Changes between Initial Version and Version 1 of Ticket #16303


Ignore:
Timestamp:
Nov 14, 2024, 10:41:32 AM (12 months ago)
Author:
Eric Pettersen
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #16303

    • Property Cc Tom Goddard added
    • Property Component Unassigned → Third Party
    • Property Owner set to Tristan Croll
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → assigned
    • Property Summary ChimeraX bug report submission → ISOLDE: 'MDFFMgr' object has no attribute 'was_deleted'

  • Ticket #16303 – Description

    initial v1  
    2848284831698 atoms, 32088 bonds, 2031 residues, 21 models selected 
    28492849
    2850 > ui mousemode right "move picked models"
    2851 
    2852 > ui mousemode right "translate selected models"
    2853 
    2854 > view matrix models
    2855 > #1,0.99163,-0.083691,-0.098314,22.128,0.09889,0.98189,0.16158,-23.116,0.08301,-0.16995,0.98195,10.873
    2856 
    2857 > ui mousemode right "move picked models"
    2858 
    2859 > isolde sim resume
    2860 
    2861 > select A
    2862 
    2863 Expected an objects specifier or a keyword 
    2864 
    2865 > select /A
    2866 
    2867 10566 atoms, 10696 bonds, 677 residues, 1 model selected 
    2868 
    2869 > view matrix models
    2870 > #1.2,1,3.4694e-17,9.7145e-17,-0.57951,2.0817e-17,1,-5.5511e-17,0.97731,0,-8.3267e-17,1,0.16641
    2871 
    2872 > view matrix models
    2873 > #1.2,1,6.0715e-17,1.1102e-16,-3.7199,1.3878e-17,1,-1.3878e-16,0.75132,1.3878e-17,-8.3267e-17,1,-1.2135
    2874 
    2875 > view matrix models
    2876 > #1.2,1,-5.6725e-16,-4.1633e-17,-4.514,-4.4929e-16,1,-4.1633e-16,6.3267,-5.4123e-16,2.498e-16,1,0.76486
    2877 
    2878 > select /A
    2879 
    2880 10566 atoms, 10696 bonds, 677 residues, 1 model selected 
    2881 
    2882 > ui mousemode right "isolde tug selection"
    2883 
    2884 > ~select
    2885 
    2886 Nothing selected 
    2887 
    2888 > ~select
    2889 
    2890 Nothing selected 
    2891 
    2892 > chains
    2893 
    2894 Unknown command: chains 
    2895 
    2896 > chains/
    2897 
    2898 Unknown command: chains/ 
    2899 
    2900 > /
    2901 
    2902 Unknown command: / 
    2903 
    2904 > select add #1.2
    2905 
    2906 31698 atoms, 32088 bonds, 2031 residues, 14 models selected 
    2907 
    2908 > select add #1.1.1
    2909 
    2910 31698 atoms, 32088 bonds, 2031 residues, 17 models selected 
    2911 
    2912 > select add #1
    2913 
    2914 31698 atoms, 32088 bonds, 2031 residues, 21 models selected 
    2915 
    2916 > select subtract #1.1.1
    2917 
    2918 31698 atoms, 32088 bonds, 2031 residues, 16 models selected 
    2919 
    2920 > select add #1.2
    2921 
    2922 31698 atoms, 32088 bonds, 2031 residues, 17 models selected 
    2923 
    2924 > select subtract #1.3
    2925 
    2926 31698 atoms, 32088 bonds, 2031 residues, 15 models selected 
    2927 
    2928 > select add #1.2
    2929 
    2930 31698 atoms, 32088 bonds, 2031 residues, 16 models selected 
    2931 
    2932 > ~select
    2933 
    2934 Nothing selected 
    2935 
    2936 > select add #1.1.1
    2937 
    2938 4 models selected 
    2939 
    2940 > ui mousemode right "translate selected models"
    2941 
    2942 > view matrix models
    2943 > #1.1.1,1,-5.0307e-17,2.6368e-16,0.51738,-1.1796e-16,1,-6.3838e-16,-5.7231,6.9389e-17,1.3878e-16,1,0.10217
    2944 
    2945 > ui mousemode right "rotate selected models"
    2946 
    2947 > view matrix models
    2948 > #1.1.1,0.98912,-0.14707,-0.0035996,18.306,0.1471,0.9884,0.037814,-25.16,-0.0020035,-0.037932,0.99928,4.5772
    2949 
    2950 > view matrix models
    2951 > #1.1.1,0.86583,-0.49895,-0.037256,74.567,0.49933,0.85694,0.1278,-60.241,-0.031839,-0.12925,0.9911,18.874
    2952 
    2953 > view matrix models
    2954 > #1.1.1,0.9799,-0.19939,-0.0062574,25.388,0.19945,0.97857,0.05124,-31.446,-0.0040934,-0.051458,0.99867,6.3666
    2955 
    2956 > view matrix models
    2957 > #1.1.1,0.99258,0.12162,-0.0012517,-11.88,-0.1216,0.99208,-0.031353,12.279,-0.0025713,0.031273,0.99951,-2.9923
    2958 
    2959 > view matrix models
    2960 > #1.1.1,0.9998,-0.020045,-0.0001605,2.7614,0.020046,0.99979,0.0051605,-8.5229,5.7023e-05,-0.0051627,0.99999,0.66479
    2961 
    2962 > view matrix models
    2963 > #1.1.1,0.99427,0.018958,-0.1052,8.6924,-0.019023,0.99982,0.00038549,-3.5055,0.10519,0.0016179,0.99445,-11.917
    2964 
    2965 > view matrix models
    2966 > #1.1.1,0.98647,-0.12373,-0.10757,25.525,0.12676,0.99169,0.021827,-21.678,0.10397,-0.035167,0.99396,-7.6817
    2967 
    2968 > ui mousemode right "translate selected models"
    2969 
    2970 > view matrix models
    2971 > #1.1.1,0.98647,-0.12373,-0.10757,30.35,0.12676,0.99169,0.021827,-13.388,0.10397,-0.035167,0.99396,-6.3941
    2972 
    2973 > ~select
    2974 
    2975 Nothing selected 
    2976 
    2977 > ui mousemode right rotate
    2978 
    2979 > ~select
    2980 
    2981 Nothing selected 
    2982 
    2983 > ui mousemode right "move picked models"
    2984 
    2985 > ui mousemode right "translate selected models"
    2986 
    2987 > select add #1.1.1
    2988 
    2989 4 models selected 
    2990 
    2991 > view matrix models
    2992 > #1.1.1,0.98647,-0.12373,-0.10757,33.311,0.12676,0.99169,0.021827,-17.645,0.10397,-0.035167,0.99396,-5.3485
    2993 
    2994 > select subtract #1.1.1
    2995 
    2996 Nothing selected 
    2997 
    2998 > ~select
    2999 
    3000 Nothing selected 
    3001 
    3002 > select /A
    3003 
    3004 10566 atoms, 10696 bonds, 677 residues, 1 model selected 
    3005 
    3006 > select /c
    3007 
    3008 10566 atoms, 10696 bonds, 677 residues, 1 model selected 
    3009 
    3010 > select /C
    3011 
    3012 10566 atoms, 10696 bonds, 677 residues, 1 model selected 
    3013 
    3014 > ui mousemode right "isolde tug selection"
    3015 
    3016 [Repeated 1 time(s)]
    3017 
    3018 > select /A
    3019 
    3020 10566 atoms, 10696 bonds, 677 residues, 1 model selected 
    3021 
    3022 > select /B
    3023 
    3024 10566 atoms, 10696 bonds, 677 residues, 1 model selected 
    3025 
    3026 > ~select
    3027 
    3028 Nothing selected 
    3029 
    3030 > select /B
    3031 
    3032 10566 atoms, 10696 bonds, 677 residues, 1 model selected 
    3033 
    3034 > ui mousemode right "isolde tug selection"
    3035 
    3036 [Repeated 1 time(s)]
    3037 
    3038 > ~select
    3039 
    3040 Nothing selected 
    3041 
    3042 > ui mousemode right "translate selected models"
    3043 
    3044 > hide atoms
    3045 
    3046 > show atoms
    3047 
    3048 > select add #1.2
    3049 
    3050 31698 atoms, 32088 bonds, 2031 residues, 14 models selected 
    3051 
    3052 > select add #1.2
    3053 
    3054 31698 atoms, 32088 bonds, 2031 residues, 14 models selected 
    3055 
    3056 > select add #1.2
    3057 
    3058 31698 atoms, 32088 bonds, 2031 residues, 14 models selected 
    3059 
    3060 > ~select
    3061 
    3062 Nothing selected 
    3063 
    3064 > select add #1.2
    3065 
    3066 31698 atoms, 32088 bonds, 2031 residues, 14 models selected 
    3067 
    3068 > select add #1.2
    3069 
    3070 31698 atoms, 32088 bonds, 2031 residues, 14 models selected 
    3071 
    3072 > ~select
    3073 
    3074 Nothing selected 
    3075 
    3076 > select add #1.1.1
    3077 
    3078 4 models selected 
    3079 
    3080 > ui mousemode right "rotate selected models"
    3081 
    3082 > view matrix models
    3083 > #1.1.1,0.95386,-0.26947,-0.13243,55.464,0.27868,0.95872,0.056438,-35.107,0.11175,-0.090739,0.98958,0.24681
    3084 
    3085 > view matrix models
    3086 > #1.1.1,0.86816,-0.46394,-0.17625,90.975,0.48447,0.86928,0.098215,-53.367,0.10765,-0.17066,0.97943,10.451
    3087 
    3088 > view matrix models
    3089 > #1.1.1,0.72836,-0.29898,-0.61652,129.46,0.4368,0.89585,0.081589,-49.148,0.52792,-0.32872,0.7831,-3.8769
    3090 
    3091 > ui mousemode right "move picked models"
    3092 
    3093 > ui mousemode right "rotate selected models"
    3094 
    3095 > view matrix models
    3096 > #1.1.1,0.85765,-0.27788,-0.43269,95.102,0.37939,0.90992,0.16766,-51.769,0.34712,-0.30795,0.88582,5.8133
    3097 
    3098 > view matrix models
    3099 > #1.1.1,0.648,-0.46752,-0.60126,156.1,0.73192,0.6006,0.32181,-73.411,0.21067,-0.64861,0.73138,73.494
    3100 
    3101 > view matrix models
    3102 > #1.1.1,0.73896,-0.48429,-0.4684,135.09,0.66602,0.63004,0.39933,-75.941,0.10172,-0.60706,0.78812,76.608
    3103 
    3104 > view matrix models
    3105 > #1.1.1,0.81976,-0.49328,-0.29098,110.35,0.57131,0.66885,0.47565,-75.991,-0.040005,-0.55616,0.83011,83.909
    3106 
    3107 > view matrix models
    3108 > #1.1.1,0.85593,-0.49206,-0.15894,93.907,0.49686,0.69745,0.51643,-74.068,-0.14326,-0.52099,0.84145,91.195
    3109 
    3110 > view matrix models
    3111 > #1.1.1,0.82413,-0.49343,-0.2781,108.68,0.56418,0.67165,0.48019,-75.872,-0.050157,-0.55263,0.83191,84.555
    3112 
    3113 > isolde sim pause
    3114 
    3115 > view matrix models
    3116 > #1.1.1,0.97678,-0.058664,-0.20603,36.223,0.14599,0.88615,0.43981,-46.365,0.15678,-0.45967,0.87414,46.017
    3117 
    3118 > ui mousemode right "move picked models"
    3119 
    3120 > view matrix models
    3121 > #1.2,1,-2.5847e-16,5.8287e-16,-6.4386,-2.949e-16,1,-1.9429e-16,6.691,-5.8287e-16,-3.3307e-16,1,-0.1065
    3122 
    3123 > isolde sim resume
    3124 
    3125 > ui mousemode right "translate selected models"
    3126 
    3127 > ui mousemode right rotate
    3128 
    3129 > ~select
    3130 
    3131 Nothing selected 
    3132 
    3133 > ~select
    3134 
    3135 Nothing selected 
    3136 
    3137 > ~select
    3138 
    3139 Nothing selected 
    3140 
    3141 > select /A
    3142 
    3143 10566 atoms, 10696 bonds, 677 residues, 1 model selected 
    3144 
    3145 > ui mousemode right "isolde tug selection"
    3146 
    3147 > select add #1
    3148 
    3149 31698 atoms, 32088 bonds, 2031 residues, 21 models selected 
    3150 
    3151 > select add #1
    3152 
    3153 31698 atoms, 32088 bonds, 2031 residues, 21 models selected 
    3154 
    3155 > select add #1
    3156 
    3157 31698 atoms, 32088 bonds, 2031 residues, 21 models selected 
    3158 
    3159 > ~select
    3160 
    3161 Nothing selected 
    3162 
    3163 > select /C
    3164 
    3165 10566 atoms, 10696 bonds, 677 residues, 1 model selected 
    3166 
    3167 > ~select
    3168 
    3169 Nothing selected 
    3170 
    3171 > rotate 30
    3172 
    3173 Unknown command: rotate 30 
    3174 
    3175 > rotate x 30
    3176 
    3177 Unknown command: rotate x 30 
    3178 
    3179 > turn 30
    3180 
    3181 Expected an axis vector or a keyword 
    3182 
    3183 > help help:user
    3184 
    3185 > turn y 30
    3186 
    3187 [Repeated 1 time(s)]
    3188 
    3189 > select /B
    3190 
    3191 10566 atoms, 10696 bonds, 677 residues, 1 model selected 
    3192 
    3193 > isolde sim pause
    3194 
    3195 > select
    3196 
    3197 31698 atoms, 32088 bonds, 2031 residues, 21 models selected 
    3198 
    3199 > ~select
    3200 
    3201 Nothing selected 
    3202 
    3203 > select add #1.1.1
    3204 
    3205 4 models selected 
    3206 
    3207 > ui mousemode right "translate selected models"
    3208 
    3209 > view matrix models
    3210 > #1.1.1,0.97678,-0.058664,-0.20603,36.443,0.14599,0.88615,0.43981,-47.931,0.15678,-0.45967,0.87414,43.486
    3211 
    3212 > ui mousemode right "rotate selected models"
    3213 
    3214 > view matrix models
    3215 > #1.1.1,0.93878,-0.072118,-0.33688,54.349,0.21104,0.89328,0.39687,-52.488,0.27231,-0.44367,0.85382,29.924
    3216 
    3217 > select add #1.1.1
    3218 
    3219 4 models selected 
    3220 
    3221 > select subtract #1.1.1
    3222 
    3223 Nothing selected 
    3224 
    3225 > ~select
    3226 
    3227 Nothing selected 
    3228 
    3229 > select add #1.2
    3230 
    3231 31698 atoms, 32088 bonds, 2031 residues, 14 models selected 
    3232 
    3233 > view matrix models
    3234 > #1.2,0.98911,-0.053048,-0.13729,11.919,0.074733,0.98461,0.15797,-14.293,0.1268,-0.16651,0.97785,3.142
    3235 
    3236 > view matrix models
    3237 > #1.2,0.98948,0.016677,-0.14373,5.221,0.0055592,0.98822,0.15294,-5.6294,0.14458,-0.15213,0.97773,-0.5454
    3238 
    3239 > view matrix models
    3240 > #1.2,0.98685,0.0096553,-0.16132,7.7496,0.012471,0.99069,0.13558,-5.287,0.16113,-0.13581,0.97754,-4.2736
    3241 
    3242 > view matrix models
    3243 > #1.2,0.98778,0.006444,-0.15574,7.4975,0.02641,0.97778,0.20796,-11.769,0.15362,-0.20953,0.96566,5.2641
    3244 
    3245 > view matrix models
    3246 > #1.2,0.8593,-0.4953,-0.12761,72.895,0.51115,0.8227,0.24878,-59.558,-0.018234,-0.27901,0.96012,34.297
    3247 
    3248 > view matrix models
    3249 > #1.2,0.98861,0.0059789,-0.15036,6.9894,0.020811,0.98418,0.17597,-9.0452,0.14903,-0.17709,0.97284,1.8859
    3250 
    3251 > ui mousemode right "move picked models"
    3252 
    3253 > ui mousemode right "translate selected models"
    3254 
    3255 > view matrix models
    3256 > #1.2,0.98861,0.0059789,-0.15036,15.778,0.020811,0.98418,0.17597,-19.022,0.14903,-0.17709,0.97284,-8.0522
    3257 
    3258 > view matrix models
    3259 > #1.2,0.98861,0.0059789,-0.15036,12.948,0.020811,0.98418,0.17597,-19.55,0.14903,-0.17709,0.97284,-4.7808
    3260 
    3261 > view matrix models
    3262 > #1.2,0.98861,0.0059789,-0.15036,8.191,0.020811,0.98418,0.17597,-20.422,0.14903,-0.17709,0.97284,-0.82751
    3263 
    3264 > isolde sim resume
    3265 
    3266 > select /A
    3267 
    3268 10566 atoms, 10696 bonds, 677 residues, 1 model selected 
    3269 
    3270 > ui mousemode right "isolde tug selection"
    3271 
    3272 [Repeated 1 time(s)]
    3273 
    3274 > ~select
    3275 
    3276 Nothing selected 
    3277 
    3278 > volume #1.1.1.1 level 0.1688
    3279 
    3280 > volume #1.1.1.1 level 0.1198
    3281 
    3282 > ui mousemode right "isolde tug selection"
    3283 
    3284 > isolde sim stop
    3285 
    3286 Sim termination reason: None 
    3287 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3288 chains... 
    3289 ISOLDE: Corrected atom nomenclature of 61 residues in model #1.2 to IUPAC-IUB
    3290 standards. 
    3291 ISOLDE: stopped sim 
    3292 
    3293 > isolde start
    3294 
    3295 > save "C:/Users/daniellem/Desktop/CryoEM workshop/Dissertation final 316W
    3296 > model/316W_diss_2.cxs"
    3297 
    3298 ——— End of log from Wed Nov 13 21:10:41 2024 ———
    3299 
    3300 opened ChimeraX session 
    3301 
    3302 > clipper isolate #1 maskRadius 16
    3303 
    3304 > isolde start
    3305 
    3306 > isolde sim start /A-C
    3307 
    3308 ISOLDE: started sim 
    3309 
    3310 > ui mousemode right "isolde tug atom"
    3311 
    3312 > ~select
    3313 
    3314 Nothing selected 
    3315 
    3316 > select /B
    3317 
    3318 10566 atoms, 10696 bonds, 677 residues, 1 model selected 
    3319 
    3320 > ui mousemode right "isolde tug selection"
    3321 
    3322 > select
    3323 
    3324 31698 atoms, 32088 bonds, 2031 residues, 24 models selected 
    3325 
    3326 > ~select
    3327 
    3328 Nothing selected 
    3329 
    3330 > select /A
    3331 
    3332 10566 atoms, 10696 bonds, 677 residues, 1 model selected 
    3333 
    3334 > ui mousemode right "isolde tug selection"
    3335 
    3336 [Repeated 1 time(s)]
    3337 
    3338 > isolde restrain distances "#1/C"
    3339 
    3340 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3341 chains... 
    3342 ISOLDE: Corrected atom nomenclature of 8 residues in model #1.2 to IUPAC-IUB
    3343 standards. 
    3344 
    3345 > ~select
    3346 
    3347 Nothing selected 
    3348 
    3349 > ui mousemode right "isolde tug residue"
    3350 
    3351 > help help:user
    3352 
    3353 > select add #1.2
    3354 
    3355 31698 atoms, 32088 bonds, 2031 residues, 17 models selected 
    3356 
    3357 > show ribbons
    3358 
    3359 > ~select
    3360 
    3361 Nothing selected 
    3362 
    3363 > ui mousemode right swapaa
    3364 
    3365 > swapaa mousemode /C:59 VAL
    3366 
    3367 Sim termination reason: coord length mismatch 
    3368 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3369 chains... 
    3370 ISOLDE: Corrected atom nomenclature of 17 residues in model #1.2 to IUPAC-IUB
    3371 standards. 
    3372 ISOLDE: stopped sim 
    3373 
    3374 > save "C:/Users/daniellem/Desktop/CryoEM workshop/Dissertation final 316W
    3375 > model/316W_diss_3.cxs"
    3376 
    3377 [Repeated 1 time(s)]
    3378 
    3379 ——— End of log from Wed Nov 13 21:59:07 2024 ———
    3380 
    3381 opened ChimeraX session 
    3382 
    3383 > open "D:\Dissertation final 316W model\316W_diss_3.cxs" format session
    3384 
    3385 Opened DeepEMhancer_Danielle_4_9.mrc as #1.1.1.1, grid size 128,128,128, pixel
    3386 1.66, shown at level 0.12, step 1, values float32 
    3387 Unable to restore session, resetting. 
    3388  
    3389 Traceback (most recent call last): 
    3390 File "C:\Program Files\ChimeraX 1.9rc202411130312\bin\Lib\site-
    3391 packages\chimerax\core\session.py", line 854, in restore 
    3392 self.add_state_manager(name, data) 
    3393 File "C:\Program Files\ChimeraX 1.9rc202411130312\bin\Lib\site-
    3394 packages\chimerax\core\session.py", line 647, in add_state_manager 
    3395 raise ValueError( 
    3396 ValueError: container "Isolde Residue Stepper Manager" of type "<class
    3397 'NoneType'>" does not have snapshot methods and does not have clear method 
    3398  
    3399 Log from Wed Nov 13 21:59:07 2024UCSF ChimeraX version: 1.8 (2024-06-10) 
    3400 © 2016-2024 Regents of the University of California. All rights reserved. 
    3401 
    3402 > open "C:\Users\daniellem\Desktop\CryoEM workshop\Dissertation final 316W
    3403 > model\316W_diss_2.cxs" format session
    3404 
    3405 Opened DeepEMhancer_Danielle_4_9.mrc as #1.1.1.1, grid size 128,128,128, pixel
    3406 1.66, shown at level 0.12, step 1, values float32 
    3407 Log from Wed Nov 13 21:10:41 2024UCSF ChimeraX version: 1.8 (2024-06-10) 
    3408 © 2016-2024 Regents of the University of California. All rights reserved. 
    3409 
    3410 > open "C:\Users\daniellem\Desktop\CryoEM workshop\Dissertation final 316W
    3411 > model\Isolde_316W.cxs" format session
    3412 
    3413 Opened DeepEMhancer_Danielle_4_9.mrc as #1, grid size 128,128,128, pixel 1.66,
    3414 shown at level 0.171, step 1, values float32 
    3415 Log from Wed Nov 13 16:05:25 2024 Startup Messages 
    3416 --- 
    3417 note | available bundle cache has not been initialized yet 
    3418  
    3419 UCSF ChimeraX version: 1.8 (2024-06-10) 
    3420 © 2016-2024 Regents of the University of California. All rights reserved. 
    3421 How to cite UCSF ChimeraX 
    3422 
    3423 > open
    3424 > C:\\\Users\\\daniellem\\\Downloads\\\ChimeraX_ISOLDE-1.8-cp311-cp311-win_amd64.whl
    3425 
    3426 Unrecognized file suffix '.whl' 
    3427 
    3428 > open "C:/Users/daniellem/Desktop/CryoEM
    3429 > workshop/DeepEMhancer_Danielle_4_9.mrc"
    3430 
    3431 Opened DeepEMhancer_Danielle_4_9.mrc as #1, grid size 128,128,128, pixel 1.66,
    3432 shown at level 0.171, step 1, values float32 
    3433 
    3434 > open
    3435 > C:/Users/daniellem/Downloads/fold_202411_11_fresh/fold_202411_11_fresh_model_0.cif
    3436 
    3437 Chain information for fold_202411_11_fresh_model_0.cif #2 
    3438 --- 
    3439 Chain | Description 
    3440 A B C | . 
    3441  
    3442 
    3443 > fitmap #2 inMap #1
    3444 
    3445 Fit molecule fold_202411_11_fresh_model_0.cif (#2) to map
    3446 DeepEMhancer_Danielle_4_9.mrc (#1) using 16827 atoms 
    3447 average map value = 0.07522, steps = 844 
    3448 shifted from previous position = 175 
    3449 rotated from previous position = 54.2 degrees 
    3450 atoms outside contour = 14504, contour level = 0.17065 
    3451  
    3452 Position of fold_202411_11_fresh_model_0.cif (#2) relative to
    3453 DeepEMhancer_Danielle_4_9.mrc (#1) coordinates: 
    3454 Matrix rotation and translation 
    3455 0.64792760 -0.62354966 -0.43746502 96.82197592 
    3456 0.74386964 0.64153909 0.18731140 110.82058535 
    3457 0.16385295 -0.44678117 0.87951055 97.73764625 
    3458 Axis -0.39073889 -0.37054262 0.84262761 
    3459 Axis point -58.82632784 190.65888686 0.00000000 
    3460 Rotation angle (degrees) 54.23312860 
    3461 Shift along axis 3.46057824 
    3462  
    3463 
    3464 > select add #2
    3465 
    3466 16827 atoms, 17253 bonds, 2103 residues, 1 model selected 
    3467 
    3468 > ui mousemode right "translate selected models"
    3469 
    3470 > ui mousemode right "rotate selected models"
    3471 
    3472 > view matrix models
    3473 > #2,0.90908,-0.24195,0.33917,98.645,-0.23659,0.3703,0.89828,112.27,-0.34293,-0.89685,0.27939,96.701
    3474 
    3475 > view matrix models
    3476 > #2,0.53124,-0.06761,0.84452,97.684,-0.82947,0.1615,0.5347,110.22,-0.17254,-0.98455,0.029713,96.843
    3477 
    3478 > view matrix models
    3479 > #2,0.41491,-0.042433,0.90887,97.121,-0.90723,-0.095219,0.40971,113.02,0.069157,-0.99455,-0.078003,97.834
    3480 
    3481 > view matrix models
    3482 > #2,0.75288,0.027834,0.65757,97.316,-0.63298,-0.24308,0.73502,119.44,0.1803,-0.96961,-0.16539,97.49
    3483 
    3484 > ui mousemode right "move picked models"
    3485 
    3486 > ui mousemode right "rotate selected models"
    3487 
    3488 > view matrix models
    3489 > #2,0.87103,0.31614,0.37598,92.913,-0.28071,-0.30778,0.90911,123.97,0.40312,-0.8974,-0.17934,97.549
    3490 
    3491 > view matrix models
    3492 > #2,0.91536,0.086966,0.39313,97.148,-0.39835,0.053566,0.91567,117.07,0.058573,-0.99477,0.083675,97.517
    3493 
    3494 > view matrix models
    3495 > #2,0.69172,-0.58695,0.42073,107.25,-0.39031,0.18632,0.90163,114.71,-0.60761,-0.78789,-0.10021,89.196
    3496 
    3497 > view matrix models
    3498 > #2,0.65444,-0.63502,0.41045,107.75,-0.39395,0.17697,0.90193,114.84,-0.64538,-0.75195,-0.13435,88.167
    3499 
    3500 > view matrix models
    3501 > #2,0.74125,-0.50299,0.44446,106.36,-0.46474,0.093202,0.88053,115.65,-0.48433,-0.85925,-0.16467,90.397
    3502 
    3503 > ui mousemode right "translate selected models"
    3504 
    3505 > view matrix models
    3506 > #2,0.74125,-0.50299,0.44446,122.67,-0.46474,0.093202,0.88053,118.02,-0.48433,-0.85925,-0.16467,90.501
    3507 
    3508 > ui mousemode right "rotate selected models"
    3509 
    3510 > view matrix models
    3511 > #2,0.83206,-0.25682,0.49165,119.4,-0.49196,0.067772,0.86798,118.23,-0.25624,-0.96408,-0.069956,93.922
    3512 
    3513 > ui mousemode right "translate selected models"
    3514 
    3515 > view matrix models
    3516 > #2,0.83206,-0.25682,0.49165,110.78,-0.49196,0.067772,0.86798,107.87,-0.25624,-0.96408,-0.069956,93.209
    3517 
    3518 > select subtract #2
    3519 
    3520 Nothing selected 
    3521 
    3522 > isolde start
    3523 
    3524 > set selectionWidth 4
    3525 
    3526 Forcefield cache not found or out of date. Regenerating from ffXML files. This
    3527 is normal if running ISOLDE for the first time, or after upgrading OpenMM. 
    3528 
    3529 Done loading forcefield 
    3530 
    3531 > isolde set simFidelityMode Medium/Medium
    3532 
    3533 ISOLDE: setting sim fidelity mode to Medium/Medium 
    3534 nonbonded_cutoff_distance = 0.900000 
    3535 use_gbsa = True 
    3536 gbsa_cutoff = 1.100000 
    3537 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3538 chains... 
    3539 ISOLDE: Corrected atom nomenclature of 277 residues in model #2 to IUPAC-IUB
    3540 standards. 
    3541 Chain information for fold_202411_11_fresh_model_0.cif 
    3542 --- 
    3543 Chain | Description 
    3544 2.2/A 2.2/B 2.2/C | . 
    3545  
    3546 Cached rota8000-val data not found. Regenerating from text file. This is
    3547 normal if running ISOLDE for the first time 
    3548 Cached rota8000-leu data not found. Regenerating from text file. This is
    3549 normal if running ISOLDE for the first time 
    3550 Cached rota8000-ile data not found. Regenerating from text file. This is
    3551 normal if running ISOLDE for the first time 
    3552 Cached rota8000-pro data not found. Regenerating from text file. This is
    3553 normal if running ISOLDE for the first time 
    3554 Cached rota8000-phe data not found. Regenerating from text file. This is
    3555 normal if running ISOLDE for the first time 
    3556 Cached rota8000-tyr data not found. Regenerating from text file. This is
    3557 normal if running ISOLDE for the first time 
    3558 Cached rota8000-trp data not found. Regenerating from text file. This is
    3559 normal if running ISOLDE for the first time 
    3560 Cached rota8000-ser data not found. Regenerating from text file. This is
    3561 normal if running ISOLDE for the first time 
    3562 Cached rota8000-thr data not found. Regenerating from text file. This is
    3563 normal if running ISOLDE for the first time 
    3564 Cached rota8000-cys data not found. Regenerating from text file. This is
    3565 normal if running ISOLDE for the first time 
    3566 Cached rota8000-met data not found. Regenerating from text file. This is
    3567 normal if running ISOLDE for the first time 
    3568 Cached rota8000-lys data not found. Regenerating from text file. This is
    3569 normal if running ISOLDE for the first time 
    3570 Cached rota8000-his data not found. Regenerating from text file. This is
    3571 normal if running ISOLDE for the first time 
    3572 Cached rota8000-arg data not found. Regenerating from text file. This is
    3573 normal if running ISOLDE for the first time 
    3574 Cached rota8000-asp data not found. Regenerating from text file. This is
    3575 normal if running ISOLDE for the first time 
    3576 Cached rota8000-asn data not found. Regenerating from text file. This is
    3577 normal if running ISOLDE for the first time 
    3578 Cached rota8000-gln data not found. Regenerating from text file. This is
    3579 normal if running ISOLDE for the first time 
    3580 Cached rota8000-glu data not found. Regenerating from text file. This is
    3581 normal if running ISOLDE for the first time 
    3582 Cached rama8000-cispro data not found. Regenerating from text file. This is
    3583 normal if running ISOLDE for the first time 
    3584 Cached rama8000-transpro data not found. Regenerating from text file. This is
    3585 normal if running ISOLDE for the first time 
    3586 Cached rama8000-gly-sym data not found. Regenerating from text file. This is
    3587 normal if running ISOLDE for the first time 
    3588 Cached rama8000-prepro-noGP data not found. Regenerating from text file. This
    3589 is normal if running ISOLDE for the first time 
    3590 Cached rama8000-ileval-nopreP data not found. Regenerating from text file.
    3591 This is normal if running ISOLDE for the first time 
    3592 Cached rama8000-general-noGPIVpreP data not found. Regenerating from text
    3593 file. This is normal if running ISOLDE for the first time 
    3594 ISOLDE: created disulfide bonds between the following residues: 
    3595 B125-B137; A125-A137; B484-B590; A120-A176; B355-B428; C484-C590; C181-C416;
    3596 A208-A219; A276-A309; B198-B227; B120-B176; A113-A185; B181-B416; B208-B219;
    3597 A181-A416; C120-C176; C125-C137; C198-C227; A484-A590; A362-A401; B583-B589;
    3598 A583-A589; C362-C401; A48-A68; B113-B185; B276-B309; C113-C185; C208-C219;
    3599 B362-B401; B48-B68; C48-C68; C276-C309; A198-A227; A355-A428; C355-C428;
    3600 C583-C589 
    3601 
    3602 > save "C:/Users/daniellem/Desktop/CryoEM workshop/Dissertation final 316W
    3603 > model/Isolde_316W.cxs"
    3604 
    3605 > select add #2
    3606 
    3607 16827 atoms, 17289 bonds, 2103 residues, 14 models selected 
    3608 
    3609 > select subtract #1
    3610 
    3611 16827 atoms, 17289 bonds, 2103 residues, 12 models selected 
    3612 
    3613 > select add #2
    3614 
    3615 16827 atoms, 17289 bonds, 2103 residues, 12 models selected 
    3616 
    3617 > select add #2
    3618 
    3619 16827 atoms, 17289 bonds, 2103 residues, 12 models selected 
    3620 
    3621 > select add #2
    3622 
    3623 16827 atoms, 17289 bonds, 2103 residues, 12 models selected 
    3624 
    3625 > select subtract #2.1
    3626 
    3627 16827 atoms, 17289 bonds, 2103 residues, 11 models selected 
    3628 
    3629 > select add #2
    3630 
    3631 16827 atoms, 17289 bonds, 2103 residues, 12 models selected 
    3632 
    3633 > save "C:/Users/daniellem/Desktop/CryoEM workshop/Dissertation final 316W
    3634 > model/Isolde_316W.cxs"
    3635 
    3636 ——— End of log from Wed Nov 13 16:05:25 2024 ———
    3637 
    3638 opened ChimeraX session 
    3639 
    3640 > ui mousemode right "rotate selected models"
    3641 
    3642 > ui mousemode right rotate
    3643 
    3644 > select add #2
    3645 
    3646 16827 atoms, 17289 bonds, 2103 residues, 15 models selected 
    3647 
    3648 > select add #2
    3649 
    3650 16827 atoms, 17289 bonds, 2103 residues, 15 models selected 
    3651 
    3652 > select subtract #2.1
    3653 
    3654 16827 atoms, 17289 bonds, 2103 residues, 14 models selected 
    3655 
    3656 > select #2
    3657 
    3658 16827 atoms, 17289 bonds, 2103 residues, 15 models selected 
    3659 
    3660 > select subtract #2.1
    3661 
    3662 16827 atoms, 17289 bonds, 2103 residues, 14 models selected 
    3663 
    3664 > select subtract #2.3
    3665 
    3666 16827 atoms, 17289 bonds, 2103 residues, 13 models selected 
    3667 
    3668 > ui mousemode right "move picked models"
    3669 
    3670 > ui mousemode right "rotate selected models"
    3671 
    3672 > stop isolde
    3673 
    3674 Expected fewer arguments 
    3675 
    3676 > select add #2
    3677 
    3678 16827 atoms, 17289 bonds, 2103 residues, 15 models selected 
    3679 
    3680 > deselect all
    3681 
    3682 Unknown command: deselect all 
    3683 
    3684 > deselect
    3685 
    3686 Unknown command: deselect 
    3687 
    3688 > ~select
    3689 
    3690 Nothing selected 
    3691 
    3692 > select add #2
    3693 
    3694 16827 atoms, 17289 bonds, 2103 residues, 15 models selected 
    3695 
    3696 > view matrix models
    3697 > #2,0.99575,-0.015637,0.090722,-4.4839,0.0014031,0.98793,0.15488,-10.121,-0.092049,-0.1541,0.98376,27.255
    3698 
    3699 > view matrix models
    3700 > #2,0.78145,0.090022,-0.61745,60.114,0.035975,0.98139,0.18861,-15.794,0.62294,-0.1696,0.76367,-35.953
    3701 
    3702 > view matrix models
    3703 > #2,0.71305,0.10657,-0.69297,71.605,-0.27531,0.95155,-0.13695,45.9,0.6448,0.28843,0.70784,-81.031
    3704 
    3705 > view matrix models
    3706 > #2,0.89446,0.22625,-0.38569,16.741,-0.28596,0.95254,-0.10439,44.648,0.34377,0.20366,0.9167,-53.518
    3707 
    3708 > view matrix models
    3709 > #2,0.94709,0.31726,0.048693,-29.856,-0.31545,0.94804,-0.041416,43.885,-0.059302,0.023864,0.99795,4.4102
    3710 
    3711 > ui mousemode right "move picked models"
    3712 
    3713 > view matrix models
    3714 > #2.2,1,5.6986e-16,-2.4286e-16,-9.5814,8.4893e-16,1,1.9082e-16,0.6637,-9.7145e-17,3.1225e-17,1,-0.41905
    3715 
    3716 > select add #2
    3717 
    3718 16827 atoms, 17289 bonds, 2103 residues, 15 models selected 
    3719 
    3720 > ~select
    3721 
    3722 Nothing selected 
    3723 
    3724 > select add #1
    3725 
    3726 2 models selected 
    3727 
    3728 > ui mousemode right "rotate selected models"
    3729 
    3730 > view matrix models
    3731 > #1,0.99565,0.0035698,-0.093147,8.6107,0.0040819,0.99664,0.081827,-7.5691,0.093126,-0.081851,0.99228,-0.9953
    3732 
    3733 > view matrix models
    3734 > #1,0.99643,0.0065949,-0.084219,7.3734,0.0032596,0.9932,0.11634,-10.247,0.084414,-0.1162,0.98963,4.0265
    3735 
    3736 > ui mousemode right rotate
    3737 
    3738 > ui mousemode right "rotate selected models"
    3739 
    3740 > view matrix models
    3741 > #1,0.98436,-0.16331,-0.066065,25.793,0.1716,0.97369,0.14993,-30.516,0.039841,-0.15892,0.98649,14.137
    3742 
    3743 > select subtract #1
    3744 
    3745 Nothing selected 
    3746 
    3747 > ~select
    3748 
    3749 Nothing selected 
    3750 
    3751 > select add #2
    3752 
    3753 16827 atoms, 17289 bonds, 2103 residues, 15 models selected 
    3754 
    3755 > ui mousemode right select
    3756 
    3757 > ~select
    3758 
    3759 Nothing selected 
    3760 
    3761 > ~select
    3762 
    3763 Nothing selected 
    3764 
    3765 > clipper associate #1 toModel #2
    3766 
    3767 Opened DeepEMhancer_Danielle_4_9.mrc as #2.1.1.1, grid size 128,128,128, pixel
    3768 1.66, shown at step 1, values float32 
    3769 
    3770 > clipper associate #1 toModel #2
    3771 
    3772 > volume #2.1.1.1 level 0.01818
    3773 
    3774 > volume #2.1.1.1 level 0.006197
    3775 
    3776 > volume #2.1.1.1 level 0.01884
    3777 
    3778 > volume #2.1.1.1 level 0.01019
    3779 
    3780 > volume #2.1.1.1 level 0.0042
    3781 
    3782 > fitmap #2.2 inMap #2.1.1.1
    3783 
    3784 Fit molecule fold_202411_11_fresh_model_0.cif (#2.2) to map
    3785 DeepEMhancer_Danielle_4_9.mrc (#2.1.1.1) using 16827 atoms 
    3786 average map value = 0, steps = 24 
    3787 shifted from previous position = 0 
    3788 rotated from previous position = 0 degrees 
    3789 atoms outside contour = 16827, contour level = 0.0042003 
    3790  
    3791 Position of fold_202411_11_fresh_model_0.cif (#2.2) relative to
    3792 DeepEMhancer_Danielle_4_9.mrc (#2.1.1.1) coordinates: 
    3793 Matrix rotation and translation 
    3794 1.00000000 0.00000000 0.00000000 0.00000000 
    3795 0.00000000 1.00000000 0.00000000 0.00000000 
    3796 0.00000000 0.00000000 1.00000000 0.00000000 
    3797 Axis 0.00000000 0.00000000 1.00000000 
    3798 Axis point 0.00000000 0.00000000 0.00000000 
    3799 Rotation angle (degrees) 0.00000000 
    3800 Shift along axis 0.00000000 
    3801  
    3802 
    3803 > volume #2.1.1.1 color #ff6f82
    3804 
    3805 > volume #2.1.1.1 orthoplanes xyz positionPlanes 64,64,64 style image region
    3806 > all
    3807 
    3808 > mousemode rightMode "move planes"
    3809 
    3810 > volume #2.1.1.1 orthoplanes xyz positionPlanes 64,64,64 style image region
    3811 > all
    3812 
    3813 > mousemode rightMode "move planes"
    3814 
    3815 > volume #2.1.1.1 orthoplanes xyz positionPlanes 64,64,64 style image region
    3816 > all
    3817 
    3818 > mousemode rightMode "move planes"
    3819 
    3820 > volume #2.1.1.1 orthoplanes xyz positionPlanes 64,64,64 style image region
    3821 > all
    3822 
    3823 > mousemode rightMode "move planes"
    3824 
    3825 > volume planes z style image imageMode "full region"
    3826 
    3827 > mousemode rightMode "move planes"
    3828 
    3829 > volume style mesh
    3830 
    3831 [Repeated 1 time(s)]
    3832 
    3833 > volume #2.1.1.1 style image region all imageMode "tilted slab"
    3834 > tiltedSlabAxis 0,0,1 tiltedSlabOffset 106.1 tiltedSlabSpacing 1.658
    3835 > tiltedSlabPlaneCount 10
    3836 
    3837 > mousemode rightMode "rotate slab"
    3838 
    3839 > volume planes z style image imageMode "full region"
    3840 
    3841 > mousemode rightMode "move planes"
    3842 
    3843 > volume #2.1.1.1 style image region all imageMode "tilted slab"
    3844 > tiltedSlabAxis 0,0,1 tiltedSlabOffset 106.1 tiltedSlabSpacing 1.658
    3845 > tiltedSlabPlaneCount 10
    3846 
    3847 > mousemode rightMode "rotate slab"
    3848 
    3849 > volume style mesh
    3850 
    3851 > volume #2.1.1.1 change image level -0.0001408,0 level 0.1705,0.8 level
    3852 > 2.096,1
    3853 
    3854 > volume #2.1.1.1 level 0.3019
    3855 
    3856 > volume #2.1.1.1 orthoplanes xyz positionPlanes 64,64,64 style image region
    3857 > all
    3858 
    3859 > mousemode rightMode "move planes"
    3860 
    3861 > volume #2.1.1.1 orthoplanes xyz positionPlanes 64,64,64 style image region
    3862 > all
    3863 
    3864 > mousemode rightMode "move planes"
    3865 
    3866 > volume zone #2.1.1.1 nearAtoms #2.2 range 9.95
    3867 
    3868 > volume region all imageMode "full region"
    3869 
    3870 > volume unzone
    3871 
    3872 > mousemode rightMode "crop volume"
    3873 
    3874 > close #2.1.1.1
    3875 
    3876 > select #1
    3877 
    3878 Nothing selected 
    3879 
    3880 > clipper associate #1 toModel #2
    3881 
    3882 > close session
    3883 
    3884 > open
    3885 > C:/Users/daniellem/Downloads/fold_202411_11_fresh/fold_202411_11_fresh_model_1.cif
    3886 
    3887 Chain information for fold_202411_11_fresh_model_1.cif #1 
    3888 --- 
    3889 Chain | Description 
    3890 A B C | . 
    3891  
    3892 
    3893 > open "C:/Users/daniellem/Desktop/CryoEM
    3894 > workshop/DeepEMhancer_Danielle_4_9.mrc"
    3895 
    3896 Opened DeepEMhancer_Danielle_4_9.mrc as #2, grid size 128,128,128, pixel 1.66,
    3897 shown at level 0.171, step 1, values float32 
    3898 
    3899 > clipper associate #2 toModel #1
    3900 
    3901 Opened DeepEMhancer_Danielle_4_9.mrc as #1.1.1.1, grid size 128,128,128, pixel
    3902 1.66, shown at level 0, step 1, values float32 
    3903 Chain information for fold_202411_11_fresh_model_1.cif 
    3904 --- 
    3905 Chain | Description 
    3906 1.2/A 1.2/B 1.2/C | . 
    3907  
    3908 
    3909 > zoom
    3910 
    3911 Pixel size at center of rotation is 0.252 
    3912 
    3913 > zoom
    3914 
    3915 Pixel size at center of rotation is 0.252 
    3916 
    3917 > volume #1.1.1.1 level 2.378e-07
    3918 
    3919 > isolde start
    3920 
    3921 > set selectionWidth 4
    3922 
    3923 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3924 chains... 
    3925 ISOLDE: Corrected atom nomenclature of 286 residues in model #1.2 to IUPAC-IUB
    3926 standards. 
    3927 Done loading forcefield 
    3928 
    3929 > isolde set simFidelityMode Medium/Medium
    3930 
    3931 ISOLDE: setting sim fidelity mode to Medium/Medium 
    3932 nonbonded_cutoff_distance = 0.900000 
    3933 use_gbsa = True 
    3934 gbsa_cutoff = 1.100000 
    3935 
    3936 > volume #1.1.1.1 region 0,2,0,11,15,12
    3937 
    3938 > set bgColor white
    3939 
    3940 > set bgColor #ffffff00
    3941 
    3942 > select add #1
    3943 
    3944 16827 atoms, 17253 bonds, 2103 residues, 15 models selected 
    3945 
    3946 > select add #1.2
    3947 
    3948 16827 atoms, 17253 bonds, 2103 residues, 15 models selected 
    3949 
    3950 > select add #1
    3951 
    3952 16827 atoms, 17253 bonds, 2103 residues, 15 models selected 
    3953 
    3954 > select add #1.2
    3955 
    3956 16827 atoms, 17253 bonds, 2103 residues, 15 models selected 
    3957 
    3958 > ~select
    3959 
    3960 Nothing selected 
    3961 
    3962 > view #1.1.1.1.2 clip false
    3963 
    3964 No displayed objects specified. 
    3965 
    3966 > view #1.1.1.1.2 clip false
    3967 
    3968 No displayed objects specified. 
    3969 
    3970 > view #1.1.1.1.2 clip false
    3971 
    3972 No displayed objects specified. 
    3973 
    3974 > show #1.1.1.1.2 target m
    3975 
    3976 > hide #1.1.1.1.2 target m
    3977 
    3978 > close #1.1.1.1.2
    3979 
    3980 > hide target m
    3981 
    3982 [Repeated 1 time(s)]
    3983 
    3984 > close
    3985 
    3986 > open
    3987 > C:\Users\daniellem\Downloads\fold_202411_11_fresh\fold_202411_11_fresh_model_1.cif
    3988 > format mmcif
    3989 
    3990 Chain information for fold_202411_11_fresh_model_1.cif #1 
    3991 --- 
    3992 Chain | Description 
    3993 A B C | . 
    3994  
    3995 
    3996 > open "C:/Users/daniellem/Desktop/CryoEM workshop/Dissertation final 316W
    3997 > model/DeepEMhancer_Danielle_4_9.mrc"
    3998 
    3999 Opened DeepEMhancer_Danielle_4_9.mrc as #2, grid size 128,128,128, pixel 1.66,
    4000 shown at level 0.171, step 1, values float32 
    4001 
    4002 > volume #2 region 0,6,0,127,127,127
    4003 
    4004 > select add #1
    4005 
    4006 16827 atoms, 17253 bonds, 2103 residues, 1 model selected 
    4007 
    4008 > volume #2 region 0,9,0,127,127,127
    4009 
    4010 > volume #2 region 0,31,0,127,127,127
    4011 
    4012 > volume #2 region 0,2,0,127,127,127
    4013 
    4014 > volume #2 region 2,2,0,127,127,127
    4015 
    4016 > volume #2 region 0,2,0,127,127,127
    4017 
    4018 > ui mousemode right "rotate selected models"
    4019 
    4020 > view matrix models
    4021 > #1,0.66525,-0.10274,0.73952,-3.3498,-0.70987,0.21988,0.66913,6.6393,-0.23135,-0.9701,0.073343,18.122
    4022 
    4023 > view matrix models
    4024 > #1,0.66436,-0.098392,0.74091,-3.4057,-0.70806,0.23457,0.66606,6.4683,-0.23933,-0.96711,0.086172,18.055
    4025 
    4026 > view matrix models
    4027 > #1,0.73489,-0.0012862,0.67819,-3.9016,-0.49398,0.68416,0.53657,1.0277,-0.46468,-0.72933,0.50214,14.374
    4028 
    4029 > view matrix models
    4030 > #1,0.48401,-0.29693,0.82315,-0.71801,-0.38327,0.77371,0.50446,-0.064179,-0.78666,-0.55965,0.26068,14.723
    4031 
    4032 > view matrix models
    4033 > #1,0.45881,-0.3301,0.82494,-0.27877,-0.38342,0.76399,0.51895,-0.033803,-0.80155,-0.5544,0.22396,14.879
    4034 
    4035 > view matrix models
    4036 > #1,0.58787,-0.42542,0.68806,1.4842,-0.33441,0.64668,0.68555,-0.022276,-0.7366,-0.63311,0.2379,15.786
    4037 
    4038 > ui mousemode right "move picked models"
    4039 
    4040 > ui mousemode right "translate selected models"
    4041 
    4042 > view matrix models
    4043 > #1,0.58787,-0.42542,0.68806,89.581,-0.33441,0.64668,0.68555,125,-0.7366,-0.63311,0.2379,28.389
    4044 
    4045 > ui mousemode right "rotate selected models"
    4046 
    4047 > view matrix models
    4048 > #1,0.69323,-0.26637,0.66969,87.572,-0.39958,0.63127,0.6647,125.4,-0.59981,-0.72838,0.33118,28.789
    4049 
    4050 > view matrix models
    4051 > #1,0.68673,-0.25861,0.67936,87.446,-0.37136,0.67861,0.63371,124.95,-0.6249,-0.68747,0.36998,28.176
    4052 
    4053 > ui mousemode right "translate selected models"
    4054 
    4055 > view matrix models
    4056 > #1,0.68673,-0.25861,0.67936,89.311,-0.37136,0.67861,0.63371,114.2,-0.6249,-0.68747,0.36998,81.84
    4057 
    4058 > ui mousemode right "move picked models"
    4059 
    4060 > view matrix models #2,1,0,0,-3.1953,0,1,0,8.6026,0,0,1,-26.98
    4061 
    4062 > ui mousemode right "rotate selected models"
    4063 
    4064 > view matrix models
    4065 > #1,0.71675,0.27424,0.64114,83.225,-0.50588,0.8373,0.20739,115.63,-0.47996,-0.47299,0.73887,76.524
    4066 
    4067 > view matrix models
    4068 > #1,-0.12708,0.40435,0.90573,81.28,-0.68048,0.62882,-0.3762,118.42,-0.72166,-0.66414,0.19524,82.162
    4069 
    4070 > ui mousemode right "translate selected atoms"
    4071 
    4072 > ui mousemode right "move picked models"
    4073 
    4074 > view matrix models #2,1,0,0,74.792,0,1,0,-99.562,0,0,1,-42.19
    4075 
    4076 > ui mousemode right "rotate selected models"
    4077 
    4078 > view matrix models
    4079 > #1,-0.064661,0.98545,0.15717,76.985,0.45325,0.16932,-0.87516,123.44,-0.88904,0.014648,-0.4576,79.166
    4080 
    4081 > view matrix models
    4082 > #1,0.20735,0.96008,0.18775,76.042,0.080933,0.17443,-0.98134,125.61,-0.97491,0.21868,-0.041534,73.66
    4083 
    4084 > view matrix models
    4085 > #1,0.52905,0.84743,0.044425,76.673,-0.40974,0.30094,-0.86113,125.75,-0.74312,0.43737,0.50644,66.766
    4086 
    4087 > view matrix models
    4088 > #1,0.66252,0.74875,-0.021062,77.638,-0.32016,0.25765,-0.91165,126.14,-0.67717,0.61073,0.41042,64.875
    4089 
    4090 > ui mousemode right "move picked models"
    4091 
    4092 > select subtract #1
    4093 
    4094 Nothing selected 
    4095 
    4096 > select add #2
    4097 
    4098 2 models selected 
    4099 
    4100 > ui mousemode right "rotate selected models"
    4101 
    4102 > view matrix models
    4103 > #2,0.36714,-0.13671,-0.92007,246.56,-0.46121,0.83223,-0.3077,-0.0059004,0.80777,0.53731,0.24249,-124.99
    4104 
    4105 > view matrix models
    4106 > #2,0.52398,-0.03222,-0.85112,210.75,-0.71814,0.52057,-0.46182,77.879,0.45795,0.85321,0.24963,-120.19
    4107 
    4108 > view matrix models
    4109 > #2,0.30109,-0.16473,-0.93926,258.99,-0.83534,0.42952,-0.3431,90.528,0.45995,0.8879,-0.0082803,-100.69
    4110 
    4111 > ui mousemode right "move picked models"
    4112 
    4113 > view matrix models
    4114 > #2,0.30109,-0.16473,-0.93926,198.41,-0.83534,0.42952,-0.3431,218.9,0.45995,0.8879,-0.0082803,-85.192
    4115 
    4116 > ui mousemode right "rotate selected models"
    4117 
    4118 > view matrix models
    4119 > #2,0.18816,-0.14391,-0.97154,212.04,-0.86165,0.45054,-0.23362,209.62,0.47133,0.88108,-0.039224,-82.925
    4120 
    4121 > view matrix models
    4122 > #2,0.18599,-0.16879,-0.96794,214.7,-0.86627,0.43672,-0.24261,212.49,0.46367,0.88362,-0.064991,-79.971
    4123 
    4124 > view matrix models
    4125 > #2,0.1282,-0.10727,-0.98593,216.22,-0.87167,0.46198,-0.16361,203.12,0.47303,0.88038,-0.034277,-83.494
    4126 
    4127 > select subtract #2
    4128 
    4129 Nothing selected 
    4130 
    4131 > fitmap map
    4132 
    4133 Missing or invalid "atomsOrMap" argument: invalid objects specifier 
    4134 
    4135 > fitmap
    4136 
    4137 Missing or invalid "atomsOrMap" argument: empty atom specifier 
    4138 
    4139 > fitmap
    4140 
    4141 Missing or invalid "atomsOrMap" argument: empty atom specifier 
    4142 
    4143 > ui mousemode right "move picked models"
    4144 
    4145 > view matrix models
    4146 > #1,0.66252,0.74875,-0.021062,121.8,-0.32016,0.25765,-0.91165,144.36,-0.67717,0.61073,0.41042,58.518
    4147 
    4148 > ui mousemode right "translate selected models"
    4149 
    4150 > ui mousemode right "rotate selected models"
    4151 
    4152 > roll
    4153 
    4154 > stop
    4155 
    4156 > ui mousemode right "translate selected models"
    4157 
    4158 > undo
    4159 
    4160 > redo
    4161 
    4162 > ui mousemode right rotate
    4163 
    4164 > ui mousemode right "move picked models"
    4165 
    4166 > volume #2 level 0.2875
    4167 
    4168 > volume #2 level 0.06889
    4169 
    4170 > clipper associate #2 toModel #1
    4171 
    4172 Opened DeepEMhancer_Danielle_4_9.mrc as #1.1.1.1, grid size 128,128,128, pixel
    4173 1.66, shown at level 0.0215, step 1, values float32 
    4174 Chain information for fold_202411_11_fresh_model_1.cif 
    4175 --- 
    4176 Chain | Description 
    4177 1.2/A 1.2/B 1.2/C | . 
    4178  
    4179 
    4180 > volume #1.1.1.1 level 0.02788
    4181 
    4182 > color #1.1.1.1 #1dffd9ff models
    4183 
    4184 > set bgColor black
    4185 
    4186 > set bgColor transparent
    4187 
    4188 > save "C:/Users/daniellem/Desktop/CryoEM workshop/Dissertation final 316W
    4189 > model/316W_diss_1.cxs"
    4190 
    4191 > select add #1
    4192 
    4193 16827 atoms, 17253 bonds, 2103 residues, 7 models selected 
    4194 
    4195 > select subtract #1
    4196 
    4197 Nothing selected 
    4198 
    4199 > select add #1.2
    4200 
    4201 16827 atoms, 17253 bonds, 2103 residues, 1 model selected 
    4202 
    4203 > select subtract #1.2
    4204 
    4205 Nothing selected 
    4206 
    4207 > select add #1.2
    4208 
    4209 16827 atoms, 17253 bonds, 2103 residues, 1 model selected 
    4210 
    4211 > select subtract #1.2
    4212 
    4213 Nothing selected 
    4214 
    4215 > close #1
    4216 
    4217 > open
    4218 > C:/Users/daniellem/Downloads/fold_202411_11_fresh/fold_202411_11_fresh_model_0.cif
    4219 
    4220 Chain information for fold_202411_11_fresh_model_0.cif #1 
    4221 --- 
    4222 Chain | Description 
    4223 A B C | . 
    4224  
    4225 
    4226 > open "C:/Users/daniellem/Desktop/CryoEM
    4227 > workshop/DeepEMhancer_Danielle_4_9.mrc"
    4228 
    4229 Opened DeepEMhancer_Danielle_4_9.mrc as #2, grid size 128,128,128, pixel 1.66,
    4230 shown at level 0.171, step 1, values float32 
    4231 
    4232 > fitmap #1 inMap #2
    4233 
    4234 Fit molecule fold_202411_11_fresh_model_0.cif (#1) to map
    4235 DeepEMhancer_Danielle_4_9.mrc (#2) using 16827 atoms 
    4236 average map value = 0.07522, steps = 844 
    4237 shifted from previous position = 175 
    4238 rotated from previous position = 54.2 degrees 
    4239 atoms outside contour = 14504, contour level = 0.17065 
    4240  
    4241 Position of fold_202411_11_fresh_model_0.cif (#1) relative to
    4242 DeepEMhancer_Danielle_4_9.mrc (#2) coordinates: 
    4243 Matrix rotation and translation 
    4244 0.64792760 -0.62354966 -0.43746502 96.82197592 
    4245 0.74386964 0.64153909 0.18731140 110.82058535 
    4246 0.16385295 -0.44678117 0.87951055 97.73764625 
    4247 Axis -0.39073889 -0.37054262 0.84262761 
    4248 Axis point -58.82632784 190.65888686 0.00000000 
    4249 Rotation angle (degrees) 54.23312860 
    4250 Shift along axis 3.46057824 
    4251  
    4252 
    4253 > select add #1
    4254 
    4255 16827 atoms, 17253 bonds, 2103 residues, 1 model selected 
    4256 
    4257 > ui mousemode right "rotate selected models"
    4258 
    4259 > view matrix models
    4260 > #1,0.99713,0.047993,-0.058537,89.39,0.058353,0.0052358,0.99828,118.88,0.048217,-0.99883,0.0024202,98.244
    4261 
    4262 > view matrix models
    4263 > #1,0.8632,-0.0503,0.50236,89.98,-0.50441,-0.12817,0.8539,116.49,0.021437,-0.99048,-0.13601,96.623
    4264 
    4265 > ui mousemode right "move picked models"
    4266 
    4267 > ui mousemode right "translate selected models"
    4268 
    4269 > view matrix models
    4270 > #1,0.8632,-0.0503,0.50236,89.369,-0.50441,-0.12817,0.8539,114.78,0.021437,-0.99048,-0.13601,96.141
    4271 
    4272 > view matrix models
    4273 > #1,0.8632,-0.0503,0.50236,51.119,-0.50441,-0.12817,0.8539,133.03,0.021437,-0.99048,-0.13601,97.843
    4274 
    4275 > view matrix models
    4276 > #1,0.8632,-0.0503,0.50236,11.287,-0.50441,-0.12817,0.8539,109.46,0.021437,-0.99048,-0.13601,101.2
    4277 
    4278 > ui mousemode right "rotate selected models"
    4279 
    4280 > ui mousemode right "translate selected models"
    4281 
    4282 > view matrix models
    4283 > #1,0.8632,-0.0503,0.50236,73.284,-0.50441,-0.12817,0.8539,117.42,0.021437,-0.99048,-0.13601,99.791
    4284 
    4285 > view matrix models
    4286 > #1,0.8632,-0.0503,0.50236,70.626,-0.50441,-0.12817,0.8539,117.88,0.021437,-0.99048,-0.13601,99.742
    4287 
    4288 > view matrix models
    4289 > #1,0.8632,-0.0503,0.50236,121.46,-0.50441,-0.12817,0.8539,114.41,0.021437,-0.99048,-0.13601,99.952
    4290 
    4291 > ui mousemode right "rotate selected models"
    4292 
    4293 > view matrix models
    4294 > #1,0.8253,-0.28919,0.48503,125.06,-0.54795,-0.20249,0.81163,115.12,-0.1365,-0.93561,-0.32557,97.173
    4295 
    4296 > view matrix models
    4297 > #1,0.8233,-0.30662,0.47766,125.28,-0.55534,-0.26109,0.78958,115.9,-0.11739,-0.91532,-0.38523,96.754
    4298 
    4299 > view matrix models
    4300 > #1,0.69075,0.22823,0.68613,117.35,-0.64306,-0.24003,0.72723,114.32,0.33067,-0.94355,-0.019031,102.83
    4301 
    4302 > view matrix models
    4303 > #1,0.74225,-0.1389,0.65557,123.62,-0.66974,-0.12076,0.73271,112.12,-0.022608,-0.98292,-0.18266,99.155
    4304 
    4305 > select subtract #1
    4306 
    4307 Nothing selected 
    4308 
    4309 > select add #2
    4310 
    4311 2 models selected 
    4312 
    4313 > view matrix models
    4314 > #2,0.9995,0.0074953,0.030735,-3.5727,-0.008337,0.99959,0.027347,-1.4932,-0.030517,-0.027589,0.99915,6.62
    4315 
    4316 > ui mousemode right "translate selected models"
    4317 
    4318 > view matrix models
    4319 > #2,0.9995,0.0074953,0.030735,23.671,-0.008337,0.99959,0.027347,4.4973,-0.030517,-0.027589,0.99915,5.6597
    4320 
    4321 > ui mousemode right rotate
    4322 
    4323 > ui mousemode right "rotate selected models"
    4324 
    4325 > view matrix models
    4326 > #2,0.97796,-0.014894,-0.20826,50.426,0.05381,0.98174,0.18248,-14.843,0.20174,-0.18966,0.9609,0.28557
    4327 
    4328 > ui mousemode right "translate selected models"
    4329 
    4330 > view matrix models
    4331 > #2,0.97796,-0.014894,-0.20826,53.888,0.05381,0.98174,0.18248,-19.638,0.20174,-0.18966,0.9609,2.2334
    4332 
    4333 > ui mousemode right "rotate selected models"
    4334 
    4335 > view matrix models
    4336 > #2,0.98566,-0.0079441,-0.16857,48.617,0.044096,0.97631,0.21182,-20.604,0.1629,-0.21622,0.96266,9.4578
    4337 
    4338 > view matrix models
    4339 > #2,0.95291,-0.0044741,-0.30321,64.289,0.14917,0.87746,0.45586,-44.084,0.26402,-0.47962,0.83681,38.3
    4340 
    4341 > view matrix models
    4342 > #2,0.92066,-0.20279,-0.33356,92.584,0.33574,0.8473,0.41154,-58.164,0.19917,-0.49088,0.84816,45.955
    4343 
    4344 > ui mousemode right "translate selected models"
    4345 
    4346 > view matrix models
    4347 > #2,0.92066,-0.20279,-0.33356,83.602,0.33574,0.8473,0.41154,-56.096,0.19917,-0.49088,0.84816,44.316
    4348 
    4349 > select add #2
    4350 
    4351 3 models selected 
    4352 
    4353 > ui mousemode right translate
    4354 
    4355 > ui mousemode right "translate selected atoms"
    4356 
    4357 > ui mousemode right "move picked models"
    4358 
    4359 > ui mousemode right select
    4360 
    4361 > select subtract #2
    4362 
    4363 Nothing selected 
    4364 
    4365 > ui mousemode right "translate selected models"
    4366 
    4367 > select add #2
    4368 
    4369 3 models selected 
    4370 
    4371 > select subtract #2
    4372 
    4373 Nothing selected 
    4374 
    4375 > ui mousemode right "move picked models"
    4376 
    4377 > ui mousemode right "rotate selected models"
    4378 
    4379 > ui mousemode right "translate selected models"
    4380 
    4381 > select add #1
    4382 
    4383 16827 atoms, 17253 bonds, 2103 residues, 1 model selected 
    4384 
    4385 > view matrix models
    4386 > #1,0.74225,-0.1389,0.65557,125.13,-0.66974,-0.12076,0.73271,107.13,-0.022608,-0.98292,-0.18266,95.753
    4387 
    4388 > select subtract #1
    4389 
    4390 Nothing selected 
    4391 
    4392 > isolde start
    4393 
    4394 > clipper associate #2 toModel #1
    4395 
    4396 Opened DeepEMhancer_Danielle_4_9.mrc as #1.1.1.1, grid size 128,128,128, pixel
    4397 1.66, shown at level 0.191, step 1, values float32 
    4398 Chain information for fold_202411_11_fresh_model_0.cif 
    4399 --- 
    4400 Chain | Description 
    4401 1.2/A 1.2/B 1.2/C | . 
    4402  
    4403 
    4404 > isolde start
    4405 
    4406 > set bgColor white
    4407 
    4408 > set bgColor #ffffff00
    4409 
    4410 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4411 chains... 
    4412 ISOLDE: Corrected atom nomenclature of 277 residues in model #1.2 to IUPAC-IUB
    4413 standards. 
    4414 ISOLDE: created disulfide bonds between the following residues: 
    4415 B125-B137; B276-B309; C181-C416; B48-B68; C276-C309; C355-C428; A355-A428;
    4416 A362-A401; C484-C590; A276-A309; A181-A416; B583-B589; A125-A137; C113-C185;
    4417 B484-B590; C583-C589; B362-B401; B113-B185; C208-C219; A48-A68; C48-C68;
    4418 A113-A185; C198-C227; B208-B219; B181-B416; A583-A589; A208-A219; B198-B227;
    4419 B355-B428; C125-C137; A198-A227; C362-C401; B120-B176; A484-A590; A120-A176;
    4420 C120-C176 
    4421 
    4422 > set silhouettes false
    4423 
    4424 > ~select
    4425 
    4426 Nothing selected 
    4427 
    4428 > set silhouettes false
    4429 
    4430 > delete ~protein
    4431 
    4432 > addh
    4433 
    4434 Summary of feedback from adding hydrogens to fold_202411_11_fresh_model_0.cif
    4435 #1.2 
    4436 --- 
    4437 notes | Termini for fold_202411_11_fresh_model_0.cif (#1.2) chain A determined from SEQRES records 
    4438 Termini for fold_202411_11_fresh_model_0.cif (#1.2) chain B determined from
    4439 SEQRES records 
    4440 Termini for fold_202411_11_fresh_model_0.cif (#1.2) chain C determined from
    4441 SEQRES records 
    4442 Chain-initial residues that are actual N termini: /A MET 1, /B MET 1, /C MET 1 
    4443 Chain-initial residues that are not actual N termini: 
    4444 Chain-final residues that are actual C termini: /A HIS 677, /B HIS 677, /C HIS
    4445 677 
    4446 Chain-final residues that are not actual C termini: 
    4447 1630 hydrogen bonds 
    4448 15663 hydrogens added 
    4449  
    4450 
    4451 > select #1
    4452 
    4453 31698 atoms, 32088 bonds, 2031 residues, 16 models selected 
    4454 
    4455 > clipper isolate #1 maskRadius 16
    4456 
    4457 > view matrix models #1,1,0,0,7.0869,0,1,0,-0.39389,0,0,1,2.602
    4458 
    4459 > ui mousemode right "rotate selected models"
    4460 
    4461 > view matrix models
    4462 > #1,0.95983,0.26995,-0.076557,-10.994,-0.24059,0.93216,0.27052,16.377,0.14439,-0.24124,0.95966,14.374
    4463 
    4464 > view matrix models
    4465 > #1,0.9876,-0.040147,-0.15174,25.439,0.021063,0.99189,-0.12534,6.9079,0.15554,0.1206,0.98044,-28.405
    4466 
    4467 > view matrix models
    4468 > #1,0.99163,-0.083691,-0.098314,25.632,0.09889,0.98189,0.16158,-23.443,0.08301,-0.16995,0.98195,12.399
    4469 
    4470 > hide atoms
    4471 
    4472 > save "C:/Users/daniellem/Desktop/CryoEM workshop/Dissertation final 316W
    4473 > model/316W_diss_1.cxs"
    4474 
    4475 > show ~HC
    4476 
    4477 > isolde restrain distances "#1/A,G"
    4478 
    4479 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4480 chains... 
    4481 
    4482 > isolde restrain distances "#1/B,F"
    4483 
    4484 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4485 chains... 
    4486 
    4487 > select #1
    4488 
    4489 31698 atoms, 32088 bonds, 2031 residues, 17 models selected 
    4490 
    4491 > isolde sim start sel
    4492 
    4493 ISOLDE: started sim 
    4494 
    4495 > ui mousemode right "isolde tug selection"
    4496 
    4497 > select /B,F@CA
    4498 
    4499 677 atoms, 677 residues, 1 model selected 
    4500 
    4501 > select /A,H@CA
    4502 
    4503 677 atoms, 677 residues, 1 model selected 
    4504 
    4505 > select /A,B,C
    4506 
    4507 31698 atoms, 32088 bonds, 2031 residues, 1 model selected 
    4508 
    4509 > ui hideFloating toggle
    4510 
    4511 [Repeated 1 time(s)]
    4512 
    4513 > ~select
    4514 
    4515 Nothing selected 
    4516 
    4517 > ~select
    4518 
    4519 Nothing selected 
    4520 
    4521 > isolde sim pause
    4522 
    4523 > select #1
    4524 
    4525 31698 atoms, 32088 bonds, 2031 residues, 21 models selected 
    4526 
    4527 > ui mousemode right "move picked models"
    4528 
    4529 > ui mousemode right "translate selected models"
    4530 
    4531 > view matrix models
    4532 > #1,0.99163,-0.083691,-0.098314,22.128,0.09889,0.98189,0.16158,-23.116,0.08301,-0.16995,0.98195,10.873
    4533 
    4534 > ui mousemode right "move picked models"
    4535 
    4536 > isolde sim resume
    4537 
    4538 > select A
    4539 
    4540 Expected an objects specifier or a keyword 
    4541 
    4542 > select /A
    4543 
    4544 10566 atoms, 10696 bonds, 677 residues, 1 model selected 
    4545 
    4546 > view matrix models
    4547 > #1.2,1,3.4694e-17,9.7145e-17,-0.57951,2.0817e-17,1,-5.5511e-17,0.97731,0,-8.3267e-17,1,0.16641
    4548 
    4549 > view matrix models
    4550 > #1.2,1,6.0715e-17,1.1102e-16,-3.7199,1.3878e-17,1,-1.3878e-16,0.75132,1.3878e-17,-8.3267e-17,1,-1.2135
    4551 
    4552 > view matrix models
    4553 > #1.2,1,-5.6725e-16,-4.1633e-17,-4.514,-4.4929e-16,1,-4.1633e-16,6.3267,-5.4123e-16,2.498e-16,1,0.76486
    4554 
    4555 > select /A
    4556 
    4557 10566 atoms, 10696 bonds, 677 residues, 1 model selected 
    4558 
    4559 > ui mousemode right "isolde tug selection"
    4560 
    4561 > ~select
    4562 
    4563 Nothing selected 
    4564 
    4565 > ~select
    4566 
    4567 Nothing selected 
    4568 
    4569 > chains
    4570 
    4571 Unknown command: chains 
    4572 
    4573 > chains/
    4574 
    4575 Unknown command: chains/ 
    4576 
    4577 > /
    4578 
    4579 Unknown command: / 
    4580 
    4581 > select add #1.2
    4582 
    4583 31698 atoms, 32088 bonds, 2031 residues, 14 models selected 
    4584 
    4585 > select add #1.1.1
    4586 
    4587 31698 atoms, 32088 bonds, 2031 residues, 17 models selected 
    4588 
    4589 > select add #1
    4590 
    4591 31698 atoms, 32088 bonds, 2031 residues, 21 models selected 
    4592 
    4593 > select subtract #1.1.1
    4594 
    4595 31698 atoms, 32088 bonds, 2031 residues, 16 models selected 
    4596 
    4597 > select add #1.2
    4598 
    4599 31698 atoms, 32088 bonds, 2031 residues, 17 models selected 
    4600 
    4601 > select subtract #1.3
    4602 
    4603 31698 atoms, 32088 bonds, 2031 residues, 15 models selected 
    4604 
    4605 > select add #1.2
    4606 
    4607 31698 atoms, 32088 bonds, 2031 residues, 16 models selected 
    4608 
    4609 > ~select
    4610 
    4611 Nothing selected 
    4612 
    4613 > select add #1.1.1
    4614 
    4615 4 models selected 
    4616 
    4617 > ui mousemode right "translate selected models"
    4618 
    4619 > view matrix models
    4620 > #1.1.1,1,-5.0307e-17,2.6368e-16,0.51738,-1.1796e-16,1,-6.3838e-16,-5.7231,6.9389e-17,1.3878e-16,1,0.10217
    4621 
    4622 > ui mousemode right "rotate selected models"
    4623 
    4624 > view matrix models
    4625 > #1.1.1,0.98912,-0.14707,-0.0035996,18.306,0.1471,0.9884,0.037814,-25.16,-0.0020035,-0.037932,0.99928,4.5772
    4626 
    4627 > view matrix models
    4628 > #1.1.1,0.86583,-0.49895,-0.037256,74.567,0.49933,0.85694,0.1278,-60.241,-0.031839,-0.12925,0.9911,18.874
    4629 
    4630 > view matrix models
    4631 > #1.1.1,0.9799,-0.19939,-0.0062574,25.388,0.19945,0.97857,0.05124,-31.446,-0.0040934,-0.051458,0.99867,6.3666
    4632 
    4633 > view matrix models
    4634 > #1.1.1,0.99258,0.12162,-0.0012517,-11.88,-0.1216,0.99208,-0.031353,12.279,-0.0025713,0.031273,0.99951,-2.9923
    4635 
    4636 > view matrix models
    4637 > #1.1.1,0.9998,-0.020045,-0.0001605,2.7614,0.020046,0.99979,0.0051605,-8.5229,5.7023e-05,-0.0051627,0.99999,0.66479
    4638 
    4639 > view matrix models
    4640 > #1.1.1,0.99427,0.018958,-0.1052,8.6924,-0.019023,0.99982,0.00038549,-3.5055,0.10519,0.0016179,0.99445,-11.917
    4641 
    4642 > view matrix models
    4643 > #1.1.1,0.98647,-0.12373,-0.10757,25.525,0.12676,0.99169,0.021827,-21.678,0.10397,-0.035167,0.99396,-7.6817
    4644 
    4645 > ui mousemode right "translate selected models"
    4646 
    4647 > view matrix models
    4648 > #1.1.1,0.98647,-0.12373,-0.10757,30.35,0.12676,0.99169,0.021827,-13.388,0.10397,-0.035167,0.99396,-6.3941
    4649 
    4650 > ~select
    4651 
    4652 Nothing selected 
    4653 
    4654 > ui mousemode right rotate
    4655 
    4656 > ~select
    4657 
    4658 Nothing selected 
    4659 
    4660 > ui mousemode right "move picked models"
    4661 
    4662 > ui mousemode right "translate selected models"
    4663 
    4664 > select add #1.1.1
    4665 
    4666 4 models selected 
    4667 
    4668 > view matrix models
    4669 > #1.1.1,0.98647,-0.12373,-0.10757,33.311,0.12676,0.99169,0.021827,-17.645,0.10397,-0.035167,0.99396,-5.3485
    4670 
    4671 > select subtract #1.1.1
    4672 
    4673 Nothing selected 
    4674 
    4675 > ~select
    4676 
    4677 Nothing selected 
    4678 
    4679 > select /A
    4680 
    4681 10566 atoms, 10696 bonds, 677 residues, 1 model selected 
    4682 
    4683 > select /c
    4684 
    4685 10566 atoms, 10696 bonds, 677 residues, 1 model selected 
    4686 
    4687 > select /C
    4688 
    4689 10566 atoms, 10696 bonds, 677 residues, 1 model selected 
    4690 
    4691 > ui mousemode right "isolde tug selection"
    4692 
    4693 [Repeated 1 time(s)]
    4694 
    4695 > select /A
    4696 
    4697 10566 atoms, 10696 bonds, 677 residues, 1 model selected 
    4698 
    4699 > select /B
    4700 
    4701 10566 atoms, 10696 bonds, 677 residues, 1 model selected 
    4702 
    4703 > ~select
    4704 
    4705 Nothing selected 
    4706 
    4707 > select /B
    4708 
    4709 10566 atoms, 10696 bonds, 677 residues, 1 model selected 
    4710 
    4711 > ui mousemode right "isolde tug selection"
    4712 
    4713 [Repeated 1 time(s)]
    4714 
    4715 > ~select
    4716 
    4717 Nothing selected 
    4718 
    4719 > ui mousemode right "translate selected models"
    4720 
    4721 > hide atoms
    4722 
    4723 > show atoms
    4724 
    4725 > select add #1.2
    4726 
    4727 31698 atoms, 32088 bonds, 2031 residues, 14 models selected 
    4728 
    4729 > select add #1.2
    4730 
    4731 31698 atoms, 32088 bonds, 2031 residues, 14 models selected 
    4732 
    4733 > select add #1.2
    4734 
    4735 31698 atoms, 32088 bonds, 2031 residues, 14 models selected 
    4736 
    4737 > ~select
    4738 
    4739 Nothing selected 
    4740 
    4741 > select add #1.2
    4742 
    4743 31698 atoms, 32088 bonds, 2031 residues, 14 models selected 
    4744 
    4745 > select add #1.2
    4746 
    4747 31698 atoms, 32088 bonds, 2031 residues, 14 models selected 
    4748 
    4749 > ~select
    4750 
    4751 Nothing selected 
    4752 
    4753 > select add #1.1.1
    4754 
    4755 4 models selected 
    4756 
    4757 > ui mousemode right "rotate selected models"
    4758 
    4759 > view matrix models
    4760 > #1.1.1,0.95386,-0.26947,-0.13243,55.464,0.27868,0.95872,0.056438,-35.107,0.11175,-0.090739,0.98958,0.24681
    4761 
    4762 > view matrix models
    4763 > #1.1.1,0.86816,-0.46394,-0.17625,90.975,0.48447,0.86928,0.098215,-53.367,0.10765,-0.17066,0.97943,10.451
    4764 
    4765 > view matrix models
    4766 > #1.1.1,0.72836,-0.29898,-0.61652,129.46,0.4368,0.89585,0.081589,-49.148,0.52792,-0.32872,0.7831,-3.8769
    4767 
    4768 > ui mousemode right "move picked models"
    4769 
    4770 > ui mousemode right "rotate selected models"
    4771 
    4772 > view matrix models
    4773 > #1.1.1,0.85765,-0.27788,-0.43269,95.102,0.37939,0.90992,0.16766,-51.769,0.34712,-0.30795,0.88582,5.8133
    4774 
    4775 > view matrix models
    4776 > #1.1.1,0.648,-0.46752,-0.60126,156.1,0.73192,0.6006,0.32181,-73.411,0.21067,-0.64861,0.73138,73.494
    4777 
    4778 > view matrix models
    4779 > #1.1.1,0.73896,-0.48429,-0.4684,135.09,0.66602,0.63004,0.39933,-75.941,0.10172,-0.60706,0.78812,76.608
    4780 
    4781 > view matrix models
    4782 > #1.1.1,0.81976,-0.49328,-0.29098,110.35,0.57131,0.66885,0.47565,-75.991,-0.040005,-0.55616,0.83011,83.909
    4783 
    4784 > view matrix models
    4785 > #1.1.1,0.85593,-0.49206,-0.15894,93.907,0.49686,0.69745,0.51643,-74.068,-0.14326,-0.52099,0.84145,91.195
    4786 
    4787 > view matrix models
    4788 > #1.1.1,0.82413,-0.49343,-0.2781,108.68,0.56418,0.67165,0.48019,-75.872,-0.050157,-0.55263,0.83191,84.555
    4789 
    4790 > isolde sim pause
    4791 
    4792 > view matrix models
    4793 > #1.1.1,0.97678,-0.058664,-0.20603,36.223,0.14599,0.88615,0.43981,-46.365,0.15678,-0.45967,0.87414,46.017
    4794 
    4795 > ui mousemode right "move picked models"
    4796 
    4797 > view matrix models
    4798 > #1.2,1,-2.5847e-16,5.8287e-16,-6.4386,-2.949e-16,1,-1.9429e-16,6.691,-5.8287e-16,-3.3307e-16,1,-0.1065
    4799 
    4800 > isolde sim resume
    4801 
    4802 > ui mousemode right "translate selected models"
    4803 
    4804 > ui mousemode right rotate
    4805 
    4806 > ~select
    4807 
    4808 Nothing selected 
    4809 
    4810 > ~select
    4811 
    4812 Nothing selected 
    4813 
    4814 > ~select
    4815 
    4816 Nothing selected 
    4817 
    4818 > select /A
    4819 
    4820 10566 atoms, 10696 bonds, 677 residues, 1 model selected 
    4821 
    4822 > ui mousemode right "isolde tug selection"
    4823 
    4824 > select add #1
    4825 
    4826 31698 atoms, 32088 bonds, 2031 residues, 21 models selected 
    4827 
    4828 > select add #1
    4829 
    4830 31698 atoms, 32088 bonds, 2031 residues, 21 models selected 
    4831 
    4832 > select add #1
    4833 
    4834 31698 atoms, 32088 bonds, 2031 residues, 21 models selected 
    4835 
    4836 > ~select
    4837 
    4838 Nothing selected 
    4839 
    4840 > select /C
    4841 
    4842 10566 atoms, 10696 bonds, 677 residues, 1 model selected 
    4843 
    4844 > ~select
    4845 
    4846 Nothing selected 
    4847 
    4848 > rotate 30
    4849 
    4850 Unknown command: rotate 30 
    4851 
    4852 > rotate x 30
    4853 
    4854 Unknown command: rotate x 30 
    4855 
    4856 > turn 30
    4857 
    4858 Expected an axis vector or a keyword 
    4859 
    4860 > help help:user
    4861 
    4862 > turn y 30
    4863 
    4864 [Repeated 1 time(s)]
    4865 
    4866 > select /B
    4867 
    4868 10566 atoms, 10696 bonds, 677 residues, 1 model selected 
    4869 
    4870 > isolde sim pause
    4871 
    4872 > select
    4873 
    4874 31698 atoms, 32088 bonds, 2031 residues, 21 models selected 
    4875 
    4876 > ~select
    4877 
    4878 Nothing selected 
    4879 
    4880 > select add #1.1.1
    4881 
    4882 4 models selected 
    4883 
    4884 > ui mousemode right "translate selected models"
    4885 
    4886 > view matrix models
    4887 > #1.1.1,0.97678,-0.058664,-0.20603,36.443,0.14599,0.88615,0.43981,-47.931,0.15678,-0.45967,0.87414,43.486
    4888 
    4889 > ui mousemode right "rotate selected models"
    4890 
    4891 > view matrix models
    4892 > #1.1.1,0.93878,-0.072118,-0.33688,54.349,0.21104,0.89328,0.39687,-52.488,0.27231,-0.44367,0.85382,29.924
    4893 
    4894 > select add #1.1.1
    4895 
    4896 4 models selected 
    4897 
    4898 > select subtract #1.1.1
    4899 
    4900 Nothing selected 
    4901 
    4902 > ~select
    4903 
    4904 Nothing selected 
    4905 
    4906 > select add #1.2
    4907 
    4908 31698 atoms, 32088 bonds, 2031 residues, 14 models selected 
    4909 
    4910 > view matrix models
    4911 > #1.2,0.98911,-0.053048,-0.13729,11.919,0.074733,0.98461,0.15797,-14.293,0.1268,-0.16651,0.97785,3.142
    4912 
    4913 > view matrix models
    4914 > #1.2,0.98948,0.016677,-0.14373,5.221,0.0055592,0.98822,0.15294,-5.6294,0.14458,-0.15213,0.97773,-0.5454
    4915 
    4916 > view matrix models
    4917 > #1.2,0.98685,0.0096553,-0.16132,7.7496,0.012471,0.99069,0.13558,-5.287,0.16113,-0.13581,0.97754,-4.2736
    4918 
    4919 > view matrix models
    4920 > #1.2,0.98778,0.006444,-0.15574,7.4975,0.02641,0.97778,0.20796,-11.769,0.15362,-0.20953,0.96566,5.2641
    4921 
    4922 > view matrix models
    4923 > #1.2,0.8593,-0.4953,-0.12761,72.895,0.51115,0.8227,0.24878,-59.558,-0.018234,-0.27901,0.96012,34.297
    4924 
    4925 > view matrix models
    4926 > #1.2,0.98861,0.0059789,-0.15036,6.9894,0.020811,0.98418,0.17597,-9.0452,0.14903,-0.17709,0.97284,1.8859
    4927 
    4928 > ui mousemode right "move picked models"
    4929 
    4930 > ui mousemode right "translate selected models"
    4931 
    4932 > view matrix models
    4933 > #1.2,0.98861,0.0059789,-0.15036,15.778,0.020811,0.98418,0.17597,-19.022,0.14903,-0.17709,0.97284,-8.0522
    4934 
    4935 > view matrix models
    4936 > #1.2,0.98861,0.0059789,-0.15036,12.948,0.020811,0.98418,0.17597,-19.55,0.14903,-0.17709,0.97284,-4.7808
    4937 
    4938 > view matrix models
    4939 > #1.2,0.98861,0.0059789,-0.15036,8.191,0.020811,0.98418,0.17597,-20.422,0.14903,-0.17709,0.97284,-0.82751
    4940 
    4941 > isolde sim resume
    4942 
    4943 > select /A
    4944 
    4945 10566 atoms, 10696 bonds, 677 residues, 1 model selected 
    4946 
    4947 > ui mousemode right "isolde tug selection"
    4948 
    4949 [Repeated 1 time(s)]
    4950 
    4951 > ~select
    4952 
    4953 Nothing selected 
    4954 
    4955 > volume #1.1.1.1 level 0.1688
    4956 
    4957 > volume #1.1.1.1 level 0.1198
    4958 
    4959 > ui mousemode right "isolde tug selection"
    4960 
    4961 > isolde sim stop
    4962 
    4963 Sim termination reason: None 
    4964 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4965 chains... 
    4966 ISOLDE: Corrected atom nomenclature of 61 residues in model #1.2 to IUPAC-IUB
    4967 standards. 
    4968 ISOLDE: stopped sim 
    4969 
    4970 > isolde start
    4971 
    4972 > save "C:/Users/daniellem/Desktop/CryoEM workshop/Dissertation final 316W
    4973 > model/316W_diss_2.cxs"
    4974 
    4975 ——— End of log from Wed Nov 13 21:10:41 2024 ———
    4976 
    4977 opened ChimeraX session 
    4978 
    4979 > clipper isolate #1 maskRadius 16
    4980 
    4981 > isolde start
    4982 
    4983 > isolde sim start /A-C
    4984 
    4985 ISOLDE: started sim 
    4986 
    4987 > ui mousemode right "isolde tug atom"
    4988 
    4989 > ~select
    4990 
    4991 Nothing selected 
    4992 
    4993 > select /B
    4994 
    4995 10566 atoms, 10696 bonds, 677 residues, 1 model selected 
    4996 
    4997 > ui mousemode right "isolde tug selection"
    4998 
    4999 > select
    5000 
    5001 31698 atoms, 32088 bonds, 2031 residues, 24 models selected 
    5002 
    5003 > ~select
    5004 
    5005 Nothing selected 
    5006 
    5007 > select /A
    5008 
    5009 10566 atoms, 10696 bonds, 677 residues, 1 model selected 
    5010 
    5011 > ui mousemode right "isolde tug selection"
    5012 
    5013 [Repeated 1 time(s)]
    5014 
    5015 > isolde restrain distances "#1/C"
    5016 
    5017 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5018 chains... 
    5019 ISOLDE: Corrected atom nomenclature of 8 residues in model #1.2 to IUPAC-IUB
    5020 standards. 
    5021 
    5022 > ~select
    5023 
    5024 Nothing selected 
    5025 
    5026 > ui mousemode right "isolde tug residue"
    5027 
    5028 > help help:user
    5029 
    5030 > select add #1.2
    5031 
    5032 31698 atoms, 32088 bonds, 2031 residues, 17 models selected 
    5033 
    5034 > show ribbons
    5035 
    5036 > ~select
    5037 
    5038 Nothing selected 
    5039 
    5040 > ui mousemode right swapaa
    5041 
    5042 > swapaa mousemode /C:59 VAL
    5043 
    5044 Sim termination reason: coord length mismatch 
    5045 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5046 chains... 
    5047 ISOLDE: Corrected atom nomenclature of 17 residues in model #1.2 to IUPAC-IUB
    5048 standards. 
    5049 ISOLDE: stopped sim 
    5050 
    5051 > save "C:/Users/daniellem/Desktop/CryoEM workshop/Dissertation final 316W
    5052 > model/316W_diss_3.cxs"
    5053 
    5054 [Repeated 1 time(s)]
    5055 
    5056 ——— End of log from Wed Nov 13 21:59:07 2024 ———
    5057 
    5058 opened ChimeraX session 
    5059 
    5060 > open "D:\Dissertation final 316W model\316W_diss_3.cxs" format session
    5061 
    5062 Opened DeepEMhancer_Danielle_4_9.mrc as #1.1.1.1, grid size 128,128,128, pixel
    5063 1.66, shown at level 0.12, step 1, values float32 
    5064 Unable to restore session, resetting. 
    5065  
    5066 Traceback (most recent call last): 
    5067 File "C:\Program Files\ChimeraX 1.9rc202411130312\bin\Lib\site-
    5068 packages\chimerax\core\session.py", line 854, in restore 
    5069 self.add_state_manager(name, data) 
    5070 File "C:\Program Files\ChimeraX 1.9rc202411130312\bin\Lib\site-
    5071 packages\chimerax\core\session.py", line 647, in add_state_manager 
    5072 raise ValueError( 
    5073 ValueError: container "Isolde Residue Stepper Manager" of type "<class
    5074 'NoneType'>" does not have snapshot methods and does not have clear method 
    5075  
    5076 Log from Wed Nov 13 21:59:07 2024UCSF ChimeraX version: 1.8 (2024-06-10) 
    5077 © 2016-2024 Regents of the University of California. All rights reserved. 
    5078 
    5079 > open "C:\Users\daniellem\Desktop\CryoEM workshop\Dissertation final 316W
    5080 > model\316W_diss_2.cxs" format session
    5081 
    5082 Opened DeepEMhancer_Danielle_4_9.mrc as #1.1.1.1, grid size 128,128,128, pixel
    5083 1.66, shown at level 0.12, step 1, values float32 
    5084 Log from Wed Nov 13 21:10:41 2024UCSF ChimeraX version: 1.8 (2024-06-10) 
    5085 © 2016-2024 Regents of the University of California. All rights reserved. 
    5086 
    5087 > open "C:\Users\daniellem\Desktop\CryoEM workshop\Dissertation final 316W
    5088 > model\Isolde_316W.cxs" format session
    5089 
    5090 Opened DeepEMhancer_Danielle_4_9.mrc as #1, grid size 128,128,128, pixel 1.66,
    5091 shown at level 0.171, step 1, values float32 
    5092 Log from Wed Nov 13 16:05:25 2024 Startup Messages 
    5093 --- 
    5094 note | available bundle cache has not been initialized yet 
    5095  
    5096 UCSF ChimeraX version: 1.8 (2024-06-10) 
    5097 © 2016-2024 Regents of the University of California. All rights reserved. 
    5098 How to cite UCSF ChimeraX 
    5099 
    5100 > open
    5101 > C:\\\Users\\\daniellem\\\Downloads\\\ChimeraX_ISOLDE-1.8-cp311-cp311-win_amd64.whl
    5102 
    5103 Unrecognized file suffix '.whl' 
    5104 
    5105 > open "C:/Users/daniellem/Desktop/CryoEM
    5106 > workshop/DeepEMhancer_Danielle_4_9.mrc"
    5107 
    5108 Opened DeepEMhancer_Danielle_4_9.mrc as #1, grid size 128,128,128, pixel 1.66,
    5109 shown at level 0.171, step 1, values float32 
    5110 
    5111 > open
    5112 > C:/Users/daniellem/Downloads/fold_202411_11_fresh/fold_202411_11_fresh_model_0.cif
    5113 
    5114 Chain information for fold_202411_11_fresh_model_0.cif #2 
    5115 --- 
    5116 Chain | Description 
    5117 A B C | . 
    5118  
    5119 
    5120 > fitmap #2 inMap #1
    5121 
    5122 Fit molecule fold_202411_11_fresh_model_0.cif (#2) to map
    5123 DeepEMhancer_Danielle_4_9.mrc (#1) using 16827 atoms 
    5124 average map value = 0.07522, steps = 844 
    5125 shifted from previous position = 175 
    5126 rotated from previous position = 54.2 degrees 
    5127 atoms outside contour = 14504, contour level = 0.17065 
    5128  
    5129 Position of fold_202411_11_fresh_model_0.cif (#2) relative to
    5130 DeepEMhancer_Danielle_4_9.mrc (#1) coordinates: 
    5131 Matrix rotation and translation 
    5132 0.64792760 -0.62354966 -0.43746502 96.82197592 
    5133 0.74386964 0.64153909 0.18731140 110.82058535 
    5134 0.16385295 -0.44678117 0.87951055 97.73764625 
    5135 Axis -0.39073889 -0.37054262 0.84262761 
    5136 Axis point -58.82632784 190.65888686 0.00000000 
    5137 Rotation angle (degrees) 54.23312860 
    5138 Shift along axis 3.46057824 
    5139  
    5140 
    5141 > select add #2
    5142 
    5143 16827 atoms, 17253 bonds, 2103 residues, 1 model selected 
    5144 
    5145 > ui mousemode right "translate selected models"
    5146 
    5147 > ui mousemode right "rotate selected models"
    5148 
    5149 > view matrix models
    5150 > #2,0.90908,-0.24195,0.33917,98.645,-0.23659,0.3703,0.89828,112.27,-0.34293,-0.89685,0.27939,96.701
    5151 
    5152 > view matrix models
    5153 > #2,0.53124,-0.06761,0.84452,97.684,-0.82947,0.1615,0.5347,110.22,-0.17254,-0.98455,0.029713,96.843
    5154 
    5155 > view matrix models
    5156 > #2,0.41491,-0.042433,0.90887,97.121,-0.90723,-0.095219,0.40971,113.02,0.069157,-0.99455,-0.078003,97.834
    5157 
    5158 > view matrix models
    5159 > #2,0.75288,0.027834,0.65757,97.316,-0.63298,-0.24308,0.73502,119.44,0.1803,-0.96961,-0.16539,97.49
    5160 
    5161 > ui mousemode right "move picked models"
    5162 
    5163 > ui mousemode right "rotate selected models"
    5164 
    5165 > view matrix models
    5166 > #2,0.87103,0.31614,0.37598,92.913,-0.28071,-0.30778,0.90911,123.97,0.40312,-0.8974,-0.17934,97.549
    5167 
    5168 > view matrix models
    5169 > #2,0.91536,0.086966,0.39313,97.148,-0.39835,0.053566,0.91567,117.07,0.058573,-0.99477,0.083675,97.517
    5170 
    5171 > view matrix models
    5172 > #2,0.69172,-0.58695,0.42073,107.25,-0.39031,0.18632,0.90163,114.71,-0.60761,-0.78789,-0.10021,89.196
    5173 
    5174 > view matrix models
    5175 > #2,0.65444,-0.63502,0.41045,107.75,-0.39395,0.17697,0.90193,114.84,-0.64538,-0.75195,-0.13435,88.167
    5176 
    5177 > view matrix models
    5178 > #2,0.74125,-0.50299,0.44446,106.36,-0.46474,0.093202,0.88053,115.65,-0.48433,-0.85925,-0.16467,90.397
    5179 
    5180 > ui mousemode right "translate selected models"
    5181 
    5182 > view matrix models
    5183 > #2,0.74125,-0.50299,0.44446,122.67,-0.46474,0.093202,0.88053,118.02,-0.48433,-0.85925,-0.16467,90.501
    5184 
    5185 > ui mousemode right "rotate selected models"
    5186 
    5187 > view matrix models
    5188 > #2,0.83206,-0.25682,0.49165,119.4,-0.49196,0.067772,0.86798,118.23,-0.25624,-0.96408,-0.069956,93.922
    5189 
    5190 > ui mousemode right "translate selected models"
    5191 
    5192 > view matrix models
    5193 > #2,0.83206,-0.25682,0.49165,110.78,-0.49196,0.067772,0.86798,107.87,-0.25624,-0.96408,-0.069956,93.209
    5194 
    5195 > select subtract #2
    5196 
    5197 Nothing selected 
    5198 
    5199 > isolde start
    5200 
    5201 > set selectionWidth 4
    5202 
    5203 Forcefield cache not found or out of date. Regenerating from ffXML files. This
    5204 is normal if running ISOLDE for the first time, or after upgrading OpenMM. 
    5205 
    5206 Done loading forcefield 
    5207 
    5208 > isolde set simFidelityMode Medium/Medium
    5209 
    5210 ISOLDE: setting sim fidelity mode to Medium/Medium 
    5211 nonbonded_cutoff_distance = 0.900000 
    5212 use_gbsa = True 
    5213 gbsa_cutoff = 1.100000 
    5214 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5215 chains... 
    5216 ISOLDE: Corrected atom nomenclature of 277 residues in model #2 to IUPAC-IUB
    5217 standards. 
    5218 Chain information for fold_202411_11_fresh_model_0.cif 
    5219 --- 
    5220 Chain | Description 
    5221 2.2/A 2.2/B 2.2/C | . 
    5222  
    5223 Cached rota8000-val data not found. Regenerating from text file. This is
    5224 normal if running ISOLDE for the first time 
    5225 Cached rota8000-leu data not found. Regenerating from text file. This is
    5226 normal if running ISOLDE for the first time 
    5227 Cached rota8000-ile data not found. Regenerating from text file. This is
    5228 normal if running ISOLDE for the first time 
    5229 Cached rota8000-pro data not found. Regenerating from text file. This is
    5230 normal if running ISOLDE for the first time 
    5231 Cached rota8000-phe data not found. Regenerating from text file. This is
    5232 normal if running ISOLDE for the first time 
    5233 Cached rota8000-tyr data not found. Regenerating from text file. This is
    5234 normal if running ISOLDE for the first time 
    5235 Cached rota8000-trp data not found. Regenerating from text file. This is
    5236 normal if running ISOLDE for the first time 
    5237 Cached rota8000-ser data not found. Regenerating from text file. This is
    5238 normal if running ISOLDE for the first time 
    5239 Cached rota8000-thr data not found. Regenerating from text file. This is
    5240 normal if running ISOLDE for the first time 
    5241 Cached rota8000-cys data not found. Regenerating from text file. This is
    5242 normal if running ISOLDE for the first time 
    5243 Cached rota8000-met data not found. Regenerating from text file. This is
    5244 normal if running ISOLDE for the first time 
    5245 Cached rota8000-lys data not found. Regenerating from text file. This is
    5246 normal if running ISOLDE for the first time 
    5247 Cached rota8000-his data not found. Regenerating from text file. This is
    5248 normal if running ISOLDE for the first time 
    5249 Cached rota8000-arg data not found. Regenerating from text file. This is
    5250 normal if running ISOLDE for the first time 
    5251 Cached rota8000-asp data not found. Regenerating from text file. This is
    5252 normal if running ISOLDE for the first time 
    5253 Cached rota8000-asn data not found. Regenerating from text file. This is
    5254 normal if running ISOLDE for the first time 
    5255 Cached rota8000-gln data not found. Regenerating from text file. This is
    5256 normal if running ISOLDE for the first time 
    5257 Cached rota8000-glu data not found. Regenerating from text file. This is
    5258 normal if running ISOLDE for the first time 
    5259 Cached rama8000-cispro data not found. Regenerating from text file. This is
    5260 normal if running ISOLDE for the first time 
    5261 Cached rama8000-transpro data not found. Regenerating from text file. This is
    5262 normal if running ISOLDE for the first time 
    5263 Cached rama8000-gly-sym data not found. Regenerating from text file. This is
    5264 normal if running ISOLDE for the first time 
    5265 Cached rama8000-prepro-noGP data not found. Regenerating from text file. This
    5266 is normal if running ISOLDE for the first time 
    5267 Cached rama8000-ileval-nopreP data not found. Regenerating from text file.
    5268 This is normal if running ISOLDE for the first time 
    5269 Cached rama8000-general-noGPIVpreP data not found. Regenerating from text
    5270 file. This is normal if running ISOLDE for the first time 
    5271 ISOLDE: created disulfide bonds between the following residues: 
    5272 B125-B137; A125-A137; B484-B590; A120-A176; B355-B428; C484-C590; C181-C416;
    5273 A208-A219; A276-A309; B198-B227; B120-B176; A113-A185; B181-B416; B208-B219;
    5274 A181-A416; C120-C176; C125-C137; C198-C227; A484-A590; A362-A401; B583-B589;
    5275 A583-A589; C362-C401; A48-A68; B113-B185; B276-B309; C113-C185; C208-C219;
    5276 B362-B401; B48-B68; C48-C68; C276-C309; A198-A227; A355-A428; C355-C428;
    5277 C583-C589 
    5278 
    5279 > save "C:/Users/daniellem/Desktop/CryoEM workshop/Dissertation final 316W
    5280 > model/Isolde_316W.cxs"
    5281 
    5282 > select add #2
    5283 
    5284 16827 atoms, 17289 bonds, 2103 residues, 14 models selected 
    5285 
    5286 > select subtract #1
    5287 
    5288 16827 atoms, 17289 bonds, 2103 residues, 12 models selected 
    5289 
    5290 > select add #2
    5291 
    5292 16827 atoms, 17289 bonds, 2103 residues, 12 models selected 
    5293 
    5294 > select add #2
    5295 
    5296 16827 atoms, 17289 bonds, 2103 residues, 12 models selected 
    5297 
    5298 > select add #2
    5299 
    5300 16827 atoms, 17289 bonds, 2103 residues, 12 models selected 
    5301 
    5302 > select subtract #2.1
    5303 
    5304 16827 atoms, 17289 bonds, 2103 residues, 11 models selected 
    5305 
    5306 > select add #2
    5307 
    5308 16827 atoms, 17289 bonds, 2103 residues, 12 models selected 
    5309 
    5310 > save "C:/Users/daniellem/Desktop/CryoEM workshop/Dissertation final 316W
    5311 > model/Isolde_316W.cxs"
    5312 
    5313 ——— End of log from Wed Nov 13 16:05:25 2024 ———
    5314 
    5315 opened ChimeraX session 
    5316 
    5317 > ui mousemode right "rotate selected models"
    5318 
    5319 > ui mousemode right rotate
    5320 
    5321 > select add #2
    5322 
    5323 16827 atoms, 17289 bonds, 2103 residues, 15 models selected 
    5324 
    5325 > select add #2
    5326 
    5327 16827 atoms, 17289 bonds, 2103 residues, 15 models selected 
    5328 
    5329 > select subtract #2.1
    5330 
    5331 16827 atoms, 17289 bonds, 2103 residues, 14 models selected 
    5332 
    5333 > select #2
    5334 
    5335 16827 atoms, 17289 bonds, 2103 residues, 15 models selected 
    5336 
    5337 > select subtract #2.1
    5338 
    5339 16827 atoms, 17289 bonds, 2103 residues, 14 models selected 
    5340 
    5341 > select subtract #2.3
    5342 
    5343 16827 atoms, 17289 bonds, 2103 residues, 13 models selected 
    5344 
    5345 > ui mousemode right "move picked models"
    5346 
    5347 > ui mousemode right "rotate selected models"
    5348 
    5349 > stop isolde
    5350 
    5351 Expected fewer arguments 
    5352 
    5353 > select add #2
    5354 
    5355 16827 atoms, 17289 bonds, 2103 residues, 15 models selected 
    5356 
    5357 > deselect all
    5358 
    5359 Unknown command: deselect all 
    5360 
    5361 > deselect
    5362 
    5363 Unknown command: deselect 
    5364 
    5365 > ~select
    5366 
    5367 Nothing selected 
    5368 
    5369 > select add #2
    5370 
    5371 16827 atoms, 17289 bonds, 2103 residues, 15 models selected 
    5372 
    5373 > view matrix models
    5374 > #2,0.99575,-0.015637,0.090722,-4.4839,0.0014031,0.98793,0.15488,-10.121,-0.092049,-0.1541,0.98376,27.255
    5375 
    5376 > view matrix models
    5377 > #2,0.78145,0.090022,-0.61745,60.114,0.035975,0.98139,0.18861,-15.794,0.62294,-0.1696,0.76367,-35.953
    5378 
    5379 > view matrix models
    5380 > #2,0.71305,0.10657,-0.69297,71.605,-0.27531,0.95155,-0.13695,45.9,0.6448,0.28843,0.70784,-81.031
    5381 
    5382 > view matrix models
    5383 > #2,0.89446,0.22625,-0.38569,16.741,-0.28596,0.95254,-0.10439,44.648,0.34377,0.20366,0.9167,-53.518
    5384 
    5385 > view matrix models
    5386 > #2,0.94709,0.31726,0.048693,-29.856,-0.31545,0.94804,-0.041416,43.885,-0.059302,0.023864,0.99795,4.4102
    5387 
    5388 > ui mousemode right "move picked models"
    5389 
    5390 > view matrix models
    5391 > #2.2,1,5.6986e-16,-2.4286e-16,-9.5814,8.4893e-16,1,1.9082e-16,0.6637,-9.7145e-17,3.1225e-17,1,-0.41905
    5392 
    5393 > select add #2
    5394 
    5395 16827 atoms, 17289 bonds, 2103 residues, 15 models selected 
    5396 
    5397 > ~select
    5398 
    5399 Nothing selected 
    5400 
    5401 > select add #1
    5402 
    5403 2 models selected 
    5404 
    5405 > ui mousemode right "rotate selected models"
    5406 
    5407 > view matrix models
    5408 > #1,0.99565,0.0035698,-0.093147,8.6107,0.0040819,0.99664,0.081827,-7.5691,0.093126,-0.081851,0.99228,-0.9953
    5409 
    5410 > view matrix models
    5411 > #1,0.99643,0.0065949,-0.084219,7.3734,0.0032596,0.9932,0.11634,-10.247,0.084414,-0.1162,0.98963,4.0265
    5412 
    5413 > ui mousemode right rotate
    5414 
    5415 > ui mousemode right "rotate selected models"
    5416 
    5417 > view matrix models
    5418 > #1,0.98436,-0.16331,-0.066065,25.793,0.1716,0.97369,0.14993,-30.516,0.039841,-0.15892,0.98649,14.137
    5419 
    5420 > select subtract #1
    5421 
    5422 Nothing selected 
    5423 
    5424 > ~select
    5425 
    5426 Nothing selected 
    5427 
    5428 > select add #2
    5429 
    5430 16827 atoms, 17289 bonds, 2103 residues, 15 models selected 
    5431 
    5432 > ui mousemode right select
    5433 
    5434 > ~select
    5435 
    5436 Nothing selected 
    5437 
    5438 > ~select
    5439 
    5440 Nothing selected 
    5441 
    5442 > clipper associate #1 toModel #2
    5443 
    5444 Opened DeepEMhancer_Danielle_4_9.mrc as #2.1.1.1, grid size 128,128,128, pixel
    5445 1.66, shown at step 1, values float32 
    5446 
    5447 > clipper associate #1 toModel #2
    5448 
    5449 > volume #2.1.1.1 level 0.01818
    5450 
    5451 > volume #2.1.1.1 level 0.006197
    5452 
    5453 > volume #2.1.1.1 level 0.01884
    5454 
    5455 > volume #2.1.1.1 level 0.01019
    5456 
    5457 > volume #2.1.1.1 level 0.0042
    5458 
    5459 > fitmap #2.2 inMap #2.1.1.1
    5460 
    5461 Fit molecule fold_202411_11_fresh_model_0.cif (#2.2) to map
    5462 DeepEMhancer_Danielle_4_9.mrc (#2.1.1.1) using 16827 atoms 
    5463 average map value = 0, steps = 24 
    5464 shifted from previous position = 0 
    5465 rotated from previous position = 0 degrees 
    5466 atoms outside contour = 16827, contour level = 0.0042003 
    5467  
    5468 Position of fold_202411_11_fresh_model_0.cif (#2.2) relative to
    5469 DeepEMhancer_Danielle_4_9.mrc (#2.1.1.1) coordinates: 
    5470 Matrix rotation and translation 
    5471 1.00000000 0.00000000 0.00000000 0.00000000 
    5472 0.00000000 1.00000000 0.00000000 0.00000000 
    5473 0.00000000 0.00000000 1.00000000 0.00000000 
    5474 Axis 0.00000000 0.00000000 1.00000000 
    5475 Axis point 0.00000000 0.00000000 0.00000000 
    5476 Rotation angle (degrees) 0.00000000 
    5477 Shift along axis 0.00000000 
    5478  
    5479 
    5480 > volume #2.1.1.1 color #ff6f82
    5481 
    5482 > volume #2.1.1.1 orthoplanes xyz positionPlanes 64,64,64 style image region
    5483 > all
    5484 
    5485 > mousemode rightMode "move planes"
    5486 
    5487 > volume #2.1.1.1 orthoplanes xyz positionPlanes 64,64,64 style image region
    5488 > all
    5489 
    5490 > mousemode rightMode "move planes"
    5491 
    5492 > volume #2.1.1.1 orthoplanes xyz positionPlanes 64,64,64 style image region
    5493 > all
    5494 
    5495 > mousemode rightMode "move planes"
    5496 
    5497 > volume #2.1.1.1 orthoplanes xyz positionPlanes 64,64,64 style image region
    5498 > all
    5499 
    5500 > mousemode rightMode "move planes"
    5501 
    5502 > volume planes z style image imageMode "full region"
    5503 
    5504 > mousemode rightMode "move planes"
    5505 
    5506 > volume style mesh
    5507 
    5508 [Repeated 1 time(s)]
    5509 
    5510 > volume #2.1.1.1 style image region all imageMode "tilted slab"
    5511 > tiltedSlabAxis 0,0,1 tiltedSlabOffset 106.1 tiltedSlabSpacing 1.658
    5512 > tiltedSlabPlaneCount 10
    5513 
    5514 > mousemode rightMode "rotate slab"
    5515 
    5516 > volume planes z style image imageMode "full region"
    5517 
    5518 > mousemode rightMode "move planes"
    5519 
    5520 > volume #2.1.1.1 style image region all imageMode "tilted slab"
    5521 > tiltedSlabAxis 0,0,1 tiltedSlabOffset 106.1 tiltedSlabSpacing 1.658
    5522 > tiltedSlabPlaneCount 10
    5523 
    5524 > mousemode rightMode "rotate slab"
    5525 
    5526 > volume style mesh
    5527 
    5528 > volume #2.1.1.1 change image level -0.0001408,0 level 0.1705,0.8 level
    5529 > 2.096,1
    5530 
    5531 > volume #2.1.1.1 level 0.3019
    5532 
    5533 > volume #2.1.1.1 orthoplanes xyz positionPlanes 64,64,64 style image region
    5534 > all
    5535 
    5536 > mousemode rightMode "move planes"
    5537 
    5538 > volume #2.1.1.1 orthoplanes xyz positionPlanes 64,64,64 style image region
    5539 > all
    5540 
    5541 > mousemode rightMode "move planes"
    5542 
    5543 > volume zone #2.1.1.1 nearAtoms #2.2 range 9.95
    5544 
    5545 > volume region all imageMode "full region"
    5546 
    5547 > volume unzone
    5548 
    5549 > mousemode rightMode "crop volume"
    5550 
    5551 > close #2.1.1.1
    5552 
    5553 > select #1
    5554 
    5555 Nothing selected 
    5556 
    5557 > clipper associate #1 toModel #2
    5558 
    5559 > close session
    5560 
    5561 > open
    5562 > C:/Users/daniellem/Downloads/fold_202411_11_fresh/fold_202411_11_fresh_model_1.cif
    5563 
    5564 Chain information for fold_202411_11_fresh_model_1.cif #1 
    5565 --- 
    5566 Chain | Description 
    5567 A B C | . 
    5568  
    5569 
    5570 > open "C:/Users/daniellem/Desktop/CryoEM
    5571 > workshop/DeepEMhancer_Danielle_4_9.mrc"
    5572 
    5573 Opened DeepEMhancer_Danielle_4_9.mrc as #2, grid size 128,128,128, pixel 1.66,
    5574 shown at level 0.171, step 1, values float32 
    5575 
    5576 > clipper associate #2 toModel #1
    5577 
    5578 Opened DeepEMhancer_Danielle_4_9.mrc as #1.1.1.1, grid size 128,128,128, pixel
    5579 1.66, shown at level 0, step 1, values float32 
    5580 Chain information for fold_202411_11_fresh_model_1.cif 
    5581 --- 
    5582 Chain | Description 
    5583 1.2/A 1.2/B 1.2/C | . 
    5584  
    5585 
    5586 > zoom
    5587 
    5588 Pixel size at center of rotation is 0.252 
    5589 
    5590 > zoom
    5591 
    5592 Pixel size at center of rotation is 0.252 
    5593 
    5594 > volume #1.1.1.1 level 2.378e-07
    5595 
    5596 > isolde start
    5597 
    5598 > set selectionWidth 4
    5599 
    5600 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5601 chains... 
    5602 ISOLDE: Corrected atom nomenclature of 286 residues in model #1.2 to IUPAC-IUB
    5603 standards. 
    5604 Done loading forcefield 
    5605 
    5606 > isolde set simFidelityMode Medium/Medium
    5607 
    5608 ISOLDE: setting sim fidelity mode to Medium/Medium 
    5609 nonbonded_cutoff_distance = 0.900000 
    5610 use_gbsa = True 
    5611 gbsa_cutoff = 1.100000 
    5612 
    5613 > volume #1.1.1.1 region 0,2,0,11,15,12
    5614 
    5615 > set bgColor white
    5616 
    5617 > set bgColor #ffffff00
    5618 
    5619 > select add #1
    5620 
    5621 16827 atoms, 17253 bonds, 2103 residues, 15 models selected 
    5622 
    5623 > select add #1.2
    5624 
    5625 16827 atoms, 17253 bonds, 2103 residues, 15 models selected 
    5626 
    5627 > select add #1
    5628 
    5629 16827 atoms, 17253 bonds, 2103 residues, 15 models selected 
    5630 
    5631 > select add #1.2
    5632 
    5633 16827 atoms, 17253 bonds, 2103 residues, 15 models selected 
    5634 
    5635 > ~select
    5636 
    5637 Nothing selected 
    5638 
    5639 > view #1.1.1.1.2 clip false
    5640 
    5641 No displayed objects specified. 
    5642 
    5643 > view #1.1.1.1.2 clip false
    5644 
    5645 No displayed objects specified. 
    5646 
    5647 > view #1.1.1.1.2 clip false
    5648 
    5649 No displayed objects specified. 
    5650 
    5651 > show #1.1.1.1.2 target m
    5652 
    5653 > hide #1.1.1.1.2 target m
    5654 
    5655 > close #1.1.1.1.2
    5656 
    5657 > hide target m
    5658 
    5659 [Repeated 1 time(s)]
    5660 
    5661 > close
    5662 
    5663 > open
    5664 > C:\Users\daniellem\Downloads\fold_202411_11_fresh\fold_202411_11_fresh_model_1.cif
    5665 > format mmcif
    5666 
    5667 Chain information for fold_202411_11_fresh_model_1.cif #1 
    5668 --- 
    5669 Chain | Description 
    5670 A B C | . 
    5671  
    5672 
    5673 > open "C:/Users/daniellem/Desktop/CryoEM workshop/Dissertation final 316W
    5674 > model/DeepEMhancer_Danielle_4_9.mrc"
    5675 
    5676 Opened DeepEMhancer_Danielle_4_9.mrc as #2, grid size 128,128,128, pixel 1.66,
    5677 shown at level 0.171, step 1, values float32 
    5678 
    5679 > volume #2 region 0,6,0,127,127,127
    5680 
    5681 > select add #1
    5682 
    5683 16827 atoms, 17253 bonds, 2103 residues, 1 model selected 
    5684 
    5685 > volume #2 region 0,9,0,127,127,127
    5686 
    5687 > volume #2 region 0,31,0,127,127,127
    5688 
    5689 > volume #2 region 0,2,0,127,127,127
    5690 
    5691 > volume #2 region 2,2,0,127,127,127
    5692 
    5693 > volume #2 region 0,2,0,127,127,127
    5694 
    5695 > ui mousemode right "rotate selected models"
    5696 
    5697 > view matrix models
    5698 > #1,0.66525,-0.10274,0.73952,-3.3498,-0.70987,0.21988,0.66913,6.6393,-0.23135,-0.9701,0.073343,18.122
    5699 
    5700 > view matrix models
    5701 > #1,0.66436,-0.098392,0.74091,-3.4057,-0.70806,0.23457,0.66606,6.4683,-0.23933,-0.96711,0.086172,18.055
    5702 
    5703 > view matrix models
    5704 > #1,0.73489,-0.0012862,0.67819,-3.9016,-0.49398,0.68416,0.53657,1.0277,-0.46468,-0.72933,0.50214,14.374
    5705 
    5706 > view matrix models
    5707 > #1,0.48401,-0.29693,0.82315,-0.71801,-0.38327,0.77371,0.50446,-0.064179,-0.78666,-0.55965,0.26068,14.723
    5708 
    5709 > view matrix models
    5710 > #1,0.45881,-0.3301,0.82494,-0.27877,-0.38342,0.76399,0.51895,-0.033803,-0.80155,-0.5544,0.22396,14.879
    5711 
    5712 > view matrix models
    5713 > #1,0.58787,-0.42542,0.68806,1.4842,-0.33441,0.64668,0.68555,-0.022276,-0.7366,-0.63311,0.2379,15.786
    5714 
    5715 > ui mousemode right "move picked models"
    5716 
    5717 > ui mousemode right "translate selected models"
    5718 
    5719 > view matrix models
    5720 > #1,0.58787,-0.42542,0.68806,89.581,-0.33441,0.64668,0.68555,125,-0.7366,-0.63311,0.2379,28.389
    5721 
    5722 > ui mousemode right "rotate selected models"
    5723 
    5724 > view matrix models
    5725 > #1,0.69323,-0.26637,0.66969,87.572,-0.39958,0.63127,0.6647,125.4,-0.59981,-0.72838,0.33118,28.789
    5726 
    5727 > view matrix models
    5728 > #1,0.68673,-0.25861,0.67936,87.446,-0.37136,0.67861,0.63371,124.95,-0.6249,-0.68747,0.36998,28.176
    5729 
    5730 > ui mousemode right "translate selected models"
    5731 
    5732 > view matrix models
    5733 > #1,0.68673,-0.25861,0.67936,89.311,-0.37136,0.67861,0.63371,114.2,-0.6249,-0.68747,0.36998,81.84
    5734 
    5735 > ui mousemode right "move picked models"
    5736 
    5737 > view matrix models #2,1,0,0,-3.1953,0,1,0,8.6026,0,0,1,-26.98
    5738 
    5739 > ui mousemode right "rotate selected models"
    5740 
    5741 > view matrix models
    5742 > #1,0.71675,0.27424,0.64114,83.225,-0.50588,0.8373,0.20739,115.63,-0.47996,-0.47299,0.73887,76.524
    5743 
    5744 > view matrix models
    5745 > #1,-0.12708,0.40435,0.90573,81.28,-0.68048,0.62882,-0.3762,118.42,-0.72166,-0.66414,0.19524,82.162
    5746 
    5747 > ui mousemode right "translate selected atoms"
    5748 
    5749 > ui mousemode right "move picked models"
    5750 
    5751 > view matrix models #2,1,0,0,74.792,0,1,0,-99.562,0,0,1,-42.19
    5752 
    5753 > ui mousemode right "rotate selected models"
    5754 
    5755 > view matrix models
    5756 > #1,-0.064661,0.98545,0.15717,76.985,0.45325,0.16932,-0.87516,123.44,-0.88904,0.014648,-0.4576,79.166
    5757 
    5758 > view matrix models
    5759 > #1,0.20735,0.96008,0.18775,76.042,0.080933,0.17443,-0.98134,125.61,-0.97491,0.21868,-0.041534,73.66
    5760 
    5761 > view matrix models
    5762 > #1,0.52905,0.84743,0.044425,76.673,-0.40974,0.30094,-0.86113,125.75,-0.74312,0.43737,0.50644,66.766
    5763 
    5764 > view matrix models
    5765 > #1,0.66252,0.74875,-0.021062,77.638,-0.32016,0.25765,-0.91165,126.14,-0.67717,0.61073,0.41042,64.875
    5766 
    5767 > ui mousemode right "move picked models"
    5768 
    5769 > select subtract #1
    5770 
    5771 Nothing selected 
    5772 
    5773 > select add #2
    5774 
    5775 2 models selected 
    5776 
    5777 > ui mousemode right "rotate selected models"
    5778 
    5779 > view matrix models
    5780 > #2,0.36714,-0.13671,-0.92007,246.56,-0.46121,0.83223,-0.3077,-0.0059004,0.80777,0.53731,0.24249,-124.99
    5781 
    5782 > view matrix models
    5783 > #2,0.52398,-0.03222,-0.85112,210.75,-0.71814,0.52057,-0.46182,77.879,0.45795,0.85321,0.24963,-120.19
    5784 
    5785 > view matrix models
    5786 > #2,0.30109,-0.16473,-0.93926,258.99,-0.83534,0.42952,-0.3431,90.528,0.45995,0.8879,-0.0082803,-100.69
    5787 
    5788 > ui mousemode right "move picked models"
    5789 
    5790 > view matrix models
    5791 > #2,0.30109,-0.16473,-0.93926,198.41,-0.83534,0.42952,-0.3431,218.9,0.45995,0.8879,-0.0082803,-85.192
    5792 
    5793 > ui mousemode right "rotate selected models"
    5794 
    5795 > view matrix models
    5796 > #2,0.18816,-0.14391,-0.97154,212.04,-0.86165,0.45054,-0.23362,209.62,0.47133,0.88108,-0.039224,-82.925
    5797 
    5798 > view matrix models
    5799 > #2,0.18599,-0.16879,-0.96794,214.7,-0.86627,0.43672,-0.24261,212.49,0.46367,0.88362,-0.064991,-79.971
    5800 
    5801 > view matrix models
    5802 > #2,0.1282,-0.10727,-0.98593,216.22,-0.87167,0.46198,-0.16361,203.12,0.47303,0.88038,-0.034277,-83.494
    5803 
    5804 > select subtract #2
    5805 
    5806 Nothing selected 
    5807 
    5808 > fitmap map
    5809 
    5810 Missing or invalid "atomsOrMap" argument: invalid objects specifier 
    5811 
    5812 > fitmap
    5813 
    5814 Missing or invalid "atomsOrMap" argument: empty atom specifier 
    5815 
    5816 > fitmap
    5817 
    5818 Missing or invalid "atomsOrMap" argument: empty atom specifier 
    5819 
    5820 > ui mousemode right "move picked models"
    5821 
    5822 > view matrix models
    5823 > #1,0.66252,0.74875,-0.021062,121.8,-0.32016,0.25765,-0.91165,144.36,-0.67717,0.61073,0.41042,58.518
    5824 
    5825 > ui mousemode right "translate selected models"
    5826 
    5827 > ui mousemode right "rotate selected models"
    5828 
    5829 > roll
    5830 
    5831 > stop
    5832 
    5833 > ui mousemode right "translate selected models"
    5834 
    5835 > undo
    5836 
    5837 > redo
    5838 
    5839 > ui mousemode right rotate
    5840 
    5841 > ui mousemode right "move picked models"
    5842 
    5843 > volume #2 level 0.2875
    5844 
    5845 > volume #2 level 0.06889
    5846 
    5847 > clipper associate #2 toModel #1
    5848 
    5849 Opened DeepEMhancer_Danielle_4_9.mrc as #1.1.1.1, grid size 128,128,128, pixel
    5850 1.66, shown at level 0.0215, step 1, values float32 
    5851 Chain information for fold_202411_11_fresh_model_1.cif 
    5852 --- 
    5853 Chain | Description 
    5854 1.2/A 1.2/B 1.2/C | . 
    5855  
    5856 
    5857 > volume #1.1.1.1 level 0.02788
    5858 
    5859 > color #1.1.1.1 #1dffd9ff models
    5860 
    5861 > set bgColor black
    5862 
    5863 > set bgColor transparent
    5864 
    5865 > save "C:/Users/daniellem/Desktop/CryoEM workshop/Dissertation final 316W
    5866 > model/316W_diss_1.cxs"
    5867 
    5868 > select add #1
    5869 
    5870 16827 atoms, 17253 bonds, 2103 residues, 7 models selected 
    5871 
    5872 > select subtract #1
    5873 
    5874 Nothing selected 
    5875 
    5876 > select add #1.2
    5877 
    5878 16827 atoms, 17253 bonds, 2103 residues, 1 model selected 
    5879 
    5880 > select subtract #1.2
    5881 
    5882 Nothing selected 
    5883 
    5884 > select add #1.2
    5885 
    5886 16827 atoms, 17253 bonds, 2103 residues, 1 model selected 
    5887 
    5888 > select subtract #1.2
    5889 
    5890 Nothing selected 
    5891 
    5892 > close #1
    5893 
    5894 > open
    5895 > C:/Users/daniellem/Downloads/fold_202411_11_fresh/fold_202411_11_fresh_model_0.cif
    5896 
    5897 Chain information for fold_202411_11_fresh_model_0.cif #1 
    5898 --- 
    5899 Chain | Description 
    5900 A B C | . 
    5901  
    5902 
    5903 > open "C:/Users/daniellem/Desktop/CryoEM
    5904 > workshop/DeepEMhancer_Danielle_4_9.mrc"
    5905 
    5906 Opened DeepEMhancer_Danielle_4_9.mrc as #2, grid size 128,128,128, pixel 1.66,
    5907 shown at level 0.171, step 1, values float32 
    5908 
    5909 > fitmap #1 inMap #2
    5910 
    5911 Fit molecule fold_202411_11_fresh_model_0.cif (#1) to map
    5912 DeepEMhancer_Danielle_4_9.mrc (#2) using 16827 atoms 
    5913 average map value = 0.07522, steps = 844 
    5914 shifted from previous position = 175 
    5915 rotated from previous position = 54.2 degrees 
    5916 atoms outside contour = 14504, contour level = 0.17065 
    5917  
    5918 Position of fold_202411_11_fresh_model_0.cif (#1) relative to
    5919 DeepEMhancer_Danielle_4_9.mrc (#2) coordinates: 
    5920 Matrix rotation and translation 
    5921 0.64792760 -0.62354966 -0.43746502 96.82197592 
    5922 0.74386964 0.64153909 0.18731140 110.82058535 
    5923 0.16385295 -0.44678117 0.87951055 97.73764625 
    5924 Axis -0.39073889 -0.37054262 0.84262761 
    5925 Axis point -58.82632784 190.65888686 0.00000000 
    5926 Rotation angle (degrees) 54.23312860 
    5927 Shift along axis 3.46057824 
    5928  
    5929 
    5930 > select add #1
    5931 
    5932 16827 atoms, 17253 bonds, 2103 residues, 1 model selected 
    5933 
    5934 > ui mousemode right "rotate selected models"
    5935 
    5936 > view matrix models
    5937 > #1,0.99713,0.047993,-0.058537,89.39,0.058353,0.0052358,0.99828,118.88,0.048217,-0.99883,0.0024202,98.244
    5938 
    5939 > view matrix models
    5940 > #1,0.8632,-0.0503,0.50236,89.98,-0.50441,-0.12817,0.8539,116.49,0.021437,-0.99048,-0.13601,96.623
    5941 
    5942 > ui mousemode right "move picked models"
    5943 
    5944 > ui mousemode right "translate selected models"
    5945 
    5946 > view matrix models
    5947 > #1,0.8632,-0.0503,0.50236,89.369,-0.50441,-0.12817,0.8539,114.78,0.021437,-0.99048,-0.13601,96.141
    5948 
    5949 > view matrix models
    5950 > #1,0.8632,-0.0503,0.50236,51.119,-0.50441,-0.12817,0.8539,133.03,0.021437,-0.99048,-0.13601,97.843
    5951 
    5952 > view matrix models
    5953 > #1,0.8632,-0.0503,0.50236,11.287,-0.50441,-0.12817,0.8539,109.46,0.021437,-0.99048,-0.13601,101.2
    5954 
    5955 > ui mousemode right "rotate selected models"
    5956 
    5957 > ui mousemode right "translate selected models"
    5958 
    5959 > view matrix models
    5960 > #1,0.8632,-0.0503,0.50236,73.284,-0.50441,-0.12817,0.8539,117.42,0.021437,-0.99048,-0.13601,99.791
    5961 
    5962 > view matrix models
    5963 > #1,0.8632,-0.0503,0.50236,70.626,-0.50441,-0.12817,0.8539,117.88,0.021437,-0.99048,-0.13601,99.742
    5964 
    5965 > view matrix models
    5966 > #1,0.8632,-0.0503,0.50236,121.46,-0.50441,-0.12817,0.8539,114.41,0.021437,-0.99048,-0.13601,99.952
    5967 
    5968 > ui mousemode right "rotate selected models"
    5969 
    5970 > view matrix models
    5971 > #1,0.8253,-0.28919,0.48503,125.06,-0.54795,-0.20249,0.81163,115.12,-0.1365,-0.93561,-0.32557,97.173
    5972 
    5973 > view matrix models
    5974 > #1,0.8233,-0.30662,0.47766,125.28,-0.55534,-0.26109,0.78958,115.9,-0.11739,-0.91532,-0.38523,96.754
    5975 
    5976 > view matrix models
    5977 > #1,0.69075,0.22823,0.68613,117.35,-0.64306,-0.24003,0.72723,114.32,0.33067,-0.94355,-0.019031,102.83
    5978 
    5979 > view matrix models
    5980 > #1,0.74225,-0.1389,0.65557,123.62,-0.66974,-0.12076,0.73271,112.12,-0.022608,-0.98292,-0.18266,99.155
    5981 
    5982 > select subtract #1
    5983 
    5984 Nothing selected 
    5985 
    5986 > select add #2
    5987 
    5988 2 models selected 
    5989 
    5990 > view matrix models
    5991 > #2,0.9995,0.0074953,0.030735,-3.5727,-0.008337,0.99959,0.027347,-1.4932,-0.030517,-0.027589,0.99915,6.62
    5992 
    5993 > ui mousemode right "translate selected models"
    5994 
    5995 > view matrix models
    5996 > #2,0.9995,0.0074953,0.030735,23.671,-0.008337,0.99959,0.027347,4.4973,-0.030517,-0.027589,0.99915,5.6597
    5997 
    5998 > ui mousemode right rotate
    5999 
    6000 > ui mousemode right "rotate selected models"
    6001 
    6002 > view matrix models
    6003 > #2,0.97796,-0.014894,-0.20826,50.426,0.05381,0.98174,0.18248,-14.843,0.20174,-0.18966,0.9609,0.28557
    6004 
    6005 > ui mousemode right "translate selected models"
    6006 
    6007 > view matrix models
    6008 > #2,0.97796,-0.014894,-0.20826,53.888,0.05381,0.98174,0.18248,-19.638,0.20174,-0.18966,0.9609,2.2334
    6009 
    6010 > ui mousemode right "rotate selected models"
    6011 
    6012 > view matrix models
    6013 > #2,0.98566,-0.0079441,-0.16857,48.617,0.044096,0.97631,0.21182,-20.604,0.1629,-0.21622,0.96266,9.4578
    6014 
    6015 > view matrix models
    6016 > #2,0.95291,-0.0044741,-0.30321,64.289,0.14917,0.87746,0.45586,-44.084,0.26402,-0.47962,0.83681,38.3
    6017 
    6018 > view matrix models
    6019 > #2,0.92066,-0.20279,-0.33356,92.584,0.33574,0.8473,0.41154,-58.164,0.19917,-0.49088,0.84816,45.955
    6020 
    6021 > ui mousemode right "translate selected models"
    6022 
    6023 > view matrix models
    6024 > #2,0.92066,-0.20279,-0.33356,83.602,0.33574,0.8473,0.41154,-56.096,0.19917,-0.49088,0.84816,44.316
    6025 
    6026 > select add #2
    6027 
    6028 3 models selected 
    6029 
    6030 > ui mousemode right translate
    6031 
    6032 > ui mousemode right "translate selected atoms"
    6033 
    6034 > ui mousemode right "move picked models"
    6035 
    6036 > ui mousemode right select
    6037 
    6038 > select subtract #2
    6039 
    6040 Nothing selected 
    6041 
    6042 > ui mousemode right "translate selected models"
    6043 
    6044 > select add #2
    6045 
    6046 3 models selected 
    6047 
    6048 > select subtract #2
    6049 
    6050 Nothing selected 
    6051 
    6052 > ui mousemode right "move picked models"
    6053 
    6054 > ui mousemode right "rotate selected models"
    6055 
    6056 > ui mousemode right "translate selected models"
    6057 
    6058 > select add #1
    6059 
    6060 16827 atoms, 17253 bonds, 2103 residues, 1 model selected 
    6061 
    6062 > view matrix models
    6063 > #1,0.74225,-0.1389,0.65557,125.13,-0.66974,-0.12076,0.73271,107.13,-0.022608,-0.98292,-0.18266,95.753
    6064 
    6065 > select subtract #1
    6066 
    6067 Nothing selected 
    6068 
    6069 > isolde start
    6070 
    6071 > clipper associate #2 toModel #1
    6072 
    6073 Opened DeepEMhancer_Danielle_4_9.mrc as #1.1.1.1, grid size 128,128,128, pixel
    6074 1.66, shown at level 0.191, step 1, values float32 
    6075 Chain information for fold_202411_11_fresh_model_0.cif 
    6076 --- 
    6077 Chain | Description 
    6078 1.2/A 1.2/B 1.2/C | . 
    6079  
    6080 
    6081 > isolde start
    6082 
    6083 > set bgColor white
    6084 
    6085 > set bgColor #ffffff00
    6086 
    6087 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6088 chains... 
    6089 ISOLDE: Corrected atom nomenclature of 277 residues in model #1.2 to IUPAC-IUB
    6090 standards. 
    6091 ISOLDE: created disulfide bonds between the following residues: 
    6092 B125-B137; B276-B309; C181-C416; B48-B68; C276-C309; C355-C428; A355-A428;
    6093 A362-A401; C484-C590; A276-A309; A181-A416; B583-B589; A125-A137; C113-C185;
    6094 B484-B590; C583-C589; B362-B401; B113-B185; C208-C219; A48-A68; C48-C68;
    6095 A113-A185; C198-C227; B208-B219; B181-B416; A583-A589; A208-A219; B198-B227;
    6096 B355-B428; C125-C137; A198-A227; C362-C401; B120-B176; A484-A590; A120-A176;
    6097 C120-C176 
    6098 
    6099 > set silhouettes false
    6100 
    6101 > ~select
    6102 
    6103 Nothing selected 
    6104 
    6105 > set silhouettes false
    6106 
    6107 > delete ~protein
    6108 
    6109 > addh
    6110 
    6111 Summary of feedback from adding hydrogens to fold_202411_11_fresh_model_0.cif
    6112 #1.2 
    6113 --- 
    6114 notes | Termini for fold_202411_11_fresh_model_0.cif (#1.2) chain A determined from SEQRES records 
    6115 Termini for fold_202411_11_fresh_model_0.cif (#1.2) chain B determined from
    6116 SEQRES records 
    6117 Termini for fold_202411_11_fresh_model_0.cif (#1.2) chain C determined from
    6118 SEQRES records 
    6119 Chain-initial residues that are actual N termini: /A MET 1, /B MET 1, /C MET 1 
    6120 Chain-initial residues that are not actual N termini: 
    6121 Chain-final residues that are actual C termini: /A HIS 677, /B HIS 677, /C HIS
    6122 677 
    6123 Chain-final residues that are not actual C termini: 
    6124 1630 hydrogen bonds 
    6125 15663 hydrogens added 
    6126  
    6127 
    6128 > select #1
    6129 
    6130 31698 atoms, 32088 bonds, 2031 residues, 16 models selected 
    6131 
    6132 > clipper isolate #1 maskRadius 16
    6133 
    6134 > view matrix models #1,1,0,0,7.0869,0,1,0,-0.39389,0,0,1,2.602
    6135 
    6136 > ui mousemode right "rotate selected models"
    6137 
    6138 > view matrix models
    6139 > #1,0.95983,0.26995,-0.076557,-10.994,-0.24059,0.93216,0.27052,16.377,0.14439,-0.24124,0.95966,14.374
    6140 
    6141 > view matrix models
    6142 > #1,0.9876,-0.040147,-0.15174,25.439,0.021063,0.99189,-0.12534,6.9079,0.15554,0.1206,0.98044,-28.405
    6143 
    6144 > view matrix models
    6145 > #1,0.99163,-0.083691,-0.098314,25.632,0.09889,0.98189,0.16158,-23.443,0.08301,-0.16995,0.98195,12.399
    6146 
    6147 > hide atoms
    6148 
    6149 > save "C:/Users/daniellem/Desktop/CryoEM workshop/Dissertation final 316W
    6150 > model/316W_diss_1.cxs"
    6151 
    6152 > show ~HC
    6153 
    6154 > isolde restrain distances "#1/A,G"
    6155 
    6156 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6157 chains... 
    6158 
    6159 > isolde restrain distances "#1/B,F"
    6160 
    6161 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6162 chains... 
    6163 
    6164 > select #1
    6165 
    6166 31698 atoms, 32088 bonds, 2031 residues, 17 models selected 
    6167 
    6168 > isolde sim start sel
    6169 
    6170 ISOLDE: started sim 
    6171 
    6172 > ui mousemode right "isolde tug selection"
    6173 
    6174 > select /B,F@CA
    6175 
    6176 677 atoms, 677 residues, 1 model selected 
    6177 
    6178 > select /A,H@CA
    6179 
    6180 677 atoms, 677 residues, 1 model selected 
    6181 
    6182 > select /A,B,C
    6183 
    6184 31698 atoms, 32088 bonds, 2031 residues, 1 model selected 
    6185 
    6186 > ui hideFloating toggle
    6187 
    6188 [Repeated 1 time(s)]
    6189 
    6190 > ~select
    6191 
    6192 Nothing selected 
    6193 
    6194 > ~select
    6195 
    6196 Nothing selected 
    6197 
    6198 > isolde sim pause
    6199 
    6200 > select #1
    6201 
    6202 31698 atoms, 32088 bonds, 2031 residues, 21 models selected 
    6203 
    6204 > ui mousemode right "move picked models"
    6205 
    6206 > ui mousemode right "translate selected models"
    6207 
    6208 > view matrix models
    6209 > #1,0.99163,-0.083691,-0.098314,22.128,0.09889,0.98189,0.16158,-23.116,0.08301,-0.16995,0.98195,10.873
    6210 
    6211 > ui mousemode right "move picked models"
    6212 
    6213 > isolde sim resume
    6214 
    6215 > select A
    6216 
    6217 Expected an objects specifier or a keyword 
    6218 
    6219 > select /A
    6220 
    6221 10566 atoms, 10696 bonds, 677 residues, 1 model selected 
    6222 
    6223 > view matrix models
    6224 > #1.2,1,3.4694e-17,9.7145e-17,-0.57951,2.0817e-17,1,-5.5511e-17,0.97731,0,-8.3267e-17,1,0.16641
    6225 
    6226 > view matrix models
    6227 > #1.2,1,6.0715e-17,1.1102e-16,-3.7199,1.3878e-17,1,-1.3878e-16,0.75132,1.3878e-17,-8.3267e-17,1,-1.2135
    6228 
    6229 > view matrix models
    6230 > #1.2,1,-5.6725e-16,-4.1633e-17,-4.514,-4.4929e-16,1,-4.1633e-16,6.3267,-5.4123e-16,2.498e-16,1,0.76486
    6231 
    6232 > select /A
    6233 
    6234 10566 atoms, 10696 bonds, 677 residues, 1 model selected 
    6235 
    6236 > ui mousemode right "isolde tug selection"
    6237 
    6238 > ~select
    6239 
    6240 Nothing selected 
    6241 
    6242 > ~select
    6243 
    6244 Nothing selected 
    6245 
    6246 > chains
    6247 
    6248 Unknown command: chains 
    6249 
    6250 > chains/
    6251 
    6252 Unknown command: chains/ 
    6253 
    6254 > /
    6255 
    6256 Unknown command: / 
    6257 
    6258 > select add #1.2
    6259 
    6260 31698 atoms, 32088 bonds, 2031 residues, 14 models selected 
    6261 
    6262 > select add #1.1.1
    6263 
    6264 31698 atoms, 32088 bonds, 2031 residues, 17 models selected 
    6265 
    6266 > select add #1
    6267 
    6268 31698 atoms, 32088 bonds, 2031 residues, 21 models selected 
    6269 
    6270 > select subtract #1.1.1
    6271 
    6272 31698 atoms, 32088 bonds, 2031 residues, 16 models selected 
    6273 
    6274 > select add #1.2
    6275 
    6276 31698 atoms, 32088 bonds, 2031 residues, 17 models selected 
    6277 
    6278 > select subtract #1.3
    6279 
    6280 31698 atoms, 32088 bonds, 2031 residues, 15 models selected 
    6281 
    6282 > select add #1.2
    6283 
    6284 31698 atoms, 32088 bonds, 2031 residues, 16 models selected 
    6285 
    6286 > ~select
    6287 
    6288 Nothing selected 
    6289 
    6290 > select add #1.1.1
    6291 
    6292 4 models selected 
    6293 
    6294 > ui mousemode right "translate selected models"
    6295 
    6296 > view matrix models
    6297 > #1.1.1,1,-5.0307e-17,2.6368e-16,0.51738,-1.1796e-16,1,-6.3838e-16,-5.7231,6.9389e-17,1.3878e-16,1,0.10217
    6298 
    6299 > ui mousemode right "rotate selected models"
    6300 
    6301 > view matrix models
    6302 > #1.1.1,0.98912,-0.14707,-0.0035996,18.306,0.1471,0.9884,0.037814,-25.16,-0.0020035,-0.037932,0.99928,4.5772
    6303 
    6304 > view matrix models
    6305 > #1.1.1,0.86583,-0.49895,-0.037256,74.567,0.49933,0.85694,0.1278,-60.241,-0.031839,-0.12925,0.9911,18.874
    6306 
    6307 > view matrix models
    6308 > #1.1.1,0.9799,-0.19939,-0.0062574,25.388,0.19945,0.97857,0.05124,-31.446,-0.0040934,-0.051458,0.99867,6.3666
    6309 
    6310 > view matrix models
    6311 > #1.1.1,0.99258,0.12162,-0.0012517,-11.88,-0.1216,0.99208,-0.031353,12.279,-0.0025713,0.031273,0.99951,-2.9923
    6312 
    6313 > view matrix models
    6314 > #1.1.1,0.9998,-0.020045,-0.0001605,2.7614,0.020046,0.99979,0.0051605,-8.5229,5.7023e-05,-0.0051627,0.99999,0.66479
    6315 
    6316 > view matrix models
    6317 > #1.1.1,0.99427,0.018958,-0.1052,8.6924,-0.019023,0.99982,0.00038549,-3.5055,0.10519,0.0016179,0.99445,-11.917
    6318 
    6319 > view matrix models
    6320 > #1.1.1,0.98647,-0.12373,-0.10757,25.525,0.12676,0.99169,0.021827,-21.678,0.10397,-0.035167,0.99396,-7.6817
    6321 
    6322 > ui mousemode right "translate selected models"
    6323 
    6324 > view matrix models
    6325 > #1.1.1,0.98647,-0.12373,-0.10757,30.35,0.12676,0.99169,0.021827,-13.388,0.10397,-0.035167,0.99396,-6.3941
    6326 
    6327 > ~select
    6328 
    6329 Nothing selected 
    6330 
    6331 > ui mousemode right rotate
    6332 
    6333 > ~select
    6334 
    6335 Nothing selected 
    6336 
    6337 > ui mousemode right "move picked models"
    6338 
    6339 > ui mousemode right "translate selected models"
    6340 
    6341 > select add #1.1.1
    6342 
    6343 4 models selected 
    6344 
    6345 > view matrix models
    6346 > #1.1.1,0.98647,-0.12373,-0.10757,33.311,0.12676,0.99169,0.021827,-17.645,0.10397,-0.035167,0.99396,-5.3485
    6347 
    6348 > select subtract #1.1.1
    6349 
    6350 Nothing selected 
    6351 
    6352 > ~select
    6353 
    6354 Nothing selected 
    6355 
    6356 > select /A
    6357 
    6358 10566 atoms, 10696 bonds, 677 residues, 1 model selected 
    6359 
    6360 > select /c
    6361 
    6362 10566 atoms, 10696 bonds, 677 residues, 1 model selected 
    6363 
    6364 > select /C
    6365 
    6366 10566 atoms, 10696 bonds, 677 residues, 1 model selected 
    6367 
    6368 > ui mousemode right "isolde tug selection"
    6369 
    6370 [Repeated 1 time(s)]
    6371 
    6372 > select /A
    6373 
    6374 10566 atoms, 10696 bonds, 677 residues, 1 model selected 
    6375 
    6376 > select /B
    6377 
    6378 10566 atoms, 10696 bonds, 677 residues, 1 model selected 
    6379 
    6380 > ~select
    6381 
    6382 Nothing selected 
    6383 
    6384 > select /B
    6385 
    6386 10566 atoms, 10696 bonds, 677 residues, 1 model selected 
    6387 
    6388 > ui mousemode right "isolde tug selection"
    6389 
    6390 [Repeated 1 time(s)]
    6391 
    6392 > ~select
    6393 
    6394 Nothing selected 
    6395 
    6396 > ui mousemode right "translate selected models"
    6397 
    6398 > hide atoms
    6399 
    6400 > show atoms
    6401 
    6402 > select add #1.2
    6403 
    6404 31698 atoms, 32088 bonds, 2031 residues, 14 models selected 
    6405 
    6406 > select add #1.2
    6407 
    6408 31698 atoms, 32088 bonds, 2031 residues, 14 models selected 
    6409 
    6410 > select add #1.2
    6411 
    6412 31698 atoms, 32088 bonds, 2031 residues, 14 models selected 
    6413 
    6414 > ~select
    6415 
    6416 Nothing selected 
    6417 
    6418 > select add #1.2
    6419 
    6420 31698 atoms, 32088 bonds, 2031 residues, 14 models selected 
    6421 
    6422 > select add #1.2
    6423 
    6424 31698 atoms, 32088 bonds, 2031 residues, 14 models selected 
    6425 
    6426 > ~select
    6427 
    6428 Nothing selected 
    6429 
    6430 > select add #1.1.1
    6431 
    6432 4 models selected 
    6433 
    6434 > ui mousemode right "rotate selected models"
    6435 
    6436 > view matrix models
    6437 > #1.1.1,0.95386,-0.26947,-0.13243,55.464,0.27868,0.95872,0.056438,-35.107,0.11175,-0.090739,0.98958,0.24681
    6438 
    6439 > view matrix models
    6440 > #1.1.1,0.86816,-0.46394,-0.17625,90.975,0.48447,0.86928,0.098215,-53.367,0.10765,-0.17066,0.97943,10.451
    6441 
    6442 > view matrix models
    6443 > #1.1.1,0.72836,-0.29898,-0.61652,129.46,0.4368,0.89585,0.081589,-49.148,0.52792,-0.32872,0.7831,-3.8769
    6444 
    6445 > ui mousemode right "move picked models"
    6446 
    6447 > ui mousemode right "rotate selected models"
    6448 
    6449 > view matrix models
    6450 > #1.1.1,0.85765,-0.27788,-0.43269,95.102,0.37939,0.90992,0.16766,-51.769,0.34712,-0.30795,0.88582,5.8133
    6451 
    6452 > view matrix models
    6453 > #1.1.1,0.648,-0.46752,-0.60126,156.1,0.73192,0.6006,0.32181,-73.411,0.21067,-0.64861,0.73138,73.494
    6454 
    6455 > view matrix models
    6456 > #1.1.1,0.73896,-0.48429,-0.4684,135.09,0.66602,0.63004,0.39933,-75.941,0.10172,-0.60706,0.78812,76.608
    6457 
    6458 > view matrix models
    6459 > #1.1.1,0.81976,-0.49328,-0.29098,110.35,0.57131,0.66885,0.47565,-75.991,-0.040005,-0.55616,0.83011,83.909
    6460 
    6461 > view matrix models
    6462 > #1.1.1,0.85593,-0.49206,-0.15894,93.907,0.49686,0.69745,0.51643,-74.068,-0.14326,-0.52099,0.84145,91.195
    6463 
    6464 > view matrix models
    6465 > #1.1.1,0.82413,-0.49343,-0.2781,108.68,0.56418,0.67165,0.48019,-75.872,-0.050157,-0.55263,0.83191,84.555
    6466 
    6467 > isolde sim pause
    6468 
    6469 > view matrix models
    6470 > #1.1.1,0.97678,-0.058664,-0.20603,36.223,0.14599,0.88615,0.43981,-46.365,0.15678,-0.45967,0.87414,46.017
    6471 
    6472 > ui mousemode right "move picked models"
    6473 
    6474 > view matrix models
    6475 > #1.2,1,-2.5847e-16,5.8287e-16,-6.4386,-2.949e-16,1,-1.9429e-16,6.691,-5.8287e-16,-3.3307e-16,1,-0.1065
    6476 
    6477 > isolde sim resume
    6478 
    6479 > ui mousemode right "translate selected models"
    6480 
    6481 > ui mousemode right rotate
    6482 
    6483 > ~select
    6484 
    6485 Nothing selected 
    6486 
    6487 > ~select
    6488 
    6489 Nothing selected 
    6490 
    6491 > ~select
    6492 
    6493 Nothing selected 
    6494 
    6495 > select /A
    6496 
    6497 10566 atoms, 10696 bonds, 677 residues, 1 model selected 
    6498 
    6499 > ui mousemode right "isolde tug selection"
    6500 
    6501 > select add #1
    6502 
    6503 31698 atoms, 32088 bonds, 2031 residues, 21 models selected 
    6504 
    6505 > select add #1
    6506 
    6507 31698 atoms, 32088 bonds, 2031 residues, 21 models selected 
    6508 
    6509 > select add #1
    6510 
    6511 31698 atoms, 32088 bonds, 2031 residues, 21 models selected 
    6512 
    6513 > ~select
    6514 
    6515 Nothing selected 
    6516 
    6517 > select /C
    6518 
    6519 10566 atoms, 10696 bonds, 677 residues, 1 model selected 
    6520 
    6521 > ~select
    6522 
    6523 Nothing selected 
    6524 
    6525 > rotate 30
    6526 
    6527 Unknown command: rotate 30 
    6528 
    6529 > rotate x 30
    6530 
    6531 Unknown command: rotate x 30 
    6532 
    6533 > turn 30
    6534 
    6535 Expected an axis vector or a keyword 
    6536 
    6537 > help help:user
    6538 
    6539 > turn y 30
    6540 
    6541 [Repeated 1 time(s)]
    6542 
    6543 > select /B
    6544 
    6545 10566 atoms, 10696 bonds, 677 residues, 1 model selected 
    6546 
    6547 > isolde sim pause
    6548 
    6549 > select
    6550 
    6551 31698 atoms, 32088 bonds, 2031 residues, 21 models selected 
    6552 
    6553 > ~select
    6554 
    6555 Nothing selected 
    6556 
    6557 > select add #1.1.1
    6558 
    6559 4 models selected 
    6560 
    6561 > ui mousemode right "translate selected models"
    6562 
    6563 > view matrix models
    6564 > #1.1.1,0.97678,-0.058664,-0.20603,36.443,0.14599,0.88615,0.43981,-47.931,0.15678,-0.45967,0.87414,43.486
    6565 
    6566 > ui mousemode right "rotate selected models"
    6567 
    6568 > view matrix models
    6569 > #1.1.1,0.93878,-0.072118,-0.33688,54.349,0.21104,0.89328,0.39687,-52.488,0.27231,-0.44367,0.85382,29.924
    6570 
    6571 > select add #1.1.1
    6572 
    6573 4 models selected 
    6574 
    6575 > select subtract #1.1.1
    6576 
    6577 Nothing selected 
    6578 
    6579 > ~select
    6580 
    6581 Nothing selected 
    6582 
    6583 > select add #1.2
    6584 
    6585 31698 atoms, 32088 bonds, 2031 residues, 14 models selected 
    6586 
    6587 > view matrix models
    6588 > #1.2,0.98911,-0.053048,-0.13729,11.919,0.074733,0.98461,0.15797,-14.293,0.1268,-0.16651,0.97785,3.142
    6589 
    6590 > view matrix models
    6591 > #1.2,0.98948,0.016677,-0.14373,5.221,0.0055592,0.98822,0.15294,-5.6294,0.14458,-0.15213,0.97773,-0.5454
    6592 
    6593 > view matrix models
    6594 > #1.2,0.98685,0.0096553,-0.16132,7.7496,0.012471,0.99069,0.13558,-5.287,0.16113,-0.13581,0.97754,-4.2736
    6595 
    6596 > view matrix models
    6597 > #1.2,0.98778,0.006444,-0.15574,7.4975,0.02641,0.97778,0.20796,-11.769,0.15362,-0.20953,0.96566,5.2641
    6598 
    6599 > view matrix models
    6600 > #1.2,0.8593,-0.4953,-0.12761,72.895,0.51115,0.8227,0.24878,-59.558,-0.018234,-0.27901,0.96012,34.297
    6601 
    6602 > view matrix models
    6603 > #1.2,0.98861,0.0059789,-0.15036,6.9894,0.020811,0.98418,0.17597,-9.0452,0.14903,-0.17709,0.97284,1.8859
    6604 
    6605 > ui mousemode right "move picked models"
    6606 
    6607 > ui mousemode right "translate selected models"
    6608 
    6609 > view matrix models
    6610 > #1.2,0.98861,0.0059789,-0.15036,15.778,0.020811,0.98418,0.17597,-19.022,0.14903,-0.17709,0.97284,-8.0522
    6611 
    6612 > view matrix models
    6613 > #1.2,0.98861,0.0059789,-0.15036,12.948,0.020811,0.98418,0.17597,-19.55,0.14903,-0.17709,0.97284,-4.7808
    6614 
    6615 > view matrix models
    6616 > #1.2,0.98861,0.0059789,-0.15036,8.191,0.020811,0.98418,0.17597,-20.422,0.14903,-0.17709,0.97284,-0.82751
    6617 
    6618 > isolde sim resume
    6619 
    6620 > select /A
    6621 
    6622 10566 atoms, 10696 bonds, 677 residues, 1 model selected 
    6623 
    6624 > ui mousemode right "isolde tug selection"
    6625 
    6626 [Repeated 1 time(s)]
    6627 
    6628 > ~select
    6629 
    6630 Nothing selected 
    6631 
    6632 > volume #1.1.1.1 level 0.1688
    6633 
    6634 > volume #1.1.1.1 level 0.1198
    6635 
    6636 > ui mousemode right "isolde tug selection"
    6637 
    6638 > isolde sim stop
    6639 
    6640 Sim termination reason: None 
    6641 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6642 chains... 
    6643 ISOLDE: Corrected atom nomenclature of 61 residues in model #1.2 to IUPAC-IUB
    6644 standards. 
    6645 ISOLDE: stopped sim 
    6646 
    6647 > isolde start
    6648 
    6649 > save "C:/Users/daniellem/Desktop/CryoEM workshop/Dissertation final 316W
    6650 > model/316W_diss_2.cxs"
    6651 
    6652 ——— End of log from Wed Nov 13 21:10:41 2024 ———
    6653 
    6654 opened ChimeraX session 
    6655 
    6656 > clipper isolate #1 maskRadius 16
    6657 
    6658 > isolde start
    6659 
    6660 > isolde sim start /A-C
    6661 
    6662 ISOLDE: started sim 
    6663 
    6664 > ui mousemode right "isolde tug atom"
    6665 
    6666 > ~select
    6667 
    6668 Nothing selected 
    6669 
    6670 > select /B
    6671 
    6672 10566 atoms, 10696 bonds, 677 residues, 1 model selected 
    6673 
    6674 > ui mousemode right "isolde tug selection"
    6675 
    6676 > select
    6677 
    6678 31698 atoms, 32088 bonds, 2031 residues, 24 models selected 
    6679 
    6680 > ~select
    6681 
    6682 Nothing selected 
    6683 
    6684 > select /A
    6685 
    6686 10566 atoms, 10696 bonds, 677 residues, 1 model selected 
    6687 
    6688 > ui mousemode right "isolde tug selection"
    6689 
    6690 [Repeated 1 time(s)]
    6691 
    6692 > isolde restrain distances "#1/C"
    6693 
    6694 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6695 chains... 
    6696 ISOLDE: Corrected atom nomenclature of 8 residues in model #1.2 to IUPAC-IUB
    6697 standards. 
    6698 
    6699 > ~select
    6700 
    6701 Nothing selected 
    6702 
    6703 > ui mousemode right "isolde tug residue"
    6704 
    6705 > help help:user
    6706 
    6707 > select add #1.2
    6708 
    6709 31698 atoms, 32088 bonds, 2031 residues, 17 models selected 
    6710 
    6711 > show ribbons
    6712 
    6713 > ~select
    6714 
    6715 Nothing selected 
    6716 
    6717 > ui mousemode right swapaa
    6718 
    6719 > swapaa mousemode /C:59 VAL
    6720 
    6721 Sim termination reason: coord length mismatch 
    6722 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6723 chains... 
    6724 ISOLDE: Corrected atom nomenclature of 17 residues in model #1.2 to IUPAC-IUB
    6725 standards. 
    6726 ISOLDE: stopped sim 
    6727 
    6728 > save "C:/Users/daniellem/Desktop/CryoEM workshop/Dissertation final 316W
    6729 > model/316W_diss_3.cxs"
    6730 
    6731 [Repeated 1 time(s)]
    6732 
    6733 ——— End of log from Wed Nov 13 21:59:07 2024 ———
    6734 
    6735 opened ChimeraX session 
    6736 
    6737 > open "D:\Dissertation final 316W model\316W_diss_3.cxs" format session
    6738 
    6739 Opened DeepEMhancer_Danielle_4_9.mrc as #1.1.1.1, grid size 128,128,128, pixel
    6740 1.66, shown at level 0.12, step 1, values float32 
    6741 Unable to restore session, resetting. 
    6742  
    6743 Traceback (most recent call last): 
    6744 File "C:\Program Files\ChimeraX 1.9rc202411130312\bin\Lib\site-
    6745 packages\chimerax\core\session.py", line 854, in restore 
    6746 self.add_state_manager(name, data) 
    6747 File "C:\Program Files\ChimeraX 1.9rc202411130312\bin\Lib\site-
    6748 packages\chimerax\core\session.py", line 647, in add_state_manager 
    6749 raise ValueError( 
    6750 ValueError: container "Isolde Residue Stepper Manager" of type "<class
    6751 'NoneType'>" does not have snapshot methods and does not have clear method 
    6752  
    6753 Log from Wed Nov 13 21:59:07 2024UCSF ChimeraX version: 1.8 (2024-06-10) 
    6754 © 2016-2024 Regents of the University of California. All rights reserved. 
    6755 
    6756 > open "C:\Users\daniellem\Desktop\CryoEM workshop\Dissertation final 316W
    6757 > model\316W_diss_2.cxs" format session
    6758 
    6759 Opened DeepEMhancer_Danielle_4_9.mrc as #1.1.1.1, grid size 128,128,128, pixel
    6760 1.66, shown at level 0.12, step 1, values float32 
    6761 Log from Wed Nov 13 21:10:41 2024UCSF ChimeraX version: 1.8 (2024-06-10) 
    6762 © 2016-2024 Regents of the University of California. All rights reserved. 
    6763 
    6764 > open "C:\Users\daniellem\Desktop\CryoEM workshop\Dissertation final 316W
    6765 > model\Isolde_316W.cxs" format session
    6766 
    6767 Opened DeepEMhancer_Danielle_4_9.mrc as #1, grid size 128,128,128, pixel 1.66,
    6768 shown at level 0.171, step 1, values float32 
    6769 Log from Wed Nov 13 16:05:25 2024 Startup Messages 
    6770 --- 
    6771 note | available bundle cache has not been initialized yet 
    6772  
    6773 UCSF ChimeraX version: 1.8 (2024-06-10) 
    6774 © 2016-2024 Regents of the University of California. All rights reserved. 
    6775 How to cite UCSF ChimeraX 
    6776 
    6777 > open
    6778 > C:\\\Users\\\daniellem\\\Downloads\\\ChimeraX_ISOLDE-1.8-cp311-cp311-win_amd64.whl
    6779 
    6780 Unrecognized file suffix '.whl' 
    6781 
    6782 > open "C:/Users/daniellem/Desktop/CryoEM
    6783 > workshop/DeepEMhancer_Danielle_4_9.mrc"
    6784 
    6785 Opened DeepEMhancer_Danielle_4_9.mrc as #1, grid size 128,128,128, pixel 1.66,
    6786 shown at level 0.171, step 1, values float32 
    6787 
    6788 > open
    6789 > C:/Users/daniellem/Downloads/fold_202411_11_fresh/fold_202411_11_fresh_model_0.cif
    6790 
    6791 Chain information for fold_202411_11_fresh_model_0.cif #2 
    6792 --- 
    6793 Chain | Description 
    6794 A B C | . 
    6795  
    6796 
    6797 > fitmap #2 inMap #1
    6798 
    6799 Fit molecule fold_202411_11_fresh_model_0.cif (#2) to map
    6800 DeepEMhancer_Danielle_4_9.mrc (#1) using 16827 atoms 
    6801 average map value = 0.07522, steps = 844 
    6802 shifted from previous position = 175 
    6803 rotated from previous position = 54.2 degrees 
    6804 atoms outside contour = 14504, contour level = 0.17065 
    6805  
    6806 Position of fold_202411_11_fresh_model_0.cif (#2) relative to
    6807 DeepEMhancer_Danielle_4_9.mrc (#1) coordinates: 
    6808 Matrix rotation and translation 
    6809 0.64792760 -0.62354966 -0.43746502 96.82197592 
    6810 0.74386964 0.64153909 0.18731140 110.82058535 
    6811 0.16385295 -0.44678117 0.87951055 97.73764625 
    6812 Axis -0.39073889 -0.37054262 0.84262761 
    6813 Axis point -58.82632784 190.65888686 0.00000000 
    6814 Rotation angle (degrees) 54.23312860 
    6815 Shift along axis 3.46057824 
    6816  
    6817 
    6818 > select add #2
    6819 
    6820 16827 atoms, 17253 bonds, 2103 residues, 1 model selected 
    6821 
    6822 > ui mousemode right "translate selected models"
    6823 
    6824 > ui mousemode right "rotate selected models"
    6825 
    6826 > view matrix models
    6827 > #2,0.90908,-0.24195,0.33917,98.645,-0.23659,0.3703,0.89828,112.27,-0.34293,-0.89685,0.27939,96.701
    6828 
    6829 > view matrix models
    6830 > #2,0.53124,-0.06761,0.84452,97.684,-0.82947,0.1615,0.5347,110.22,-0.17254,-0.98455,0.029713,96.843
    6831 
    6832 > view matrix models
    6833 > #2,0.41491,-0.042433,0.90887,97.121,-0.90723,-0.095219,0.40971,113.02,0.069157,-0.99455,-0.078003,97.834
    6834 
    6835 > view matrix models
    6836 > #2,0.75288,0.027834,0.65757,97.316,-0.63298,-0.24308,0.73502,119.44,0.1803,-0.96961,-0.16539,97.49
    6837 
    6838 > ui mousemode right "move picked models"
    6839 
    6840 > ui mousemode right "rotate selected models"
    6841 
    6842 > view matrix models
    6843 > #2,0.87103,0.31614,0.37598,92.913,-0.28071,-0.30778,0.90911,123.97,0.40312,-0.8974,-0.17934,97.549
    6844 
    6845 > view matrix models
    6846 > #2,0.91536,0.086966,0.39313,97.148,-0.39835,0.053566,0.91567,117.07,0.058573,-0.99477,0.083675,97.517
    6847 
    6848 > view matrix models
    6849 > #2,0.69172,-0.58695,0.42073,107.25,-0.39031,0.18632,0.90163,114.71,-0.60761,-0.78789,-0.10021,89.196
    6850 
    6851 > view matrix models
    6852 > #2,0.65444,-0.63502,0.41045,107.75,-0.39395,0.17697,0.90193,114.84,-0.64538,-0.75195,-0.13435,88.167
    6853 
    6854 > view matrix models
    6855 > #2,0.74125,-0.50299,0.44446,106.36,-0.46474,0.093202,0.88053,115.65,-0.48433,-0.85925,-0.16467,90.397
    6856 
    6857 > ui mousemode right "translate selected models"
    6858 
    6859 > view matrix models
    6860 > #2,0.74125,-0.50299,0.44446,122.67,-0.46474,0.093202,0.88053,118.02,-0.48433,-0.85925,-0.16467,90.501
    6861 
    6862 > ui mousemode right "rotate selected models"
    6863 
    6864 > view matrix models
    6865 > #2,0.83206,-0.25682,0.49165,119.4,-0.49196,0.067772,0.86798,118.23,-0.25624,-0.96408,-0.069956,93.922
    6866 
    6867 > ui mousemode right "translate selected models"
    6868 
    6869 > view matrix models
    6870 > #2,0.83206,-0.25682,0.49165,110.78,-0.49196,0.067772,0.86798,107.87,-0.25624,-0.96408,-0.069956,93.209
    6871 
    6872 > select subtract #2
    6873 
    6874 Nothing selected 
    6875 
    6876 > isolde start
    6877 
    6878 > set selectionWidth 4
    6879 
    6880 Forcefield cache not found or out of date. Regenerating from ffXML files. This
    6881 is normal if running ISOLDE for the first time, or after upgrading OpenMM. 
    6882 
    6883 Done loading forcefield 
    6884 
    6885 > isolde set simFidelityMode Medium/Medium
    6886 
    6887 ISOLDE: setting sim fidelity mode to Medium/Medium 
    6888 nonbonded_cutoff_distance = 0.900000 
    6889 use_gbsa = True 
    6890 gbsa_cutoff = 1.100000 
    6891 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6892 chains... 
    6893 ISOLDE: Corrected atom nomenclature of 277 residues in model #2 to IUPAC-IUB
    6894 standards. 
    6895 Chain information for fold_202411_11_fresh_model_0.cif 
    6896 --- 
    6897 Chain | Description 
    6898 2.2/A 2.2/B 2.2/C | . 
    6899  
    6900 Cached rota8000-val data not found. Regenerating from text file. This is
    6901 normal if running ISOLDE for the first time 
    6902 Cached rota8000-leu data not found. Regenerating from text file. This is
    6903 normal if running ISOLDE for the first time 
    6904 Cached rota8000-ile data not found. Regenerating from text file. This is
    6905 normal if running ISOLDE for the first time 
    6906 Cached rota8000-pro data not found. Regenerating from text file. This is
    6907 normal if running ISOLDE for the first time 
    6908 Cached rota8000-phe data not found. Regenerating from text file. This is
    6909 normal if running ISOLDE for the first time 
    6910 Cached rota8000-tyr data not found. Regenerating from text file. This is
    6911 normal if running ISOLDE for the first time 
    6912 Cached rota8000-trp data not found. Regenerating from text file. This is
    6913 normal if running ISOLDE for the first time 
    6914 Cached rota8000-ser data not found. Regenerating from text file. This is
    6915 normal if running ISOLDE for the first time 
    6916 Cached rota8000-thr data not found. Regenerating from text file. This is
    6917 normal if running ISOLDE for the first time 
    6918 Cached rota8000-cys data not found. Regenerating from text file. This is
    6919 normal if running ISOLDE for the first time 
    6920 Cached rota8000-met data not found. Regenerating from text file. This is
    6921 normal if running ISOLDE for the first time 
    6922 Cached rota8000-lys data not found. Regenerating from text file. This is
    6923 normal if running ISOLDE for the first time 
    6924 Cached rota8000-his data not found. Regenerating from text file. This is
    6925 normal if running ISOLDE for the first time 
    6926 Cached rota8000-arg data not found. Regenerating from text file. This is
    6927 normal if running ISOLDE for the first time 
    6928 Cached rota8000-asp data not found. Regenerating from text file. This is
    6929 normal if running ISOLDE for the first time 
    6930 Cached rota8000-asn data not found. Regenerating from text file. This is
    6931 normal if running ISOLDE for the first time 
    6932 Cached rota8000-gln data not found. Regenerating from text file. This is
    6933 normal if running ISOLDE for the first time 
    6934 Cached rota8000-glu data not found. Regenerating from text file. This is
    6935 normal if running ISOLDE for the first time 
    6936 Cached rama8000-cispro data not found. Regenerating from text file. This is
    6937 normal if running ISOLDE for the first time 
    6938 Cached rama8000-transpro data not found. Regenerating from text file. This is
    6939 normal if running ISOLDE for the first time 
    6940 Cached rama8000-gly-sym data not found. Regenerating from text file. This is
    6941 normal if running ISOLDE for the first time 
    6942 Cached rama8000-prepro-noGP data not found. Regenerating from text file. This
    6943 is normal if running ISOLDE for the first time 
    6944 Cached rama8000-ileval-nopreP data not found. Regenerating from text file.
    6945 This is normal if running ISOLDE for the first time 
    6946 Cached rama8000-general-noGPIVpreP data not found. Regenerating from text
    6947 file. This is normal if running ISOLDE for the first time 
    6948 ISOLDE: created disulfide bonds between the following residues: 
    6949 B125-B137; A125-A137; B484-B590; A120-A176; B355-B428; C484-C590; C181-C416;
    6950 A208-A219; A276-A309; B198-B227; B120-B176; A113-A185; B181-B416; B208-B219;
    6951 A181-A416; C120-C176; C125-C137; C198-C227; A484-A590; A362-A401; B583-B589;
    6952 A583-A589; C362-C401; A48-A68; B113-B185; B276-B309; C113-C185; C208-C219;
    6953 B362-B401; B48-B68; C48-C68; C276-C309; A198-A227; A355-A428; C355-C428;
    6954 C583-C589 
    6955 
    6956 > save "C:/Users/daniellem/Desktop/CryoEM workshop/Dissertation final 316W
    6957 > model/Isolde_316W.cxs"
    6958 
    6959 > select add #2
    6960 
    6961 16827 atoms, 17289 bonds, 2103 residues, 14 models selected 
    6962 
    6963 > select subtract #1
    6964 
    6965 16827 atoms, 17289 bonds, 2103 residues, 12 models selected 
    6966 
    6967 > select add #2
    6968 
    6969 16827 atoms, 17289 bonds, 2103 residues, 12 models selected 
    6970 
    6971 > select add #2
    6972 
    6973 16827 atoms, 17289 bonds, 2103 residues, 12 models selected 
    6974 
    6975 > select add #2
    6976 
    6977 16827 atoms, 17289 bonds, 2103 residues, 12 models selected 
    6978 
    6979 > select subtract #2.1
    6980 
    6981 16827 atoms, 17289 bonds, 2103 residues, 11 models selected 
    6982 
    6983 > select add #2
    6984 
    6985 16827 atoms, 17289 bonds, 2103 residues, 12 models selected 
    6986 
    6987 > save "C:/Users/daniellem/Desktop/CryoEM workshop/Dissertation final 316W
    6988 > model/Isolde_316W.cxs"
    6989 
    6990 ——— End of log from Wed Nov 13 16:05:25 2024 ———
    6991 
    6992 opened ChimeraX session 
    6993 
    6994 > ui mousemode right "rotate selected models"
    6995 
    6996 > ui mousemode right rotate
    6997 
    6998 > select add #2
    6999 
    7000 16827 atoms, 17289 bonds, 2103 residues, 15 models selected 
    7001 
    7002 > select add #2
    7003 
    7004 16827 atoms, 17289 bonds, 2103 residues, 15 models selected 
    7005 
    7006 > select subtract #2.1
    7007 
    7008 16827 atoms, 17289 bonds, 2103 residues, 14 models selected 
    7009 
    7010 > select #2
    7011 
    7012 16827 atoms, 17289 bonds, 2103 residues, 15 models selected 
    7013 
    7014 > select subtract #2.1
    7015 
    7016 16827 atoms, 17289 bonds, 2103 residues, 14 models selected 
    7017 
    7018 > select subtract #2.3
    7019 
    7020 16827 atoms, 17289 bonds, 2103 residues, 13 models selected 
    7021 
    7022 > ui mousemode right "move picked models"
    7023 
    7024 > ui mousemode right "rotate selected models"
    7025 
    7026 > stop isolde
    7027 
    7028 Expected fewer arguments 
    7029 
    7030 > select add #2
    7031 
    7032 16827 atoms, 17289 bonds, 2103 residues, 15 models selected 
    7033 
    7034 > deselect all
    7035 
    7036 Unknown command: deselect all 
    7037 
    7038 > deselect
    7039 
    7040 Unknown command: deselect 
    7041 
    7042 > ~select
    7043 
    7044 Nothing selected 
    7045 
    7046 > select add #2
    7047 
    7048 16827 atoms, 17289 bonds, 2103 residues, 15 models selected 
    7049 
    7050 > view matrix models
    7051 > #2,0.99575,-0.015637,0.090722,-4.4839,0.0014031,0.98793,0.15488,-10.121,-0.092049,-0.1541,0.98376,27.255
    7052 
    7053 > view matrix models
    7054 > #2,0.78145,0.090022,-0.61745,60.114,0.035975,0.98139,0.18861,-15.794,0.62294,-0.1696,0.76367,-35.953
    7055 
    7056 > view matrix models
    7057 > #2,0.71305,0.10657,-0.69297,71.605,-0.27531,0.95155,-0.13695,45.9,0.6448,0.28843,0.70784,-81.031
    7058 
    7059 > view matrix models
    7060 > #2,0.89446,0.22625,-0.38569,16.741,-0.28596,0.95254,-0.10439,44.648,0.34377,0.20366,0.9167,-53.518
    7061 
    7062 > view matrix models
    7063 > #2,0.94709,0.31726,0.048693,-29.856,-0.31545,0.94804,-0.041416,43.885,-0.059302,0.023864,0.99795,4.4102
    7064 
    7065 > ui mousemode right "move picked models"
    7066 
    7067 > view matrix models
    7068 > #2.2,1,5.6986e-16,-2.4286e-16,-9.5814,8.4893e-16,1,1.9082e-16,0.6637,-9.7145e-17,3.1225e-17,1,-0.41905
    7069 
    7070 > select add #2
    7071 
    7072 16827 atoms, 17289 bonds, 2103 residues, 15 models selected 
    7073 
    7074 > ~select
    7075 
    7076 Nothing selected 
    7077 
    7078 > select add #1
    7079 
    7080 2 models selected 
    7081 
    7082 > ui mousemode right "rotate selected models"
    7083 
    7084 > view matrix models
    7085 > #1,0.99565,0.0035698,-0.093147,8.6107,0.0040819,0.99664,0.081827,-7.5691,0.093126,-0.081851,0.99228,-0.9953
    7086 
    7087 > view matrix models
    7088 > #1,0.99643,0.0065949,-0.084219,7.3734,0.0032596,0.9932,0.11634,-10.247,0.084414,-0.1162,0.98963,4.0265
    7089 
    7090 > ui mousemode right rotate
    7091 
    7092 > ui mousemode right "rotate selected models"
    7093 
    7094 > view matrix models
    7095 > #1,0.98436,-0.16331,-0.066065,25.793,0.1716,0.97369,0.14993,-30.516,0.039841,-0.15892,0.98649,14.137
    7096 
    7097 > select subtract #1
    7098 
    7099 Nothing selected 
    7100 
    7101 > ~select
    7102 
    7103 Nothing selected 
    7104 
    7105 > select add #2
    7106 
    7107 16827 atoms, 17289 bonds, 2103 residues, 15 models selected 
    7108 
    7109 > ui mousemode right select
    7110 
    7111 > ~select
    7112 
    7113 Nothing selected 
    7114 
    7115 > ~select
    7116 
    7117 Nothing selected 
    7118 
    7119 > clipper associate #1 toModel #2
    7120 
    7121 Opened DeepEMhancer_Danielle_4_9.mrc as #2.1.1.1, grid size 128,128,128, pixel
    7122 1.66, shown at step 1, values float32 
    7123 
    7124 > clipper associate #1 toModel #2
    7125 
    7126 > volume #2.1.1.1 level 0.01818
    7127 
    7128 > volume #2.1.1.1 level 0.006197
    7129 
    7130 > volume #2.1.1.1 level 0.01884
    7131 
    7132 > volume #2.1.1.1 level 0.01019
    7133 
    7134 > volume #2.1.1.1 level 0.0042
    7135 
    7136 > fitmap #2.2 inMap #2.1.1.1
    7137 
    7138 Fit molecule fold_202411_11_fresh_model_0.cif (#2.2) to map
    7139 DeepEMhancer_Danielle_4_9.mrc (#2.1.1.1) using 16827 atoms 
    7140 average map value = 0, steps = 24 
    7141 shifted from previous position = 0 
    7142 rotated from previous position = 0 degrees 
    7143 atoms outside contour = 16827, contour level = 0.0042003 
    7144  
    7145 Position of fold_202411_11_fresh_model_0.cif (#2.2) relative to
    7146 DeepEMhancer_Danielle_4_9.mrc (#2.1.1.1) coordinates: 
    7147 Matrix rotation and translation 
    7148 1.00000000 0.00000000 0.00000000 0.00000000 
    7149 0.00000000 1.00000000 0.00000000 0.00000000 
    7150 0.00000000 0.00000000 1.00000000 0.00000000 
    7151 Axis 0.00000000 0.00000000 1.00000000 
    7152 Axis point 0.00000000 0.00000000 0.00000000 
    7153 Rotation angle (degrees) 0.00000000 
    7154 Shift along axis 0.00000000 
    7155  
    7156 
    7157 > volume #2.1.1.1 color #ff6f82
    7158 
    7159 > volume #2.1.1.1 orthoplanes xyz positionPlanes 64,64,64 style image region
    7160 > all
    7161 
    7162 > mousemode rightMode "move planes"
    7163 
    7164 > volume #2.1.1.1 orthoplanes xyz positionPlanes 64,64,64 style image region
    7165 > all
    7166 
    7167 > mousemode rightMode "move planes"
    7168 
    7169 > volume #2.1.1.1 orthoplanes xyz positionPlanes 64,64,64 style image region
    7170 > all
    7171 
    7172 > mousemode rightMode "move planes"
    7173 
    7174 > volume #2.1.1.1 orthoplanes xyz positionPlanes 64,64,64 style image region
    7175 > all
    7176 
    7177 > mousemode rightMode "move planes"
    7178 
    7179 > volume planes z style image imageMode "full region"
    7180 
    7181 > mousemode rightMode "move planes"
    7182 
    7183 > volume style mesh
    7184 
    7185 [Repeated 1 time(s)]
    7186 
    7187 > volume #2.1.1.1 style image region all imageMode "tilted slab"
    7188 > tiltedSlabAxis 0,0,1 tiltedSlabOffset 106.1 tiltedSlabSpacing 1.658
    7189 > tiltedSlabPlaneCount 10
    7190 
    7191 > mousemode rightMode "rotate slab"
    7192 
    7193 > volume planes z style image imageMode "full region"
    7194 
    7195 > mousemode rightMode "move planes"
    7196 
    7197 > volume #2.1.1.1 style image region all imageMode "tilted slab"
    7198 > tiltedSlabAxis 0,0,1 tiltedSlabOffset 106.1 tiltedSlabSpacing 1.658
    7199 > tiltedSlabPlaneCount 10
    7200 
    7201 > mousemode rightMode "rotate slab"
    7202 
    7203 > volume style mesh
    7204 
    7205 > volume #2.1.1.1 change image level -0.0001408,0 level 0.1705,0.8 level
    7206 > 2.096,1
    7207 
    7208 > volume #2.1.1.1 level 0.3019
    7209 
    7210 > volume #2.1.1.1 orthoplanes xyz positionPlanes 64,64,64 style image region
    7211 > all
    7212 
    7213 > mousemode rightMode "move planes"
    7214 
    7215 > volume #2.1.1.1 orthoplanes xyz positionPlanes 64,64,64 style image region
    7216 > all
    7217 
    7218 > mousemode rightMode "move planes"
    7219 
    7220 > volume zone #2.1.1.1 nearAtoms #2.2 range 9.95
    7221 
    7222 > volume region all imageMode "full region"
    7223 
    7224 > volume unzone
    7225 
    7226 > mousemode rightMode "crop volume"
    7227 
    7228 > close #2.1.1.1
    7229 
    7230 > select #1
    7231 
    7232 Nothing selected 
    7233 
    7234 > clipper associate #1 toModel #2
    7235 
    7236 > close session
    7237 
    7238 > open
    7239 > C:/Users/daniellem/Downloads/fold_202411_11_fresh/fold_202411_11_fresh_model_1.cif
    7240 
    7241 Chain information for fold_202411_11_fresh_model_1.cif #1 
    7242 --- 
    7243 Chain | Description 
    7244 A B C | . 
    7245  
    7246 
    7247 > open "C:/Users/daniellem/Desktop/CryoEM
    7248 > workshop/DeepEMhancer_Danielle_4_9.mrc"
    7249 
    7250 Opened DeepEMhancer_Danielle_4_9.mrc as #2, grid size 128,128,128, pixel 1.66,
    7251 shown at level 0.171, step 1, values float32 
    7252 
    7253 > clipper associate #2 toModel #1
    7254 
    7255 Opened DeepEMhancer_Danielle_4_9.mrc as #1.1.1.1, grid size 128,128,128, pixel
    7256 1.66, shown at level 0, step 1, values float32 
    7257 Chain information for fold_202411_11_fresh_model_1.cif 
    7258 --- 
    7259 Chain | Description 
    7260 1.2/A 1.2/B 1.2/C | . 
    7261  
    7262 
    7263 > zoom
    7264 
    7265 Pixel size at center of rotation is 0.252 
    7266 
    7267 > zoom
    7268 
    7269 Pixel size at center of rotation is 0.252 
    7270 
    7271 > volume #1.1.1.1 level 2.378e-07
    7272 
    7273 > isolde start
    7274 
    7275 > set selectionWidth 4
    7276 
    7277 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7278 chains... 
    7279 ISOLDE: Corrected atom nomenclature of 286 residues in model #1.2 to IUPAC-IUB
    7280 standards. 
    7281 Done loading forcefield 
    7282 
    7283 > isolde set simFidelityMode Medium/Medium
    7284 
    7285 ISOLDE: setting sim fidelity mode to Medium/Medium 
    7286 nonbonded_cutoff_distance = 0.900000 
    7287 use_gbsa = True 
    7288 gbsa_cutoff = 1.100000 
    7289 
    7290 > volume #1.1.1.1 region 0,2,0,11,15,12
    7291 
    7292 > set bgColor white
    7293 
    7294 > set bgColor #ffffff00
    7295 
    7296 > select add #1
    7297 
    7298 16827 atoms, 17253 bonds, 2103 residues, 15 models selected 
    7299 
    7300 > select add #1.2
    7301 
    7302 16827 atoms, 17253 bonds, 2103 residues, 15 models selected 
    7303 
    7304 > select add #1
    7305 
    7306 16827 atoms, 17253 bonds, 2103 residues, 15 models selected 
    7307 
    7308 > select add #1.2
    7309 
    7310 16827 atoms, 17253 bonds, 2103 residues, 15 models selected 
    7311 
    7312 > ~select
    7313 
    7314 Nothing selected 
    7315 
    7316 > view #1.1.1.1.2 clip false
    7317 
    7318 No displayed objects specified. 
    7319 
    7320 > view #1.1.1.1.2 clip false
    7321 
    7322 No displayed objects specified. 
    7323 
    7324 > view #1.1.1.1.2 clip false
    7325 
    7326 No displayed objects specified. 
    7327 
    7328 > show #1.1.1.1.2 target m
    7329 
    7330 > hide #1.1.1.1.2 target m
    7331 
    7332 > close #1.1.1.1.2
    7333 
    7334 > hide target m
    7335 
    7336 [Repeated 1 time(s)]
    7337 
    7338 > close
    7339 
    7340 > open
    7341 > C:\Users\daniellem\Downloads\fold_202411_11_fresh\fold_202411_11_fresh_model_1.cif
    7342 > format mmcif
    7343 
    7344 Chain information for fold_202411_11_fresh_model_1.cif #1 
    7345 --- 
    7346 Chain | Description 
    7347 A B C | . 
    7348  
    7349 
    7350 > open "C:/Users/daniellem/Desktop/CryoEM workshop/Dissertation final 316W
    7351 > model/DeepEMhancer_Danielle_4_9.mrc"
    7352 
    7353 Opened DeepEMhancer_Danielle_4_9.mrc as #2, grid size 128,128,128, pixel 1.66,
    7354 shown at level 0.171, step 1, values float32 
    7355 
    7356 > volume #2 region 0,6,0,127,127,127
    7357 
    7358 > select add #1
    7359 
    7360 16827 atoms, 17253 bonds, 2103 residues, 1 model selected 
    7361 
    7362 > volume #2 region 0,9,0,127,127,127
    7363 
    7364 > volume #2 region 0,31,0,127,127,127
    7365 
    7366 > volume #2 region 0,2,0,127,127,127
    7367 
    7368 > volume #2 region 2,2,0,127,127,127
    7369 
    7370 > volume #2 region 0,2,0,127,127,127
    7371 
    7372 > ui mousemode right "rotate selected models"
    7373 
    7374 > view matrix models
    7375 > #1,0.66525,-0.10274,0.73952,-3.3498,-0.70987,0.21988,0.66913,6.6393,-0.23135,-0.9701,0.073343,18.122
    7376 
    7377 > view matrix models
    7378 > #1,0.66436,-0.098392,0.74091,-3.4057,-0.70806,0.23457,0.66606,6.4683,-0.23933,-0.96711,0.086172,18.055
    7379 
    7380 > view matrix models
    7381 > #1,0.73489,-0.0012862,0.67819,-3.9016,-0.49398,0.68416,0.53657,1.0277,-0.46468,-0.72933,0.50214,14.374
    7382 
    7383 > view matrix models
    7384 > #1,0.48401,-0.29693,0.82315,-0.71801,-0.38327,0.77371,0.50446,-0.064179,-0.78666,-0.55965,0.26068,14.723
    7385 
    7386 > view matrix models
    7387 > #1,0.45881,-0.3301,0.82494,-0.27877,-0.38342,0.76399,0.51895,-0.033803,-0.80155,-0.5544,0.22396,14.879
    7388 
    7389 > view matrix models
    7390 > #1,0.58787,-0.42542,0.68806,1.4842,-0.33441,0.64668,0.68555,-0.022276,-0.7366,-0.63311,0.2379,15.786
    7391 
    7392 > ui mousemode right "move picked models"
    7393 
    7394 > ui mousemode right "translate selected models"
    7395 
    7396 > view matrix models
    7397 > #1,0.58787,-0.42542,0.68806,89.581,-0.33441,0.64668,0.68555,125,-0.7366,-0.63311,0.2379,28.389
    7398 
    7399 > ui mousemode right "rotate selected models"
    7400 
    7401 > view matrix models
    7402 > #1,0.69323,-0.26637,0.66969,87.572,-0.39958,0.63127,0.6647,125.4,-0.59981,-0.72838,0.33118,28.789
    7403 
    7404 > view matrix models
    7405 > #1,0.68673,-0.25861,0.67936,87.446,-0.37136,0.67861,0.63371,124.95,-0.6249,-0.68747,0.36998,28.176
    7406 
    7407 > ui mousemode right "translate selected models"
    7408 
    7409 > view matrix models
    7410 > #1,0.68673,-0.25861,0.67936,89.311,-0.37136,0.67861,0.63371,114.2,-0.6249,-0.68747,0.36998,81.84
    7411 
    7412 > ui mousemode right "move picked models"
    7413 
    7414 > view matrix models #2,1,0,0,-3.1953,0,1,0,8.6026,0,0,1,-26.98
    7415 
    7416 > ui mousemode right "rotate selected models"
    7417 
    7418 > view matrix models
    7419 > #1,0.71675,0.27424,0.64114,83.225,-0.50588,0.8373,0.20739,115.63,-0.47996,-0.47299,0.73887,76.524
    7420 
    7421 > view matrix models
    7422 > #1,-0.12708,0.40435,0.90573,81.28,-0.68048,0.62882,-0.3762,118.42,-0.72166,-0.66414,0.19524,82.162
    7423 
    7424 > ui mousemode right "translate selected atoms"
    7425 
    7426 > ui mousemode right "move picked models"
    7427 
    7428 > view matrix models #2,1,0,0,74.792,0,1,0,-99.562,0,0,1,-42.19
    7429 
    7430 > ui mousemode right "rotate selected models"
    7431 
    7432 > view matrix models
    7433 > #1,-0.064661,0.98545,0.15717,76.985,0.45325,0.16932,-0.87516,123.44,-0.88904,0.014648,-0.4576,79.166
    7434 
    7435 > view matrix models
    7436 > #1,0.20735,0.96008,0.18775,76.042,0.080933,0.17443,-0.98134,125.61,-0.97491,0.21868,-0.041534,73.66
    7437 
    7438 > view matrix models
    7439 > #1,0.52905,0.84743,0.044425,76.673,-0.40974,0.30094,-0.86113,125.75,-0.74312,0.43737,0.50644,66.766
    7440 
    7441 > view matrix models
    7442 > #1,0.66252,0.74875,-0.021062,77.638,-0.32016,0.25765,-0.91165,126.14,-0.67717,0.61073,0.41042,64.875
    7443 
    7444 > ui mousemode right "move picked models"
    7445 
    7446 > select subtract #1
    7447 
    7448 Nothing selected 
    7449 
    7450 > select add #2
    7451 
    7452 2 models selected 
    7453 
    7454 > ui mousemode right "rotate selected models"
    7455 
    7456 > view matrix models
    7457 > #2,0.36714,-0.13671,-0.92007,246.56,-0.46121,0.83223,-0.3077,-0.0059004,0.80777,0.53731,0.24249,-124.99
    7458 
    7459 > view matrix models
    7460 > #2,0.52398,-0.03222,-0.85112,210.75,-0.71814,0.52057,-0.46182,77.879,0.45795,0.85321,0.24963,-120.19
    7461 
    7462 > view matrix models
    7463 > #2,0.30109,-0.16473,-0.93926,258.99,-0.83534,0.42952,-0.3431,90.528,0.45995,0.8879,-0.0082803,-100.69
    7464 
    7465 > ui mousemode right "move picked models"
    7466 
    7467 > view matrix models
    7468 > #2,0.30109,-0.16473,-0.93926,198.41,-0.83534,0.42952,-0.3431,218.9,0.45995,0.8879,-0.0082803,-85.192
    7469 
    7470 > ui mousemode right "rotate selected models"
    7471 
    7472 > view matrix models
    7473 > #2,0.18816,-0.14391,-0.97154,212.04,-0.86165,0.45054,-0.23362,209.62,0.47133,0.88108,-0.039224,-82.925
    7474 
    7475 > view matrix models
    7476 > #2,0.18599,-0.16879,-0.96794,214.7,-0.86627,0.43672,-0.24261,212.49,0.46367,0.88362,-0.064991,-79.971
    7477 
    7478 > view matrix models
    7479 > #2,0.1282,-0.10727,-0.98593,216.22,-0.87167,0.46198,-0.16361,203.12,0.47303,0.88038,-0.034277,-83.494
    7480 
    7481 > select subtract #2
    7482 
    7483 Nothing selected 
    7484 
    7485 > fitmap map
    7486 
    7487 Missing or invalid "atomsOrMap" argument: invalid objects specifier 
    7488 
    7489 > fitmap
    7490 
    7491 Missing or invalid "atomsOrMap" argument: empty atom specifier 
    7492 
    7493 > fitmap
    7494 
    7495 Missing or invalid "atomsOrMap" argument: empty atom specifier 
    7496 
    7497 > ui mousemode right "move picked models"
    7498 
    7499 > view matrix models
    7500 > #1,0.66252,0.74875,-0.021062,121.8,-0.32016,0.25765,-0.91165,144.36,-0.67717,0.61073,0.41042,58.518
    7501 
    7502 > ui mousemode right "translate selected models"
    7503 
    7504 > ui mousemode right "rotate selected models"
    7505 
    7506 > roll
    7507 
    7508 > stop
    7509 
    7510 > ui mousemode right "translate selected models"
    7511 
    7512 > undo
    7513 
    7514 > redo
    7515 
    7516 > ui mousemode right rotate
    7517 
    7518 > ui mousemode right "move picked models"
    7519 
    7520 > volume #2 level 0.2875
    7521 
    7522 > volume #2 level 0.06889
    7523 
    7524 > clipper associate #2 toModel #1
    7525 
    7526 Opened DeepEMhancer_Danielle_4_9.mrc as #1.1.1.1, grid size 128,128,128, pixel
    7527 1.66, shown at level 0.0215, step 1, values float32 
    7528 Chain information for fold_202411_11_fresh_model_1.cif 
    7529 --- 
    7530 Chain | Description 
    7531 1.2/A 1.2/B 1.2/C | . 
    7532  
    7533 
    7534 > volume #1.1.1.1 level 0.02788
    7535 
    7536 > color #1.1.1.1 #1dffd9ff models
    7537 
    7538 > set bgColor black
    7539 
    7540 > set bgColor transparent
    7541 
    7542 > save "C:/Users/daniellem/Desktop/CryoEM workshop/Dissertation final 316W
    7543 > model/316W_diss_1.cxs"
    7544 
    7545 > select add #1
    7546 
    7547 16827 atoms, 17253 bonds, 2103 residues, 7 models selected 
    7548 
    7549 > select subtract #1
    7550 
    7551 Nothing selected 
    7552 
    7553 > select add #1.2
    7554 
    7555 16827 atoms, 17253 bonds, 2103 residues, 1 model selected 
    7556 
    7557 > select subtract #1.2
    7558 
    7559 Nothing selected 
    7560 
    7561 > select add #1.2
    7562 
    7563 16827 atoms, 17253 bonds, 2103 residues, 1 model selected 
    7564 
    7565 > select subtract #1.2
    7566 
    7567 Nothing selected 
    7568 
    7569 > close #1
    7570 
    7571 > open
    7572 > C:/Users/daniellem/Downloads/fold_202411_11_fresh/fold_202411_11_fresh_model_0.cif
    7573 
    7574 Chain information for fold_202411_11_fresh_model_0.cif #1 
    7575 --- 
    7576 Chain | Description 
    7577 A B C | . 
    7578  
    7579 
    7580 > open "C:/Users/daniellem/Desktop/CryoEM
    7581 > workshop/DeepEMhancer_Danielle_4_9.mrc"
    7582 
    7583 Opened DeepEMhancer_Danielle_4_9.mrc as #2, grid size 128,128,128, pixel 1.66,
    7584 shown at level 0.171, step 1, values float32 
    7585 
    7586 > fitmap #1 inMap #2
    7587 
    7588 Fit molecule fold_202411_11_fresh_model_0.cif (#1) to map
    7589 DeepEMhancer_Danielle_4_9.mrc (#2) using 16827 atoms 
    7590 average map value = 0.07522, steps = 844 
    7591 shifted from previous position = 175 
    7592 rotated from previous position = 54.2 degrees 
    7593 atoms outside contour = 14504, contour level = 0.17065 
    7594  
    7595 Position of fold_202411_11_fresh_model_0.cif (#1) relative to
    7596 DeepEMhancer_Danielle_4_9.mrc (#2) coordinates: 
    7597 Matrix rotation and translation 
    7598 0.64792760 -0.62354966 -0.43746502 96.82197592 
    7599 0.74386964 0.64153909 0.18731140 110.82058535 
    7600 0.16385295 -0.44678117 0.87951055 97.73764625 
    7601 Axis -0.39073889 -0.37054262 0.84262761 
    7602 Axis point -58.82632784 190.65888686 0.00000000 
    7603 Rotation angle (degrees) 54.23312860 
    7604 Shift along axis 3.46057824 
    7605  
    7606 
    7607 > select add #1
    7608 
    7609 16827 atoms, 17253 bonds, 2103 residues, 1 model selected 
    7610 
    7611 > ui mousemode right "rotate selected models"
    7612 
    7613 > view matrix models
    7614 > #1,0.99713,0.047993,-0.058537,89.39,0.058353,0.0052358,0.99828,118.88,0.048217,-0.99883,0.0024202,98.244
    7615 
    7616 > view matrix models
    7617 > #1,0.8632,-0.0503,0.50236,89.98,-0.50441,-0.12817,0.8539,116.49,0.021437,-0.99048,-0.13601,96.623
    7618 
    7619 > ui mousemode right "move picked models"
    7620 
    7621 > ui mousemode right "translate selected models"
    7622 
    7623 > view matrix models
    7624 > #1,0.8632,-0.0503,0.50236,89.369,-0.50441,-0.12817,0.8539,114.78,0.021437,-0.99048,-0.13601,96.141
    7625 
    7626 > view matrix models
    7627 > #1,0.8632,-0.0503,0.50236,51.119,-0.50441,-0.12817,0.8539,133.03,0.021437,-0.99048,-0.13601,97.843
    7628 
    7629 > view matrix models
    7630 > #1,0.8632,-0.0503,0.50236,11.287,-0.50441,-0.12817,0.8539,109.46,0.021437,-0.99048,-0.13601,101.2
    7631 
    7632 > ui mousemode right "rotate selected models"
    7633 
    7634 > ui mousemode right "translate selected models"
    7635 
    7636 > view matrix models
    7637 > #1,0.8632,-0.0503,0.50236,73.284,-0.50441,-0.12817,0.8539,117.42,0.021437,-0.99048,-0.13601,99.791
    7638 
    7639 > view matrix models
    7640 > #1,0.8632,-0.0503,0.50236,70.626,-0.50441,-0.12817,0.8539,117.88,0.021437,-0.99048,-0.13601,99.742
    7641 
    7642 > view matrix models
    7643 > #1,0.8632,-0.0503,0.50236,121.46,-0.50441,-0.12817,0.8539,114.41,0.021437,-0.99048,-0.13601,99.952
    7644 
    7645 > ui mousemode right "rotate selected models"
    7646 
    7647 > view matrix models
    7648 > #1,0.8253,-0.28919,0.48503,125.06,-0.54795,-0.20249,0.81163,115.12,-0.1365,-0.93561,-0.32557,97.173
    7649 
    7650 > view matrix models
    7651 > #1,0.8233,-0.30662,0.47766,125.28,-0.55534,-0.26109,0.78958,115.9,-0.11739,-0.91532,-0.38523,96.754
    7652 
    7653 > view matrix models
    7654 > #1,0.69075,0.22823,0.68613,117.35,-0.64306,-0.24003,0.72723,114.32,0.33067,-0.94355,-0.019031,102.83
    7655 
    7656 > view matrix models
    7657 > #1,0.74225,-0.1389,0.65557,123.62,-0.66974,-0.12076,0.73271,112.12,-0.022608,-0.98292,-0.18266,99.155
    7658 
    7659 > select subtract #1
    7660 
    7661 Nothing selected 
    7662 
    7663 > select add #2
    7664 
    7665 2 models selected 
    7666 
    7667 > view matrix models
    7668 > #2,0.9995,0.0074953,0.030735,-3.5727,-0.008337,0.99959,0.027347,-1.4932,-0.030517,-0.027589,0.99915,6.62
    7669 
    7670 > ui mousemode right "translate selected models"
    7671 
    7672 > view matrix models
    7673 > #2,0.9995,0.0074953,0.030735,23.671,-0.008337,0.99959,0.027347,4.4973,-0.030517,-0.027589,0.99915,5.6597
    7674 
    7675 > ui mousemode right rotate
    7676 
    7677 > ui mousemode right "rotate selected models"
    7678 
    7679 > view matrix models
    7680 > #2,0.97796,-0.014894,-0.20826,50.426,0.05381,0.98174,0.18248,-14.843,0.20174,-0.18966,0.9609,0.28557
    7681 
    7682 > ui mousemode right "translate selected models"
    7683 
    7684 > view matrix models
    7685 > #2,0.97796,-0.014894,-0.20826,53.888,0.05381,0.98174,0.18248,-19.638,0.20174,-0.18966,0.9609,2.2334
    7686 
    7687 > ui mousemode right "rotate selected models"
    7688 
    7689 > view matrix models
    7690 > #2,0.98566,-0.0079441,-0.16857,48.617,0.044096,0.97631,0.21182,-20.604,0.1629,-0.21622,0.96266,9.4578
    7691 
    7692 > view matrix models
    7693 > #2,0.95291,-0.0044741,-0.30321,64.289,0.14917,0.87746,0.45586,-44.084,0.26402,-0.47962,0.83681,38.3
    7694 
    7695 > view matrix models
    7696 > #2,0.92066,-0.20279,-0.33356,92.584,0.33574,0.8473,0.41154,-58.164,0.19917,-0.49088,0.84816,45.955
    7697 
    7698 > ui mousemode right "translate selected models"
    7699 
    7700 > view matrix models
    7701 > #2,0.92066,-0.20279,-0.33356,83.602,0.33574,0.8473,0.41154,-56.096,0.19917,-0.49088,0.84816,44.316
    7702 
    7703 > select add #2
    7704 
    7705 3 models selected 
    7706 
    7707 > ui mousemode right translate
    7708 
    7709 > ui mousemode right "translate selected atoms"
    7710 
    7711 > ui mousemode right "move picked models"
    7712 
    7713 > ui mousemode right select
    7714 
    7715 > select subtract #2
    7716 
    7717 Nothing selected 
    7718 
    7719 > ui mousemode right "translate selected models"
    7720 
    7721 > select add #2
    7722 
    7723 3 models selected 
    7724 
    7725 > select subtract #2
    7726 
    7727 Nothing selected 
    7728 
    7729 > ui mousemode right "move picked models"
    7730 
    7731 > ui mousemode right "rotate selected models"
    7732 
    7733 > ui mousemode right "translate selected models"
    7734 
    7735 > select add #1
    7736 
    7737 16827 atoms, 17253 bonds, 2103 residues, 1 model selected 
    7738 
    7739 > view matrix models
    7740 > #1,0.74225,-0.1389,0.65557,125.13,-0.66974,-0.12076,0.73271,107.13,-0.022608,-0.98292,-0.18266,95.753
    7741 
    7742 > select subtract #1
    7743 
    7744 Nothing selected 
    7745 
    7746 > isolde start
    7747 
    7748 > clipper associate #2 toModel #1
    7749 
    7750 Opened DeepEMhancer_Danielle_4_9.mrc as #1.1.1.1, grid size 128,128,128, pixel
    7751 1.66, shown at level 0.191, step 1, values float32 
    7752 Chain information for fold_202411_11_fresh_model_0.cif 
    7753 --- 
    7754 Chain | Description 
    7755 1.2/A 1.2/B 1.2/C | . 
    7756  
    7757 
    7758 > isolde start
    7759 
    7760 > set bgColor white
    7761 
    7762 > set bgColor #ffffff00
    7763 
    7764 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7765 chains... 
    7766 ISOLDE: Corrected atom nomenclature of 277 residues in model #1.2 to IUPAC-IUB
    7767 standards. 
    7768 ISOLDE: created disulfide bonds between the following residues: 
    7769 B125-B137; B276-B309; C181-C416; B48-B68; C276-C309; C355-C428; A355-A428;
    7770 A362-A401; C484-C590; A276-A309; A181-A416; B583-B589; A125-A137; C113-C185;
    7771 B484-B590; C583-C589; B362-B401; B113-B185; C208-C219; A48-A68; C48-C68;
    7772 A113-A185; C198-C227; B208-B219; B181-B416; A583-A589; A208-A219; B198-B227;
    7773 B355-B428; C125-C137; A198-A227; C362-C401; B120-B176; A484-A590; A120-A176;
    7774 C120-C176 
    7775 
    7776 > set silhouettes false
    7777 
    7778 > ~select
    7779 
    7780 Nothing selected 
    7781 
    7782 > set silhouettes false
    7783 
    7784 > delete ~protein
    7785 
    7786 > addh
    7787 
    7788 Summary of feedback from adding hydrogens to fold_202411_11_fresh_model_0.cif
    7789 #1.2 
    7790 --- 
    7791 notes | Termini for fold_202411_11_fresh_model_0.cif (#1.2) chain A determined from SEQRES records 
    7792 Termini for fold_202411_11_fresh_model_0.cif (#1.2) chain B determined from
    7793 SEQRES records 
    7794 Termini for fold_202411_11_fresh_model_0.cif (#1.2) chain C determined from
    7795 SEQRES records 
    7796 Chain-initial residues that are actual N termini: /A MET 1, /B MET 1, /C MET 1 
    7797 Chain-initial residues that are not actual N termini: 
    7798 Chain-final residues that are actual C termini: /A HIS 677, /B HIS 677, /C HIS
    7799 677 
    7800 Chain-final residues that are not actual C termini: 
    7801 1630 hydrogen bonds 
    7802 15663 hydrogens added 
    7803  
    7804 
    7805 > select #1
    7806 
    7807 31698 atoms, 32088 bonds, 2031 residues, 16 models selected 
    7808 
    7809 > clipper isolate #1 maskRadius 16
    7810 
    7811 > view matrix models #1,1,0,0,7.0869,0,1,0,-0.39389,0,0,1,2.602
    7812 
    7813 > ui mousemode right "rotate selected models"
    7814 
    7815 > view matrix models
    7816 > #1,0.95983,0.26995,-0.076557,-10.994,-0.24059,0.93216,0.27052,16.377,0.14439,-0.24124,0.95966,14.374
    7817 
    7818 > view matrix models
    7819 > #1,0.9876,-0.040147,-0.15174,25.439,0.021063,0.99189,-0.12534,6.9079,0.15554,0.1206,0.98044,-28.405
    7820 
    7821 > view matrix models
    7822 > #1,0.99163,-0.083691,-0.098314,25.632,0.09889,0.98189,0.16158,-23.443,0.08301,-0.16995,0.98195,12.399
    7823 
    7824 > hide atoms
    7825 
    7826 > save "C:/Users/daniellem/Desktop/CryoEM workshop/Dissertation final 316W
    7827 > model/316W_diss_1.cxs"
    7828 
    7829 > show ~HC
    7830 
    7831 > isolde restrain distances "#1/A,G"
    7832 
    7833 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7834 chains... 
    7835 
    7836 > isolde restrain distances "#1/B,F"
    7837 
    7838 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7839 chains... 
    7840 
    7841 > select #1
    7842 
    7843 31698 atoms, 32088 bonds, 2031 residues, 17 models selected 
    7844 
    7845 > isolde sim start sel
    7846 
    7847 ISOLDE: started sim 
    7848 
    7849 > ui mousemode right "isolde tug selection"
    7850 
    7851 > select /B,F@CA
    7852 
    7853 677 atoms, 677 residues, 1 model selected 
    7854 
    7855 > select /A,H@CA
    7856 
    7857 677 atoms, 677 residues, 1 model selected 
    7858 
    7859 > select /A,B,C
    7860 
    7861 31698 atoms, 32088 bonds, 2031 residues, 1 model selected 
    7862 
    7863 > ui hideFloating toggle
    7864 
    7865 [Repeated 1 time(s)]
    7866 
    7867 > ~select
    7868 
    7869 Nothing selected 
    7870 
    7871 > ~select
    7872 
    7873 Nothing selected 
    7874 
    7875 > isolde sim pause
    7876 
    7877 > select #1
    7878 
    7879 31698 atoms, 32088 bonds, 2031 residues, 21 models selected 
    7880 
    7881 > ui mousemode right "move picked models"
    7882 
    7883 > ui mousemode right "translate selected models"
    7884 
    7885 > view matrix models
    7886 > #1,0.99163,-0.083691,-0.098314,22.128,0.09889,0.98189,0.16158,-23.116,0.08301,-0.16995,0.98195,10.873
    7887 
    7888 > ui mousemode right "move picked models"
    7889 
    7890 > isolde sim resume
    7891 
    7892 > select A
    7893 
    7894 Expected an objects specifier or a keyword 
    7895 
    7896 > select /A
    7897 
    7898 10566 atoms, 10696 bonds, 677 residues, 1 model selected 
    7899 
    7900 > view matrix models
    7901 > #1.2,1,3.4694e-17,9.7145e-17,-0.57951,2.0817e-17,1,-5.5511e-17,0.97731,0,-8.3267e-17,1,0.16641
    7902 
    7903 > view matrix models
    7904 > #1.2,1,6.0715e-17,1.1102e-16,-3.7199,1.3878e-17,1,-1.3878e-16,0.75132,1.3878e-17,-8.3267e-17,1,-1.2135
    7905 
    7906 > view matrix models
    7907 > #1.2,1,-5.6725e-16,-4.1633e-17,-4.514,-4.4929e-16,1,-4.1633e-16,6.3267,-5.4123e-16,2.498e-16,1,0.76486
    7908 
    7909 > select /A
    7910 
    7911 10566 atoms, 10696 bonds, 677 residues, 1 model selected 
    7912 
    7913 > ui mousemode right "isolde tug selection"
    7914 
    7915 > ~select
    7916 
    7917 Nothing selected 
    7918 
    7919 > ~select
    7920 
    7921 Nothing selected 
    7922 
    7923 > chains
    7924 
    7925 Unknown command: chains 
    7926 
    7927 > chains/
    7928 
    7929 Unknown command: chains/ 
    7930 
    7931 > /
    7932 
    7933 Unknown command: / 
    7934 
    7935 > select add #1.2
    7936 
    7937 31698 atoms, 32088 bonds, 2031 residues, 14 models selected 
    7938 
    7939 > select add #1.1.1
    7940 
    7941 31698 atoms, 32088 bonds, 2031 residues, 17 models selected 
    7942 
    7943 > select add #1
    7944 
    7945 31698 atoms, 32088 bonds, 2031 residues, 21 models selected 
    7946 
    7947 > select subtract #1.1.1
    7948 
    7949 31698 atoms, 32088 bonds, 2031 residues, 16 models selected 
    7950 
    7951 > select add #1.2
    7952 
    7953 31698 atoms, 32088 bonds, 2031 residues, 17 models selected 
    7954 
    7955 > select subtract #1.3
    7956 
    7957 31698 atoms, 32088 bonds, 2031 residues, 15 models selected 
    7958 
    7959 > select add #1.2
    7960 
    7961 31698 atoms, 32088 bonds, 2031 residues, 16 models selected 
    7962 
    7963 > ~select
    7964 
    7965 Nothing selected 
    7966 
    7967 > select add #1.1.1
    7968 
    7969 4 models selected 
    7970 
    7971 > ui mousemode right "translate selected models"
    7972 
    7973 > view matrix models
    7974 > #1.1.1,1,-5.0307e-17,2.6368e-16,0.51738,-1.1796e-16,1,-6.3838e-16,-5.7231,6.9389e-17,1.3878e-16,1,0.10217
    7975 
    7976 > ui mousemode right "rotate selected models"
    7977 
    7978 > view matrix models
    7979 > #1.1.1,0.98912,-0.14707,-0.0035996,18.306,0.1471,0.9884,0.037814,-25.16,-0.0020035,-0.037932,0.99928,4.5772
    7980 
    7981 > view matrix models
    7982 > #1.1.1,0.86583,-0.49895,-0.037256,74.567,0.49933,0.85694,0.1278,-60.241,-0.031839,-0.12925,0.9911,18.874
    7983 
    7984 > view matrix models
    7985 > #1.1.1,0.9799,-0.19939,-0.0062574,25.388,0.19945,0.97857,0.05124,-31.446,-0.0040934,-0.051458,0.99867,6.3666
    7986 
    7987 > view matrix models
    7988 > #1.1.1,0.99258,0.12162,-0.0012517,-11.88,-0.1216,0.99208,-0.031353,12.279,-0.0025713,0.031273,0.99951,-2.9923
    7989 
    7990 > view matrix models
    7991 > #1.1.1,0.9998,-0.020045,-0.0001605,2.7614,0.020046,0.99979,0.0051605,-8.5229,5.7023e-05,-0.0051627,0.99999,0.66479
    7992 
    7993 > view matrix models
    7994 > #1.1.1,0.99427,0.018958,-0.1052,8.6924,-0.019023,0.99982,0.00038549,-3.5055,0.10519,0.0016179,0.99445,-11.917
    7995 
    7996 > view matrix models
    7997 > #1.1.1,0.98647,-0.12373,-0.10757,25.525,0.12676,0.99169,0.021827,-21.678,0.10397,-0.035167,0.99396,-7.6817
    7998 
    7999 > ui mousemode right "translate selected models"
     2850[deleted to fit within ticket limits]
    80002851
    80012852> view matrix models