
    8940 
    8941 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8942 chains... 
    8943 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    8944 standards. 
    8945 ISOLDE: stopped sim 
    8946 
    8947 > isolde sim start sel
    8948 
    8949 ISOLDE: started sim 
    8950 
    8951 > ui tool show "Ramachandran Plot"
    8952 
    8953 > select clear
    8954 
    8955 > ui tool show "Ramachandran Plot"
    8956 
    8957 > select clear
    8958 
    8959 > ui tool show "Ramachandran Plot"
    8960 
    8961 > select clear
    8962 
    8963 > ui tool show "Ramachandran Plot"
    8964 
    8965 > isolde sim stop
    8966 
    8967 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8968 chains... 
    8969 ISOLDE: stopped sim 
    8970 
    8971 > ui tool show "Ramachandran Plot"
    8972 
    8973 > isolde sim start sel
    8974 
    8975 ISOLDE: started sim 
    8976 
    8977 > ui tool show "Ramachandran Plot"
    8978 
    8979 > select clear
    8980 
    8981 > isolde pepflip sel
    8982 
    8983 Flipping the peptide bond for 1 residues 
    8984 
    8985 > select clear
    8986 
    8987 > ui tool show "Ramachandran Plot"
    8988 
    8989 > isolde sim stop
    8990 
    8991 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8992 chains... 
    8993 ISOLDE: stopped sim 
    8994 
    8995 > ui tool show "Ramachandran Plot"
    8996 
    8997 > isolde sim start sel
    8998 
    8999 ISOLDE: started sim 
    9000 
    9001 > ui tool show "Ramachandran Plot"
    9002 
    9003 > isolde sim stop
    9004 
    9005 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9006 chains... 
    9007 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    9008 standards. 
    9009 ISOLDE: stopped sim 
    9010 
    9011 > isolde sim start sel
    9012 
    9013 ISOLDE: started sim 
    9014 
    9015 > select clear
    9016 
    9017 > isolde pepflip sel
    9018 
    9019 Flipping the peptide bond for 1 residues 
    9020 
    9021 > isolde pepflip sel
    9022 
    9023 Flipping the peptide bond for 1 residues 
    9024 
    9025 > isolde pepflip sel
    9026 
    9027 Flipping the peptide bond for 1 residues 
    9028 
    9029 > isolde pepflip sel
    9030 
    9031 Flipping the peptide bond for 1 residues 
    9032 
    9033 > ui tool show "Ramachandran Plot"
    9034 
    9035 > isolde pepflip sel
    9036 
    9037 Flipping the peptide bond for 1 residues 
    9038 
    9039 > select clear
    9040 
    9041 > isolde pepflip sel
    9042 
    9043 Flipping the peptide bond for 1 residues 
    9044 
    9045 > isolde pepflip sel
    9046 
    9047 Flipping the peptide bond for 1 residues 
    9048 
    9049 > select clear
    9050 
    9051 > isolde pepflip sel
    9052 
    9053 Flipping the peptide bond for 1 residues 
    9054 
    9055 > ui tool show "Ramachandran Plot"
    9056 
    9057 > select clear
    9058 
    9059 > ui tool show "Ramachandran Plot"
    9060 
    9061 > isolde sim stop
    9062 
    9063 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9064 chains... 
    9065 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    9066 standards. 
    9067 ISOLDE: stopped sim 
    9068 
    9069 > ui tool show "Ramachandran Plot"
    9070 
    9071 > isolde sim start sel
    9072 
    9073 ISOLDE: started sim 
    9074 
    9075 > ui tool show "Ramachandran Plot"
    9076 
    9077 > select clear
    9078 
    9079 > isolde sim stop
    9080 
    9081 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9082 chains... 
    9083 ISOLDE: stopped sim 
    9084 
    9085 > ui tool show "Ramachandran Plot"
    9086 
    9087 > isolde sim start sel
    9088 
    9089 ISOLDE: started sim 
    9090 
    9091 > isolde pepflip sel
    9092 
    9093 Flipping the peptide bond for 1 residues 
    9094 
    9095 > select clear
    9096 
    9097 > isolde pepflip sel
    9098 
    9099 Flipping the peptide bond for 1 residues 
    9100 
    9101 > select clear
    9102 
    9103 > isolde pepflip sel
    9104 
    9105 Flipping the peptide bond for 1 residues 
    9106 
    9107 > isolde pepflip sel
    9108 
    9109 Flipping the peptide bond for 1 residues 
    9110 
    9111 > select clear
    9112 
    9113 > ui tool show "Ramachandran Plot"
    9114 
    9115 > select clear
    9116 
    9117 > ui tool show "Ramachandran Plot"
    9118 
    9119 > isolde pepflip sel
    9120 
    9121 Flipping the peptide bond for 1 residues 
    9122 
    9123 > isolde pepflip sel
    9124 
    9125 Flipping the peptide bond for 1 residues 
    9126 
    9127 > ui tool show "Ramachandran Plot"
    9128 
    9129 > select clear
    9130 
    9131 > isolde sim stop
    9132 
    9133 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9134 chains... 
    9135 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    9136 standards. 
    9137 ISOLDE: stopped sim 
    9138 
    9139 > ui tool show "Ramachandran Plot"
    9140 
    9141 > isolde sim start sel
    9142 
    9143 ISOLDE: started sim 
    9144 
    9145 > select clear
    9146 
    9147 > ui tool show "Ramachandran Plot"
    9148 
    9149 > view #1/d:155
    9150 
    9151 > select clear
    9152 
    9153 > isolde sim stop
    9154 
    9155 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9156 chains... 
    9157 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    9158 standards. 
    9159 ISOLDE: stopped sim 
    9160 
    9161 > ui tool show "Ramachandran Plot"
    9162 
    9163 > isolde sim start sel
    9164 
    9165 ISOLDE: started sim 
    9166 
    9167 > isolde pepflip sel
    9168 
    9169 Flipping the peptide bond for 1 residues 
    9170 
    9171 > ui tool show "Ramachandran Plot"
    9172 
    9173 > select clear
    9174 
    9175 > isolde sim pause
    9176 
    9177 > isolde sim resume
    9178 
    9179 > ui tool show "Ramachandran Plot"
    9180 
    9181 > isolde sim stop
    9182 
    9183 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9184 chains... 
    9185 ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
    9186 standards. 
    9187 ISOLDE: stopped sim 
    9188 
    9189 > ui tool show "Ramachandran Plot"
    9190 
    9191 > isolde sim start sel
    9192 
    9193 ISOLDE: started sim 
    9194 
    9195 > isolde pepflip sel
    9196 
    9197 Flipping the peptide bond for 1 residues 
    9198 
    9199 > isolde pepflip sel
    9200 
    9201 Flipping the peptide bond for 1 residues 
    9202 
    9203 > isolde pepflip sel
    9204 
    9205 Flipping the peptide bond for 1 residues 
    9206 
    9207 > isolde pepflip sel
    9208 
    9209 Flipping the peptide bond for 1 residues 
    9210 
    9211 > isolde pepflip sel
    9212 
    9213 Flipping the peptide bond for 1 residues 
    9214 
    9215 > select clear
    9216 
    9217 > isolde pepflip sel
    9218 
    9219 Flipping the peptide bond for 1 residues 
    9220 
    9221 > isolde pepflip sel
    9222 
    9223 Flipping the peptide bond for 1 residues 
    9224 
    9225 > isolde pepflip sel
    9226 
    9227 Flipping the peptide bond for 1 residues 
    9228 
    9229 > isolde pepflip sel
    9230 
    9231 Flipping the peptide bond for 1 residues 
    9232 
    9233 > select clear
    9234 
    9235 > ui tool show "Ramachandran Plot"
    9236 
    9237 > isolde sim pause
    9238 
    9239 > isolde sim resume
    9240 
    9241 > ui tool show "Ramachandran Plot"
    9242 
    9243 > isolde sim stop
    9244 
    9245 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9246 chains... 
    9247 ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
    9248 standards. 
    9249 ISOLDE: stopped sim 
    9250 
    9251 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    9252 > mut8-no-C-ter/20-1-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
    9253 > step20-1.cxs
    9254 
    9255 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    9256 
    9257 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    9258 > mut8-no-C-ter/20-1-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
    9259 > step20-1.pdb
    9260 
    9261 > ui tool show "Ramachandran Plot"
    9262 
    9263 > isolde sim start sel
    9264 
    9265 ISOLDE: started sim 
    9266 
    9267 > select clear
    9268 
    9269 > ui tool show "Ramachandran Plot"
    9270 
    9271 > select clear
    9272 
    9273 > isolde sim stop
    9274 
    9275 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9276 chains... 
    9277 ISOLDE: stopped sim 
    9278 
    9279 > ui tool show "Ramachandran Plot"
    9280 
    9281 > isolde sim start sel
    9282 
    9283 ISOLDE: started sim 
    9284 
    9285 > ui tool show "Ramachandran Plot"
    9286 
    9287 > select clear
    9288 
    9289 > ui tool show "Ramachandran Plot"
    9290 
    9291 > isolde pepflip sel
    9292 
    9293 Flipping the peptide bond for 1 residues 
    9294 
    9295 > select clear
    9296 
    9297 > isolde pepflip sel
    9298 
    9299 Flipping the peptide bond for 1 residues 
    9300 
    9301 > select clear
    9302 
    9303 > ui tool show "Ramachandran Plot"
    9304 
    9305 > select clear
    9306 
    9307 > view #1/q:29
    9308 
    9309 > isolde sim pause
    9310 
    9311 > ui tool show "Ramachandran Plot"
    9312 
    9313 Traceback (most recent call last): 
    9314 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9315 packages/matplotlib/cbook/__init__.py", line 287, in process 
    9316 func(*args, **kwargs) 
    9317 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    9318 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    9319 on_resize 
    9320 c.draw() 
    9321 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9322 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    9323 self.figure.draw(self.renderer) 
    9324 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9325 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    9326 result = draw(artist, renderer, *args, **kwargs) 
    9327 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9328 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    9329 return draw(artist, renderer) 
    9330 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9331 packages/matplotlib/figure.py", line 2796, in draw 
    9332 artists = self._get_draw_artists(renderer) 
    9333 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9334 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    9335 ax.apply_aspect() 
    9336 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9337 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    9338 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    9339 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9340 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    9341 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    9342 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    9343 
    9344 > ui tool show "Ramachandran Plot"
    9345 
    9346 Traceback (most recent call last): 
    9347 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9348 packages/matplotlib/cbook/__init__.py", line 287, in process 
    9349 func(*args, **kwargs) 
    9350 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    9351 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    9352 on_resize 
    9353 c.draw() 
    9354 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9355 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    9356 self.figure.draw(self.renderer) 
    9357 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9358 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    9359 result = draw(artist, renderer, *args, **kwargs) 
    9360 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9361 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    9362 return draw(artist, renderer) 
    9363 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9364 packages/matplotlib/figure.py", line 2796, in draw 
    9365 artists = self._get_draw_artists(renderer) 
    9366 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9367 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    9368 ax.apply_aspect() 
    9369 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9370 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    9371 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    9372 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9373 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    9374 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    9375 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    9376 
    9377 > isolde sim resume
    9378 
    9379 > isolde sim pause
    9380 
    9381 > isolde sim resume
    9382 
    9383 > select clear
    9384 
    9385 > isolde pepflip sel
    9386 
    9387 Flipping the peptide bond for 1 residues 
    9388 
    9389 > select clear
    9390 
    9391 > isolde sim pause
    9392 
    9393 > isolde sim resume
    9394 
    9395 > select clear
    9396 
    9397 > isolde pepflip sel
    9398 
    9399 Flipping the peptide bond for 1 residues 
    9400 
    9401 > isolde pepflip sel
    9402 
    9403 Flipping the peptide bond for 1 residues 
    9404 
    9405 > select clear
    9406 
    9407 > ui tool show "Ramachandran Plot"
    9408 
    9409 > select clear
    9410 
    9411 > isolde sim pause
    9412 
    9413 > ui tool show "Ramachandran Plot"
    9414 
    9415 > isolde sim resume
    9416 
    9417 > select clear
    9418 
    9419 > isolde pepflip sel
    9420 
    9421 Flipping the peptide bond for 1 residues 
    9422 
    9423 > isolde pepflip sel
    9424 
    9425 Flipping the peptide bond for 1 residues 
    9426 
    9427 > isolde pepflip sel
    9428 
    9429 Flipping the peptide bond for 1 residues 
    9430 
    9431 > isolde pepflip sel
    9432 
    9433 Flipping the peptide bond for 1 residues 
    9434 
    9435 > isolde pepflip sel
    9436 
    9437 Flipping the peptide bond for 1 residues 
    9438 
    9439 > isolde pepflip sel
    9440 
    9441 Flipping the peptide bond for 1 residues 
    9442 
    9443 > ui tool show "Ramachandran Plot"
    9444 
    9445 > select clear
    9446 
    9447 > isolde sim pause
    9448 
    9449 > ui tool show "Ramachandran Plot"
    9450 
    9451 > select clear
    9452 
    9453 > isolde sim resume
    9454 
    9455 > isolde pepflip sel
    9456 
    9457 Flipping the peptide bond for 1 residues 
    9458 
    9459 > select clear
    9460 
    9461 > isolde pepflip sel
    9462 
    9463 Flipping the peptide bond for 1 residues 
    9464 
    9465 > ui tool show "Ramachandran Plot"
    9466 
    9467 > select clear
    9468 
    9469 > isolde sim pause
    9470 
    9471 > isolde sim resume
    9472 
    9473 > ui tool show "Ramachandran Plot"
    9474 
    9475 > select clear
    9476 
    9477 > isolde pepflip sel
    9478 
    9479 Flipping the peptide bond for 1 residues 
    9480 
    9481 > ui tool show "Ramachandran Plot"
    9482 
    9483 > select clear
    9484 
    9485 > ui tool show "Ramachandran Plot"
    9486 
    9487 > select clear
    9488 
    9489 > ui tool show "Ramachandran Plot"
    9490 
    9491 Traceback (most recent call last): 
    9492 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9493 packages/matplotlib/cbook/__init__.py", line 287, in process 
    9494 func(*args, **kwargs) 
    9495 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    9496 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    9497 on_resize 
    9498 c.draw() 
    9499 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9500 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    9501 self.figure.draw(self.renderer) 
    9502 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9503 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    9504 result = draw(artist, renderer, *args, **kwargs) 
    9505 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9506 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    9507 return draw(artist, renderer) 
    9508 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9509 packages/matplotlib/figure.py", line 2796, in draw 
    9510 artists = self._get_draw_artists(renderer) 
    9511 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9512 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    9513 ax.apply_aspect() 
    9514 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9515 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    9516 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    9517 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9518 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    9519 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    9520 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    9521 
    9522 > select clear
    9523 
    9524 > ui tool show "Ramachandran Plot"
    9525 
    9526 > select clear
    9527 
    9528 > ui tool show "Ramachandran Plot"
    9529 
    9530 > style #1/q:34|/q:39 sphere
    9531 
    9532 Changed 38 atom styles 
    9533 
    9534 > style #1/q:34|/q:39 stick
    9535 
    9536 Changed 38 atom styles 
    9537 
    9538 > ui tool show "Ramachandran Plot"
    9539 
    9540 > select clear
    9541 
    9542 > isolde sim pause
    9543 
    9544 > style #1/q:34|/q:39|/q:32 sphere
    9545 
    9546 Changed 57 atom styles 
    9547 
    9548 > style #1/q:34|/q:39|/q:32 stick
    9549 
    9550 Changed 57 atom styles 
    9551 
    9552 > ui tool show "Ramachandran Plot"
    9553 
    9554 > isolde sim resume
    9555 
    9556 > isolde sim stop
    9557 
    9558 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9559 chains... 
    9560 ISOLDE: stopped sim 
    9561 
    9562 > isolde sim start sel
    9563 
    9564 ISOLDE: started sim 
    9565 
    9566 > select clear
    9567 
    9568 > isolde pepflip sel
    9569 
    9570 Flipping the peptide bond for 1 residues 
    9571 
    9572 > isolde pepflip sel
    9573 
    9574 Flipping the peptide bond for 1 residues 
    9575 
    9576 > isolde pepflip sel
    9577 
    9578 Flipping the peptide bond for 1 residues 
    9579 
    9580 > isolde pepflip sel
    9581 
    9582 Flipping the peptide bond for 1 residues 
    9583 
    9584 > isolde pepflip sel
    9585 
    9586 Flipping the peptide bond for 1 residues 
    9587 
    9588 > isolde pepflip sel
    9589 
    9590 Flipping the peptide bond for 1 residues 
    9591 
    9592 > isolde pepflip sel
    9593 
    9594 Flipping the peptide bond for 1 residues 
    9595 
    9596 > isolde sim pause
    9597 
    9598 > isolde sim resume
    9599 
    9600 > ui tool show "Ramachandran Plot"
    9601 
    9602 > select clear
    9603 
    9604 > ui tool show "Ramachandran Plot"
    9605 
    9606 > isolde pepflip sel
    9607 
    9608 Flipping the peptide bond for 1 residues 
    9609 
    9610 > select clear
    9611 
    9612 > isolde pepflip sel
    9613 
    9614 Flipping the peptide bond for 1 residues 
    9615 
    9616 > isolde pepflip sel
    9617 
    9618 Flipping the peptide bond for 1 residues 
    9619 
    9620 > select clear
    9621 
    9622 > style #1/q:23-24 sphere
    9623 
    9624 Changed 35 atom styles 
    9625 
    9626 > style #1/q:23-24 stick
    9627 
    9628 Changed 35 atom styles 
    9629 
    9630 > ui tool show "Ramachandran Plot"
    9631 
    9632 > select clear
    9633 
    9634 > ui tool show "Ramachandran Plot"
    9635 
    9636 > select clear
    9637 
    9638 > isolde sim pause
    9639 
    9640 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    9641 > mut8-no-C-ter/20-2-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
    9642 > step20-2.pdb
    9643 
    9644 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    9645 > mut8-no-C-ter/20-2-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
    9646 > step20-2.cxs
    9647 
    9648 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    9649 
    9650 > isolde sim resume
    9651 
    9652 > ui tool show "Ramachandran Plot"
    9653 
    9654 Traceback (most recent call last): 
    9655 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9656 packages/matplotlib/cbook/__init__.py", line 287, in process 
    9657 func(*args, **kwargs) 
    9658 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    9659 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    9660 on_resize 
    9661 c.draw() 
    9662 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9663 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    9664 self.figure.draw(self.renderer) 
    9665 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9666 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    9667 result = draw(artist, renderer, *args, **kwargs) 
    9668 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9669 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    9670 return draw(artist, renderer) 
    9671 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9672 packages/matplotlib/figure.py", line 2796, in draw 
    9673 artists = self._get_draw_artists(renderer) 
    9674 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9675 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    9676 ax.apply_aspect() 
    9677 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9678 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    9679 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    9680 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    9681 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    9682 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    9683 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    9684 
    9685 > isolde sim pause
    9686 
    9687 > view #1/q:24
    9688 
    9689 > isolde sim resume
    9690 
    9691 > select clear
    9692 
    9693 > isolde pepflip sel
    9694 
    9695 Flipping the peptide bond for 1 residues 
    9696 
    9697 > select clear
    9698 
    9699 > ui tool show "Ramachandran Plot"
    9700 
    9701 > style #1/i:23-24|/n:68 sphere
    9702 
    9703 Changed 53 atom styles 
    9704 
    9705 > style #1/i:23-24|/n:68 stick]
    9706 
    9707 Expected a keyword 
    9708 
    9709 > style #1/i:23-24|/n:68 stick
    9710 
    9711 Changed 53 atom styles 
    9712 
    9713 > style #1/q:23-24|/n:68 sphere
    9714 
    9715 Changed 59 atom styles 
    9716 
    9717 > style #1/q:23-24|/n:68 stick
    9718 
    9719 Changed 59 atom styles 
    9720 
    9721 > ui tool show "Ramachandran Plot"
    9722 
    9723 > isolde sim stop
    9724 
    9725 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9726 chains... 
    9727 ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
    9728 standards. 
    9729 ISOLDE: stopped sim 
    9730 
    9731 > view #1/q:41
    9732 
    9733 > select #1/q:41
    9734 
    9735 24 atoms, 23 bonds, 1 residue, 1 model selected 
    9736 
    9737 > isolde sim start sel
    9738 
    9739 ISOLDE: started sim 
    9740 
    9741 > ui tool show "Ramachandran Plot"
    9742 
    9743 > select clear
    9744 
    9745 > isolde sim stop
    9746 
    9747 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9748 chains... 
    9749 ISOLDE: stopped sim 
    9750 
    9751 > isolde sim start sel
    9752 
    9753 ISOLDE: started sim 
    9754 
    9755 > ui tool show "Ramachandran Plot"
    9756 
    9757 > select clear
    9758 
    9759 > isolde pepflip sel
    9760 
    9761 Flipping the peptide bond for 1 residues 
    9762 
    9763 > isolde pepflip sel
    9764 
    9765 Flipping the peptide bond for 1 residues 
    9766 
    9767 > isolde pepflip sel
    9768 
    9769 Flipping the peptide bond for 1 residues 
    9770 
    9771 > isolde sim stop discardTo start
    9772 
    9773 reverting to start 
    9774 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9775 chains... 
    9776 ISOLDE: stopped sim 
    9777 
    9778 > isolde sim start sel
    9779 
    9780 ISOLDE: started sim 
    9781 
    9782 > ui tool show "Ramachandran Plot"
    9783 
    9784 > select clear
    9785 
    9786 > isolde pepflip sel
    9787 
    9788 Flipping the peptide bond for 1 residues 
    9789 
    9790 > select clear
    9791 
    9792 > isolde pepflip sel
    9793 
    9794 Flipping the peptide bond for 1 residues 
    9795 
    9796 > isolde pepflip sel
    9797 
    9798 Flipping the peptide bond for 1 residues 
    9799 
    9800 > select clear
    9801 
    9802 > isolde pepflip sel
    9803 
    9804 Flipping the peptide bond for 1 residues 
    9805 
    9806 > isolde pepflip sel
    9807 
    9808 Flipping the peptide bond for 1 residues 
    9809 
    9810 > isolde pepflip sel
    9811 
    9812 Flipping the peptide bond for 1 residues 
    9813 
    9814 > isolde pepflip sel
    9815 
    9816 Flipping the peptide bond for 1 residues 
    9817 
    9818 > isolde pepflip sel
    9819 
    9820 Flipping the peptide bond for 1 residues 
    9821 
    9822 > select clear
    9823 
    9824 > ui tool show "Ramachandran Plot"
    9825 
    9826 > isolde sim stop
    9827 
    9828 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9829 chains... 
    9830 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    9831 standards. 
    9832 ISOLDE: stopped sim 
    9833 
    9834 > view #1/q:41
    9835 
    9836 > select #1/q:41
    9837 
    9838 24 atoms, 23 bonds, 1 residue, 1 model selected 
    9839 
    9840 > isolde sim start sel
    9841 
    9842 ISOLDE: started sim 
    9843 
    9844 > ui tool show "Ramachandran Plot"
    9845 
    9846 > select clear
    9847 
    9848 > isolde sim stop
    9849 
    9850 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9851 chains... 
    9852 ISOLDE: stopped sim 
    9853 
    9854 > ui tool show "Ramachandran Plot"
    9855 
    9856 > isolde sim start sel
    9857 
    9858 ISOLDE: started sim 
    9859 
    9860 > isolde pepflip sel
    9861 
    9862 Flipping the peptide bond for 1 residues 
    9863 
    9864 > isolde pepflip sel
    9865 
    9866 Flipping the peptide bond for 1 residues 
    9867 
    9868 > select clear
    9869 
    9870 > ui tool show "Ramachandran Plot"
    9871 
    9872 > isolde pepflip sel
    9873 
    9874 Flipping the peptide bond for 1 residues 
    9875 
    9876 > select clear
    9877 
    9878 > ui tool show "Ramachandran Plot"
    9879 
    9880 > select clear
    9881 
    9882 > isolde sim stop
    9883 
    9884 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9885 chains... 
    9886 ISOLDE: stopped sim 
    9887 
    9888 > ui tool show "Ramachandran Plot"
    9889 
    9890 > isolde sim start sel
    9891 
    9892 ISOLDE: started sim 
    9893 
    9894 > ui tool show "Ramachandran Plot"
    9895 
    9896 > select clear
    9897 
    9898 > isolde sim stop
    9899 
    9900 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9901 chains... 
    9902 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    9903 standards. 
    9904 ISOLDE: stopped sim 
    9905 
    9906 > ui tool show "Ramachandran Plot"
    9907 
    9908 > isolde sim start sel
    9909 
    9910 ISOLDE: started sim 
    9911 
    9912 > ui tool show "Ramachandran Plot"
    9913 
    9914 > select clear
    9915 
    9916 > ui tool show "Ramachandran Plot"
    9917 
    9918 > isolde sim stop
    9919 
    9920 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9921 chains... 
    9922 ISOLDE: stopped sim 
    9923 
    9924 > ui tool show "Ramachandran Plot"
    9925 
    9926 > isolde sim start sel
    9927 
    9928 ISOLDE: started sim 
    9929 
    9930 > ui tool show "Ramachandran Plot"
    9931 
    9932 > isolde pepflip sel
    9933 
    9934 Flipping the peptide bond for 1 residues 
    9935 
    9936 > isolde pepflip sel
    9937 
    9938 Flipping the peptide bond for 1 residues 
    9939 
    9940 > isolde pepflip sel
    9941 
    9942 Flipping the peptide bond for 1 residues 
    9943 
    9944 > isolde pepflip sel
    9945 
    9946 Flipping the peptide bond for 1 residues 
    9947 
    9948 > select clear
    9949 
    9950 > isolde pepflip sel
    9951 
    9952 Flipping the peptide bond for 1 residues 
    9953 
    9954 > select clear
    9955 
    9956 > ui tool show "Ramachandran Plot"
    9957 
    9958 > select clear
    9959 
    9960 > ui tool show "Ramachandran Plot"
    9961 
    9962 > select clear
    9963 
    9964 > isolde pepflip sel
    9965 
    9966 Flipping the peptide bond for 1 residues 
    9967 
    9968 > select clear
    9969 
    9970 > ui tool show "Ramachandran Plot"
    9971 
    9972 > select clear
    9973 
    9974 > isolde sim stop
    9975 
    9976 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9977 chains... 
    9978 ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
    9979 standards. 
    9980 ISOLDE: stopped sim 
    9981 
    9982 > ui tool show "Ramachandran Plot"
    9983 
    9984 > isolde sim start sel
    9985 
    9986 ISOLDE: started sim 
    9987 
    9988 > isolde pepflip sel
    9989 
    9990 Flipping the peptide bond for 1 residues 
    9991 
    9992 > isolde pepflip sel
    9993 
    9994 Flipping the peptide bond for 1 residues 
    9995 
    9996 > isolde pepflip sel
    9997 
    9998 Flipping the peptide bond for 1 residues 
    9999 
    10000 > select clear
    10001 
    10002 > isolde pepflip sel
    10003 
    10004 Flipping the peptide bond for 1 residues 
    10005 
    10006 > isolde pepflip sel
    10007 
    10008 Flipping the peptide bond for 1 residues 
    10009 
    10010 > select clear
    10011 
    10012 > isolde pepflip sel
    10013 
    10014 Flipping the peptide bond for 1 residues 
    10015 
    10016 > isolde pepflip sel
    10017 
    10018 Flipping the peptide bond for 1 residues 
    10019 
    10020 > select clear
    10021 
    10022 > ui tool show "Ramachandran Plot"
    10023 
    10024 > select clear
    10025 
    10026 > isolde pepflip sel
    10027 
    10028 Flipping the peptide bond for 1 residues 
    10029 
    10030 > select clear
    10031 
    10032 > ui tool show "Ramachandran Plot"
    10033 
    10034 > select clear
    10035 
    10036 > isolde pepflip sel
    10037 
    10038 Flipping the peptide bond for 1 residues 
    10039 
    10040 > select clear
    10041 
    10042 > isolde pepflip sel
    10043 
    10044 Flipping the peptide bond for 1 residues 
    10045 
    10046 > isolde pepflip sel
    10047 
    10048 Flipping the peptide bond for 1 residues 
    10049 
    10050 > isolde pepflip sel
    10051 
    10052 Flipping the peptide bond for 1 residues 
    10053 
    10054 > select clear
    10055 
    10056 > isolde sim pause
    10057 
    10058 > isolde sim resume
    10059 
    10060 > isolde sim stop
    10061 
    10062 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10063 chains... 
    10064 ISOLDE: stopped sim 
    10065 
    10066 > select #1/o:74-81|/o:12
    10067 
    10068 140 atoms, 138 bonds, 9 residues, 1 model selected 
    10069 
    10070 > isolde sim start sel
    10071 
    10072 ISOLDE: started sim 
    10073 
    10074 > isolde pepflip sel
    10075 
    10076 Flipping the peptide bond for 1 residues 
    10077 
    10078 Multiple residues selected! Going to the first... 
    10079 
    10080 > view #1/o:74
    10081 
    10082 > select clear
    10083 
    10084 > ui tool show "Ramachandran Plot"
    10085 
    10086 > isolde pepflip sel
    10087 
    10088 Flipping the peptide bond for 1 residues 
    10089 
    10090 > isolde pepflip sel
    10091 
    10092 Flipping the peptide bond for 1 residues 
    10093 
    10094 > select clear
    10095 
    10096 > isolde pepflip sel
    10097 
    10098 Flipping the peptide bond for 1 residues 
    10099 
    10100 > select clear
    10101 
    10102 > ui tool show "Ramachandran Plot"
    10103 
    10104 > view #1/o:74
    10105 
    10106 > select clear
    10107 
    10108 > ui tool show "Ramachandran Plot"
    10109 
    10110 > select clear
    10111 
    10112 Traceback (most recent call last): 
    10113 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10114 packages/matplotlib/cbook/__init__.py", line 287, in process 
    10115 func(*args, **kwargs) 
    10116 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    10117 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    10118 on_resize 
    10119 c.draw() 
    10120 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10121 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    10122 self.figure.draw(self.renderer) 
    10123 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10124 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    10125 result = draw(artist, renderer, *args, **kwargs) 
    10126 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10127 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    10128 return draw(artist, renderer) 
    10129 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10130 packages/matplotlib/figure.py", line 2796, in draw 
    10131 artists = self._get_draw_artists(renderer) 
    10132 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10133 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    10134 ax.apply_aspect() 
    10135 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10136 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    10137 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    10138 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    10139 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    10140 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    10141 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    10142 
    10143 > select clear
    10144 
    10145 > isolde pepflip sel
    10146 
    10147 Flipping the peptide bond for 1 residues 
    10148 
    10149 > isolde pepflip sel
    10150 
    10151 Flipping the peptide bond for 1 residues 
    10152 
    10153 > select clear
    10154 
    10155 > view #1/o:74
    10156 
    10157 > isolde sim pause
    10158 
    10159 > ui tool show "Ramachandran Plot"
    10160 
    10161 > isolde sim resume
    10162 
    10163 > ui tool show "Ramachandran Plot"
    10164 
    10165 > select clear
    10166 
    10167 > ui tool show "Ramachandran Plot"
    10168 
    10169 > isolde sim pause
    10170 
    10171 > ui tool show "Ramachandran Plot"
    10172 
    10173 > view #1/o:74
    10174 
    10175 > isolde sim resume
    10176 
    10177 > ui tool show "Ramachandran Plot"
    10178 
    10179 > isolde sim pause
    10180 
    10181 > isolde sim stop
    10182 
    10183 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10184 chains... 
    10185 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    10186 standards. 
    10187 ISOLDE: stopped sim 
    10188 
    10189 > isolde sim start sel
    10190 
    10191 ISOLDE: started sim 
    10192 
    10193 > ui tool show "Ramachandran Plot"
    10194 
    10195 > select clear
    10196 
    10197 > isolde sim stop
    10198 
    10199 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10200 chains... 
    10201 ISOLDE: stopped sim 
    10202 
    10203 > view #1/o:74
    10204 
    10205 > view #1/o:74-81|/o:12
    10206 
    10207 > select #1/o:74-81|/o:12
    10208 
    10209 140 atoms, 138 bonds, 9 residues, 1 model selected 
    10210 
    10211 > isolde sim start sel
    10212 
    10213 ISOLDE: started sim 
    10214 
    10215 > ui tool show "Ramachandran Plot"
    10216 
    10217 > select clear
    10218 
    10219 > isolde sim stop
    10220 
    10221 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10222 chains... 
    10223 ISOLDE: stopped sim 
    10224 
    10225 > select #1/o:74
    10226 
    10227 11 atoms, 10 bonds, 1 residue, 1 model selected 
    10228 
    10229 > view #1/o:74
    10230 
    10231 > isolde sim start sel
    10232 
    10233 ISOLDE: started sim 
    10234 
    10235 > ui tool show "Ramachandran Plot"
    10236 
    10237 > select clear
    10238 
    10239 > ui tool show "Ramachandran Plot"
    10240 
    10241 > isolde sim stop
    10242 
    10243 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10244 chains... 
    10245 ISOLDE: stopped sim 
    10246 
    10247 > ui tool show "Ramachandran Plot"
    10248 
    10249 > isolde sim start sel
    10250 
    10251 ISOLDE: started sim 
    10252 
    10253 > ui tool show "Ramachandran Plot"
    10254 
    10255 > select clear
    10256 
    10257 > ui tool show "Ramachandran Plot"
    10258 
    10259 > isolde sim stop
    10260 
    10261 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10262 chains... 
    10263 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    10264 standards. 
    10265 ISOLDE: stopped sim 
    10266 
    10267 > ui tool show "Ramachandran Plot"
    10268 
    10269 > isolde sim start sel
    10270 
    10271 ISOLDE: started sim 
    10272 
    10273 > select clear
    10274 
    10275 > ui tool show "Ramachandran Plot"
    10276 
    10277 > isolde sim pause
    10278 
    10279 > isolde sim resume
    10280 
    10281 > isolde pepflip sel
    10282 
    10283 Flipping the peptide bond for 1 residues 
    10284 
    10285 > isolde pepflip sel
    10286 
    10287 Flipping the peptide bond for 1 residues 
    10288 
    10289 > isolde pepflip sel
    10290 
    10291 Flipping the peptide bond for 1 residues 
    10292 
    10293 > isolde pepflip sel
    10294 
    10295 Flipping the peptide bond for 1 residues 
    10296 
    10297 > select clear
    10298 
    10299 > isolde pepflip sel
    10300 
    10301 Flipping the peptide bond for 1 residues 
    10302 
    10303 > isolde pepflip sel
    10304 
    10305 Flipping the peptide bond for 1 residues 
    10306 
    10307 > select clear
    10308 
    10309 > ui tool show "Ramachandran Plot"
    10310 
    10311 > select clear
    10312 
    10313 > view #1/l:33
    10314 
    10315 > select clear
    10316 
    10317 > isolde pepflip sel
    10318 
    10319 Flipping the peptide bond for 1 residues 
    10320 
    10321 > select clear
    10322 
    10323 > ui tool show "Ramachandran Plot"
    10324 
    10325 > select clear
    10326 
    10327 > isolde sim pause
    10328 
    10329 > isolde sim resume
    10330 
    10331 > ui tool show "Ramachandran Plot"
    10332 
    10333 > isolde sim pause
    10334 
    10335 > isolde sim stop
    10336 
    10337 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10338 chains... 
    10339 ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
    10340 standards. 
    10341 ISOLDE: stopped sim 
    10342 
    10343 > isolde sim start sel
    10344 
    10345 ISOLDE: started sim 
    10346 
    10347 > ui tool show "Ramachandran Plot"
    10348 
    10349 > select clear
    10350 
    10351 > isolde sim pause
    10352 
    10353 > isolde sim resume
    10354 
    10355 > ui tool show "Ramachandran Plot"
    10356 
    10357 > select clear
    10358 
    10359 > isolde pepflip sel
    10360 
    10361 Flipping the peptide bond for 1 residues 
    10362 
    10363 > isolde pepflip sel
    10364 
    10365 Flipping the peptide bond for 1 residues 
    10366 
    10367 > isolde pepflip sel
    10368 
    10369 Flipping the peptide bond for 1 residues 
    10370 
    10371 > ui tool show "Ramachandran Plot"
    10372 
    10373 > select clear
    10374 
    10375 > ui tool show "Ramachandran Plot"
    10376 
    10377 > select clear
    10378 
    10379 > isolde pepflip sel
    10380 
    10381 Flipping the peptide bond for 1 residues 
    10382 
    10383 > isolde pepflip sel
    10384 
    10385 Flipping the peptide bond for 1 residues 
    10386 
    10387 > ui tool show "Ramachandran Plot"
    10388 
    10389 > select clear
    10390 
    10391 > isolde sim stop
    10392 
    10393 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10394 chains... 
    10395 ISOLDE: stopped sim 
    10396 
    10397 > view #1/l:33
    10398 
    10399 > select #1/l:33
    10400 
    10401 17 atoms, 16 bonds, 1 residue, 1 model selected 
    10402 
    10403 > isolde sim start sel
    10404 
    10405 ISOLDE: started sim 
    10406 
    10407 > ui tool show "Ramachandran Plot"
    10408 
    10409 > select clear
    10410 
    10411 > ui tool show "Ramachandran Plot"
    10412 
    10413 > isolde sim stop
    10414 
    10415 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10416 chains... 
    10417 ISOLDE: stopped sim 
    10418 
    10419 > isolde sim start sel
    10420 
    10421 ISOLDE: started sim 
    10422 
    10423 > select clear
    10424 
    10425 > ui tool show "Ramachandran Plot"
    10426 
    10427 > isolde pepflip sel
    10428 
    10429 Flipping the peptide bond for 1 residues 
    10430 
    10431 > select clear
    10432 
    10433 > ui tool show "Ramachandran Plot"
    10434 
    10435 > select clear
    10436 
    10437 > ui tool show "Ramachandran Plot"
    10438 
    10439 > isolde sim pause
    10440 
    10441 > isolde sim resume
    10442 
    10443 > ui tool show "Ramachandran Plot"
    10444 
    10445 > isolde sim stop
    10446 
    10447 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10448 chains... 
    10449 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    10450 standards. 
    10451 ISOLDE: stopped sim 
    10452 
    10453 > view #1/l:33
    10454 
    10455 > select #1/l:33
    10456 
    10457 17 atoms, 16 bonds, 1 residue, 1 model selected 
    10458 
    10459 > isolde sim start sel
    10460 
    10461 ISOLDE: started sim 
    10462 
    10463 > ui tool show "Ramachandran Plot"
    10464 
    10465 > select clear
    10466 
    10467 > ui tool show "Ramachandran Plot"
    10468 
    10469 > isolde sim stop
    10470 
    10471 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10472 chains... 
    10473 ISOLDE: stopped sim 
    10474 
    10475 > ui tool show "Ramachandran Plot"
    10476 
    10477 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    10478 > mut8-no-C-ter/20-3-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
    10479 > step20-3-afterStep1d2.cxs
    10480 
    10481 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    10482 
    10483 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    10484 > mut8-no-C-ter/20-3-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
    10485 > step20-3-afterStep1d2.pdb
    10486 
    10487 > ui tool show "Ramachandran Plot"
    10488 
    10489 > isolde sim start sel
    10490 
    10491 ISOLDE: started sim 
    10492 
    10493 > select clear
    10494 
    10495 > isolde sim pause
    10496 
    10497 > select clear
    10498 
    10499 > isolde sim resume
    10500 
    10501 > select clear
    10502 
    10503 > ui tool show "Ramachandran Plot"
    10504 
    10505 > select clear
    10506 
    10507 > isolde sim pause
    10508 
    10509 > isolde sim resume
    10510 
    10511 > ui tool show "Ramachandran Plot"
    10512 
    10513 > isolde sim stop
    10514 
    10515 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10516 chains... 
    10517 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    10518 standards. 
    10519 ISOLDE: stopped sim 
    10520 
    10521 > select #1/u:100-109
    10522 
    10523 161 atoms, 160 bonds, 10 residues, 1 model selected 
    10524 
    10525 > isolde sim start sel
    10526 
    10527 ISOLDE: started sim 
    10528 
    10529 > ui tool show "Ramachandran Plot"
    10530 
    10531 > isolde sim pause
    10532 
    10533 > ui tool show "Ramachandran Plot"
    10534 
    10535 > isolde sim resume
    10536 
    10537 > ui tool show "Ramachandran Plot"
    10538 
    10539 > isolde sim pause
    10540 
    10541 > isolde sim resume
    10542 
    10543 > isolde sim stop
    10544 
    10545 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10546 chains... 
    10547 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    10548 standards. 
    10549 ISOLDE: stopped sim 
    10550 
    10551 > select #1/u:115-116
    10552 
    10553 43 atoms, 42 bonds, 2 residues, 1 model selected 
    10554 
    10555 > isolde sim start sel
    10556 
    10557 ISOLDE: started sim 
    10558 
    10559 > select clear
    10560 
    10561 > isolde pepflip sel
    10562 
    10563 Flipping the peptide bond for 1 residues 
    10564 
    10565 > ui tool show "Ramachandran Plot"
    10566 
    10567 > view #1/u:115-116
    10568 
    10569 > isolde sim pause
    10570 
    10571 > ui tool show "Ramachandran Plot"
    10572 
    10573 > isolde sim resume
    10574 
    10575 > isolde sim stop
    10576 
    10577 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10578 chains... 
    10579 ISOLDE: stopped sim 
    10580 
    10581 > isolde sim start sel
    10582 
    10583 ISOLDE: started sim 
    10584 
    10585 > isolde sim pause
    10586 
    10587 > isolde sim resume
    10588 
    10589 > isolde sim pause
    10590 
    10591 > isolde sim resume
    10592 
    10593 > ui tool show "Ramachandran Plot"
    10594 
    10595 > isolde sim stop
    10596 
    10597 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10598 chains... 
    10599 ISOLDE: stopped sim 
    10600 
    10601 > select #1/t:127-131
    10602 
    10603 85 atoms, 85 bonds, 5 residues, 1 model selected 
    10604 
    10605 > isolde sim start sel
    10606 
    10607 ISOLDE: started sim 
    10608 
    10609 > isolde pepflip sel
    10610 
    10611 Flipping the peptide bond for 1 residues 
    10612 
    10613 > isolde pepflip sel
    10614 
    10615 Flipping the peptide bond for 1 residues 
    10616 
    10617 > ui tool show "Ramachandran Plot"
    10618 
    10619 > select clear
    10620 
    10621 > isolde sim pause
    10622 
    10623 > ui tool show "Ramachandran Plot"
    10624 
    10625 > isolde sim resume
    10626 
    10627 > isolde pepflip sel
    10628 
    10629 Flipping the peptide bond for 1 residues 
    10630 
    10631 > isolde pepflip sel
    10632 
    10633 Flipping the peptide bond for 1 residues 
    10634 
    10635 > isolde sim stop
    10636 
    10637 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10638 chains... 
    10639 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    10640 standards. 
    10641 ISOLDE: stopped sim 
    10642 
    10643 > select #1/t:107-111
    10644 
    10645 85 atoms, 85 bonds, 5 residues, 1 model selected 
    10646 
    10647 > isolde sim start sel
    10648 
    10649 ISOLDE: started sim 
    10650 
    10651 > select clear
    10652 
    10653 > isolde pepflip sel
    10654 
    10655 Flipping the peptide bond for 1 residues 
    10656 
    10657 > isolde pepflip sel
    10658 
    10659 Flipping the peptide bond for 1 residues 
    10660 
    10661 > isolde pepflip sel
    10662 
    10663 Flipping the peptide bond for 1 residues 
    10664 
    10665 > isolde pepflip sel
    10666 
    10667 Flipping the peptide bond for 1 residues 
    10668 
    10669 > ui tool show "Ramachandran Plot"
    10670 
    10671 > select clear
    10672 
    10673 > isolde sim pause
    10674 
    10675 3 models selected 
    10676 
    10677 > select clear
    10678 
    10679 > isolde sim resume
    10680 
    10681 > select clear
    10682 
    10683 > ui tool show "Ramachandran Plot"
    10684 
    10685 > select clear
    10686 
    10687 > isolde sim stop
    10688 
    10689 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10690 chains... 
    10691 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    10692 standards. 
    10693 ISOLDE: stopped sim 
    10694 
    10695 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    10696 > mut8-no-C-ter/20-4-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
    10697 > step20-4.pdb
    10698 
    10699 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    10700 > mut8-no-C-ter/20-4-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
    10701 > step20-4.cxs
    10702 
    10703 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    10704 
    10705 > ui tool show "Ramachandran Plot"
    10706 
    10707 > isolde sim start sel
    10708 
    10709 ISOLDE: started sim 
    10710 
    10711 > ui tool show "Ramachandran Plot"
    10712 
    10713 > isolde sim stop
    10714 
    10715 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10716 chains... 
    10717 ISOLDE: stopped sim 
    10718 
    10719 > view #1/t:86
    10720 
    10721 > select #1/t:86
    10722 
    10723 17 atoms, 17 bonds, 1 residue, 1 model selected 
    10724 
    10725 > isolde sim start sel
    10726 
    10727 ISOLDE: started sim 
    10728 
    10729 > ui tool show "Ramachandran Plot"
    10730 
    10731 > isolde sim pause
    10732 
    10733 > isolde sim resume
    10734 
    10735 > ui tool show "Ramachandran Plot"
    10736 
    10737 > isolde sim pause
    10738 
    10739 > isolde sim stop
    10740 
    10741 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10742 chains... 
    10743 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    10744 standards. 
    10745 ISOLDE: stopped sim 
    10746 
    10747 > isolde sim start sel
    10748 
    10749 ISOLDE: started sim 
    10750 
    10751 > ui tool show "Ramachandran Plot"
    10752 
    10753 > select clear
    10754 
    10755 > isolde sim pause
    10756 
    10757 > ui tool show "Ramachandran Plot"
    10758 
    10759 > isolde sim stop
    10760 
    10761 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10762 chains... 
    10763 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    10764 standards. 
    10765 ISOLDE: stopped sim 
    10766 
    10767 > isolde sim start sel
    10768 
    10769 ISOLDE: started sim 
    10770 
    10771 > ui tool show "Ramachandran Plot"
    10772 
    10773 > isolde sim stop
    10774 
    10775 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10776 chains... 
    10777 ISOLDE: stopped sim 
    10778 
    10779 > view #1/t:125
    10780 
    10781 > select #1/t:125
    10782 
    10783 15 atoms, 14 bonds, 1 residue, 1 model selected 
    10784 
    10785 > isolde sim start sel
    10786 
    10787 ISOLDE: started sim 
    10788 
    10789 > select clear
    10790 
    10791 > isolde sim pause
    10792 
    10793 > isolde sim stop
    10794 
    10795 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10796 chains... 
    10797 ISOLDE: stopped sim 
    10798 
    10799 > isolde sim start sel
    10800 
    10801 ISOLDE: started sim 
    10802 
    10803 > ui tool show "Ramachandran Plot"
    10804 
    10805 > isolde sim pause
    10806 
    10807 > ui tool show "Ramachandran Plot"
    10808 
    10809 > isolde sim stop
    10810 
    10811 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10812 chains... 
    10813 ISOLDE: stopped sim 
    10814 
    10815 > isolde sim start sel
    10816 
    10817 ISOLDE: started sim 
    10818 
    10819 > ui tool show "Ramachandran Plot"
    10820 
    10821 > isolde sim pause
    10822 
    10823 > isolde sim resume
    10824 
    10825 > isolde sim pause
    10826 
    10827 > isolde sim resume
    10828 
    10829 > ui tool show "Ramachandran Plot"
    10830 
    10831 > isolde sim pause
    10832 
    10833 > isolde sim stop
    10834 
    10835 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10836 chains... 
    10837 ISOLDE: stopped sim 
    10838 
    10839 > select #1/t:60-61
    10840 
    10841 24 atoms, 24 bonds, 2 residues, 1 model selected 
    10842 
    10843 > isolde sim start sel
    10844 
    10845 ISOLDE: started sim 
    10846 
    10847 > isolde sim pause
    10848 
    10849 > isolde sim resume
    10850 
    10851 > ui tool show "Ramachandran Plot"
    10852 
    10853 > select clear
    10854 
    10855 > isolde pepflip sel
    10856 
    10857 Flipping the peptide bond for 1 residues 
    10858 
    10859 > isolde pepflip sel
    10860 
    10861 Flipping the peptide bond for 1 residues 
    10862 
    10863 > isolde pepflip sel
    10864 
    10865 Flipping the peptide bond for 1 residues 
    10866 
    10867 > select clear
    10868 
    10869 > isolde pepflip sel
    10870 
    10871 Flipping the peptide bond for 1 residues 
    10872 
    10873 > isolde pepflip sel
    10874 
    10875 Flipping the peptide bond for 1 residues 
    10876 
    10877 > isolde pepflip sel
    10878 
    10879 Flipping the peptide bond for 1 residues 
    10880 Unable to flip peptide bond after 50 rounds. Giving up. 
    10881 
    10882 > isolde pepflip sel
    10883 
    10884 Flipping the peptide bond for 1 residues 
    10885 
    10886 > isolde pepflip sel
    10887 
    10888 Flipping the peptide bond for 1 residues 
    10889 
    10890 > isolde pepflip sel
    10891 
    10892 Flipping the peptide bond for 1 residues 
    10893 
    10894 > select clear
    10895 
    10896 > ui tool show "Ramachandran Plot"
    10897 
    10898 > select clear
    10899 
    10900 > ui tool show "Ramachandran Plot"
    10901 
    10902 > isolde sim stop
    10903 
    10904 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10905 chains... 
    10906 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    10907 standards. 
    10908 ISOLDE: stopped sim 
    10909 
    10910 > ui tool show "Ramachandran Plot"
    10911 
    10912 > view #1/t:55
    10913 
    10914 > select #1/t:55
    10915 
    10916 17 atoms, 17 bonds, 1 residue, 1 model selected 
    10917 
    10918 > isolde sim start sel
    10919 
    10920 ISOLDE: started sim 
    10921 
    10922 > ui tool show "Ramachandran Plot"
    10923 
    10924 > isolde sim stop
    10925 
    10926 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10927 chains... 
    10928 ISOLDE: stopped sim 
    10929 
    10930 > view #1/t:47]
    10931 
    10932 No objects specified. 
    10933 
    10934 > view #1/t:47
    10935 
    10936 > select #1/t:47
    10937 
    10938 24 atoms, 23 bonds, 1 residue, 1 model selected 
    10939 
    10940 > isolde sim start sel
    10941 
    10942 ISOLDE: started sim 
    10943 
    10944 > ui tool show "Ramachandran Plot"
    10945 
    10946 > isolde sim stop
    10947 
    10948 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10949 chains... 
    10950 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    10951 standards. 
    10952 ISOLDE: stopped sim 
    10953 
    10954 > view #1/t:125
    10955 
    10956 > select #1/t:125
    10957 
    10958 15 atoms, 14 bonds, 1 residue, 1 model selected 
    10959 
    10960 > isolde sim start sel
    10961 
    10962 ISOLDE: started sim 
    10963 
    10964 > ui tool show "Ramachandran Plot"
    10965 
    10966 > isolde sim stop
    10967 
    10968 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10969 chains... 
    10970 ISOLDE: stopped sim 
    10971 
    10972 > select #1/t:125
    10973 
    10974 15 atoms, 14 bonds, 1 residue, 1 model selected 
    10975 
    10976 > isolde sim start sel
    10977 
    10978 ISOLDE: started sim 
    10979 
    10980 > select clear
    10981 
    10982 > ui tool show "Ramachandran Plot"
    10983 
    10984 > isolde sim stop
    10985 
    10986 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10987 chains... 
    10988 ISOLDE: stopped sim 
    10989 
    10990 > select #1/t:86
    10991 
    10992 17 atoms, 17 bonds, 1 residue, 1 model selected 
    10993 
    10994 > view #1/t:86
    10995 
    10996 > isolde sim start sel
    10997 
    10998 ISOLDE: started sim 
    10999 
    11000 > ui tool show "Ramachandran Plot"
    11001 
    11002 > select clear
    11003 
    11004 > isolde sim stop
    11005 
    11006 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11007 chains... 
    11008 ISOLDE: stopped sim 
    11009 
    11010 > view #1/u:87
    11011 
    11012 > select #1/u:87
    11013 
    11014 24 atoms, 23 bonds, 1 residue, 1 model selected 
    11015 
    11016 > isolde sim start sel
    11017 
    11018 ISOLDE: started sim 
    11019 
    11020 > ui tool show "Ramachandran Plot"
    11021 
    11022 > select clear
    11023 
    11024 > isolde sim stop
    11025 
    11026 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11027 chains... 
    11028 ISOLDE: stopped sim 
    11029 
    11030 > view #1/t:107-111
    11031 
    11032 > select #1/t:107-111
    11033 
    11034 85 atoms, 85 bonds, 5 residues, 1 model selected 
    11035 
    11036 > isolde sim start sel
    11037 
    11038 ISOLDE: started sim 
    11039 
    11040 > ui tool show "Ramachandran Plot"
    11041 
    11042 > select clear
    11043 
    11044 > isolde pepflip sel
    11045 
    11046 Flipping the peptide bond for 1 residues 
    11047 
    11048 > ui tool show "Ramachandran Plot"
    11049 
    11050 > isolde pepflip sel
    11051 
    11052 Flipping the peptide bond for 1 residues 
    11053 
    11054 > ui tool show "Ramachandran Plot"
    11055 
    11056 > isolde sim pause
    11057 
    11058 > view #1/t:100
    11059 
    11060 > select #1/t:100
    11061 
    11062 16 atoms, 15 bonds, 1 residue, 1 model selected 
    11063 
    11064 > isolde sim start sel
    11065 
    11066 Simulation already running! 
    11067 
    11068 > isolde sim stop
    11069 
    11070 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11071 chains... 
    11072 ISOLDE: stopped sim 
    11073 
    11074 > select #1/t:100
    11075 
    11076 16 atoms, 15 bonds, 1 residue, 1 model selected 
    11077 
    11078 > isolde sim start sel
    11079 
    11080 ISOLDE: started sim 
    11081 
    11082 > ui tool show "Ramachandran Plot"
    11083 
    11084 > isolde sim pause
    11085 
    11086 > isolde sim stop
    11087 
    11088 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11089 chains... 
    11090 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    11091 standards. 
    11092 ISOLDE: stopped sim 
    11093 
    11094 > isolde sim start sel
    11095 
    11096 ISOLDE: started sim 
    11097 
    11098 > select clear
    11099 
    11100 > isolde pepflip sel
    11101 
    11102 Flipping the peptide bond for 1 residues 
    11103 
    11104 > isolde pepflip sel
    11105 
    11106 Flipping the peptide bond for 1 residues 
    11107 
    11108 > isolde pepflip sel
    11109 
    11110 Flipping the peptide bond for 1 residues 
    11111 
    11112 > isolde pepflip sel
    11113 
    11114 Flipping the peptide bond for 1 residues 
    11115 
    11116 > select clear
    11117 
    11118 > ui tool show "Ramachandran Plot"
    11119 
    11120 > isolde pepflip sel
    11121 
    11122 Flipping the peptide bond for 1 residues 
    11123 
    11124 > ui tool show "Ramachandran Plot"
    11125 
    11126 > isolde sim pause
    11127 
    11128 > isolde sim resume
    11129 
    11130 > isolde pepflip sel
    11131 
    11132 Flipping the peptide bond for 1 residues 
    11133 
    11134 > ui tool show "Ramachandran Plot"
    11135 
    11136 > isolde sim stop
    11137 
    11138 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11139 chains... 
    11140 ISOLDE: stopped sim 
    11141 
    11142 > select #1/t:100
    11143 
    11144 16 atoms, 15 bonds, 1 residue, 1 model selected 
    11145 
    11146 > isolde sim start sel
    11147 
    11148 ISOLDE: started sim 
    11149 
    11150 > ui tool show "Ramachandran Plot"
    11151 
    11152 > isolde sim pause
    11153 
    11154 > ui tool show "Ramachandran Plot"
    11155 
    11156 > isolde sim resume
    11157 
    11158 > isolde pepflip sel
    11159 
    11160 Flipping the peptide bond for 1 residues 
    11161 
    11162 > isolde sim pause
    11163 
    11164 > ui tool show "Ramachandran Plot"
    11165 
    11166 > isolde sim resume
    11167 
    11168 > isolde pepflip sel
    11169 
    11170 Flipping the peptide bond for 1 residues 
    11171 
    11172 > isolde pepflip sel
    11173 
    11174 Flipping the peptide bond for 1 residues 
    11175 
    11176 > isolde pepflip sel
    11177 
    11178 Flipping the peptide bond for 1 residues 
    11179 
    11180 > isolde sim pause
    11181 
    11182 > isolde sim stop
    11183 
    11184 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11185 chains... 
    11186 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    11187 standards. 
    11188 ISOLDE: stopped sim 
    11189 
    11190 > isolde sim start sel
    11191 
    11192 ISOLDE: started sim 
    11193 
    11194 > isolde sim stop
    11195 
    11196 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11197 chains... 
    11198 ISOLDE: stopped sim 
    11199 
    11200 > select #1/t:80|t:75
    11201 
    11202 Expected an objects specifier or a keyword 
    11203 
    11204 > select #1/t:80|/t:75
    11205 
    11206 36 atoms, 35 bonds, 2 residues, 1 model selected 
    11207 
    11208 > isolde sim start sel
    11209 
    11210 ISOLDE: started sim 
    11211 
    11212 > select clear
    11213 
    11214 > isolde sim pause
    11215 
    11216 > isolde sim resume
    11217 
    11218 > isolde pepflip sel
    11219 
    11220 Flipping the peptide bond for 1 residues 
    11221 
    11222 > select clear
    11223 
    11224 > isolde pepflip sel
    11225 
    11226 Flipping the peptide bond for 1 residues 
    11227 
    11228 > select clear
    11229 
    11230 > ui tool show "Ramachandran Plot"
    11231 
    11232 > isolde sim pause
    11233 
    11234 > isolde sim resume
    11235 
    11236 > select clear
    11237 
    11238 > ui tool show "Ramachandran Plot"
    11239 
    11240 > isolde sim stop
    11241 
    11242 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11243 chains... 
    11244 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    11245 standards. 
    11246 ISOLDE: stopped sim 
    11247 
    11248 > view #1/t:80
    11249 
    11250 > select #1/t:80
    11251 
    11252 14 atoms, 14 bonds, 1 residue, 1 model selected 
    11253 
    11254 > isolde sim start sel
    11255 
    11256 ISOLDE: started sim 
    11257 
    11258 > ui tool show "Ramachandran Plot"
    11259 
    11260 > isolde sim stop
    11261 
    11262 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11263 chains... 
    11264 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    11265 standards. 
    11266 ISOLDE: stopped sim 
    11267 
    11268 > view #1/t:100
    11269 
    11270 > select #1/t:100
    11271 
    11272 16 atoms, 15 bonds, 1 residue, 1 model selected 
    11273 
    11274 > isolde sim start sel
    11275 
    11276 ISOLDE: started sim 
    11277 
    11278 > ui tool show "Ramachandran Plot"
    11279 
    11280 > isolde sim stop
    11281 
    11282 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11283 chains... 
    11284 ISOLDE: stopped sim 
    11285 
    11286 > view #1/t:107-111
    11287 
    11288 > select #1/t:107-111
    11289 
    11290 85 atoms, 85 bonds, 5 residues, 1 model selected 
    11291 
    11292 > isolde sim start sel
    11293 
    11294 ISOLDE: started sim 
    11295 
    11296 > ui tool show "Ramachandran Plot"
    11297 
    11298 > isolde sim stop
    11299 
    11300 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11301 chains... 
    11302 ISOLDE: stopped sim 
    11303 
    11304 > view #1/t:127-131
    11305 
    11306 > select #1/t:127-131
    11307 
    11308 85 atoms, 85 bonds, 5 residues, 1 model selected 
    11309 
    11310 > isolde sim start sel
    11311 
    11312 ISOLDE: started sim 
    11313 
    11314 > ui tool show "Ramachandran Plot"
    11315 
    11316 > isolde sim stop
    11317 
    11318 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11319 chains... 
    11320 ISOLDE: stopped sim 
    11321 
    11322 > view #1/u:115-116
    11323 
    11324 > select #1/u:115-116
    11325 
    11326 43 atoms, 42 bonds, 2 residues, 1 model selected 
    11327 
    11328 > isolde sim start sel
    11329 
    11330 ISOLDE: started sim 
    11331 
    11332 > ui tool show "Ramachandran Plot"
    11333 
    11334 > isolde sim pause
    11335 
    11336 > isolde sim resume
    11337 
    11338 > ui tool show "Ramachandran Plot"
    11339 
    11340 > isolde sim stop
    11341 
    11342 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11343 chains... 
    11344 ISOLDE: stopped sim 
    11345 
    11346 > view #1/u:100-109
    11347 
    11348 > select #1/u:100-109
    11349 
    11350 161 atoms, 160 bonds, 10 residues, 1 model selected 
    11351 
    11352 > isolde sim start sel
    11353 
    11354 ISOLDE: started sim 
    11355 
    11356 > ui tool show "Ramachandran Plot"
    11357 
    11358 > isolde sim stop
    11359 
    11360 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11361 chains... 
    11362 ISOLDE: stopped sim 
    11363 
    11364 > select clear
    11365 
    11366 > view #1/u:101
    11367 
    11368 > select #1/u:101
    11369 
    11370 11 atoms, 10 bonds, 1 residue, 1 model selected 
    11371 
    11372 > isolde sim start sel
    11373 
    11374 ISOLDE: started sim 
    11375 
    11376 > ui tool show "Ramachandran Plot"
    11377 
    11378 > isolde sim stop
    11379 
    11380 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11381 chains... 
    11382 ISOLDE: stopped sim 
    11383 
    11384 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    11385 > mut8-no-C-ter/20-5-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
    11386 > step20-5.cxs
    11387 
    11388 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    11389 
    11390 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    11391 > mut8-no-C-ter/20-5-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
    11392 > step20-5.pdb
    11393 
    11394 > isolde sim start sel
    11395 
    11396 ISOLDE: started sim 
    11397 
    11398 > ui tool show "Ramachandran Plot"
    11399 
    11400 > isolde sim stop
    11401 
    11402 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11403 chains... 
    11404 ISOLDE: stopped sim 
    11405 
    11406 > isolde sim start sel
    11407 
    11408 ISOLDE: started sim 
    11409 
    11410 > ui tool show "Ramachandran Plot"
    11411 
    11412 > isolde sim stop
    11413 
    11414 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11415 chains... 
    11416 ISOLDE: stopped sim 
    11417 
    11418 > isolde sim start sel
    11419 
    11420 ISOLDE: started sim 
    11421 
    11422 > ui tool show "Ramachandran Plot"
    11423 
    11424 > isolde sim stop
    11425 
    11426 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11427 chains... 
    11428 ISOLDE: stopped sim 
    11429 
    11430 > isolde sim start sel
    11431 
    11432 ISOLDE: started sim 
    11433 
    11434 > ui tool show "Ramachandran Plot"
    11435 
    11436 > select clear
    11437 
    11438 > isolde sim stop
    11439 
    11440 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11441 chains... 
    11442 ISOLDE: stopped sim 
    11443 
    11444 > isolde sim start sel
    11445 
    11446 ISOLDE: started sim 
    11447 
    11448 > ui tool show "Ramachandran Plot"
    11449 
    11450 > isolde sim stop
    11451 
    11452 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11453 chains... 
    11454 ISOLDE: stopped sim 
    11455 
    11456 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    11457 > mut8-no-C-ter/20-6-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
    11458 > step20-6-fixedNewTwistedBonds.pdb
    11459 
    11460 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/KSRP-
    11461 > mut8-no-C-ter/20-6-continuingNew-FirstSteps-RefiningBEFORE-Annealing-
    11462 > step20-6-fixedNewTwistedBonds.cxs
    11463 
    11464 Taking snapshot of stepper: 5opt-concatenated-Map-Mut8-40S-noCter.pdb 
    11465 
    11466 > ui tool show "Ramachandran Plot"
    11467 
    11468 > isolde sim start sel
    11469 
    11470 ISOLDE: started sim 
    11471 
    11472 > isolde pepflip sel
    11473 
    11474 Flipping the peptide bond for 1 residues 
    11475 
    11476 > isolde pepflip sel
    11477 
    11478 Flipping the peptide bond for 1 residues 
    11479 
    11480 > ui tool show "Ramachandran Plot"
    11481 
    11482 > isolde sim stop
    11483 
    11484 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11485 chains... 
    11486 ISOLDE: stopped sim 
    11487 
    11488 > ui tool show "Ramachandran Plot"
    11489 
    11490 > isolde sim start sel
    11491 
    11492 ISOLDE: started sim 
    11493 
    11494 > ui tool show "Ramachandran Plot"
    11495 
    11496 > select clear
    11497 
    11498 > isolde pepflip sel
    11499 
    11500 Flipping the peptide bond for 1 residues 
    11501 
    11502 > ui tool show "Ramachandran Plot"
    11503 
    11504 > isolde sim stop
    11505 
    11506 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11507 chains... 
    11508 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    11509 standards. 
    11510 ISOLDE: stopped sim 
    11511 
    11512 > ui tool show "Ramachandran Plot"
    11513 
    11514 > isolde sim start sel
    11515 
    11516 ISOLDE: started sim 
    11517 
    11518 > isolde pepflip sel
    11519 
    11520 Flipping the peptide bond for 1 residues 
    11521 
    11522 > ui tool show "Ramachandran Plot"
    11523 
    11524 > view #1/f:43
    11525 
    11526 > ui tool show "Ramachandran Plot"
    11527 
    11528 > isolde sim stop
    11529 
    11530 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11531 chains... 
    11532 ISOLDE: stopped sim 
    11533 
    11534 > ui tool show "Ramachandran Plot"
    11535 
    11536 > isolde sim start sel
    11537 
    11538 ISOLDE: started sim 
    11539 
    11540 > isolde pepflip sel
    11541 
    11542 Flipping the peptide bond for 1 residues 
    11543 
    11544 > ui tool show "Ramachandran Plot"
    11545 
    11546 > select clear
    11547 
    11548 > ui tool show "Ramachandran Plot"
    11549 
    11550 > isolde sim stop
    11551 
    11552 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11553 chains... 
    11554 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    11555 standards. 
    11556 ISOLDE: stopped sim 
    11557 
    11558 > ui tool show "Ramachandran Plot"
    11559 
    11560 > hide #!1.2 models
    11561 
    11562 > show #!1.2 models
    11563 
    11564 > hide #!1.2 models
    11565 
    11566 > show #!1.2 models
    11567 
    11568 > hide #!1.2 models
    11569 
    11570 > show #!1.2 models
    11571 
    11572 > hide #!1.1 models
    11573 
    11574 > show #!1.1 models
    11575 
    11576 > hide #!1.2 models
    11577 
    11578 > show #!1.2 models
    11579 
    11580 > hide #!1.2 models
    11581 
    11582 > show #!1.2 models
    11583 
    11584 > ui tool show "Ramachandran Plot"
    11585 
    11586 > isolde sim start sel
    11587 
    11588 ISOLDE: started sim 
    11589 
    11590 > ui tool show "Ramachandran Plot"
    11591 
    11592 > isolde pepflip sel
    11593 
    11594 Flipping the peptide bond for 1 residues 
    11595 
    11596 > select clear
    11597 
    11598 > ui tool show "Ramachandran Plot"
    11599 
    11600 > isolde sim stop
    11601 
    11602 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11603 chains... 
    11604 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    11605 standards. 
    11606 ISOLDE: stopped sim 
    11607 
    11608 > ui tool show "Ramachandran Plot"
    11609 
    11610 > isolde sim start sel
    11611 
    11612 ISOLDE: started sim 
    11613 
    11614 > isolde pepflip sel
    11615 
    11616 Flipping the peptide bond for 1 residues 
    11617 
    11618 > ui tool show "Ramachandran Plot"
    11619 
    11620 > isolde sim pause
    11621 
    11622 > isolde sim resume
    11623 
    11624 > isolde sim stop
    11625 
    11626 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11627 chains... 
    11628 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    11629 standards. 
    11630 ISOLDE: stopped sim 
    11631 
    11632 > ui tool show "Ramachandran Plot"
    11633 
    11634 > isolde sim start sel
    11635 
    11636 ISOLDE: started sim 
    11637 
    11638 > isolde pepflip sel
    11639 
    11640 Flipping the peptide bond for 1 residues 
    11641 
    11642 > ui tool show "Ramachandran Plot"
    11643 
    11644 > isolde sim pause
    11645 
    11646 > ui tool show "Ramachandran Plot"
    11647 
    11648 > isolde sim stop
    11649 
    11650 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11651 chains... 
    11652 ISOLDE: stopped sim 
    11653 
    11654 > isolde sim start sel
    11655 
    11656 ISOLDE: started sim 
    11657 
    11658 > isolde pepflip sel
    11659 
    11660 Flipping the peptide bond for 1 residues 
    11661 
    11662 > isolde pepflip sel
    11663 
    11664 Flipping the peptide bond for 1 residues 
    11665 
    11666 > isolde pepflip sel
    11667 
    11668 Flipping the peptide bond for 1 residues 
    11669 
    11670 > ui tool show "Ramachandran Plot"
    11671 
    11672 > select clear
    11673 
    11674 > ui tool show "Ramachandran Plot"
    11675 
    11676 > isolde sim pause
    11677 
    11678 > ui tool show "Ramachandran Plot"
    11679 
    11680 > isolde sim resume
    11681 
    11682 > isolde sim stop
    11683 
    11684 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11685 chains... 
    11686 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    11687 standards. 
    11688 ISOLDE: stopped sim 
    11689 
    11690 > isolde sim start sel
    11691 
    11692 ISOLDE: started sim 
    11693 
    11694 > select clear
    11695 
    11696 > ui tool show "Ramachandran Plot"
    11697 
    11698 > isolde sim pause
    11699 
    11700 > select clear
    11701 
    11702 > ui tool show "Ramachandran Plot"
    11703 
    11704 > isolde sim stop
    11705 
    11706 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11707 chains... 
    11708 ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
    11709 standards. 
    11710 ISOLDE: stopped sim 
    11711 
    11712 > isolde sim start sel
    11713 
    11714 ISOLDE: started sim 
    11715 
    11716 > ui tool show "Ramachandran Plot"
    11717 
    11718 > isolde sim pause
    11719 
    11720 > isolde sim resume
    11721 
    11722 > select clear
    11723 
    11724 > ui tool show "Ramachandran Plot"
    11725 
    11726 > isolde sim stop
    11727 
    11728 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11729 chains... 
    11730 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    11731 standards. 
    11732 ISOLDE: stopped sim 
    11733 
    11734 > view #1/k:137
    11735 
    11736 > select #1/k:137
    11737 
    11738 17 atoms, 16 bonds, 1 residue, 1 model selected 
    11739 
    11740 > isolde sim start sel
    11741 
    11742 ISOLDE: started sim 
    11743 
    11744 > ui tool show "Ramachandran Plot"
    11745 
    11746 > isolde sim stop
    11747 
    11748 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11749 chains... 
    11750 ISOLDE: stopped sim 
    11751 
    11752 > view #1/k:142
    11753 
    11754 > select #1/k:142
    11755 
    11756 15 atoms, 14 bonds, 1 residue, 1 model selected 
    11757 
    11758 > isolde sim start sel
    11759 
    11760 ISOLDE: started sim 
    11761 
    11762 > ui tool show "Ramachandran Plot"
    11763 
    11764 > isolde sim stop
    11765 
    11766 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11767 chains... 
    11768 ISOLDE: stopped sim 
    11769 
    11770 > view #1/k:149
    11771 
    11772 > select #1/k:149
    11773 
    11774 10 atoms, 9 bonds, 1 residue, 1 model selected 
    11775 
    11776 > isolde sim start sel
    11777 
    11778 ISOLDE: started sim 
    11779 
    11780 > ui tool show "Ramachandran Plot"
    11781 
    11782 > isolde sim stop
    11783 
    11784 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11785 chains... 
    11786 ISOLDE: stopped sim 
    11787 
    11788 > ui tool show "Ramachandran Plot"
    11789 
    11790 > isolde sim start sel
    11791 
    11792 ISOLDE: started sim 
    11793 
    11794 > ui tool show "Ramachandran Plot"
    11795 
    11796 > isolde pepflip sel
    11797 
    11798 Flipping the peptide bond for 1 residues 
    11799 
    11800 > isolde pepflip sel
    11801 
    11802 Flipping the peptide bond for 1 residues 
    11803 
    11804 > isolde pepflip sel
    11805 
    11806 Flipping the peptide bond for 1 residues 
    11807 
    11808 > isolde pepflip sel
    11809 
    11810 Flipping the peptide bond for 1 residues 
    11811 
    11812 > ui tool show "Ramachandran Plot"
    11813 
    11814 > isolde sim pause
    11815 
    11816 > isolde sim resume
    11817 
    11818 > isolde pepflip sel
    11819 
    11820 Flipping the peptide bond for 1 residues 
    11821 
    11822 > isolde pepflip sel
    11823 
    11824 Flipping the peptide bond for 1 residues 
    11825 
    11826 > isolde pepflip sel
    11827 
    11828 Flipping the peptide bond for 1 residues 
    11829 
    11830 > select clear
    11831 
    11832 > isolde sim pause
    11833 
    11834 > isolde sim resume
    11835 
    11836 > select clear
    11837 
    11838 > isolde sim pause
    11839 
    11840 > isolde sim resume
    11841 
    11842 > ui tool show "Ramachandran Plot"
    11843 
    11844 > isolde sim stop
    11845 
    11846 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11847 chains... 
    11848 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    11849 standards. 
    11850 ISOLDE: stopped sim 
    11851 
    11852 > isolde sim start sel
    11853 
    11854 ISOLDE: started sim 
    11855 
    11856 > ui tool show "Ramachandran Plot"
    11857 
    11858 > isolde sim pause
    11859 
    11860 > ui tool show "Ramachandran Plot"
    11861 
    11862 > isolde sim stop
    11863 
    11864 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11865 chains... 
    11866 ISOLDE: stopped sim 
    11867 
    11868 > isolde sim start sel
    11869 
    11870 ISOLDE: started sim 
    11871 
    11872 > ui tool show "Ramachandran Plot"
    11873 
    11874 > isolde pepflip sel
    11875 
    11876 Flipping the peptide bond for 1 residues 
    11877 
    11878 > ui tool show "Ramachandran Plot"
    11879 
    11880 > isolde pepflip sel
    11881 
    11882 Flipping the peptide bond for 1 residues 
    11883 
    11884 > select clear
     2986[had to delete a bunch of the log to fit within ticket limits]
    118852987
    118862988> ui tool show "Ramachandran Plot"