Changes between Initial Version and Version 1 of Ticket #19299


Ignore:
Timestamp:
Nov 6, 2025, 1:40:41 PM (4 weeks ago)
Author:
Eric Pettersen
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #19299

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

  • Ticket #19299 – Description

    initial v1  
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     143[deleted to fit within ticket limits]
     144
    2282145],
    2283146  "sharedCache" : {
    … …  
    291778079 atoms, 81 bonds, 9 residues, 1 model selected 
    2918781
    2919 > select up
    2920 
    2921 1459 atoms, 1497 bonds, 181 residues, 1 model selected 
    2922 
    2923 > ui tool show "Color Actions"
    2924 
    2925 > color sel blue
    2926 
    2927 > color sel royal blue
    2928 
    2929 > show #6 models
    2930 
    2931 > hide #6 models
    2932 
    2933 > show #4 models
    2934 
    2935 > hide #4 models
    2936 
    2937 > show #!3 models
    2938 
    2939 > hide #!3 models
    2940 
    2941 > show #!1 models
    2942 
    2943 > hide #!1 models
    2944 
    2945 > show #!3 models
    2946 
    2947 > hide #!3 models
    2948 
    2949 > show #4 models
    2950 
    2951 > select clear
    2952 
    2953 > hide #2 models
    2954 
    2955 > select #4/A:71
    2956 
    2957 20 atoms, 20 bonds, 1 residue, 1 model selected 
    2958 
    2959 > select up
    2960 
    2961 150 atoms, 151 bonds, 9 residues, 1 model selected 
    2962 
    2963 > select up
    2964 
    2965 2813 atoms, 2852 bonds, 174 residues, 1 model selected 
    2966 
    2967 > color sel dark sea green
    2968 
    2969 > color sel olive drab
    2970 
    2971 > color sel medium sea green
    2972 
    2973 > color sel forest green
    2974 
    2975 > select clear
    2976 
    2977 > show #5 models
    2978 
    2979 > hide #4 models
    2980 
    2981 > select #5/A:70
    2982 
    2983 19 atoms, 18 bonds, 1 residue, 1 model selected 
    2984 
    2985 > select up
    2986 
    2987 155 atoms, 156 bonds, 9 residues, 1 model selected 
    2988 
    2989 > select up
    2990 
    2991 2845 atoms, 2882 bonds, 174 residues, 1 model selected 
    2992 
    2993 > color sel sienna
    2994 
    2995 > color sel indian red
    2996 
    2997 > color sel saddle brown
    2998 
    2999 > color sel maroon
    3000 
    3001 > select clear
    3002 
    3003 > hide #5 models
    3004 
    3005 > show #6 models
    3006 
    3007 > show #7 models
    3008 
    3009 > hide #6 models
    3010 
    3011 > select #7/G:81
    3012 
    3013 17 atoms, 16 bonds, 1 residue, 1 model selected 
    3014 
    3015 > select add #7/H:21
    3016 
    3017 28 atoms, 26 bonds, 2 residues, 1 model selected 
    3018 
    3019 > select up
    3020 
    3021 183 atoms, 182 bonds, 12 residues, 1 model selected 
    3022 
    3023 > select up
    3024 
    3025 3494 atoms, 3537 bonds, 236 residues, 1 model selected 
    3026 
    3027 > color sel silver
    3028 
    3029 > select #7/A:104
    3030 
    3031 22 atoms, 21 bonds, 1 residue, 1 model selected 
    3032 
    3033 > select up
    3034 
    3035 147 atoms, 147 bonds, 8 residues, 1 model selected 
    3036 
    3037 > select up
    3038 
    3039 2806 atoms, 2845 bonds, 174 residues, 1 model selected 
    3040 
    3041 > color sel midnight blue
    3042 
    3043 > select clear
    3044 
    3045 > show #!1 models
    3046 
    3047 > hide #7 models
    3048 
    3049 > show #6 models
    3050 
    3051 > hide #6 models
    3052 
    3053 > show #5 models
    3054 
    3055 > hide #!1 models
    3056 
    3057 > show #6 models
    3058 
    3059 > hide #6 models
    3060 
    3061 > show #!1 models
    3062 
    3063 > hide #5 models
    3064 
    3065 > show #5 models
    3066 
    3067 > hide #5 models
    3068 
    3069 > show #4 models
    3070 
    3071 > show #5 models
    3072 
    3073 > show #!3 models
    3074 
    3075 > hide #!3 models
    3076 
    3077 > show #2 models
    3078 
    3079 > hide #2 models
    3080 
    3081 > hide #4 models
    3082 
    3083 > hide #!1 models
    3084 
    3085 > show #2 models
    3086 
    3087 > show #6 models
    3088 
    3089 > hide #5 models
    3090 
    3091 > hide #2 models
    3092 
    3093 > show #5 models
    3094 
    3095 > show #7 models
    3096 
    3097 > hide #6 models
    3098 
    3099 > show #6 models
    3100 
    3101 > show #4 models
    3102 
    3103 > show #!3 models
    3104 
    3105 > hide #!3 models
    3106 
    3107 > show #!1 models
    3108 
    3109 > hide #!1 models
    3110 
    3111 > tile
    3112 
    3113 4 models tiled 
    3114 
    3115 > hide #5 models
    3116 
    3117 > show #5 models
    3118 
    3119 > select clear
    3120 
    3121 > select #5/G:124
    3122 
    3123 14 atoms, 13 bonds, 1 residue, 1 model selected 
    3124 
    3125 > select add #5/H:67
    3126 
    3127 25 atoms, 23 bonds, 2 residues, 1 model selected 
    3128 
    3129 > select up
    3130 
    3131 161 atoms, 160 bonds, 11 residues, 1 model selected 
    3132 
    3133 > select up
    3134 
    3135 3494 atoms, 3537 bonds, 236 residues, 1 model selected 
    3136 
    3137 > ui tool show Matchmaker
    3138 
    3139 > matchmaker #4,6-7#!1 to #5 & sel
    3140 
    3141 Parameters 
    3142 --- 
    3143 Chain pairing | bb 
    3144 Alignment algorithm | Needleman-Wunsch 
    3145 Similarity matrix | BLOSUM-62 
    3146 SS fraction | 0.3 
    3147 Gap open (HH/SS/other) | 18/18/6 
    3148 Gap extend | 1 
    3149 SS matrix |  |  | H | S | O 
    3150 ---|---|---|--- 
    3151 H | 6 | -9 | -6 
    3152 S |  | 6 | -6 
    3153 O |  |  | 4 
    3154 Iteration cutoff | 2 
    3155  
    3156 Matchmaker design_start.pdb, chain G (#5) with Cluster2c_lib1.pdb, chain G
    3157 (#4), sequence alignment score = 665.8 
    3158 RMSD between 126 pruned atom pairs is 0.098 angstroms; (across all 126 pairs:
    3159 0.098) 
    3160  
    3161 Matchmaker design_start.pdb, chain G (#5) with RMSD4_NNK1.pdb, chain G (#6),
    3162 sequence alignment score = 665.8 
    3163 RMSD between 126 pruned atom pairs is 0.168 angstroms; (across all 126 pairs:
    3164 0.168) 
    3165  
    3166 Matchmaker design_start.pdb, chain G (#5) with RMSD6_NNK1.pdb, chain G (#7),
    3167 sequence alignment score = 665.8 
    3168 RMSD between 126 pruned atom pairs is 0.200 angstroms; (across all 126 pairs:
    3169 0.200) 
    3170  
    3171 Matchmaker design_start.pdb, chain G (#5) with
    3172 231023_poly310-DH270UCA3_refine_001.pdb, chain H (#1), sequence alignment
    3173 score = 638.8 
    3174 RMSD between 125 pruned atom pairs is 0.800 angstroms; (across all 126 pairs:
    3175 0.817) 
    3176  
    3177 
    3178 > hide #5 models
    3179 
    3180 > show #5 models
    3181 
    3182 > hide #5 models
    3183 
    3184 > show #5 models
    3185 
    3186 > hide #4 models
    3187 
    3188 > hide #6 models
    3189 
    3190 > hide #7 models
    3191 
    3192 > show #7 models
    3193 
    3194 > matchmaker #4,6-7#!1 to #5 & sel
    3195 
    3196 Parameters 
    3197 --- 
    3198 Chain pairing | bb 
    3199 Alignment algorithm | Needleman-Wunsch 
    3200 Similarity matrix | BLOSUM-62 
    3201 SS fraction | 0.3 
    3202 Gap open (HH/SS/other) | 18/18/6 
    3203 Gap extend | 1 
    3204 SS matrix |  |  | H | S | O 
    3205 ---|---|---|--- 
    3206 H | 6 | -9 | -6 
    3207 S |  | 6 | -6 
    3208 O |  |  | 4 
    3209 Iteration cutoff | 2 
    3210  
    3211 Matchmaker design_start.pdb, chain G (#5) with Cluster2c_lib1.pdb, chain G
    3212 (#4), sequence alignment score = 665.8 
    3213 RMSD between 126 pruned atom pairs is 0.098 angstroms; (across all 126 pairs:
    3214 0.098) 
    3215  
    3216 Matchmaker design_start.pdb, chain G (#5) with RMSD4_NNK1.pdb, chain G (#6),
    3217 sequence alignment score = 665.8 
    3218 RMSD between 126 pruned atom pairs is 0.168 angstroms; (across all 126 pairs:
    3219 0.168) 
    3220  
    3221 Matchmaker design_start.pdb, chain G (#5) with RMSD6_NNK1.pdb, chain G (#7),
    3222 sequence alignment score = 665.8 
    3223 RMSD between 126 pruned atom pairs is 0.200 angstroms; (across all 126 pairs:
    3224 0.200) 
    3225  
    3226 Matchmaker design_start.pdb, chain G (#5) with
    3227 231023_poly310-DH270UCA3_refine_001.pdb, chain H (#1), sequence alignment
    3228 score = 638.8 
    3229 RMSD between 125 pruned atom pairs is 0.800 angstroms; (across all 126 pairs:
    3230 0.817) 
    3231  
    3232 
    3233 > hide #7 models
    3234 
    3235 > show #6 models
    3236 
    3237 > matchmaker #4,6-7#!1 to #5 & sel
    3238 
    3239 Parameters 
    3240 --- 
    3241 Chain pairing | bb 
    3242 Alignment algorithm | Needleman-Wunsch 
    3243 Similarity matrix | BLOSUM-62 
    3244 SS fraction | 0.3 
    3245 Gap open (HH/SS/other) | 18/18/6 
    3246 Gap extend | 1 
    3247 SS matrix |  |  | H | S | O 
    3248 ---|---|---|--- 
    3249 H | 6 | -9 | -6 
    3250 S |  | 6 | -6 
    3251 O |  |  | 4 
    3252 Iteration cutoff | 2 
    3253  
    3254 Matchmaker design_start.pdb, chain G (#5) with Cluster2c_lib1.pdb, chain G
    3255 (#4), sequence alignment score = 665.8 
    3256 RMSD between 126 pruned atom pairs is 0.098 angstroms; (across all 126 pairs:
    3257 0.098) 
    3258  
    3259 Matchmaker design_start.pdb, chain G (#5) with RMSD4_NNK1.pdb, chain G (#6),
    3260 sequence alignment score = 665.8 
    3261 RMSD between 126 pruned atom pairs is 0.168 angstroms; (across all 126 pairs:
    3262 0.168) 
    3263  
    3264 Matchmaker design_start.pdb, chain G (#5) with RMSD6_NNK1.pdb, chain G (#7),
    3265 sequence alignment score = 665.8 
    3266 RMSD between 126 pruned atom pairs is 0.200 angstroms; (across all 126 pairs:
    3267 0.200) 
    3268  
    3269 Matchmaker design_start.pdb, chain G (#5) with
    3270 231023_poly310-DH270UCA3_refine_001.pdb, chain H (#1), sequence alignment
    3271 score = 638.8 
    3272 RMSD between 125 pruned atom pairs is 0.800 angstroms; (across all 126 pairs:
    3273 0.817) 
    3274  
    3275 
    3276 > hide #6 models
    3277 
    3278 > show #4 models
    3279 
    3280 > matchmaker #4,6-7#!1 to #5 & sel
    3281 
    3282 Parameters 
    3283 --- 
    3284 Chain pairing | bb 
    3285 Alignment algorithm | Needleman-Wunsch 
    3286 Similarity matrix | BLOSUM-62 
    3287 SS fraction | 0.3 
    3288 Gap open (HH/SS/other) | 18/18/6 
    3289 Gap extend | 1 
    3290 SS matrix |  |  | H | S | O 
    3291 ---|---|---|--- 
    3292 H | 6 | -9 | -6 
    3293 S |  | 6 | -6 
    3294 O |  |  | 4 
    3295 Iteration cutoff | 2 
    3296  
    3297 Matchmaker design_start.pdb, chain G (#5) with Cluster2c_lib1.pdb, chain G
    3298 (#4), sequence alignment score = 665.8 
    3299 RMSD between 126 pruned atom pairs is 0.098 angstroms; (across all 126 pairs:
    3300 0.098) 
    3301  
    3302 Matchmaker design_start.pdb, chain G (#5) with RMSD4_NNK1.pdb, chain G (#6),
    3303 sequence alignment score = 665.8 
    3304 RMSD between 126 pruned atom pairs is 0.168 angstroms; (across all 126 pairs:
    3305 0.168) 
    3306  
    3307 Matchmaker design_start.pdb, chain G (#5) with RMSD6_NNK1.pdb, chain G (#7),
    3308 sequence alignment score = 665.8 
    3309 RMSD between 126 pruned atom pairs is 0.200 angstroms; (across all 126 pairs:
    3310 0.200) 
    3311  
    3312 Matchmaker design_start.pdb, chain G (#5) with
    3313 231023_poly310-DH270UCA3_refine_001.pdb, chain H (#1), sequence alignment
    3314 score = 638.8 
    3315 RMSD between 125 pruned atom pairs is 0.800 angstroms; (across all 126 pairs:
    3316 0.817) 
    3317  
    3318 
    3319 > hide #4 models
    3320 
    3321 > show #!1 models
    3322 
    3323 > matchmaker #4,6-7#!1 to #5 & sel
    3324 
    3325 Parameters 
    3326 --- 
    3327 Chain pairing | bb 
    3328 Alignment algorithm | Needleman-Wunsch 
    3329 Similarity matrix | BLOSUM-62 
    3330 SS fraction | 0.3 
    3331 Gap open (HH/SS/other) | 18/18/6 
    3332 Gap extend | 1 
    3333 SS matrix |  |  | H | S | O 
    3334 ---|---|---|--- 
    3335 H | 6 | -9 | -6 
    3336 S |  | 6 | -6 
    3337 O |  |  | 4 
    3338 Iteration cutoff | 2 
    3339  
    3340 Matchmaker design_start.pdb, chain G (#5) with Cluster2c_lib1.pdb, chain G
    3341 (#4), sequence alignment score = 665.8 
    3342 RMSD between 126 pruned atom pairs is 0.098 angstroms; (across all 126 pairs:
    3343 0.098) 
    3344  
    3345 Matchmaker design_start.pdb, chain G (#5) with RMSD4_NNK1.pdb, chain G (#6),
    3346 sequence alignment score = 665.8 
    3347 RMSD between 126 pruned atom pairs is 0.168 angstroms; (across all 126 pairs:
    3348 0.168) 
    3349  
    3350 Matchmaker design_start.pdb, chain G (#5) with RMSD6_NNK1.pdb, chain G (#7),
    3351 sequence alignment score = 665.8 
    3352 RMSD between 126 pruned atom pairs is 0.200 angstroms; (across all 126 pairs:
    3353 0.200) 
    3354  
    3355 Matchmaker design_start.pdb, chain G (#5) with
    3356 231023_poly310-DH270UCA3_refine_001.pdb, chain H (#1), sequence alignment
    3357 score = 638.8 
    3358 RMSD between 125 pruned atom pairs is 0.800 angstroms; (across all 126 pairs:
    3359 0.817) 
    3360  
    3361 
    3362 > matchmaker #4,6-7#!1 to #5 & sel
    3363 
    3364 Parameters 
    3365 --- 
    3366 Chain pairing | bb 
    3367 Alignment algorithm | Needleman-Wunsch 
    3368 Similarity matrix | BLOSUM-62 
    3369 SS fraction | 0.3 
    3370 Gap open (HH/SS/other) | 18/18/6 
    3371 Gap extend | 1 
    3372 SS matrix |  |  | H | S | O 
    3373 ---|---|---|--- 
    3374 H | 6 | -9 | -6 
    3375 S |  | 6 | -6 
    3376 O |  |  | 4 
    3377 Iteration cutoff | 2 
    3378  
    3379 Matchmaker design_start.pdb, chain G (#5) with Cluster2c_lib1.pdb, chain G
    3380 (#4), sequence alignment score = 665.8 
    3381 RMSD between 126 pruned atom pairs is 0.098 angstroms; (across all 126 pairs:
    3382 0.098) 
    3383  
    3384 Matchmaker design_start.pdb, chain G (#5) with RMSD4_NNK1.pdb, chain G (#6),
    3385 sequence alignment score = 665.8 
    3386 RMSD between 126 pruned atom pairs is 0.168 angstroms; (across all 126 pairs:
    3387 0.168) 
    3388  
    3389 Matchmaker design_start.pdb, chain G (#5) with RMSD6_NNK1.pdb, chain G (#7),
    3390 sequence alignment score = 665.8 
    3391 RMSD between 126 pruned atom pairs is 0.200 angstroms; (across all 126 pairs:
    3392 0.200) 
    3393  
    3394 Matchmaker design_start.pdb, chain G (#5) with
    3395 231023_poly310-DH270UCA3_refine_001.pdb, chain H (#1), sequence alignment
    3396 score = 638.8 
    3397 RMSD between 125 pruned atom pairs is 0.800 angstroms; (across all 126 pairs:
    3398 0.817) 
    3399  
    3400 
    3401 > hide #5 models
    3402 
    3403 > select #1/L:106
    3404 
    3405 6 atoms, 5 bonds, 1 residue, 1 model selected 
    3406 
    3407 > select add #1/H:112C
    3408 
    3409 12 atoms, 10 bonds, 2 residues, 1 model selected 
    3410 
    3411 > select add #1/H:110
    3412 
    3413 20 atoms, 17 bonds, 3 residues, 1 model selected 
    3414 
    3415 > select add #1/H:59
    3416 
    3417 28 atoms, 24 bonds, 4 residues, 1 model selected 
    3418 
    3419 > select add #1/H:35
    3420 
    3421 35 atoms, 30 bonds, 5 residues, 1 model selected 
    3422 
    3423 > select up
    3424 
    3425 307 atoms, 318 bonds, 39 residues, 1 model selected 
    3426 
    3427 > select up
    3428 
    3429 3334 atoms, 3411 bonds, 444 residues, 1 model selected 
    3430 
    3431 > select down
    3432 
    3433 307 atoms, 318 bonds, 39 residues, 1 model selected 
    3434 
    3435 > select add #1/H:38
    3436 
    3437 319 atoms, 330 bonds, 40 residues, 1 model selected 
    3438 
    3439 > select up
    3440 
    3441 331 atoms, 344 bonds, 41 residues, 1 model selected 
    3442 
    3443 > select add #1/H:40
    3444 
    3445 341 atoms, 354 bonds, 42 residues, 1 model selected 
    3446 
    3447 > select add #1/H:67
    3448 
    3449 353 atoms, 366 bonds, 43 residues, 1 model selected 
    3450 
    3451 > select up
    3452 
    3453 417 atoms, 434 bonds, 50 residues, 1 model selected 
    3454 
    3455 > show #5 models
    3456 
    3457 > matchmaker #!1 & sel to #5 & sel
    3458 
    3459 No 'to' model specified 
    3460 
    3461 > matchmaker #!1 & sel to #5 & sel
    3462 
    3463 No 'to' model specified 
    3464 
    3465 > matchmaker #!1 & sel to #5 & sel
    3466 
    3467 No 'to' model specified 
    3468 
    3469 > matchmaker #!1 & sel to #5
    3470 
    3471 Parameters 
    3472 --- 
    3473 Chain pairing | bb 
    3474 Alignment algorithm | Needleman-Wunsch 
    3475 Similarity matrix | BLOSUM-62 
    3476 SS fraction | 0.3 
    3477 Gap open (HH/SS/other) | 18/18/6 
    3478 Gap extend | 1 
    3479 SS matrix |  |  | H | S | O 
    3480 ---|---|---|--- 
    3481 H | 6 | -9 | -6 
    3482 S |  | 6 | -6 
    3483 O |  |  | 4 
    3484 Iteration cutoff | 2 
    3485  
    3486 Matchmaker design_start.pdb, chain G (#5) with
    3487 231023_poly310-DH270UCA3_refine_001.pdb, chain H (#1), sequence alignment
    3488 score = 227.4 
    3489 RMSD between 42 pruned atom pairs is 0.783 angstroms; (across all 42 pairs:
    3490 0.783) 
    3491  
    3492 
    3493 > select add #5/G:109
    3494 
    3495 428 atoms, 444 bonds, 51 residues, 2 models selected 
    3496 
    3497 > select up
    3498 
    3499 744 atoms, 770 bonds, 72 residues, 2 models selected 
    3500 
    3501 > select add #5/G:72
    3502 
    3503 768 atoms, 793 bonds, 73 residues, 2 models selected 
    3504 
    3505 > select up
    3506 
    3507 841 atoms, 866 bonds, 78 residues, 2 models selected 
    3508 
    3509 > select up
    3510 
    3511 5259 atoms, 5364 bonds, 570 residues, 2 models selected 
    3512 
    3513 > select down
    3514 
    3515 841 atoms, 866 bonds, 78 residues, 2 models selected 
    3516 
    3517 > select add #5/G:80
    3518 
    3519 862 atoms, 887 bonds, 79 residues, 2 models selected 
    3520 
    3521 > select up
    3522 
    3523 937 atoms, 962 bonds, 84 residues, 2 models selected 
    3524 
    3525 > select add #5/G:75
    3526 
    3527 948 atoms, 972 bonds, 85 residues, 2 models selected 
    3528 
    3529 > select up
    3530 
    3531 992 atoms, 1018 bonds, 88 residues, 2 models selected 
    3532 
    3533 > matchmaker #!1 & sel to #5
    3534 
    3535 Parameters 
    3536 --- 
    3537 Chain pairing | bb 
    3538 Alignment algorithm | Needleman-Wunsch 
    3539 Similarity matrix | BLOSUM-62 
    3540 SS fraction | 0.3 
    3541 Gap open (HH/SS/other) | 18/18/6 
    3542 Gap extend | 1 
    3543 SS matrix |  |  | H | S | O 
    3544 ---|---|---|--- 
    3545 H | 6 | -9 | -6 
    3546 S |  | 6 | -6 
    3547 O |  |  | 4 
    3548 Iteration cutoff | 2 
    3549  
    3550 Matchmaker design_start.pdb, chain G (#5) with
    3551 231023_poly310-DH270UCA3_refine_001.pdb, chain H (#1), sequence alignment
    3552 score = 227.4 
    3553 RMSD between 42 pruned atom pairs is 0.783 angstroms; (across all 42 pairs:
    3554 0.783) 
    3555  
    3556 
    3557 > select add #5/G:56
    3558 
    3559 999 atoms, 1024 bonds, 89 residues, 2 models selected 
    3560 
    3561 > select subtract #5/G:56
    3562 
    3563 992 atoms, 1018 bonds, 88 residues, 2 models selected 
    3564 
    3565 > select clear
    3566 
    3567 > select #1/H:111C
    3568 
    3569 12 atoms, 12 bonds, 1 residue, 1 model selected 
    3570 
    3571 > select add #5/G:102
    3572 
    3573 31 atoms, 30 bonds, 2 residues, 2 models selected 
    3574 
    3575 > select up
    3576 
    3577 508 atoms, 526 bonds, 44 residues, 2 models selected 
    3578 
    3579 > matchmaker #!1 & sel to #5 & sel
    3580 
    3581 Parameters 
    3582 --- 
    3583 Chain pairing | bb 
    3584 Alignment algorithm | Needleman-Wunsch 
    3585 Similarity matrix | BLOSUM-62 
    3586 SS fraction | 0.3 
    3587 Gap open (HH/SS/other) | 18/18/6 
    3588 Gap extend | 1 
    3589 SS matrix |  |  | H | S | O 
    3590 ---|---|---|--- 
    3591 H | 6 | -9 | -6 
    3592 S |  | 6 | -6 
    3593 O |  |  | 4 
    3594 Iteration cutoff | 2 
    3595  
    3596 Matchmaker design_start.pdb, chain G (#5) with
    3597 231023_poly310-DH270UCA3_refine_001.pdb, chain H (#1), sequence alignment
    3598 score = 121.6 
    3599 RMSD between 22 pruned atom pairs is 0.765 angstroms; (across all 22 pairs:
    3600 0.765) 
    3601  
    3602 
    3603 > matchmaker #!1 & sel to #5 & sel
    3604 
    3605 Parameters 
    3606 --- 
    3607 Chain pairing | bb 
    3608 Alignment algorithm | Needleman-Wunsch 
    3609 Similarity matrix | BLOSUM-62 
    3610 SS fraction | 0.3 
    3611 Gap open (HH/SS/other) | 18/18/6 
    3612 Gap extend | 1 
    3613 SS matrix |  |  | H | S | O 
    3614 ---|---|---|--- 
    3615 H | 6 | -9 | -6 
    3616 S |  | 6 | -6 
    3617 O |  |  | 4 
    3618 Iteration cutoff | 2 
    3619  
    3620 Matchmaker design_start.pdb, chain G (#5) with
    3621 231023_poly310-DH270UCA3_refine_001.pdb, chain H (#1), sequence alignment
    3622 score = 121.6 
    3623 RMSD between 22 pruned atom pairs is 0.765 angstroms; (across all 22 pairs:
    3624 0.765) 
    3625  
    3626 Desktop color scheme is dark 
    3627 Traceback (most recent call last): 
    3628 File
    3629 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3630 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    3631 self.status(self._last_message, self._last_color) 
    3632 File
    3633 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3634 packages/chimerax/ui/statusbar.py", line 164, in status 
    3635 r.draw_background() 
    3636 File
    3637 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3638 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    3639 GL.glClear(flags) 
    3640 File "src/errorchecker.pyx", line 59, in
    3641 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3642 OpenGL.error.GLError: GLError( 
    3643 err = 1286, 
    3644 description = b'invalid framebuffer operation', 
    3645 baseOperation = glClear, 
    3646 cArguments = (16640,) 
    3647 ) 
    3648  
    3649 
    3650 Window position QRect(2345,363 600x300) outside any known screen, using
    3651 primary screen 
    3652 
    3653 OpenGL.error.GLError: GLError( 
    3654 err = 1286, 
    3655 description = b'invalid framebuffer operation', 
    3656 baseOperation = glClear, 
    3657 cArguments = (16640,) 
    3658 ) 
    3659  
    3660 File "src/errorchecker.pyx", line 59, in
    3661 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3662  
    3663 See log for complete Python traceback. 
    3664  
    3665 Traceback (most recent call last): 
    3666 File
    3667 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3668 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    3669 self.status(self._last_message, self._last_color) 
    3670 File
    3671 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3672 packages/chimerax/ui/statusbar.py", line 164, in status 
    3673 r.draw_background() 
    3674 File
    3675 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3676 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    3677 GL.glClear(flags) 
    3678 File "src/errorchecker.pyx", line 59, in
    3679 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3680 OpenGL.error.GLError: GLError( 
    3681 err = 1286, 
    3682 description = b'invalid framebuffer operation', 
    3683 baseOperation = glClear, 
    3684 cArguments = (16640,) 
    3685 ) 
    3686  
    3687 OpenGL.error.GLError: GLError( 
    3688 err = 1286, 
    3689 description = b'invalid framebuffer operation', 
    3690 baseOperation = glClear, 
    3691 cArguments = (16640,) 
    3692 ) 
    3693  
    3694 File "src/errorchecker.pyx", line 59, in
    3695 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3696  
    3697 See log for complete Python traceback. 
    3698  
    3699 Traceback (most recent call last): 
    3700 File
    3701 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3702 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    3703 self.status(self._last_message, self._last_color) 
    3704 File
    3705 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3706 packages/chimerax/ui/statusbar.py", line 164, in status 
    3707 r.draw_background() 
    3708 File
    3709 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3710 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    3711 GL.glClear(flags) 
    3712 File "src/errorchecker.pyx", line 59, in
    3713 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3714 OpenGL.error.GLError: GLError( 
    3715 err = 1286, 
    3716 description = b'invalid framebuffer operation', 
    3717 baseOperation = glClear, 
    3718 cArguments = (16640,) 
    3719 ) 
    3720  
    3721 OpenGL.error.GLError: GLError( 
    3722 err = 1286, 
    3723 description = b'invalid framebuffer operation', 
    3724 baseOperation = glClear, 
    3725 cArguments = (16640,) 
    3726 ) 
    3727  
    3728 File "src/errorchecker.pyx", line 59, in
    3729 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3730  
    3731 See log for complete Python traceback. 
    3732  
    3733 Traceback (most recent call last): 
    3734 File
    3735 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3736 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    3737 self.status(self._last_message, self._last_color) 
    3738 File
    3739 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3740 packages/chimerax/ui/statusbar.py", line 164, in status 
    3741 r.draw_background() 
    3742 File
    3743 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3744 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    3745 GL.glClear(flags) 
    3746 File "src/errorchecker.pyx", line 59, in
    3747 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3748 OpenGL.error.GLError: GLError( 
    3749 err = 1286, 
    3750 description = b'invalid framebuffer operation', 
    3751 baseOperation = glClear, 
    3752 cArguments = (16640,) 
    3753 ) 
    3754  
    3755 OpenGL.error.GLError: GLError( 
    3756 err = 1286, 
    3757 description = b'invalid framebuffer operation', 
    3758 baseOperation = glClear, 
    3759 cArguments = (16640,) 
    3760 ) 
    3761  
    3762 File "src/errorchecker.pyx", line 59, in
    3763 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3764  
    3765 See log for complete Python traceback. 
    3766  
    3767 Traceback (most recent call last): 
    3768 File
    3769 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3770 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    3771 self.status(self._last_message, self._last_color) 
    3772 File
    3773 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3774 packages/chimerax/ui/statusbar.py", line 164, in status 
    3775 r.draw_background() 
    3776 File
    3777 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3778 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    3779 GL.glClear(flags) 
    3780 File "src/errorchecker.pyx", line 59, in
    3781 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3782 OpenGL.error.GLError: GLError( 
    3783 err = 1286, 
    3784 description = b'invalid framebuffer operation', 
    3785 baseOperation = glClear, 
    3786 cArguments = (16640,) 
    3787 ) 
    3788  
    3789 OpenGL.error.GLError: GLError( 
    3790 err = 1286, 
    3791 description = b'invalid framebuffer operation', 
    3792 baseOperation = glClear, 
    3793 cArguments = (16640,) 
    3794 ) 
    3795  
    3796 File "src/errorchecker.pyx", line 59, in
    3797 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3798  
    3799 See log for complete Python traceback. 
    3800  
    3801 Traceback (most recent call last): 
    3802 File
    3803 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3804 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    3805 self.status(self._last_message, self._last_color) 
    3806 File
    3807 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3808 packages/chimerax/ui/statusbar.py", line 164, in status 
    3809 r.draw_background() 
    3810 File
    3811 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3812 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    3813 GL.glClear(flags) 
    3814 File "src/errorchecker.pyx", line 59, in
    3815 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3816 OpenGL.error.GLError: GLError( 
    3817 err = 1286, 
    3818 description = b'invalid framebuffer operation', 
    3819 baseOperation = glClear, 
    3820 cArguments = (16640,) 
    3821 ) 
    3822  
    3823 OpenGL.error.GLError: GLError( 
    3824 err = 1286, 
    3825 description = b'invalid framebuffer operation', 
    3826 baseOperation = glClear, 
    3827 cArguments = (16640,) 
    3828 ) 
    3829  
    3830 File "src/errorchecker.pyx", line 59, in
    3831 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3832  
    3833 See log for complete Python traceback. 
    3834  
    3835 Traceback (most recent call last): 
    3836 File
    3837 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3838 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    3839 self.status(self._last_message, self._last_color) 
    3840 File
    3841 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3842 packages/chimerax/ui/statusbar.py", line 164, in status 
    3843 r.draw_background() 
    3844 File
    3845 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3846 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    3847 GL.glClear(flags) 
    3848 File "src/errorchecker.pyx", line 59, in
    3849 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3850 OpenGL.error.GLError: GLError( 
    3851 err = 1286, 
    3852 description = b'invalid framebuffer operation', 
    3853 baseOperation = glClear, 
    3854 cArguments = (16640,) 
    3855 ) 
    3856  
    3857 OpenGL.error.GLError: GLError( 
    3858 err = 1286, 
    3859 description = b'invalid framebuffer operation', 
    3860 baseOperation = glClear, 
    3861 cArguments = (16640,) 
    3862 ) 
    3863  
    3864 File "src/errorchecker.pyx", line 59, in
    3865 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3866  
    3867 See log for complete Python traceback. 
    3868  
    3869 Traceback (most recent call last): 
    3870 File
    3871 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3872 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    3873 self.status(self._last_message, self._last_color) 
    3874 File
    3875 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3876 packages/chimerax/ui/statusbar.py", line 164, in status 
    3877 r.draw_background() 
    3878 File
    3879 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3880 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    3881 GL.glClear(flags) 
    3882 File "src/errorchecker.pyx", line 59, in
    3883 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3884 OpenGL.error.GLError: GLError( 
    3885 err = 1286, 
    3886 description = b'invalid framebuffer operation', 
    3887 baseOperation = glClear, 
    3888 cArguments = (16640,) 
    3889 ) 
    3890  
    3891 OpenGL.error.GLError: GLError( 
    3892 err = 1286, 
    3893 description = b'invalid framebuffer operation', 
    3894 baseOperation = glClear, 
    3895 cArguments = (16640,) 
    3896 ) 
    3897  
    3898 File "src/errorchecker.pyx", line 59, in
    3899 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3900  
    3901 See log for complete Python traceback. 
    3902  
    3903 Desktop color scheme is light 
    3904 Traceback (most recent call last): 
    3905 File
    3906 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3907 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    3908 self.status(self._last_message, self._last_color) 
    3909 File
    3910 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3911 packages/chimerax/ui/statusbar.py", line 164, in status 
    3912 r.draw_background() 
    3913 File
    3914 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3915 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    3916 GL.glClear(flags) 
    3917 File "src/errorchecker.pyx", line 59, in
    3918 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3919 OpenGL.error.GLError: GLError( 
    3920 err = 1286, 
    3921 description = b'invalid framebuffer operation', 
    3922 baseOperation = glClear, 
    3923 cArguments = (16640,) 
    3924 ) 
    3925  
    3926 OpenGL.error.GLError: GLError( 
    3927 err = 1286, 
    3928 description = b'invalid framebuffer operation', 
    3929 baseOperation = glClear, 
    3930 cArguments = (16640,) 
    3931 ) 
    3932  
    3933 File "src/errorchecker.pyx", line 59, in
    3934 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3935  
    3936 See log for complete Python traceback. 
    3937  
    3938 Traceback (most recent call last): 
    3939 File
    3940 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3941 packages/chimerax/ui/gui.py", line 873, in customEvent 
    3942 func(*args, **kw) 
    3943 File
    3944 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3945 packages/chimerax/core/logger.py", line 522, in status 
    3946 StatusLogger.status(self, msg, **kw) 
    3947 File
    3948 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3949 packages/chimerax/core/logger.py", line 220, in status 
    3950 if l.status(msg, color, secondary) and getattr( 
    3951 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    3952 File
    3953 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3954 packages/chimerax/ui/gui.py", line 1085, in status 
    3955 sbar.status(msg, color, secondary) 
    3956 File
    3957 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3958 packages/chimerax/ui/statusbar.py", line 164, in status 
    3959 r.draw_background() 
    3960 File
    3961 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3962 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    3963 GL.glClear(flags) 
    3964 File "src/errorchecker.pyx", line 59, in
    3965 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3966 OpenGL.error.GLError: GLError( 
    3967 err = 1286, 
    3968 description = b'invalid framebuffer operation', 
    3969 baseOperation = glClear, 
    3970 cArguments = (16640,) 
    3971 ) 
    3972  
    3973 OpenGL.error.GLError: GLError( 
    3974 err = 1286, 
    3975 description = b'invalid framebuffer operation', 
    3976 baseOperation = glClear, 
    3977 cArguments = (16640,) 
    3978 ) 
    3979  
    3980 File "src/errorchecker.pyx", line 59, in
    3981 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    3982  
    3983 See log for complete Python traceback. 
    3984  
    3985 Traceback (most recent call last): 
    3986 File
    3987 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3988 packages/chimerax/ui/gui.py", line 172, in _update_color_scheme 
    3989 self.session.logger.status(msg) 
    3990 File
    3991 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3992 packages/chimerax/core/logger.py", line 522, in status 
    3993 StatusLogger.status(self, msg, **kw) 
    3994 File
    3995 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    3996 packages/chimerax/core/logger.py", line 220, in status 
    3997 if l.status(msg, color, secondary) and getattr( 
    3998 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    3999 File
    4000 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4001 packages/chimerax/ui/gui.py", line 1085, in status 
    4002 sbar.status(msg, color, secondary) 
    4003 File
    4004 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4005 packages/chimerax/ui/statusbar.py", line 164, in status 
    4006 r.draw_background() 
    4007 File
    4008 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4009 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    4010 GL.glClear(flags) 
    4011 File "src/errorchecker.pyx", line 59, in
    4012 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4013 OpenGL.error.GLError: GLError( 
    4014 err = 1286, 
    4015 description = b'invalid framebuffer operation', 
    4016 baseOperation = glClear, 
    4017 cArguments = (16640,) 
    4018 ) 
    4019  
    4020 OpenGL.error.GLError: GLError( 
    4021 err = 1286, 
    4022 description = b'invalid framebuffer operation', 
    4023 baseOperation = glClear, 
    4024 cArguments = (16640,) 
    4025 ) 
    4026  
    4027 File "src/errorchecker.pyx", line 59, in
    4028 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4029  
    4030 See log for complete Python traceback. 
    4031  
    4032 Traceback (most recent call last): 
    4033 File
    4034 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4035 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    4036 self.status(self._last_message, self._last_color) 
    4037 File
    4038 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4039 packages/chimerax/ui/statusbar.py", line 164, in status 
    4040 r.draw_background() 
    4041 File
    4042 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4043 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    4044 GL.glClear(flags) 
    4045 File "src/errorchecker.pyx", line 59, in
    4046 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4047 OpenGL.error.GLError: GLError( 
    4048 err = 1286, 
    4049 description = b'invalid framebuffer operation', 
    4050 baseOperation = glClear, 
    4051 cArguments = (16640,) 
    4052 ) 
    4053  
    4054 OpenGL.error.GLError: GLError( 
    4055 err = 1286, 
    4056 description = b'invalid framebuffer operation', 
    4057 baseOperation = glClear, 
    4058 cArguments = (16640,) 
    4059 ) 
    4060  
    4061 File "src/errorchecker.pyx", line 59, in
    4062 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4063  
    4064 See log for complete Python traceback. 
    4065  
    4066 Traceback (most recent call last): 
    4067 File
    4068 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4069 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    4070 self.status(self._last_message, self._last_color) 
    4071 File
    4072 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4073 packages/chimerax/ui/statusbar.py", line 164, in status 
    4074 r.draw_background() 
    4075 File
    4076 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4077 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    4078 GL.glClear(flags) 
    4079 File "src/errorchecker.pyx", line 59, in
    4080 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4081 OpenGL.error.GLError: GLError( 
    4082 err = 1286, 
    4083 description = b'invalid framebuffer operation', 
    4084 baseOperation = glClear, 
    4085 cArguments = (16640,) 
    4086 ) 
    4087  
    4088 OpenGL.error.GLError: GLError( 
    4089 err = 1286, 
    4090 description = b'invalid framebuffer operation', 
    4091 baseOperation = glClear, 
    4092 cArguments = (16640,) 
    4093 ) 
    4094  
    4095 File "src/errorchecker.pyx", line 59, in
    4096 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4097  
    4098 See log for complete Python traceback. 
    4099  
    4100 Traceback (most recent call last): 
    4101 File
    4102 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4103 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    4104 self.status(self._last_message, self._last_color) 
    4105 File
    4106 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4107 packages/chimerax/ui/statusbar.py", line 164, in status 
    4108 r.draw_background() 
    4109 File
    4110 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4111 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    4112 GL.glClear(flags) 
    4113 File "src/errorchecker.pyx", line 59, in
    4114 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4115 OpenGL.error.GLError: GLError( 
    4116 err = 1286, 
    4117 description = b'invalid framebuffer operation', 
    4118 baseOperation = glClear, 
    4119 cArguments = (16640,) 
    4120 ) 
    4121  
    4122 OpenGL.error.GLError: GLError( 
    4123 err = 1286, 
    4124 description = b'invalid framebuffer operation', 
    4125 baseOperation = glClear, 
    4126 cArguments = (16640,) 
    4127 ) 
    4128  
    4129 File "src/errorchecker.pyx", line 59, in
    4130 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4131  
    4132 See log for complete Python traceback. 
    4133  
    4134 Traceback (most recent call last): 
    4135 File
    4136 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4137 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    4138 self.status(self._last_message, self._last_color) 
    4139 File
    4140 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4141 packages/chimerax/ui/statusbar.py", line 164, in status 
    4142 r.draw_background() 
    4143 File
    4144 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4145 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    4146 GL.glClear(flags) 
    4147 File "src/errorchecker.pyx", line 59, in
    4148 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4149 OpenGL.error.GLError: GLError( 
    4150 err = 1286, 
    4151 description = b'invalid framebuffer operation', 
    4152 baseOperation = glClear, 
    4153 cArguments = (16640,) 
    4154 ) 
    4155  
    4156 OpenGL.error.GLError: GLError( 
    4157 err = 1286, 
    4158 description = b'invalid framebuffer operation', 
    4159 baseOperation = glClear, 
    4160 cArguments = (16640,) 
    4161 ) 
    4162  
    4163 File "src/errorchecker.pyx", line 59, in
    4164 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4165  
    4166 See log for complete Python traceback. 
    4167  
    4168 Traceback (most recent call last): 
    4169 File
    4170 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4171 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    4172 self.status(self._last_message, self._last_color) 
    4173 File
    4174 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4175 packages/chimerax/ui/statusbar.py", line 164, in status 
    4176 r.draw_background() 
    4177 File
    4178 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4179 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    4180 GL.glClear(flags) 
    4181 File "src/errorchecker.pyx", line 59, in
    4182 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4183 OpenGL.error.GLError: GLError( 
    4184 err = 1286, 
    4185 description = b'invalid framebuffer operation', 
    4186 baseOperation = glClear, 
    4187 cArguments = (16640,) 
    4188 ) 
    4189  
    4190 OpenGL.error.GLError: GLError( 
    4191 err = 1286, 
    4192 description = b'invalid framebuffer operation', 
    4193 baseOperation = glClear, 
    4194 cArguments = (16640,) 
    4195 ) 
    4196  
    4197 File "src/errorchecker.pyx", line 59, in
    4198 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4199  
    4200 See log for complete Python traceback. 
    4201  
    4202 Traceback (most recent call last): 
    4203 File
    4204 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4205 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    4206 self.status(self._last_message, self._last_color) 
    4207 File
    4208 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4209 packages/chimerax/ui/statusbar.py", line 164, in status 
    4210 r.draw_background() 
    4211 File
    4212 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4213 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    4214 GL.glClear(flags) 
    4215 File "src/errorchecker.pyx", line 59, in
    4216 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4217 OpenGL.error.GLError: GLError( 
    4218 err = 1286, 
    4219 description = b'invalid framebuffer operation', 
    4220 baseOperation = glClear, 
    4221 cArguments = (16640,) 
    4222 ) 
    4223  
    4224 OpenGL.error.GLError: GLError( 
    4225 err = 1286, 
    4226 description = b'invalid framebuffer operation', 
    4227 baseOperation = glClear, 
    4228 cArguments = (16640,) 
    4229 ) 
    4230  
    4231 File "src/errorchecker.pyx", line 59, in
    4232 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4233  
    4234 See log for complete Python traceback. 
    4235  
    4236 Traceback (most recent call last): 
    4237 File
    4238 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4239 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    4240 self.status(self._last_message, self._last_color) 
    4241 File
    4242 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4243 packages/chimerax/ui/statusbar.py", line 164, in status 
    4244 r.draw_background() 
    4245 File
    4246 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4247 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    4248 GL.glClear(flags) 
    4249 File "src/errorchecker.pyx", line 59, in
    4250 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4251 OpenGL.error.GLError: GLError( 
    4252 err = 1286, 
    4253 description = b'invalid framebuffer operation', 
    4254 baseOperation = glClear, 
    4255 cArguments = (16640,) 
    4256 ) 
    4257  
    4258 OpenGL.error.GLError: GLError( 
    4259 err = 1286, 
    4260 description = b'invalid framebuffer operation', 
    4261 baseOperation = glClear, 
    4262 cArguments = (16640,) 
    4263 ) 
    4264  
    4265 File "src/errorchecker.pyx", line 59, in
    4266 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4267  
    4268 See log for complete Python traceback. 
    4269  
    4270 Traceback (most recent call last): 
    4271 File
    4272 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4273 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    4274 self.status(self._last_message, self._last_color) 
    4275 File
    4276 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4277 packages/chimerax/ui/statusbar.py", line 164, in status 
    4278 r.draw_background() 
    4279 File
    4280 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4281 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    4282 GL.glClear(flags) 
    4283 File "src/errorchecker.pyx", line 59, in
    4284 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4285 OpenGL.error.GLError: GLError( 
    4286 err = 1286, 
    4287 description = b'invalid framebuffer operation', 
    4288 baseOperation = glClear, 
    4289 cArguments = (16640,) 
    4290 ) 
    4291  
    4292 OpenGL.error.GLError: GLError( 
    4293 err = 1286, 
    4294 description = b'invalid framebuffer operation', 
    4295 baseOperation = glClear, 
    4296 cArguments = (16640,) 
    4297 ) 
    4298  
    4299 File "src/errorchecker.pyx", line 59, in
    4300 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4301  
    4302 See log for complete Python traceback. 
    4303  
    4304 Traceback (most recent call last): 
    4305 File
    4306 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4307 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    4308 self.status(self._last_message, self._last_color) 
    4309 File
    4310 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4311 packages/chimerax/ui/statusbar.py", line 164, in status 
    4312 r.draw_background() 
    4313 File
    4314 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4315 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    4316 GL.glClear(flags) 
    4317 File "src/errorchecker.pyx", line 59, in
    4318 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4319 OpenGL.error.GLError: GLError( 
    4320 err = 1286, 
    4321 description = b'invalid framebuffer operation', 
    4322 baseOperation = glClear, 
    4323 cArguments = (16640,) 
    4324 ) 
    4325  
    4326 OpenGL.error.GLError: GLError( 
    4327 err = 1286, 
    4328 description = b'invalid framebuffer operation', 
    4329 baseOperation = glClear, 
    4330 cArguments = (16640,) 
    4331 ) 
    4332  
    4333 File "src/errorchecker.pyx", line 59, in
    4334 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4335  
    4336 See log for complete Python traceback. 
    4337  
    4338 Traceback (most recent call last): 
    4339 File
    4340 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4341 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    4342 self.status(self._last_message, self._last_color) 
    4343 File
    4344 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4345 packages/chimerax/ui/statusbar.py", line 164, in status 
    4346 r.draw_background() 
    4347 File
    4348 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4349 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    4350 GL.glClear(flags) 
    4351 File "src/errorchecker.pyx", line 59, in
    4352 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4353 OpenGL.error.GLError: GLError( 
    4354 err = 1286, 
    4355 description = b'invalid framebuffer operation', 
    4356 baseOperation = glClear, 
    4357 cArguments = (16640,) 
    4358 ) 
    4359  
    4360 OpenGL.error.GLError: GLError( 
    4361 err = 1286, 
    4362 description = b'invalid framebuffer operation', 
    4363 baseOperation = glClear, 
    4364 cArguments = (16640,) 
    4365 ) 
    4366  
    4367 File "src/errorchecker.pyx", line 59, in
    4368 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4369  
    4370 See log for complete Python traceback. 
    4371  
    4372 Traceback (most recent call last): 
    4373 File
    4374 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4375 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    4376 self.status(self._last_message, self._last_color) 
    4377 File
    4378 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4379 packages/chimerax/ui/statusbar.py", line 164, in status 
    4380 r.draw_background() 
    4381 File
    4382 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4383 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    4384 GL.glClear(flags) 
    4385 File "src/errorchecker.pyx", line 59, in
    4386 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4387 OpenGL.error.GLError: GLError( 
    4388 err = 1286, 
    4389 description = b'invalid framebuffer operation', 
    4390 baseOperation = glClear, 
    4391 cArguments = (16640,) 
    4392 ) 
    4393  
    4394 OpenGL.error.GLError: GLError( 
    4395 err = 1286, 
    4396 description = b'invalid framebuffer operation', 
    4397 baseOperation = glClear, 
    4398 cArguments = (16640,) 
    4399 ) 
    4400  
    4401 File "src/errorchecker.pyx", line 59, in
    4402 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4403  
    4404 See log for complete Python traceback. 
    4405  
    4406 Traceback (most recent call last): 
    4407 File
    4408 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4409 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    4410 self.status(self._last_message, self._last_color) 
    4411 File
    4412 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4413 packages/chimerax/ui/statusbar.py", line 164, in status 
    4414 r.draw_background() 
    4415 File
    4416 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4417 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    4418 GL.glClear(flags) 
    4419 File "src/errorchecker.pyx", line 59, in
    4420 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4421 OpenGL.error.GLError: GLError( 
    4422 err = 1286, 
    4423 description = b'invalid framebuffer operation', 
    4424 baseOperation = glClear, 
    4425 cArguments = (16640,) 
    4426 ) 
    4427  
    4428 OpenGL.error.GLError: GLError( 
    4429 err = 1286, 
    4430 description = b'invalid framebuffer operation', 
    4431 baseOperation = glClear, 
    4432 cArguments = (16640,) 
    4433 ) 
    4434  
    4435 File "src/errorchecker.pyx", line 59, in
    4436 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4437  
    4438 See log for complete Python traceback. 
    4439  
    4440 Desktop color scheme is light 
    4441 Traceback (most recent call last): 
    4442 File
    4443 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4444 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    4445 self.status(self._last_message, self._last_color) 
    4446 File
    4447 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4448 packages/chimerax/ui/statusbar.py", line 164, in status 
    4449 r.draw_background() 
    4450 File
    4451 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4452 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    4453 GL.glClear(flags) 
    4454 File "src/errorchecker.pyx", line 59, in
    4455 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4456 OpenGL.error.GLError: GLError( 
    4457 err = 1286, 
    4458 description = b'invalid framebuffer operation', 
    4459 baseOperation = glClear, 
    4460 cArguments = (16640,) 
    4461 ) 
    4462  
    4463 OpenGL.error.GLError: GLError( 
    4464 err = 1286, 
    4465 description = b'invalid framebuffer operation', 
    4466 baseOperation = glClear, 
    4467 cArguments = (16640,) 
    4468 ) 
    4469  
    4470 File "src/errorchecker.pyx", line 59, in
    4471 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4472  
    4473 See log for complete Python traceback. 
    4474  
    4475 Traceback (most recent call last): 
    4476 File
    4477 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4478 packages/chimerax/ui/gui.py", line 873, in customEvent 
    4479 func(*args, **kw) 
    4480 File
    4481 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4482 packages/chimerax/core/logger.py", line 522, in status 
    4483 StatusLogger.status(self, msg, **kw) 
    4484 File
    4485 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4486 packages/chimerax/core/logger.py", line 220, in status 
    4487 if l.status(msg, color, secondary) and getattr( 
    4488 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    4489 File
    4490 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4491 packages/chimerax/ui/gui.py", line 1085, in status 
    4492 sbar.status(msg, color, secondary) 
    4493 File
    4494 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4495 packages/chimerax/ui/statusbar.py", line 164, in status 
    4496 r.draw_background() 
    4497 File
    4498 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4499 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    4500 GL.glClear(flags) 
    4501 File "src/errorchecker.pyx", line 59, in
    4502 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4503 OpenGL.error.GLError: GLError( 
    4504 err = 1286, 
    4505 description = b'invalid framebuffer operation', 
    4506 baseOperation = glClear, 
    4507 cArguments = (16640,) 
    4508 ) 
    4509  
    4510 OpenGL.error.GLError: GLError( 
    4511 err = 1286, 
    4512 description = b'invalid framebuffer operation', 
    4513 baseOperation = glClear, 
    4514 cArguments = (16640,) 
    4515 ) 
    4516  
    4517 File "src/errorchecker.pyx", line 59, in
    4518 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4519  
    4520 See log for complete Python traceback. 
    4521  
    4522 Traceback (most recent call last): 
    4523 File
    4524 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4525 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    4526 self.status(self._last_message, self._last_color) 
    4527 File
    4528 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4529 packages/chimerax/ui/statusbar.py", line 164, in status 
    4530 r.draw_background() 
    4531 File
    4532 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4533 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    4534 GL.glClear(flags) 
    4535 File "src/errorchecker.pyx", line 59, in
    4536 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4537 OpenGL.error.GLError: GLError( 
    4538 err = 1286, 
    4539 description = b'invalid framebuffer operation', 
    4540 baseOperation = glClear, 
    4541 cArguments = (16640,) 
    4542 ) 
    4543  
    4544 OpenGL.error.GLError: GLError( 
    4545 err = 1286, 
    4546 description = b'invalid framebuffer operation', 
    4547 baseOperation = glClear, 
    4548 cArguments = (16640,) 
    4549 ) 
    4550  
    4551 File "src/errorchecker.pyx", line 59, in
    4552 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4553  
    4554 See log for complete Python traceback. 
    4555  
    4556 Traceback (most recent call last): 
    4557 File
    4558 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4559 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    4560 self.status(self._last_message, self._last_color) 
    4561 File
    4562 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4563 packages/chimerax/ui/statusbar.py", line 164, in status 
    4564 r.draw_background() 
    4565 File
    4566 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4567 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    4568 GL.glClear(flags) 
    4569 File "src/errorchecker.pyx", line 59, in
    4570 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4571 OpenGL.error.GLError: GLError( 
    4572 err = 1286, 
    4573 description = b'invalid framebuffer operation', 
    4574 baseOperation = glClear, 
    4575 cArguments = (16640,) 
    4576 ) 
    4577  
    4578 OpenGL.error.GLError: GLError( 
    4579 err = 1286, 
    4580 description = b'invalid framebuffer operation', 
    4581 baseOperation = glClear, 
    4582 cArguments = (16640,) 
    4583 ) 
    4584  
    4585 File "src/errorchecker.pyx", line 59, in
    4586 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4587  
    4588 See log for complete Python traceback. 
    4589  
    4590 Traceback (most recent call last): 
    4591 File
    4592 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4593 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    4594 self.status(self._last_message, self._last_color) 
    4595 File
    4596 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4597 packages/chimerax/ui/statusbar.py", line 164, in status 
    4598 r.draw_background() 
    4599 File
    4600 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4601 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    4602 GL.glClear(flags) 
    4603 File "src/errorchecker.pyx", line 59, in
    4604 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4605 OpenGL.error.GLError: GLError( 
    4606 err = 1286, 
    4607 description = b'invalid framebuffer operation', 
    4608 baseOperation = glClear, 
    4609 cArguments = (16640,) 
    4610 ) 
    4611  
    4612 OpenGL.error.GLError: GLError( 
    4613 err = 1286, 
    4614 description = b'invalid framebuffer operation', 
    4615 baseOperation = glClear, 
    4616 cArguments = (16640,) 
    4617 ) 
    4618  
    4619 File "src/errorchecker.pyx", line 59, in
    4620 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4621  
    4622 See log for complete Python traceback. 
    4623  
    4624 
    4625 > show #2 models
    4626 
    4627 > hide #!1 models
    4628 
    4629 > hide #5 models
    4630 
    4631 > select add #1
    4632 
    4633 4974 atoms, 5093 bonds, 7 pseudobonds, 630 residues, 4 models selected 
    4634 Traceback (most recent call last): 
    4635 File
    4636 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4637 packages/chimerax/model_panel/tool.py", line 475, in _tree_change_cb 
    4638 run(self.session, "select " + mode + " #" + model.id_string) 
    4639 File
    4640 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4641 packages/chimerax/core/commands/run.py", line 49, in run 
    4642 results = command.run(text, log=log, return_json=return_json) 
    4643 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    4644 File
    4645 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4646 packages/chimerax/core/commands/cli.py", line 3221, in run 
    4647 result = ci.function(session, **kw_args) 
    4648 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    4649 File
    4650 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4651 packages/chimerax/std_commands/select.py", line 120, in select_add 
    4652 report_selection(session) 
    4653 File
    4654 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4655 packages/chimerax/std_commands/select.py", line 192, in report_selection 
    4656 session.logger.status(', '.join(lines) + ' selected', log = True) 
    4657 File
    4658 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4659 packages/chimerax/core/logger.py", line 522, in status 
    4660 StatusLogger.status(self, msg, **kw) 
    4661 File
    4662 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4663 packages/chimerax/core/logger.py", line 220, in status 
    4664 if l.status(msg, color, secondary) and getattr( 
    4665 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    4666 File
    4667 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4668 packages/chimerax/ui/gui.py", line 1085, in status 
    4669 sbar.status(msg, color, secondary) 
    4670 File
    4671 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4672 packages/chimerax/ui/statusbar.py", line 164, in status 
    4673 r.draw_background() 
    4674 File
    4675 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4676 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    4677 GL.glClear(flags) 
    4678 File "src/errorchecker.pyx", line 59, in
    4679 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4680 OpenGL.error.GLError: GLError( 
    4681 err = 1286, 
    4682 description = b'invalid framebuffer operation', 
    4683 baseOperation = glClear, 
    4684 cArguments = (16640,) 
    4685 ) 
    4686  
    4687 OpenGL.error.GLError: GLError( 
    4688 err = 1286, 
    4689 description = b'invalid framebuffer operation', 
    4690 baseOperation = glClear, 
    4691 cArguments = (16640,) 
    4692 ) 
    4693  
    4694 File "src/errorchecker.pyx", line 59, in
    4695 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4696  
    4697 See log for complete Python traceback. 
    4698  
    4699 
    4700 > select add #5
    4701 
    4702 10986 atoms, 11176 bonds, 7 pseudobonds, 1018 residues, 4 models selected 
    4703 Traceback (most recent call last): 
    4704 File
    4705 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4706 packages/chimerax/model_panel/tool.py", line 475, in _tree_change_cb 
    4707 run(self.session, "select " + mode + " #" + model.id_string) 
    4708 File
    4709 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4710 packages/chimerax/core/commands/run.py", line 49, in run 
    4711 results = command.run(text, log=log, return_json=return_json) 
    4712 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    4713 File
    4714 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4715 packages/chimerax/core/commands/cli.py", line 3221, in run 
    4716 result = ci.function(session, **kw_args) 
    4717 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    4718 File
    4719 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4720 packages/chimerax/std_commands/select.py", line 120, in select_add 
    4721 report_selection(session) 
    4722 File
    4723 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4724 packages/chimerax/std_commands/select.py", line 192, in report_selection 
    4725 session.logger.status(', '.join(lines) + ' selected', log = True) 
    4726 File
    4727 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4728 packages/chimerax/core/logger.py", line 522, in status 
    4729 StatusLogger.status(self, msg, **kw) 
    4730 File
    4731 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4732 packages/chimerax/core/logger.py", line 220, in status 
    4733 if l.status(msg, color, secondary) and getattr( 
    4734 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    4735 File
    4736 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4737 packages/chimerax/ui/gui.py", line 1085, in status 
    4738 sbar.status(msg, color, secondary) 
    4739 File
    4740 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4741 packages/chimerax/ui/statusbar.py", line 164, in status 
    4742 r.draw_background() 
    4743 File
    4744 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4745 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    4746 GL.glClear(flags) 
    4747 File "src/errorchecker.pyx", line 59, in
    4748 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4749 OpenGL.error.GLError: GLError( 
    4750 err = 1286, 
    4751 description = b'invalid framebuffer operation', 
    4752 baseOperation = glClear, 
    4753 cArguments = (16640,) 
    4754 ) 
    4755  
    4756 OpenGL.error.GLError: GLError( 
    4757 err = 1286, 
    4758 description = b'invalid framebuffer operation', 
    4759 baseOperation = glClear, 
    4760 cArguments = (16640,) 
    4761 ) 
    4762  
    4763 File "src/errorchecker.pyx", line 59, in
    4764 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4765  
    4766 See log for complete Python traceback. 
    4767  
    4768 
    4769 > select subtract #1
    4770 
    4771 6339 atoms, 6419 bonds, 410 residues, 1 model selected 
    4772 Traceback (most recent call last): 
    4773 File
    4774 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4775 packages/chimerax/model_panel/tool.py", line 475, in _tree_change_cb 
    4776 run(self.session, "select " + mode + " #" + model.id_string) 
    4777 File
    4778 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4779 packages/chimerax/core/commands/run.py", line 49, in run 
    4780 results = command.run(text, log=log, return_json=return_json) 
    4781 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    4782 File
    4783 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4784 packages/chimerax/core/commands/cli.py", line 3221, in run 
    4785 result = ci.function(session, **kw_args) 
    4786 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    4787 File
    4788 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4789 packages/chimerax/std_commands/select.py", line 132, in select_subtract 
    4790 report_selection(session) 
    4791 File
    4792 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4793 packages/chimerax/std_commands/select.py", line 192, in report_selection 
    4794 session.logger.status(', '.join(lines) + ' selected', log = True) 
    4795 File
    4796 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4797 packages/chimerax/core/logger.py", line 522, in status 
    4798 StatusLogger.status(self, msg, **kw) 
    4799 File
    4800 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4801 packages/chimerax/core/logger.py", line 220, in status 
    4802 if l.status(msg, color, secondary) and getattr( 
    4803 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    4804 File
    4805 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4806 packages/chimerax/ui/gui.py", line 1085, in status 
    4807 sbar.status(msg, color, secondary) 
    4808 File
    4809 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4810 packages/chimerax/ui/statusbar.py", line 164, in status 
    4811 r.draw_background() 
    4812 File
    4813 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4814 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    4815 GL.glClear(flags) 
    4816 File "src/errorchecker.pyx", line 59, in
    4817 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4818 OpenGL.error.GLError: GLError( 
    4819 err = 1286, 
    4820 description = b'invalid framebuffer operation', 
    4821 baseOperation = glClear, 
    4822 cArguments = (16640,) 
    4823 ) 
    4824  
    4825 OpenGL.error.GLError: GLError( 
    4826 err = 1286, 
    4827 description = b'invalid framebuffer operation', 
    4828 baseOperation = glClear, 
    4829 cArguments = (16640,) 
    4830 ) 
    4831  
    4832 File "src/errorchecker.pyx", line 59, in
    4833 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4834  
    4835 See log for complete Python traceback. 
    4836  
    4837 
    4838 > select subtract #5
    4839 
    4840 Nothing selected 
    4841 Traceback (most recent call last): 
    4842 File
    4843 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4844 packages/chimerax/model_panel/tool.py", line 475, in _tree_change_cb 
    4845 run(self.session, "select " + mode + " #" + model.id_string) 
    4846 File
    4847 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4848 packages/chimerax/core/commands/run.py", line 49, in run 
    4849 results = command.run(text, log=log, return_json=return_json) 
    4850 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    4851 File
    4852 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4853 packages/chimerax/core/commands/cli.py", line 3221, in run 
    4854 result = ci.function(session, **kw_args) 
    4855 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    4856 File
    4857 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4858 packages/chimerax/std_commands/select.py", line 132, in select_subtract 
    4859 report_selection(session) 
    4860 File
    4861 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4862 packages/chimerax/std_commands/select.py", line 192, in report_selection 
    4863 session.logger.status(', '.join(lines) + ' selected', log = True) 
    4864 File
    4865 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4866 packages/chimerax/core/logger.py", line 522, in status 
    4867 StatusLogger.status(self, msg, **kw) 
    4868 File
    4869 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4870 packages/chimerax/core/logger.py", line 220, in status 
    4871 if l.status(msg, color, secondary) and getattr( 
    4872 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    4873 File
    4874 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4875 packages/chimerax/ui/gui.py", line 1085, in status 
    4876 sbar.status(msg, color, secondary) 
    4877 File
    4878 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4879 packages/chimerax/ui/statusbar.py", line 164, in status 
    4880 r.draw_background() 
    4881 File
    4882 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4883 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    4884 GL.glClear(flags) 
    4885 File "src/errorchecker.pyx", line 59, in
    4886 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4887 OpenGL.error.GLError: GLError( 
    4888 err = 1286, 
    4889 description = b'invalid framebuffer operation', 
    4890 baseOperation = glClear, 
    4891 cArguments = (16640,) 
    4892 ) 
    4893  
    4894 OpenGL.error.GLError: GLError( 
    4895 err = 1286, 
    4896 description = b'invalid framebuffer operation', 
    4897 baseOperation = glClear, 
    4898 cArguments = (16640,) 
    4899 ) 
    4900  
    4901 File "src/errorchecker.pyx", line 59, in
    4902 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4903  
    4904 See log for complete Python traceback. 
    4905  
    4906 
    4907 > view orient
    4908 
    4909 > hide #2 models
    4910 
    4911 > show #!1 models
    4912 
    4913 > view orient
    4914 
    4915 Traceback (most recent call last): 
    4916 File
    4917 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4918 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    4919 self.status(self._last_message, self._last_color) 
    4920 File
    4921 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4922 packages/chimerax/ui/statusbar.py", line 164, in status 
    4923 r.draw_background() 
    4924 File
    4925 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4926 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    4927 GL.glClear(flags) 
    4928 File "src/errorchecker.pyx", line 59, in
    4929 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4930 OpenGL.error.GLError: GLError( 
    4931 err = 1286, 
    4932 description = b'invalid framebuffer operation', 
    4933 baseOperation = glClear, 
    4934 cArguments = (16640,) 
    4935 ) 
    4936  
    4937 OpenGL.error.GLError: GLError( 
    4938 err = 1286, 
    4939 description = b'invalid framebuffer operation', 
    4940 baseOperation = glClear, 
    4941 cArguments = (16640,) 
    4942 ) 
    4943  
    4944 File "src/errorchecker.pyx", line 59, in
    4945 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4946  
    4947 See log for complete Python traceback. 
    4948  
    4949 Traceback (most recent call last): 
    4950 File
    4951 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4952 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    4953 self.status(self._last_message, self._last_color) 
    4954 File
    4955 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4956 packages/chimerax/ui/statusbar.py", line 164, in status 
    4957 r.draw_background() 
    4958 File
    4959 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4960 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    4961 GL.glClear(flags) 
    4962 File "src/errorchecker.pyx", line 59, in
    4963 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4964 OpenGL.error.GLError: GLError( 
    4965 err = 1286, 
    4966 description = b'invalid framebuffer operation', 
    4967 baseOperation = glClear, 
    4968 cArguments = (16640,) 
    4969 ) 
    4970  
    4971 OpenGL.error.GLError: GLError( 
    4972 err = 1286, 
    4973 description = b'invalid framebuffer operation', 
    4974 baseOperation = glClear, 
    4975 cArguments = (16640,) 
    4976 ) 
    4977  
    4978 File "src/errorchecker.pyx", line 59, in
    4979 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4980  
    4981 See log for complete Python traceback. 
    4982  
    4983 Traceback (most recent call last): 
    4984 File
    4985 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4986 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    4987 self.status(self._last_message, self._last_color) 
    4988 File
    4989 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4990 packages/chimerax/ui/statusbar.py", line 164, in status 
    4991 r.draw_background() 
    4992 File
    4993 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    4994 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    4995 GL.glClear(flags) 
    4996 File "src/errorchecker.pyx", line 59, in
    4997 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    4998 OpenGL.error.GLError: GLError( 
    4999 err = 1286, 
    5000 description = b'invalid framebuffer operation', 
    5001 baseOperation = glClear, 
    5002 cArguments = (16640,) 
    5003 ) 
    5004  
    5005 OpenGL.error.GLError: GLError( 
    5006 err = 1286, 
    5007 description = b'invalid framebuffer operation', 
    5008 baseOperation = glClear, 
    5009 cArguments = (16640,) 
    5010 ) 
    5011  
    5012 File "src/errorchecker.pyx", line 59, in
    5013 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5014  
    5015 See log for complete Python traceback. 
    5016  
    5017 Traceback (most recent call last): 
    5018 File
    5019 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5020 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    5021 self.status(self._last_message, self._last_color) 
    5022 File
    5023 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5024 packages/chimerax/ui/statusbar.py", line 164, in status 
    5025 r.draw_background() 
    5026 File
    5027 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5028 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    5029 GL.glClear(flags) 
    5030 File "src/errorchecker.pyx", line 59, in
    5031 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5032 OpenGL.error.GLError: GLError( 
    5033 err = 1286, 
    5034 description = b'invalid framebuffer operation', 
    5035 baseOperation = glClear, 
    5036 cArguments = (16640,) 
    5037 ) 
    5038  
    5039 OpenGL.error.GLError: GLError( 
    5040 err = 1286, 
    5041 description = b'invalid framebuffer operation', 
    5042 baseOperation = glClear, 
    5043 cArguments = (16640,) 
    5044 ) 
    5045  
    5046 File "src/errorchecker.pyx", line 59, in
    5047 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5048  
    5049 See log for complete Python traceback. 
    5050  
    5051 
    5052 > show #4 models
    5053 
    5054 > hide #4 models
    5055 
    5056 > show #5 models
    5057 
    5058 > hide #!1 models
    5059 
    5060 > show #6 models
    5061 
    5062 > show #7 models
    5063 
    5064 > show #4 models
    5065 
    5066 > show #!1 models
    5067 
    5068 Traceback (most recent call last): 
    5069 File
    5070 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5071 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    5072 self.status(self._last_message, self._last_color) 
    5073 File
    5074 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5075 packages/chimerax/ui/statusbar.py", line 164, in status 
    5076 r.draw_background() 
    5077 File
    5078 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5079 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    5080 GL.glClear(flags) 
    5081 File "src/errorchecker.pyx", line 59, in
    5082 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5083 OpenGL.error.GLError: GLError( 
    5084 err = 1286, 
    5085 description = b'invalid framebuffer operation', 
    5086 baseOperation = glClear, 
    5087 cArguments = (16640,) 
    5088 ) 
    5089  
    5090 OpenGL.error.GLError: GLError( 
    5091 err = 1286, 
    5092 description = b'invalid framebuffer operation', 
    5093 baseOperation = glClear, 
    5094 cArguments = (16640,) 
    5095 ) 
    5096  
    5097 File "src/errorchecker.pyx", line 59, in
    5098 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5099  
    5100 See log for complete Python traceback. 
    5101  
    5102 Traceback (most recent call last): 
    5103 File
    5104 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5105 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    5106 self.status(self._last_message, self._last_color) 
    5107 File
    5108 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5109 packages/chimerax/ui/statusbar.py", line 164, in status 
    5110 r.draw_background() 
    5111 File
    5112 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5113 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    5114 GL.glClear(flags) 
    5115 File "src/errorchecker.pyx", line 59, in
    5116 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5117 OpenGL.error.GLError: GLError( 
    5118 err = 1286, 
    5119 description = b'invalid framebuffer operation', 
    5120 baseOperation = glClear, 
    5121 cArguments = (16640,) 
    5122 ) 
    5123  
    5124 OpenGL.error.GLError: GLError( 
    5125 err = 1286, 
    5126 description = b'invalid framebuffer operation', 
    5127 baseOperation = glClear, 
    5128 cArguments = (16640,) 
    5129 ) 
    5130  
    5131 File "src/errorchecker.pyx", line 59, in
    5132 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5133  
    5134 See log for complete Python traceback. 
    5135  
    5136 Traceback (most recent call last): 
    5137 File
    5138 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5139 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    5140 self.status(self._last_message, self._last_color) 
    5141 File
    5142 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5143 packages/chimerax/ui/statusbar.py", line 164, in status 
    5144 r.draw_background() 
    5145 File
    5146 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5147 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    5148 GL.glClear(flags) 
    5149 File "src/errorchecker.pyx", line 59, in
    5150 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5151 OpenGL.error.GLError: GLError( 
    5152 err = 1286, 
    5153 description = b'invalid framebuffer operation', 
    5154 baseOperation = glClear, 
    5155 cArguments = (16640,) 
    5156 ) 
    5157  
    5158 OpenGL.error.GLError: GLError( 
    5159 err = 1286, 
    5160 description = b'invalid framebuffer operation', 
    5161 baseOperation = glClear, 
    5162 cArguments = (16640,) 
    5163 ) 
    5164  
    5165 File "src/errorchecker.pyx", line 59, in
    5166 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5167  
    5168 See log for complete Python traceback. 
    5169  
    5170 Traceback (most recent call last): 
    5171 File
    5172 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5173 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    5174 self.status(self._last_message, self._last_color) 
    5175 File
    5176 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5177 packages/chimerax/ui/statusbar.py", line 164, in status 
    5178 r.draw_background() 
    5179 File
    5180 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5181 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    5182 GL.glClear(flags) 
    5183 File "src/errorchecker.pyx", line 59, in
    5184 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5185 OpenGL.error.GLError: GLError( 
    5186 err = 1286, 
    5187 description = b'invalid framebuffer operation', 
    5188 baseOperation = glClear, 
    5189 cArguments = (16640,) 
    5190 ) 
    5191  
    5192 OpenGL.error.GLError: GLError( 
    5193 err = 1286, 
    5194 description = b'invalid framebuffer operation', 
    5195 baseOperation = glClear, 
    5196 cArguments = (16640,) 
    5197 ) 
    5198  
    5199 File "src/errorchecker.pyx", line 59, in
    5200 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5201  
    5202 See log for complete Python traceback. 
    5203  
    5204 Traceback (most recent call last): 
    5205 File
    5206 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5207 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    5208 self.status(self._last_message, self._last_color) 
    5209 File
    5210 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5211 packages/chimerax/ui/statusbar.py", line 164, in status 
    5212 r.draw_background() 
    5213 File
    5214 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5215 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    5216 GL.glClear(flags) 
    5217 File "src/errorchecker.pyx", line 59, in
    5218 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5219 OpenGL.error.GLError: GLError( 
    5220 err = 1286, 
    5221 description = b'invalid framebuffer operation', 
    5222 baseOperation = glClear, 
    5223 cArguments = (16640,) 
    5224 ) 
    5225  
    5226 OpenGL.error.GLError: GLError( 
    5227 err = 1286, 
    5228 description = b'invalid framebuffer operation', 
    5229 baseOperation = glClear, 
    5230 cArguments = (16640,) 
    5231 ) 
    5232  
    5233 File "src/errorchecker.pyx", line 59, in
    5234 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5235  
    5236 See log for complete Python traceback. 
    5237  
    5238 Traceback (most recent call last): 
    5239 File
    5240 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5241 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    5242 self.status(self._last_message, self._last_color) 
    5243 File
    5244 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5245 packages/chimerax/ui/statusbar.py", line 164, in status 
    5246 r.draw_background() 
    5247 File
    5248 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5249 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    5250 GL.glClear(flags) 
    5251 File "src/errorchecker.pyx", line 59, in
    5252 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5253 OpenGL.error.GLError: GLError( 
    5254 err = 1286, 
    5255 description = b'invalid framebuffer operation', 
    5256 baseOperation = glClear, 
    5257 cArguments = (16640,) 
    5258 ) 
    5259  
    5260 OpenGL.error.GLError: GLError( 
    5261 err = 1286, 
    5262 description = b'invalid framebuffer operation', 
    5263 baseOperation = glClear, 
    5264 cArguments = (16640,) 
    5265 ) 
    5266  
    5267 File "src/errorchecker.pyx", line 59, in
    5268 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5269  
    5270 See log for complete Python traceback. 
    5271  
    5272 Traceback (most recent call last): 
    5273 File
    5274 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5275 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    5276 self.status(self._last_message, self._last_color) 
    5277 File
    5278 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5279 packages/chimerax/ui/statusbar.py", line 164, in status 
    5280 r.draw_background() 
    5281 File
    5282 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5283 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    5284 GL.glClear(flags) 
    5285 File "src/errorchecker.pyx", line 59, in
    5286 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5287 OpenGL.error.GLError: GLError( 
    5288 err = 1286, 
    5289 description = b'invalid framebuffer operation', 
    5290 baseOperation = glClear, 
    5291 cArguments = (16640,) 
    5292 ) 
    5293  
    5294 OpenGL.error.GLError: GLError( 
    5295 err = 1286, 
    5296 description = b'invalid framebuffer operation', 
    5297 baseOperation = glClear, 
    5298 cArguments = (16640,) 
    5299 ) 
    5300  
    5301 File "src/errorchecker.pyx", line 59, in
    5302 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5303  
    5304 See log for complete Python traceback. 
    5305  
    5306 Traceback (most recent call last): 
    5307 File
    5308 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5309 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    5310 self.status(self._last_message, self._last_color) 
    5311 File
    5312 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5313 packages/chimerax/ui/statusbar.py", line 164, in status 
    5314 r.draw_background() 
    5315 File
    5316 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5317 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    5318 GL.glClear(flags) 
    5319 File "src/errorchecker.pyx", line 59, in
    5320 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5321 OpenGL.error.GLError: GLError( 
    5322 err = 1286, 
    5323 description = b'invalid framebuffer operation', 
    5324 baseOperation = glClear, 
    5325 cArguments = (16640,) 
    5326 ) 
    5327  
    5328 OpenGL.error.GLError: GLError( 
    5329 err = 1286, 
    5330 description = b'invalid framebuffer operation', 
    5331 baseOperation = glClear, 
    5332 cArguments = (16640,) 
    5333 ) 
    5334  
    5335 File "src/errorchecker.pyx", line 59, in
    5336 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5337  
    5338 See log for complete Python traceback. 
    5339  
    5340 Traceback (most recent call last): 
    5341 File
    5342 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5343 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    5344 self.status(self._last_message, self._last_color) 
    5345 File
    5346 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5347 packages/chimerax/ui/statusbar.py", line 164, in status 
    5348 r.draw_background() 
    5349 File
    5350 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5351 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    5352 GL.glClear(flags) 
    5353 File "src/errorchecker.pyx", line 59, in
    5354 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5355 OpenGL.error.GLError: GLError( 
    5356 err = 1286, 
    5357 description = b'invalid framebuffer operation', 
    5358 baseOperation = glClear, 
    5359 cArguments = (16640,) 
    5360 ) 
    5361  
    5362 OpenGL.error.GLError: GLError( 
    5363 err = 1286, 
    5364 description = b'invalid framebuffer operation', 
    5365 baseOperation = glClear, 
    5366 cArguments = (16640,) 
    5367 ) 
    5368  
    5369 File "src/errorchecker.pyx", line 59, in
    5370 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5371  
    5372 See log for complete Python traceback. 
    5373  
    5374 Traceback (most recent call last): 
    5375 File
    5376 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5377 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    5378 self.status(self._last_message, self._last_color) 
    5379 File
    5380 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5381 packages/chimerax/ui/statusbar.py", line 164, in status 
    5382 r.draw_background() 
    5383 File
    5384 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5385 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    5386 GL.glClear(flags) 
    5387 File "src/errorchecker.pyx", line 59, in
    5388 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5389 OpenGL.error.GLError: GLError( 
    5390 err = 1286, 
    5391 description = b'invalid framebuffer operation', 
    5392 baseOperation = glClear, 
    5393 cArguments = (16640,) 
    5394 ) 
    5395  
    5396 OpenGL.error.GLError: GLError( 
    5397 err = 1286, 
    5398 description = b'invalid framebuffer operation', 
    5399 baseOperation = glClear, 
    5400 cArguments = (16640,) 
    5401 ) 
    5402  
    5403 File "src/errorchecker.pyx", line 59, in
    5404 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5405  
    5406 See log for complete Python traceback. 
    5407  
    5408 Traceback (most recent call last): 
    5409 File
    5410 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5411 packages/chimerax/ui/gui.py", line 172, in _update_color_scheme 
    5412 self.session.logger.status(msg) 
    5413 File
    5414 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5415 packages/chimerax/core/logger.py", line 522, in status 
    5416 StatusLogger.status(self, msg, **kw) 
    5417 File
    5418 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5419 packages/chimerax/core/logger.py", line 220, in status 
    5420 if l.status(msg, color, secondary) and getattr( 
    5421 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    5422 File
    5423 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5424 packages/chimerax/ui/gui.py", line 1085, in status 
    5425 sbar.status(msg, color, secondary) 
    5426 File
    5427 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5428 packages/chimerax/ui/statusbar.py", line 164, in status 
    5429 r.draw_background() 
    5430 File
    5431 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5432 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    5433 GL.glClear(flags) 
    5434 File "src/errorchecker.pyx", line 59, in
    5435 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5436 OpenGL.error.GLError: GLError( 
    5437 err = 1286, 
    5438 description = b'invalid framebuffer operation', 
    5439 baseOperation = glClear, 
    5440 cArguments = (16640,) 
    5441 ) 
    5442  
    5443 OpenGL.error.GLError: GLError( 
    5444 err = 1286, 
    5445 description = b'invalid framebuffer operation', 
    5446 baseOperation = glClear, 
    5447 cArguments = (16640,) 
    5448 ) 
    5449  
    5450 File "src/errorchecker.pyx", line 59, in
    5451 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5452  
    5453 See log for complete Python traceback. 
    5454  
    5455 Traceback (most recent call last): 
    5456 File
    5457 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5458 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    5459 self.status(self._last_message, self._last_color) 
    5460 File
    5461 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5462 packages/chimerax/ui/statusbar.py", line 164, in status 
    5463 r.draw_background() 
    5464 File
    5465 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5466 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    5467 GL.glClear(flags) 
    5468 File "src/errorchecker.pyx", line 59, in
    5469 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5470 OpenGL.error.GLError: GLError( 
    5471 err = 1286, 
    5472 description = b'invalid framebuffer operation', 
    5473 baseOperation = glClear, 
    5474 cArguments = (16640,) 
    5475 ) 
    5476  
    5477 OpenGL.error.GLError: GLError( 
    5478 err = 1286, 
    5479 description = b'invalid framebuffer operation', 
    5480 baseOperation = glClear, 
    5481 cArguments = (16640,) 
    5482 ) 
    5483  
    5484 File "src/errorchecker.pyx", line 59, in
    5485 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5486  
    5487 See log for complete Python traceback. 
    5488  
    5489 Traceback (most recent call last): 
    5490 File
    5491 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5492 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    5493 self.status(self._last_message, self._last_color) 
    5494 File
    5495 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5496 packages/chimerax/ui/statusbar.py", line 164, in status 
    5497 r.draw_background() 
    5498 File
    5499 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5500 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    5501 GL.glClear(flags) 
    5502 File "src/errorchecker.pyx", line 59, in
    5503 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5504 OpenGL.error.GLError: GLError( 
    5505 err = 1286, 
    5506 description = b'invalid framebuffer operation', 
    5507 baseOperation = glClear, 
    5508 cArguments = (16640,) 
    5509 ) 
    5510  
    5511 OpenGL.error.GLError: GLError( 
    5512 err = 1286, 
    5513 description = b'invalid framebuffer operation', 
    5514 baseOperation = glClear, 
    5515 cArguments = (16640,) 
    5516 ) 
    5517  
    5518 File "src/errorchecker.pyx", line 59, in
    5519 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5520  
    5521 See log for complete Python traceback. 
    5522  
    5523 Traceback (most recent call last): 
    5524 File
    5525 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5526 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    5527 self.status(self._last_message, self._last_color) 
    5528 File
    5529 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5530 packages/chimerax/ui/statusbar.py", line 164, in status 
    5531 r.draw_background() 
    5532 File
    5533 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5534 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    5535 GL.glClear(flags) 
    5536 File "src/errorchecker.pyx", line 59, in
    5537 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5538 OpenGL.error.GLError: GLError( 
    5539 err = 1286, 
    5540 description = b'invalid framebuffer operation', 
    5541 baseOperation = glClear, 
    5542 cArguments = (16640,) 
    5543 ) 
    5544  
    5545 OpenGL.error.GLError: GLError( 
    5546 err = 1286, 
    5547 description = b'invalid framebuffer operation', 
    5548 baseOperation = glClear, 
    5549 cArguments = (16640,) 
    5550 ) 
    5551  
    5552 File "src/errorchecker.pyx", line 59, in
    5553 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5554  
    5555 See log for complete Python traceback. 
    5556  
    5557 Traceback (most recent call last): 
    5558 File
    5559 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5560 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    5561 self.status(self._last_message, self._last_color) 
    5562 File
    5563 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5564 packages/chimerax/ui/statusbar.py", line 164, in status 
    5565 r.draw_background() 
    5566 File
    5567 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5568 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    5569 GL.glClear(flags) 
    5570 File "src/errorchecker.pyx", line 59, in
    5571 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5572 OpenGL.error.GLError: GLError( 
    5573 err = 1286, 
    5574 description = b'invalid framebuffer operation', 
    5575 baseOperation = glClear, 
    5576 cArguments = (16640,) 
    5577 ) 
    5578  
    5579 OpenGL.error.GLError: GLError( 
    5580 err = 1286, 
    5581 description = b'invalid framebuffer operation', 
    5582 baseOperation = glClear, 
    5583 cArguments = (16640,) 
    5584 ) 
    5585  
    5586 File "src/errorchecker.pyx", line 59, in
    5587 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5588  
    5589 See log for complete Python traceback. 
    5590  
    5591 Traceback (most recent call last): 
    5592 File
    5593 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5594 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    5595 self.status(self._last_message, self._last_color) 
    5596 File
    5597 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5598 packages/chimerax/ui/statusbar.py", line 164, in status 
    5599 r.draw_background() 
    5600 File
    5601 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5602 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    5603 GL.glClear(flags) 
    5604 File "src/errorchecker.pyx", line 59, in
    5605 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5606 OpenGL.error.GLError: GLError( 
    5607 err = 1286, 
    5608 description = b'invalid framebuffer operation', 
    5609 baseOperation = glClear, 
    5610 cArguments = (16640,) 
    5611 ) 
    5612  
    5613 OpenGL.error.GLError: GLError( 
    5614 err = 1286, 
    5615 description = b'invalid framebuffer operation', 
    5616 baseOperation = glClear, 
    5617 cArguments = (16640,) 
    5618 ) 
    5619  
    5620 File "src/errorchecker.pyx", line 59, in
    5621 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5622  
    5623 See log for complete Python traceback. 
    5624  
    5625 Traceback (most recent call last): 
    5626 File
    5627 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5628 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    5629 self.status(self._last_message, self._last_color) 
    5630 File
    5631 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5632 packages/chimerax/ui/statusbar.py", line 164, in status 
    5633 r.draw_background() 
    5634 File
    5635 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5636 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    5637 GL.glClear(flags) 
    5638 File "src/errorchecker.pyx", line 59, in
    5639 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5640 OpenGL.error.GLError: GLError( 
    5641 err = 1286, 
    5642 description = b'invalid framebuffer operation', 
    5643 baseOperation = glClear, 
    5644 cArguments = (16640,) 
    5645 ) 
    5646  
    5647 OpenGL.error.GLError: GLError( 
    5648 err = 1286, 
    5649 description = b'invalid framebuffer operation', 
    5650 baseOperation = glClear, 
    5651 cArguments = (16640,) 
    5652 ) 
    5653  
    5654 File "src/errorchecker.pyx", line 59, in
    5655 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5656  
    5657 See log for complete Python traceback. 
    5658  
    5659 Traceback (most recent call last): 
    5660 File
    5661 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5662 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    5663 self.status(self._last_message, self._last_color) 
    5664 File
    5665 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5666 packages/chimerax/ui/statusbar.py", line 164, in status 
    5667 r.draw_background() 
    5668 File
    5669 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5670 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    5671 GL.glClear(flags) 
    5672 File "src/errorchecker.pyx", line 59, in
    5673 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5674 OpenGL.error.GLError: GLError( 
    5675 err = 1286, 
    5676 description = b'invalid framebuffer operation', 
    5677 baseOperation = glClear, 
    5678 cArguments = (16640,) 
    5679 ) 
    5680  
    5681 OpenGL.error.GLError: GLError( 
    5682 err = 1286, 
    5683 description = b'invalid framebuffer operation', 
    5684 baseOperation = glClear, 
    5685 cArguments = (16640,) 
    5686 ) 
    5687  
    5688 File "src/errorchecker.pyx", line 59, in
    5689 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5690  
    5691 See log for complete Python traceback. 
    5692  
    5693 Traceback (most recent call last): 
    5694 File
    5695 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5696 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    5697 self.status(self._last_message, self._last_color) 
    5698 File
    5699 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5700 packages/chimerax/ui/statusbar.py", line 164, in status 
    5701 r.draw_background() 
    5702 File
    5703 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5704 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    5705 GL.glClear(flags) 
    5706 File "src/errorchecker.pyx", line 59, in
    5707 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5708 OpenGL.error.GLError: GLError( 
    5709 err = 1286, 
    5710 description = b'invalid framebuffer operation', 
    5711 baseOperation = glClear, 
    5712 cArguments = (16640,) 
    5713 ) 
    5714  
    5715 OpenGL.error.GLError: GLError( 
    5716 err = 1286, 
    5717 description = b'invalid framebuffer operation', 
    5718 baseOperation = glClear, 
    5719 cArguments = (16640,) 
    5720 ) 
    5721  
    5722 File "src/errorchecker.pyx", line 59, in
    5723 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5724  
    5725 See log for complete Python traceback. 
    5726  
    5727 Traceback (most recent call last): 
    5728 File
    5729 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5730 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    5731 self.status(self._last_message, self._last_color) 
    5732 File
    5733 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5734 packages/chimerax/ui/statusbar.py", line 164, in status 
    5735 r.draw_background() 
    5736 File
    5737 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5738 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    5739 GL.glClear(flags) 
    5740 File "src/errorchecker.pyx", line 59, in
    5741 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5742 OpenGL.error.GLError: GLError( 
    5743 err = 1286, 
    5744 description = b'invalid framebuffer operation', 
    5745 baseOperation = glClear, 
    5746 cArguments = (16640,) 
    5747 ) 
    5748  
    5749 OpenGL.error.GLError: GLError( 
    5750 err = 1286, 
    5751 description = b'invalid framebuffer operation', 
    5752 baseOperation = glClear, 
    5753 cArguments = (16640,) 
    5754 ) 
    5755  
    5756 File "src/errorchecker.pyx", line 59, in
    5757 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5758  
    5759 See log for complete Python traceback. 
    5760  
    5761 Desktop color scheme is light 
    5762 Traceback (most recent call last): 
    5763 File
    5764 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5765 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    5766 self.status(self._last_message, self._last_color) 
    5767 File
    5768 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5769 packages/chimerax/ui/statusbar.py", line 164, in status 
    5770 r.draw_background() 
    5771 File
    5772 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5773 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    5774 GL.glClear(flags) 
    5775 File "src/errorchecker.pyx", line 59, in
    5776 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5777 OpenGL.error.GLError: GLError( 
    5778 err = 1286, 
    5779 description = b'invalid framebuffer operation', 
    5780 baseOperation = glClear, 
    5781 cArguments = (16640,) 
    5782 ) 
    5783  
    5784 OpenGL.error.GLError: GLError( 
    5785 err = 1286, 
    5786 description = b'invalid framebuffer operation', 
    5787 baseOperation = glClear, 
    5788 cArguments = (16640,) 
    5789 ) 
    5790  
    5791 File "src/errorchecker.pyx", line 59, in
    5792 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5793  
    5794 See log for complete Python traceback. 
    5795  
    5796 Traceback (most recent call last): 
    5797 File
    5798 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5799 packages/chimerax/ui/gui.py", line 873, in customEvent 
    5800 func(*args, **kw) 
    5801 File
    5802 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5803 packages/chimerax/core/logger.py", line 522, in status 
    5804 StatusLogger.status(self, msg, **kw) 
    5805 File
    5806 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5807 packages/chimerax/core/logger.py", line 220, in status 
    5808 if l.status(msg, color, secondary) and getattr( 
    5809 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    5810 File
    5811 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5812 packages/chimerax/ui/gui.py", line 1085, in status 
    5813 sbar.status(msg, color, secondary) 
    5814 File
    5815 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5816 packages/chimerax/ui/statusbar.py", line 164, in status 
    5817 r.draw_background() 
    5818 File
    5819 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5820 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    5821 GL.glClear(flags) 
    5822 File "src/errorchecker.pyx", line 59, in
    5823 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5824 OpenGL.error.GLError: GLError( 
    5825 err = 1286, 
    5826 description = b'invalid framebuffer operation', 
    5827 baseOperation = glClear, 
    5828 cArguments = (16640,) 
    5829 ) 
    5830  
    5831 OpenGL.error.GLError: GLError( 
    5832 err = 1286, 
    5833 description = b'invalid framebuffer operation', 
    5834 baseOperation = glClear, 
    5835 cArguments = (16640,) 
    5836 ) 
    5837  
    5838 File "src/errorchecker.pyx", line 59, in
    5839 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5840  
    5841 See log for complete Python traceback. 
    5842  
    5843 Traceback (most recent call last): 
    5844 File
    5845 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5846 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    5847 self.status(self._last_message, self._last_color) 
    5848 File
    5849 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5850 packages/chimerax/ui/statusbar.py", line 164, in status 
    5851 r.draw_background() 
    5852 File
    5853 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5854 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    5855 GL.glClear(flags) 
    5856 File "src/errorchecker.pyx", line 59, in
    5857 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5858 OpenGL.error.GLError: GLError( 
    5859 err = 1286, 
    5860 description = b'invalid framebuffer operation', 
    5861 baseOperation = glClear, 
    5862 cArguments = (16640,) 
    5863 ) 
    5864  
    5865 OpenGL.error.GLError: GLError( 
    5866 err = 1286, 
    5867 description = b'invalid framebuffer operation', 
    5868 baseOperation = glClear, 
    5869 cArguments = (16640,) 
    5870 ) 
    5871  
    5872 File "src/errorchecker.pyx", line 59, in
    5873 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5874  
    5875 See log for complete Python traceback. 
    5876  
    5877 Traceback (most recent call last): 
    5878 File
    5879 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5880 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    5881 self.status(self._last_message, self._last_color) 
    5882 File
    5883 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5884 packages/chimerax/ui/statusbar.py", line 164, in status 
    5885 r.draw_background() 
    5886 File
    5887 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5888 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    5889 GL.glClear(flags) 
    5890 File "src/errorchecker.pyx", line 59, in
    5891 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5892 OpenGL.error.GLError: GLError( 
    5893 err = 1286, 
    5894 description = b'invalid framebuffer operation', 
    5895 baseOperation = glClear, 
    5896 cArguments = (16640,) 
    5897 ) 
    5898  
    5899 OpenGL.error.GLError: GLError( 
    5900 err = 1286, 
    5901 description = b'invalid framebuffer operation', 
    5902 baseOperation = glClear, 
    5903 cArguments = (16640,) 
    5904 ) 
    5905  
    5906 File "src/errorchecker.pyx", line 59, in
    5907 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5908  
    5909 See log for complete Python traceback. 
    5910  
    5911 Traceback (most recent call last): 
    5912 File
    5913 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5914 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    5915 self.status(self._last_message, self._last_color) 
    5916 File
    5917 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5918 packages/chimerax/ui/statusbar.py", line 164, in status 
    5919 r.draw_background() 
    5920 File
    5921 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5922 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    5923 GL.glClear(flags) 
    5924 File "src/errorchecker.pyx", line 59, in
    5925 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5926 OpenGL.error.GLError: GLError( 
    5927 err = 1286, 
    5928 description = b'invalid framebuffer operation', 
    5929 baseOperation = glClear, 
    5930 cArguments = (16640,) 
    5931 ) 
    5932  
    5933 OpenGL.error.GLError: GLError( 
    5934 err = 1286, 
    5935 description = b'invalid framebuffer operation', 
    5936 baseOperation = glClear, 
    5937 cArguments = (16640,) 
    5938 ) 
    5939  
    5940 File "src/errorchecker.pyx", line 59, in
    5941 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5942  
    5943 See log for complete Python traceback. 
    5944  
    5945 Traceback (most recent call last): 
    5946 File
    5947 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5948 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    5949 self.status(self._last_message, self._last_color) 
    5950 File
    5951 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5952 packages/chimerax/ui/statusbar.py", line 164, in status 
    5953 r.draw_background() 
    5954 File
    5955 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5956 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    5957 GL.glClear(flags) 
    5958 File "src/errorchecker.pyx", line 59, in
    5959 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5960 OpenGL.error.GLError: GLError( 
    5961 err = 1286, 
    5962 description = b'invalid framebuffer operation', 
    5963 baseOperation = glClear, 
    5964 cArguments = (16640,) 
    5965 ) 
    5966  
    5967 OpenGL.error.GLError: GLError( 
    5968 err = 1286, 
    5969 description = b'invalid framebuffer operation', 
    5970 baseOperation = glClear, 
    5971 cArguments = (16640,) 
    5972 ) 
    5973  
    5974 File "src/errorchecker.pyx", line 59, in
    5975 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5976  
    5977 See log for complete Python traceback. 
    5978  
    5979 Traceback (most recent call last): 
    5980 File
    5981 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5982 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    5983 self.status(self._last_message, self._last_color) 
    5984 File
    5985 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5986 packages/chimerax/ui/statusbar.py", line 164, in status 
    5987 r.draw_background() 
    5988 File
    5989 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    5990 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    5991 GL.glClear(flags) 
    5992 File "src/errorchecker.pyx", line 59, in
    5993 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    5994 OpenGL.error.GLError: GLError( 
    5995 err = 1286, 
    5996 description = b'invalid framebuffer operation', 
    5997 baseOperation = glClear, 
    5998 cArguments = (16640,) 
    5999 ) 
    6000  
    6001 OpenGL.error.GLError: GLError( 
    6002 err = 1286, 
    6003 description = b'invalid framebuffer operation', 
    6004 baseOperation = glClear, 
    6005 cArguments = (16640,) 
    6006 ) 
    6007  
    6008 File "src/errorchecker.pyx", line 59, in
    6009 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    6010  
    6011 See log for complete Python traceback. 
    6012  
    6013 Traceback (most recent call last): 
    6014 File
    6015 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6016 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    6017 self.status(self._last_message, self._last_color) 
    6018 File
    6019 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6020 packages/chimerax/ui/statusbar.py", line 164, in status 
    6021 r.draw_background() 
    6022 File
    6023 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6024 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    6025 GL.glClear(flags) 
    6026 File "src/errorchecker.pyx", line 59, in
    6027 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    6028 OpenGL.error.GLError: GLError( 
    6029 err = 1286, 
    6030 description = b'invalid framebuffer operation', 
    6031 baseOperation = glClear, 
    6032 cArguments = (16640,) 
    6033 ) 
    6034  
    6035 OpenGL.error.GLError: GLError( 
    6036 err = 1286, 
    6037 description = b'invalid framebuffer operation', 
    6038 baseOperation = glClear, 
    6039 cArguments = (16640,) 
    6040 ) 
    6041  
    6042 File "src/errorchecker.pyx", line 59, in
    6043 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    6044  
    6045 See log for complete Python traceback. 
    6046  
    6047 Traceback (most recent call last): 
    6048 File
    6049 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6050 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    6051 self.status(self._last_message, self._last_color) 
    6052 File
    6053 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6054 packages/chimerax/ui/statusbar.py", line 164, in status 
    6055 r.draw_background() 
    6056 File
    6057 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6058 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    6059 GL.glClear(flags) 
    6060 File "src/errorchecker.pyx", line 59, in
    6061 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    6062 OpenGL.error.GLError: GLError( 
    6063 err = 1286, 
    6064 description = b'invalid framebuffer operation', 
    6065 baseOperation = glClear, 
    6066 cArguments = (16640,) 
    6067 ) 
    6068  
    6069 OpenGL.error.GLError: GLError( 
    6070 err = 1286, 
    6071 description = b'invalid framebuffer operation', 
    6072 baseOperation = glClear, 
    6073 cArguments = (16640,) 
    6074 ) 
    6075  
    6076 File "src/errorchecker.pyx", line 59, in
    6077 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    6078  
    6079 See log for complete Python traceback. 
    6080  
    6081 Traceback (most recent call last): 
    6082 File
    6083 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6084 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    6085 self.status(self._last_message, self._last_color) 
    6086 File
    6087 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6088 packages/chimerax/ui/statusbar.py", line 164, in status 
    6089 r.draw_background() 
    6090 File
    6091 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6092 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    6093 GL.glClear(flags) 
    6094 File "src/errorchecker.pyx", line 59, in
    6095 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    6096 OpenGL.error.GLError: GLError( 
    6097 err = 1286, 
    6098 description = b'invalid framebuffer operation', 
    6099 baseOperation = glClear, 
    6100 cArguments = (16640,) 
    6101 ) 
    6102  
    6103 OpenGL.error.GLError: GLError( 
    6104 err = 1286, 
    6105 description = b'invalid framebuffer operation', 
    6106 baseOperation = glClear, 
    6107 cArguments = (16640,) 
    6108 ) 
    6109  
    6110 File "src/errorchecker.pyx", line 59, in
    6111 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    6112  
    6113 See log for complete Python traceback. 
    6114  
    6115 Traceback (most recent call last): 
    6116 File
    6117 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6118 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    6119 self.status(self._last_message, self._last_color) 
    6120 File
    6121 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6122 packages/chimerax/ui/statusbar.py", line 164, in status 
    6123 r.draw_background() 
    6124 File
    6125 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6126 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    6127 GL.glClear(flags) 
    6128 File "src/errorchecker.pyx", line 59, in
    6129 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    6130 OpenGL.error.GLError: GLError( 
    6131 err = 1286, 
    6132 description = b'invalid framebuffer operation', 
    6133 baseOperation = glClear, 
    6134 cArguments = (16640,) 
    6135 ) 
    6136  
    6137 OpenGL.error.GLError: GLError( 
    6138 err = 1286, 
    6139 description = b'invalid framebuffer operation', 
    6140 baseOperation = glClear, 
    6141 cArguments = (16640,) 
    6142 ) 
    6143  
    6144 File "src/errorchecker.pyx", line 59, in
    6145 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    6146  
    6147 See log for complete Python traceback. 
    6148  
    6149 Traceback (most recent call last): 
    6150 File
    6151 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6152 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    6153 self.status(self._last_message, self._last_color) 
    6154 File
    6155 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6156 packages/chimerax/ui/statusbar.py", line 164, in status 
    6157 r.draw_background() 
    6158 File
    6159 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6160 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    6161 GL.glClear(flags) 
    6162 File "src/errorchecker.pyx", line 59, in
    6163 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    6164 OpenGL.error.GLError: GLError( 
    6165 err = 1286, 
    6166 description = b'invalid framebuffer operation', 
    6167 baseOperation = glClear, 
    6168 cArguments = (16640,) 
    6169 ) 
    6170  
    6171 OpenGL.error.GLError: GLError( 
    6172 err = 1286, 
    6173 description = b'invalid framebuffer operation', 
    6174 baseOperation = glClear, 
    6175 cArguments = (16640,) 
    6176 ) 
    6177  
    6178 File "src/errorchecker.pyx", line 59, in
    6179 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    6180  
    6181 See log for complete Python traceback. 
    6182  
    6183 Traceback (most recent call last): 
    6184 File
    6185 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6186 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    6187 self.status(self._last_message, self._last_color) 
    6188 File
    6189 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6190 packages/chimerax/ui/statusbar.py", line 164, in status 
    6191 r.draw_background() 
    6192 File
    6193 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6194 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    6195 GL.glClear(flags) 
    6196 File "src/errorchecker.pyx", line 59, in
    6197 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    6198 OpenGL.error.GLError: GLError( 
    6199 err = 1286, 
    6200 description = b'invalid framebuffer operation', 
    6201 baseOperation = glClear, 
    6202 cArguments = (16640,) 
    6203 ) 
    6204  
    6205 OpenGL.error.GLError: GLError( 
    6206 err = 1286, 
    6207 description = b'invalid framebuffer operation', 
    6208 baseOperation = glClear, 
    6209 cArguments = (16640,) 
    6210 ) 
    6211  
    6212 File "src/errorchecker.pyx", line 59, in
    6213 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    6214  
    6215 See log for complete Python traceback. 
    6216  
    6217 Traceback (most recent call last): 
    6218 File
    6219 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6220 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    6221 self.status(self._last_message, self._last_color) 
    6222 File
    6223 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6224 packages/chimerax/ui/statusbar.py", line 164, in status 
    6225 r.draw_background() 
    6226 File
    6227 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6228 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    6229 GL.glClear(flags) 
    6230 File "src/errorchecker.pyx", line 59, in
    6231 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    6232 OpenGL.error.GLError: GLError( 
    6233 err = 1286, 
    6234 description = b'invalid framebuffer operation', 
    6235 baseOperation = glClear, 
    6236 cArguments = (16640,) 
    6237 ) 
    6238  
    6239 OpenGL.error.GLError: GLError( 
    6240 err = 1286, 
    6241 description = b'invalid framebuffer operation', 
    6242 baseOperation = glClear, 
    6243 cArguments = (16640,) 
    6244 ) 
    6245  
    6246 File "src/errorchecker.pyx", line 59, in
    6247 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    6248  
    6249 See log for complete Python traceback. 
    6250  
    6251 Traceback (most recent call last): 
    6252 File
    6253 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6254 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    6255 self.status(self._last_message, self._last_color) 
    6256 File
    6257 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6258 packages/chimerax/ui/statusbar.py", line 164, in status 
    6259 r.draw_background() 
    6260 File
    6261 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6262 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    6263 GL.glClear(flags) 
    6264 File "src/errorchecker.pyx", line 59, in
    6265 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    6266 OpenGL.error.GLError: GLError( 
    6267 err = 1286, 
    6268 description = b'invalid framebuffer operation', 
    6269 baseOperation = glClear, 
    6270 cArguments = (16640,) 
    6271 ) 
    6272  
    6273 OpenGL.error.GLError: GLError( 
    6274 err = 1286, 
    6275 description = b'invalid framebuffer operation', 
    6276 baseOperation = glClear, 
    6277 cArguments = (16640,) 
    6278 ) 
    6279  
    6280 File "src/errorchecker.pyx", line 59, in
    6281 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    6282  
    6283 See log for complete Python traceback. 
    6284  
    6285 Traceback (most recent call last): 
    6286 File
    6287 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6288 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    6289 self.status(self._last_message, self._last_color) 
    6290 File
    6291 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6292 packages/chimerax/ui/statusbar.py", line 164, in status 
    6293 r.draw_background() 
    6294 File
    6295 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6296 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    6297 GL.glClear(flags) 
    6298 File "src/errorchecker.pyx", line 59, in
    6299 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    6300 OpenGL.error.GLError: GLError( 
    6301 err = 1286, 
    6302 description = b'invalid framebuffer operation', 
    6303 baseOperation = glClear, 
    6304 cArguments = (16640,) 
    6305 ) 
    6306  
    6307 OpenGL.error.GLError: GLError( 
    6308 err = 1286, 
    6309 description = b'invalid framebuffer operation', 
    6310 baseOperation = glClear, 
    6311 cArguments = (16640,) 
    6312 ) 
    6313  
    6314 File "src/errorchecker.pyx", line 59, in
    6315 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    6316  
    6317 See log for complete Python traceback. 
    6318  
    6319 Traceback (most recent call last): 
    6320 File
    6321 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6322 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    6323 self.status(self._last_message, self._last_color) 
    6324 File
    6325 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6326 packages/chimerax/ui/statusbar.py", line 164, in status 
    6327 r.draw_background() 
    6328 File
    6329 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6330 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    6331 GL.glClear(flags) 
    6332 File "src/errorchecker.pyx", line 59, in
    6333 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    6334 OpenGL.error.GLError: GLError( 
    6335 err = 1286, 
    6336 description = b'invalid framebuffer operation', 
    6337 baseOperation = glClear, 
    6338 cArguments = (16640,) 
    6339 ) 
    6340  
    6341 OpenGL.error.GLError: GLError( 
    6342 err = 1286, 
    6343 description = b'invalid framebuffer operation', 
    6344 baseOperation = glClear, 
    6345 cArguments = (16640,) 
    6346 ) 
    6347  
    6348 File "src/errorchecker.pyx", line 59, in
    6349 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    6350  
    6351 See log for complete Python traceback. 
    6352  
    6353 Traceback (most recent call last): 
    6354 File
    6355 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6356 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    6357 self.status(self._last_message, self._last_color) 
    6358 File
    6359 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6360 packages/chimerax/ui/statusbar.py", line 164, in status 
    6361 r.draw_background() 
    6362 File
    6363 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6364 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    6365 GL.glClear(flags) 
    6366 File "src/errorchecker.pyx", line 59, in
    6367 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    6368 OpenGL.error.GLError: GLError( 
    6369 err = 1286, 
    6370 description = b'invalid framebuffer operation', 
    6371 baseOperation = glClear, 
    6372 cArguments = (16640,) 
    6373 ) 
    6374  
    6375 OpenGL.error.GLError: GLError( 
    6376 err = 1286, 
    6377 description = b'invalid framebuffer operation', 
    6378 baseOperation = glClear, 
    6379 cArguments = (16640,) 
    6380 ) 
    6381  
    6382 File "src/errorchecker.pyx", line 59, in
    6383 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    6384  
    6385 See log for complete Python traceback. 
    6386  
    6387 Traceback (most recent call last): 
    6388 File
    6389 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6390 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    6391 self.status(self._last_message, self._last_color) 
    6392 File
    6393 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6394 packages/chimerax/ui/statusbar.py", line 164, in status 
    6395 r.draw_background() 
    6396 File
    6397 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6398 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    6399 GL.glClear(flags) 
    6400 File "src/errorchecker.pyx", line 59, in
    6401 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    6402 OpenGL.error.GLError: GLError( 
    6403 err = 1286, 
    6404 description = b'invalid framebuffer operation', 
    6405 baseOperation = glClear, 
    6406 cArguments = (16640,) 
    6407 ) 
    6408  
    6409 OpenGL.error.GLError: GLError( 
    6410 err = 1286, 
    6411 description = b'invalid framebuffer operation', 
    6412 baseOperation = glClear, 
    6413 cArguments = (16640,) 
    6414 ) 
    6415  
    6416 File "src/errorchecker.pyx", line 59, in
    6417 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    6418  
    6419 See log for complete Python traceback. 
    6420  
    6421 Traceback (most recent call last): 
    6422 File
    6423 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6424 packages/chimerax/ui/statusbar.py", line 98, in _expose_event 
    6425 self.status(self._last_message, self._last_color) 
    6426 File
    6427 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6428 packages/chimerax/ui/statusbar.py", line 164, in status 
    6429 r.draw_background() 
    6430 File
    6431 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6432 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    6433 GL.glClear(flags) 
    6434 File "src/errorchecker.pyx", line 59, in
    6435 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    6436 OpenGL.error.GLError: GLError( 
    6437 err = 1286, 
    6438 description = b'invalid framebuffer operation', 
    6439 baseOperation = glClear, 
    6440 cArguments = (16640,) 
    6441 ) 
    6442  
    6443 OpenGL.error.GLError: GLError( 
    6444 err = 1286, 
    6445 description = b'invalid framebuffer operation', 
    6446 baseOperation = glClear, 
    6447 cArguments = (16640,) 
    6448 ) 
    6449  
    6450 File "src/errorchecker.pyx", line 59, in
    6451 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    6452  
    6453 See log for complete Python traceback. 
    6454  
    6455 
    6456 > hide #!1 models
    6457 
    6458 > hide #4 models
    6459 
    6460 > hide #6 models
    6461 
    6462 > hide #7 models
    6463 
    6464 > show #6 models
    6465 
    6466 > hide #6 models
    6467 
    6468 > select clear
    6469 
    6470 Traceback (most recent call last): 
    6471 File
    6472 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6473 packages/chimerax/mouse_modes/mousemodes.py", line 656, in   
    6474 gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
    6475 "mouse_up") 
    6476 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    6477 File
    6478 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6479 packages/chimerax/mouse_modes/mousemodes.py", line 556, in
    6480 _dispatch_mouse_event 
    6481 f(MouseEvent(event, modifiers=modifiers)) 
    6482 File
    6483 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6484 packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up 
    6485 mouse_select(event, mode, self.session, self.view) 
    6486 File
    6487 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6488 packages/chimerax/mouse_modes/std_modes.py", line 210, in mouse_select 
    6489 select_pick(session, pick, mode) 
    6490 File
    6491 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6492 packages/chimerax/mouse_modes/std_modes.py", line 227, in select_pick 
    6493 session.logger.status('cleared selection') 
    6494 File
    6495 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6496 packages/chimerax/core/logger.py", line 522, in status 
    6497 StatusLogger.status(self, msg, **kw) 
    6498 File
    6499 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6500 packages/chimerax/core/logger.py", line 220, in status 
    6501 if l.status(msg, color, secondary) and getattr( 
    6502 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    6503 File
    6504 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6505 packages/chimerax/ui/gui.py", line 1085, in status 
    6506 sbar.status(msg, color, secondary) 
    6507 File
    6508 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6509 packages/chimerax/ui/statusbar.py", line 164, in status 
    6510 r.draw_background() 
    6511 File
    6512 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6513 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    6514 GL.glClear(flags) 
    6515 File "src/errorchecker.pyx", line 59, in
    6516 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    6517 OpenGL.error.GLError: GLError( 
    6518 err = 1286, 
    6519 description = b'invalid framebuffer operation', 
    6520 baseOperation = glClear, 
    6521 cArguments = (16640,) 
    6522 ) 
    6523  
    6524 OpenGL.error.GLError: GLError( 
    6525 err = 1286, 
    6526 description = b'invalid framebuffer operation', 
    6527 baseOperation = glClear, 
    6528 cArguments = (16640,) 
    6529 ) 
    6530  
    6531 File "src/errorchecker.pyx", line 59, in
    6532 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    6533  
    6534 See log for complete Python traceback. 
    6535  
    6536 
    6537 > select #5/H:39
    6538 
    6539 17 atoms, 16 bonds, 1 residue, 1 model selected 
    6540 Traceback (most recent call last): 
    6541 File
    6542 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6543 packages/chimerax/mouse_modes/mousemodes.py", line 656, in   
    6544 gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
    6545 "mouse_up") 
    6546 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    6547 File
    6548 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6549 packages/chimerax/mouse_modes/mousemodes.py", line 556, in
    6550 _dispatch_mouse_event 
    6551 f(MouseEvent(event, modifiers=modifiers)) 
    6552 File
    6553 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6554 packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up 
    6555 mouse_select(event, mode, self.session, self.view) 
    6556 File
    6557 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6558 packages/chimerax/mouse_modes/std_modes.py", line 210, in mouse_select 
    6559 select_pick(session, pick, mode) 
    6560 File
    6561 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6562 packages/chimerax/mouse_modes/std_modes.py", line 241, in select_pick 
    6563 run(session, 'select %s' % spec) 
    6564 File
    6565 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6566 packages/chimerax/core/commands/run.py", line 49, in run 
    6567 results = command.run(text, log=log, return_json=return_json) 
    6568 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    6569 File
    6570 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6571 packages/chimerax/core/commands/cli.py", line 3221, in run 
    6572 result = ci.function(session, **kw_args) 
    6573 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    6574 File
    6575 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6576 packages/chimerax/std_commands/select.py", line 62, in select 
    6577 report_selection(session) 
    6578 File
    6579 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6580 packages/chimerax/std_commands/select.py", line 192, in report_selection 
    6581 session.logger.status(', '.join(lines) + ' selected', log = True) 
    6582 File
    6583 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6584 packages/chimerax/core/logger.py", line 522, in status 
    6585 StatusLogger.status(self, msg, **kw) 
    6586 File
    6587 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6588 packages/chimerax/core/logger.py", line 220, in status 
    6589 if l.status(msg, color, secondary) and getattr( 
    6590 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    6591 File
    6592 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6593 packages/chimerax/ui/gui.py", line 1085, in status 
    6594 sbar.status(msg, color, secondary) 
    6595 File
    6596 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6597 packages/chimerax/ui/statusbar.py", line 164, in status 
    6598 r.draw_background() 
    6599 File
    6600 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6601 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    6602 GL.glClear(flags) 
    6603 File "src/errorchecker.pyx", line 59, in
    6604 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    6605 OpenGL.error.GLError: GLError( 
    6606 err = 1286, 
    6607 description = b'invalid framebuffer operation', 
    6608 baseOperation = glClear, 
    6609 cArguments = (16640,) 
    6610 ) 
    6611  
    6612 OpenGL.error.GLError: GLError( 
    6613 err = 1286, 
    6614 description = b'invalid framebuffer operation', 
    6615 baseOperation = glClear, 
    6616 cArguments = (16640,) 
    6617 ) 
    6618  
    6619 File "src/errorchecker.pyx", line 59, in
    6620 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    6621  
    6622 See log for complete Python traceback. 
    6623  
    6624 
    6625 > select add #5/G:93
    6626 
    6627 33 atoms, 31 bonds, 2 residues, 1 model selected 
    6628 Traceback (most recent call last): 
    6629 File
    6630 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6631 packages/chimerax/mouse_modes/mousemodes.py", line 656, in   
    6632 gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
    6633 "mouse_up") 
    6634 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    6635 File
    6636 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6637 packages/chimerax/mouse_modes/mousemodes.py", line 556, in
    6638 _dispatch_mouse_event 
    6639 f(MouseEvent(event, modifiers=modifiers)) 
    6640 File
    6641 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6642 packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up 
    6643 mouse_select(event, mode, self.session, self.view) 
    6644 File
    6645 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6646 packages/chimerax/mouse_modes/std_modes.py", line 210, in mouse_select 
    6647 select_pick(session, pick, mode) 
    6648 File
    6649 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6650 packages/chimerax/mouse_modes/std_modes.py", line 245, in select_pick 
    6651 run(session, 'select %s %s' % (operation, spec)) 
    6652 File
    6653 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6654 packages/chimerax/core/commands/run.py", line 49, in run 
    6655 results = command.run(text, log=log, return_json=return_json) 
    6656 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    6657 File
    6658 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6659 packages/chimerax/core/commands/cli.py", line 3221, in run 
    6660 result = ci.function(session, **kw_args) 
    6661 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    6662 File
    6663 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6664 packages/chimerax/std_commands/select.py", line 120, in select_add 
    6665 report_selection(session) 
    6666 File
    6667 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6668 packages/chimerax/std_commands/select.py", line 192, in report_selection 
    6669 session.logger.status(', '.join(lines) + ' selected', log = True) 
    6670 File
    6671 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6672 packages/chimerax/core/logger.py", line 522, in status 
    6673 StatusLogger.status(self, msg, **kw) 
    6674 File
    6675 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6676 packages/chimerax/core/logger.py", line 220, in status 
    6677 if l.status(msg, color, secondary) and getattr( 
    6678 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    6679 File
    6680 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6681 packages/chimerax/ui/gui.py", line 1085, in status 
    6682 sbar.status(msg, color, secondary) 
    6683 File
    6684 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6685 packages/chimerax/ui/statusbar.py", line 164, in status 
    6686 r.draw_background() 
    6687 File
    6688 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6689 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    6690 GL.glClear(flags) 
    6691 File "src/errorchecker.pyx", line 59, in
    6692 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    6693 OpenGL.error.GLError: GLError( 
    6694 err = 1286, 
    6695 description = b'invalid framebuffer operation', 
    6696 baseOperation = glClear, 
    6697 cArguments = (16640,) 
    6698 ) 
    6699  
    6700 OpenGL.error.GLError: GLError( 
    6701 err = 1286, 
    6702 description = b'invalid framebuffer operation', 
    6703 baseOperation = glClear, 
    6704 cArguments = (16640,) 
    6705 ) 
    6706  
    6707 File "src/errorchecker.pyx", line 59, in
    6708 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    6709  
    6710 See log for complete Python traceback. 
    6711  
    6712 
    6713 > select up
    6714 
    6715 218 atoms, 221 bonds, 13 residues, 1 model selected 
    6716 Traceback (most recent call last): 
    6717 File
    6718 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6719 packages/chimerax/ui/gui.py", line 393, in forward_keystroke 
    6720 run(self.session, 'select up') 
    6721 File
    6722 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6723 packages/chimerax/core/commands/run.py", line 49, in run 
    6724 results = command.run(text, log=log, return_json=return_json) 
    6725 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    6726 File
    6727 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6728 packages/chimerax/core/commands/cli.py", line 3221, in run 
    6729 result = ci.function(session, **kw_args) 
    6730 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    6731 File
    6732 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6733 packages/chimerax/std_commands/select.py", line 145, in select_up 
    6734 report_selection(session) 
    6735 File
    6736 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6737 packages/chimerax/std_commands/select.py", line 192, in report_selection 
    6738 session.logger.status(', '.join(lines) + ' selected', log = True) 
    6739 File
    6740 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6741 packages/chimerax/core/logger.py", line 522, in status 
    6742 StatusLogger.status(self, msg, **kw) 
    6743 File
    6744 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6745 packages/chimerax/core/logger.py", line 220, in status 
    6746 if l.status(msg, color, secondary) and getattr( 
    6747 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    6748 File
    6749 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6750 packages/chimerax/ui/gui.py", line 1085, in status 
    6751 sbar.status(msg, color, secondary) 
    6752 File
    6753 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6754 packages/chimerax/ui/statusbar.py", line 164, in status 
    6755 r.draw_background() 
    6756 File
    6757 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6758 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    6759 GL.glClear(flags) 
    6760 File "src/errorchecker.pyx", line 59, in
    6761 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    6762 OpenGL.error.GLError: GLError( 
    6763 err = 1286, 
    6764 description = b'invalid framebuffer operation', 
    6765 baseOperation = glClear, 
    6766 cArguments = (16640,) 
    6767 ) 
    6768  
    6769 OpenGL.error.GLError: GLError( 
    6770 err = 1286, 
    6771 description = b'invalid framebuffer operation', 
    6772 baseOperation = glClear, 
    6773 cArguments = (16640,) 
    6774 ) 
    6775  
    6776 File "src/errorchecker.pyx", line 59, in
    6777 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    6778  
    6779 See log for complete Python traceback. 
    6780  
    6781 
    6782 > select up
    6783 
    6784 3494 atoms, 3537 bonds, 236 residues, 1 model selected 
    6785 Traceback (most recent call last): 
    6786 File
    6787 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6788 packages/chimerax/ui/gui.py", line 393, in forward_keystroke 
    6789 run(self.session, 'select up') 
    6790 File
    6791 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6792 packages/chimerax/core/commands/run.py", line 49, in run 
    6793 results = command.run(text, log=log, return_json=return_json) 
    6794 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    6795 File
    6796 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6797 packages/chimerax/core/commands/cli.py", line 3221, in run 
    6798 result = ci.function(session, **kw_args) 
    6799 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    6800 File
    6801 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6802 packages/chimerax/std_commands/select.py", line 145, in select_up 
    6803 report_selection(session) 
    6804 File
    6805 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6806 packages/chimerax/std_commands/select.py", line 192, in report_selection 
    6807 session.logger.status(', '.join(lines) + ' selected', log = True) 
    6808 File
    6809 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6810 packages/chimerax/core/logger.py", line 522, in status 
    6811 StatusLogger.status(self, msg, **kw) 
    6812 File
    6813 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6814 packages/chimerax/core/logger.py", line 220, in status 
    6815 if l.status(msg, color, secondary) and getattr( 
    6816 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    6817 File
    6818 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6819 packages/chimerax/ui/gui.py", line 1085, in status 
    6820 sbar.status(msg, color, secondary) 
    6821 File
    6822 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6823 packages/chimerax/ui/statusbar.py", line 164, in status 
    6824 r.draw_background() 
    6825 File
    6826 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6827 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    6828 GL.glClear(flags) 
    6829 File "src/errorchecker.pyx", line 59, in
    6830 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    6831 OpenGL.error.GLError: GLError( 
    6832 err = 1286, 
    6833 description = b'invalid framebuffer operation', 
    6834 baseOperation = glClear, 
    6835 cArguments = (16640,) 
    6836 ) 
    6837  
    6838 OpenGL.error.GLError: GLError( 
    6839 err = 1286, 
    6840 description = b'invalid framebuffer operation', 
    6841 baseOperation = glClear, 
    6842 cArguments = (16640,) 
    6843 ) 
    6844  
    6845 File "src/errorchecker.pyx", line 59, in
    6846 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    6847  
    6848 See log for complete Python traceback. 
    6849  
    6850 
    6851 > show #6 models
    6852 
    6853 > show #7 models
    6854 
    6855 > show #4 models
    6856 
    6857 > ui tool show Matchmaker
    6858 
    6859 [Repeated 1 time(s)]
    6860 
    6861 > matchmaker #4,6-7 to #5 & sel
    6862 
    6863 Parameters 
    6864 --- 
    6865 Chain pairing | bb 
    6866 Alignment algorithm | Needleman-Wunsch 
    6867 Similarity matrix | BLOSUM-62 
    6868 SS fraction | 0.3 
    6869 Gap open (HH/SS/other) | 18/18/6 
    6870 Gap extend | 1 
    6871 SS matrix |  |  | H | S | O 
    6872 ---|---|---|--- 
    6873 H | 6 | -9 | -6 
    6874 S |  | 6 | -6 
    6875 O |  |  | 4 
    6876 Iteration cutoff | 2 
    6877  
    6878 Matchmaker design_start.pdb, chain G (#5) with Cluster2c_lib1.pdb, chain G
    6879 (#4), sequence alignment score = 665.8 
    6880 Traceback (most recent call last): 
    6881 File
    6882 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6883 packages/chimerax/match_maker/tool.py", line 175, in   
    6884 bbox.button(qbbox.Apply).clicked.connect(lambda *args:
    6885 self.run_matchmaker(apply=True)) 
    6886 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    6887 File
    6888 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6889 packages/chimerax/match_maker/tool.py", line 312, in run_matchmaker 
    6890 run(self.session, cmd) 
    6891 File
    6892 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6893 packages/chimerax/core/commands/run.py", line 49, in run 
    6894 results = command.run(text, log=log, return_json=return_json) 
    6895 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    6896 File
    6897 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6898 packages/chimerax/core/commands/cli.py", line 3221, in run 
    6899 result = ci.function(session, **kw_args) 
    6900 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    6901 File
    6902 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6903 packages/chimerax/match_maker/match.py", line 777, in cmd_match 
    6904 ret_vals = match(session, pairing, match_items, matrix, alg, gap_open,
    6905 gap_extend, 
    6906 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    6907 File
    6908 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6909 packages/chimerax/match_maker/match.py", line 552, in match 
    6910 logger.status("Matchmaker %s (#%s) with %s (#%s)," 
    6911 File
    6912 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6913 packages/chimerax/core/logger.py", line 522, in status 
    6914 StatusLogger.status(self, msg, **kw) 
    6915 File
    6916 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6917 packages/chimerax/core/logger.py", line 220, in status 
    6918 if l.status(msg, color, secondary) and getattr( 
    6919 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
    6920 File
    6921 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6922 packages/chimerax/ui/gui.py", line 1085, in status 
    6923 sbar.status(msg, color, secondary) 
    6924 File
    6925 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6926 packages/chimerax/ui/statusbar.py", line 164, in status 
    6927 r.draw_background() 
    6928 File
    6929 "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
    6930 packages/chimerax/graphics/opengl.py", line 1238, in draw_background 
    6931 GL.glClear(flags) 
    6932 File "src/errorchecker.pyx", line 59, in
    6933 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    6934 OpenGL.error.GLError: GLError( 
    6935 err = 1286, 
    6936 description = b'invalid framebuffer operation', 
    6937 baseOperation = glClear, 
    6938 cArguments = (16640,) 
    6939 ) 
    6940  
    6941 OpenGL.error.GLError: GLError( 
    6942 err = 1286, 
    6943 description = b'invalid framebuffer operation', 
    6944 baseOperation = glClear, 
    6945 cArguments = (16640,) 
    6946 ) 
    6947  
    6948 File "src/errorchecker.pyx", line 59, in
    6949 OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError 
    6950  
    6951 See log for complete Python traceback. 
    6952  
    6953 
    6954 > save /Users/oswanson/Desktop/Primocalins/Structures/initial_models.cxs
    6955 
    6956 ——— End of log from Fri Oct 31 13:49:15 2025 ———
    6957 
    6958 > view name session-start
    6959 
    6960 opened ChimeraX session 
    6961 
    6962 > ui tool show Matchmaker
    6963 
    6964 > matchmaker #4,6-7 to #5 & sel
    6965 
    6966 Parameters 
    6967 --- 
    6968 Chain pairing | bb 
    6969 Alignment algorithm | Needleman-Wunsch 
    6970 Similarity matrix | BLOSUM-62 
    6971 SS fraction | 0.3 
    6972 Gap open (HH/SS/other) | 18/18/6 
    6973 Gap extend | 1 
    6974 SS matrix |  |  | H | S | O 
    6975 ---|---|---|--- 
    6976 H | 6 | -9 | -6 
    6977 S |  | 6 | -6 
    6978 O |  |  | 4 
    6979 Iteration cutoff | 2 
    6980  
    6981 Matchmaker design_start.pdb, chain G (#5) with Cluster2c_lib1.pdb, chain G
    6982 (#4), sequence alignment score = 665.8 
    6983 RMSD between 126 pruned atom pairs is 0.098 angstroms; (across all 126 pairs:
    6984 0.098) 
    6985  
    6986 Matchmaker design_start.pdb, chain G (#5) with RMSD4_NNK1.pdb, chain G (#6),
    6987 sequence alignment score = 665.8 
    6988 RMSD between 126 pruned atom pairs is 0.168 angstroms; (across all 126 pairs:
    6989 0.168) 
    6990  
    6991 Matchmaker design_start.pdb, chain G (#5) with RMSD6_NNK1.pdb, chain G (#7),
    6992 sequence alignment score = 665.8 
    6993 RMSD between 126 pruned atom pairs is 0.200 angstroms; (across all 126 pairs:
    6994 0.200) 
    6995  
    6996 
    6997 > select clear
    6998 
    6999 > hide #5 models
    7000 
    7001 > hide #4 models
    7002 
    7003 > hide #6 models
    7004 
    7005 > select #7/G:101
    7006 
    7007 24 atoms, 25 bonds, 1 residue, 1 model selected 
    7008 
    7009 > select up
    7010 
    7011 327 atoms, 336 bonds, 22 residues, 1 model selected 
    7012 
    7013 > select subtract #7/G:120
    7014 
    7015 320 atoms, 329 bonds, 21 residues, 1 model selected 
    7016 
    7017 > select #7/G:23
    7018 
    7019 22 atoms, 21 bonds, 1 residue, 1 model selected 
    7020 
    7021 > select up
    7022 
    7023 118 atoms, 117 bonds, 8 residues, 1 model selected 
    7024 
    7025 > select up
    7026 
    7027 1925 atoms, 1953 bonds, 126 residues, 1 model selected 
    7028 
    7029 > ui tool show "Color Actions"
    7030 
    7031 > color sel pale goldenrod
    7032 
    7033 > select #7/H:22
    7034 
    7035 10 atoms, 9 bonds, 1 residue, 1 model selected 
    7036 
    7037 > select up
    7038 
    7039 87 atoms, 86 bonds, 6 residues, 1 model selected 
    7040 
    7041 > select up
    7042 
    7043 1569 atoms, 1584 bonds, 110 residues, 1 model selected 
    7044 
    7045 > color sel cornsilk
    7046 
    7047 > color sel floral white
    7048 
    7049 > color sel light yellow
    7050 
    7051 > select clear
    7052 
    7053 Drag select of 1 residues 
    7054 
    7055 > select up
    7056 
    7057 327 atoms, 336 bonds, 22 residues, 1 model selected 
    7058 
    7059 > select subtract #7/G:113
    7060 
    7061 313 atoms, 321 bonds, 21 residues, 1 model selected 
    7062 
    7063 > select subtract #7/G:114
    7064 
    7065 293 atoms, 300 bonds, 20 residues, 1 model selected 
    7066 
    7067 > select subtract #7/G:116
    7068 
    7069 272 atoms, 277 bonds, 19 residues, 1 model selected 
    7070 
    7071 > select subtract #7/G:115
    7072 
    7073 260 atoms, 266 bonds, 18 residues, 1 model selected 
    7074 
    7075 > select subtract #7/G:117
    7076 
    7077 236 atoms, 240 bonds, 17 residues, 1 model selected 
    7078 
    7079 > select subtract #7/G:118
    7080 
    7081 229 atoms, 233 bonds, 16 residues, 1 model selected 
    7082 
    7083 > select subtract #7/G:120
    7084 
    7085 222 atoms, 226 bonds, 15 residues, 1 model selected 
    7086 
    7087 > select add #7/G:113
    7088 
    7089 236 atoms, 239 bonds, 16 residues, 1 model selected 
    7090 
    7091 > select add #7/G:114
    7092 
    7093 256 atoms, 259 bonds, 17 residues, 1 model selected 
    7094 
    7095 > select add #7/G:115
    7096 
    7097 268 atoms, 270 bonds, 18 residues, 1 model selected 
    7098 
    7099 > select add #7/G:116
    7100 
    7101 289 atoms, 291 bonds, 19 residues, 1 model selected 
    7102 
    7103 > select add #7/G:117
    7104 
    7105 313 atoms, 316 bonds, 20 residues, 1 model selected 
    7106 
    7107 > select add #7/G:98
    7108 
    7109 337 atoms, 339 bonds, 21 residues, 1 model selected 
    7110 
    7111 > select subtract #7/G:119
    7112 
    7113 320 atoms, 323 bonds, 20 residues, 1 model selected 
    7114 
    7115 > select subtract #7/G:117
    7116 
    7117 296 atoms, 298 bonds, 19 residues, 1 model selected 
    7118 
    7119 > color sel royal blue
    7120 
    7121 > color sel cornflower blue
    7122 
    7123 > color sel deep sky blue
    7124 
    7125 > lighting soft
    7126 
    7127 > lighting shadows true intensity 0.5
    7128 
    7129 > graphics silhouettes true
    7130 
    7131 > lighting shadows false
    7132 
    7133 > lighting soft
    7134 
    7135 > lighting full
    7136 
    7137 > lighting flat
    7138 
    7139 > lighting full
    7140 
    7141 > lighting soft
    7142 
    7143 > lighting shadows true intensity 0.5
    7144 
    7145 > lighting shadows false
    7146 
    7147 > lighting shadows true
    7148 
    7149 > lighting shadows false
    7150 
    7151 > lighting simple
    7152 
    7153 > lighting soft
    7154 
    7155 > ui tool show "Side View"
    7156 
    7157 > color sel deep sky blue
    7158 
    7159 > color sel light steel blue
    7160 
    7161 > color sel sky blue
    7162 
    7163 > color sel light sky blue
    7164 
    7165 > color sel light cyan
    7166 
    7167 > color sel sky blue
    7168 
    7169 > select clear
    7170 
    7171 > select #7/A:70
    7172 
    7173 24 atoms, 23 bonds, 1 residue, 1 model selected 
    7174 
    7175 > select up
    7176 
    7177 155 atoms, 156 bonds, 9 residues, 1 model selected 
    7178 
    7179 > select up
    7180 
    7181 2806 atoms, 2845 bonds, 174 residues, 1 model selected 
    7182 
    7183 > show #!1 models
    7184 
    7185 > hide #!1 models
    7186 
    7187 > matchmaker #!1 to #5 & sel
    7188 
    7189 No 'to' model specified 
    7190 
    7191 > matchmaker #!1 to #5
    7192 
    7193 Parameters 
    7194 --- 
    7195 Chain pairing | bb 
    7196 Alignment algorithm | Needleman-Wunsch 
    7197 Similarity matrix | BLOSUM-62 
    7198 SS fraction | 0.3 
    7199 Gap open (HH/SS/other) | 18/18/6 
    7200 Gap extend | 1 
    7201 SS matrix |  |  | H | S | O 
    7202 ---|---|---|--- 
    7203 H | 6 | -9 | -6 
    7204 S |  | 6 | -6 
    7205 O |  |  | 4 
    7206 Iteration cutoff | 2 
    7207  
    7208 Matchmaker design_start.pdb, chain A (#5) with
    7209 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1), sequence alignment
    7210 score = 709.7 
    7211 RMSD between 150 pruned atom pairs is 0.630 angstroms; (across all 164 pairs:
    7212 1.402) 
    7213  
    7214 
    7215 > show #!1 models
    7216 
    7217 > hide #!1 models
    7218 
    7219 > show #5 models
    7220 
    7221 > hide #7 models
    7222 
    7223 > select #5/G:5
    7224 
    7225 16 atoms, 15 bonds, 1 residue, 1 model selected 
    7226 
    7227 > select up
    7228 
    7229 69 atoms, 68 bonds, 4 residues, 1 model selected 
    7230 
    7231 > select up
    7232 
    7233 1925 atoms, 1953 bonds, 126 residues, 1 model selected 
    7234 
    7235 > select up
    7236 
    7237 6339 atoms, 6419 bonds, 410 residues, 1 model selected 
    7238 
    7239 > select down
    7240 
    7241 1925 atoms, 1953 bonds, 126 residues, 1 model selected 
    7242 
    7243 > matchmaker #!1 to #5 & sel
    7244 
    7245 Parameters 
    7246 --- 
    7247 Chain pairing | bb 
    7248 Alignment algorithm | Needleman-Wunsch 
    7249 Similarity matrix | BLOSUM-62 
    7250 SS fraction | 0.3 
    7251 Gap open (HH/SS/other) | 18/18/6 
    7252 Gap extend | 1 
    7253 SS matrix |  |  | H | S | O 
    7254 ---|---|---|--- 
    7255 H | 6 | -9 | -6 
    7256 S |  | 6 | -6 
    7257 O |  |  | 4 
    7258 Iteration cutoff | 2 
    7259  
    7260 Matchmaker design_start.pdb, chain G (#5) with
    7261 231023_poly310-DH270UCA3_refine_001.pdb, chain H (#1), sequence alignment
    7262 score = 638.8 
    7263 RMSD between 125 pruned atom pairs is 0.800 angstroms; (across all 126 pairs:
    7264 0.817) 
    7265  
    7266 
    7267 > show #!1 models
    7268 
    7269 > hide #5 models
    7270 
    7271 > show #6 models
    7272 
    7273 > show #7 models
    7274 
    7275 > hide #7 models
    7276 
    7277 > hide #6 models
    7278 
    7279 > show #6 models
    7280 
    7281 > show #7 models
    7282 
    7283 > select clear
    7284 
    7285 > select #6/A:130
    7286 
    7287 21 atoms, 21 bonds, 1 residue, 1 model selected 
    7288 
    7289 > select up
    7290 
    7291 167 atoms, 170 bonds, 10 residues, 1 model selected 
    7292 
    7293 > select up
    7294 
    7295 2815 atoms, 2853 bonds, 174 residues, 1 model selected 
    7296 
    7297 > color sel pink
    7298 
    7299 > hide #!1 models
    7300 
    7301 > hide #7 models
    7302 
    7303 > select #6/G:5
    7304 
    7305 16 atoms, 15 bonds, 1 residue, 1 model selected 
    7306 
    7307 > select up
    7308 
    7309 69 atoms, 68 bonds, 4 residues, 1 model selected 
    7310 
    7311 > select up
    7312 
    7313 1925 atoms, 1953 bonds, 126 residues, 1 model selected 
    7314 
    7315 > color sel pale goldenrod
    7316 
    7317 > select #6/H:22
    7318 
    7319 10 atoms, 9 bonds, 1 residue, 1 model selected 
    7320 
    7321 > select up
    7322 
    7323 87 atoms, 86 bonds, 6 residues, 1 model selected 
    7324 
    7325 > select up
    7326 
    7327 1569 atoms, 1584 bonds, 110 residues, 1 model selected 
    7328 
    7329 > color sel light yellow
    7330 
    7331 > select clear
    7332 
    7333 > select #6/G:102
    7334 
    7335 19 atoms, 18 bonds, 1 residue, 1 model selected 
    7336 
    7337 > select up
    7338 
    7339 327 atoms, 336 bonds, 22 residues, 1 model selected 
    7340 
    7341 > select #6/G:120
    7342 
    7343 7 atoms, 6 bonds, 1 residue, 1 model selected 
    7344 
    7345 > select #6/G:103
    7346 
    7347 11 atoms, 10 bonds, 1 residue, 1 model selected 
    7348 
    7349 > select up
    7350 
    7351 327 atoms, 336 bonds, 22 residues, 1 model selected 
    7352 
    7353 > select subtract #6/G:120
    7354 
    7355 320 atoms, 329 bonds, 21 residues, 1 model selected 
    7356 
    7357 > select subtract #6/G:119
    7358 
    7359 303 atoms, 312 bonds, 20 residues, 1 model selected 
    7360 
    7361 > select subtract #6/G:118
    7362 
    7363 296 atoms, 305 bonds, 19 residues, 1 model selected 
    7364 
    7365 > select subtract #6/G:117
    7366 
    7367 272 atoms, 279 bonds, 18 residues, 1 model selected 
    7368 
    7369 > color sel sky blue
    7370 
    7371 > select clear
    7372 
    7373 > show #7 models
    7374 
    7375 > hide #7 models
    7376 
    7377 > select #6/G:98
    7378 
    7379 24 atoms, 23 bonds, 1 residue, 1 model selected 
    7380 
    7381 > color sel sky blue
    7382 
    7383 > select clear
    7384 
    7385 > show #7 models
    7386 
    7387 > hide #6 models
    7388 
    7389 > show #6 models
    7390 
    7391 > hide #7 models
    7392 
    7393 > preset cartoons/nucleotides licorice/ovals
    7394 
    7395 Using preset: Cartoons/Nucleotides / Licorice/Ovals 
    7396 Changed 0 atom styles 
    7397 Preset expands to these ChimeraX commands:
    7398 
    7399    
    7400    
    7401     show nucleic
    7402     hide protein|solvent|H
    7403     surf hide
    7404     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    7405     ~worm
    7406     cartoon
    7407     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    7408     cartoon style ~(nucleic|strand) x round
    7409     cartoon style (nucleic|strand) x rect
    7410     cartoon style protein modeh default arrows f x round width 1 thick 1
    7411     cartoon style nucleic x round width 1.6 thick 1.6
    7412     nucleotides tube/slab shape ellipsoid
    7413 
    7414  
    7415 
    7416 > preset cartoons/nucleotides cylinders/stubs
    7417 
    7418 Using preset: Cartoons/Nucleotides / Cylinders/Stubs 
    7419 Changed 0 atom styles 
    7420 Preset expands to these ChimeraX commands:
    7421 
    7422    
    7423    
    7424     show nucleic
    7425     hide protein|solvent|H
    7426     surf hide
    7427     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    7428     ~worm
    7429     cartoon
    7430     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    7431     cartoon style ~(nucleic|strand) x round
    7432     cartoon style (nucleic|strand) x rect
    7433     cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    7434     cartoon style nucleic x round width 1.6 thick 1.6
    7435     nucleotides stubs
    7436 
    7437  
    7438 
    7439 > preset cartoons/nucleotides ribbons/slabs
    7440 
    7441 Using preset: Cartoons/Nucleotides / Ribbons/Slabs 
    7442 Changed 0 atom styles 
    7443 Preset expands to these ChimeraX commands:
    7444 
    7445    
    7446    
    7447     show nucleic
    7448     hide protein|solvent|H
    7449     surf hide
    7450     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    7451     ~worm
    7452     cartoon
    7453     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    7454     cartoon style ~(nucleic|strand) x round
    7455     cartoon style (nucleic|strand) x rect
    7456     nucleotides tube/slab shape box
    7457 
    7458  
    7459 
    7460 > show #7 models
    7461 
    7462 > hide #6 models
    7463 
    7464 > show #6 models
    7465 
    7466 > hide #7 models
    7467 
    7468 > hide #6 models
    7469 
    7470 > show #4 models
    7471 
    7472 > show #6 models
    7473 
    7474 > hide #6 models
    7475 
    7476 > select #4/G:47
    7477 
    7478 24 atoms, 25 bonds, 1 residue, 1 model selected 
    7479 
    7480 > select up
    7481 
    7482 75 atoms, 76 bonds, 4 residues, 1 model selected 
    7483 
    7484 > select up
    7485 
    7486 1925 atoms, 1953 bonds, 126 residues, 1 model selected 
    7487 
    7488 > color sel pale goldenrod
    7489 
    7490 > select #4/H:87
    7491 
    7492 12 atoms, 11 bonds, 1 residue, 1 model selected 
    7493 
    7494 > select up
    7495 
    7496 124 atoms, 126 bonds, 9 residues, 1 model selected 
    7497 
    7498 > select up
    7499 
    7500 1569 atoms, 1584 bonds, 110 residues, 1 model selected 
    7501 
    7502 > color sel light yellow
    7503 
    7504 > select clear
    7505 
    7506 > select #4/G:101
    7507 
    7508 24 atoms, 25 bonds, 1 residue, 1 model selected 
    7509 
    7510 > select up
    7511 
    7512 327 atoms, 336 bonds, 22 residues, 1 model selected 
    7513 
    7514 > select #4/G:98
    7515 
    7516 24 atoms, 23 bonds, 1 residue, 1 model selected 
    7517 
    7518 > select clear
    7519 
    7520 > select #4/G:109
    7521 
    7522 11 atoms, 10 bonds, 1 residue, 1 model selected 
    7523 
    7524 > select up
    7525 
    7526 327 atoms, 336 bonds, 22 residues, 1 model selected 
    7527 
    7528 > select add #4/G:98
    7529 
    7530 351 atoms, 359 bonds, 23 residues, 1 model selected 
    7531 
    7532 > select subtract #4/G:116
    7533 
    7534 330 atoms, 336 bonds, 22 residues, 1 model selected 
    7535 
    7536 > select subtract #4/G:117
    7537 
    7538 306 atoms, 310 bonds, 21 residues, 1 model selected 
    7539 
    7540 > select subtract #4/G:119
    7541 
    7542 289 atoms, 292 bonds, 20 residues, 1 model selected 
    7543 
    7544 > select add #4/G:95
    7545 
    7546 310 atoms, 313 bonds, 21 residues, 1 model selected 
    7547 
    7548 > select add #4/G:119
    7549 
    7550 327 atoms, 329 bonds, 22 residues, 1 model selected 
    7551 
    7552 > select subtract #4/G:95
    7553 
    7554 306 atoms, 308 bonds, 21 residues, 1 model selected 
    7555 
    7556 > select subtract #4/G:118
    7557 
    7558 299 atoms, 302 bonds, 20 residues, 1 model selected 
    7559 
    7560 > select subtract #4/G:119
    7561 
    7562 282 atoms, 286 bonds, 19 residues, 1 model selected 
    7563 
    7564 > select subtract #4/G:120
    7565 
    7566 275 atoms, 280 bonds, 18 residues, 1 model selected 
    7567 
    7568 > color sel sky blue
    7569 
    7570 > show #6 models
    7571 
    7572 > hide #6 models
    7573 
    7574 > show #7 models
    7575 
    7576 > hide #7 models
    7577 
    7578 > select clear
    7579 
    7580 > show #6 models
    7581 
    7582 > hide #6 models
    7583 
    7584 > show #!1 models
    7585 
    7586 > show #6 models
    7587 
    7588 > show #7 models
    7589 
    7590 > hide #4 models
    7591 
    7592 > hide #6 models
    7593 
    7594 > show #6 models
    7595 
    7596 > hide #!1 models
    7597 
    7598 > hide #7 models
    7599 
    7600 > show #7 models
    7601 
    7602 > hide #6 models
    7603 
    7604 > show #6 models
    7605 
    7606 > hide #7 models
    7607 
    7608 > show #4 models
    7609 
    7610 > hide #6 models
    7611 
    7612 > show #6 models
    7613 
    7614 > hide #4 models
    7615 
    7616 > show #7 models
    7617 
    7618 > hide #6 models
    7619 
    7620 > show #6 models
    7621 
    7622 > hide #6 models
    7623 
    7624 > show #5 models
    7625 
    7626 > hide #5 models
    7627 
    7628 > show #4 models
    7629 
    7630 > hide #4 models
    7631 
    7632 > show #6 models
    7633 
    7634 > select clear
    7635 
    7636 > select #6/A:76
    7637 
    7638 10 atoms, 9 bonds, 1 residue, 1 model selected 
    7639 
    7640 > select up
    7641 
    7642 178 atoms, 180 bonds, 11 residues, 1 model selected 
    7643 
    7644 > select up
    7645 
    7646 2815 atoms, 2853 bonds, 174 residues, 1 model selected 
    7647 
    7648 > select up
    7649 
    7650 6309 atoms, 6390 bonds, 410 residues, 1 model selected 
    7651 
    7652 > select down
    7653 
    7654 2815 atoms, 2853 bonds, 174 residues, 1 model selected 
    7655 
    7656 > matchmaker #7 to #6 & sel
    7657 
    7658 Parameters 
    7659 --- 
    7660 Chain pairing | bb 
    7661 Alignment algorithm | Needleman-Wunsch 
    7662 Similarity matrix | BLOSUM-62 
    7663 SS fraction | 0.3 
    7664 Gap open (HH/SS/other) | 18/18/6 
    7665 Gap extend | 1 
    7666 SS matrix |  |  | H | S | O 
    7667 ---|---|---|--- 
    7668 H | 6 | -9 | -6 
    7669 S |  | 6 | -6 
    7670 O |  |  | 4 
    7671 Iteration cutoff | 2 
    7672  
    7673 Matchmaker RMSD4_NNK1.pdb, chain A (#6) with RMSD6_NNK1.pdb, chain A (#7),
    7674 sequence alignment score = 841.6 
    7675 RMSD between 174 pruned atom pairs is 0.233 angstroms; (across all 174 pairs:
    7676 0.233) 
    7677  
    7678 
    7679 > select clear
    7680 
    7681 > hide #7 models
    7682 
    7683 > hide #6 models
    7684 
    7685 > show #7 models
    7686 
    7687 > show #6 models
    7688 
    7689 > hide #7 models
    7690 
    7691 > show #7 models
    7692 
    7693 > hide #7 models
    7694 
    7695 > show #7 models
    7696 
    7697 > hide #6 models
    7698 
    7699 > show #6 models
    7700 
    7701 > hide #7 models
    7702 
    7703 > select clear
    7704 
    7705 > select #6/G:105
    7706 
    7707 21 atoms, 21 bonds, 1 residue, 1 model selected 
    7708 
    7709 > select up
    7710 
    7711 327 atoms, 336 bonds, 22 residues, 1 model selected 
    7712 
    7713 > ui tool show Contacts
    7714 
    7715 > contacts sel restrict cross interModel false intraMol false
    7716 > ignoreHiddenModels true select true color #ffd479 reveal true log true
    7717    
    7718    
    7719     Allowed overlap: -0.4
    7720     H-bond overlap reduction: 0.4
    7721     Ignore contacts between atoms separated by 4 bonds or less
    7722     Detect intra-residue contacts: False
    7723     Detect intra-molecule contacts: False
    7724    
    7725     98 contacts
    7726                  atom1                            atom2               overlap  distance
    7727     RMSD4_NNK1.pdb #6/G GLY 110 O    RMSD4_NNK1.pdb #6/H LEU 34 3HD1   0.347    2.133
    7728     RMSD4_NNK1.pdb #6/G ASP 107 H    RMSD4_NNK1.pdb #6/A GLU 79 OE1    0.259    1.821
    7729     RMSD4_NNK1.pdb #6/G PHE 114 H    RMSD4_NNK1.pdb #6/H TYR 38 OH     0.241    1.859
    7730     RMSD4_NNK1.pdb #6/G PHE 114 H    RMSD4_NNK1.pdb #6/H LEU 48 2HD1   0.178    1.822
    7731     RMSD4_NNK1.pdb #6/G PRO 112 O    RMSD4_NNK1.pdb #6/H TYR 38 HH     0.172    1.908
    7732     RMSD4_NNK1.pdb #6/G TYR 111 CE2  RMSD4_NNK1.pdb #6/H LEU 34 CD2    0.152    3.248
    7733     RMSD4_NNK1.pdb #6/G TYR 106 CD2  RMSD4_NNK1.pdb #6/A LEU 70 1HD2   0.132    2.568
    7734     RMSD4_NNK1.pdb #6/G ASP 115 OD1  RMSD4_NNK1.pdb #6/H TYR 51 HH     0.130    1.950
    7735     RMSD4_NNK1.pdb #6/G GLY 110 O    RMSD4_NNK1.pdb #6/H LEU 34 CD1    0.120    3.060
    7736     RMSD4_NNK1.pdb #6/G ASP 115 OD1  RMSD4_NNK1.pdb #6/H LEU 48 3HD1   0.112    2.368
    7737     RMSD4_NNK1.pdb #6/G TYR 111 CE2  RMSD4_NNK1.pdb #6/H LEU 34 1HD2   0.104    2.596
    7738     RMSD4_NNK1.pdb #6/G GLY 110 O    RMSD4_NNK1.pdb #6/H TYR 93 1HB    0.064    2.416
    7739     RMSD4_NNK1.pdb #6/G TYR 111 OH   RMSD4_NNK1.pdb #6/A VAL 77 3HG1   0.048    2.452
    7740     RMSD4_NNK1.pdb #6/G PHE 114 HD1  RMSD4_NNK1.pdb #6/H TYR 38 OH     0.047    2.453
    7741     RMSD4_NNK1.pdb #6/G ASP 115 CG   RMSD4_NNK1.pdb #6/H TYR 51 OH     0.031    3.169
    7742     RMSD4_NNK1.pdb #6/G TRP 117 CZ3  RMSD4_NNK1.pdb #6/H PRO 46 CG     0.022    3.378
    7743     RMSD4_NNK1.pdb #6/G PHE 114 H    RMSD4_NNK1.pdb #6/H LEU 48 CD1    0.008    2.692
    7744     RMSD4_NNK1.pdb #6/G PHE 114 CD1  RMSD4_NNK1.pdb #6/H TYR 38 OH     -0.013    3.213
    7745     RMSD4_NNK1.pdb #6/G TRP 117 CE3  RMSD4_NNK1.pdb #6/H PRO 46 CG     -0.014    3.414
    7746     RMSD4_NNK1.pdb #6/G TYR 106 CD2  RMSD4_NNK1.pdb #6/A LEU 70 CD2    -0.018    3.418
    7747     RMSD4_NNK1.pdb #6/G TYR 111 CD2  RMSD4_NNK1.pdb #6/H LEU 34 CD2    -0.019    3.419
    7748     RMSD4_NNK1.pdb #6/G TYR 111 CD2  RMSD4_NNK1.pdb #6/H LEU 34 2HD2   -0.019    2.719
    7749     RMSD4_NNK1.pdb #6/G PHE 114 N    RMSD4_NNK1.pdb #6/H LEU 48 2HD1   -0.033    2.658
    7750     RMSD4_NNK1.pdb #6/G PHE 114 O    RMSD4_NNK1.pdb #6/H TYR 38 HE2    -0.033    2.513
    7751     RMSD4_NNK1.pdb #6/G ASP 115 OD1  RMSD4_NNK1.pdb #6/H TYR 51 OH     -0.033    2.613
    7752     RMSD4_NNK1.pdb #6/G PHE 114 N    RMSD4_NNK1.pdb #6/H TYR 38 OH     -0.042    2.767
    7753     RMSD4_NNK1.pdb #6/G TRP 117 CD2  RMSD4_NNK1.pdb #6/H PRO 46 1HG    -0.046    2.746
    7754     RMSD4_NNK1.pdb #6/G ASP 115 CG   RMSD4_NNK1.pdb #6/H TYR 51 HH     -0.065    2.765
    7755     RMSD4_NNK1.pdb #6/G PHE 114 CE1  RMSD4_NNK1.pdb #6/H PHE 101 HZ    -0.082    2.782
    7756     RMSD4_NNK1.pdb #6/G TYR 105 CE2  RMSD4_NNK1.pdb #6/A LEU 36 1HD2   -0.083    2.783
    7757     RMSD4_NNK1.pdb #6/G TYR 111 HH   RMSD4_NNK1.pdb #6/A VAL 77 3HG1   -0.085    2.085
    7758     RMSD4_NNK1.pdb #6/G PHE 114 HE1  RMSD4_NNK1.pdb #6/H PHE 101 HZ    -0.093    2.093
    7759     RMSD4_NNK1.pdb #6/G ASP 107 H    RMSD4_NNK1.pdb #6/A GLU 79 CD     -0.093    2.793
    7760     RMSD4_NNK1.pdb #6/G TRP 117 CE3  RMSD4_NNK1.pdb #6/H PRO 46 1HG    -0.104    2.804
    7761     RMSD4_NNK1.pdb #6/G ASP 107 N    RMSD4_NNK1.pdb #6/A GLU 79 OE1    -0.107    2.812
    7762     RMSD4_NNK1.pdb #6/G TYR 105 OH   RMSD4_NNK1.pdb #6/A VAL 41 3HG1   -0.112    2.612
    7763     RMSD4_NNK1.pdb #6/G TYR 105 HE2  RMSD4_NNK1.pdb #6/A LEU 36 1HD2   -0.122    2.122
    7764     RMSD4_NNK1.pdb #6/G PHE 114 N    RMSD4_NNK1.pdb #6/H LEU 48 CD1    -0.134    3.459
    7765     RMSD4_NNK1.pdb #6/G TYR 105 HE2  RMSD4_NNK1.pdb #6/A VAL 41 2HG2   -0.140    2.140
    7766     RMSD4_NNK1.pdb #6/G TYR 111 CZ   RMSD4_NNK1.pdb #6/H LEU 34 1HD2   -0.146    2.846
    7767     RMSD4_NNK1.pdb #6/G GLY 110 CA   RMSD4_NNK1.pdb #6/H TYR 93 CD1    -0.152    3.552
    7768     RMSD4_NNK1.pdb #6/G GLY 110 C    RMSD4_NNK1.pdb #6/H LEU 34 3HD1   -0.156    2.856
    7769     RMSD4_NNK1.pdb #6/G PHE 114 HD1  RMSD4_NNK1.pdb #6/H TYR 38 CZ     -0.169    2.869
    7770     RMSD4_NNK1.pdb #6/G TRP 117 CZ3  RMSD4_NNK1.pdb #6/H PRO 46 2HG    -0.173    2.873
    7771     RMSD4_NNK1.pdb #6/G TRP 117 CE2  RMSD4_NNK1.pdb #6/H PRO 46 1HG    -0.174    2.874
    7772     RMSD4_NNK1.pdb #6/G TYR 105 CE2  RMSD4_NNK1.pdb #6/A LEU 36 CD2    -0.174    3.574
    7773     RMSD4_NNK1.pdb #6/G GLY 110 O    RMSD4_NNK1.pdb #6/H TYR 93 CB     -0.182    3.362
    7774     RMSD4_NNK1.pdb #6/G TYR 111 OH   RMSD4_NNK1.pdb #6/A VAL 77 CG1    -0.191    3.391
    7775     RMSD4_NNK1.pdb #6/G TYR 105 CD1  RMSD4_NNK1.pdb #6/A MET 49 CE     -0.196    3.596
    7776     RMSD4_NNK1.pdb #6/G PRO 112 1HG  RMSD4_NNK1.pdb #6/H SER 36 HG     -0.205    2.205
    7777     RMSD4_NNK1.pdb #6/G PRO 112 O    RMSD4_NNK1.pdb #6/H TYR 38 OH     -0.208    2.788
    7778     RMSD4_NNK1.pdb #6/G ASN 113 OD1  RMSD4_NNK1.pdb #6/H TYR 51 CE1    -0.209    3.389
    7779     RMSD4_NNK1.pdb #6/G ASP 115 OD1  RMSD4_NNK1.pdb #6/H LEU 48 CD1    -0.215    3.395
    7780     RMSD4_NNK1.pdb #6/G GLY 110 2HA  RMSD4_NNK1.pdb #6/H TYR 93 CE1    -0.217    2.917
    7781     RMSD4_NNK1.pdb #6/G TRP 117 CH2  RMSD4_NNK1.pdb #6/H PRO 46 CG     -0.221    3.621
    7782     RMSD4_NNK1.pdb #6/G PRO 112 C    RMSD4_NNK1.pdb #6/H TYR 38 HH     -0.222    2.922
    7783     RMSD4_NNK1.pdb #6/G TYR 106 1HB  RMSD4_NNK1.pdb #6/A GLU 79 OE1    -0.235    2.715
    7784     RMSD4_NNK1.pdb #6/G TYR 106 OH   RMSD4_NNK1.pdb #6/A TYR 72 CD2    -0.240    3.440
    7785     RMSD4_NNK1.pdb #6/G PRO 112 1HG  RMSD4_NNK1.pdb #6/H SER 36 OG     -0.249    2.749
    7786     RMSD4_NNK1.pdb #6/G GLY 110 2HA  RMSD4_NNK1.pdb #6/H TYR 93 CD1    -0.250    2.950
    7787     RMSD4_NNK1.pdb #6/G TYR 105 CE1  RMSD4_NNK1.pdb #6/A MET 49 SD     -0.251    3.733
    7788     RMSD4_NNK1.pdb #6/G TYR 105 OH   RMSD4_NNK1.pdb #6/A VAL 41 HA     -0.257    2.757
    7789     RMSD4_NNK1.pdb #6/G PHE 114 CB   RMSD4_NNK1.pdb #6/H TYR 38 OH     -0.259    3.459
    7790     RMSD4_NNK1.pdb #6/G TRP 117 CZ3  RMSD4_NNK1.pdb #6/H PRO 46 1HG    -0.276    2.976
    7791     RMSD4_NNK1.pdb #6/G ASP 107 CB   RMSD4_NNK1.pdb #6/A GLU 79 OE1    -0.280    3.460
    7792     RMSD4_NNK1.pdb #6/G GLY 110 CA   RMSD4_NNK1.pdb #6/H TYR 93 CE1    -0.281    3.681
    7793     RMSD4_NNK1.pdb #6/G TYR 111 CE2  RMSD4_NNK1.pdb #6/H LEU 34 2HD2   -0.282    2.982
    7794     RMSD4_NNK1.pdb #6/G ASN 113 HA   RMSD4_NNK1.pdb #6/H LEU 48 CD1    -0.284    2.984
    7795     RMSD4_NNK1.pdb #6/G TRP 117 CD2  RMSD4_NNK1.pdb #6/H PRO 46 CG     -0.287    3.687
    7796     RMSD4_NNK1.pdb #6/G TYR 111 HH   RMSD4_NNK1.pdb #6/A VAL 77 CG1    -0.297    2.997
    7797     RMSD4_NNK1.pdb #6/G PHE 114 H    RMSD4_NNK1.pdb #6/H TYR 38 HH     -0.321    2.321
    7798     RMSD4_NNK1.pdb #6/G TYR 111 CZ   RMSD4_NNK1.pdb #6/H LEU 34 CD2    -0.328    3.728
    7799     RMSD4_NNK1.pdb #6/G TYR 106 OH   RMSD4_NNK1.pdb #6/A TYR 72 CE2    -0.329    3.529
    7800     RMSD4_NNK1.pdb #6/G TYR 106 CG   RMSD4_NNK1.pdb #6/A LEU 70 1HD2   -0.332    3.032
    7801     RMSD4_NNK1.pdb #6/G TYR 105 CD1  RMSD4_NNK1.pdb #6/A MET 49 3HE    -0.332    3.032
    7802     RMSD4_NNK1.pdb #6/G TYR 105 CG   RMSD4_NNK1.pdb #6/A MET 49 CE     -0.332    3.732
    7803     RMSD4_NNK1.pdb #6/G TRP 117 CE3  RMSD4_NNK1.pdb #6/H PRO 46 CD     -0.334    3.734
    7804     RMSD4_NNK1.pdb #6/G PRO 112 O    RMSD4_NNK1.pdb #6/H SER 36 HG     -0.334    2.414
    7805     RMSD4_NNK1.pdb #6/G PHE 114 1HB  RMSD4_NNK1.pdb #6/H TYR 38 OH     -0.339    2.839
    7806     RMSD4_NNK1.pdb #6/G ASP 107 2HB  RMSD4_NNK1.pdb #6/A GLU 79 OE1    -0.340    2.820
    7807     RMSD4_NNK1.pdb #6/G ASN 113 HA   RMSD4_NNK1.pdb #6/H LEU 48 1HD1   -0.341    2.341
    7808     RMSD4_NNK1.pdb #6/G PHE 114 HE1  RMSD4_NNK1.pdb #6/H PHE 101 CZ    -0.343    3.043
    7809     RMSD4_NNK1.pdb #6/G GLY 110 O    RMSD4_NNK1.pdb #6/H TYR 93 CG     -0.343    3.523
    7810     RMSD4_NNK1.pdb #6/G PHE 114 1HB  RMSD4_NNK1.pdb #6/H TYR 38 CE2    -0.347    3.047
    7811     RMSD4_NNK1.pdb #6/G TYR 105 CE2  RMSD4_NNK1.pdb #6/A PHE 40 HE1    -0.349    3.049
    7812     RMSD4_NNK1.pdb #6/G TRP 117 HZ2  RMSD4_NNK1.pdb #6/H TYR 38 CE2    -0.360    3.060
    7813     RMSD4_NNK1.pdb #6/G TYR 105 HE2  RMSD4_NNK1.pdb #6/A LEU 36 CD2    -0.366    3.066
    7814     RMSD4_NNK1.pdb #6/G TRP 117 CE3  RMSD4_NNK1.pdb #6/H PRO 46 1HD    -0.367    3.067
    7815     RMSD4_NNK1.pdb #6/G PHE 114 CA   RMSD4_NNK1.pdb #6/H TYR 38 OH     -0.368    3.568
    7816     RMSD4_NNK1.pdb #6/G TRP 117 CZ2  RMSD4_NNK1.pdb #6/H PRO 46 1HG    -0.371    3.071
    7817     RMSD4_NNK1.pdb #6/G ASN 113 OD1  RMSD4_NNK1.pdb #6/H TYR 51 CD1    -0.372    3.552
    7818     RMSD4_NNK1.pdb #6/G PHE 114 H    RMSD4_NNK1.pdb #6/H TYR 38 CZ     -0.373    3.073
    7819     RMSD4_NNK1.pdb #6/G TYR 106 CE2  RMSD4_NNK1.pdb #6/A LEU 70 1HD2   -0.376    3.076
    7820     RMSD4_NNK1.pdb #6/G GLY 110 O    RMSD4_NNK1.pdb #6/H TYR 93 CD1    -0.380    3.560
    7821     RMSD4_NNK1.pdb #6/G TYR 105 CZ   RMSD4_NNK1.pdb #6/A MET 49 SD     -0.388    3.870
    7822     RMSD4_NNK1.pdb #6/G TRP 117 CH2  RMSD4_NNK1.pdb #6/H PRO 46 2HG    -0.391    3.091
    7823     RMSD4_NNK1.pdb #6/G GLY 110 C    RMSD4_NNK1.pdb #6/H LEU 34 CD1    -0.398    3.798
    7824     RMSD4_NNK1.pdb #6/G TRP 117 CH2  RMSD4_NNK1.pdb #6/H PRO 46 1HG    -0.399    3.099
    7825    
    7826 
    7827  
    7828 98 contacts 
    7829 
    7830 > undo
    7831 
    7832 > hide sel atoms
    7833 
    7834 > select up
    7835 
    7836 310 atoms, 302 bonds, 17 residues, 1 model selected 
    7837 
    7838 > hide sel atoms
    7839 
    7840 > select add #6/G:111
    7841 
    7842 331 atoms, 323 bonds, 18 residues, 1 model selected 
    7843 
    7844 > select up
    7845 
    7846 1781 atoms, 1810 bonds, 112 residues, 1 model selected 
    7847 
    7848 > hide sel atoms
    7849 
    7850 > select clear
    7851 
    7852 > select #6/A:71
    7853 
    7854 20 atoms, 20 bonds, 1 residue, 1 model selected 
    7855 
    7856 > select up
    7857 
    7858 152 atoms, 154 bonds, 9 residues, 1 model selected 
    7859 
    7860 > select up
    7861 
    7862 2815 atoms, 2853 bonds, 174 residues, 1 model selected 
    7863 
    7864 > contacts ignoreHiddenModels true color #ff2600
    7865 
    7866 4408 contacts 
    7867 
    7868 > undo
    7869 
    7870 > select #6/A:70
    7871 
    7872 19 atoms, 18 bonds, 1 residue, 1 model selected 
    7873 
    7874 > select up
    7875 
    7876 152 atoms, 154 bonds, 9 residues, 1 model selected 
    7877 
    7878 > select up
    7879 
    7880 2815 atoms, 2853 bonds, 174 residues, 1 model selected 
    7881 
    7882 > contacts sel restrict cross ignoreHiddenModels true color #ff2600
    7883 
    7884 57 contacts 
    7885 
    7886 > contacts sel restrict cross interModel false intraMol false
    7887 > ignoreHiddenModels true select true color #ff2600 reveal true
    7888 
    7889 57 contacts 
    7890 
    7891 > select up
    7892 
    7893 400 atoms, 387 bonds, 24 residues, 1 model selected 
    7894 
    7895 > color sel byhetero
    7896 
    7897 > show #!1 models
    7898 
    7899 > show #7 models
    7900 
    7901 > hide #7 models
    7902 
    7903 > select #6/A:71
    7904 
    7905 20 atoms, 20 bonds, 1 residue, 1 model selected 
    7906 
    7907 > select up
    7908 
    7909 152 atoms, 154 bonds, 9 residues, 1 model selected 
    7910 
    7911 > select up
    7912 
    7913 2815 atoms, 2853 bonds, 174 residues, 1 model selected 
    7914 
    7915 > matchmaker #!1 to #6 & sel
    7916 
    7917 Parameters 
    7918 --- 
    7919 Chain pairing | bb 
    7920 Alignment algorithm | Needleman-Wunsch 
    7921 Similarity matrix | BLOSUM-62 
    7922 SS fraction | 0.3 
    7923 Gap open (HH/SS/other) | 18/18/6 
    7924 Gap extend | 1 
    7925 SS matrix |  |  | H | S | O 
    7926 ---|---|---|--- 
    7927 H | 6 | -9 | -6 
    7928 S |  | 6 | -6 
    7929 O |  |  | 4 
    7930 Iteration cutoff | 2 
    7931  
    7932 Matchmaker RMSD4_NNK1.pdb, chain A (#6) with
    7933 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1), sequence alignment
    7934 score = 692.2 
    7935 RMSD between 150 pruned atom pairs is 0.641 angstroms; (across all 164 pairs:
    7936 1.442) 
    7937  
    7938 
    7939 > show #7 models
    7940 
    7941 > hide #!6 models
    7942 
    7943 > show #!6 models
    7944 
    7945 > hide #7 models
    7946 
    7947 > select clear
    7948 
    7949 > hide #!1 models
    7950 
    7951 > show #!1 models
    7952 
    7953 > hide #!1 models
    7954 
    7955 > hide #!6 models
    7956 
    7957 > show #7 models
    7958 
    7959 > select #7/A:70
    7960 
    7961 24 atoms, 23 bonds, 1 residue, 1 model selected 
    7962 
    7963 > select up
    7964 
    7965 155 atoms, 156 bonds, 9 residues, 1 model selected 
    7966 
    7967 > select up
    7968 
    7969 2806 atoms, 2845 bonds, 174 residues, 1 model selected 
    7970 
    7971 > contacts sel restrict cross interModel false intraMol false
    7972 > ignoreHiddenModels true select true color #ff2600 name contacts_RMSD6 reveal
    7973 > true
    7974 
    7975 63 contacts 
    7976 
    7977 > select up
    7978 
    7979 344 atoms, 338 bonds, 20 residues, 1 model selected 
    7980 
    7981 > color sel byhetero
    7982 
    7983 > select clear
    7984 
    7985 > hide #8 models
    7986 
    7987 > hide #!7 models
    7988 
    7989 > show #!1 models
    7990 
    7991 > select #1/E:79
    7992 
    7993 7 atoms, 6 bonds, 1 residue, 1 model selected 
    7994 
    7995 > select up
    7996 
    7997 78 atoms, 80 bonds, 9 residues, 1 model selected 
    7998 
    7999 > select up
    8000 
    8001 709 atoms, 728 bonds, 90 residues, 1 model selected 
    8002 
    8003 > select up
    8004 
    8005 727 atoms, 746 bonds, 92 residues, 1 model selected 
    8006 
    8007 > select up
    8008 
    8009 1313 atoms, 1346 bonds, 164 residues, 1 model selected 
    8010 
    8011 > select up
    8012 
    8013 4647 atoms, 4757 bonds, 608 residues, 1 model selected 
    8014 
    8015 > select down
    8016 
    8017 1313 atoms, 1346 bonds, 164 residues, 1 model selected 
    8018 
    8019 > contacts sel restrict cross interModel false intraMol false
    8020 > ignoreHiddenModels true select true color #ff2600 name contacts_poly310
    8021 > reveal true
    8022 
    8023 64 contacts 
    8024 
    8025 > select up
    8026 
    8027 237 atoms, 233 bonds, 27 residues, 1 model selected 
    8028 
    8029 > color sel byhetero
    8030 
    8031 > hide #!1 models
    8032 
    8033 > show #!1 models
    8034 
    8035 > select clear
    8036 
    8037 > select #1/H:126
    8038 
    8039 7 atoms, 6 bonds, 1 residue, 1 model selected 
    8040 
    8041 > select up
    8042 
    8043 36 atoms, 35 bonds, 5 residues, 1 model selected 
    8044 
    8045 > select up
    8046 
    8047 1725 atoms, 1772 bonds, 228 residues, 1 model selected 
    8048 
    8049 > color sel pale goldenrod
    8050 
    8051 > select #1/L:105
    8052 
    8053 6 atoms, 5 bonds, 1 residue, 1 model selected 
    8054 
    8055 > select up
    8056 
    8057 67 atoms, 69 bonds, 8 residues, 1 model selected 
    8058 
    8059 > select up
    8060 
    8061 1609 atoms, 1639 bonds, 216 residues, 1 model selected 
    8062 
    8063 > color sel light yellow
    8064 
    8065 > select clear
    8066 
    8067 > select #1/H:111C
    8068 
    8069 12 atoms, 12 bonds, 1 residue, 1 model selected 
    8070 
    8071 > select up
    8072 
    8073 181 atoms, 190 bonds, 22 residues, 1 model selected 
    8074 
    8075 > select subtract #1/H:119
    8076 
    8077 177 atoms, 185 bonds, 21 residues, 1 model selected 
    8078 
    8079 > select subtract #1/H:120
    8080 
    8081 168 atoms, 176 bonds, 20 residues, 1 model selected 
    8082 
    8083 > select subtract #1/H:121
    8084 
    8085 164 atoms, 173 bonds, 19 residues, 1 model selected 
    8086 
    8087 > select subtract #1/H:118
    8088 
    8089 150 atoms, 157 bonds, 18 residues, 1 model selected 
    8090 
    8091 > select subtract #1/H:117
    8092 
    8093 138 atoms, 144 bonds, 17 residues, 1 model selected 
    8094 
    8095 > color sel sky blue
    8096 
    8097 > select add #1
    8098 
    8099 4647 atoms, 4757 bonds, 71 pseudobonds, 608 residues, 4 models selected 
    8100 
    8101 > color sel byhetero
    8102 
    8103 > select clear
    8104 
    8105 > hide #!1 models
    8106 
    8107 > show #!6 models
    8108 
    8109 > select add #6
    8110 
    8111 6309 atoms, 6390 bonds, 114 pseudobonds, 410 residues, 3 models selected 
    8112 
    8113 > select add #7
    8114 
    8115 12609 atoms, 12772 bonds, 177 pseudobonds, 820 residues, 5 models selected 
    8116 
    8117 > show #!7 models
    8118 
    8119 > select H
    8120 
    8121 12439 atoms, 19 pseudobonds, 1640 residues, 7 models selected 
    8122 
    8123 > select clear
    8124 
    8125 > select add #6
    8126 
    8127 6309 atoms, 6390 bonds, 114 pseudobonds, 410 residues, 3 models selected 
    8128 
    8129 > select add #7
    8130 
    8131 12609 atoms, 12772 bonds, 177 pseudobonds, 820 residues, 5 models selected 
    8132 
    8133 > select H
    8134 
    8135 12439 atoms, 19 pseudobonds, 1640 residues, 7 models selected 
    8136 
    8137 > delete atoms (#!6-7 & sel)
    8138 
    8139 > delete bonds (#!6-7 & sel)
    8140 
    8141 > hide #!6 models
    8142 
    8143 > show #!6 models
    8144 
    8145 > hide #!7 models
    8146 
    8147 > show #!7 models
    8148 
    8149 > show #!1 models
    8150 
    8151 > show #2 models
    8152 
    8153 > hide #2 models
    8154 
    8155 > hide #!1 models
    8156 
    8157 > select clear
    8158 
    8159 > hide #!7 models
    8160 
    8161 > show #!1 models
    8162 
    8163 > hide #!6 models
    8164 
    8165 > show #4 models
    8166 
    8167 > hide #4 models
    8168 
    8169 > show #!6 models
    8170 
    8171 > hide #6.1 models
    8172 
    8173 > hide #!6 models
    8174 
    8175 > show #!7 models
    8176 
    8177 > hide #!7 models
    8178 
    8179 > select #1/E:33
    8180 
    8181 7 atoms, 6 bonds, 1 residue, 1 model selected 
    8182 
    8183 > select up
    8184 
    8185 74 atoms, 76 bonds, 10 residues, 1 model selected 
    8186 
    8187 > select up
    8188 
    8189 709 atoms, 728 bonds, 90 residues, 1 model selected 
    8190 
    8191 > select up
    8192 
    8193 727 atoms, 746 bonds, 92 residues, 1 model selected 
    8194 
    8195 > select up
    8196 
    8197 1313 atoms, 1346 bonds, 164 residues, 1 model selected 
    8198 
    8199 > show #5 models
    8200 
    8201 > hide #5 models
    8202 
    8203 > show #!6 models
    8204 
    8205 > select clear
    8206 
    8207 > show #!7 models
    8208 
    8209 > hide #!7 models
    8210 
    8211 > select #6/A:131
    8212 
    8213 9 atoms, 8 bonds, 1 residue, 1 model selected 
    8214 
    8215 > select up
    8216 
    8217 88 atoms, 91 bonds, 10 residues, 1 model selected 
    8218 
    8219 > select up
    8220 
    8221 1416 atoms, 1454 bonds, 174 residues, 1 model selected 
    8222 
    8223 > show #8 models
    8224 
    8225 > matchmaker #4 to #6 & sel
    8226 
    8227 Parameters 
    8228 --- 
    8229 Chain pairing | bb 
    8230 Alignment algorithm | Needleman-Wunsch 
    8231 Similarity matrix | BLOSUM-62 
    8232 SS fraction | 0.3 
    8233 Gap open (HH/SS/other) | 18/18/6 
    8234 Gap extend | 1 
    8235 SS matrix |  |  | H | S | O 
    8236 ---|---|---|--- 
    8237 H | 6 | -9 | -6 
    8238 S |  | 6 | -6 
    8239 O |  |  | 4 
    8240 Iteration cutoff | 2 
    8241  
    8242 Matchmaker RMSD4_NNK1.pdb, chain A (#6) with Cluster2c_lib1.pdb, chain A (#4),
    8243 sequence alignment score = 808.5 
    8244 RMSD between 174 pruned atom pairs is 0.223 angstroms; (across all 174 pairs:
    8245 0.223) 
    8246  
    8247 
    8248 > hide #!6 models
    8249 
    8250 > show #4 models
    8251 
    8252 > hide #4 models
    8253 
    8254 > hide #1.3 models
    8255 
    8256 > hide #1.1 models
    8257 
    8258 > show #1.3 models
    8259 
    8260 > select #1/E:43
    8261 
    8262 11 atoms, 10 bonds, 1 residue, 1 model selected 
    8263 
    8264 > select up
    8265 
    8266 113 atoms, 114 bonds, 14 residues, 1 model selected 
    8267 
    8268 > select subtract #1/E:52
    8269 
    8270 102 atoms, 102 bonds, 13 residues, 1 model selected 
    8271 
    8272 > select subtract #1/E:50
    8273 
    8274 93 atoms, 92 bonds, 12 residues, 1 model selected 
    8275 
    8276 > select subtract #1/E:51
    8277 
    8278 85 atoms, 85 bonds, 11 residues, 1 model selected 
    8279 
    8280 > select subtract #1/E:49
    8281 
    8282 80 atoms, 80 bonds, 10 residues, 1 model selected 
    8283 
    8284 > show sel atoms
    8285 
    8286 > hide sel atoms
    8287 
    8288 > select #1/E:37
    8289 
    8290 5 atoms, 4 bonds, 1 residue, 1 model selected 
    8291 
    8292 > select add #1/E:133
    8293 
    8294 16 atoms, 15 bonds, 2 residues, 1 model selected 
    8295 
    8296 > select add #1/E:134
    8297 
    8298 24 atoms, 22 bonds, 3 residues, 1 model selected 
    8299 
    8300 > select add #1/E:38
    8301 
    8302 28 atoms, 25 bonds, 4 residues, 1 model selected 
    8303 
    8304 > select add #1/E:135
    8305 
    8306 36 atoms, 32 bonds, 5 residues, 1 model selected 
    8307 
    8308 > show sel atoms
    8309 
    8310 > color sel byhetero
    8311 
    8312 > select clear
    8313 
    8314 > hide #!1 models
    8315 
    8316 > show #!6 models
    8317 
    8318 > show #!7 models
    8319 
    8320 > hide #!6 models
    8321 
    8322 > show #!6 models
    8323 
    8324 > hide #!7 models
    8325 
    8326 > show #!7 models
    8327 
    8328 > hide #!6 models
    8329 
    8330 > hide #!7 models
    8331 
    8332 > show #6.1 models
    8333 
    8334 > show #!7 models
    8335 
    8336 > hide #!6 models
    8337 
    8338 > show #!6 models
    8339 
    8340 > hide #!6 models
    8341 
    8342 > show #!6 models
    8343 
    8344 > hide #!7 models
    8345 
    8346 > show #!7 models
    8347 
    8348 > hide #!6 models
    8349 
    8350 > hide #!7 models
    8351 
    8352 > show #!6 models
    8353 
    8354 > hide #!6 models
    8355 
    8356 > show #!7 models
    8357 
    8358 > show #!6 models
    8359 
    8360 > hide #!7 models
    8361 
    8362 > show #!7 models
    8363 
    8364 > hide #!7 models
    8365 
    8366 > show #!7 models
    8367 
    8368 > hide #!6 models
    8369 
    8370 > show #!6 models
    8371 
    8372 > hide #!7 models
    8373 
    8374 > show #!7 models
    8375 
    8376 > hide #!6 models
    8377 
    8378 > hide #!7 models
    8379 
    8380 > show #!6 models
    8381 
    8382 > show #!7 models
    8383 
    8384 > hide #!7 models
    8385 
    8386 > show #!7 models
    8387 
    8388 > hide #!6 models
    8389 
    8390 > show #!6 models
    8391 
    8392 > hide #!7 models
    8393 
    8394 > hide #6.1 models
    8395 
    8396 > show #6.1 models
    8397 
    8398 > hide #6.1 models
    8399 
    8400 > hide #8 models
    8401 
    8402 > show #8 models
    8403 
    8404 > select add #8
    8405 
    8406 21 pseudobonds, 1 model selected 
    8407 
    8408 > select add #6.1
    8409 
    8410 42 pseudobonds, 2 models selected 
    8411 
    8412 > hide #!6 cartoons
    8413 
    8414 > show #!6 cartoons
    8415 
    8416 > hide #!6 atoms
    8417 
    8418 > select clear
    8419 
    8420 > hide #8 models
    8421 
    8422 > show #!7 models
    8423 
    8424 > select add #7
    8425 
    8426 3204 atoms, 3286 bonds, 20 pseudobonds, 410 residues, 2 models selected 
    8427 
    8428 > hide sel atoms
    8429 
    8430 > select clear
    8431 
    8432 > hide #1.3 models
    8433 
    8434 > hide #1.2 models
    8435 
    8436 > hide #!6 models
    8437 
    8438 > hide #7.1 models
    8439 
    8440 > show #!6 models
    8441 
    8442 > hide #!6 models
    8443 
    8444 > show #!6 models
    8445 
    8446 > hide #!7 models
    8447 
    8448 > show #!7 models
    8449 
    8450 > hide #!7 models
    8451 
    8452 > show #!7 models
    8453 
    8454 > hide #!6 models
    8455 
    8456 > show #!6 models
    8457 
    8458 > lighting soft
    8459 
    8460 > hide #!6 models
    8461 
    8462 > lighting gentle
    8463 
    8464 > graphics silhouettes false
    8465 
    8466 > graphics silhouettes true
    8467 
    8468 > graphics silhouettes false
    8469 
    8470 > graphics silhouettes true
    8471 
    8472 > lighting shadows true intensity 0.5
    8473 
    8474 > lighting shadows false
    8475 
    8476 > save view init_design
    8477 
    8478 Cannot determine format for 'view' 
    8479 
    8480 > view name init_design
    8481 
    8482 > view list
    8483 
    8484 Named views: init_design, session-start 
    8485 
    8486 > show #!6 models
    8487 
    8488 > hide #!7 models
    8489 
    8490 > select #6/A:68
    8491 
    8492 6 atoms, 5 bonds, 1 residue, 1 model selected 
    8493 
    8494 > select up
    8495 
    8496 78 atoms, 80 bonds, 9 residues, 1 model selected 
    8497 
    8498 > select up
    8499 
    8500 1416 atoms, 1454 bonds, 174 residues, 1 model selected 
    8501 
    8502 > color sel pink
    8503 
    8504 > color sel pale violet red
    8505 
    8506 > color sel dark sea green
    8507 
    8508 > color sel salmon
    8509 
    8510 > color sel dark salmon
    8511 
    8512 > color sel coral
    8513 
    8514 > color sel pale violet red
    8515 
    8516 > select clear
    8517 
    8518 > select #6/H:20
    8519 
    8520 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8521 
    8522 > select up
    8523 
    8524 42 atoms, 41 bonds, 6 residues, 1 model selected 
    8525 
    8526 > select up
    8527 
    8528 797 atoms, 812 bonds, 110 residues, 1 model selected 
    8529 
    8530 > color sel pale goldenrod
    8531 
    8532 > select #6/G:4
    8533 
    8534 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8535 
    8536 > select up
    8537 
    8538 33 atoms, 32 bonds, 4 residues, 1 model selected 
    8539 
    8540 > select up
    8541 
    8542 990 atoms, 1018 bonds, 126 residues, 1 model selected 
    8543 
    8544 > color sel burly wood
    8545 
    8546 > color sel goldenrod
    8547 
    8548 > color sel dark goldenrod
    8549 
    8550 > select clear
    8551 
    8552 > select #6/G:4
    8553 
    8554 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8555 
    8556 > select #6/G:107
    8557 
    8558 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8559 
    8560 > select up
    8561 
    8562 181 atoms, 190 bonds, 22 residues, 1 model selected 
    8563 
    8564 > select subtract #6/G:115
    8565 
    8566 173 atoms, 181 bonds, 21 residues, 1 model selected 
    8567 
    8568 > select add #6/G:97
    8569 
    8570 178 atoms, 185 bonds, 22 residues, 1 model selected 
    8571 
    8572 > select subtract #6/G:97
    8573 
    8574 173 atoms, 181 bonds, 21 residues, 1 model selected 
    8575 
    8576 > select subtract #6/G:116
    8577 
    8578 161 atoms, 168 bonds, 20 residues, 1 model selected 
    8579 
    8580 > select subtract #6/G:117
    8581 
    8582 147 atoms, 152 bonds, 19 residues, 1 model selected 
    8583 
    8584 > select subtract #6/G:118
    8585 
    8586 143 atoms, 148 bonds, 18 residues, 1 model selected 
    8587 
    8588 > select subtract #6/G:119
    8589 
    8590 134 atoms, 139 bonds, 17 residues, 1 model selected 
    8591 
    8592 > select subtract #6/G:120
    8593 
    8594 130 atoms, 136 bonds, 16 residues, 1 model selected 
    8595 
    8596 > color sel navy
    8597 
    8598 > color sel steel blue
    8599 
    8600 > color sel teal
    8601 
    8602 > color sel dark cyan
    8603 
    8604 > select clear
    8605 
    8606 > show #!7 models
    8607 
    8608 > hide #!6 models
    8609 
    8610 > select #7/H:48
    8611 
    8612 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8613 
    8614 > select up
    8615 
    8616 33 atoms, 32 bonds, 4 residues, 1 model selected 
    8617 
    8618 > select up
    8619 
    8620 797 atoms, 812 bonds, 110 residues, 1 model selected 
    8621 
    8622 > color sel pale goldenrod
    8623 
    8624 > select #7/G:122
    8625 
    8626 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8627 
    8628 > select up
    8629 
    8630 36 atoms, 35 bonds, 5 residues, 1 model selected 
    8631 
    8632 > select up
    8633 
    8634 990 atoms, 1018 bonds, 126 residues, 1 model selected 
    8635 
    8636 > select up
    8637 
    8638 3204 atoms, 3286 bonds, 410 residues, 1 model selected 
    8639 
    8640 > select down
    8641 
    8642 990 atoms, 1018 bonds, 126 residues, 1 model selected 
    8643 
    8644 > color sel goldenrod
    8645 
    8646 > select clear
    8647 
    8648 > select #7/G:101
    8649 
    8650 14 atoms, 15 bonds, 1 residue, 1 model selected 
    8651 
    8652 > select up
    8653 
    8654 181 atoms, 190 bonds, 22 residues, 1 model selected 
    8655 
    8656 > select add #7/G:98
    8657 
    8658 192 atoms, 200 bonds, 23 residues, 1 model selected 
    8659 
    8660 > select subtract #7/G:116
    8661 
    8662 180 atoms, 186 bonds, 22 residues, 1 model selected 
    8663 
    8664 > select subtract #7/G:117
    8665 
    8666 166 atoms, 170 bonds, 21 residues, 1 model selected 
    8667 
    8668 > select subtract #7/G:118
    8669 
    8670 162 atoms, 166 bonds, 20 residues, 1 model selected 
    8671 
    8672 > select subtract #7/G:119
    8673 
    8674 153 atoms, 157 bonds, 19 residues, 1 model selected 
    8675 
    8676 > select subtract #7/G:120
    8677 
    8678 149 atoms, 154 bonds, 18 residues, 1 model selected 
    8679 
    8680 > color sel dark cyan
    8681 
    8682 > select clear
    8683 
    8684 > view list
    8685 
    8686 Named views: init_design, session-start 
    8687 
    8688 > view init_design
    8689 
    8690 > show #!6 models
    8691 
    8692 > hide #!7 models
    8693 
    8694 > show #!7 models
    8695 
    8696 > hide #!6 models
    8697 
    8698 > select #7/A:68
    8699 
    8700 6 atoms, 5 bonds, 1 residue, 1 model selected 
    8701 
    8702 > select up
    8703 
    8704 77 atoms, 78 bonds, 9 residues, 1 model selected 
    8705 
    8706 > select up
    8707 
    8708 1417 atoms, 1456 bonds, 174 residues, 1 model selected 
    8709 
    8710 > color sel olive drab
    8711 
    8712 > color sel dark khaki
    8713 
    8714 > color sel dark sea green
    8715 
    8716 > color sel light green
    8717 
    8718 > color sel pale green
    8719 
    8720 > color sel green yellow
    8721 
    8722 > color sel forest green
    8723 
    8724 > color sel green
    8725 
    8726 > color sel lime
    8727 
    8728 > color sel lawn green
    8729 
    8730 > color sel blue
    8731 
    8732 > color sel medium blue
    8733 
    8734 > color sel dark blue
    8735 
    8736 > color sel medium sea green
    8737 
    8738 > color sel sea green
    8739 
    8740 > color sel olive drab
    8741 
    8742 > color sel green
    8743 
    8744 > color sel dark blue
    8745 
    8746 > color sel navy
    8747 
    8748 > color sel indigo
    8749 
    8750 > color sel navy
    8751 
    8752 > color sel dark blue
    8753 
    8754 > color sel navy
    8755 
    8756 > color sel medium blue
    8757 
    8758 > select clear
    8759 
    8760 > select #7/A:80
    8761 
    8762 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8763 
    8764 > select up
    8765 
    8766 90 atoms, 92 bonds, 11 residues, 1 model selected 
    8767 
    8768 > select up
    8769 
    8770 1417 atoms, 1456 bonds, 174 residues, 1 model selected 
    8771 
    8772 > color sel dark blue
    8773 
    8774 > select clear
    8775 
    8776 > show #!6 models
    8777 
    8778 > hide #!7 models
    8779 
    8780 > select #6/A:80
    8781 
    8782 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8783 
    8784 > select up
    8785 
    8786 90 atoms, 92 bonds, 11 residues, 1 model selected 
    8787 
    8788 > select up
    8789 
    8790 1416 atoms, 1454 bonds, 174 residues, 1 model selected 
    8791 
    8792 > show sel surfaces
    8793 
    8794 > transparency sel 50
    8795 
    8796 > transparency sel 70
    8797 
    8798 > select clear
    8799 
    8800 > show #!7 models
    8801 
    8802 > hide #!6 models
    8803 
    8804 > select #7/A:36
    8805 
    8806 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8807 
    8808 > select up
    8809 
    8810 74 atoms, 76 bonds, 10 residues, 1 model selected 
    8811 
    8812 > select up
    8813 
    8814 1417 atoms, 1456 bonds, 174 residues, 1 model selected 
    8815 
    8816 > volume style surface
    8817 
    8818 No volumes specified 
    8819 
    8820 > select clear
    8821 
    8822 > select #7/A:81
    8823 
    8824 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8825 
    8826 > select up
    8827 
    8828 90 atoms, 92 bonds, 11 residues, 1 model selected 
    8829 
    8830 > select up
    8831 
    8832 1417 atoms, 1456 bonds, 174 residues, 1 model selected 
    8833 
    8834 > show sel surfaces
    8835 
    8836 > transparency sel 50
    8837 
    8838 > transparency sel 70
    8839 
    8840 > select clear
    8841 
    8842 > show #!6 models
    8843 
    8844 > hide #6.2 models
    8845 
    8846 > show #6.2 models
    8847 
    8848 > hide #6.2 models
    8849 
    8850 > hide #!7 models
    8851 
    8852 > show #!7 models
    8853 
    8854 > show #6.2 models
    8855 
    8856 > hide #!7 models
    8857 
    8858 > hide #6.2 models
    8859 
    8860 > show #6.2 models
    8861 
    8862 > hide #!6 models
    8863 
    8864 > show #!7 models
    8865 
    8866 > show #!6 models
    8867 
    8868 > hide #!7 models
    8869 
    8870 > show #!7 models
    8871 
    8872 > hide #!6 models
    8873 
    8874 > show #!6 models
    8875 
    8876 > hide #!6 models
    8877 
    8878 > show #!6 models
    8879 
    8880 > hide #!7 models
    8881 
    8882 > show #!7 models
    8883 
    8884 > hide #!6 models
    8885 
    8886 > preset cartoons/nucleotides licorice/ovals
    8887 
    8888 Using preset: Cartoons/Nucleotides / Licorice/Ovals 
    8889 Changed 0 atom styles 
    8890 Preset expands to these ChimeraX commands:
    8891 
    8892    
    8893    
    8894     show nucleic
    8895     hide protein|solvent|H
    8896     surf hide
    8897     style (protein|nucleic|solvent) & @@draw_mode=0 stick
    8898     ~worm
    8899     cartoon
    8900     cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    8901     cartoon style ~(nucleic|strand) x round
    8902     cartoon style (nucleic|strand) x rect
    8903     cartoon style protein modeh default arrows f x round width 1 thick 1
    8904     cartoon style nucleic x round width 1.6 thick 1.6
    8905     nucleotides tube/slab shape ellipsoid
    8906 
    8907  
    8908 
    8909 > select #7/A:108
    8910 
    8911 7 atoms, 6 bonds, 1 residue, 1 model selected 
    8912 
    8913 > select up
    8914 
    8915 67 atoms, 67 bonds, 8 residues, 2 models selected 
    8916 
    8917 > select up
    8918 
    8919 1417 atoms, 1456 bonds, 174 residues, 2 models selected 
    8920 
    8921 > show sel surfaces
    8922 
    8923 > show #!6 models
    8924 
    8925 > hide #!7 models
    8926 
    8927 > select #6/A:168
    8928 
    8929 11 atoms, 11 bonds, 1 residue, 1 model selected 
    8930 
    8931 > select up
    8932 
    8933 99 atoms, 101 bonds, 13 residues, 2 models selected 
    8934 
    8935 > select up
    8936 
    8937 1416 atoms, 1454 bonds, 174 residues, 2 models selected 
    8938 
    8939 > show sel surfaces
    8940 
    8941 > select clear
    8942 
    8943 > show #!7 models
    8944 
    8945 > hide #!6 models
    8946 
    8947 > select #7/A:45@CG
    8948 
    8949 1 atom, 1 residue, 1 model selected 
    8950 
    8951 > select up
    8952 
    8953 8 atoms, 7 bonds, 1 residue, 2 models selected 
    8954 
    8955 > select up
    8956 
    8957 129 atoms, 133 bonds, 14 residues, 2 models selected 
    8958 
    8959 > select up
    8960 
    8961 1417 atoms, 1456 bonds, 174 residues, 2 models selected 
    8962 
    8963 > hide sel surfaces
    8964 
    8965 > color sel slate gray
    8966 
    8967 > color sel dim gray
    8968 
    8969 > show #!6 models
    8970 
    8971 > hide #!6 models
    8972 
    8973 > show #!6 models
    8974 
    8975 > hide #!6 models
    8976 
    8977 > hide #!7 models
    8978 
    8979 > show #!7 models
    8980 
    8981 > color sel dark orange
    8982 
    8983 > color sel chocolate
    8984 
    8985 > color sel dark red
    8986 
    8987 > color sel maroon
    8988 
    8989 > show sel surfaces
    8990 
    8991 > transparency sel 70
    8992 
    8993 > select clear
    8994 
    8995 > show #!6 models
    8996 
    8997 > hide #!7 models
    8998 
    8999 > show #5 models
    9000 
    9001 > hide #5 models
    9002 
    9003 > show #!7 models
    9004 
    9005 > hide #!6 models
    9006 
    9007 > select #7/A:46@CA
    9008 
    9009 1 atom, 1 residue, 1 model selected 
    9010 
    9011 > select up
    9012 
    9013 8 atoms, 7 bonds, 1 residue, 2 models selected 
    9014 
    9015 > select up
    9016 
    9017 129 atoms, 133 bonds, 14 residues, 2 models selected 
    9018 
    9019 > select up
    9020 
    9021 1417 atoms, 1456 bonds, 174 residues, 2 models selected 
    9022 
    9023 > color sel medium aquamarine
    9024 
    9025 > transparency sel 70
    9026 
    9027 > select clear
    9028 
    9029 > select #7/G:98
    9030 
    9031 11 atoms, 10 bonds, 1 residue, 1 model selected 
    9032 
    9033 > select up
    9034 
    9035 58 atoms, 59 bonds, 7 residues, 1 model selected 
    9036 
    9037 > select up
    9038 
    9039 990 atoms, 1018 bonds, 126 residues, 1 model selected 
    9040 
    9041 > select down
    9042 
    9043 58 atoms, 59 bonds, 7 residues, 1 model selected 
    9044 
    9045 > select #7/G:101
    9046 
    9047 14 atoms, 15 bonds, 1 residue, 1 model selected 
    9048 
    9049 > select up
    9050 
    9051 181 atoms, 190 bonds, 22 residues, 1 model selected 
    9052 
    9053 > select subtract #7/G:116
    9054 
    9055 169 atoms, 176 bonds, 21 residues, 1 model selected 
    9056 
    9057 > select subtract #7/G:117
    9058 
    9059 155 atoms, 160 bonds, 20 residues, 1 model selected 
    9060 
    9061 > select subtract #7/G:118
    9062 
    9063 151 atoms, 156 bonds, 19 residues, 1 model selected 
    9064 
    9065 > select subtract #7/G:119
    9066 
    9067 142 atoms, 147 bonds, 18 residues, 1 model selected 
    9068 
    9069 > select subtract #7/G:120
    9070 
    9071 138 atoms, 144 bonds, 17 residues, 1 model selected 
    9072 
    9073 > select add #7/G:98
    9074 
    9075 149 atoms, 154 bonds, 18 residues, 1 model selected 
    9076 
    9077 > color sel navy
    9078 
    9079 > color sel dark blue
    9080 
    9081 > color sel medium aquamarine
    9082 
    9083 > color sel blue
    9084 
    9085 > color sel medium blue
    9086 
    9087 > color sel dark blue
    9088 
    9089 > color sel navy
    9090 
    9091 > color sel indigo
    9092 
    9093 > color sel midnight blue
    9094 
    9095 > show #!6 models
    9096 
    9097 > hide #!7 models
    9098 
    9099 > hide #!6 models
    9100 
    9101 > show #!7 models
    9102 
    9103 > show #!6 models
    9104 
    9105 > hide #!7 models
    9106 
    9107 > show #!7 models
    9108 
    9109 > hide #!6 models
    9110 
    9111 > hide #!7 models
    9112 
    9113 > show #!6 models
    9114 
    9115 > select #6/G:107
    9116 
    9117 8 atoms, 7 bonds, 1 residue, 1 model selected 
    9118 
    9119 > select up
    9120 
    9121 181 atoms, 190 bonds, 22 residues, 1 model selected 
    9122 
    9123 > select subtract #6/G:120
    9124 
    9125 177 atoms, 186 bonds, 21 residues, 1 model selected 
    9126 
    9127 > select subtract #6/G:119
    9128 
    9129 168 atoms, 177 bonds, 20 residues, 1 model selected 
    9130 
    9131 > select subtract #6/G:118
    9132 
    9133 164 atoms, 173 bonds, 19 residues, 1 model selected 
    9134 
    9135 > select subtract #6/G:117
    9136 
    9137 150 atoms, 157 bonds, 18 residues, 1 model selected 
    9138 
    9139 > select subtract #6/G:115
    9140 
    9141 142 atoms, 148 bonds, 17 residues, 1 model selected 
    9142 
    9143 > select subtract #6/G:116
    9144 
    9145 130 atoms, 136 bonds, 16 residues, 1 model selected 
    9146 
    9147 > color sel midnight blue
    9148 
    9149 > show #!7 models
    9150 
    9151 > hide #!7 models
    9152 
    9153 > select clear
    9154 
    9155 > show #!7 models
    9156 
    9157 > hide #!6 models
    9158 
    9159 > select #7/G:108
    9160 
    9161 6 atoms, 5 bonds, 1 residue, 1 model selected 
    9162 
    9163 > select #7/G:109
    9164 
    9165 6 atoms, 5 bonds, 1 residue, 1 model selected 
    9166 
    9167 > select #7/G:110
    9168 
    9169 4 atoms, 3 bonds, 1 residue, 1 model selected 
    9170 
    9171 > select add #7/G:111
    9172 
    9173 16 atoms, 15 bonds, 2 residues, 1 model selected 
    9174 
    9175 > select add #7/G:112
    9176 
    9177 23 atoms, 22 bonds, 3 residues, 1 model selected 
    9178 
    9179 > select add #7/G:113
    9180 
    9181 31 atoms, 29 bonds, 4 residues, 1 model selected 
    9182 
    9183 > select add #7/G:114
    9184 
    9185 42 atoms, 40 bonds, 5 residues, 1 model selected 
    9186 
    9187 > select add #7/G:115
    9188 
    9189 50 atoms, 47 bonds, 6 residues, 1 model selected 
    9190 
    9191 > select add #7/G:98
    9192 
    9193 61 atoms, 57 bonds, 7 residues, 1 model selected 
    9194 
    9195 > select add #7/G:99
    9196 
    9197 65 atoms, 60 bonds, 8 residues, 1 model selected 
    9198 
    9199 > select add #7/G:100
    9200 
    9201 69 atoms, 63 bonds, 9 residues, 1 model selected 
    9202 
    9203 > select add #7/G:101
    9204 
    9205 83 atoms, 78 bonds, 10 residues, 1 model selected 
    9206 
    9207 > select add #7/G:102
    9208 
    9209 91 atoms, 85 bonds, 11 residues, 1 model selected 
    9210 
    9211 > select add #7/G:103
    9212 
    9213 97 atoms, 90 bonds, 12 residues, 1 model selected 
    9214 
    9215 > select add #7/G:104
    9216 
    9217 105 atoms, 97 bonds, 13 residues, 1 model selected 
    9218 
    9219 > color sel goldenrod
    9220 
    9221 > select clear
    9222 
    9223 > show #!6 models
    9224 
    9225 > hide #!7 models
    9226 
    9227 > name view init_des2
    9228 
    9229 "init_des2": invalid atom specifier 
    9230 
    9231 > view name init_des2
    9232 
    9233 > show #!7 models
    9234 
    9235 > hide #!7 models
    9236 
    9237 > select add #6/G:114
    9238 
    9239 11 atoms, 11 bonds, 1 residue, 1 model selected 
    9240 
    9241 > select add #6/G:99
    9242 
    9243 15 atoms, 14 bonds, 2 residues, 1 model selected 
    9244 
    9245 > select add #6/G:100
    9246 
    9247 19 atoms, 17 bonds, 3 residues, 1 model selected 
    9248 
    9249 > select add #6/G:101
    9250 
    9251 33 atoms, 32 bonds, 4 residues, 1 model selected 
    9252 
    9253 > select add #6/G:102
    9254 
    9255 41 atoms, 39 bonds, 5 residues, 1 model selected 
    9256 
    9257 > select add #6/G:105
    9258 
    9259 53 atoms, 51 bonds, 6 residues, 1 model selected 
    9260 
    9261 > select subtract #6/G:105
    9262 
    9263 41 atoms, 39 bonds, 5 residues, 1 model selected 
    9264 Drag select of RMSD4_NNK1.pdb_A SES surface, 12 of 169006 triangles, 1
    9265 residues 
    9266 
    9267 > select add #6/G:104
    9268 
    9269 55 atoms, 46 bonds, 7 residues, 1 model selected 
    9270 
    9271 > select add #6/G:110
    9272 
    9273 59 atoms, 49 bonds, 8 residues, 1 model selected 
    9274 
    9275 > select add #6/G:111
    9276 
    9277 71 atoms, 61 bonds, 9 residues, 1 model selected 
    9278 
    9279 > select add #6/G:112
    9280 
    9281 78 atoms, 68 bonds, 10 residues, 1 model selected 
    9282 
    9283 > select add #6/G:113
    9284 
    9285 86 atoms, 75 bonds, 11 residues, 1 model selected 
    9286 
    9287 > color sel goldenrod
    9288 
    9289 > select clear
    9290 
    9291 > select #6/G:98
    9292 
    9293 11 atoms, 10 bonds, 1 residue, 1 model selected 
    9294 
    9295 > select up
    9296 
    9297 58 atoms, 59 bonds, 7 residues, 1 model selected 
    9298 
    9299 > select up
    9300 
    9301 990 atoms, 1018 bonds, 126 residues, 1 model selected 
    9302 
    9303 > select subtract #6/G:109
    9304 
    9305 984 atoms, 1011 bonds, 125 residues, 1 model selected 
    9306 
    9307 > select subtract #6/G:108
    9308 
    9309 978 atoms, 1005 bonds, 124 residues, 1 model selected 
    9310 
    9311 > select subtract #6/G:107
    9312 
    9313 970 atoms, 997 bonds, 123 residues, 1 model selected 
    9314 
    9315 > select subtract #6/G:105
    9316 
    9317 958 atoms, 983 bonds, 122 residues, 1 model selected 
    9318 
    9319 > select subtract #6/G:106
    9320 
    9321 946 atoms, 971 bonds, 121 residues, 1 model selected 
    9322 
    9323 > color sel goldenrod
    9324 
    9325 > select clear
    9326 
    9327 > view init_des2
    9328 
    9329 > show #!7 models
    9330 
    9331 > hide #!6 models
    9332 
    9333 > show #!6 models
    9334 
    9335 > hide #!7 models
    9336 
    9337 > show #!7 models
    9338 
    9339 > view init_des2
    9340 
    9341 > hide #!6 models
    9342 
    9343 > select clear
    9344 
    9345 > show #!6 models
    9346 
    9347 > hide #!7 models
    9348 
    9349 > save /Users/oswanson/Desktop/Primocalins/Structures/initial_models.cxs
    9350 
    9351 Desktop color scheme is dark 
    9352 Desktop color scheme is light 
    9353 Desktop color scheme is dark 
    9354 Desktop color scheme is light 
    9355 Desktop color scheme is dark 
    9356 Desktop color scheme is light 
    9357 
    9358 > show #!1 models
    9359 
    9360 > hide #!6 models
    9361 
    9362 > show #!3 models
    9363 
    9364 > hide #!3 models
    9365 
    9366 > show #1.2 models
    9367 
    9368 > show #1.3 models
    9369 
    9370 > select add #1.3
    9371 
    9372 64 pseudobonds, 1 model selected 
    9373 
    9374 > show #!1 atoms
    9375 
    9376 > select up
    9377 
    9378 71 pseudobonds, 3 models selected 
    9379 
    9380 > select #1/E:36@CA
    9381 
    9382 1 atom, 1 residue, 1 model selected 
    9383 
    9384 > select #1/E:36
    9385 
    9386 8 atoms, 7 bonds, 1 residue, 1 model selected 
    9387 
    9388 > select add #1/H:111B
    9389 
    9390 20 atoms, 19 bonds, 2 residues, 1 model selected 
    9391 
    9392 > select add #1/E:50
    9393 
    9394 29 atoms, 27 bonds, 1 pseudobond, 3 residues, 2 models selected 
    9395 
    9396 > select add #1/E:49
    9397 
    9398 34 atoms, 31 bonds, 1 pseudobond, 4 residues, 2 models selected 
    9399 
    9400 > select add #1/H:111C
    9401 
    9402 46 atoms, 43 bonds, 1 pseudobond, 5 residues, 2 models selected 
    9403 
    9404 > select add #1/H:109
    9405 
    9406 60 atoms, 58 bonds, 1 pseudobond, 6 residues, 2 models selected 
    9407 
    9408 > select add #1/E:128
    9409 
    9410 68 atoms, 65 bonds, 1 pseudobond, 7 residues, 2 models selected 
    9411 
    9412 > select add #1/E:68
    9413 
    9414 76 atoms, 72 bonds, 1 pseudobond, 8 residues, 2 models selected 
    9415 
    9416 > select add #1/H:59
    9417 
    9418 84 atoms, 79 bonds, 1 pseudobond, 9 residues, 2 models selected 
    9419 
    9420 > select add #1/H:62
    9421 
    9422 90 atoms, 84 bonds, 1 pseudobond, 10 residues, 2 models selected 
    9423 
    9424 > select add #1/H:110
    9425 
    9426 98 atoms, 91 bonds, 1 pseudobond, 11 residues, 2 models selected 
    9427 
    9428 > select add #1/E:72
    9429 
    9430 105 atoms, 98 bonds, 1 pseudobond, 12 residues, 2 models selected 
    9431 
    9432 > select add #1/H:66
    9433 
    9434 113 atoms, 105 bonds, 1 pseudobond, 13 residues, 2 models selected 
    9435 
    9436 > select add #1/E:74
    9437 
    9438 122 atoms, 113 bonds, 1 pseudobond, 14 residues, 2 models selected 
    9439 
    9440 > select add #1/H:112D
    9441 
    9442 130 atoms, 120 bonds, 1 pseudobond, 15 residues, 2 models selected 
    9443 
    9444 > select add #1/E:52
    9445 
    9446 141 atoms, 131 bonds, 1 pseudobond, 16 residues, 2 models selected 
    9447 
    9448 > select add #1/H:111A
    9449 
    9450 149 atoms, 138 bonds, 1 pseudobond, 17 residues, 2 models selected 
    9451 
    9452 > select ~sel & ##selected
    9453 
    9454 4498 atoms, 4613 bonds, 41 pseudobonds, 591 residues, 4 models selected 
    9455 
    9456 > hide sel atoms
    9457 
    9458 > undo
    9459 
    9460 > redo
    9461 
    9462 > select clear
    9463 
    9464 > select #1/H:111C
    9465 
    9466 12 atoms, 12 bonds, 1 residue, 1 model selected 
    9467 
    9468 > hide sel atoms
    9469 
    9470 > select clear
    9471 
    9472 > select add #1.3
    9473 
    9474 64 pseudobonds, 1 model selected 
    9475 
    9476 > select add #1.2
    9477 
    9478 70 pseudobonds, 2 models selected 
    9479 
    9480 > view orient
    9481 
    9482 > select subtract #1.3
    9483 
    9484 6 pseudobonds, 1 model selected 
    9485 
    9486 > select subtract #1.2
    9487 
    9488 Nothing selected 
    9489 
    9490 > select #1/H:111C
    9491 
    9492 12 atoms, 12 bonds, 1 residue, 1 model selected 
    9493 
    9494 > select up
    9495 
    9496 181 atoms, 190 bonds, 22 residues, 1 model selected 
    9497 
    9498 > select up
    9499 
    9500 1725 atoms, 1772 bonds, 228 residues, 1 model selected 
    9501 
    9502 > select up
    9503 
    9504 4647 atoms, 4757 bonds, 608 residues, 1 model selected 
    9505 
    9506 > select down
    9507 
    9508 1725 atoms, 1772 bonds, 228 residues, 1 model selected 
    9509 
    9510 > style sel sphere
    9511 
    9512 Changed 1725 atom styles 
    9513 
    9514 > select up
    9515 
    9516 4647 atoms, 4757 bonds, 608 residues, 1 model selected 
    9517 
    9518 > style sel sphere
    9519 
    9520 Changed 4647 atom styles 
    9521 
    9522 > style sel ball
    9523 
    9524 Changed 4647 atom styles 
    9525 
    9526 > nucleotides sel atoms
    9527 
    9528 > style nucleic & sel stick
    9529 
    9530 Changed 0 atom styles 
    9531 
    9532 > nucleotides sel atoms
    9533 
    9534 > style nucleic & sel stick
    9535 
    9536 Changed 0 atom styles 
    9537 
    9538 > style sel stick
    9539 
    9540 Changed 4647 atom styles 
    9541 
    9542 > hide #1.3 models
    9543 
    9544 > open
    9545 > /Users/oswanson/Desktop/Primocalins/Structures/folds_2025_11_03_22_26/y513_gspy_uca3_notags/fold_y513_gspy_uca3_notags_full_data_0.json
    9546 
    9547 Failed opening file
    9548 /Users/oswanson/Desktop/Primocalins/Structures/folds_2025_11_03_22_26/y513_gspy_uca3_notags/fold_y513_gspy_uca3_notags_full_data_0.json: 
    9549 Opening an AlphaFold PAE file requires first opening the predicted atomic
    9550 model. Did not find an open atomic model from the same directory. If the
    9551 atomic model is already open choose it using menu 
    9552  
    9553 Tools / Structure Prediction / AlphaFold Error Plot 
    9554  
    9555 or use the open command structure option, for example 
    9556  
    9557 open
    9558 /Users/oswanson/Desktop/Primocalins/Structures/folds_2025_11_03_22_26/y513_gspy_uca3_notags/fold_y513_gspy_uca3_notags_full_data_0.json
    9559 structure #1 
    9560  
    9561 If you are trying to open a JSON file that is not AlphaFold PAE data then you
    9562 need to specify the specific JSON format such as 
    9563  
    9564 open mole_channels.json format mole 
    9565 
    9566 > open
    9567 > /Users/oswanson/Desktop/Primocalins/Structures/folds_2025_11_03_22_26/y513_gspy_uca3_notags/fold_y513_gspy_uca3_notags_model_0.cif
    9568 
    9569 Chain information for fold_y513_gspy_uca3_notags_model_0.cif #9 
    9570 --- 
    9571 Chain | Description 
    9572 A | . 
    9573 B | . 
    9574 C | . 
    9575  
    9576 Computing secondary structure 
    9577 
    9578 > open
    9579 > /Users/oswanson/Desktop/Primocalins/Structures/folds_2025_11_03_22_26/poly310_uca3/fold_poly310_uca3_model_0.cif
    9580 
    9581 Chain information for fold_poly310_uca3_model_0.cif #10 
    9582 --- 
    9583 Chain | Description 
    9584 A | . 
    9585 B | . 
    9586 C | . 
    9587  
    9588 Computing secondary structure 
    9589 
    9590 > open
    9591 > /Users/oswanson/Desktop/Primocalins/Structures/folds_2025_11_03_22_26/poly28_uca3/fold_poly28_uca3_model_0.cif
    9592 
    9593 Chain information for fold_poly28_uca3_model_0.cif #11 
    9594 --- 
    9595 Chain | Description 
    9596 A | . 
    9597 B | . 
    9598 C | . 
    9599  
    9600 Computing secondary structure 
    9601 
    9602 > ui tool show Matchmaker
    9603 
    9604 > select #1/E:132
    9605 
    9606 9 atoms, 8 bonds, 1 residue, 1 model selected 
    9607 
    9608 > select up
    9609 
    9610 63 atoms, 63 bonds, 8 residues, 1 model selected 
    9611 
    9612 > select up
    9613 
    9614 604 atoms, 618 bonds, 74 residues, 1 model selected 
    9615 
    9616 > select up
    9617 
    9618 616 atoms, 629 bonds, 76 residues, 1 model selected 
    9619 
    9620 > select up
    9621 
    9622 1313 atoms, 1346 bonds, 164 residues, 1 model selected 
    9623 
    9624 > matchmaker #9-11 to #1 & sel
    9625 
    9626 Parameters 
    9627 --- 
    9628 Chain pairing | bb 
    9629 Alignment algorithm | Needleman-Wunsch 
    9630 Similarity matrix | BLOSUM-62 
    9631 SS fraction | 0.3 
    9632 Gap open (HH/SS/other) | 18/18/6 
    9633 Gap extend | 1 
    9634 SS matrix |  |  | H | S | O 
    9635 ---|---|---|--- 
    9636 H | 6 | -9 | -6 
    9637 S |  | 6 | -6 
    9638 O |  |  | 4 
    9639 Iteration cutoff | 2 
    9640  
    9641 Matchmaker 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1) with
    9642 fold_y513_gspy_uca3_notags_model_0.cif, chain A (#9), sequence alignment score
    9643 = 675.4 
    9644 RMSD between 152 pruned atom pairs is 0.658 angstroms; (across all 164 pairs:
    9645 1.656) 
    9646  
    9647 Matchmaker 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1) with
    9648 fold_poly310_uca3_model_0.cif, chain A (#10), sequence alignment score = 803.4 
    9649 RMSD between 153 pruned atom pairs is 0.635 angstroms; (across all 164 pairs:
    9650 1.380) 
    9651  
    9652 Matchmaker 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1) with
    9653 fold_poly28_uca3_model_0.cif, chain A (#11), sequence alignment score = 766 
    9654 RMSD between 157 pruned atom pairs is 0.633 angstroms; (across all 164 pairs:
    9655 1.406) 
    9656  
    9657 
    9658 > hide #9 models
    9659 
    9660 > hide #11 models
    9661 
    9662 > show #11 models
    9663 
    9664 > hide #10 models
    9665 
    9666 > show #!6 models
    9667 
    9668 > hide #!6 models
    9669 
    9670 > show #5 models
    9671 
    9672 > hide #5 models
    9673 
    9674 > show #4 models
    9675 
    9676 > hide #4 models
    9677 
    9678 > show #4 models
    9679 
    9680 > hide #4 models
    9681 
    9682 > show #4 models
    9683 
    9684 > hide #4 models
    9685 
    9686 > show #9 models
    9687 
    9688 > hide #11 models
    9689 
    9690 > show #2 models
    9691 
    9692 > matchmaker #2 to #1 & sel
    9693 
    9694 Parameters 
    9695 --- 
    9696 Chain pairing | bb 
    9697 Alignment algorithm | Needleman-Wunsch 
    9698 Similarity matrix | BLOSUM-62 
    9699 SS fraction | 0.3 
    9700 Gap open (HH/SS/other) | 18/18/6 
    9701 Gap extend | 1 
    9702 SS matrix |  |  | H | S | O 
    9703 ---|---|---|--- 
    9704 H | 6 | -9 | -6 
    9705 S |  | 6 | -6 
    9706 O |  |  | 4 
    9707 Iteration cutoff | 2 
    9708  
    9709 Matchmaker 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1) with
    9710 Y513apo_refine_31.pdb, chain B (#2), sequence alignment score = 692 
    9711 RMSD between 154 pruned atom pairs is 0.689 angstroms; (across all 164 pairs:
    9712 1.591) 
    9713  
    9714 
    9715 > matchmaker #5 to #1 & sel
    9716 
    9717 Parameters 
    9718 --- 
    9719 Chain pairing | bb 
    9720 Alignment algorithm | Needleman-Wunsch 
    9721 Similarity matrix | BLOSUM-62 
    9722 SS fraction | 0.3 
    9723 Gap open (HH/SS/other) | 18/18/6 
    9724 Gap extend | 1 
    9725 SS matrix |  |  | H | S | O 
    9726 ---|---|---|--- 
    9727 H | 6 | -9 | -6 
    9728 S |  | 6 | -6 
    9729 O |  |  | 4 
    9730 Iteration cutoff | 2 
    9731  
    9732 Matchmaker 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1) with
    9733 design_start.pdb, chain A (#5), sequence alignment score = 709.7 
    9734 RMSD between 150 pruned atom pairs is 0.630 angstroms; (across all 164 pairs:
    9735 1.402) 
    9736  
    9737 
    9738 > show #5 models
    9739 
    9740 > hide #2 models
    9741 
    9742 > hide #9 models
    9743 
    9744 > hide #5 models
    9745 
    9746 > show #5 models
    9747 
    9748 > hide #5 models
    9749 
    9750 > show #5 models
    9751 
    9752 > hide #!1 models
    9753 
    9754 > show #11 models
    9755 
    9756 > hide #11 models
    9757 
    9758 > show #9 models
    9759 
    9760 > hide #9 models
    9761 
    9762 > show #!1 models
    9763 
    9764 > show #2 models
    9765 
    9766 > hide #!1 models
    9767 
    9768 > hide #5 models
    9769 
    9770 > show #9 models
    9771 
    9772 > hide #1.2 models
    9773 
    9774 > hide #2 models
    9775 
    9776 > show #2 models
    9777 
    9778 > hide #2 models
    9779 
    9780 > show #2 models
    9781 
    9782 > hide #2 models
    9783 
    9784 > show #2 models
    9785 
    9786 > hide #2 models
    9787 
    9788 > select #9/A:85
    9789 
    9790 10 atoms, 10 bonds, 1 residue, 1 model selected 
    9791 
    9792 > select up
    9793 
    9794 93 atoms, 96 bonds, 11 residues, 1 model selected 
    9795 
    9796 > select up
    9797 
    9798 1449 atoms, 1487 bonds, 184 residues, 1 model selected 
    9799 
    9800 > color bfactor sel
    9801 
    9802 1449 atoms, 184 residues, atom bfactor range 15.7 to 97.6 
    9803 
    9804 > select clear
    9805 
    9806 > select #9/A:3
    9807 
    9808 11 atoms, 11 bonds, 1 residue, 1 model selected 
    9809 
    9810 > select up
    9811 
    9812 129 atoms, 134 bonds, 18 residues, 1 model selected 
    9813 
    9814 > select subtract #9/A:18
    9815 
    9816 122 atoms, 126 bonds, 17 residues, 1 model selected 
    9817 
    9818 > select subtract #9/A:17
    9819 
    9820 115 atoms, 118 bonds, 16 residues, 1 model selected 
    9821 
    9822 > select subtract #9/A:16
    9823 
    9824 110 atoms, 113 bonds, 15 residues, 1 model selected 
    9825 
    9826 > select subtract #9/A:15
    9827 
    9828 103 atoms, 105 bonds, 14 residues, 1 model selected 
    9829 
    9830 > select subtract #9/A:14
    9831 
    9832 95 atoms, 97 bonds, 13 residues, 1 model selected 
    9833 
    9834 > select subtract #9/A:13
    9835 
    9836 90 atoms, 92 bonds, 12 residues, 1 model selected 
    9837 
    9838 > hide sel cartoons
    9839 
    9840 > select #9/A:86
    9841 
    9842 8 atoms, 7 bonds, 1 residue, 1 model selected 
    9843 
    9844 > select up
    9845 
    9846 93 atoms, 96 bonds, 11 residues, 1 model selected 
    9847 
    9848 > select up
    9849 
    9850 1449 atoms, 1487 bonds, 184 residues, 1 model selected 
    9851 
    9852 > ui tool show Contacts
    9853 
    9854 > contacts sel restrict cross interModel false intraMol false
    9855 > ignoreHiddenModels true select true color #ff2600 name contacts_AF3_Y513
    9856 > reveal true log true
    9857    
    9858    
    9859     Allowed overlap: -0.4
    9860     H-bond overlap reduction: 0.4
    9861     Ignore contacts between atoms separated by 4 bonds or less
    9862     Detect intra-residue contacts: False
    9863     Detect intra-molecule contacts: False
    9864    
    9865     116 contacts
    9866                              atom1                                                    atom2                           overlap  distance
    9867     fold_y513_gspy_uca3_notags_model_0.cif #9/A THR 8 CG2    fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 O     1.315    1.985
    9868     fold_y513_gspy_uca3_notags_model_0.cif #9/A GLU 107 O    fold_y513_gspy_uca3_notags_model_0.cif #9/B TRP 101 CD1   0.992    2.188
    9869     fold_y513_gspy_uca3_notags_model_0.cif #9/A MET 131 SD   fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CB    0.884    2.766
    9870     fold_y513_gspy_uca3_notags_model_0.cif #9/A ASN 135 ND2  fold_y513_gspy_uca3_notags_model_0.cif #9/B ASN 113 ND2   0.667    2.613
    9871     fold_y513_gspy_uca3_notags_model_0.cif #9/A THR 8 CB     fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 106 CA    0.633    3.127
    9872     fold_y513_gspy_uca3_notags_model_0.cif #9/A PHE 112 CE2  fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CE2   0.606    2.914
    9873     fold_y513_gspy_uca3_notags_model_0.cif #9/A THR 8 CG2    fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 C     0.598    2.892
    9874     fold_y513_gspy_uca3_notags_model_0.cif #9/A GLY 108 CA   fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 32 OH     0.541    2.799
    9875     fold_y513_gspy_uca3_notags_model_0.cif #9/A THR 8 CB     fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 O     0.531    2.769
    9876     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 NZ    fold_y513_gspy_uca3_notags_model_0.cif #9/B SER 109 O     0.504    2.156
    9877     fold_y513_gspy_uca3_notags_model_0.cif #9/A PHE 112 CZ   fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CE2   0.481    3.039
    9878     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 2 CE     fold_y513_gspy_uca3_notags_model_0.cif #9/B TRP 50 CH2    0.470    3.170
    9879     fold_y513_gspy_uca3_notags_model_0.cif #9/A TRP 7 CH2    fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CD1   0.459    3.061
    9880     fold_y513_gspy_uca3_notags_model_0.cif #9/A GLN 87 NE2   fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 OH    0.413    2.287
    9881     fold_y513_gspy_uca3_notags_model_0.cif #9/A THR 8 OG1    fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 106 CA    0.412    2.928
    9882     fold_y513_gspy_uca3_notags_model_0.cif #9/A PHE 112 CE2  fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CD2   0.393    3.127
    9883     fold_y513_gspy_uca3_notags_model_0.cif #9/A TRP 7 CH2    fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CE1   0.383    3.137
    9884     fold_y513_gspy_uca3_notags_model_0.cif #9/A GLU 107 O    fold_y513_gspy_uca3_notags_model_0.cif #9/B TRP 101 NE1   0.355    2.305
    9885     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 CE    fold_y513_gspy_uca3_notags_model_0.cif #9/C TYR 93 CE1    0.313    3.327
    9886     fold_y513_gspy_uca3_notags_model_0.cif #9/A ARG 136 NH2  fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 106 CE2   0.258    3.142
    9887     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 2 CG     fold_y513_gspy_uca3_notags_model_0.cif #9/B TRP 50 CH2    0.199    3.441
    9888     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 CE    fold_y513_gspy_uca3_notags_model_0.cif #9/C TYR 93 CZ     0.198    3.292
    9889     fold_y513_gspy_uca3_notags_model_0.cif #9/A ASP 106 CG   fold_y513_gspy_uca3_notags_model_0.cif #9/B THR 28 OG1    0.193    3.147
    9890     fold_y513_gspy_uca3_notags_model_0.cif #9/A MET 74 SD    fold_y513_gspy_uca3_notags_model_0.cif #9/B LEU 104 CD2   0.177    3.473
    9891     fold_y513_gspy_uca3_notags_model_0.cif #9/A THR 8 CB     fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 C     0.135    3.355
    9892     fold_y513_gspy_uca3_notags_model_0.cif #9/A HIS 85 CG    fold_y513_gspy_uca3_notags_model_0.cif #9/B LEU 104 CD1   0.116    3.374
    9893     fold_y513_gspy_uca3_notags_model_0.cif #9/A GLN 87 NE2   fold_y513_gspy_uca3_notags_model_0.cif #9/B LEU 104 CD2   0.112    3.408
    9894     fold_y513_gspy_uca3_notags_model_0.cif #9/A GLN 87 NE2   fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CZ    0.093    3.157
    9895     fold_y513_gspy_uca3_notags_model_0.cif #9/A VAL 4 CG1    fold_y513_gspy_uca3_notags_model_0.cif #9/B ASP 107 CG    0.089    3.671
    9896     fold_y513_gspy_uca3_notags_model_0.cif #9/A PHE 112 CZ   fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CZ    0.084    3.286
    9897     fold_y513_gspy_uca3_notags_model_0.cif #9/A ASP 133 OD2  fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 106 OH    0.078    2.402
    9898     fold_y513_gspy_uca3_notags_model_0.cif #9/A LEU 109 CB   fold_y513_gspy_uca3_notags_model_0.cif #9/B TRP 101 CZ2   0.067    3.573
    9899     fold_y513_gspy_uca3_notags_model_0.cif #9/A THR 8 CG2    fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 106 CA    0.063    3.697
    9900     fold_y513_gspy_uca3_notags_model_0.cif #9/A HIS 85 ND1   fold_y513_gspy_uca3_notags_model_0.cif #9/B LEU 104 CD1   0.055    3.465
    9901     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 2 CD     fold_y513_gspy_uca3_notags_model_0.cif #9/B TRP 50 CH2    0.053    3.587
    9902     fold_y513_gspy_uca3_notags_model_0.cif #9/A TRP 7 CZ2    fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CD1   0.052    3.468
    9903     fold_y513_gspy_uca3_notags_model_0.cif #9/A GLU 107 CG   fold_y513_gspy_uca3_notags_model_0.cif #9/B THR 28 CB     0.044    3.716
    9904     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 CE    fold_y513_gspy_uca3_notags_model_0.cif #9/B SER 109 O     0.040    3.260
    9905     fold_y513_gspy_uca3_notags_model_0.cif #9/A GLN 87 CD    fold_y513_gspy_uca3_notags_model_0.cif #9/B LEU 104 CD2   0.039    3.451
    9906     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 NZ    fold_y513_gspy_uca3_notags_model_0.cif #9/B SER 109 C     0.037    3.213
    9907     fold_y513_gspy_uca3_notags_model_0.cif #9/A MET 131 SD   fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CG    0.035    3.345
    9908     fold_y513_gspy_uca3_notags_model_0.cif #9/A ARG 136 CZ   fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 106 CE2   0.033    3.337
    9909     fold_y513_gspy_uca3_notags_model_0.cif #9/A ASP 133 CG   fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 106 OH    0.022    3.318
    9910     fold_y513_gspy_uca3_notags_model_0.cif #9/A HIS 85 CB    fold_y513_gspy_uca3_notags_model_0.cif #9/B LEU 104 CD1   0.008    3.752
    9911     fold_y513_gspy_uca3_notags_model_0.cif #9/A VAL 4 CG1    fold_y513_gspy_uca3_notags_model_0.cif #9/B ASP 107 OD2   -0.019    3.319
    9912     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 CB    fold_y513_gspy_uca3_notags_model_0.cif #9/C LEU 34 CD1    -0.022    3.782
    9913     fold_y513_gspy_uca3_notags_model_0.cif #9/A GLU 107 C    fold_y513_gspy_uca3_notags_model_0.cif #9/B TRP 101 CD1   -0.034    3.404
    9914     fold_y513_gspy_uca3_notags_model_0.cif #9/A LEU 109 CD2  fold_y513_gspy_uca3_notags_model_0.cif #9/B TRP 101 CH2   -0.048    3.688
    9915     fold_y513_gspy_uca3_notags_model_0.cif #9/A THR 8 CG2    fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CA    -0.055    3.815
    9916     fold_y513_gspy_uca3_notags_model_0.cif #9/A THR 8 CB     fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 106 N     -0.060    3.580
    9917     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 2 CE     fold_y513_gspy_uca3_notags_model_0.cif #9/B TRP 50 CZ3    -0.069    3.709
    9918     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 CE    fold_y513_gspy_uca3_notags_model_0.cif #9/C TYR 93 OH     -0.088    3.428
    9919     fold_y513_gspy_uca3_notags_model_0.cif #9/A HIS 85 CD2   fold_y513_gspy_uca3_notags_model_0.cif #9/B LEU 104 CD1   -0.089    3.729
    9920     fold_y513_gspy_uca3_notags_model_0.cif #9/A GLN 87 NE2   fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CE2   -0.090    3.490
    9921     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 CG    fold_y513_gspy_uca3_notags_model_0.cif #9/C LEU 34 CD1    -0.107    3.867
    9922     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 2 CE     fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 33 OH     -0.120    3.460
    9923     fold_y513_gspy_uca3_notags_model_0.cif #9/A ASP 106 CB   fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 27 CA     -0.128    3.888
    9924     fold_y513_gspy_uca3_notags_model_0.cif #9/A THR 8 OG1    fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 C     -0.128    3.198
    9925     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 NZ    fold_y513_gspy_uca3_notags_model_0.cif #9/B SER 109 N     -0.140    3.420
    9926     fold_y513_gspy_uca3_notags_model_0.cif #9/A THR 8 CG2    fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 106 N     -0.140    3.660
    9927     fold_y513_gspy_uca3_notags_model_0.cif #9/A PHE 89 CZ    fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 OH    -0.142    3.362
    9928     fold_y513_gspy_uca3_notags_model_0.cif #9/A GLU 107 CG   fold_y513_gspy_uca3_notags_model_0.cif #9/B THR 28 OG1    -0.147    3.487
    9929     fold_y513_gspy_uca3_notags_model_0.cif #9/A ARG 136 NE   fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 106 CE2   -0.147    3.547
    9930     fold_y513_gspy_uca3_notags_model_0.cif #9/A TRP 7 CZ2    fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CE1   -0.149    3.669
    9931     fold_y513_gspy_uca3_notags_model_0.cif #9/A GLN 87 OE1   fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CE2   -0.154    3.334
    9932     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 2 CG     fold_y513_gspy_uca3_notags_model_0.cif #9/B GLY 57 CA     -0.158    3.918
    9933     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 CG    fold_y513_gspy_uca3_notags_model_0.cif #9/C TYR 93 CE2    -0.161    3.801
    9934     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 2 CG     fold_y513_gspy_uca3_notags_model_0.cif #9/B TRP 50 CZ3    -0.165    3.805
    9935     fold_y513_gspy_uca3_notags_model_0.cif #9/A PHE 112 CZ   fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CD2   -0.167    3.687
    9936     fold_y513_gspy_uca3_notags_model_0.cif #9/A ASN 135 CG   fold_y513_gspy_uca3_notags_model_0.cif #9/B ASN 113 ND2   -0.180    3.430
    9937     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 CD    fold_y513_gspy_uca3_notags_model_0.cif #9/C LEU 34 CD1    -0.183    3.943
    9938     fold_y513_gspy_uca3_notags_model_0.cif #9/A ALA 13 CB    fold_y513_gspy_uca3_notags_model_0.cif #9/C ASN 33 ND2    -0.184    3.704
    9939     fold_y513_gspy_uca3_notags_model_0.cif #9/A MET 131 CE   fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CB    -0.186    3.946
    9940     fold_y513_gspy_uca3_notags_model_0.cif #9/A ARG 136 CB   fold_y513_gspy_uca3_notags_model_0.cif #9/C GLU 52 OE2    -0.194    3.494
    9941     fold_y513_gspy_uca3_notags_model_0.cif #9/A THR 8 CB     fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 106 CB    -0.200    3.960
    9942     fold_y513_gspy_uca3_notags_model_0.cif #9/A ASP 106 CG   fold_y513_gspy_uca3_notags_model_0.cif #9/B THR 28 N      -0.204    3.724
    9943     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 CD    fold_y513_gspy_uca3_notags_model_0.cif #9/B ASP 107 O     -0.208    3.508
    9944     fold_y513_gspy_uca3_notags_model_0.cif #9/A ARG 136 NH2  fold_y513_gspy_uca3_notags_model_0.cif #9/B SER 108 CB    -0.210    3.730
    9945     fold_y513_gspy_uca3_notags_model_0.cif #9/A LEU 109 CD2  fold_y513_gspy_uca3_notags_model_0.cif #9/B TRP 101 CZ2   -0.214    3.854
    9946     fold_y513_gspy_uca3_notags_model_0.cif #9/A GLU 107 C    fold_y513_gspy_uca3_notags_model_0.cif #9/B TRP 101 NE1   -0.215    3.465
    9947     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 2 NZ     fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 33 OH     -0.218    2.918
    9948     fold_y513_gspy_uca3_notags_model_0.cif #9/A HIS 85 CE1   fold_y513_gspy_uca3_notags_model_0.cif #9/B LEU 104 CD1   -0.219    3.859
    9949     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 2 CB     fold_y513_gspy_uca3_notags_model_0.cif #9/B GLY 57 CA     -0.234    3.994
    9950     fold_y513_gspy_uca3_notags_model_0.cif #9/A MET 131 SD   fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CD2   -0.237    3.767
    9951     fold_y513_gspy_uca3_notags_model_0.cif #9/A VAL 4 CG1    fold_y513_gspy_uca3_notags_model_0.cif #9/B ASP 107 CB    -0.243    4.003
    9952     fold_y513_gspy_uca3_notags_model_0.cif #9/A ALA 5 CB     fold_y513_gspy_uca3_notags_model_0.cif #9/B LEU 104 O     -0.254    3.554
    9953     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 2 CE     fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 33 CE1    -0.255    3.895
    9954     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 NZ    fold_y513_gspy_uca3_notags_model_0.cif #9/B SER 108 CA    -0.257    3.777
    9955     fold_y513_gspy_uca3_notags_model_0.cif #9/A ARG 136 NH1  fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 111 CE2   -0.262    3.662
    9956     fold_y513_gspy_uca3_notags_model_0.cif #9/A PHE 112 CZ   fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 OH    -0.269    3.489
    9957     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 NZ    fold_y513_gspy_uca3_notags_model_0.cif #9/B SER 108 C     -0.270    3.520
    9958     fold_y513_gspy_uca3_notags_model_0.cif #9/A LEU 9 O      fold_y513_gspy_uca3_notags_model_0.cif #9/B ASP 107 O     -0.271    3.111
    9959     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 CE    fold_y513_gspy_uca3_notags_model_0.cif #9/C TYR 93 CE2    -0.272    3.912
    9960     fold_y513_gspy_uca3_notags_model_0.cif #9/A GLN 87 OE1   fold_y513_gspy_uca3_notags_model_0.cif #9/B LEU 104 CD2   -0.274    3.574
    9961     fold_y513_gspy_uca3_notags_model_0.cif #9/A GLN 87 CD    fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 OH    -0.286    3.356
    9962     fold_y513_gspy_uca3_notags_model_0.cif #9/A ASN 135 CA   fold_y513_gspy_uca3_notags_model_0.cif #9/C TYR 51 CE2    -0.290    3.930
    9963     fold_y513_gspy_uca3_notags_model_0.cif #9/A PHE 112 CE2  fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 CZ    -0.296    3.666
    9964     fold_y513_gspy_uca3_notags_model_0.cif #9/A GLY 108 N    fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 32 OH     -0.298    2.998
    9965     fold_y513_gspy_uca3_notags_model_0.cif #9/A GLU 107 CG   fold_y513_gspy_uca3_notags_model_0.cif #9/B THR 28 CG2    -0.300    4.060
    9966     fold_y513_gspy_uca3_notags_model_0.cif #9/A LEU 109 CD1  fold_y513_gspy_uca3_notags_model_0.cif #9/B TRP 101 CH2   -0.301    3.941
    9967     fold_y513_gspy_uca3_notags_model_0.cif #9/A THR 8 O      fold_y513_gspy_uca3_notags_model_0.cif #9/B ASP 107 CB    -0.304    3.604
    9968     fold_y513_gspy_uca3_notags_model_0.cif #9/A LEU 109 CB   fold_y513_gspy_uca3_notags_model_0.cif #9/B TRP 101 CH2   -0.308    3.948
    9969     fold_y513_gspy_uca3_notags_model_0.cif #9/A GLU 107 O    fold_y513_gspy_uca3_notags_model_0.cif #9/B TRP 101 CG    -0.310    3.340
    9970     fold_y513_gspy_uca3_notags_model_0.cif #9/A GLU 107 C    fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 32 OH     -0.314    3.384
    9971     fold_y513_gspy_uca3_notags_model_0.cif #9/A ARG 136 NH1  fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 111 CD2   -0.323    3.723
    9972     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 2 NZ     fold_y513_gspy_uca3_notags_model_0.cif #9/B SER 109 CB    -0.334    3.854
    9973     fold_y513_gspy_uca3_notags_model_0.cif #9/A ASN 135 CB   fold_y513_gspy_uca3_notags_model_0.cif #9/C TYR 51 CE2    -0.336    3.976
    9974     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 CE    fold_y513_gspy_uca3_notags_model_0.cif #9/C TYR 93 CD1    -0.339    3.979
    9975     fold_y513_gspy_uca3_notags_model_0.cif #9/A HIS 85 CB    fold_y513_gspy_uca3_notags_model_0.cif #9/B LEU 104 CD2   -0.347    4.107
    9976     fold_y513_gspy_uca3_notags_model_0.cif #9/A THR 8 OG1    fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 106 C     -0.368    3.438
    9977     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 NZ    fold_y513_gspy_uca3_notags_model_0.cif #9/B SER 109 CA    -0.375    3.895
    9978     fold_y513_gspy_uca3_notags_model_0.cif #9/A GLY 108 CA   fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 32 CZ     -0.383    3.873
    9979     fold_y513_gspy_uca3_notags_model_0.cif #9/A ASP 133 CB   fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 106 OH    -0.384    3.724
    9980     fold_y513_gspy_uca3_notags_model_0.cif #9/A PHE 89 CE1   fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 OH    -0.393    3.613
    9981     fold_y513_gspy_uca3_notags_model_0.cif #9/A ASP 133 OD2  fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 106 CZ    -0.396    3.426
    9982     fold_y513_gspy_uca3_notags_model_0.cif #9/A ASP 106 O    fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 32 CE1    -0.400    3.580
    9983    
    9984 
    9985  
    9986 116 contacts 
    9987 
    9988 > select up
    9989 
    9990 373 atoms, 366 bonds, 41 residues, 1 model selected 
    9991 
    9992 > show sel cartoons
    9993 
    9994 > select clear
    9995 
    9996 > select #9/A:9
    9997 
    9998 8 atoms, 7 bonds, 1 residue, 1 model selected 
    9999 
    10000 > select up
    10001 
    10002 129 atoms, 134 bonds, 18 residues, 1 model selected 
    10003 
    10004 > select subtract #9/A:13
    10005 
    10006 124 atoms, 128 bonds, 17 residues, 1 model selected 
    10007 
    10008 > select subtract #9/A:14
    10009 
    10010 116 atoms, 120 bonds, 16 residues, 1 model selected 
    10011 
    10012 > select subtract #9/A:15
    10013 
    10014 109 atoms, 112 bonds, 15 residues, 1 model selected 
    10015 
    10016 > select subtract #9/A:16
    10017 
    10018 104 atoms, 107 bonds, 14 residues, 1 model selected 
    10019 
    10020 > select subtract #9/A:17
    10021 
    10022 97 atoms, 99 bonds, 13 residues, 1 model selected 
    10023 
    10024 > select subtract #9/A:18
    10025 
    10026 90 atoms, 92 bonds, 12 residues, 1 model selected 
    10027 
    10028 > hide sel atoms
    10029 
    10030 > hide sel cartoons
    10031 
    10032 > select #9/A:77
    10033 
    10034 11 atoms, 11 bonds, 1 residue, 1 model selected 
    10035 
    10036 > select up
    10037 
    10038 73 atoms, 74 bonds, 9 residues, 1 model selected 
    10039 
    10040 > select up
    10041 
    10042 1449 atoms, 1487 bonds, 184 residues, 1 model selected 
    10043 
    10044 > ui tool show H-Bonds
    10045 
    10046 > hbonds sel color #ffd479 restrict cross interModel false distSlop 0.8
    10047 > intraMol false intraRes false select true reveal true log true
    10048    
    10049    
    10050     Finding intramodel H-bonds
    10051     Constraints relaxed by 0.8 angstroms and 20 degrees
    10052     Models used:
    10053         9 fold_y513_gspy_uca3_notags_model_0.cif
    10054    
    10055     12 H-bonds
    10056     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    10057     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 2 NZ    fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 33 OH    no hydrogen  2.918  N/A
    10058     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 2 NZ    fold_y513_gspy_uca3_notags_model_0.cif #9/B ASP 107 OD1  no hydrogen  3.757  N/A
    10059     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 2 NZ    fold_y513_gspy_uca3_notags_model_0.cif #9/B SER 109 OG   no hydrogen  3.788  N/A
    10060     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 NZ   fold_y513_gspy_uca3_notags_model_0.cif #9/B ASP 107 O    no hydrogen  3.089  N/A
    10061     fold_y513_gspy_uca3_notags_model_0.cif #9/A LYS 10 NZ   fold_y513_gspy_uca3_notags_model_0.cif #9/B SER 109 O    no hydrogen  2.156  N/A
    10062     fold_y513_gspy_uca3_notags_model_0.cif #9/A GLN 87 NE2  fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 105 OH   no hydrogen  2.287  N/A
    10063     fold_y513_gspy_uca3_notags_model_0.cif #9/B THR 28 N    fold_y513_gspy_uca3_notags_model_0.cif #9/A ASP 106 O    no hydrogen  3.544  N/A
    10064     fold_y513_gspy_uca3_notags_model_0.cif #9/B THR 28 OG1  fold_y513_gspy_uca3_notags_model_0.cif #9/A ASP 106 OD1  no hydrogen  2.990  N/A
    10065     fold_y513_gspy_uca3_notags_model_0.cif #9/B THR 28 OG1  fold_y513_gspy_uca3_notags_model_0.cif #9/A ASP 106 OD2  no hydrogen  2.993  N/A
    10066     fold_y513_gspy_uca3_notags_model_0.cif #9/B TYR 106 OH  fold_y513_gspy_uca3_notags_model_0.cif #9/A ASP 133 OD2  no hydrogen  2.402  N/A
    10067     fold_y513_gspy_uca3_notags_model_0.cif #9/B ASP 107 N   fold_y513_gspy_uca3_notags_model_0.cif #9/A LEU 9 O      no hydrogen  3.520  N/A
    10068     fold_y513_gspy_uca3_notags_model_0.cif #9/C LYS 55 NZ   fold_y513_gspy_uca3_notags_model_0.cif #9/A ASN 135 O    no hydrogen  3.388  N/A
    10069    
    10070 
    10071  
    10072 12 hydrogen bonds found 
    10073 
    10074 > hide #9.1 models
    10075 
    10076 > select up
    10077 
    10078 6 atoms, 3 bonds, 3 residues, 1 model selected 
    10079 
    10080 > select up
    10081 
    10082 26 atoms, 24 bonds, 3 residues, 1 model selected 
    10083 
    10084 > hide sel atoms
    10085 
    10086 > show #2 models
    10087 
    10088 > select #2/B:100
    10089 
    10090 8 atoms, 7 bonds, 1 residue, 1 model selected 
    10091 
    10092 > select up
    10093 
    10094 150 atoms, 152 bonds, 21 residues, 1 model selected 
    10095 
    10096 > show sel atoms
    10097 
    10098 > select clear
    10099 
    10100 > hide #2 models
    10101 
    10102 > hide #!9 models
    10103 
    10104 > show #10 models
    10105 
    10106 > select #10/A:74
    10107 
    10108 12 atoms, 12 bonds, 1 residue, 1 model selected 
    10109 
    10110 > select up
    10111 
    10112 70 atoms, 71 bonds, 8 residues, 1 model selected 
    10113 
    10114 > select up
    10115 
    10116 1533 atoms, 1572 bonds, 191 residues, 1 model selected 
    10117 
    10118 > color bfactor sel
    10119 
    10120 1533 atoms, 191 residues, atom bfactor range 23 to 97.7 
    10121 
    10122 > select clear
    10123 
    10124 > select #10/A:33
    10125 
    10126 5 atoms, 4 bonds, 1 residue, 1 model selected 
    10127 
    10128 > select up
    10129 
    10130 74 atoms, 76 bonds, 10 residues, 1 model selected 
    10131 
    10132 > select up
    10133 
    10134 1533 atoms, 1572 bonds, 191 residues, 1 model selected 
    10135 
    10136 > hbonds sel color #ffd479 restrict cross interModel false distSlop 0.8
    10137 > intraMol false intraRes false select true reveal true log true
    10138    
    10139    
    10140     Finding intramodel H-bonds
    10141     Constraints relaxed by 0.8 angstroms and 20 degrees
    10142     Models used:
    10143         10 fold_poly310_uca3_model_0.cif
    10144    
    10145     27 H-bonds
    10146     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    10147     fold_poly310_uca3_model_0.cif #10/A HIS 1 NE2    fold_poly310_uca3_model_0.cif #10/B ASN 54 O     no hydrogen  3.290  N/A
    10148     fold_poly310_uca3_model_0.cif #10/A LYS 42 NZ    fold_poly310_uca3_model_0.cif #10/B THR 74 O     no hydrogen  2.445  N/A
    10149     fold_poly310_uca3_model_0.cif #10/A THR 50 OG1   fold_poly310_uca3_model_0.cif #10/B TYR 105 OH   no hydrogen  3.816  N/A
    10150     fold_poly310_uca3_model_0.cif #10/A LYS 70 NZ    fold_poly310_uca3_model_0.cif #10/B TYR 116 OH   no hydrogen  3.243  N/A
    10151     fold_poly310_uca3_model_0.cif #10/A LYS 94 NZ    fold_poly310_uca3_model_0.cif #10/B ASP 107 OD1  no hydrogen  2.708  N/A
    10152     fold_poly310_uca3_model_0.cif #10/A ARG 123 NH1  fold_poly310_uca3_model_0.cif #10/B GLY 103 O    no hydrogen  1.975  N/A
    10153     fold_poly310_uca3_model_0.cif #10/A ARG 123 NH1  fold_poly310_uca3_model_0.cif #10/B TYR 106 O    no hydrogen  3.125  N/A
    10154     fold_poly310_uca3_model_0.cif #10/A ASN 125 ND2  fold_poly310_uca3_model_0.cif #10/B THR 58 O     no hydrogen  3.150  N/A
    10155     fold_poly310_uca3_model_0.cif #10/A GLU 189 N    fold_poly310_uca3_model_0.cif #10/C GLU 52 OE1   no hydrogen  3.690  N/A
    10156     fold_poly310_uca3_model_0.cif #10/B THR 28 OG1   fold_poly310_uca3_model_0.cif #10/A ASP 43 OD1   no hydrogen  3.445  N/A
    10157     fold_poly310_uca3_model_0.cif #10/B THR 28 OG1   fold_poly310_uca3_model_0.cif #10/A ASP 43 OD2   no hydrogen  2.892  N/A
    10158     fold_poly310_uca3_model_0.cif #10/B THR 30 OG1   fold_poly310_uca3_model_0.cif #10/A GLU 40 OE1   no hydrogen  2.847  N/A
    10159     fold_poly310_uca3_model_0.cif #10/B THR 30 OG1   fold_poly310_uca3_model_0.cif #10/A GLU 40 OE2   no hydrogen  3.309  N/A
    10160     fold_poly310_uca3_model_0.cif #10/B TYR 33 OH    fold_poly310_uca3_model_0.cif #10/A ASP 124 OD1  no hydrogen  2.574  N/A
    10161     fold_poly310_uca3_model_0.cif #10/B TYR 33 OH    fold_poly310_uca3_model_0.cif #10/A ASP 124 OD2  no hydrogen  3.482  N/A
    10162     fold_poly310_uca3_model_0.cif #10/B ASN 52 ND2   fold_poly310_uca3_model_0.cif #10/A ASP 124 OD2  no hydrogen  2.754  N/A
    10163     fold_poly310_uca3_model_0.cif #10/B ASN 54 ND2   fold_poly310_uca3_model_0.cif #10/A ALA 36 O     no hydrogen  2.530  N/A
    10164     fold_poly310_uca3_model_0.cif #10/B SER 55 OG    fold_poly310_uca3_model_0.cif #10/A ASP 124 OD2  no hydrogen  3.777  N/A
    10165     fold_poly310_uca3_model_0.cif #10/B ARG 72 NH2   fold_poly310_uca3_model_0.cif #10/A HIS 1 NE2    no hydrogen  3.406  N/A
    10166     fold_poly310_uca3_model_0.cif #10/B ARG 98 NH1   fold_poly310_uca3_model_0.cif #10/A ASP 69 OD2   no hydrogen  2.768  N/A
    10167     fold_poly310_uca3_model_0.cif #10/B ARG 98 NH2   fold_poly310_uca3_model_0.cif #10/A ASP 69 OD2   no hydrogen  3.151  N/A
    10168     fold_poly310_uca3_model_0.cif #10/B TYR 105 OH   fold_poly310_uca3_model_0.cif #10/A THR 50 OG1   no hydrogen  3.816  N/A
    10169     fold_poly310_uca3_model_0.cif #10/B TYR 105 OH   fold_poly310_uca3_model_0.cif #10/A ASP 64 OD1   no hydrogen  3.083  N/A
    10170     fold_poly310_uca3_model_0.cif #10/B TYR 105 OH   fold_poly310_uca3_model_0.cif #10/A ASP 64 OD2   no hydrogen  3.375  N/A
    10171     fold_poly310_uca3_model_0.cif #10/C LYS 55 NZ    fold_poly310_uca3_model_0.cif #10/A TRP 187 O    no hydrogen  3.072  N/A
    10172     fold_poly310_uca3_model_0.cif #10/C TYR 93 OH    fold_poly310_uca3_model_0.cif #10/A ASP 96 OD2   no hydrogen  1.879  N/A
    10173     fold_poly310_uca3_model_0.cif #10/C SER 97 N     fold_poly310_uca3_model_0.cif #10/A ASP 96 OD2   no hydrogen  3.403  N/A
    10174    
    10175 
    10176  
    10177 27 hydrogen bonds found 
    10178 
    10179 > show #!1 models
    10180 
    10181 > show #1.2 models
    10182 
    10183 > hide #1.2 models
    10184 
    10185 > hide #!1 models
    10186 
    10187 > select #10/A:119
    10188 
    10189 11 atoms, 11 bonds, 1 residue, 1 model selected 
    10190 
    10191 > select up
    10192 
    10193 72 atoms, 74 bonds, 9 residues, 1 model selected 
    10194 
    10195 > select up
    10196 
    10197 1533 atoms, 1572 bonds, 191 residues, 1 model selected 
    10198 
    10199 > contacts sel restrict cross interModel false intraMol false
    10200 > ignoreHiddenModels true select true color #ff2600 name contacts_AF3_Y513
    10201 > reveal true log true
    10202    
    10203    
    10204     Allowed overlap: -0.4
    10205     H-bond overlap reduction: 0.4
    10206     Ignore contacts between atoms separated by 4 bonds or less
    10207     Detect intra-residue contacts: False
    10208     Detect intra-molecule contacts: False
    10209    
    10210     149 contacts
    10211                          atom1                                            atom2                       overlap  distance
    10212     fold_poly310_uca3_model_0.cif #10/A LEU 190 CD2  fold_poly310_uca3_model_0.cif #10/B TYR 111 OH    1.410    1.930
    10213     fold_poly310_uca3_model_0.cif #10/A ARG 77 NH2   fold_poly310_uca3_model_0.cif #10/B TYR 105 CE1   0.724    2.676
    10214     fold_poly310_uca3_model_0.cif #10/A LEU 32 CD2   fold_poly310_uca3_model_0.cif #10/B LEU 104 CD1   0.708    3.052
    10215     fold_poly310_uca3_model_0.cif #10/A ARG 123 NH1  fold_poly310_uca3_model_0.cif #10/B GLY 103 O     0.685    1.975
    10216     fold_poly310_uca3_model_0.cif #10/A ARG 77 NH1   fold_poly310_uca3_model_0.cif #10/B TYR 105 CD1   0.681    2.719
    10217     fold_poly310_uca3_model_0.cif #10/A MET 73 SD    fold_poly310_uca3_model_0.cif #10/B TRP 101 CE3   0.672    2.858
    10218     fold_poly310_uca3_model_0.cif #10/A ASP 96 OD2   fold_poly310_uca3_model_0.cif #10/C TYR 93 OH     0.601    1.879
    10219     fold_poly310_uca3_model_0.cif #10/A ARG 123 CD   fold_poly310_uca3_model_0.cif #10/B TYR 106 O     0.432    2.868
    10220     fold_poly310_uca3_model_0.cif #10/A LEU 32 CD1   fold_poly310_uca3_model_0.cif #10/B LEU 104 CD1   0.425    3.335
    10221     fold_poly310_uca3_model_0.cif #10/A LEU 190 CD1  fold_poly310_uca3_model_0.cif #10/B TYR 106 CD1   0.423    3.217
    10222     fold_poly310_uca3_model_0.cif #10/A ASP 96 CG    fold_poly310_uca3_model_0.cif #10/C TYR 93 OH     0.406    2.934
    10223     fold_poly310_uca3_model_0.cif #10/A LYS 94 NZ    fold_poly310_uca3_model_0.cif #10/B ASP 107 CG    0.401    3.119
    10224     fold_poly310_uca3_model_0.cif #10/A LYS 94 NZ    fold_poly310_uca3_model_0.cif #10/B GLY 110 N     0.359    2.921
    10225     fold_poly310_uca3_model_0.cif #10/A GLU 186 CG   fold_poly310_uca3_model_0.cif #10/C TYR 51 OH     0.353    2.987
    10226     fold_poly310_uca3_model_0.cif #10/A ARG 77 NH1   fold_poly310_uca3_model_0.cif #10/B TYR 105 CE1   0.336    3.064
    10227     fold_poly310_uca3_model_0.cif #10/A LEU 130 CD2  fold_poly310_uca3_model_0.cif #10/B LEU 104 CB    0.324    3.436
    10228     fold_poly310_uca3_model_0.cif #10/A PHE 48 CZ    fold_poly310_uca3_model_0.cif #10/B LEU 104 CD1   0.314    3.326
    10229     fold_poly310_uca3_model_0.cif #10/A LEU 90 CD2   fold_poly310_uca3_model_0.cif #10/B TYR 105 O     0.283    3.017
    10230     fold_poly310_uca3_model_0.cif #10/A LEU 130 CD2  fold_poly310_uca3_model_0.cif #10/B TYR 105 CD2   0.271    3.369
    10231     fold_poly310_uca3_model_0.cif #10/A PHE 48 CE1   fold_poly310_uca3_model_0.cif #10/B LEU 104 CD1   0.262    3.378
    10232     fold_poly310_uca3_model_0.cif #10/A ASP 96 CG    fold_poly310_uca3_model_0.cif #10/C SER 96 N      0.249    3.271
    10233     fold_poly310_uca3_model_0.cif #10/A LYS 94 CB    fold_poly310_uca3_model_0.cif #10/C TYR 93 CE2    0.241    3.399
    10234     fold_poly310_uca3_model_0.cif #10/A LEU 190 CD2  fold_poly310_uca3_model_0.cif #10/B TYR 111 CZ    0.239    3.251
    10235     fold_poly310_uca3_model_0.cif #10/A ASP 43 OD2   fold_poly310_uca3_model_0.cif #10/B THR 28 CA     0.220    3.080
    10236     fold_poly310_uca3_model_0.cif #10/A LYS 42 NZ    fold_poly310_uca3_model_0.cif #10/B THR 74 O      0.215    2.445
    10237     fold_poly310_uca3_model_0.cif #10/A LYS 94 CD    fold_poly310_uca3_model_0.cif #10/C TYR 93 CZ     0.147    3.343
    10238     fold_poly310_uca3_model_0.cif #10/A ASP 43 OD2   fold_poly310_uca3_model_0.cif #10/B THR 28 CG2    0.144    3.156
    10239     fold_poly310_uca3_model_0.cif #10/A ALA 36 O     fold_poly310_uca3_model_0.cif #10/B ASN 54 ND2    0.130    2.530
    10240     fold_poly310_uca3_model_0.cif #10/A ARG 77 CZ    fold_poly310_uca3_model_0.cif #10/B TYR 105 CE1   0.120    3.250
    10241     fold_poly310_uca3_model_0.cif #10/A ASP 43 OD2   fold_poly310_uca3_model_0.cif #10/B THR 28 CB     0.119    3.181
    10242     fold_poly310_uca3_model_0.cif #10/A ARG 123 NH1  fold_poly310_uca3_model_0.cif #10/B GLY 103 C     0.107    3.143
    10243     fold_poly310_uca3_model_0.cif #10/A HIS 188 ND1  fold_poly310_uca3_model_0.cif #10/C GLU 52 OE2    0.102    2.558
    10244     fold_poly310_uca3_model_0.cif #10/A ARG 77 NH1   fold_poly310_uca3_model_0.cif #10/B TYR 106 CB    0.100    3.420
    10245     fold_poly310_uca3_model_0.cif #10/A MET 73 SD    fold_poly310_uca3_model_0.cif #10/B TRP 101 CB    0.095    3.555
    10246     fold_poly310_uca3_model_0.cif #10/A LYS 94 CD    fold_poly310_uca3_model_0.cif #10/C TYR 93 OH     0.094    3.246
    10247     fold_poly310_uca3_model_0.cif #10/A LYS 94 NZ    fold_poly310_uca3_model_0.cif #10/B SER 109 OG    0.092    2.608
    10248     fold_poly310_uca3_model_0.cif #10/A LEU 190 CD1  fold_poly310_uca3_model_0.cif #10/B TYR 106 CB    0.058    3.702
    10249     fold_poly310_uca3_model_0.cif #10/A PRO 68 CG    fold_poly310_uca3_model_0.cif #10/B TYR 32 OH     0.044    3.296
    10250     fold_poly310_uca3_model_0.cif #10/A ASN 92 OD1   fold_poly310_uca3_model_0.cif #10/B ASP 107 CB    0.034    3.266
    10251     fold_poly310_uca3_model_0.cif #10/A ARG 123 CG   fold_poly310_uca3_model_0.cif #10/B ASP 107 CG    0.031    3.729
    10252     fold_poly310_uca3_model_0.cif #10/A ARG 123 CZ   fold_poly310_uca3_model_0.cif #10/B GLY 103 O     0.025    3.005
    10253     fold_poly310_uca3_model_0.cif #10/A ARG 77 NH2   fold_poly310_uca3_model_0.cif #10/B TYR 105 CD1   0.014    3.386
    10254     fold_poly310_uca3_model_0.cif #10/A ARG 123 CD   fold_poly310_uca3_model_0.cif #10/B ASP 107 CA    0.014    3.746
    10255     fold_poly310_uca3_model_0.cif #10/A LYS 94 CD    fold_poly310_uca3_model_0.cif #10/C TYR 93 CE1    0.012    3.628
    10256     fold_poly310_uca3_model_0.cif #10/A ARG 123 CG   fold_poly310_uca3_model_0.cif #10/B ASP 107 CB    -0.004    3.764
    10257     fold_poly310_uca3_model_0.cif #10/A LYS 94 CE    fold_poly310_uca3_model_0.cif #10/B ASP 107 CG    -0.012    3.772
    10258     fold_poly310_uca3_model_0.cif #10/A LEU 32 CG    fold_poly310_uca3_model_0.cif #10/B LEU 104 CD1   -0.028    3.788
    10259     fold_poly310_uca3_model_0.cif #10/A LYS 94 NZ    fold_poly310_uca3_model_0.cif #10/B SER 109 N     -0.035    3.315
    10260     fold_poly310_uca3_model_0.cif #10/A ARG 123 O    fold_poly310_uca3_model_0.cif #10/B ASP 107 OD2   -0.042    2.882
    10261     fold_poly310_uca3_model_0.cif #10/A LEU 190 CD1  fold_poly310_uca3_model_0.cif #10/B TYR 106 CG    -0.044    3.534
    10262     fold_poly310_uca3_model_0.cif #10/A PHE 119 CD2  fold_poly310_uca3_model_0.cif #10/B TYR 105 CB    -0.044    3.684
    10263     fold_poly310_uca3_model_0.cif #10/A LYS 94 CE    fold_poly310_uca3_model_0.cif #10/B GLY 110 N     -0.046    3.566
    10264     fold_poly310_uca3_model_0.cif #10/A LYS 94 NZ    fold_poly310_uca3_model_0.cif #10/B ASP 107 OD1   -0.048    2.708
    10265     fold_poly310_uca3_model_0.cif #10/A LEU 190 CG   fold_poly310_uca3_model_0.cif #10/B TYR 111 OH    -0.059    3.399
    10266     fold_poly310_uca3_model_0.cif #10/A ARG 77 CZ    fold_poly310_uca3_model_0.cif #10/B TYR 105 CD1   -0.059    3.429
    10267     fold_poly310_uca3_model_0.cif #10/A LYS 42 NZ    fold_poly310_uca3_model_0.cif #10/B SER 75 CA     -0.066    3.586
    10268     fold_poly310_uca3_model_0.cif #10/A ASP 96 OD2   fold_poly310_uca3_model_0.cif #10/C TYR 93 CZ     -0.069    3.099
    10269     fold_poly310_uca3_model_0.cif #10/A ASP 124 CG   fold_poly310_uca3_model_0.cif #10/B TYR 33 OH     -0.070    3.410
    10270     fold_poly310_uca3_model_0.cif #10/A GLU 40 CD    fold_poly310_uca3_model_0.cif #10/B THR 30 OG1    -0.076    3.416
    10271     fold_poly310_uca3_model_0.cif #10/A PRO 68 CB    fold_poly310_uca3_model_0.cif #10/B TYR 32 OH     -0.077    3.417
    10272     fold_poly310_uca3_model_0.cif #10/A ASP 69 OD2   fold_poly310_uca3_model_0.cif #10/B VAL 2 CG2     -0.078    3.378
    10273     fold_poly310_uca3_model_0.cif #10/A MET 73 SD    fold_poly310_uca3_model_0.cif #10/B TRP 101 CD2   -0.082    3.462
    10274     fold_poly310_uca3_model_0.cif #10/A ARG 123 CG   fold_poly310_uca3_model_0.cif #10/B ASP 107 CA    -0.083    3.843
    10275     fold_poly310_uca3_model_0.cif #10/A ASP 124 OD2  fold_poly310_uca3_model_0.cif #10/B ASN 52 ND2    -0.094    2.754
    10276     fold_poly310_uca3_model_0.cif #10/A ASP 124 OD1  fold_poly310_uca3_model_0.cif #10/B TYR 33 OH     -0.094    2.574
    10277     fold_poly310_uca3_model_0.cif #10/A LEU 99 CD2   fold_poly310_uca3_model_0.cif #10/B ASP 107 OD2   -0.107    3.407
    10278     fold_poly310_uca3_model_0.cif #10/A ASP 69 OD2   fold_poly310_uca3_model_0.cif #10/B ARG 98 NH1    -0.108    2.768
    10279     fold_poly310_uca3_model_0.cif #10/A HIS 188 ND1  fold_poly310_uca3_model_0.cif #10/B TYR 111 CE2   -0.110    3.510
    10280     fold_poly310_uca3_model_0.cif #10/A HIS 188 CE1  fold_poly310_uca3_model_0.cif #10/C GLU 52 OE2    -0.121    3.301
    10281     fold_poly310_uca3_model_0.cif #10/A ARG 123 CD   fold_poly310_uca3_model_0.cif #10/B TYR 106 C     -0.122    3.612
    10282     fold_poly310_uca3_model_0.cif #10/A HIS 1 NE2    fold_poly310_uca3_model_0.cif #10/B ARG 72 NH2    -0.126    3.406
    10283     fold_poly310_uca3_model_0.cif #10/A ARG 77 CD    fold_poly310_uca3_model_0.cif #10/B TYR 106 CB    -0.136    3.896
    10284     fold_poly310_uca3_model_0.cif #10/A GLU 40 OE2   fold_poly310_uca3_model_0.cif #10/B THR 30 CG2    -0.141    3.441
    10285     fold_poly310_uca3_model_0.cif #10/A ASP 64 OD2   fold_poly310_uca3_model_0.cif #10/B TYR 105 CE1   -0.143    3.323
    10286     fold_poly310_uca3_model_0.cif #10/A ARG 77 NH1   fold_poly310_uca3_model_0.cif #10/B TYR 106 CD2   -0.145    3.545
    10287     fold_poly310_uca3_model_0.cif #10/A LYS 94 CB    fold_poly310_uca3_model_0.cif #10/C TYR 93 CZ     -0.146    3.636
    10288     fold_poly310_uca3_model_0.cif #10/A LYS 94 CG    fold_poly310_uca3_model_0.cif #10/C TYR 93 CE2    -0.154    3.794
    10289     fold_poly310_uca3_model_0.cif #10/A LYS 94 NZ    fold_poly310_uca3_model_0.cif #10/B SER 109 CB    -0.164    3.684
    10290     fold_poly310_uca3_model_0.cif #10/A MET 73 CE    fold_poly310_uca3_model_0.cif #10/B TRP 101 CB    -0.167    3.927
    10291     fold_poly310_uca3_model_0.cif #10/A MET 73 SD    fold_poly310_uca3_model_0.cif #10/B TRP 101 CZ3   -0.172    3.702
    10292     fold_poly310_uca3_model_0.cif #10/A ASP 43 CG    fold_poly310_uca3_model_0.cif #10/B THR 28 OG1    -0.172    3.512
    10293     fold_poly310_uca3_model_0.cif #10/A ASP 64 CG    fold_poly310_uca3_model_0.cif #10/B TYR 105 OH    -0.181    3.521
    10294     fold_poly310_uca3_model_0.cif #10/A ASP 96 OD2   fold_poly310_uca3_model_0.cif #10/C SER 96 CA     -0.184    3.484
    10295     fold_poly310_uca3_model_0.cif #10/A MET 73 CG    fold_poly310_uca3_model_0.cif #10/B TRP 101 CE3   -0.188    3.828
    10296     fold_poly310_uca3_model_0.cif #10/A ASP 69 CB    fold_poly310_uca3_model_0.cif #10/B TYR 32 OH     -0.189    3.529
    10297     fold_poly310_uca3_model_0.cif #10/A ASP 69 CG    fold_poly310_uca3_model_0.cif #10/B VAL 2 CG2     -0.190    3.950
    10298     fold_poly310_uca3_model_0.cif #10/A LYS 70 CE    fold_poly310_uca3_model_0.cif #10/B TYR 116 OH    -0.194    3.534
    10299     fold_poly310_uca3_model_0.cif #10/A LYS 94 NZ    fold_poly310_uca3_model_0.cif #10/B SER 109 CA    -0.198    3.718
    10300     fold_poly310_uca3_model_0.cif #10/A HIS 188 CE1  fold_poly310_uca3_model_0.cif #10/B ASN 113 ND2   -0.198    3.598
    10301     fold_poly310_uca3_model_0.cif #10/A ASP 96 OD2   fold_poly310_uca3_model_0.cif #10/C SER 96 N      -0.207    2.867
    10302     fold_poly310_uca3_model_0.cif #10/A ASP 69 CG    fold_poly310_uca3_model_0.cif #10/B ARG 98 NH1    -0.208    3.728
    10303     fold_poly310_uca3_model_0.cif #10/A VAL 75 CG2   fold_poly310_uca3_model_0.cif #10/B TYR 106 OH    -0.210    3.550
    10304     fold_poly310_uca3_model_0.cif #10/A ARG 123 NH1  fold_poly310_uca3_model_0.cif #10/B ILE 102 CG2   -0.212    3.732
    10305     fold_poly310_uca3_model_0.cif #10/A ILE 93 CG2   fold_poly310_uca3_model_0.cif #10/B TYR 111 OH    -0.216    3.556
    10306     fold_poly310_uca3_model_0.cif #10/A ARG 123 O    fold_poly310_uca3_model_0.cif #10/B ASP 107 CG    -0.221    3.521
    10307     fold_poly310_uca3_model_0.cif #10/A LYS 94 CB    fold_poly310_uca3_model_0.cif #10/C TYR 93 OH     -0.227    3.567
    10308     fold_poly310_uca3_model_0.cif #10/A TRP 187 C    fold_poly310_uca3_model_0.cif #10/C LYS 55 NZ     -0.229    3.479
    10309     fold_poly310_uca3_model_0.cif #10/A TYR 102 CE2  fold_poly310_uca3_model_0.cif #10/B TYR 105 C     -0.234    3.604
    10310     fold_poly310_uca3_model_0.cif #10/A LEU 190 CD1  fold_poly310_uca3_model_0.cif #10/B TYR 106 CE1   -0.237    3.877
    10311     fold_poly310_uca3_model_0.cif #10/A LEU 99 CD1   fold_poly310_uca3_model_0.cif #10/B ASP 107 OD2   -0.238    3.538
    10312     fold_poly310_uca3_model_0.cif #10/A SER 95 N     fold_poly310_uca3_model_0.cif #10/C TYR 32 CE1    -0.239    3.639
    10313     fold_poly310_uca3_model_0.cif #10/A GLU 189 CG   fold_poly310_uca3_model_0.cif #10/C LYS 55 NZ     -0.242    3.762
    10314     fold_poly310_uca3_model_0.cif #10/A ASP 96 OD1   fold_poly310_uca3_model_0.cif #10/C GLY 95 CA     -0.242    3.542
    10315     fold_poly310_uca3_model_0.cif #10/A LEU 130 CD2  fold_poly310_uca3_model_0.cif #10/B LEU 104 O     -0.244    3.544
    10316     fold_poly310_uca3_model_0.cif #10/A VAL 75 CG2   fold_poly310_uca3_model_0.cif #10/B TRP 101 CZ3   -0.245    3.885
    10317     fold_poly310_uca3_model_0.cif #10/A LYS 94 NZ    fold_poly310_uca3_model_0.cif #10/B GLY 110 CA    -0.247    3.767
    10318     fold_poly310_uca3_model_0.cif #10/A PHE 119 CE2  fold_poly310_uca3_model_0.cif #10/B TYR 105 CD1   -0.250    3.770
    10319     fold_poly310_uca3_model_0.cif #10/A LYS 42 NZ    fold_poly310_uca3_model_0.cif #10/B THR 74 C      -0.254    3.504
    10320     fold_poly310_uca3_model_0.cif #10/A VAL 75 CG2   fold_poly310_uca3_model_0.cif #10/B TYR 106 CZ    -0.257    3.747
    10321     fold_poly310_uca3_model_0.cif #10/A HIS 1 CD2    fold_poly310_uca3_model_0.cif #10/B ARG 72 NH2    -0.261    3.661
    10322     fold_poly310_uca3_model_0.cif #10/A LYS 94 CG    fold_poly310_uca3_model_0.cif #10/C TYR 93 CZ     -0.264    3.754
    10323     fold_poly310_uca3_model_0.cif #10/A VAL 75 CG2   fold_poly310_uca3_model_0.cif #10/B TYR 106 CE2   -0.266    3.906
    10324     fold_poly310_uca3_model_0.cif #10/A HIS 188 ND1  fold_poly310_uca3_model_0.cif #10/C GLU 52 CD     -0.267    3.787
    10325     fold_poly310_uca3_model_0.cif #10/A ASP 43 CG    fold_poly310_uca3_model_0.cif #10/B THR 28 CG2    -0.271    4.031
    10326     fold_poly310_uca3_model_0.cif #10/A ASP 96 CG    fold_poly310_uca3_model_0.cif #10/C GLY 95 CA     -0.279    4.039
    10327     fold_poly310_uca3_model_0.cif #10/A ARG 77 NH1   fold_poly310_uca3_model_0.cif #10/B TYR 105 C     -0.281    3.531
    10328     fold_poly310_uca3_model_0.cif #10/A ASP 124 CG   fold_poly310_uca3_model_0.cif #10/B TRP 50 CH2    -0.282    3.922
    10329     fold_poly310_uca3_model_0.cif #10/A TRP 187 O    fold_poly310_uca3_model_0.cif #10/C LYS 55 CD     -0.284    3.584
    10330     fold_poly310_uca3_model_0.cif #10/A PRO 68 CB    fold_poly310_uca3_model_0.cif #10/B TRP 101 NE1   -0.286    3.806
    10331     fold_poly310_uca3_model_0.cif #10/A LYS 94 CD    fold_poly310_uca3_model_0.cif #10/C TYR 93 CE2    -0.293    3.933
    10332     fold_poly310_uca3_model_0.cif #10/A LYS 94 CE    fold_poly310_uca3_model_0.cif #10/B ASP 107 O     -0.297    3.597
    10333     fold_poly310_uca3_model_0.cif #10/A ILE 93 CG2   fold_poly310_uca3_model_0.cif #10/B TYR 111 CE1   -0.297    3.937
    10334     fold_poly310_uca3_model_0.cif #10/A ASP 96 CG    fold_poly310_uca3_model_0.cif #10/C SER 96 CA     -0.298    4.058
    10335     fold_poly310_uca3_model_0.cif #10/A LYS 94 CA    fold_poly310_uca3_model_0.cif #10/C TYR 32 CE1    -0.310    3.950
    10336     fold_poly310_uca3_model_0.cif #10/A PHE 119 CE2  fold_poly310_uca3_model_0.cif #10/B TYR 105 CG    -0.310    3.680
    10337     fold_poly310_uca3_model_0.cif #10/A LYS 94 CE    fold_poly310_uca3_model_0.cif #10/B GLY 110 CA    -0.322    4.082
    10338     fold_poly310_uca3_model_0.cif #10/A TRP 187 CB   fold_poly310_uca3_model_0.cif #10/C LYS 55 NZ     -0.333    3.853
    10339     fold_poly310_uca3_model_0.cif #10/A LYS 94 CE    fold_poly310_uca3_model_0.cif #10/B ASP 107 OD1   -0.334    3.634
    10340     fold_poly310_uca3_model_0.cif #10/A LYS 42 NZ    fold_poly310_uca3_model_0.cif #10/B SER 75 C      -0.350    3.600
    10341     fold_poly310_uca3_model_0.cif #10/A ASP 69 OD2   fold_poly310_uca3_model_0.cif #10/B ARG 98 CZ     -0.354    3.384
    10342     fold_poly310_uca3_model_0.cif #10/A GLU 186 CG   fold_poly310_uca3_model_0.cif #10/C TYR 51 CZ     -0.355    3.845
    10343     fold_poly310_uca3_model_0.cif #10/A LEU 190 CD2  fold_poly310_uca3_model_0.cif #10/B TYR 111 CE2   -0.365    4.005
    10344     fold_poly310_uca3_model_0.cif #10/A ASP 124 CG   fold_poly310_uca3_model_0.cif #10/B ASN 52 ND2    -0.366    3.886
    10345     fold_poly310_uca3_model_0.cif #10/A ASP 124 OD1  fold_poly310_uca3_model_0.cif #10/B TYR 33 CE1    -0.366    3.546
    10346     fold_poly310_uca3_model_0.cif #10/A HIS 188 CA   fold_poly310_uca3_model_0.cif #10/C GLU 52 OE2    -0.367    3.667
    10347     fold_poly310_uca3_model_0.cif #10/A GLU 40 OE1   fold_poly310_uca3_model_0.cif #10/B THR 30 OG1    -0.367    2.847
    10348     fold_poly310_uca3_model_0.cif #10/A LYS 42 CE    fold_poly310_uca3_model_0.cif #10/B THR 74 O      -0.369    3.669
    10349     fold_poly310_uca3_model_0.cif #10/A HIS 188 CA   fold_poly310_uca3_model_0.cif #10/C LYS 55 NZ     -0.371    3.891
    10350     fold_poly310_uca3_model_0.cif #10/A PHE 119 CZ   fold_poly310_uca3_model_0.cif #10/B TYR 105 CD2   -0.375    3.895
    10351     fold_poly310_uca3_model_0.cif #10/A ASP 69 OD1   fold_poly310_uca3_model_0.cif #10/B VAL 2 CG2     -0.375    3.675
    10352     fold_poly310_uca3_model_0.cif #10/A ASP 43 CG    fold_poly310_uca3_model_0.cif #10/B THR 28 CB     -0.379    4.139
    10353     fold_poly310_uca3_model_0.cif #10/A TYR 102 CE2  fold_poly310_uca3_model_0.cif #10/B TYR 105 O     -0.381    3.561
    10354     fold_poly310_uca3_model_0.cif #10/A ARG 77 NH1   fold_poly310_uca3_model_0.cif #10/B TYR 105 O     -0.381    3.041
    10355     fold_poly310_uca3_model_0.cif #10/A ASP 124 CB   fold_poly310_uca3_model_0.cif #10/B TRP 50 CH2    -0.382    4.022
    10356     fold_poly310_uca3_model_0.cif #10/A PHE 119 CZ   fold_poly310_uca3_model_0.cif #10/B TYR 105 CE2   -0.384    3.904
    10357     fold_poly310_uca3_model_0.cif #10/A ASP 124 OD2  fold_poly310_uca3_model_0.cif #10/B ASN 52 CB     -0.386    3.686
    10358     fold_poly310_uca3_model_0.cif #10/A VAL 75 CG1   fold_poly310_uca3_model_0.cif #10/B TYR 106 CE2   -0.393    4.033
    10359     fold_poly310_uca3_model_0.cif #10/A ARG 123 NH1  fold_poly310_uca3_model_0.cif #10/B GLY 103 N     -0.393    3.673
    10360     fold_poly310_uca3_model_0.cif #10/A PHE 119 CD2  fold_poly310_uca3_model_0.cif #10/B TYR 105 CG    -0.399    3.769
    10361    
    10362 
    10363  
    10364 149 contacts 
    10365 
    10366 > hide #10.2 models
    10367 
    10368 > hide #!10 models
    10369 
    10370 > select add #10
    10371 
    10372 3324 atoms, 3406 bonds, 176 pseudobonds, 428 residues, 3 models selected 
    10373 
    10374 > select subtract #10
    10375 
    10376 Nothing selected 
    10377 
    10378 > show #11 models
    10379 
    10380 > select #11/A:35
    10381 
    10382 7 atoms, 6 bonds, 1 residue, 1 model selected 
    10383 
    10384 > select up
    10385 
    10386 74 atoms, 76 bonds, 10 residues, 1 model selected 
    10387 
    10388 > select up
    10389 
    10390 1590 atoms, 1630 bonds, 197 residues, 1 model selected 
    10391 
    10392 > color bfactor sel
    10393 
    10394 1590 atoms, 197 residues, atom bfactor range 14.1 to 97.5 
    10395 
    10396 > hbonds sel color #ffd479 restrict cross interModel false distSlop 0.8
    10397 > intraMol false intraRes false select true reveal true log true
    10398    
    10399    
    10400     Finding intramodel H-bonds
    10401     Constraints relaxed by 0.8 angstroms and 20 degrees
    10402     Models used:
    10403         11 fold_poly28_uca3_model_0.cif
    10404    
    10405     8 H-bonds
    10406     H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    10407     fold_poly28_uca3_model_0.cif #11/A SER 7 OG    fold_poly28_uca3_model_0.cif #11/C ASN 33 OD1  no hydrogen  3.348  N/A
    10408     fold_poly28_uca3_model_0.cif #11/B THR 28 OG1  fold_poly28_uca3_model_0.cif #11/A SER 101 O   no hydrogen  3.603  N/A
    10409     fold_poly28_uca3_model_0.cif #11/B ASN 54 ND2  fold_poly28_uca3_model_0.cif #11/A TYR 80 O    no hydrogen  3.294  N/A
    10410     fold_poly28_uca3_model_0.cif #11/B LEU 104 N   fold_poly28_uca3_model_0.cif #11/A GLU 81 OE2  no hydrogen  3.487  N/A
    10411     fold_poly28_uca3_model_0.cif #11/C TYR 32 OH   fold_poly28_uca3_model_0.cif #11/A GLU 46 OE1  no hydrogen  2.872  N/A
    10412     fold_poly28_uca3_model_0.cif #11/C TYR 51 OH   fold_poly28_uca3_model_0.cif #11/A ASN 131 O   no hydrogen  2.250  N/A
    10413     fold_poly28_uca3_model_0.cif #11/C SER 54 OG   fold_poly28_uca3_model_0.cif #11/A ASP 8 OD1   no hydrogen  2.636  N/A
    10414     fold_poly28_uca3_model_0.cif #11/C SER 96 N    fold_poly28_uca3_model_0.cif #11/A GLU 46 OE2  no hydrogen  3.304  N/A
    10415    
    10416 
    10417  
    10418 8 hydrogen bonds found 
    10419 
    10420 > select #11/A:138
    10421 
    10422 7 atoms, 6 bonds, 1 residue, 1 model selected 
    10423 
    10424 > select up
    10425 
    10426 76 atoms, 77 bonds, 9 residues, 1 model selected 
     782[deleted to fit within ticket limits]
    10427783
    10428784> select up