Changes between Initial Version and Version 1 of Ticket #17446


Ignore:
Timestamp:
Apr 21, 2025, 2:35:23 PM (6 months ago)
Author:
pett
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #17446

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

  • Ticket #17446 – Description

    initial v1  
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    1483     "name" : "_imagingmath.cpython-311-darwin.so"
    1484   },
    1485   {
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    1492     "name" : "libsystem_kernel.dylib"
    1493   },
    1494   {
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    1499     "uuid" : "642faf7a-874e-37e6-8aba-2b0cc09a3025",
    1500     "path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
    1501     "name" : "libsystem_pthread.dylib"
    1502   },
    1503   {
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    1519     "name" : "libsystem_platform.dylib"
    1520   },
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    1542     "name" : "SkyLight"
    1543   },
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    1552   },
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     72[deleted to fit within ticket limits]
     73
    160074],
    160175  "sharedCache" : {
    … …  
    28241298 
    28251299
    2826 > open
    2827 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_Model/RealSpaceRefine_6/mOCT1-VB1-coot-11_real_space_refined_006.pdb
    2828 
    2829 Chain information for mOCT1-VB1-coot-11_real_space_refined_006.pdb #4 
    2830 --- 
    2831 Chain | Description 
    2832 A | No description available 
    2833  
    2834 
    2835 > open
    2836 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_Model/mOCT1-VB1_real_space_refined_014.pdb
    2837 
    2838 Chain information for mOCT1-VB1_real_space_refined_014.pdb #5 
    2839 --- 
    2840 Chain | Description 
    2841 A | No description available 
    2842  
    2843 
    2844 > close #3#4
    2845 
    2846 > volume #2 color #ffffb296
    2847 
    2848 > volume #2 color #ffffb2c8
    2849 
    2850 > volume #2 level 0.4304
    2851 
    2852 > volume #2 level 0.3677
    2853 
    2854 > select /A:601@C15
    2855 
    2856 1 atom, 1 residue, 1 model selected 
    2857 
    2858 > select up
    2859 
    2860 18 atoms, 19 bonds, 1 residue, 1 model selected 
    2861 
    2862 > view sel
    2863 
    2864 > select clear
    2865 
    2866 > open
    2867 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-ABC_Model/mOCT1-ABC_real_space_refined_009.pdb
    2868 
    2869 Chain information for mOCT1-ABC_real_space_refined_009.pdb #3 
    2870 --- 
    2871 Chain | Description 
    2872 A | No description available 
    2873  
    2874 
    2875 > open
    2876 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-ABC_20220411_cryoSPARC/J142_2.25A_clip-240/cryosparc_P3_J150__localfilter_240.mrc
    2877 
    2878 Opened cryosparc_P3_J150__localfilter_240.mrc as #4, grid size 240,240,240,
    2879 pixel 0.553, shown at level 0.229, step 1, values float32 
    2880 
    2881 > volume #4 level 0.7041
    2882 
    2883 > hide #!2 models
    2884 
    2885 > hide #!3 models
    2886 
    2887 > hide #!5 models
    2888 
    2889 > show #!3 models
    2890 
    2891 > select ::name="ABC"
    2892 
    2893 42 atoms, 48 bonds, 2 residues, 1 model selected 
    2894 
    2895 > view sel
    2896 
    2897 > volume #4 level 0.5273
    2898 
    2899 > hide #!4 models
    2900 
    2901 > show #!4 models
    2902 
    2903 > show #!1 models
    2904 
    2905 > hide #!3 models
    2906 
    2907 > save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
    2908 > density.cxs" includeMaps true
    2909 
    2910 QXcbConnection: XCB error: 3 (BadWindow), sequence: 57982, resource id:
    2911 35654641, major code: 40 (TranslateCoords), minor code: 0 
    2912 
    2913 > hide #!1 models
    2914 
    2915 > rename #1 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    2916 
    2917 > rename #2 mOCT1-VB1_cryosparc_P3_J154__localfilter_240_VB1.mrc
    2918 
    2919 > rename #4 mOCT1-ABC_cryosparc_P3_J150__localfilter_240.mrc
    2920 
    2921 > show #!3 models
    2922 
    2923 > select clear
    2924 
    2925 > hide #!4 models
    2926 
    2927 > select ::name="ABC"
    2928 
    2929 42 atoms, 48 bonds, 2 residues, 1 model selected 
    2930 
    2931 > select add #3
    2932 
    2933 3550 atoms, 3613 bonds, 1 pseudobond, 490 residues, 2 models selected 
    2934 
    2935 > color (#!3 & sel) white
    2936 
    2937 > select clear
    2938 
    2939 > select ::name="ABC"
    2940 
    2941 42 atoms, 48 bonds, 2 residues, 1 model selected 
    2942 
    2943 > color sel red
    2944 
    2945 > show #!4 models
    2946 
    2947 > ui tool show "Color Zone"
    2948 
    2949 > color zone #4 near #3 distance 3.32
    2950 
    2951 > volume splitbyzone #4
    2952 
    2953 Opened mOCT1-ABC_cryosparc_P3_J150__localfilter_240.mrc 0 as #6.1, grid size
    2954 240,240,240, pixel 0.553, shown at level 0.527, step 1, values float32 
    2955 Opened mOCT1-ABC_cryosparc_P3_J150__localfilter_240.mrc 1 as #6.2, grid size
    2956 240,240,240, pixel 0.553, shown at level 0.527, step 1, values float32 
    2957 Opened mOCT1-ABC_cryosparc_P3_J150__localfilter_240.mrc 2 as #6.3, grid size
    2958 240,240,240, pixel 0.553, shown at level 0.527, step 1, values float32 
    2959 
    2960 > hide #!3 models
    2961 
    2962 > select add #3
    2963 
    2964 3550 atoms, 3613 bonds, 1 pseudobond, 490 residues, 2 models selected 
    2965 
    2966 > select subtract #3
    2967 
    2968 Nothing selected 
    2969 
    2970 > hide #!6.1 models
    2971 
    2972 > hide #!6.3 models
    2973 
    2974 > show #!6.3 models
    2975 
    2976 > hide #!6.2 models
    2977 
    2978 > close #6.1-2
    2979 
    2980 > save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
    2981 > density.cxs" includeMaps true
    2982 
    2983 QXcbConnection: XCB error: 3 (BadWindow), sequence: 18121, resource id:
    2984 35654647, major code: 40 (TranslateCoords), minor code: 0 
    2985 
    2986 > show #!3 models
    2987 
    2988 > color #3 #fffffbff
    2989 
    2990 > color #3 #ddddaaff
    2991 
    2992 > color #3 #dda0deff
    2993 
    2994 > color #3 plum
    2995 
    2996 > select add #3
    2997 
    2998 3550 atoms, 3613 bonds, 1 pseudobond, 490 residues, 2 models selected 
    2999 
    3000 > color (#!3 & sel) byhetero
    3001 
    3002 > color #6.3 #ddddaaff models
    3003 
    3004 > color #6.3 plum models
    3005 
    3006 > color #6.3 #ffffb2ff models
    3007 
    3008 Drag select of 6.3 mOCT1-ABC_cryosparc_P3_J150__localfilter_240.mrc 2 , 5
    3009 atoms, 5 residues, 5 bonds 
    3010 
    3011 > select clear
    3012 
    3013 > color #6.3 #ffffb2c8 models
    3014 
    3015 > select ::name="ABC"
    3016 
    3017 42 atoms, 48 bonds, 2 residues, 1 model selected 
    3018 
    3019 > view sel
    3020 
    3021 > select #3/A:234
    3022 
    3023 11 atoms, 10 bonds, 1 residue, 1 model selected 
    3024 
    3025 > color #6.3 #ffffb296 models
    3026 
    3027 > show #!2 models
    3028 
    3029 > hide #!2 models
    3030 
    3031 > show #!2 models
    3032 
    3033 > hide #!3 models
    3034 
    3035 > hide #!6 models
    3036 
    3037 > hide #!6.3 models
    3038 
    3039 > show #!4 models
    3040 
    3041 > hide #!4 models
    3042 
    3043 > show #!5 models
    3044 
    3045 > show #!3 models
    3046 
    3047 > hide #!3 models
    3048 
    3049 > select #5/A:36
    3050 
    3051 12 atoms, 12 bonds, 1 residue, 1 model selected 
    3052 
    3053 > show sel atoms
    3054 
    3055 > hide #!5 models
    3056 
    3057 > hide #!2 models
    3058 
    3059 > show #!1 models
    3060 
    3061 > view
    3062 
    3063 > save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
    3064 > density.cxs" includeMaps true
    3065 
    3066 QXcbConnection: XCB error: 3 (BadWindow), sequence: 5156, resource id:
    3067 35654673, major code: 40 (TranslateCoords), minor code: 0 
    3068 
    3069 > open
    3070 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-3TC_20240411/job207/relion_locres_filtered.mrc
    3071 
    3072 Opened relion_locres_filtered.mrc as #7, grid size 320,320,320, pixel 0.83,
    3073 shown at level 0.00144, step 2, values float32 
    3074 
    3075 > volume #7 level 0.01204
    3076 
    3077 > select add #7
    3078 
    3079 12 atoms, 12 bonds, 1 residue, 3 models selected 
    3080 
    3081 > select add #5
    3082 
    3083 3526 atoms, 3584 bonds, 1 pseudobond, 489 residues, 4 models selected 
    3084 
    3085 > select subtract #5
    3086 
    3087 2 models selected 
    3088 
    3089 > ui mousemode right "translate selected models"
    3090 
    3091 > view matrix models #7,1,0,0,-67.025,0,1,0,-62.171,0,0,1,-62.016
    3092 
    3093 > view matrix models #7,1,0,0,-65.422,0,1,0,-60.829,0,0,1,-69.057
    3094 
    3095 > ui mousemode right "rotate selected models"
    3096 
    3097 > view matrix models
    3098 > #7,-0.44906,0.62428,0.63923,-47.882,-0.83076,-0.55508,-0.041522,263.31,0.32891,-0.5497,0.76789,-6.0495
    3099 
    3100 > ui mousemode right "translate selected models"
    3101 
    3102 > view matrix models
    3103 > #7,-0.44906,0.62428,0.63923,-43.112,-0.83076,-0.55508,-0.041522,259.52,0.32891,-0.5497,0.76789,-3.3226
    3104 
    3105 > view matrix models
    3106 > #7,-0.44906,0.62428,0.63923,-46.691,-0.83076,-0.55508,-0.041522,257.64,0.32891,-0.5497,0.76789,-5.4256
    3107 
    3108 > view matrix models
    3109 > #7,-0.44906,0.62428,0.63923,-43.086,-0.83076,-0.55508,-0.041522,254.57,0.32891,-0.5497,0.76789,-5.2175
    3110 
    3111 > ui tool show "Fit in Map"
    3112 
    3113 > fitmap #7 inMap #1
    3114 
    3115 Fit map relion_locres_filtered.mrc in map
    3116 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc using 3812 points 
    3117 correlation = 0.2373, correlation about mean = 0.07089, overlap = 11.07 
    3118 steps = 116, shift = 1.21, angle = 8.84 degrees 
    3119  
    3120 Position of relion_locres_filtered.mrc (#7) relative to
    3121 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    3122 Matrix rotation and translation 
    3123 -0.36461695 0.73265397 0.57469351 -59.14787422 
    3124 -0.87490183 -0.48082660 0.05790126 236.29988230 
    3125 0.31874951 -0.48168862 0.81631784 -18.80617873 
    3126 Axis -0.31464704 0.14924672 -0.93740208 
    3127 Axis point 41.71559551 127.71968026 0.00000000 
    3128 Rotation angle (degrees) 120.96824033 
    3129 Shift along axis 71.50663710 
    3130  
    3131 
    3132 > rename #7 mOCT1-3TC
    3133 
    3134 > select clear
    3135 
    3136 [Repeated 1 time(s)]
    3137 
    3138 > rename #7 mOCT1-3TC.mrc
    3139 
    3140 > open
    3141 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-3TC_Model/RealSpaceRefine_6/mOCT1-3TC-
    3142 > coot-14_real_space_refined_006.pdb
    3143 
    3144 Chain information for mOCT1-3TC-coot-14_real_space_refined_006.pdb #8 
    3145 --- 
    3146 Chain | Description 
    3147 A | No description available 
    3148  
    3149 
    3150 > ui tool show Matchmaker
    3151 
    3152 > matchmaker #!8 to #5
    3153 
    3154 Parameters 
    3155 --- 
    3156 Chain pairing | bb 
    3157 Alignment algorithm | Needleman-Wunsch 
    3158 Similarity matrix | BLOSUM-62 
    3159 SS fraction | 0.3 
    3160 Gap open (HH/SS/other) | 18/18/6 
    3161 Gap extend | 1 
    3162 SS matrix |  |  | H | S | O 
    3163 ---|---|---|--- 
    3164 H | 6 | -9 | -6 
    3165 S |  | 6 | -6 
    3166 O |  |  | 4 
    3167 Iteration cutoff | 2 
    3168  
    3169 Matchmaker mOCT1-VB1_real_space_refined_014.pdb, chain A (#5) with mOCT1-3TC-
    3170 coot-14_real_space_refined_006.pdb, chain A (#8), sequence alignment score =
    3171 2352.2 
    3172 RMSD between 450 pruned atom pairs is 0.409 angstroms; (across all 450 pairs:
    3173 0.409) 
    3174  
    3175 
    3176 > hide #!1 models
    3177 
    3178 > hide #!7 models
    3179 
    3180 > show #!1 models
    3181 
    3182 > hide #!8 models
    3183 
    3184 > show #!7 models
    3185 
    3186 > select add #7
    3187 
    3188 2 models selected 
    3189 
    3190 > ui mousemode right "rotate selected models"
    3191 
    3192 > view matrix models
    3193 > #7,0.49719,-0.57211,-0.6523,173.98,0.80196,0.58997,0.093813,-133.23,0.33116,-0.56976,0.75214,0.34956
    3194 
    3195 > ui mousemode right "translate selected models"
    3196 
    3197 > view matrix models
    3198 > #7,0.49719,-0.57211,-0.6523,164.87,0.80196,0.58997,0.093813,-137.47,0.33116,-0.56976,0.75214,-2.3096
    3199 
    3200 > fitmap #7 inMap #1
    3201 
    3202 Fit map mOCT1-3TC.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    3203 using 3812 points 
    3204 correlation = 0.9181, correlation about mean = 0.7496, overlap = 65.08 
    3205 steps = 160, shift = 6.4, angle = 20.1 degrees 
    3206  
    3207 Position of mOCT1-3TC.mrc (#7) relative to
    3208 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    3209 Matrix rotation and translation 
    3210 0.27009123 -0.75134279 -0.60210857 210.67160095 
    3211 0.83888334 0.49056205 -0.23584655 -78.20606144 
    3212 0.47257322 -0.44139877 0.76278546 -39.17036140 
    3213 Axis -0.10648785 -0.55674686 0.82382842 
    3214 Axis point 169.78551241 113.86943556 0.00000000 
    3215 Rotation angle (degrees) 74.82789173 
    3216 Shift along axis -11.16264322 
    3217  
    3218 
    3219 > fitmap #8 inMap #7
    3220 
    3221 Fit molecule mOCT1-3TC-coot-14_real_space_refined_006.pdb (#8) to map
    3222 mOCT1-3TC.mrc (#7) using 7048 atoms 
    3223 average map value = 0.01706, steps = 60 
    3224 shifted from previous position = 0.0823 
    3225 rotated from previous position = 0.357 degrees 
    3226 atoms outside contour = 4146, contour level = 0.012041 
    3227  
    3228 Position of mOCT1-3TC-coot-14_real_space_refined_006.pdb (#8) relative to
    3229 mOCT1-3TC.mrc (#7) coordinates: 
    3230 Matrix rotation and translation 
    3231 0.99999991 -0.00005602 -0.00043067 0.07339565 
    3232 0.00005621 0.99999991 0.00043709 -0.06044298 
    3233 0.00043064 -0.00043712 0.99999982 0.02180230 
    3234 Axis -0.70938425 -0.69891365 0.09106970 
    3235 Axis point 0.00000000 51.44490735 150.82453668 
    3236 Rotation angle (degrees) 0.03530433 
    3237 Shift along axis -0.00783577 
    3238  
    3239 
    3240 > show #!8 models
    3241 
    3242 > hide #!8 models
    3243 
    3244 > select subtract #7
    3245 
    3246 Nothing selected 
    3247 
    3248 > hide #!1 models
    3249 
    3250 > show #!8 models
    3251 
    3252 > select ::name="3TC"
    3253 
    3254 26 atoms, 27 bonds, 1 residue, 1 model selected 
    3255 
    3256 > select add #8
    3257 
    3258 7048 atoms, 7109 bonds, 1 pseudobond, 486 residues, 2 models selected 
    3259 
    3260 > color (#!8 & sel) white
    3261 
    3262 > select ::name="3TC"
    3263 
    3264 26 atoms, 27 bonds, 1 residue, 1 model selected 
    3265 
    3266 > color sel red
    3267 
    3268 > view sel
    3269 
    3270 > volume #7 step 1
    3271 
    3272 > color zone #7 near #8 distance 4.98
    3273 
    3274 > volume splitbyzone #7
    3275 
    3276 Opened mOCT1-3TC.mrc 0 as #9.1, grid size 320,320,320, pixel 0.83, shown at
    3277 level 0.012, step 1, values float32 
    3278 Opened mOCT1-3TC.mrc 1 as #9.2, grid size 320,320,320, pixel 0.83, shown at
    3279 level 0.012, step 1, values float32 
    3280 Opened mOCT1-3TC.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at
    3281 level 0.012, step 1, values float32 
    3282 
    3283 > close #9.2
    3284 
    3285 > close #9.1
    3286 
    3287 > color #9.3 white models
    3288 
    3289 > color #9.3 #ffffb2ff models
    3290 
    3291 > color #9.3 #ffffb296 models
    3292 
    3293 > select #8/A:447
    3294 
    3295 19 atoms, 18 bonds, 1 residue, 1 model selected 
    3296 
    3297 > select add #8
    3298 
    3299 7048 atoms, 7109 bonds, 1 pseudobond, 486 residues, 2 models selected 
    3300 
    3301 > color #8 #bb22ffff
    3302 
    3303 > color #8 #b2fffbff
    3304 
    3305 > color #8 #b2ffb2ff
    3306 
    3307 > color (#!8 & sel) byhetero
    3308 
    3309 > select clear
    3310 
    3311 [Repeated 1 time(s)]
    3312 
    3313 > save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
    3314 > density.cxs" includeMaps true
    3315 
    3316 > hide #!9.3 models
    3317 
    3318 > hide #!9 models
    3319 
    3320 > hide #!8 models
    3321 
    3322 > open
    3323 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-AZT_20240413/job307/relion_locres_filtered_flipz.mrc
    3324 
    3325 Opened relion_locres_filtered_flipz.mrc as #10, grid size 320,320,320, pixel
    3326 0.83, shown at level 0.00125, step 2, values float32 
    3327 
    3328 > show #!1 models
    3329 
    3330 > view
    3331 
    3332 > volume #1 level 0.3063
    3333 
    3334 > volume #10 step 1
    3335 
    3336 > volume #10 level 0.01019
    3337 
    3338 > rename #10 mOCT1-AZT.mrc
    3339 
    3340 > select add #10
    3341 
    3342 2 models selected 
    3343 
    3344 > view matrix models #10,1,0,0,-48.383,0,1,0,-77.671,0,0,1,-67.093
    3345 
    3346 > view matrix models #10,1,0,0,-54.836,0,1,0,-59.483,0,0,1,-63.826
    3347 
    3348 > ui mousemode right "rotate selected models"
    3349 
    3350 > view matrix models
    3351 > #10,0.55307,0.83192,0.044939,-108.96,-0.78881,0.54024,-0.29312,148.24,-0.26813,0.12666,0.95502,-37.718
    3352 
    3353 > ui mousemode right "translate selected models"
    3354 
    3355 > view matrix models
    3356 > #10,0.55307,0.83192,0.044939,-120.39,-0.78881,0.54024,-0.29312,136.85,-0.26813,0.12666,0.95502,-39.969
    3357 
    3358 > view matrix models
    3359 > #10,0.55307,0.83192,0.044939,-121.53,-0.78881,0.54024,-0.29312,137.41,-0.26813,0.12666,0.95502,-39.609
    3360 
    3361 > fitmap #10 inMap #1
    3362 
    3363 Fit map mOCT1-AZT.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    3364 using 33175 points 
    3365 correlation = 0.9169, correlation about mean = 0.7611, overlap = 495.2 
    3366 steps = 172, shift = 3.01, angle = 24.4 degrees 
    3367  
    3368 Position of mOCT1-AZT.mrc (#10) relative to
    3369 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    3370 Matrix rotation and translation 
    3371 0.17958596 0.98366820 0.01207312 -89.49221412 
    3372 -0.89232990 0.16805236 -0.41893408 218.60375344 
    3373 -0.41412105 0.06446147 0.90793639 -7.62218964 
    3374 Axis 0.24369569 0.21485858 -0.94575272 
    3375 Axis point 81.50821029 166.97786454 0.00000000 
    3376 Rotation angle (degrees) 82.65824965 
    3377 Shift along axis 32.36873253 
    3378  
    3379 
    3380 > view
    3381 
    3382 > view orient
    3383 
    3384 > ui tool show "Side View"
    3385 
    3386 > open
    3387 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-AZT_Model/RealSpaceRefine_4/mOCT1-AZT_14_real_space_refined_004.pdb
    3388 
    3389 Chain information for mOCT1-AZT_14_real_space_refined_004.pdb #11 
    3390 --- 
    3391 Chain | Description 
    3392 A | No description available 
    3393  
    3394 
    3395 > ui tool show Matchmaker
    3396 
    3397 > matchmaker #!11 to #5
    3398 
    3399 Parameters 
    3400 --- 
    3401 Chain pairing | bb 
    3402 Alignment algorithm | Needleman-Wunsch 
    3403 Similarity matrix | BLOSUM-62 
    3404 SS fraction | 0.3 
    3405 Gap open (HH/SS/other) | 18/18/6 
    3406 Gap extend | 1 
    3407 SS matrix |  |  | H | S | O 
    3408 ---|---|---|--- 
    3409 H | 6 | -9 | -6 
    3410 S |  | 6 | -6 
    3411 O |  |  | 4 
    3412 Iteration cutoff | 2 
    3413  
    3414 Matchmaker mOCT1-VB1_real_space_refined_014.pdb, chain A (#5) with
    3415 mOCT1-AZT_14_real_space_refined_004.pdb, chain A (#11), sequence alignment
    3416 score = 2367.3 
    3417 RMSD between 449 pruned atom pairs is 0.415 angstroms; (across all 449 pairs:
    3418 0.415) 
    3419  
    3420 
    3421 > fitmap #11 inMap #10
    3422 
    3423 Fit molecule mOCT1-AZT_14_real_space_refined_004.pdb (#11) to map
    3424 mOCT1-AZT.mrc (#10) using 7017 atoms 
    3425 average map value = 0.01592, steps = 48 
    3426 shifted from previous position = 0.0651 
    3427 rotated from previous position = 0.278 degrees 
    3428 atoms outside contour = 3029, contour level = 0.010186 
    3429  
    3430 Position of mOCT1-AZT_14_real_space_refined_004.pdb (#11) relative to
    3431 mOCT1-AZT.mrc (#10) coordinates: 
    3432 Matrix rotation and translation 
    3433 -0.89530533 -0.39092164 -0.21356179 331.89133766 
    3434 0.43778783 -0.68362766 -0.58394781 243.21431714 
    3435 0.08228108 -0.61630634 0.78319622 99.39179726 
    3436 Axis -0.03674901 -0.33598352 0.94115067 
    3437 Axis point 137.92729950 180.24940846 0.00000000 
    3438 Rotation angle (degrees) 153.87927506 
    3439 Shift along axis -0.37002346 
    3440  
    3441 
    3442 > hide #!1 models
    3443 
    3444 > select ::name="AZZ"
    3445 
    3446 19 atoms, 20 bonds, 1 residue, 1 model selected 
    3447 
    3448 > hide #!10 models
    3449 
    3450 > select add #11
    3451 
    3452 7017 atoms, 7080 bonds, 1 pseudobond, 483 residues, 2 models selected 
    3453 
    3454 > select subtract #11
    3455 
    3456 Nothing selected 
    3457 
    3458 > select add #11
    3459 
    3460 7017 atoms, 7080 bonds, 1 pseudobond, 483 residues, 2 models selected 
    3461 
    3462 > color (#!11 & sel) white
    3463 
    3464 > color #11 #aaaaffff
    3465 
    3466 > color (#!11 & sel) white
    3467 
    3468 > select ::name="AZZ"
    3469 
    3470 19 atoms, 20 bonds, 1 residue, 1 model selected 
    3471 
    3472 > color sel red
    3473 
    3474 > color zone #10 near #11 distance 4.98
    3475 
    3476 > show #!10 models
    3477 
    3478 > volume splitbyzone #10
    3479 
    3480 Opened mOCT1-AZT.mrc 0 as #12.1, grid size 320,320,320, pixel 0.83, shown at
    3481 level 0.0102, step 1, values float32 
    3482 Opened mOCT1-AZT.mrc 1 as #12.2, grid size 320,320,320, pixel 0.83, shown at
    3483 level 0.0102, step 1, values float32 
    3484 Opened mOCT1-AZT.mrc 2 as #12.3, grid size 320,320,320, pixel 0.83, shown at
    3485 level 0.0102, step 1, values float32 
    3486 
    3487 > close #12.2
    3488 
    3489 > close #12.1
    3490 
    3491 > color #12.3 #ff0000fe models
    3492 
    3493 > color #12.3 #ff000096 models
    3494 
    3495 > color #12.3 #ffffff96 models
    3496 
    3497 > color #12.3 #ffffb296 models
    3498 
    3499 > color #11 #aaffffff
    3500 
    3501 > color #11 #aaaaffff
    3502 
    3503 > select add #11
    3504 
    3505 7017 atoms, 7080 bonds, 1 pseudobond, 483 residues, 2 models selected 
    3506 
    3507 > color (#!11 & sel) byhetero
    3508 
    3509 > select clear
    3510 
    3511 > show #!3 models
    3512 
    3513 > hide #!3 models
    3514 
    3515 > save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
    3516 > density.cxs" includeMaps true
    3517 
    3518 > hide #!12.3 models
    3519 
    3520 > hide #!12 models
    3521 
    3522 > hide #!11 models
    3523 
    3524 > show #!1 models
    3525 
    3526 > open
    3527 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-MTF_20240702/job350/postprocess.mrc
    3528 
    3529 Opened postprocess.mrc as #13, grid size 320,320,320, pixel 0.83, shown at
    3530 level 0.00595, step 2, values float32 
    3531 
    3532 > volume #13 step 1
    3533 
    3534 > volume #13 level 0.02012
    3535 
    3536 > select add #13
    3537 
    3538 2 models selected 
    3539 
    3540 > view matrix models #13,1,0,0,-56.643,0,1,0,-72.238,0,0,1,-68.565
    3541 
    3542 > ui mousemode right "rotate selected models"
    3543 
    3544 > view matrix models
    3545 > #13,0.02465,-0.61986,0.78433,49.618,-0.43145,0.70114,0.56768,-50.105,-0.9018,-0.35239,-0.25015,252.26
    3546 
    3547 > ui mousemode right "translate selected models"
    3548 
    3549 > view matrix models
    3550 > #13,0.02465,-0.61986,0.78433,42.91,-0.43145,0.70114,0.56768,-47.812,-0.9018,-0.35239,-0.25015,260.75
    3551 
    3552 > view matrix models
    3553 > #13,0.02465,-0.61986,0.78433,45.137,-0.43145,0.70114,0.56768,-48.218,-0.9018,-0.35239,-0.25015,267.86
    3554 
    3555 > rename #13 mOCT1-MTF.mrc
    3556 
    3557 > open
    3558 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-MTF_20240603/RealSpaceRefine_3/mOCT1_MTF-
    3559 > coot-9_real_space_refined_003.pdb
    3560 
    3561 Chain information for mOCT1_MTF-coot-9_real_space_refined_003.pdb #14 
    3562 --- 
    3563 Chain | Description 
    3564 A | No description available 
    3565  
    3566 
    3567 > fitmap #13 inMap #1
    3568 
    3569 Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    3570 using 17817 points 
    3571 correlation = 0.2983, correlation about mean = 0.07385, overlap = 82.29 
    3572 steps = 200, shift = 2.4, angle = 7.61 degrees 
    3573  
    3574 Position of mOCT1-MTF.mrc (#13) relative to
    3575 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    3576 Matrix rotation and translation 
    3577 -0.05771312 -0.64461025 0.76232987 59.74942259 
    3578 -0.34050237 0.73052504 0.59193860 -66.21901607 
    3579 -0.93847075 -0.22541250 -0.26165220 256.68697920 
    3580 Axis -0.42762978 0.88984156 0.15910615 
    3581 Axis point 123.33045199 0.00000000 117.21732044 
    3582 Rotation angle (degrees) 107.12276965 
    3583 Shift along axis -43.63458901 
    3584  
    3585 
    3586 > select subtract #13
    3587 
    3588 Nothing selected 
    3589 
    3590 > select add #13
    3591 
    3592 2 models selected 
    3593 
    3594 > ui mousemode right "rotate selected models"
    3595 
    3596 > view matrix models
    3597 > #13,0.50114,0.40107,-0.76681,42.081,-0.045209,-0.87277,-0.48604,255.79,-0.86419,0.27824,-0.41924,198.29
    3598 
    3599 > ui mousemode right "translate selected models"
    3600 
    3601 > view matrix models
    3602 > #13,0.50114,0.40107,-0.76681,41.903,-0.045209,-0.87277,-0.48604,247.49,-0.86419,0.27824,-0.41924,198.18
    3603 
    3604 > view matrix models
    3605 > #13,0.50114,0.40107,-0.76681,53.046,-0.045209,-0.87277,-0.48604,251.12,-0.86419,0.27824,-0.41924,198.38
    3606 
    3607 > fitmap #13 inMap #1
    3608 
    3609 Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    3610 using 17817 points 
    3611 correlation = 0.2273, correlation about mean = 0.06656, overlap = 59.06 
    3612 steps = 120, shift = 2.59, angle = 4.72 degrees 
    3613  
    3614 Position of mOCT1-MTF.mrc (#13) relative to
    3615 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    3616 Matrix rotation and translation 
    3617 0.43566959 0.38627366 -0.81300964 69.55864121 
    3618 -0.07375796 -0.88487887 -0.45994473 251.91510217 
    3619 -0.89707959 0.26034986 -0.35702406 194.41028021 
    3620 Axis 0.83873143 0.09789343 -0.53567385 
    3621 Axis point 0.00000000 97.27212052 153.57991582 
    3622 Rotation angle (degrees) 154.57081238 
    3623 Shift along axis -21.13865268 
    3624  
    3625 
    3626 > view matrix models
    3627 > #13,0.43567,0.38627,-0.81301,67.4,-0.073758,-0.88488,-0.45994,259.27,-0.89708,0.26035,-0.35702,197.15
    3628 
    3629 > ui mousemode right "rotate selected models"
    3630 
    3631 > view matrix models
    3632 > #13,0.3307,0.47313,-0.81657,68.962,0.20831,-0.88051,-0.42581,219.2,-0.92046,-0.029281,-0.38974,244.12
    3633 
    3634 > view matrix models
    3635 > #13,0.3796,0.48184,-0.78977,58.246,0.18592,-0.87598,-0.44507,223.83,-0.90628,0.022112,-0.42211,239.42
    3636 
    3637 > ui mousemode right "translate selected models"
    3638 
    3639 > view matrix models
    3640 > #13,0.3796,0.48184,-0.78977,53.846,0.18592,-0.87598,-0.44507,217.81,-0.90628,0.022112,-0.42211,235.11
    3641 
    3642 > fitmap #13 inMap #1
    3643 
    3644 Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    3645 using 17817 points 
    3646 correlation = 0.2652, correlation about mean = 0.06679, overlap = 73.72 
    3647 steps = 92, shift = 1.81, angle = 5.01 degrees 
    3648  
    3649 Position of mOCT1-MTF.mrc (#13) relative to
    3650 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    3651 Matrix rotation and translation 
    3652 0.31415893 0.53789144 -0.78228958 53.81386032 
    3653 0.19698588 -0.84300825 -0.50053338 220.95415625 
    3654 -0.92870918 0.00314703 -0.37079559 234.49017112 
    3655 Axis 0.80514260 0.23405449 -0.54494394 
    3656 Axis point 0.00000000 81.07236056 158.23174632 
    3657 Rotation angle (degrees) 161.77257653 
    3658 Shift along axis -32.74085292 
    3659  
    3660 
    3661 > view matrix models
    3662 > #13,0.31416,0.53789,-0.78229,60.198,0.19699,-0.84301,-0.50053,217.39,-0.92871,0.003147,-0.3708,234.22
    3663 
    3664 > fitmap #13 inMap #1
    3665 
    3666 Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    3667 using 17817 points 
    3668 correlation = 0.2449, correlation about mean = 0.05515, overlap = 65.5 
    3669 steps = 80, shift = 1.45, angle = 5.73 degrees 
    3670  
    3671 Position of mOCT1-MTF.mrc (#13) relative to
    3672 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    3673 Matrix rotation and translation 
    3674 0.28419679 0.60053681 -0.74738728 50.81854511 
    3675 0.27816291 -0.79764719 -0.53514891 205.19579930 
    3676 -0.91752798 -0.05580782 -0.39373584 245.12613641 
    3677 Axis 0.79598780 0.28253351 -0.53533003 
    3678 Axis point 0.00000000 71.54715698 160.41463451 
    3679 Rotation angle (degrees) 162.47642045 
    3680 Shift along axis -32.79775064 
    3681  
    3682 
    3683 > view matrix models
    3684 > #13,0.2842,0.60054,-0.74739,49.177,0.27816,-0.79765,-0.53515,206.5,-0.91753,-0.055808,-0.39374,243.99
    3685 
    3686 > fitmap #13 inMap #1
    3687 
    3688 Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    3689 using 17817 points 
    3690 correlation = 0.3559, correlation about mean = 0.151, overlap = 107.2 
    3691 steps = 88, shift = 2.33, angle = 2.34 degrees 
    3692  
    3693 Position of mOCT1-MTF.mrc (#13) relative to
    3694 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    3695 Matrix rotation and translation 
    3696 0.29378487 0.57675594 -0.76226180 52.65591556 
    3697 0.29516509 -0.81321822 -0.50155130 203.18767751 
    3698 -0.90915787 -0.07764488 -0.40914943 245.95334709 
    3699 Axis 0.80029578 0.27732609 -0.53161726 
    3700 Axis point 0.00000000 73.19686532 158.33534093 
    3701 Rotation angle (degrees) 164.64234082 
    3702 Shift along axis -32.26349399 
    3703  
    3704 
    3705 > view matrix models
    3706 > #13,0.29378,0.57676,-0.76226,50.19,0.29517,-0.81322,-0.50155,203.5,-0.90916,-0.077645,-0.40915,251.78
    3707 
    3708 > fitmap #13 inMap #1
    3709 
    3710 Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    3711 using 17817 points 
    3712 correlation = 0.9033, correlation about mean = 0.6277, overlap = 419.6 
    3713 steps = 52, shift = 1.52, angle = 1.92 degrees 
    3714  
    3715 Position of mOCT1-MTF.mrc (#13) relative to
    3716 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    3717 Matrix rotation and translation 
    3718 0.29574252 0.60146473 -0.74214321 45.38180479 
    3719 0.29484975 -0.79643687 -0.52796964 204.44935424 
    3720 -0.90862533 -0.06267767 -0.41288198 249.74597785 
    3721 Axis 0.80005949 0.28626242 -0.52721784 
    3722 Axis point 0.00000000 72.71544700 159.79227740 
    3723 Rotation angle (degrees) 163.09499009 
    3724 Shift along axis -36.83622428 
    3725  
    3726 
    3727 > ui tool show Matchmaker
    3728 
    3729 > matchmaker #!14 to #5
    3730 
    3731 Parameters 
    3732 --- 
    3733 Chain pairing | bb 
    3734 Alignment algorithm | Needleman-Wunsch 
    3735 Similarity matrix | BLOSUM-62 
    3736 SS fraction | 0.3 
    3737 Gap open (HH/SS/other) | 18/18/6 
    3738 Gap extend | 1 
    3739 SS matrix |  |  | H | S | O 
    3740 ---|---|---|--- 
    3741 H | 6 | -9 | -6 
    3742 S |  | 6 | -6 
    3743 O |  |  | 4 
    3744 Iteration cutoff | 2 
    3745  
    3746 Matchmaker mOCT1-VB1_real_space_refined_014.pdb, chain A (#5) with mOCT1_MTF-
    3747 coot-9_real_space_refined_003.pdb, chain A (#14), sequence alignment score =
    3748 2355.8 
    3749 RMSD between 450 pruned atom pairs is 0.377 angstroms; (across all 450 pairs:
    3750 0.377) 
    3751  
    3752 
    3753 > select add #14
    3754 
    3755 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 4 models selected 
    3756 
    3757 > select subtract #13
    3758 
    3759 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected 
    3760 
    3761 > hide #!1 models
    3762 
    3763 > save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
    3764 > density.cxs" includeMaps true
    3765 
    3766 QXcbConnection: XCB error: 3 (BadWindow), sequence: 5891, resource id:
    3767 35654810, major code: 40 (TranslateCoords), minor code: 0 
    3768 
    3769 > color #14 #95cacdff
    3770 
    3771 > select ::name="MF8"
    3772 
    3773 22 atoms, 21 bonds, 1 residue, 1 model selected 
    3774 
    3775 > select add #14
    3776 
    3777 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected 
    3778 
    3779 > select subtract #14
    3780 
    3781 Nothing selected 
    3782 
    3783 > select add #14
    3784 
    3785 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected 
    3786 
    3787 > color (#!14 & sel) white
    3788 
    3789 > select ::name="MF8"
    3790 
    3791 22 atoms, 21 bonds, 1 residue, 1 model selected 
    3792 
    3793 > color sel red
    3794 
    3795 > color zone #10 near #11 distance 4.98
    3796 
    3797 > color zone #13 near #14 distance 4.98
    3798 
    3799 > hide #!14 models
    3800 
    3801 > show #!14 models
    3802 
    3803 > volume #13 level 0.0238
    3804 
    3805 > volume #13 level 0.02122
    3806 
    3807 > volume #13 level 0.01423
    3808 
    3809 > volume splitbyzone #13
    3810 
    3811 Opened mOCT1-MTF.mrc 0 as #15.1, grid size 320,320,320, pixel 0.83, shown at
    3812 level 0.0142, step 1, values float32 
    3813 Opened mOCT1-MTF.mrc 1 as #15.2, grid size 320,320,320, pixel 0.83, shown at
    3814 level 0.0142, step 1, values float32 
    3815 Opened mOCT1-MTF.mrc 2 as #15.3, grid size 320,320,320, pixel 0.83, shown at
    3816 level 0.0142, step 1, values float32 
    3817 
    3818 > close #15.1
    3819 
    3820 > close #15.2
    3821 
    3822 > volume #15.3 level 0.009273
    3823 
    3824 > volume #15.3 level 0.01703
    3825 
    3826 > close #15#15.3
    3827 
    3828 > select add #14
    3829 
    3830 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected 
    3831 
    3832 > show #!13 models
    3833 
    3834 > color zone #13 near #14 distance 4.88
    3835 
    3836 > color zone #13 near #14 distance 4.78
    3837 
    3838 > color zone #13 near #14 distance 4.68
    3839 
    3840 > color zone #13 near #14 distance 4.58
    3841 
    3842 > color zone #13 near #14 distance 4.48
    3843 
    3844 > color zone #13 near #14 distance 4.38
    3845 
    3846 > color zone #13 near #14 distance 4.28
    3847 
    3848 > color zone #13 near #14 distance 4.18
    3849 
    3850 > color zone #13 near #14 distance 4.08
    3851 
    3852 > color zone #13 near #14 distance 3.98
    3853 
    3854 > color zone #13 near #14 distance 3.88
    3855 
    3856 > color zone #13 near #14 distance 3.78
    3857 
    3858 > color zone #13 near #14 distance 3.68
    3859 
    3860 > color zone #13 near #14 distance 3.58
    3861 
    3862 > color zone #13 near #14 distance 3.48
    3863 
    3864 > color zone #13 near #14 distance 3.38
    3865 
    3866 [Repeated 1 time(s)]
    3867 
    3868 > volume splitbyzone #13
    3869 
    3870 Opened mOCT1-MTF.mrc 0 as #15.1, grid size 320,320,320, pixel 0.83, shown at
    3871 level 0.0142, step 1, values float32 
    3872 Opened mOCT1-MTF.mrc 1 as #15.2, grid size 320,320,320, pixel 0.83, shown at
    3873 level 0.0142, step 1, values float32 
    3874 Opened mOCT1-MTF.mrc 2 as #15.3, grid size 320,320,320, pixel 0.83, shown at
    3875 level 0.0142, step 1, values float32 
    3876 
    3877 > close #15.1-2
    3878 
    3879 > volume #15.3 level 0.009634
    3880 
    3881 > color zone #13 near #14 distance 3.28
    3882 
    3883 > color zone #13 near #14 distance 3.18
    3884 
    3885 > color zone #13 near #14 distance 3.08
    3886 
    3887 > close #15#15.3
    3888 
    3889 > show #!13 models
    3890 
    3891 > select add #13
    3892 
    3893 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 4 models selected 
    3894 
    3895 > select subtract #13
    3896 
    3897 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected 
    3898 
    3899 > color zone #13 near #14 distance 2.98
    3900 
    3901 > color zone #13 near #14 distance 2.88
    3902 
    3903 > color zone #13 near #14 distance 2.78
    3904 
    3905 > color zone #13 near #14 distance 2.68
    3906 
    3907 > color zone #13 near #14 distance 2.58
    3908 
    3909 > color zone #13 near #14 distance 2.48
    3910 
    3911 > volume #13 level 0.01681
    3912 
    3913 > fitmap #14 inMap #13
    3914 
    3915 Fit molecule mOCT1_MTF-coot-9_real_space_refined_003.pdb (#14) to map
    3916 mOCT1-MTF.mrc (#13) using 7044 atoms 
    3917 average map value = 0.01572, steps = 48 
    3918 shifted from previous position = 0.0765 
    3919 rotated from previous position = 0.266 degrees 
    3920 atoms outside contour = 4386, contour level = 0.016807 
    3921  
    3922 Position of mOCT1_MTF-coot-9_real_space_refined_003.pdb (#14) relative to
    3923 mOCT1-MTF.mrc (#13) coordinates: 
    3924 Matrix rotation and translation 
    3925 0.99946408 0.01781074 -0.02746495 0.87693504 
    3926 -0.01720783 0.99960910 0.02203450 -1.16466203 
    3927 0.02784666 -0.02155008 0.99937988 -1.14535630 
    3928 Axis -0.55418255 -0.70329295 -0.44526478 
    3929 Axis point 28.72708736 -0.00000000 48.38067452 
    3930 Rotation angle (degrees) 2.25364092 
    3931 Shift along axis 0.84310332 
    3932  
    3933 
    3934 > color zone #13 near #14 distance 2.48
    3935 
    3936 [Repeated 1 time(s)]
    3937 
    3938 > color single #13
    3939 
    3940 > color zone #13 near #14 distance 2.48
    3941 
    3942 > color zone #13 near #14 distance 2.38
    3943 
    3944 > color zone #13 near #14 distance 2.28
    3945 
    3946 > color zone #13 near #14 distance 2.18
    3947 
    3948 > color zone #13 near #14 distance 2.08
    3949 
    3950 > color zone #13 near #14 distance 1.98
    3951 
    3952 > color zone #13 near #14 distance 1.88
    3953 
    3954 > color zone #13 near #14 distance 1.78
    3955 
    3956 > color zone #13 near #14 distance 1.68
    3957 
    3958 > color zone #13 near #14 distance 1.58
    3959 
    3960 > color zone #13 near #14 distance 1.48
    3961 
    3962 > color zone #13 near #14 distance 1.38
    3963 
    3964 > color zone #13 near #14 distance 1.48
    3965 
    3966 > color zone #13 near #14 distance 1.58
    3967 
    3968 > color zone #13 near #14 distance 1.68
    3969 
    3970 > color zone #13 near #14 distance 1.78
    3971 
    3972 > color zone #13 near #14 distance 1.88
    3973 
    3974 > color zone #13 near #14 distance 1.98
    3975 
    3976 > volume #13 level 0.01957
    3977 
    3978 > color zone #13 near #14 distance 1.98
    3979 
    3980 > volume splitbyzone #13
    3981 
    3982 Opened mOCT1-MTF.mrc 0 as #15.1, grid size 320,320,320, pixel 0.83, shown at
    3983 level 0.0196, step 1, values float32 
    3984 Opened mOCT1-MTF.mrc 1 as #15.2, grid size 320,320,320, pixel 0.83, shown at
    3985 level 0.0196, step 1, values float32 
    3986 Opened mOCT1-MTF.mrc 2 as #15.3, grid size 320,320,320, pixel 0.83, shown at
    3987 level 0.0196, step 1, values float32 
    3988 
    3989 > close #15.1-2
    3990 
    3991 > color #15.3 yellow models
    3992 
    3993 > color #15.3 white models
    3994 
    3995 > color #15.3 #ffffb2ff models
    3996 
    3997 > color #15.3 #ffffb296 models
    3998 
    3999 > volume #15.3 level 0.01524
    4000 
    4001 > volume #15.3 level 0.0119
    4002 
    4003 > select subtract #14
    4004 
    4005 Nothing selected 
    4006 
    4007 > select add #14
    4008 
    4009 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected 
    4010 
    4011 > color #14 #55dd44ff
    4012 
    4013 > color #14 #5d42cdff
    4014 
    4015 > color #14 #5858cdff
    4016 
    4017 > color #14 #7d76cdff
    4018 
    4019 > color #14 #9d7bcdff
    4020 
    4021 > color #14 #cd75baff
    4022 
    4023 > color #14 #9381cdff
    4024 
    4025 > color (#!14 & sel) byhetero
    4026 
    4027 > select clear
    4028 
    4029 > save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
    4030 > density.cxs" includeMaps true
    4031 
    4032 > hide #!15.3 models
    4033 
    4034 > hide #!15 models
    4035 
    4036 > hide #!14 models
    4037 
    4038 > show #!1 models
    4039 
    4040 > open
    4041 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/job321/relion_locres_filtered.mrc
    4042 
    4043 Opened relion_locres_filtered.mrc as #16, grid size 320,320,320, pixel 0.83,
    4044 shown at level 0.00147, step 2, values float32 
    4045 
    4046 > volume #13 level 0.01846
    4047 
    4048 > volume #16 step 1
    4049 
    4050 > volume #16 level 0.01137
    4051 
    4052 > select add #16
    4053 
    4054 2 models selected 
    4055 
    4056 > ui mousemode right "rotate selected models"
    4057 
    4058 > view matrix models
    4059 > #16,0.91726,-0.046522,0.39555,-35.801,-0.13266,0.90075,0.41357,-25.02,-0.37554,-0.43183,0.82006,127.4
    4060 
    4061 > view matrix models
    4062 > #16,0.97308,0.0084656,-0.23031,32.94,-0.035652,0.99283,-0.11414,20.659,0.2277,0.11927,0.9664,-40.203
    4063 
    4064 > view matrix models
    4065 > #16,0.95291,-0.013325,0.30296,-32.366,-0.094841,0.93583,0.33946,-24.554,-0.28805,-0.35221,0.89049,96.605
    4066 
    4067 > view matrix models
    4068 > #16,0.68405,0.72927,0.015283,-53.826,0.65561,-0.6055,-0.45117,179.02,-0.31977,0.31864,-0.89231,251.74
    4069 
    4070 > view matrix models
    4071 > #16,-0.14871,0.82898,-0.53915,114.85,0.43367,-0.43531,-0.78894,230.9,-0.88872,-0.35114,-0.29476,331.38
    4072 
    4073 > view matrix models
    4074 > #16,-0.59154,0.6904,-0.41646,173.56,0.69281,0.17103,-0.70054,108.52,-0.41243,-0.70292,-0.57948,352.16
    4075 
    4076 > ui mousemode right "translate selected models"
    4077 
    4078 > view matrix models
    4079 > #16,-0.59154,0.6904,-0.41646,98.473,0.69281,0.17103,-0.70054,82.195,-0.41243,-0.70292,-0.57948,295.09
    4080 
    4081 > view matrix models
    4082 > #16,-0.59154,0.6904,-0.41646,115.7,0.69281,0.17103,-0.70054,51.467,-0.41243,-0.70292,-0.57948,297.87
    4083 
    4084 > view matrix models
    4085 > #16,-0.59154,0.6904,-0.41646,109.24,0.69281,0.17103,-0.70054,49.803,-0.41243,-0.70292,-0.57948,297.08
    4086 
    4087 > view matrix models
    4088 > #16,-0.59154,0.6904,-0.41646,112.5,0.69281,0.17103,-0.70054,41.909,-0.41243,-0.70292,-0.57948,292.69
    4089 
    4090 > ui mousemode right "rotate selected models"
    4091 
    4092 > view matrix models
    4093 > #16,-0.52634,0.62911,-0.57201,132.47,0.46428,-0.35094,-0.81319,152.81,-0.71233,-0.69359,-0.10737,267.76
    4094 
    4095 > view matrix models
    4096 > #16,-0.56071,0.74447,-0.36245,94.475,0.40226,-0.13769,-0.90511,145.91,-0.72373,-0.6533,-0.22227,279.35
    4097 
    4098 > ui mousemode right "translate selected models"
    4099 
    4100 > view matrix models
    4101 > #16,-0.56071,0.74447,-0.36245,91.988,0.40226,-0.13769,-0.90511,152.84,-0.72373,-0.6533,-0.22227,276.37
    4102 
    4103 > ui mousemode right "rotate selected models"
    4104 
    4105 > view matrix models
    4106 > #16,-0.69312,0.68147,-0.23491,100.24,0.41746,0.11382,-0.90154,118.42,-0.58764,-0.72294,-0.36338,286.3
    4107 
    4108 > rename #16 hOCT1-VB1.mrc
    4109 
    4110 > fitmap #16 inMap #1
    4111 
    4112 Fit map hOCT1-VB1.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    4113 using 29501 points 
    4114 correlation = 0.336, correlation about mean = 0.1558, overlap = 114.4 
    4115 steps = 148, shift = 3.34, angle = 5.64 degrees 
    4116  
    4117 Position of hOCT1-VB1.mrc (#16) relative to
    4118 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    4119 Matrix rotation and translation 
    4120 -0.66774800 0.66848229 -0.32748134 111.59775010 
    4121 0.47076725 0.03845367 -0.88141903 115.78397104 
    4122 -0.57662015 -0.74273329 -0.34037693 282.67572866 
    4123 Axis 0.39969377 0.71802066 -0.56981683 
    4124 Axis point 39.62225841 0.00000000 179.67701786 
    4125 Rotation angle (degrees) 170.00920250 
    4126 Shift along axis -33.33317846 
    4127  
    4128 
    4129 > ui mousemode right "translate selected models"
    4130 
    4131 > view matrix models
    4132 > #16,-0.66775,0.66848,-0.32748,111.72,0.47077,0.038454,-0.88142,115.95,-0.57662,-0.74273,-0.34038,288.9
    4133 
    4134 > fitmap #16 inMap #1
    4135 
    4136 Fit map hOCT1-VB1.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    4137 using 29501 points 
    4138 correlation = 0.7772, correlation about mean = 0.5328, overlap = 352.7 
    4139 steps = 60, shift = 1.34, angle = 1.92 degrees 
    4140  
    4141 Position of hOCT1-VB1.mrc (#16) relative to
    4142 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    4143 Matrix rotation and translation 
    4144 -0.68896253 0.65809895 -0.30370448 111.90845021 
    4145 0.45027206 0.06027049 -0.89085495 116.65862228 
    4146 -0.56796628 -0.75051532 -0.33784768 287.44343290 
    4147 Axis 0.38522072 0.72537689 -0.57046767 
    4148 Axis point 41.86637964 0.00000000 181.62562393 
    4149 Rotation angle (degrees) 169.50470225 
    4150 Shift along axis -36.24626372 
    4151  
    4152 
    4153 > view matrix models
    4154 > #16,-0.68896,0.6581,-0.3037,110.15,0.45027,0.06027,-0.89085,119.19,-0.56797,-0.75052,-0.33785,287.46
    4155 
    4156 > fitmap #16 inMap #1
    4157 
    4158 Fit map hOCT1-VB1.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    4159 using 29501 points 
    4160 correlation = 0.7772, correlation about mean = 0.5327, overlap = 352.7 
    4161 steps = 72, shift = 3.09, angle = 0.0182 degrees 
    4162  
    4163 Position of hOCT1-VB1.mrc (#16) relative to
    4164 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    4165 Matrix rotation and translation 
    4166 -0.68902052 0.65795875 -0.30387662 111.96278841 
    4167 0.45022908 0.06002731 -0.89089309 116.69902951 
    4168 -0.56793001 -0.75065771 -0.33759222 287.41226501 
    4169 Axis 0.38519550 0.72529614 -0.57058737 
    4170 Axis point 41.87016659 0.00000000 181.64241189 
    4171 Rotation angle (degrees) 169.51189271 
    4172 Shift along axis -36.22489055 
    4173  
    4174 
    4175 > fitmap #16 inMap #1
    4176 
    4177 Fit map hOCT1-VB1.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    4178 using 29501 points 
    4179 correlation = 0.7772, correlation about mean = 0.5328, overlap = 352.7 
    4180 steps = 36, shift = 0.00448, angle = 0.00722 degrees 
    4181  
    4182 Position of hOCT1-VB1.mrc (#16) relative to
    4183 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    4184 Matrix rotation and translation 
    4185 -0.68898476 0.65802671 -0.30381055 111.93916561 
    4186 0.45024501 0.06010903 -0.89087953 116.68451889 
    4187 -0.56796077 -0.75059160 -0.33768744 287.42460080 
    4188 Axis 0.38521270 0.72532270 -0.57054198 
    4189 Axis point 41.86758112 0.00000000 181.63640339 
    4190 Rotation angle (degrees) 169.50839167 
    4191 Shift along axis -36.23348002 
    4192  
    4193 
    4194 > open
    4195 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/RealSpaceRefine_10/hOCT1-VB_Dock2_real_space_refined_010.pdb
    4196 
    4197 Chain information for hOCT1-VB_Dock2_real_space_refined_010.pdb #17 
    4198 --- 
    4199 Chain | Description 
    4200 A | No description available 
    4201  
    4202 
    4203 > ui tool show Matchmaker
    4204 
    4205 > matchmaker #!17 to #5
    4206 
    4207 Parameters 
    4208 --- 
    4209 Chain pairing | bb 
    4210 Alignment algorithm | Needleman-Wunsch 
    4211 Similarity matrix | BLOSUM-62 
    4212 SS fraction | 0.3 
    4213 Gap open (HH/SS/other) | 18/18/6 
    4214 Gap extend | 1 
    4215 SS matrix |  |  | H | S | O 
    4216 ---|---|---|--- 
    4217 H | 6 | -9 | -6 
    4218 S |  | 6 | -6 
    4219 O |  |  | 4 
    4220 Iteration cutoff | 2 
    4221  
    4222 Matchmaker mOCT1-VB1_real_space_refined_014.pdb, chain A (#5) with
    4223 hOCT1-VB_Dock2_real_space_refined_010.pdb, chain A (#17), sequence alignment
    4224 score = 1980 
    4225 RMSD between 416 pruned atom pairs is 0.792 angstroms; (across all 446 pairs:
    4226 1.346) 
    4227  
    4228 
    4229 > fitmap #17 inMap #16
    4230 
    4231 Fit molecule hOCT1-VB_Dock2_real_space_refined_010.pdb (#17) to map
    4232 hOCT1-VB1.mrc (#16) using 3479 atoms 
    4233 average map value = 0.02025, steps = 64 
    4234 shifted from previous position = 0.153 
    4235 rotated from previous position = 0.521 degrees 
    4236 atoms outside contour = 1063, contour level = 0.011373 
    4237  
    4238 Position of hOCT1-VB_Dock2_real_space_refined_010.pdb (#17) relative to
    4239 hOCT1-VB1.mrc (#16) coordinates: 
    4240 Matrix rotation and translation 
    4241 0.99999651 0.00186028 0.00187897 -0.40239474 
    4242 -0.00185675 0.99999652 -0.00187607 0.55801929 
    4243 -0.00188246 0.00187257 0.99999648 0.09469763 
    4244 Axis 0.57831092 0.58028383 -0.57343453 
    4245 Axis point 61.09212114 0.00000000 225.59585813 
    4246 Rotation angle (degrees) 0.18569746 
    4247 Shift along axis 0.03679741 
    4248  
    4249 
    4250 > fitmap #17 inMap #16
    4251 
    4252 Fit molecule hOCT1-VB_Dock2_real_space_refined_010.pdb (#17) to map
    4253 hOCT1-VB1.mrc (#16) using 3479 atoms 
    4254 average map value = 0.02025, steps = 28 
    4255 shifted from previous position = 0.0153 
    4256 rotated from previous position = 0.0146 degrees 
    4257 atoms outside contour = 1064, contour level = 0.011373 
    4258  
    4259 Position of hOCT1-VB_Dock2_real_space_refined_010.pdb (#17) relative to
    4260 hOCT1-VB1.mrc (#16) coordinates: 
    4261 Matrix rotation and translation 
    4262 0.99999599 0.00211002 0.00188874 -0.43726655 
    4263 -0.00210638 0.99999592 -0.00192887 0.59237860 
    4264 -0.00189280 0.00192488 0.99999636 0.07510223 
    4265 Axis 0.56254941 0.55200867 -0.61548727 
    4266 Axis point 271.69369003 217.02489508 0.00000000 
    4267 Rotation angle (degrees) 0.19625280 
    4268 Shift along axis 0.03478962 
    4269  
    4270 
    4271 > hide #!1 models
    4272 
    4273 > select add #17
    4274 
    4275 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 4 models selected 
    4276 
    4277 > select subtract #16
    4278 
    4279 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 2 models selected 
    4280 
    4281 > color (#!17 & sel) white
    4282 
    4283 > select clear
    4284 
    4285 > select ::name="VIB"
    4286 
    4287 18 atoms, 19 bonds, 1 residue, 1 model selected 
    4288 
    4289 > color sel red
    4290 
    4291 > color zone #16 near #17 distance 4.98
    4292 
    4293 > color zone #16 near #17 distance 4.88
    4294 
    4295 > color zone #16 near #17 distance 4.78
    4296 
    4297 > color zone #16 near #17 distance 4.68
    4298 
    4299 > color zone #16 near #17 distance 4.58
    4300 
    4301 > color zone #16 near #17 distance 4.48
    4302 
    4303 > color zone #16 near #17 distance 4.38
    4304 
    4305 > color zone #16 near #17 distance 4.28
    4306 
    4307 > color zone #16 near #17 distance 4.18
    4308 
    4309 > color zone #16 near #17 distance 4.08
    4310 
    4311 > color zone #16 near #17 distance 3.98
    4312 
    4313 > color zone #16 near #17 distance 3.88
    4314 
    4315 > color zone #16 near #17 distance 3.78
    4316 
    4317 > color zone #16 near #17 distance 3.68
    4318 
    4319 > color zone #16 near #17 distance 3.58
    4320 
    4321 > color zone #16 near #17 distance 3.48
    4322 
    4323 > color zone #16 near #17 distance 3.38
    4324 
    4325 > color zone #16 near #17 distance 3.28
    4326 
    4327 > color sel white
    4328 
    4329 > select ::name="VIB"
    4330 
    4331 18 atoms, 19 bonds, 1 residue, 1 model selected 
    4332 
    4333 > color sel red
    4334 
    4335 > select add #16
    4336 
    4337 18 atoms, 19 bonds, 1 residue, 3 models selected 
    4338 
    4339 > select add #17
    4340 
    4341 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 4 models selected 
    4342 
    4343 > select subtract #17
    4344 
    4345 2 models selected 
    4346 
    4347 > color #16.1 white
    4348 
    4349 > color zone #16 near #17 distance 3.28
    4350 
    4351 > color zone #16 near #17 distance 3.18
    4352 
    4353 > color zone #16 near #17 distance 3.08
    4354 
    4355 > color zone #16 near #17 distance 2.98
    4356 
    4357 > color zone #16 near #17 distance 2.88
    4358 
    4359 > color zone #16 near #17 distance 2.98
    4360 
    4361 > color zone #16 near #17 distance 3.08
    4362 
    4363 > color zone #16 near #17 distance 3.18
    4364 
    4365 > color zone #16 near #17 distance 3.28
    4366 
    4367 > color zone #16 near #17 distance 3.38
    4368 
    4369 [Repeated 1 time(s)]
    4370 
    4371 > volume splitbyzone #16
    4372 
    4373 Opened hOCT1-VB1.mrc 0 as #18.1, grid size 320,320,320, pixel 0.83, shown at
    4374 level 0.0114, step 1, values float32 
    4375 Opened hOCT1-VB1.mrc 1 as #18.2, grid size 320,320,320, pixel 0.83, shown at
    4376 level 0.0114, step 1, values float32 
    4377 Opened hOCT1-VB1.mrc 2 as #18.3, grid size 320,320,320, pixel 0.83, shown at
    4378 level 0.0114, step 1, values float32 
    4379 
    4380 > close #18.1-2
    4381 
    4382 > color #18.3 yellow models
    4383 
    4384 > color #18.3 white models
    4385 
    4386 > color #18.3 #ffffb2ff models
    4387 
    4388 > color #18.3 #ffffb296 models
    4389 
    4390 > select add #17
    4391 
    4392 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 4 models selected 
    4393 
    4394 > select subtract #16
    4395 
    4396 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 2 models selected 
    4397 
    4398 > color #17 #6622bbff
    4399 
    4400 > color #17 #62be40ff
    4401 
    4402 > color (#!17 & sel) byhetero
    4403 
    4404 Drag select of 1 atoms, 1 bonds 
    4405 
    4406 > volume #18.3 level 0.006511
    4407 
    4408 > volume #18.3 level 0.01112
    4409 
    4410 > close #18#18.3
    4411 
    4412 > select add #17
    4413 
    4414 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 2 models selected 
    4415 
    4416 > color (#!17 & sel) white
    4417 
    4418 > select ::name="VIB"
    4419 
    4420 18 atoms, 19 bonds, 1 residue, 1 model selected 
    4421 
    4422 > color sel red
    4423 
    4424 > show #!16 models
    4425 
    4426 > color zone #16 near #17 distance 3.28
    4427 
    4428 > color zone #16 near #17 distance 3.18
    4429 
    4430 > color zone #16 near #17 distance 3.08
    4431 
    4432 > color zone #16 near #17 distance 2.98
    4433 
    4434 > color zone #16 near #17 distance 2.88
    4435 
    4436 > color zone #16 near #17 distance 2.78
    4437 
    4438 > color zone #16 near #17 distance 2.68
    4439 
    4440 > color zone #16 near #17 distance 2.58
    4441 
    4442 > color zone #16 near #17 distance 2.48
    4443 
    4444 > color zone #16 near #17 distance 2.38
    4445 
    4446 > color zone #16 near #17 distance 2.28
    4447 
    4448 > color zone #16 near #17 distance 2.18
    4449 
    4450 > color zone #16 near #17 distance 2.08
    4451 
    4452 > color zone #16 near #17 distance 1.98
    4453 
    4454 > color zone #16 near #17 distance 1.88
    4455 
    4456 > color zone #16 near #17 distance 1.78
    4457 
    4458 > color zone #16 near #17 distance 1.68
    4459 
    4460 > color zone #16 near #17 distance 1.78
    4461 
    4462 > color zone #16 near #17 distance 1.88
    4463 
    4464 > color zone #16 near #17 distance 1.98
    4465 
    4466 > color zone #16 near #17 distance 2.08
    4467 
    4468 > volume splitbyzone #16
    4469 
    4470 Opened hOCT1-VB1.mrc 0 as #18.1, grid size 320,320,320, pixel 0.83, shown at
    4471 level 0.0114, step 1, values float32 
    4472 Opened hOCT1-VB1.mrc 1 as #18.2, grid size 320,320,320, pixel 0.83, shown at
    4473 level 0.0114, step 1, values float32 
    4474 Opened hOCT1-VB1.mrc 2 as #18.3, grid size 320,320,320, pixel 0.83, shown at
    4475 level 0.0114, step 1, values float32 
    4476 
    4477 > close #18.1-2
    4478 
    4479 > color #18.3 white models
    4480 
    4481 > color #18.3 #ffffb2ff models
    4482 
    4483 > select add #18.3
    4484 
    4485 18 atoms, 19 bonds, 1 residue, 3 models selected 
    4486 
    4487 > color #18.3 #ffffb296 models
    4488 
    4489 > select subtract #18.3
    4490 
    4491 18 atoms, 19 bonds, 1 residue, 1 model selected 
    4492 
    4493 > select add #17
    4494 
    4495 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 2 models selected 
    4496 
    4497 > select subtract #17
    4498 
    4499 Nothing selected 
    4500 
    4501 > select add #17
    4502 
    4503 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 2 models selected 
    4504 
    4505 > color #17 #6622bbff
    4506 
    4507 > color #17 #62be40ff
    4508 
    4509 > color (#!17 & sel) byhetero
    4510 
    4511 > view
    4512 
    4513 > hide #!18.3 models
    4514 
    4515 > hide #!18 models
    4516 
    4517 > hide #!17 models
    4518 
    4519 > select subtract #17
    4520 
    4521 Nothing selected 
    4522 
    4523 > show #!1 models
    4524 
    4525 > open
    4526 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241004Krios_hOCT1-AZT/job154/postprocess_masked.mrc
    4527 
    4528 Opened postprocess_masked.mrc as #19, grid size 320,320,320, pixel 0.83, shown
    4529 at level 2.83e-06, step 2, values float32 
    4530 
    4531 > volume #19 step 1
    4532 
    4533 > volume #19 level 0.0131
    4534 
    4535 > select add #19
    4536 
    4537 2 models selected 
    4538 
    4539 > ui mousemode right "rotate selected models"
    4540 
    4541 > view matrix models
    4542 > #19,-0.93986,0.28611,-0.18654,253.04,-0.10485,-0.76147,-0.63967,340.05,-0.32506,-0.58164,0.74567,158.04
    4543 
    4544 > ui mousemode right "translate selected models"
    4545 
    4546 > view matrix models
    4547 > #19,-0.93986,0.28611,-0.18654,175.89,-0.10485,-0.76147,-0.63967,293,-0.32506,-0.58164,0.74567,91.801
    4548 
    4549 > view matrix models
    4550 > #19,-0.93986,0.28611,-0.18654,185.27,-0.10485,-0.76147,-0.63967,269.77,-0.32506,-0.58164,0.74567,91.027
    4551 
    4552 > view matrix models
    4553 > #19,-0.93986,0.28611,-0.18654,178.6,-0.10485,-0.76147,-0.63967,268.3,-0.32506,-0.58164,0.74567,89.593
    4554 
    4555 > rename #19 hOCT1-AZT.mrc
    4556 
    4557 > fitmap #19 inMap #16
    4558 
    4559 Fit map hOCT1-AZT.mrc in map hOCT1-VB1.mrc using 23475 points 
    4560 correlation = 0.9652, correlation about mean = 0.8232, overlap = 14.07 
    4561 steps = 112, shift = 2.59, angle = 19.3 degrees 
    4562  
    4563 Position of hOCT1-AZT.mrc (#19) relative to hOCT1-VB1.mrc (#16) coordinates: 
    4564 Matrix rotation and translation 
    4565 0.86934918 -0.02079803 -0.49376051 87.20318527 
    4566 -0.45396874 0.36123943 -0.81450504 253.58267245 
    4567 0.19530587 0.93224113 0.30460154 -57.13169181 
    4568 Axis 0.90642923 -0.35757337 -0.22478286 
    4569 Axis point 0.00000000 185.25380563 166.58335969 
    4570 Rotation angle (degrees) 74.47879004 
    4571 Shift along axis 1.21133072 
    4572  
    4573 
    4574 > open
    4575 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241004Krios_hOCT1-AZT/RealSpaceRefine_6/hOCT1_AZT-
    4576 > coot-2_real_space_refined_006.pdb
    4577 
    4578 Chain information for hOCT1_AZT-coot-2_real_space_refined_006.pdb #20 
    4579 --- 
    4580 Chain | Description 
    4581 A | No description available 
    4582  
    4583 
    4584 > ui tool show Matchmaker
    4585 
    4586 > matchmaker #!20 to #5
    4587 
    4588 Parameters 
    4589 --- 
    4590 Chain pairing | bb 
    4591 Alignment algorithm | Needleman-Wunsch 
    4592 Similarity matrix | BLOSUM-62 
    4593 SS fraction | 0.3 
    4594 Gap open (HH/SS/other) | 18/18/6 
    4595 Gap extend | 1 
    4596 SS matrix |  |  | H | S | O 
    4597 ---|---|---|--- 
    4598 H | 6 | -9 | -6 
    4599 S |  | 6 | -6 
    4600 O |  |  | 4 
    4601 Iteration cutoff | 2 
    4602  
    4603 Matchmaker mOCT1-VB1_real_space_refined_014.pdb, chain A (#5) with hOCT1_AZT-
    4604 coot-2_real_space_refined_006.pdb, chain A (#20), sequence alignment score =
    4605 1978 
    4606 RMSD between 414 pruned atom pairs is 0.849 angstroms; (across all 446 pairs:
    4607 1.482) 
    4608  
    4609 
    4610 > hide #!1 models
    4611 
    4612 > color #19 white models
    4613 
    4614 > select add #20
    4615 
    4616 3578 atoms, 3672 bonds, 1 pseudobond, 463 residues, 4 models selected 
    4617 
    4618 > color #20 white
    4619 
    4620 > hide #!19 models
    4621 
    4622 > select subtract #19
    4623 
    4624 3578 atoms, 3672 bonds, 1 pseudobond, 463 residues, 2 models selected 
    4625 
    4626 > select up
    4627 
    4628 2 atoms, 1 bond, 1 residue, 1 model selected 
    4629 
    4630 > select up
    4631 
    4632 19 atoms, 20 bonds, 1 residue, 1 model selected 
    4633 
    4634 > color sel red
    4635 
    4636 > color zone #19 near #20 distance 4.98
    4637 
    4638 > show #!19 models
    4639 
    4640 > select add #19
    4641 
    4642 19 atoms, 20 bonds, 1 residue, 3 models selected 
    4643 
    4644 > select subtract #19
    4645 
    4646 19 atoms, 20 bonds, 1 residue, 1 model selected 
    4647 
    4648 > color zone #19 near #20 distance 4.88
    4649 
    4650 > color zone #19 near #20 distance 4.78
    4651 
    4652 > color zone #19 near #20 distance 4.68
    4653 
    4654 > color zone #19 near #20 distance 4.58
    4655 
    4656 > color zone #19 near #20 distance 4.48
    4657 
    4658 > color zone #19 near #20 distance 4.38
    4659 
    4660 > color zone #19 near #20 distance 4.28
    4661 
    4662 > color zone #19 near #20 distance 4.18
    4663 
    4664 > color zone #19 near #20 distance 4.08
    4665 
    4666 > color zone #19 near #20 distance 3.98
    4667 
    4668 > color zone #19 near #20 distance 3.88
    4669 
    4670 > color zone #19 near #20 distance 3.78
    4671 
    4672 > color zone #19 near #20 distance 3.68
    4673 
    4674 > color zone #19 near #20 distance 3.58
    4675 
    4676 > color zone #19 near #20 distance 3.48
    4677 
    4678 > volume #19 level 0.01039
    4679 
    4680 > color zone #19 near #20 distance 3.38
    4681 
    4682 > color zone #19 near #20 distance 3.28
    4683 
    4684 > color zone #19 near #20 distance 3.18
    4685 
    4686 > color zone #19 near #20 distance 3.08
    4687 
    4688 > color zone #19 near #20 distance 2.98
    4689 
    4690 > color zone #19 near #20 distance 2.88
    4691 
    4692 > color zone #19 near #20 distance 2.78
    4693 
    4694 > color zone #19 near #20 distance 2.68
    4695 
    4696 > color zone #19 near #20 distance 2.58
    4697 
    4698 > color zone #19 near #20 distance 2.48
    4699 
    4700 > color zone #19 near #20 distance 2.38
    4701 
    4702 > color zone #19 near #20 distance 2.28
    4703 
    4704 > color zone #19 near #20 distance 2.18
    4705 
    4706 > color zone #19 near #20 distance 2.08
    4707 
    4708 > color zone #19 near #20 distance 1.98
    4709 
    4710 > color zone #19 near #20 distance 1.88
    4711 
    4712 > color zone #19 near #20 distance 1.78
    4713 
    4714 > color zone #19 near #20 distance 1.88
    4715 
    4716 > color zone #19 near #20 distance 1.98
    4717 
    4718 > color zone #19 near #20 distance 2.08
    4719 
    4720 [Repeated 1 time(s)]
    4721 
    4722 > volume splitbyzone #19
    4723 
    4724 Opened hOCT1-AZT.mrc 0 as #21.1, grid size 320,320,320, pixel 0.83, shown at
    4725 level 0.0104, step 1, values float32 
    4726 Opened hOCT1-AZT.mrc 1 as #21.2, grid size 320,320,320, pixel 0.83, shown at
    4727 level 0.0104, step 1, values float32 
    4728 Opened hOCT1-AZT.mrc 2 as #21.3, grid size 320,320,320, pixel 0.83, shown at
    4729 level 0.0104, step 1, values float32 
    4730 
    4731 > close #21.1-2
    4732 
    4733 > select add #20
    4734 
    4735 3578 atoms, 3672 bonds, 1 pseudobond, 463 residues, 2 models selected 
    4736 
    4737 > select subtract #20
    4738 
    4739 Nothing selected 
    4740 
    4741 > select add #20
    4742 
    4743 3578 atoms, 3672 bonds, 1 pseudobond, 463 residues, 2 models selected 
    4744 
    4745 > color #20 #773333ff
    4746 
    4747 > color #20 #733551ff
    4748 
    4749 > color (#!20 & sel) byhetero
    4750 
    4751 > select clear
    4752 
    4753 > color #21.3 #ff000096 models
    4754 
    4755 > color #21.3 #ffffff96 models
    4756 
    4757 > color #21.3 #ffffb296 models
    4758 
    4759 > volume #21.3 level 0.008896
    4760 
    4761 > hide #!21.3 models
    4762 
    4763 > hide #!21 models
    4764 
    4765 > hide #!20 models
    4766 
    4767 > save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
    4768 > density.cxs" includeMaps true
    4769 
    4770 QXcbConnection: XCB error: 3 (BadWindow), sequence: 59019, resource id:
    4771 35654939, major code: 40 (TranslateCoords), minor code: 0 
    4772 
    4773 > show #!3 models
    4774 
    4775 > show #!6.3 models
    4776 
    4777 > select ::name="ABC"
    4778 
    4779 42 atoms, 48 bonds, 2 residues, 1 model selected 
    4780 
    4781 > view sel
    4782 
    4783 > select clear
    4784 
    4785 > hide #!6.3 models
    4786 
    4787 > hide #!6 models
    4788 
    4789 > hide #!3 models
    4790 
    4791 > show #!2 models
    4792 
    4793 > show #!5 models
    4794 
    4795 > hide #!5 models
    4796 
    4797 > hide #!2 models
    4798 
    4799 > show #!8 models
    4800 
    4801 > show #!9.3 models
    4802 
    4803 > hide #!9.3 models
    4804 
    4805 > hide #!9 models
    4806 
    4807 > hide #!8 models
    4808 
    4809 > show #!11 models
    4810 
    4811 > show #!12.3 models
    4812 
    4813 > hide #!12.3 models
    4814 
    4815 > hide #!12 models
    4816 
    4817 > hide #!11 models
    4818 
    4819 > show #!14 models
    4820 
    4821 > show #!15 models
    4822 
    4823 > hide #!15 models
    4824 
    4825 > show #!15.3 models
    4826 
    4827 > hide #!14 models
    4828 
    4829 > hide #!15 models
    4830 
    4831 > hide #!15.3 models
    4832 
    4833 > show #!17 models
    4834 
    4835 > show #!18.3 models
    4836 
    4837 > hide #!18.3 models
    4838 
    4839 > hide #!18 models
    4840 
    4841 > hide #!17 models
    4842 
    4843 > show #!20 models
    4844 
    4845 > show #!21.3 models
    4846 
    4847 > save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
    4848 > density.cxs" includeMaps true
    4849 
    4850 > save
    4851 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1_structures_ligand_density.cxs
    4852 > includeMaps true
    4853 
    4854 [Repeated 1 time(s)]
    4855 
    4856 > close session
    4857 
    4858 > open
    4859 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AZT_20240729/0-coot-
    4860 > history.scm
    4861 
    4862 Unrecognized file suffix '.scm' 
    4863 
    4864 > open
    4865 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AZT_20240729/RealSpaceRefine_2/rOAT1-AZT_coot-4_real_space_refined_002.cif
    4866 
    4867 Summary of feedback from opening
    4868 /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AZT_20240729/RealSpaceRefine_2/rOAT1-AZT_coot-4_real_space_refined_002.cif 
    4869 --- 
    4870 warnings | Skipping chem_comp category: Missing column 'type' near line 187 
    4871 Missing entity information. Treating each chain as a separate entity. 
    4872 Bad residue range for struct_conf "3" near line 98 
    4873 Bad residue range for struct_conf "4" near line 99 
    4874 Bad residue range for struct_conf "5" near line 100 
    4875 Bad residue range for struct_conf "6" near line 101 
    4876 Bad residue range for struct_conf "7" near line 102 
    4877 15 messages similar to the above omitted 
    4878 Invalid sheet range for struct_sheet_range "2 1" near line 183 
    4879 Invalid sheet range for struct_sheet_range "3 1" near line 184 
    4880 Invalid sheet range for struct_sheet_range "4 1" near line 186 
    4881 Missing or incomplete sequence information. Inferred polymer connectivity. 
    4882 Skipping chem_comp category: Missing column 'type' near line 4361 
    4883  
    4884 Chain information for rOAT1-AZT_coot-4_real_space_refined_002.cif #1 
    4885 --- 
    4886 Chain | Description 
    4887 A | No description available 
    4888  
    4889 
    4890 > close session
    4891 
    4892 > open
    4893 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AZT_20240729/RealSpaceRefine_2/rOAT1-AZT_coot-4_real_space_refined_002.pdb
    4894 
    4895 Chain information for rOAT1-AZT_coot-4_real_space_refined_002.pdb #1 
    4896 --- 
    4897 Chain | Description 
    4898 A | No description available 
    4899  
    4900 
    4901 QXcbConnection: XCB error: 3 (BadWindow), sequence: 10568, resource id:
    4902 35655077, major code: 40 (TranslateCoords), minor code: 0 
    4903 
    4904 > open
    4905 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/inward_j156_2.7A/postprocess.mrc
    4906 
    4907 Opened postprocess.mrc as #2, grid size 320,320,320, pixel 0.83, shown at
    4908 level 0.00421, step 2, values float32 
    4909 
    4910 > rename #2 rOAT1-AZT.mrc
    4911 
    4912 > volume #2 step 1
    4913 
    4914 > volume #2 level 0.01415
    4915 
    4916 > save
    4917 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    4918 > includeMaps true
    4919 
    4920 > select add #1
    4921 
    4922 3905 atoms, 3986 bonds, 515 residues, 1 model selected 
    4923 
    4924 > ui mousemode right "rotate selected models"
    4925 
    4926 > view matrix models
    4927 > #1,-0.81264,-0.025153,-0.58222,300.85,0.24435,0.8923,-0.37961,31.685,0.52906,-0.45075,-0.71897,210.07
    4928 
    4929 > ui mousemode right "translate selected models"
    4930 
    4931 > view matrix models
    4932 > #1,-0.81264,-0.025153,-0.58222,320.11,0.24435,0.8923,-0.37961,31.387,0.52906,-0.45075,-0.71897,214.5
    4933 
    4934 > ui mousemode right "rotate selected models"
    4935 
    4936 > view matrix models
    4937 > #1,-0.62181,-0.74054,-0.25487,347.35,-0.028985,0.34697,-0.93743,205.98,0.78263,-0.57551,-0.23722,138.33
    4938 
    4939 > ui mousemode right "translate selected models"
    4940 
    4941 > view matrix models
    4942 > #1,-0.62181,-0.74054,-0.25487,344.94,-0.028985,0.34697,-0.93743,211.72,0.78263,-0.57551,-0.23722,135.34
    4943 
    4944 > view matrix models
    4945 > #1,-0.62181,-0.74054,-0.25487,347.37,-0.028985,0.34697,-0.93743,211.37,0.78263,-0.57551,-0.23722,136.41
    4946 
    4947 > ui tool show "Fit in Map"
    4948 
    4949 > fitmap #1 inMap #2
    4950 
    4951 Fit molecule rOAT1-AZT_coot-4_real_space_refined_002.pdb (#1) to map
    4952 rOAT1-AZT.mrc (#2) using 3905 atoms 
    4953 average map value = 0.01965, steps = 108 
    4954 shifted from previous position = 2.32 
    4955 rotated from previous position = 12.8 degrees 
    4956 atoms outside contour = 1436, contour level = 0.014154 
    4957  
    4958 Position of rOAT1-AZT_coot-4_real_space_refined_002.pdb (#1) relative to
    4959 rOAT1-AZT.mrc (#2) coordinates: 
    4960 Matrix rotation and translation 
    4961 -0.62427498 -0.78041245 -0.03517318 323.27181278 
    4962 -0.15760640 0.16991691 -0.97277359 257.26632447 
    4963 0.76514114 -0.60173470 -0.22907287 142.60270901 
    4964 Axis 0.34360458 -0.74113973 0.57675627 
    4965 Axis point 193.37147122 0.00000000 235.15956508 
    4966 Rotation angle (degrees) 147.32171525 
    4967 Shift along axis 2.65438788 
    4968  
    4969 
    4970 > select subtract #1
    4971 
    4972 Nothing selected 
    4973 
    4974 > select add #1
    4975 
    4976 3905 atoms, 3986 bonds, 515 residues, 1 model selected 
    4977 
    4978 > color sel white
    4979 
    4980 > select ::name="AZZ"
    4981 
    4982 19 atoms, 20 bonds, 1 residue, 1 model selected 
    4983 
    4984 > color sel red
    4985 
    4986 > ui tool show "Color Zone"
    4987 
    4988 > color zone #2 near #1 distance 4.98
    4989 
    4990 > volume #2 level 0.0105
    4991 
    4992 > color zone #2 near #1 distance 4.88
    4993 
    4994 > color zone #2 near #1 distance 4.78
    4995 
    4996 > color zone #2 near #1 distance 4.68
    4997 
    4998 > color zone #2 near #1 distance 4.58
    4999 
    5000 > color zone #2 near #1 distance 4.48
    5001 
    5002 > color zone #2 near #1 distance 4.38
    5003 
    5004 > color zone #2 near #1 distance 4.28
    5005 
    5006 > color zone #2 near #1 distance 4.18
    5007 
    5008 > color zone #2 near #1 distance 4.08
    5009 
    5010 > color zone #2 near #1 distance 3.98
    5011 
    5012 > color zone #2 near #1 distance 3.88
    5013 
    5014 > color zone #2 near #1 distance 3.78
    5015 
    5016 > color zone #2 near #1 distance 3.68
    5017 
    5018 > color zone #2 near #1 distance 3.58
    5019 
    5020 > color zone #2 near #1 distance 3.48
    5021 
    5022 > color zone #2 near #1 distance 3.38
    5023 
    5024 > color zone #2 near #1 distance 3.28
    5025 
    5026 > color zone #2 near #1 distance 3.18
    5027 
    5028 > color zone #2 near #1 distance 3.08
    5029 
    5030 > color zone #2 near #1 distance 2.98
    5031 
    5032 > color zone #2 near #1 distance 2.88
    5033 
    5034 > color zone #2 near #1 distance 2.78
    5035 
    5036 > color zone #2 near #1 distance 2.68
    5037 
    5038 > color zone #2 near #1 distance 2.58
    5039 
    5040 > color zone #2 near #1 distance 2.48
    5041 
    5042 > color zone #2 near #1 distance 2.38
    5043 
    5044 > color zone #2 near #1 distance 2.28
    5045 
    5046 > color zone #2 near #1 distance 2.18
    5047 
    5048 > color zone #2 near #1 distance 2.08
    5049 
    5050 > color zone #2 near #1 distance 1.98
    5051 
    5052 > color zone #2 near #1 distance 1.88
    5053 
    5054 > color zone #2 near #1 distance 1.78
    5055 
    5056 > volume #2 level 0.008069
    5057 
    5058 > volume splitbyzone #2
    5059 
    5060 Opened rOAT1-AZT.mrc 0 as #3.1, grid size 320,320,320, pixel 0.83, shown at
    5061 level 0.00807, step 1, values float32 
    5062 Opened rOAT1-AZT.mrc 1 as #3.2, grid size 320,320,320, pixel 0.83, shown at
    5063 level 0.00807, step 1, values float32 
    5064 Opened rOAT1-AZT.mrc 2 as #3.3, grid size 320,320,320, pixel 0.83, shown at
    5065 level 0.00807, step 1, values float32 
    5066 
    5067 > close #3.1-2
    5068 
    5069 > color #3.3 white models
    5070 
    5071 > color #3.3 #ffffb2ff models
    5072 
    5073 > select add #1
    5074 
    5075 3905 atoms, 3986 bonds, 515 residues, 1 model selected 
    5076 
    5077 > color #1 #dd22bbff
    5078 
    5079 > color #1 tan
    5080 
    5081 > color sel byhetero
    5082 
    5083 > color #3.3 #ffffb296 models
    5084 
    5085 > save
    5086 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    5087 > includeMaps true
    5088 
    5089 QXcbConnection: XCB error: 3 (BadWindow), sequence: 355, resource id:
    5090 35655128, major code: 40 (TranslateCoords), minor code: 0 
    5091 
    5092 QXcbConnection: XCB error: 3 (BadWindow), sequence: 366, resource id:
    5093 35655123, major code: 40 (TranslateCoords), minor code: 0 
    5094 
    5095 > save
    5096 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    5097 > includeMaps true
    5098 
    5099 QXcbConnection: XCB error: 3 (BadWindow), sequence: 14345, resource id:
    5100 35655133, major code: 40 (TranslateCoords), minor code: 0 
    5101 
    5102 > rename #1 rOAT1-AZT_IF.pdb
    5103 
    5104 > rename #2 rOAT1-AZT_IF.mrc
    5105 
    5106 > rename #3 "rOAT1-AZT_IF.mrc split"
    5107 
    5108 > rename #3.3 "rOAT1-AZT_IF.mrc 2"
    5109 
    5110 > save
    5111 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    5112 > includeMaps true
    5113 
    5114 QXcbConnection: XCB error: 3 (BadWindow), sequence: 23455, resource id:
    5115 35655148, major code: 40 (TranslateCoords), minor code: 0 
    5116 
    5117 > open
    5118 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/outward_j170_2.7A/run_class001.mrc
    5119 
    5120 Opened run_class001.mrc as #4, grid size 320,320,320, pixel 0.83, shown at
    5121 level 0.00134, step 2, values float32 
    5122 
    5123 > close #4
    5124 
    5125 > open
    5126 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/outward_j170_2.7A/postprocess.mrc
    5127 
    5128 Opened postprocess.mrc as #4, grid size 320,320,320, pixel 0.83, shown at
    5129 level 0.00459, step 2, values float32 
    5130 
    5131 > volume #4 step 1
    5132 
    5133 > volume #4 level 0.01366
    5134 
    5135 > rename #4 rOAT1-AZT_OF.mrc
    5136 
    5137 > open
    5138 > /home/dout2/isilon/PROJECTS/OAT1/cryoEM/rOAT1-PBD_LMNG_combined_20230419_20230217_OF/rOAT1-PBD_OF-
    5139 > coot-7_real_space_refined_008.pdb
    5140 
    5141 Chain information for rOAT1-PBD_OF-coot-7_real_space_refined_008.pdb #5 
    5142 --- 
    5143 Chain | Description 
    5144 A | No description available 
    5145  
    5146 
    5147 > select subtract #1
    5148 
    5149 Nothing selected 
    5150 
    5151 > select add #5
    5152 
    5153 3792 atoms, 3881 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    5154 
    5155 > hide #!3 models
    5156 
    5157 > hide #!3.3 models
    5158 
    5159 > hide #1 models
    5160 
    5161 > view matrix models #5,1,0,0,68.569,0,1,0,64.41,0,0,1,67.632
    5162 
    5163 > view matrix models #5,1,0,0,67.083,0,1,0,66.14,0,0,1,66.95
    5164 
    5165 > fitmap #5 inMap #4
    5166 
    5167 Fit molecule rOAT1-PBD_OF-coot-7_real_space_refined_008.pdb (#5) to map
    5168 rOAT1-AZT_OF.mrc (#4) using 3792 atoms 
    5169 average map value = 0.01938, steps = 84 
    5170 shifted from previous position = 0.803 
    5171 rotated from previous position = 4.35 degrees 
    5172 atoms outside contour = 1323, contour level = 0.013659 
    5173  
    5174 Position of rOAT1-PBD_OF-coot-7_real_space_refined_008.pdb (#5) relative to
    5175 rOAT1-AZT_OF.mrc (#4) coordinates: 
    5176 Matrix rotation and translation 
    5177 0.99822969 -0.04531644 -0.03852150 72.45731875 
    5178 0.04345449 0.99790785 -0.04787105 67.21065914 
    5179 0.04061025 0.04611237 0.99811044 61.32293455 
    5180 Axis 0.62004547 -0.52206316 0.58565662 
    5181 Axis point 0.00000000 -669.59173064 1932.22009801 
    5182 Rotation angle (degrees) 4.34647273 
    5183 Shift along axis 45.75280586 
    5184  
    5185 
    5186 > save
    5187 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/outward_j170_2.7A/rOAT1-AZT_OF.pdb
    5188 > models #5 relModel #4
    5189 
    5190 > save
    5191 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/inward_j156_2.7A/rOAT1-AZT_IF.pdb
    5192 > models #1
    5193 
    5194 > close #5
    5195 
    5196 > open
    5197 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/outward_j170_2.7A/postprocess.mrc
    5198 
    5199 Opened rOAT1-AZT_OF.mrc as #5, grid size 320,320,320, pixel 0.83, shown at
    5200 level 0.00459, step 2, values float32 
    5201 
    5202 > close #5
    5203 
    5204 > open
    5205 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/outward_j170_2.7A/rOAT1-AZT_OF-
    5206 > coot-0_real_space_refined_003.pdb
    5207 
    5208 Chain information for rOAT1-AZT_OF-coot-0_real_space_refined_003.pdb #5 
    5209 --- 
    5210 Chain | Description 
    5211 A | No description available 
    5212  
    5213 
    5214 > select add #4
    5215 
    5216 2 models selected 
    5217 
    5218 > select subtract #4
    5219 
    5220 Nothing selected 
    5221 
    5222 > select add #5
    5223 
    5224 3774 atoms, 3864 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    5225 
    5226 > select clear
    5227 
    5228 > select add #5
    5229 
    5230 3774 atoms, 3864 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    5231 
    5232 > color #5 white
    5233 
    5234 > color #4 white models
    5235 
    5236 > color #2 white models
    5237 
    5238 > select #5/A:601@O4
    5239 
    5240 1 atom, 1 residue, 1 model selected 
    5241 
    5242 > select up
    5243 
    5244 19 atoms, 20 bonds, 1 residue, 1 model selected 
    5245 
    5246 > color sel red
    5247 
    5248 > color zone #4 near #5 distance 4.98
    5249 
    5250 > color zone #4 near #5 distance 4.88
    5251 
    5252 > color zone #4 near #5 distance 4.78
    5253 
    5254 > color zone #4 near #5 distance 4.68
    5255 
    5256 > color zone #4 near #5 distance 4.58
    5257 
    5258 > color zone #4 near #5 distance 4.48
    5259 
    5260 > color zone #4 near #5 distance 4.38
    5261 
    5262 > color zone #4 near #5 distance 4.28
    5263 
    5264 > color zone #4 near #5 distance 4.18
    5265 
    5266 > color zone #4 near #5 distance 4.08
    5267 
    5268 > color zone #4 near #5 distance 3.98
    5269 
    5270 > color zone #4 near #5 distance 3.88
    5271 
    5272 > color zone #4 near #5 distance 3.78
    5273 
    5274 > color zone #4 near #5 distance 3.68
    5275 
    5276 > color zone #4 near #5 distance 3.58
    5277 
    5278 > color zone #4 near #5 distance 3.48
    5279 
    5280 > color zone #4 near #5 distance 3.38
    5281 
    5282 > color zone #4 near #5 distance 3.28
    5283 
    5284 > color zone #4 near #5 distance 3.18
    5285 
    5286 > color zone #4 near #5 distance 3.08
    5287 
    5288 > color zone #4 near #5 distance 2.98
    5289 
    5290 > color zone #4 near #5 distance 2.88
    5291 
    5292 > color zone #4 near #5 distance 2.78
    5293 
    5294 > color zone #4 near #5 distance 2.68
    5295 
    5296 > color zone #4 near #5 distance 2.58
    5297 
    5298 > color zone #4 near #5 distance 2.48
    5299 
    5300 > color zone #4 near #5 distance 2.38
    5301 
    5302 > color zone #4 near #5 distance 2.28
    5303 
    5304 > color zone #4 near #5 distance 2.18
    5305 
    5306 > color zone #4 near #5 distance 2.08
    5307 
    5308 > color zone #4 near #5 distance 1.98
    5309 
    5310 > color zone #4 near #5 distance 1.88
    5311 
    5312 > color zone #4 near #5 distance 1.78
    5313 
    5314 > color zone #4 near #5 distance 1.68
    5315 
    5316 > color zone #4 near #5 distance 1.58
    5317 
    5318 > color zone #4 near #5 distance 1.48
    5319 
    5320 > color zone #4 near #5 distance 1.58
    5321 
    5322 > color zone #4 near #5 distance 1.68
    5323 
    5324 > color zone #4 near #5 distance 1.78
    5325 
    5326 > color zone #4 near #5 distance 1.88
    5327 
    5328 > volume splitbyzone #4
    5329 
    5330 Opened rOAT1-AZT_OF.mrc 0 as #6.1, grid size 320,320,320, pixel 0.83, shown at
    5331 level 0.0137, step 1, values float32 
    5332 Opened rOAT1-AZT_OF.mrc 1 as #6.2, grid size 320,320,320, pixel 0.83, shown at
    5333 level 0.0137, step 1, values float32 
    5334 Opened rOAT1-AZT_OF.mrc 2 as #6.3, grid size 320,320,320, pixel 0.83, shown at
    5335 level 0.0137, step 1, values float32 
    5336 
    5337 > close #6.1-2
    5338 
    5339 > volume #6.3 level 0.0116
    5340 
    5341 > select add #5
    5342 
    5343 3774 atoms, 3864 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    5344 
    5345 > select subtract #5
    5346 
    5347 Nothing selected 
    5348 
    5349 > color #6.3 yellow models
    5350 
    5351 > color #6.3 white models
    5352 
    5353 > color #6.3 #ffffb2ff models
    5354 
    5355 > select add #5
    5356 
    5357 3774 atoms, 3864 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    5358 
    5359 > color #5 #ffaa88ff
    5360 
    5361 > color #5 salmon
    5362 
    5363 > color (#!5 & sel) byhetero
    5364 
    5365 > color #6.3 #ffffb296 models
    5366 
    5367 > select clear
    5368 
    5369 > save
    5370 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    5371 > includeMaps true
    5372 
    5373 > show #!2 models
    5374 
    5375 > hide #!5 models
    5376 
    5377 > hide #!6 models
    5378 
    5379 > hide #!6.3 models
    5380 
    5381 > volume #2 level 0.01456
    5382 
    5383 > color #2 #a5a5a5ff models
    5384 
    5385 > open
    5386 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20230419_rOAT1-PBD/inward_j261_2.6A/postprocess.mrc
    5387 
    5388 Opened postprocess.mrc as #7, grid size 320,320,320, pixel 0.83, shown at
    5389 level 0.00408, step 2, values float32 
    5390 
    5391 > rename #7 rOAT1-PBD_IF.mrc
    5392 
    5393 > volume #2 level 0.01983
    5394 
    5395 > volume #2 level 0.0151
    5396 
    5397 > hide #!7 models
    5398 
    5399 > volume #7 level 0.01185
    5400 
    5401 > volume #7 step 1
    5402 
    5403 > volume #7 level 0.01094
    5404 
    5405 > hide #!2 models
    5406 
    5407 > open
    5408 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20230419_rOAT1-PBD/inward_j261_2.6A/rOAT1-PBD-
    5409 > coot-6.pdb
    5410 
    5411 Chain information for rOAT1-PBD-coot-6.pdb #8 
    5412 --- 
    5413 Chain | Description 
    5414 A | No description available 
    5415  
    5416 
    5417 > select add #8
    5418 
    5419 3912 atoms, 3985 bonds, 522 residues, 1 model selected 
    5420 
    5421 > ui mousemode right "translate selected models"
    5422 
    5423 > view matrix models #8,1,0,0,55.004,0,1,0,73.737,0,0,1,58.702
    5424 
    5425 > view matrix models #8,1,0,0,66.378,0,1,0,64.897,0,0,1,63.973
    5426 
    5427 > fitmap #8 inMap #7
    5428 
    5429 Fit molecule rOAT1-PBD-coot-6.pdb (#8) to map rOAT1-PBD_IF.mrc (#7) using 3912
    5430 atoms 
    5431 average map value = 0.02737, steps = 56 
    5432 shifted from previous position = 2.6 
    5433 rotated from previous position = 0.396 degrees 
    5434 atoms outside contour = 571, contour level = 0.010939 
    5435  
    5436 Position of rOAT1-PBD-coot-6.pdb (#8) relative to rOAT1-PBD_IF.mrc (#7)
    5437 coordinates: 
    5438 Matrix rotation and translation 
    5439 0.99998387 0.00531886 -0.00199304 66.36205660 
    5440 -0.00532668 0.99997806 -0.00393867 67.06308709 
    5441 0.00197205 0.00394922 0.99999026 65.65327743 
    5442 Axis 0.57034742 -0.28670293 -0.76974363 
    5443 Axis point 10937.66555565 -15865.74627304 0.00000000 
    5444 Rotation angle (degrees) 0.39620277 
    5445 Shift along axis -31.91394767 
    5446  
    5447 
    5448 > rename #8 rOAT1-PBD_IF.pdb
    5449 
    5450 > save
    5451 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    5452 > includeMaps true
    5453 
    5454 QXcbConnection: XCB error: 3 (BadWindow), sequence: 51376, resource id:
    5455 35655645, major code: 40 (TranslateCoords), minor code: 0 
    5456 
    5457 QXcbConnection: XCB error: 3 (BadWindow), sequence: 51388, resource id:
    5458 35655640, major code: 40 (TranslateCoords), minor code: 0 
    5459 
    5460 > color #8 white
    5461 
    5462 > hide #!7 models
    5463 
    5464 > select up
    5465 
    5466 2 atoms, 1 bond, 1 residue, 1 model selected 
    5467 
    5468 > select up
    5469 
    5470 19 atoms, 19 bonds, 1 residue, 1 model selected 
    5471 
    5472 > color sel red
    5473 
    5474 > show #!7 models
    5475 
    5476 > color zone #7 near #8 distance 4.98
    5477 
    5478 > color zone #7 near #8 distance 4.88
    5479 
    5480 > color zone #7 near #8 distance 4.78
    5481 
    5482 > color zone #7 near #8 distance 4.68
    5483 
    5484 > color zone #7 near #8 distance 4.58
    5485 
    5486 > color zone #7 near #8 distance 4.48
    5487 
    5488 > color zone #7 near #8 distance 4.38
    5489 
    5490 > color zone #7 near #8 distance 4.28
    5491 
    5492 > color zone #7 near #8 distance 4.18
    5493 
    5494 > color zone #7 near #8 distance 4.08
    5495 
    5496 > color zone #7 near #8 distance 3.98
    5497 
    5498 > color zone #7 near #8 distance 3.88
    5499 
    5500 > color zone #7 near #8 distance 3.78
    5501 
    5502 > color zone #7 near #8 distance 3.68
    5503 
    5504 > volume #7 level 0.02515
    5505 
    5506 > volume #7 level 0.01677
    5507 
    5508 > volume #7 level 0.0124
    5509 
    5510 > volume #7 level 0.01476
    5511 
    5512 > color zone #7 near #8 distance 3.58
    5513 
    5514 > color zone #7 near #8 distance 3.48
    5515 
    5516 > color zone #7 near #8 distance 3.38
    5517 
    5518 > color zone #7 near #8 distance 3.28
    5519 
    5520 > color zone #7 near #8 distance 3.18
    5521 
    5522 > color zone #7 near #8 distance 3.08
    5523 
    5524 > color zone #7 near #8 distance 2.98
    5525 
    5526 > color zone #7 near #8 distance 2.88
    5527 
    5528 > color zone #7 near #8 distance 2.78
    5529 
    5530 > color zone #7 near #8 distance 2.68
    5531 
    5532 > color zone #7 near #8 distance 2.58
    5533 
    5534 > color zone #7 near #8 distance 2.48
    5535 
    5536 > color zone #7 near #8 distance 2.38
    5537 
    5538 > color zone #7 near #8 distance 2.28
    5539 
    5540 > volume #7 level 0.01112
    5541 
    5542 > color zone #7 near #8 distance 2.18
    5543 
    5544 > color zone #7 near #8 distance 2.08
    5545 
    5546 > color zone #7 near #8 distance 1.98
    5547 
    5548 > color zone #7 near #8 distance 1.88
    5549 
    5550 > color zone #7 near #8 distance 1.98
    5551 
    5552 > color zone #7 near #8 distance 2.08
    5553 
    5554 > volume splitbyzone #7
    5555 
    5556 Opened rOAT1-PBD_IF.mrc 0 as #9.1, grid size 320,320,320, pixel 0.83, shown at
    5557 level 0.0111, step 1, values float32 
    5558 Opened rOAT1-PBD_IF.mrc 1 as #9.2, grid size 320,320,320, pixel 0.83, shown at
    5559 level 0.0111, step 1, values float32 
    5560 Opened rOAT1-PBD_IF.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at
    5561 level 0.0111, step 1, values float32 
    5562 
    5563 > close #9.1-2
    5564 
    5565 > color #9.3 #ff000096 models
    5566 
    5567 > color #9.3 #ffff0096 models
    5568 
    5569 > color #9.3 #ffffff96 models
    5570 
    5571 > color #9.3 #ffffb296 models
    5572 
    5573 > select add #8
    5574 
    5575 3912 atoms, 3985 bonds, 522 residues, 1 model selected 
    5576 
    5577 > color #8 #ffffddff
    5578 
    5579 > color #8 gold
    5580 
    5581 > select clear
    5582 
    5583 > select add #8
    5584 
    5585 3912 atoms, 3985 bonds, 522 residues, 1 model selected 
    5586 
    5587 > color sel byhetero
    5588 
    5589 > select clear
    5590 
    5591 > save
    5592 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    5593 > includeMaps true
    5594 
    5595 QXcbConnection: XCB error: 3 (BadWindow), sequence: 19133, resource id:
    5596 35655670, major code: 40 (TranslateCoords), minor code: 0 
    5597 
    5598 > open
    5599 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20230419_rOAT1-PBD/outward_j272_3.0A/postprocess.mrc
    5600 
    5601 Opened postprocess.mrc as #10, grid size 320,320,320, pixel 0.83, shown at
    5602 level 0.00409, step 2, values float32 
    5603 
    5604 QXcbConnection: XCB error: 3 (BadWindow), sequence: 23804, resource id:
    5605 35655680, major code: 40 (TranslateCoords), minor code: 0 
    5606 
    5607 > open
    5608 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20230419_rOAT1-PBD/outward_j272_3.0A/rOAT1-PBD_OF-
    5609 > coot-0.pdb
    5610 
    5611 Chain information for rOAT1-PBD_OF-coot-0.pdb #11 
    5612 --- 
    5613 Chain | Description 
    5614 A | No description available 
    5615  
    5616 
    5617 > hide #!9 models
    5618 
    5619 > hide #8 models
    5620 
    5621 > rename #10 rOAT1-PBD_OF
    5622 
    5623 > rename #10 rOAT1-PBD_OF.mrc
    5624 
    5625 > show #!2 models
    5626 
    5627 > volume #10 level 0.004712
    5628 
    5629 > volume #10 step 1
    5630 
    5631 > volume #10 level 0.01128
    5632 
    5633 > hide #!2 models
    5634 
    5635 > select add #11
    5636 
    5637 3872 atoms, 3966 bonds, 500 residues, 1 model selected 
    5638 
    5639 > view matrix models #11,1,0,0,65.11,0,1,0,69.986,0,0,1,61.035
    5640 
    5641 > view matrix models #11,1,0,0,68.61,0,1,0,68.058,0,0,1,65.073
    5642 
    5643 > view matrix models #11,1,0,0,67.516,0,1,0,68.105,0,0,1,67.386
    5644 
    5645 > fitmap #11 inMap #10
    5646 
    5647 Fit molecule rOAT1-PBD_OF-coot-0.pdb (#11) to map rOAT1-PBD_OF.mrc (#10) using
    5648 3872 atoms 
    5649 average map value = 0.01531, steps = 56 
    5650 shifted from previous position = 2.42 
    5651 rotated from previous position = 0.764 degrees 
    5652 atoms outside contour = 1505, contour level = 0.011277 
    5653  
    5654 Position of rOAT1-PBD_OF-coot-0.pdb (#11) relative to rOAT1-PBD_OF.mrc (#10)
    5655 coordinates: 
    5656 Matrix rotation and translation 
    5657 0.99995211 0.00939248 0.00274947 65.65298070 
    5658 -0.00936721 0.99991506 -0.00906240 67.47749964 
    5659 -0.00283436 0.00903621 0.99995516 65.83404461 
    5660 Axis 0.67891074 0.20945939 -0.70370943 
    5661 Axis point 6981.74049553 -6059.62250131 0.00000000 
    5662 Rotation angle (degrees) 0.76372650 
    5663 Shift along axis 12.37827175 
    5664  
    5665 
    5666 > show sel atoms
    5667 
    5668 > hide #!10 models
    5669 
    5670 > show #!10 models
    5671 
    5672 > open
    5673 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-PBD_LMNG_combined_20230419_20230217_OF/rOAT1-PBD_OF-
    5674 > coot-7_real_space_refined_008.pdb
    5675 
    5676 Chain information for rOAT1-PBD_OF-coot-7_real_space_refined_008.pdb #12 
    5677 --- 
    5678 Chain | Description 
    5679 A | No description available 
    5680  
    5681 
    5682 > ui tool show Matchmaker
    5683 
    5684 > matchmaker #!12 to #11
    5685 
    5686 Parameters 
    5687 --- 
    5688 Chain pairing | bb 
    5689 Alignment algorithm | Needleman-Wunsch 
    5690 Similarity matrix | BLOSUM-62 
    5691 SS fraction | 0.3 
    5692 Gap open (HH/SS/other) | 18/18/6 
    5693 Gap extend | 1 
    5694 SS matrix |  |  | H | S | O 
    5695 ---|---|---|--- 
    5696 H | 6 | -9 | -6 
    5697 S |  | 6 | -6 
    5698 O |  |  | 4 
    5699 Iteration cutoff | 2 
    5700  
    5701 Matchmaker rOAT1-PBD_OF-coot-0.pdb, chain A (#11) with rOAT1-PBD_OF-
    5702 coot-7_real_space_refined_008.pdb, chain A (#12), sequence alignment score =
    5703 2423.1 
    5704 RMSD between 470 pruned atom pairs is 0.696 angstroms; (across all 485 pairs:
    5705 1.080) 
    5706  
    5707 
    5708 > hide #11 models
    5709 
    5710 > select subtract #11
    5711 
    5712 Nothing selected 
    5713 
    5714 > show #11 models
    5715 
    5716 > hide #!12 models
    5717 
    5718 > hide #!10 models
    5719 
    5720 > show #!12 models
    5721 
    5722 > close #11
    5723 
    5724 > color #12 #bb4455ff
    5725 
    5726 > color #12 #b4503bff
    5727 
    5728 QXcbConnection: XCB error: 3 (BadWindow), sequence: 15705, resource id:
    5729 35655708, major code: 40 (TranslateCoords), minor code: 0 
    5730 
    5731 > show #!10 models
    5732 
    5733 > save
    5734 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    5735 > includeMaps true
    5736 
    5737 QXcbConnection: XCB error: 3 (BadWindow), sequence: 19760, resource id:
    5738 35655718, major code: 40 (TranslateCoords), minor code: 0 
    5739 
    5740 QXcbConnection: XCB error: 3 (BadWindow), sequence: 19772, resource id:
    5741 35655713, major code: 40 (TranslateCoords), minor code: 0 
    5742 
    5743 > color #10 #ffb2ff96 models
    5744 
    5745 > volume #10 level 0.009218
    5746 
    5747 > volume #10 level 0.008059
    5748 
    5749 > color #10 #ffb2ffff models
    5750 
    5751 > select add #12
    5752 
    5753 3792 atoms, 3881 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    5754 
    5755 > hide #!10 models
    5756 
    5757 > color #12 white
    5758 
    5759 > select clear
    5760 
    5761 > select #12/B:601@C11
    5762 
    5763 1 atom, 1 residue, 1 model selected 
    5764 
    5765 > select up
    5766 
    5767 37 atoms, 37 bonds, 1 residue, 1 model selected 
    5768 
    5769 > color sel red
    5770 
    5771 > color #10 white models
    5772 
    5773 > select add #10
    5774 
    5775 37 atoms, 37 bonds, 1 residue, 3 models selected 
    5776 
    5777 > select subtract #10
    5778 
    5779 37 atoms, 37 bonds, 1 residue, 1 model selected 
    5780 
    5781 > show #!10 models
    5782 
    5783 > color zone #10 near #12 distance 2
    5784 
    5785 > color zone #10 near #12 distance 1.9
    5786 
    5787 > color zone #10 near #12 distance 1.8
    5788 
    5789 > color zone #10 near #12 distance 1.7
    5790 
    5791 > color zone #10 near #12 distance 1.8
    5792 
    5793 > color zone #10 near #12 distance 1.9
    5794 
    5795 > color zone #10 near #12 distance 2
    5796 
    5797 [Repeated 1 time(s)]
    5798 
    5799 > volume splitbyzone #10
    5800 
    5801 Opened rOAT1-PBD_OF.mrc 0 as #11.1, grid size 320,320,320, pixel 0.83, shown
    5802 at level 0.00806, step 1, values float32 
    5803 Opened rOAT1-PBD_OF.mrc 1 as #11.2, grid size 320,320,320, pixel 0.83, shown
    5804 at level 0.00806, step 1, values float32 
    5805 Opened rOAT1-PBD_OF.mrc 2 as #11.3, grid size 320,320,320, pixel 0.83, shown
    5806 at level 0.00806, step 1, values float32 
    5807 
    5808 > volume splitbyzone #10
    5809 
    5810 Opened rOAT1-PBD_OF.mrc 0 as #13.1, grid size 320,320,320, pixel 0.83, shown
    5811 at level 0.00806, step 1, values float32 
    5812 Opened rOAT1-PBD_OF.mrc 1 as #13.2, grid size 320,320,320, pixel 0.83, shown
    5813 at level 0.00806, step 1, values float32 
    5814 Opened rOAT1-PBD_OF.mrc 2 as #13.3, grid size 320,320,320, pixel 0.83, shown
    5815 at level 0.00806, step 1, values float32 
    5816 
    5817 > close #11.1-2
    5818 
    5819 > hide #!12 models
    5820 
    5821 > hide #!11.3 models
    5822 
    5823 > hide #!11 models
    5824 
    5825 > select add #12
    5826 
    5827 3792 atoms, 3881 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    5828 
    5829 > select subtract #12
    5830 
    5831 Nothing selected 
    5832 
    5833 > close #13.1-2
    5834 
    5835 > show #!12 models
    5836 
    5837 > color #11.3 white models
    5838 
    5839 > color #11.3 #ffffb2ff models
    5840 
    5841 > color #13.3 white models
    5842 
    5843 > color #13.3 #ffffb2ff models
    5844 
    5845 > select add #12
    5846 
    5847 3792 atoms, 3881 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    5848 
    5849 > color #12 #bb4455ff
    5850 
    5851 > color #12 #b4503bff
    5852 
    5853 > color (#!12 & sel) byhetero
    5854 
    5855 > select #12/A:440
    5856 
    5857 6 atoms, 5 bonds, 1 residue, 1 model selected 
    5858 
    5859 > select add #12
    5860 
    5861 3792 atoms, 3881 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    5862 
    5863 > select subtract #12
    5864 
    5865 Nothing selected 
    5866 
    5867 > save
    5868 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    5869 > includeMaps true
    5870 
    5871 > hide #!13 models
    5872 
    5873 > hide #!13.3 models
    5874 
    5875 > hide #!12 models
    5876 
    5877 > open
    5878 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240831_rOAT1-TFV/inward_j152_2.7A/postprocess.mrc
    5879 
    5880 Opened postprocess.mrc as #14, grid size 320,320,320, pixel 0.83, shown at
    5881 level 0.00408, step 2, values float32 
    5882 
    5883 QXcbConnection: XCB error: 3 (BadWindow), sequence: 27239, resource id:
    5884 35655778, major code: 40 (TranslateCoords), minor code: 0 
    5885 
    5886 > show #!2 models
    5887 
    5888 > hide #!2 models
    5889 
    5890 > rename #14 rOAT1-TFV_IF.mrc
    5891 
    5892 > show #1 models
    5893 
    5894 > hide #!14 models
    5895 
    5896 > save
    5897 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/IF/rOAT1-TFV_IF.pdb
    5898 > models #1 relModel #14
    5899 
    5900 > open
    5901 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/RealSpaceRefine_5/rOAT1-TFV_IF-
    5902 > coot-2_real_space_refined_005.pdb
    5903 
    5904 Chain information for rOAT1-TFV_IF-coot-2_real_space_refined_005.pdb #15 
    5905 --- 
    5906 Chain | Description 
    5907 A | No description available 
    5908  
    5909 
    5910 > hide #1 models
    5911 
    5912 > show #!14 models
    5913 
    5914 > color #15 white
    5915 
    5916 > color #14 white models
    5917 
    5918 > select ::name="TFV"
    5919 
    5920 31 atoms, 32 bonds, 1 residue, 1 model selected 
    5921 
    5922 > color sel red
    5923 
    5924 > color zone #14 near #15 distance 4.68
    5925 
    5926 > color zone #14 near #15 distance 4.58
    5927 
    5928 > color zone #14 near #15 distance 4.48
    5929 
    5930 > color zone #14 near #15 distance 4.38
    5931 
    5932 > color zone #14 near #15 distance 4.28
    5933 
    5934 > color zone #14 near #15 distance 4.18
    5935 
    5936 > color zone #14 near #15 distance 4.08
    5937 
    5938 > color zone #14 near #15 distance 3.98
    5939 
    5940 > color zone #14 near #15 distance 3.88
    5941 
    5942 > color zone #14 near #15 distance 3.78
    5943 
    5944 > color zone #14 near #15 distance 3.68
    5945 
    5946 > color zone #14 near #15 distance 3.58
    5947 
    5948 > color zone #14 near #15 distance 3.48
    5949 
    5950 > color zone #14 near #15 distance 3.38
    5951 
    5952 > color zone #14 near #15 distance 3.28
    5953 
    5954 > color zone #14 near #15 distance 3.18
    5955 
    5956 > color zone #14 near #15 distance 3.08
    5957 
    5958 > color zone #14 near #15 distance 2.98
    5959 
    5960 > color zone #14 near #15 distance 2.88
    5961 
    5962 > color zone #14 near #15 distance 2.78
    5963 
    5964 > color zone #14 near #15 distance 2.68
    5965 
    5966 > volume #14 level 0.007613
    5967 
    5968 > color zone #14 near #15 distance 2.78
    5969 
    5970 > color zone #14 near #15 distance 2.88
    5971 
    5972 > color zone #14 near #15 distance 2.98
    5973 
    5974 > color zone #14 near #15 distance 2.88
    5975 
    5976 > color zone #14 near #15 distance 2.78
    5977 
    5978 > color zone #14 near #15 distance 2.68
    5979 
    5980 > color zone #14 near #15 distance 2.58
    5981 
    5982 > color zone #14 near #15 distance 2.48
    5983 
    5984 > color zone #14 near #15 distance 2.38
    5985 
    5986 > volume #14 level 0.005915
    5987 
    5988 > volume #14 level 0.005632
    5989 
    5990 > volume splitbyzone #14
    5991 
    5992 Opened rOAT1-TFV_IF.mrc 0 as #16.1, grid size 320,320,320, pixel 0.83, shown
    5993 at level 0.00563, step 1, values float32 
    5994 Opened rOAT1-TFV_IF.mrc 1 as #16.2, grid size 320,320,320, pixel 0.83, shown
    5995 at level 0.00563, step 1, values float32 
    5996 Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
    5997 at level 0.00563, step 1, values float32 
    5998 
    5999 > close #16.1-2
    6000 
    6001 > color zone #14 near #15 distance 2.09
    6002 
    6003 > close #16#16.3
    6004 
    6005 > show #!14 models
    6006 
    6007 > color zone #14 near #15 distance 1.99
    6008 
    6009 > color zone #14 near #15 distance 2.09
    6010 
    6011 > color zone #14 near #15 distance 2.19
    6012 
    6013 > color zone #14 near #15 distance 2.29
    6014 
    6015 > color zone #14 near #15 distance 2.39
    6016 
    6017 > color zone #14 near #15 distance 2.29
    6018 
    6019 > volume splitbyzone #14
    6020 
    6021 Opened rOAT1-TFV_IF.mrc 0 as #16.1, grid size 320,320,320, pixel 0.83, shown
    6022 at level 0.00563, step 1, values float32 
    6023 Opened rOAT1-TFV_IF.mrc 1 as #16.2, grid size 320,320,320, pixel 0.83, shown
    6024 at level 0.00563, step 1, values float32 
    6025 Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
    6026 at level 0.00563, step 1, values float32 
    6027 
    6028 > close #16.1-2
    6029 
    6030 > select add #15
    6031 
    6032 3917 atoms, 3998 bonds, 515 residues, 1 model selected 
    6033 
    6034 > color #16.3 #ff5500ff models
    6035 
    6036 > color #16.3 #aa0000ff models
    6037 
    6038 > color #16.3 #ff5500ff models
    6039 
    6040 > color #16.3 #ff557fff models
    6041 
    6042 > color #15 #ff557fff
    6043 
    6044 > color #16.3 white models
    6045 
    6046 > color #16.3 #ffffb2ff models
    6047 
    6048 > color #16.3 #ffffb296 models
    6049 
    6050 > open
    6051 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/IF/rOAT1-TFV_IF-
    6052 > coot-3.pdb
    6053 
    6054 Chain information for rOAT1-TFV_IF-coot-3.pdb #17 
    6055 --- 
    6056 Chain | Description 
    6057 A | No description available 
    6058  
    6059 
    6060 > close #17#16#16.3
    6061 
    6062 > close #15
    6063 
    6064 > open
    6065 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/IF/rOAT1-TFV_IF-
    6066 > coot-3.pdb
    6067 
    6068 Chain information for rOAT1-TFV_IF-coot-3.pdb #15 
    6069 --- 
    6070 Chain | Description 
    6071 A | No description available 
    6072  
    6073 
    6074 QXcbConnection: XCB error: 3 (BadWindow), sequence: 28850, resource id:
    6075 35656402, major code: 40 (TranslateCoords), minor code: 0 
    6076 
    6077 > show #!14 models
    6078 
    6079 > select add #15
    6080 
    6081 3917 atoms, 3998 bonds, 515 residues, 1 model selected 
    6082 
    6083 > select subtract #15
    6084 
    6085 Nothing selected 
    6086 
    6087 > select add #15
    6088 
    6089 3917 atoms, 3998 bonds, 515 residues, 1 model selected 
    6090 
    6091 > color #15 white
    6092 
    6093 > color zone #14 near #15 distance 2.29
    6094 
    6095 > select ::name="TFV"
    6096 
    6097 31 atoms, 32 bonds, 1 residue, 1 model selected 
    6098 
    6099 > color sel red
    6100 
    6101 > color zone #14 near #15 distance 2.29
    6102 
    6103 > color zone #14 near #15 distance 2.19
    6104 
    6105 > color zone #14 near #15 distance 2.09
    6106 
    6107 > color zone #14 near #15 distance 1.99
    6108 
    6109 > color zone #14 near #15 distance 1.89
    6110 
    6111 > color zone #14 near #15 distance 1.79
    6112 
    6113 > color zone #14 near #15 distance 1.69
    6114 
    6115 > color zone #14 near #15 distance 1.59
    6116 
    6117 > color zone #14 near #15 distance 1.49
    6118 
    6119 > color zone #14 near #15 distance 1.39
    6120 
    6121 > color zone #14 near #15 distance 1.29
    6122 
    6123 > color zone #14 near #15 distance 1.19
    6124 
    6125 > color zone #14 near #15 distance 1.09
    6126 
    6127 > color zone #14 near #15 distance 1.19
    6128 
    6129 > color zone #14 near #15 distance 1.29
    6130 
    6131 > color zone #14 near #15 distance 1.39
    6132 
    6133 > color zone #14 near #15 distance 1.49
    6134 
    6135 > color zone #14 near #15 distance 1.59
    6136 
    6137 > color zone #14 near #15 distance 1.69
    6138 
    6139 > color zone #14 near #15 distance 1.79
    6140 
    6141 > color zone #14 near #15 distance 1.89
    6142 
    6143 > color zone #14 near #15 distance 1.99
    6144 
    6145 > color zone #14 near #15 distance 2.09
    6146 
    6147 [Repeated 1 time(s)]
    6148 
    6149 > volume splitbyzone #14
    6150 
    6151 Opened rOAT1-TFV_IF.mrc 0 as #16.1, grid size 320,320,320, pixel 0.83, shown
    6152 at level 0.00563, step 1, values float32 
    6153 Opened rOAT1-TFV_IF.mrc 1 as #16.2, grid size 320,320,320, pixel 0.83, shown
    6154 at level 0.00563, step 1, values float32 
    6155 Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
    6156 at level 0.00563, step 1, values float32 
    6157 
    6158 > close #16.1-2
    6159 
    6160 > color #16.3 white models
    6161 
    6162 > color #16.3 #ffffb2ff models
    6163 
    6164 > color #16.3 #ffffb296 models
    6165 
    6166 > color #15 #ff5500ff
    6167 
    6168 > color #15 #ff557fff
    6169 
    6170 > select add #15
    6171 
    6172 3917 atoms, 3998 bonds, 515 residues, 1 model selected 
    6173 
    6174 > color sel byhetero
    6175 
    6176 > select clear
    6177 
    6178 > save
    6179 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    6180 > includeMaps true
    6181 
    6182 > open
    6183 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240831_rOAT1-TFV/outward_j170_2.7A/postprocess.mrc
    6184 
    6185 Opened postprocess.mrc as #17, grid size 320,320,320, pixel 0.83, shown at
    6186 level 0.00401, step 2, values float32 
    6187 
    6188 > rename #17 rOAT1-TVF_OF.mrc
    6189 
    6190 > hide #15 models
    6191 
    6192 > hide #!16 models
    6193 
    6194 > show #8 models
    6195 
    6196 > hide #8 models
    6197 
    6198 > show #!11.3 models
    6199 
    6200 > hide #!11 models
    6201 
    6202 > hide #!11.3 models
    6203 
    6204 > show #!12 models
    6205 
    6206 > volume #17 step 1
    6207 
    6208 > volume #17 level 0.01305
    6209 
    6210 > save
    6211 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240831_rOAT1-TFV/outward_j170_2.7A/rOAT1-TFV_OF.pdb
    6212 > models #12 relModel #17
    6213 
    6214 > hide #!16.3 models
    6215 
    6216 > hide #!12 models
    6217 
    6218 > open
    6219 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240831_rOAT1-TFV/outward_j170_2.7A/rOAT1-TFV_OF.pdb
    6220 
    6221 Chain information for rOAT1-TFV_OF.pdb #18 
    6222 --- 
    6223 Chain | Description 
    6224 A | No description available 
    6225  
    6226 
    6227 > save
    6228 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    6229 > includeMaps true
    6230 
    6231 > close #18
    6232 
    6233 > open
    6234 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/RealSpaceRefine_7/rOAT1-TFV_OF-
    6235 > coot-1_real_space_refined_007.pdb
    6236 
    6237 Chain information for rOAT1-TFV_OF-coot-1_real_space_refined_007.pdb #18 
    6238 --- 
    6239 Chain | Description 
    6240 A | No description available 
    6241  
    6242 
    6243 > select add #18
    6244 
    6245 3786 atoms, 3876 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    6246 
    6247 > color #18 white
    6248 
    6249 > color #17 white models
    6250 
    6251 > select #18/A:601@H131
    6252 
    6253 1 atom, 1 residue, 1 model selected 
    6254 
    6255 > select up
    6256 
    6257 31 atoms, 32 bonds, 1 residue, 1 model selected 
    6258 
    6259 > color sel red
    6260 
    6261 > volume #17 level 0.011
    6262 
    6263 > color zone #17 near #18 distance 4.98
    6264 
    6265 > color zone #17 near #18 distance 4.88
    6266 
    6267 > color zone #17 near #18 distance 4.78
    6268 
    6269 > color zone #17 near #18 distance 4.68
    6270 
    6271 > color zone #17 near #18 distance 4.58
    6272 
    6273 > color zone #17 near #18 distance 4.48
    6274 
    6275 > color zone #17 near #18 distance 4.38
    6276 
    6277 > color zone #17 near #18 distance 4.28
    6278 
    6279 > color zone #17 near #18 distance 4.18
    6280 
    6281 > color zone #17 near #18 distance 4.08
    6282 
    6283 > color zone #17 near #18 distance 3.98
    6284 
    6285 > color zone #17 near #18 distance 3.88
    6286 
    6287 > color zone #17 near #18 distance 3.78
    6288 
    6289 > color zone #17 near #18 distance 3.68
    6290 
    6291 > color zone #17 near #18 distance 3.58
    6292 
    6293 > color zone #17 near #18 distance 3.48
    6294 
    6295 > color zone #17 near #18 distance 3.38
    6296 
    6297 > color zone #17 near #18 distance 3.28
    6298 
    6299 > color zone #17 near #18 distance 3.18
    6300 
    6301 > color zone #17 near #18 distance 3.08
    6302 
    6303 > color zone #17 near #18 distance 2.98
    6304 
    6305 > volume splitbyzone #17
    6306 
    6307 Opened rOAT1-TVF_OF.mrc 0 as #19.1, grid size 320,320,320, pixel 0.83, shown
    6308 at level 0.011, step 1, values float32 
    6309 Opened rOAT1-TVF_OF.mrc 1 as #19.2, grid size 320,320,320, pixel 0.83, shown
    6310 at level 0.011, step 1, values float32 
    6311 Opened rOAT1-TVF_OF.mrc 2 as #19.3, grid size 320,320,320, pixel 0.83, shown
    6312 at level 0.011, step 1, values float32 
    6313 
    6314 > close #19.1-2
    6315 
    6316 > color #19.3 white models
    6317 
    6318 > color #19.3 #ffffb2ff models
    6319 
    6320 > select add #18
    6321 
    6322 3786 atoms, 3876 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    6323 
    6324 > color #18 #337744ff
    6325 
    6326 > color #18 #374c02ff
    6327 
    6328 > color (#!18 & sel) byhetero
    6329 
    6330 > select clear
    6331 
    6332 > color #19.3 #ffffb296 models
    6333 
    6334 > save
    6335 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    6336 > includeMaps true
    6337 
    6338 > open
    6339 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20250129_rOAT1-AAI/inward_j112_2.6A/postprocess.mrc
    6340 
    6341 Opened postprocess.mrc as #20, grid size 320,320,320, pixel 0.83, shown at
    6342 level 0.00494, step 2, values float32 
    6343 
    6344 > volume #20 step 1
    6345 
    6346 > hide #!19 models
    6347 
    6348 > hide #!18 models
    6349 
    6350 > rename #20 rOAT1-AAI_IF.mrc
    6351 
    6352 > volume #20 level 0.0194
    6353 
    6354 QXcbConnection: XCB error: 3 (BadWindow), sequence: 35473, resource id:
    6355 35656688, major code: 40 (TranslateCoords), minor code: 0 
    6356 
    6357 > show #!2 models
    6358 
    6359 > hide #!2 models
    6360 
    6361 > show #1 models
    6362 
    6363 > save
    6364 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/IF/rOAT1-AAI_IF.pdb
    6365 > models #1 relModel #20
    6366 
    6367 > hide #1 models
    6368 
    6369 > open
    6370 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/IF/rOAT1-AAI_IF.pdb
    6371 
    6372 Chain information for rOAT1-AAI_IF.pdb #21 
    6373 --- 
    6374 Chain | Description 
    6375 A | No description available 
    6376  
    6377 
    6378 > close #21
    6379 
    6380 > open
    6381 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/RealSpaceRefine_1/rOAT1-AAI_IF_real_space_refined_001.pdb
    6382 
    6383 Chain information for rOAT1-AAI_IF_real_space_refined_001.pdb #21 
    6384 --- 
    6385 Chain | Description 
    6386 A | No description available 
    6387  
    6388 
    6389 QXcbConnection: XCB error: 3 (BadWindow), sequence: 12758, resource id:
    6390 35656914, major code: 40 (TranslateCoords), minor code: 0 
    6391 
    6392 > close #21
    6393 
    6394 > open
    6395 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/RealSpaceRefine_3/rOAT1-AAI_IF-
    6396 > coot-1_real_space_refined_003_initial.geo
    6397 
    6398 Unrecognized file suffix '.geo' 
    6399 
    6400 > open
    6401 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/RealSpaceRefine_3/rOAT1-AAI_IF-
    6402 > coot-1_real_space_refined_003.pdb
    6403 
    6404 Chain information for rOAT1-AAI_IF-coot-1_real_space_refined_003.pdb #21 
    6405 --- 
    6406 Chain | Description 
    6407 A | No description available 
    6408  
    6409 
    6410 QXcbConnection: XCB error: 3 (BadWindow), sequence: 49188, resource id:
    6411 35657106, major code: 40 (TranslateCoords), minor code: 0 
    6412 
    6413 > select add #21
    6414 
    6415 3956 atoms, 4042 bonds, 516 residues, 1 model selected 
    6416 
    6417 > color #21 white
    6418 
    6419 > color #20 white models
    6420 
    6421 > select clear
    6422 
    6423 > select #21/A:602@O24
    6424 
    6425 1 atom, 1 residue, 1 model selected 
    6426 
    6427 > select up
    6428 
    6429 35 atoms, 38 bonds, 1 residue, 1 model selected 
    6430 
    6431 > select #21/A:601@O20
    6432 
    6433 1 atom, 1 residue, 1 model selected 
    6434 
    6435 > select add #21/A:602@C23
    6436 
    6437 2 atoms, 2 residues, 1 model selected 
    6438 
    6439 > select up
    6440 
    6441 70 atoms, 76 bonds, 2 residues, 1 model selected 
    6442 
    6443 > color sel red
    6444 
    6445 > color zone #20 near #21 distance 4.98
    6446 
    6447 > color zone #20 near #21 distance 4.88
    6448 
    6449 > color zone #20 near #21 distance 4.78
    6450 
    6451 > color zone #20 near #21 distance 4.68
    6452 
    6453 > color zone #20 near #21 distance 4.58
    6454 
    6455 > color zone #20 near #21 distance 4.48
    6456 
    6457 > color zone #20 near #21 distance 4.38
    6458 
    6459 > color zone #20 near #21 distance 4.28
    6460 
    6461 > color zone #20 near #21 distance 4.18
    6462 
    6463 > color zone #20 near #21 distance 4.08
    6464 
    6465 > color zone #20 near #21 distance 3.98
    6466 
    6467 > color zone #20 near #21 distance 3.88
    6468 
    6469 > color zone #20 near #21 distance 3.78
    6470 
    6471 > color zone #20 near #21 distance 3.68
    6472 
    6473 > color zone #20 near #21 distance 3.58
    6474 
    6475 > color zone #20 near #21 distance 3.48
    6476 
    6477 > color zone #20 near #21 distance 3.38
    6478 
    6479 > color zone #20 near #21 distance 3.28
    6480 
    6481 > color zone #20 near #21 distance 3.18
    6482 
    6483 > color zone #20 near #21 distance 3.08
    6484 
    6485 > color zone #20 near #21 distance 2.98
    6486 
    6487 > color zone #20 near #21 distance 2.88
    6488 
    6489 > volume splitbyzone #20
    6490 
    6491 Opened rOAT1-AAI_IF.mrc 0 as #22.1, grid size 320,320,320, pixel 0.83, shown
    6492 at level 0.0194, step 1, values float32 
    6493 Opened rOAT1-AAI_IF.mrc 1 as #22.2, grid size 320,320,320, pixel 0.83, shown
    6494 at level 0.0194, step 1, values float32 
    6495 Opened rOAT1-AAI_IF.mrc 2 as #22.3, grid size 320,320,320, pixel 0.83, shown
    6496 at level 0.0194, step 1, values float32 
    6497 
    6498 > close #22.1-2
    6499 
    6500 > color #22.3 yellow models
    6501 
    6502 > color #22.3 white models
    6503 
    6504 > color #22.3 #ffffb2ff models
    6505 
    6506 > color #22.3 #ffffb296 models
    6507 
    6508 > select add #21
    6509 
    6510 3956 atoms, 4042 bonds, 516 residues, 1 model selected 
    6511 
    6512 > color #21 #668855ff
    6513 
    6514 > color #21 #685d73ff
    6515 
    6516 > color sel byhetero
    6517 
    6518 > select clear
    6519 
    6520 [Repeated 1 time(s)]
    6521 
    6522 > save
    6523 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    6524 > includeMaps true
    6525 
    6526 QXcbConnection: XCB error: 3 (BadWindow), sequence: 7603, resource id:
    6527 35657141, major code: 40 (TranslateCoords), minor code: 0 
    6528 
    6529 QXcbConnection: XCB error: 3 (BadWindow), sequence: 7615, resource id:
    6530 35657136, major code: 40 (TranslateCoords), minor code: 0 
    6531 
    6532 > hide #!22.3 models
    6533 
    6534 > hide #!22 models
    6535 
    6536 > hide #21 models
    6537 
    6538 > open
    6539 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20250129_rOAT1-AAI/outward_j122_2.5A/postprocess.mrc
    6540 
    6541 Opened postprocess.mrc as #23, grid size 320,320,320, pixel 0.83, shown at
    6542 level 0.00494, step 2, values float32 
    6543 
    6544 > volume #23 level 0.01307
    6545 
    6546 > volume #23 step 1
    6547 
    6548 > volume #23 level 0.01684
    6549 
    6550 > show #1 models
    6551 
    6552 > hide #1 models
    6553 
    6554 > show #!5 models
    6555 
    6556 > rename #23 rOAT1-AAI_OF.mrc
    6557 
    6558 > save
    6559 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20250129_rOAT1-AAI/outward_j122_2.5A/rOAT1-AAI_OF.pdb
    6560 > models #5 relModel #23
    6561 
    6562 > open
    6563 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/RealSpaceRefine_4/rOAT1-AAI_OF-
    6564 > coot-1_real_space_refined_004.pdb
    6565 
    6566 Chain information for rOAT1-AAI_OF-coot-1_real_space_refined_004.pdb #24 
    6567 --- 
    6568 Chain | Description 
    6569 A | No description available 
    6570  
    6571 
    6572 > color #23 white models
    6573 
    6574 > color #24 white
    6575 
    6576 > hide #!5 models
    6577 
    6578 > select add #24/A:601@O24
    6579 
    6580 1 atom, 1 residue, 1 model selected 
    6581 
    6582 > select add #24/A:230@OH
    6583 
    6584 2 atoms, 2 residues, 1 model selected 
    6585 
    6586 > select clear
    6587 
    6588 > select add #24/A:601@O24
    6589 
    6590 1 atom, 1 residue, 1 model selected 
    6591 
    6592 > select up
    6593 
    6594 35 atoms, 38 bonds, 1 residue, 1 model selected 
    6595 
    6596 > color sel red
    6597 
    6598 > color zone #23 near #24 distance 4.98
    6599 
    6600 > volume splitbyzone #23
    6601 
    6602 Opened rOAT1-AAI_OF.mrc 0 as #25.1, grid size 320,320,320, pixel 0.83, shown
    6603 at level 0.0168, step 1, values float32 
    6604 Opened rOAT1-AAI_OF.mrc 1 as #25.2, grid size 320,320,320, pixel 0.83, shown
    6605 at level 0.0168, step 1, values float32 
    6606 Opened rOAT1-AAI_OF.mrc 2 as #25.3, grid size 320,320,320, pixel 0.83, shown
    6607 at level 0.0168, step 1, values float32 
    6608 
    6609 > close #25.1-2
    6610 
    6611 > select add #24
    6612 
    6613 3790 atoms, 3882 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    6614 
    6615 > select subtract #24
    6616 
    6617 Nothing selected 
    6618 
    6619 > color #25.3 white models
    6620 
    6621 > color #25.3 #ffffb2ff models
    6622 
    6623 > select add #24
    6624 
    6625 3790 atoms, 3882 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    6626 
    6627 > color #24 #1177ccff
    6628 
    6629 > color #24 #17c127ff
    6630 
    6631 > color (#!24 & sel) byhetero
    6632 
    6633 > select #24/A:438@CE2
    6634 
    6635 1 atom, 1 residue, 1 model selected 
    6636 Drag select of 1 atoms, 1 bonds 
    6637 
    6638 > select clear
    6639 
    6640 > color #25.3 #ffffb296 models
    6641 
    6642 > select clear
    6643 
    6644 > save
    6645 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    6646 > includeMaps true
    6647 
    6648 > open
    6649 > /home/dout2/isilon/PROJECTS/OAT1/cryoEM/rOAT1-PAH_20220730_20230218/rOAT1-PAH-
    6650 > coot-7_real_space_refined_007.pdb
    6651 
    6652 Chain information for rOAT1-PAH-coot-7_real_space_refined_007.pdb #26 
    6653 --- 
    6654 Chain | Description 
    6655 A | No description available 
    6656  
    6657 
    6658 QXcbConnection: XCB error: 3 (BadWindow), sequence: 7338, resource id:
    6659 35657291, major code: 40 (TranslateCoords), minor code: 0 
    6660 
    6661 > open
    6662 > /home/dout2/isilon/PROJECTS/OAT1/cryoEM/rOAT1-PAH_20220730_20230218/cryosparc_P4_J89__localfilter_160.mrc
    6663 
    6664 Opened cryosparc_P4_J89__localfilter_160.mrc as #27, grid size 160,160,160,
    6665 pixel 0.83, shown at level 0.134, step 1, values float32 
    6666 
    6667 > hide #!24 models
    6668 
    6669 > hide #!25.3 models
    6670 
    6671 > hide #!25 models
    6672 
    6673 > view
    6674 
    6675 > show #!2 models
    6676 
    6677 > select add #26
    6678 
    6679 3865 atoms, 3947 bonds, 1 pseudobond, 506 residues, 2 models selected 
    6680 
    6681 > select add #27
    6682 
    6683 3865 atoms, 3947 bonds, 1 pseudobond, 506 residues, 4 models selected 
    6684 
    6685 > view matrix models
    6686 > #26,1,0,0,55.434,0,1,0,82.728,0,0,1,62.865,#27,1,0,0,55.434,0,1,0,82.728,0,0,1,62.865
    6687 
    6688 > view matrix models
    6689 > #26,1,0,0,67.067,0,1,0,66.938,0,0,1,64.563,#27,1,0,0,67.067,0,1,0,66.938,0,0,1,64.563
    6690 
    6691 > rename #27 rOAT1-PAH
    6692 
    6693 > rename #27 rOAT1-PAH.mrc
    6694 
    6695 > view
    6696 
    6697 > fitmap #26 inMap #27
    6698 
    6699 Fit molecule rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) to map
    6700 rOAT1-PAH.mrc (#27) using 3865 atoms 
    6701 average map value = 0.3441, steps = 44 
    6702 shifted from previous position = 0.0131 
    6703 rotated from previous position = 0.0158 degrees 
    6704 atoms outside contour = 699, contour level = 0.13428 
    6705  
    6706 Position of rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) relative to
    6707 rOAT1-PAH.mrc (#27) coordinates: 
    6708 Matrix rotation and translation 
    6709 0.99999996 -0.00021122 0.00016567 0.00535685 
    6710 0.00021123 0.99999998 -0.00006568 0.00053709 
    6711 -0.00016566 0.00006571 0.99999998 -0.00148379 
    6712 Axis 0.23771757 0.59945172 0.76429575 
    6713 Axis point -1.23064203 24.84299856 0.00000000 
    6714 Rotation angle (degrees) 0.01583428 
    6715 Shift along axis 0.00046132 
    6716  
    6717 
    6718 > hide #!2 models
    6719 
    6720 > color #27 white models
    6721 
    6722 > color #26 white
    6723 
    6724 > hide #!26 models
    6725 
    6726 > select subtract #27
    6727 
    6728 3865 atoms, 3947 bonds, 1 pseudobond, 506 residues, 2 models selected 
    6729 
    6730 > select subtract #26
    6731 
    6732 Nothing selected 
    6733 
    6734 > hide #!27 models
    6735 
    6736 > show #!26 models
    6737 
    6738 > select #26/B:601@C07
    6739 
    6740 1 atom, 1 residue, 1 model selected 
    6741 
    6742 > select up
    6743 
    6744 23 atoms, 23 bonds, 1 residue, 1 model selected 
    6745 
    6746 > color sel red
    6747 
    6748 > show #!27 models
    6749 
    6750 > color zone #27 near #26 distance 4.98
    6751 
    6752 > color zone #27 near #26 distance 4.88
    6753 
    6754 > color zone #27 near #26 distance 4.78
    6755 
    6756 > color zone #27 near #26 distance 4.68
    6757 
    6758 > color zone #27 near #26 distance 4.58
    6759 
    6760 > color zone #27 near #26 distance 4.48
    6761 
    6762 > color zone #27 near #26 distance 4.38
    6763 
    6764 > color zone #27 near #26 distance 4.28
    6765 
    6766 > color zone #27 near #26 distance 4.18
    6767 
    6768 > color zone #27 near #26 distance 4.08
    6769 
    6770 > color zone #27 near #26 distance 3.98
    6771 
    6772 > color zone #27 near #26 distance 3.88
    6773 
    6774 > color zone #27 near #26 distance 3.78
    6775 
    6776 > color zone #27 near #26 distance 3.68
    6777 
    6778 > color zone #27 near #26 distance 3.58
    6779 
    6780 > color zone #27 near #26 distance 3.48
    6781 
    6782 > color zone #27 near #26 distance 3.38
    6783 
    6784 > color zone #27 near #26 distance 3.28
    6785 
    6786 > color zone #27 near #26 distance 3.18
    6787 
    6788 > color zone #27 near #26 distance 3.08
    6789 
    6790 > color zone #27 near #26 distance 2.98
    6791 
    6792 > color zone #27 near #26 distance 2.88
    6793 
    6794 > color zone #27 near #26 distance 2.78
    6795 
    6796 > color zone #27 near #26 distance 2.68
    6797 
    6798 > color zone #27 near #26 distance 2.58
    6799 
    6800 > color zone #27 near #26 distance 2.48
    6801 
    6802 > color zone #27 near #26 distance 2.38
    6803 
    6804 > color zone #27 near #26 distance 2.28
    6805 
    6806 > volume #27 level 0.1207
    6807 
    6808 > color zone #27 near #26 distance 2.18
    6809 
    6810 > color zone #27 near #26 distance 2.08
    6811 
    6812 > hide #!27 models
    6813 
    6814 > show #!27 models
    6815 
    6816 > fitmap #26 inMap #27
    6817 
    6818 Fit molecule rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) to map
    6819 rOAT1-PAH.mrc (#27) using 3865 atoms 
    6820 average map value = 0.3441, steps = 44 
    6821 shifted from previous position = 0.00509 
    6822 rotated from previous position = 0.0145 degrees 
    6823 atoms outside contour = 605, contour level = 0.12073 
    6824  
    6825 Position of rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) relative to
    6826 rOAT1-PAH.mrc (#27) coordinates: 
    6827 Matrix rotation and translation 
    6828 1.00000000 -0.00003177 0.00004592 0.00408484 
    6829 0.00003177 1.00000000 0.00006809 -0.00110606 
    6830 -0.00004592 -0.00006809 1.00000000 0.00040828 
    6831 Axis -0.77323345 0.52146975 0.36080373 
    6832 Axis point 0.00000000 25.00840435 -11.23310139 
    6833 Rotation angle (degrees) 0.00504562 
    6834 Shift along axis -0.00358800 
    6835  
    6836 
    6837 > fitmap #26 inMap #27
    6838 
    6839 Fit molecule rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) to map
    6840 rOAT1-PAH.mrc (#27) using 3865 atoms 
    6841 average map value = 0.3441, steps = 40 
    6842 shifted from previous position = 0.0153 
    6843 rotated from previous position = 0.0197 degrees 
    6844 atoms outside contour = 607, contour level = 0.12073 
    6845  
    6846 Position of rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) relative to
    6847 rOAT1-PAH.mrc (#27) coordinates: 
    6848 Matrix rotation and translation 
    6849 0.99999998 -0.00017402 -0.00004728 0.01145050 
    6850 0.00017401 0.99999996 -0.00023139 -0.00012574 
    6851 0.00004732 0.00023138 0.99999997 -0.01696563 
    6852 Axis 0.78875519 -0.16123857 0.59318410 
    6853 Axis point 0.00000000 70.72803400 -1.26127659 
    6854 Rotation angle (degrees) 0.01680827 
    6855 Shift along axis -0.00101183 
    6856  
    6857 
    6858 > volume splitbyzone #27
    6859 
    6860 Opened rOAT1-PAH.mrc 0 as #28.1, grid size 160,160,160, pixel 0.83, shown at
    6861 level 0.121, step 1, values float32 
    6862 Opened rOAT1-PAH.mrc 1 as #28.2, grid size 160,160,160, pixel 0.83, shown at
    6863 level 0.121, step 1, values float32 
    6864 Opened rOAT1-PAH.mrc 2 as #28.3, grid size 160,160,160, pixel 0.83, shown at
    6865 level 0.121, step 1, values float32 
    6866 
    6867 > close #28.1-2
    6868 
    6869 > volume #28.3 level 0.05463
    6870 
    6871 > color #28.3 white models
    6872 
    6873 > color #28.3 #ffffb2ff models
    6874 
    6875 > color #28.3 #ffffb296 models
    6876 
    6877 > select add #26
    6878 
    6879 3865 atoms, 3947 bonds, 1 pseudobond, 506 residues, 2 models selected 
    6880 
    6881 > color #26 #bf3434ff
    6882 
    6883 > select subtract #26
    6884 
    6885 Nothing selected 
    6886 
    6887 > hide #!26 models
    6888 
    6889 > hide #!28 models
    6890 
    6891 > hide #!28.3 models
    6892 
    6893 > show #!28 models
    6894 
    6895 > show #!28.3 models
    6896 
    6897 > hide #!28 models
    6898 
    6899 > show #!28 models
    6900 
    6901 > show #!26 models
    6902 
    6903 > save
    6904 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    6905 > includeMaps true
    6906 
    6907 QXcbConnection: XCB error: 3 (BadWindow), sequence: 59852, resource id:
    6908 35657337, major code: 40 (TranslateCoords), minor code: 0 
    6909 
    6910 > hide #!26 models
    6911 
    6912 > hide #!28 models
    6913 
    6914 > hide #!28.3 models
    6915 
    6916 > open
    6917 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20220525_rOAT1-FBP/inward_j46_2.8A/postprocess.mrc
    6918 
    6919 Opened postprocess.mrc as #29, grid size 320,320,320, pixel 0.83, shown at
    6920 level 0.0068, step 2, values float32 
    6921 
    6922 > open
    6923 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-FBP_model/rOAT1-FBP_Model04_RSR_004.pdb
    6924 
    6925 Chain information for rOAT1-FBP_Model04_RSR_004.pdb #30 
    6926 --- 
    6927 Chain | Description 
    6928 A | No description available 
    6929  
    6930 
    6931 > show #!2 models
    6932 
    6933 > volume #29 step 1
    6934 
    6935 > volume #29 level 0.01695
    6936 
    6937 > select add #30
    6938 
    6939 4327 atoms, 4393 bonds, 591 residues, 1 model selected 
    6940 
    6941 > view matrix models #30,1,0,0,75.395,0,1,0,59.328,0,0,1,65.467
    6942 
    6943 > view matrix models #30,1,0,0,69.37,0,1,0,69.752,0,0,1,66.8
    6944 
    6945 > view matrix models #30,1,0,0,64.899,0,1,0,72.303,0,0,1,66.211
    6946 
    6947 > view matrix models #30,1,0,0,67.675,0,1,0,68.154,0,0,1,64.823
    6948 
    6949 > rename #29 rOAT1-FBP.mrc
    6950 
    6951 > fitmap #30 inMap #29
    6952 
    6953 Fit molecule rOAT1-FBP_Model04_RSR_004.pdb (#30) to map rOAT1-FBP.mrc (#29)
    6954 using 4327 atoms 
    6955 average map value = 0.02366, steps = 64 
    6956 shifted from previous position = 2.15 
    6957 rotated from previous position = 1.57 degrees 
    6958 atoms outside contour = 1497, contour level = 0.016951 
    6959  
    6960 Position of rOAT1-FBP_Model04_RSR_004.pdb (#30) relative to rOAT1-FBP.mrc
    6961 (#29) coordinates: 
    6962 Matrix rotation and translation 
    6963 0.99965949 -0.01809184 -0.01880406 69.16631575 
    6964 0.01825291 0.99979787 0.00842953 64.90387685 
    6965 0.01864775 -0.00876989 0.99978765 65.39100171 
    6966 Axis -0.31300664 -0.68157330 0.66142625 
    6967 Axis point -4271.01743380 0.00000000 3378.83285764 
    6968 Rotation angle (degrees) 1.57437238 
    6969 Shift along axis -22.63494048 
    6970  
    6971 
    6972 > fitmap #29 inMap #28.3
    6973 
    6974 Fit map rOAT1-FBP.mrc in map rOAT1-PAH.mrc 2 using 25401 points 
    6975 correlation = 0.04397, correlation about mean = 0.03331, overlap = 0.1449 
    6976 steps = 2000, shift = 8.88, angle = 34.9 degrees 
    6977  
    6978 Position of rOAT1-FBP.mrc (#29) relative to rOAT1-PAH.mrc 2 (#28.3)
    6979 coordinates: 
    6980 Matrix rotation and translation 
    6981 0.83021101 -0.04922054 -0.55527201 36.70411652 
    6982 0.13130357 0.98533433 0.10897540 -101.23145590 
    6983 0.54176475 -0.16338178 0.82449824 -98.97434819 
    6984 Axis -0.23793623 -0.95839145 0.15770918 
    6985 Axis point 214.13564799 0.00000000 31.76591481 
    6986 Rotation angle (degrees) 34.91302477 
    6987 Shift along axis 72.67695975 
    6988  
    6989 
    6990 > fitmap #29 inMap #28.3
    6991 
    6992 Fit map rOAT1-FBP.mrc in map rOAT1-PAH.mrc 2 using 25401 points 
    6993 correlation = 0.06352, correlation about mean = 0.0448, overlap = 0.3215 
    6994 steps = 1976, shift = 9.79, angle = 47.5 degrees 
    6995  
    6996 Position of rOAT1-FBP.mrc (#29) relative to rOAT1-PAH.mrc 2 (#28.3)
    6997 coordinates: 
    6998 Matrix rotation and translation 
    6999 0.44591506 0.03168285 -0.89451437 128.47676238 
    7000 -0.42572042 0.88660402 -0.18081879 31.25418163 
    7001 0.78735118 0.46144286 0.40883812 -156.17744024 
    7002 Axis 0.34576253 -0.90543486 -0.24624374 
    7003 Axis point 186.53313716 0.00000000 6.98625710 
    7004 Rotation angle (degrees) 68.24252592 
    7005 Shift along axis 54.58154231 
    7006  
    7007 
    7008 > fitmap #29 inMap #2
    7009 
    7010 Fit map rOAT1-FBP.mrc in map rOAT1-AZT_IF.mrc using 25401 points 
    7011 correlation = 0.2561, correlation about mean = 0.04268, overlap = 2.051 
    7012 steps = 232, shift = 3.32, angle = 8.56 degrees 
    7013  
    7014 Position of rOAT1-FBP.mrc (#29) relative to rOAT1-AZT_IF.mrc (#2) coordinates: 
    7015 Matrix rotation and translation 
    7016 0.54964589 -0.00012465 -0.83539774 175.75622877 
    7017 -0.44507129 0.84621907 -0.29295875 119.06565669 
    7018 0.70696602 0.53283512 0.46506536 -99.09845418 
    7019 Axis 0.45744920 -0.85439368 -0.24647856 
    7020 Axis point 210.95352936 0.00000000 94.96801349 
    7021 Rotation angle (degrees) 64.50291620 
    7022 Shift along axis 3.09624573 
    7023  
    7024 
    7025 > select add #29
    7026 
    7027 4327 atoms, 4393 bonds, 591 residues, 3 models selected 
    7028 
    7029 > hide #!2 models
    7030 
    7031 > show #!2 models
    7032 
    7033 > hide #!2 models
    7034 
    7035 > show #!27 models
    7036 
    7037 > view matrix models
    7038 > #29,0.54965,-0.00012465,-0.8354,176.85,-0.44507,0.84622,-0.29296,120.37,0.70697,0.53284,0.46507,-99.177,#30,0.99966,-0.018092,-0.018804,70.259,0.018253,0.9998,0.0084295,66.206,0.018648,-0.0087699,0.99979,65.312
    7039 
    7040 > select subtract #30
    7041 
    7042 2 models selected 
    7043 
    7044 > ui mousemode right "rotate selected models"
    7045 
    7046 > view matrix models
    7047 > #29,0.93603,-0.13155,0.32642,-36.684,0.29946,0.78494,-0.54239,70.054,-0.18487,0.60545,0.77412,-40.4
    7048 
    7049 > view matrix models
    7050 > #29,0.99097,-0.1328,0.018694,4.0787,0.13411,0.98118,-0.13891,3.4116,0.00010362,0.14016,0.99013,-37.407
    7051 
    7052 > ui mousemode right "translate selected models"
    7053 
    7054 > view matrix models
    7055 > #29,0.99097,-0.1328,0.018694,17.811,0.13411,0.98118,-0.13891,8.06,0.00010362,0.14016,0.99013,-17.751
    7056 
    7057 > view matrix models
    7058 > #29,0.99097,-0.1328,0.018694,18.852,0.13411,0.98118,-0.13891,3.5023,0.00010362,0.14016,0.99013,-19.331
    7059 
    7060 > fitmap #29 inMap #2
    7061 
    7062 Fit map rOAT1-FBP.mrc in map rOAT1-AZT_IF.mrc using 25401 points 
    7063 correlation = 0.937, correlation about mean = 0.7119, overlap = 14.98 
    7064 steps = 260, shift = 2.93, angle = 16.7 degrees 
    7065  
    7066 Position of rOAT1-FBP.mrc (#29) relative to rOAT1-AZT_IF.mrc (#2) coordinates: 
    7067 Matrix rotation and translation 
    7068 0.99338416 0.10541244 -0.04556454 -5.89234048 
    7069 -0.10461957 0.99432199 0.01945563 14.33237930 
    7070 0.04735669 -0.01455997 0.99877192 -4.89753719 
    7071 Axis -0.14650897 -0.40022199 -0.90463113 
    7072 Axis point 131.78683646 64.78395429 0.00000000 
    7073 Rotation angle (degrees) 6.66633138 
    7074 Shift along axis -0.44238796 
    7075  
    7076 
    7077 > fitmap #30 inMap #29
    7078 
    7079 Fit molecule rOAT1-FBP_Model04_RSR_004.pdb (#30) to map rOAT1-FBP.mrc (#29)
    7080 using 4327 atoms 
    7081 average map value = 0.02366, steps = 84 
    7082 shifted from previous position = 1.18 
    7083 rotated from previous position = 6.66 degrees 
    7084 atoms outside contour = 1496, contour level = 0.016951 
    7085  
    7086 Position of rOAT1-FBP_Model04_RSR_004.pdb (#30) relative to rOAT1-FBP.mrc
    7087 (#29) coordinates: 
    7088 Matrix rotation and translation 
    7089 0.99966027 -0.01808767 -0.01876641 69.16021058 
    7090 0.01824668 0.99979876 0.00833662 64.90031908 
    7091 0.01861185 -0.00867622 0.99978914 65.39198117 
    7092 Axis -0.31026139 -0.68166338 0.66262576 
    7093 Axis point -4271.35731029 0.00000000 3392.84555643 
    7094 Rotation angle (degrees) 1.57107230 
    7095 Shift along axis -22.36750269 
    7096  
    7097 
    7098 > select subtract #29
    7099 
    7100 Nothing selected 
    7101 
    7102 > hide #!27 models
    7103 
    7104 > color #29 white models
    7105 
    7106 > color #30 white
    7107 
    7108 > select ::name="FBP"
    7109 
    7110 18 atoms, 19 bonds, 1 residue, 1 model selected 
    7111 
    7112 > color sel red
    7113 
    7114 > color zone #29 near #30 distance 4.98
    7115 
    7116 > volume #29 level 0.01043
    7117 
    7118 > volume splitbyzone #29
    7119 
    7120 Opened rOAT1-FBP.mrc 0 as #31.1, grid size 320,320,320, pixel 0.83, shown at
    7121 level 0.0104, step 1, values float32 
    7122 Opened rOAT1-FBP.mrc 1 as #31.2, grid size 320,320,320, pixel 0.83, shown at
    7123 level 0.0104, step 1, values float32 
    7124 Opened rOAT1-FBP.mrc 2 as #31.3, grid size 320,320,320, pixel 0.83, shown at
    7125 level 0.0104, step 1, values float32 
    7126 
    7127 > close #31.1-2
    7128 
    7129 > volume #31.3 level 0.002491
    7130 
    7131 > volume #31.3 level 0.005476
    7132 
    7133 > close #31#31.3
    7134 
    7135 > show #!29 models
    7136 
    7137 > color zone #29 near #30 distance 2
    7138 
    7139 [Repeated 1 time(s)]
    7140 
    7141 > volume splitbyzone #29
    7142 
    7143 Opened rOAT1-FBP.mrc 0 as #31.1, grid size 320,320,320, pixel 0.83, shown at
    7144 level 0.0104, step 1, values float32 
    7145 Opened rOAT1-FBP.mrc 1 as #31.2, grid size 320,320,320, pixel 0.83, shown at
    7146 level 0.0104, step 1, values float32 
    7147 Opened rOAT1-FBP.mrc 2 as #31.3, grid size 320,320,320, pixel 0.83, shown at
    7148 level 0.0104, step 1, values float32 
    7149 
    7150 > close #31.1-2
    7151 
    7152 > volume #31.3 level 0.003802
    7153 
    7154 > color #31.3 white models
    7155 
    7156 > color #31.3 #ffffb2ff models
    7157 
    7158 > color #31.3 #ffffb20f models
    7159 
    7160 > color #31.3 #ffffb296 models
    7161 
    7162 > select add #30
    7163 
    7164 4327 atoms, 4393 bonds, 591 residues, 1 model selected 
    7165 
    7166 > color #30 #889944ff
    7167 
    7168 > color #30 #894a08ff
    7169 
    7170 > save
    7171 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    7172 > includeMaps true
    7173 
    7174 > hide #!31.3 models
    7175 
    7176 > hide #!31 models
    7177 
    7178 > select subtract #30
    7179 
    7180 Nothing selected 
    7181 
    7182 > hide #30 models
    7183 
    7184 > show #!2 models
    7185 
    7186 > open
    7187 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20220609_rOAT1-CFM/inward_j194_2.7A/postprocess.mrc
    7188 
    7189 Opened postprocess.mrc as #32, grid size 320,320,320, pixel 0.83, shown at
    7190 level 0.00396, step 2, values float32 
    7191 
    7192 QXcbConnection: XCB error: 3 (BadWindow), sequence: 4668, resource id:
    7193 35657387, major code: 40 (TranslateCoords), minor code: 0 
    7194 
    7195 > volume #32 step 1
    7196 
    7197 > volume #32 level 0.01186
    7198 
    7199 > rename #32 rOAT1-CFM.mrc
    7200 
    7201 > fitmap #31.3 inMap #32
    7202 
    7203 Fit map rOAT1-FBP.mrc 2 in map rOAT1-CFM.mrc using 186 points 
    7204 correlation = 0.7788, correlation about mean = 0.1794, overlap = 0.008643 
    7205 steps = 80, shift = 1.06, angle = 39.7 degrees 
    7206  
    7207 Position of rOAT1-FBP.mrc 2 (#31.3) relative to rOAT1-CFM.mrc (#32)
    7208 coordinates: 
    7209 Matrix rotation and translation 
    7210 0.74404465 0.65679786 0.12253212 -67.09990326 
    7211 -0.66239846 0.70118044 0.26376935 89.56606533 
    7212 0.08732602 -0.27742126 0.95677145 29.93219993 
    7213 Axis -0.37942983 0.02468307 -0.92489121 
    7214 Axis point 75.79903236 131.70903838 0.00000000 
    7215 Rotation angle (degrees) 45.49284979 
    7216 Shift along axis -0.01355792 
    7217  
    7218 
    7219 > fitmap #31.3 inMap #2
    7220 
    7221 Fit map rOAT1-FBP.mrc 2 in map rOAT1-AZT_IF.mrc using 186 points 
    7222 correlation = 0.8514, correlation about mean = 0.3895, overlap = 0.01295 
    7223 steps = 76, shift = 0.987, angle = 35 degrees 
    7224  
    7225 Position of rOAT1-FBP.mrc 2 (#31.3) relative to rOAT1-AZT_IF.mrc (#2)
    7226 coordinates: 
    7227 Matrix rotation and translation 
    7228 0.98357109 0.17790518 -0.03062105 -15.98050765 
    7229 -0.17592201 0.98266732 0.05844983 19.75924781 
    7230 0.04048883 -0.05210265 0.99782061 1.12732183 
    7231 Axis -0.29288928 -0.18839308 -0.93740275 
    7232 Axis point 102.41456930 99.44616144 0.00000000 
    7233 Rotation angle (degrees) 10.87852675 
    7234 Shift along axis -0.09874061 
    7235  
    7236 
    7237 > fitmap #32 inMap #2
    7238 
    7239 Fit map rOAT1-CFM.mrc in map rOAT1-AZT_IF.mrc using 30016 points 
    7240 correlation = 0.9542, correlation about mean = 0.7898, overlap = 13.57 
    7241 steps = 72, shift = 2.43, angle = 7.06 degrees 
    7242  
    7243 Position of rOAT1-CFM.mrc (#32) relative to rOAT1-AZT_IF.mrc (#2) coordinates: 
    7244 Matrix rotation and translation 
    7245 0.99240829 0.11776796 -0.03544703 -8.88787383 
    7246 -0.11778889 0.99303752 0.00150464 18.44106769 
    7247 0.03537743 0.00268205 0.99937042 -5.69387210 
    7248 Axis 0.00478670 -0.28793162 -0.95763901 
    7249 Axis point 151.76616064 85.25679566 0.00000000 
    7250 Rotation angle (degrees) 7.06459913 
    7251 Shift along axis 0.10036409 
    7252  
    7253 
    7254 > save
    7255 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-CFM/rOAT1-CFM_IF.pdb
    7256 > models #30 relModel #32
    7257 
    7258 > open
    7259 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-CFM/rOAT1-CFM_IF.pdb
    7260 
    7261 Chain information for rOAT1-CFM_IF.pdb #33 
    7262 --- 
    7263 Chain | Description 
    7264 A | No description available 
    7265  
    7266 
    7267 > color #33 #ffff7fff
    7268 
    7269 > color #33 #55aaffff
    7270 
    7271 > select add #33
    7272 
    7273 4327 atoms, 4393 bonds, 591 residues, 1 model selected 
    7274 
    7275 > view matrix models #33,1,0,0,-3.2206,0,1,0,10.827,0,0,1,-3.1224
    7276 
    7277 > view matrix models #33,1,0,0,-4.4307,0,1,0,11.668,0,0,1,-3.5924
    7278 
    7279 > view matrix models #33,1,0,0,-4.3326,0,1,0,9.3726,0,0,1,-2.8036
    7280 
    7281 > fitmap #33 inMap #32
    7282 
    7283 Fit molecule rOAT1-CFM_IF.pdb (#33) to map rOAT1-CFM.mrc (#32) using 4327
    7284 atoms 
    7285 average map value = 0.0191, steps = 80 
    7286 shifted from previous position = 1.1 
    7287 rotated from previous position = 7.12 degrees 
    7288 atoms outside contour = 1362, contour level = 0.01186 
    7289  
    7290 Position of rOAT1-CFM_IF.pdb (#33) relative to rOAT1-CFM.mrc (#32)
    7291 coordinates: 
    7292 Matrix rotation and translation 
    7293 0.99999299 -0.00023005 -0.00373680 -4.70643521 
    7294 0.00021365 0.99999035 -0.00438786 8.58155234 
    7295 0.00373777 0.00438703 0.99998339 -3.97966882 
    7296 Axis 0.76069466 -0.64796926 0.03846397 
    7297 Axis point 0.00000000 827.85989235 581.48051316 
    7298 Rotation angle (degrees) 0.33046593 
    7299 Shift along axis -9.29381608 
    7300  
    7301 
    7302 > save /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-CFM/rOAT1-CFM.pdb
    7303 > models #33 relModel #32
    7304 
    7305 QXcbConnection: XCB error: 3 (BadWindow), sequence: 60371, resource id:
    7306 35657459, major code: 40 (TranslateCoords), minor code: 0 
    7307 
    7308 > hide #33 models
    7309 
    7310 > hide #!32 models
    7311 
    7312 > select subtract #33
    7313 
    7314 Nothing selected 
    7315 
    7316 > show #!17 models
    7317 
    7318 > hide #!17 models
    7319 
    7320 > show #!17 models
    7321 
    7322 > hide #!2 models
    7323 
    7324 > open
    7325 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/RealSpaceRefine_7/rOAT1-TFV-
    7326 > Cl_OF-coot-2.pdb
    7327 
    7328 Chain information for rOAT1-TFV-Cl_OF-coot-2.pdb #34 
    7329 --- 
    7330 Chain | Description 
    7331 A | No description available 
    7332  
    7333 
    7334 > select ::name="CL"
    7335 
    7336 1 atom, 1 residue, 1 model selected 
    7337 
    7338 > hide #!17 models
    7339 
    7340 > show sel atoms
    7341 
    7342 > show #!17 models
    7343 
    7344 > style sel stick
    7345 
    7346 Changed 1 atom style 
    7347 
    7348 > color zone #17 near #34 distance 2.98
    7349 
    7350 > select add #34
    7351 
    7352 3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 2 models selected 
    7353 
    7354 > color #34 white
    7355 
    7356 > color zone #17 near #34 distance 2.98
    7357 
    7358 > select ::name="CL"
    7359 
    7360 1 atom, 1 residue, 1 model selected 
    7361 
    7362 > color sel red
    7363 
    7364 > color zone #17 near #34 distance 2.98
    7365 
    7366 > volume splitbyzone #17
    7367 
    7368 Opened rOAT1-TVF_OF.mrc 0 as #35.1, grid size 320,320,320, pixel 0.83, shown
    7369 at level 0.011, step 1, values float32 
    7370 Opened rOAT1-TVF_OF.mrc 1 as #35.2, grid size 320,320,320, pixel 0.83, shown
    7371 at level 0.011, step 1, values float32 
    7372 Opened rOAT1-TVF_OF.mrc 2 as #35.3, grid size 320,320,320, pixel 0.83, shown
    7373 at level 0.011, step 1, values float32 
    7374 
    7375 > rename #35 "rOAT1-TVF-Cl_OF.mrc split"
    7376 
    7377 > close #35.1-2
    7378 
    7379 > rename #35.3 "rOAT1-TVF-Cl_OF.mrc 2"
    7380 
    7381 > hide #!35.3 models
    7382 
    7383 > select #34/B:1@CL
    7384 
    7385 1 atom, 1 residue, 1 model selected 
    7386 
    7387 > ui tool show Contacts
    7388 
    7389 > contacts sel interModel false ignoreHiddenModels true select true
    7390 
    7391 6 contacts 
    7392 
    7393 > ui tool show Contacts
    7394 
    7395 > contacts sel intraRes true ignoreHiddenModels true select true
    7396 
    7397 15 contacts 
    7398 
    7399 > show sel atoms
    7400 
    7401 > color #34 yellow
    7402 
    7403 > show sel atoms
    7404 
    7405 > close #36
    7406 
    7407 > select add #34
    7408 
    7409 3787 atoms, 3876 bonds, 11 pseudobonds, 487 residues, 3 models selected 
    7410 
    7411 > color #34 white
    7412 
    7413 > hide sel atoms
    7414 
    7415 > select ::name="CL"
    7416 
    7417 1 atom, 1 residue, 1 model selected 
    7418 
    7419 > show sel atoms
    7420 
    7421 > hide #35.3.1 models
    7422 
    7423 > show #35.3.1 models
    7424 
    7425 > close #34.2
    7426 
    7427 > hide #!35.3 models
    7428 
    7429 > hide #35.3.1 models
    7430 
    7431 > hide #!35 models
    7432 
    7433 > hide #34.1 models
    7434 
    7435 > select #34/B:1@CL
    7436 
    7437 1 atom, 1 residue, 1 model selected 
    7438 
    7439 > select #34/A:216
    7440 
    7441 8 atoms, 7 bonds, 1 residue, 1 model selected 
    7442 
    7443 > show sel atoms
    7444 
    7445 > select #34/A:511
    7446 
    7447 7 atoms, 7 bonds, 1 residue, 1 model selected 
    7448 
    7449 > show sel atoms
    7450 
    7451 > select #34: 219
    7452 
    7453 11 atoms, 10 bonds, 1 residue, 1 model selected 
    7454 
    7455 > show sel atoms
    7456 
    7457 > select #34: 273
    7458 
    7459 11 atoms, 10 bonds, 1 residue, 1 model selected 
    7460 
    7461 > show sel atoms
    7462 
    7463 > select #34/A:4
    7464 
    7465 8 atoms, 7 bonds, 1 residue, 1 model selected 
    7466 
    7467 > show sel atoms
    7468 
    7469 > select add #34/A:511
    7470 
    7471 15 atoms, 14 bonds, 2 residues, 1 model selected 
    7472 
    7473 > show sel atoms
    7474 
    7475 > select add #34/A:512
    7476 
    7477 23 atoms, 21 bonds, 3 residues, 1 model selected 
    7478 
    7479 > show sel atoms
    7480 
    7481 > select #34/B:1@CL
    7482 
    7483 1 atom, 1 residue, 1 model selected 
    7484 
    7485 > color sel lime
    7486 
    7487 > color #35.3.1 white
    7488 
    7489 > color #35.3.1 #ffffb2ff
    7490 
    7491 > color #35.3.1 #ffffb296
    7492 
    7493 > select #34/B:1@CL
    7494 
    7495 1 atom, 1 residue, 1 model selected 
    7496 
    7497 > select add #34
    7498 
    7499 3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 2 models selected 
    7500 
    7501 > color #34 #374c02ff
    7502 
    7503 > select #34/B:1@CL
    7504 
    7505 1 atom, 1 residue, 1 model selected 
    7506 
    7507 > color sel lime
    7508 
    7509 > select add #34
    7510 
    7511 3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 2 models selected 
    7512 
    7513 > color (#!34 & sel) byhetero
    7514 
    7515 > select #34/A:2
    7516 
    7517 5 atoms, 4 bonds, 1 residue, 1 model selected 
    7518 
    7519 > show sel atoms
    7520 
    7521 > select #34/A:3
    7522 
    7523 11 atoms, 11 bonds, 1 residue, 1 model selected 
    7524 
    7525 > show sel atoms
    7526 
    7527 > select add #34/A:215
    7528 
    7529 18 atoms, 18 bonds, 2 residues, 1 model selected 
    7530 
    7531 > show sel atoms
    7532 
    7533 > select #34/B:1@CL
    7534 
    7535 1 atom, 1 residue, 1 model selected 
    7536 
    7537 > show #35.3.1 models
    7538 
    7539 > view sel
    7540 
    7541 > hide #35.3.1 models
    7542 
    7543 > hide #!35.3 models
    7544 
    7545 > hide #!35 models
    7546 
    7547 > hide #!34 models
    7548 
    7549 > select add #34
    7550 
    7551 3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 2 models selected 
    7552 
    7553 > select subtract #34
    7554 
    7555 Nothing selected 
    7556 
    7557 > show #1 models
    7558 
    7559 > view
    7560 
    7561 > hide #1 models
    7562 
    7563 > show #21 models
    7564 
    7565 > select add #21/A:602@C12
    7566 
    7567 1 atom, 1 residue, 1 model selected 
    7568 
    7569 > select up
    7570 
    7571 3 atoms, 1 bond, 2 residues, 1 model selected 
    7572 
    7573 > select up
    7574 
    7575 44 atoms, 46 bonds, 2 residues, 1 model selected 
    7576 
    7577 > select clear
    7578 
    7579 > select #21/A:602@O14
    7580 
    7581 1 atom, 1 residue, 1 model selected 
    7582 
    7583 > select add #21/A:601@C04
    7584 
    7585 2 atoms, 2 residues, 1 model selected 
    7586 
    7587 > select up
    7588 
    7589 70 atoms, 76 bonds, 2 residues, 1 model selected 
    7590 
    7591 > view sel
    7592 
    7593 > show #!22.3 models
    7594 
    7595 > hide #!22.3 models
    7596 
    7597 > hide #!22 models
    7598 
    7599 > hide #21 models
    7600 
    7601 > select add #21
    7602 
    7603 3956 atoms, 4042 bonds, 516 residues, 1 model selected 
    7604 
    7605 > select subtract #21
    7606 
    7607 Nothing selected 
    7608 
    7609 > save
    7610 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    7611 > includeMaps true
    7612 
    7613 QXcbConnection: XCB error: 3 (BadWindow), sequence: 40781, resource id:
    7614 35657669, major code: 40 (TranslateCoords), minor code: 0 
    7615 
    7616 > open
    7617 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20241127_hOAT1-TFV/inward_j62_3.2A/postprocess.mrc
    7618 
    7619 Opened postprocess.mrc as #36, grid size 320,320,320, pixel 0.83, shown at
    7620 level 0.00418, step 2, values float32 
    7621 
    7622 > open
    7623 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20241127_hOAT1-TFV/inward_j62_3.2A/hOAT1_AF-Q4U2R8-F1-model_v4.pdb
    7624 
    7625 hOAT1_AF-Q4U2R8-F1-model_v4.pdb title: 
    7626 Alphafold monomer V2.0 prediction for solute carrier family 22 member 6
    7627 (Q4U2R8) [more info...] 
    7628  
    7629 Chain information for hOAT1_AF-Q4U2R8-F1-model_v4.pdb #37 
    7630 --- 
    7631 Chain | Description | UniProt 
    7632 A | solute carrier family 22 member 6 | S22A6_HUMAN 1-563 
    7633  
    7634 
    7635 > rename #36 hOAT1-TFV.mrc
    7636 
    7637 > volume #36 step 1
    7638 
    7639 > volume #36 level 0.008515
    7640 
    7641 > rename #37 hOAT1-TFV_IF.pdb
    7642 
    7643 > view
    7644 
    7645 > show #!2 models
    7646 
    7647 > hide #!2 models
    7648 
    7649 > ui tool show Matchmaker
    7650 
    7651 > matchmaker #37 to #1
    7652 
    7653 Parameters 
    7654 --- 
    7655 Chain pairing | bb 
    7656 Alignment algorithm | Needleman-Wunsch 
    7657 Similarity matrix | BLOSUM-62 
    7658 SS fraction | 0.3 
    7659 Gap open (HH/SS/other) | 18/18/6 
    7660 Gap extend | 1 
    7661 SS matrix |  |  | H | S | O 
    7662 ---|---|---|--- 
    7663 H | 6 | -9 | -6 
    7664 S |  | 6 | -6 
    7665 O |  |  | 4 
    7666 Iteration cutoff | 2 
    7667  
    7668 Matchmaker rOAT1-AZT_IF.pdb, chain A (#1) with hOAT1-TFV_IF.pdb, chain A
    7669 (#37), sequence alignment score = 2359.6 
    7670 RMSD between 490 pruned atom pairs is 0.806 angstroms; (across all 500 pairs:
    7671 0.862) 
    7672  
    7673 
    7674 > matchmaker #37 to #1
    7675 
    7676 Parameters 
    7677 --- 
    7678 Chain pairing | bb 
    7679 Alignment algorithm | Needleman-Wunsch 
    7680 Similarity matrix | BLOSUM-62 
    7681 SS fraction | 0.3 
    7682 Gap open (HH/SS/other) | 18/18/6 
    7683 Gap extend | 1 
    7684 SS matrix |  |  | H | S | O 
    7685 ---|---|---|--- 
    7686 H | 6 | -9 | -6 
    7687 S |  | 6 | -6 
    7688 O |  |  | 4 
    7689 Iteration cutoff | 2 
    7690  
    7691 Matchmaker rOAT1-AZT_IF.pdb, chain A (#1) with hOAT1-TFV_IF.pdb, chain A
    7692 (#37), sequence alignment score = 2359.6 
    7693 RMSD between 490 pruned atom pairs is 0.806 angstroms; (across all 500 pairs:
    7694 0.862) 
    7695  
    7696 
    7697 > save
    7698 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20241127_hOAT1-TFV/inward_j62_3.2A/hOAT1-TVF_IF.pdb
    7699 > models #37 relModel #36
    7700 
    7701 > rename #36 hOAT1-TFV_IF.mrc
    7702 
    7703 > hide #37 models
    7704 
    7705 > hide #!36 models
    7706 
    7707 > open
    7708 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20241127_hOAT1-TFV/inward_j62_3.2A/hOAT1_AF-Q4U2R8-F1-model_v4.pdb
    7709 
    7710 hOAT1_AF-Q4U2R8-F1-model_v4.pdb title: 
    7711 Alphafold monomer V2.0 prediction for solute carrier family 22 member 6
    7712 (Q4U2R8) [more info...] 
    7713  
    7714 Chain information for hOAT1_AF-Q4U2R8-F1-model_v4.pdb #38 
    7715 --- 
    7716 Chain | Description | UniProt 
    7717 A | solute carrier family 22 member 6 | S22A6_HUMAN 1-563 
    7718  
    7719 
    7720 > close #38
    7721 
    7722 > close #37
    7723 
    7724 > open
    7725 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/RealSpaceRefine_2/hOAT1-TVF_IF-
    7726 > coot-1_real_space_refined_002.pdb
    7727 
    7728 Chain information for hOAT1-TVF_IF-coot-1_real_space_refined_002.pdb #37 
    7729 --- 
    7730 Chain | Description 
    7731 A | No description available 
    7732  
    7733 
    7734 > show #!36 models
    7735 
    7736 > color #36 white models
    7737 
    7738 > color #37 white
    7739 
    7740 > hide #!36 models
    7741 
    7742 > select up
    7743 
    7744 2 atoms, 1 bond, 1 residue, 1 model selected 
    7745 
    7746 > select #37/A:601@C08
    7747 
    7748 1 atom, 1 residue, 1 model selected 
    7749 
    7750 > select up
    7751 
    7752 31 atoms, 32 bonds, 1 residue, 1 model selected 
    7753 
    7754 > color sel red
    7755 
    7756 > show #!36 models
    7757 
    7758 > color zone #36 near #37 distance 4.98
    7759 
    7760 > color zone #36 near #37 distance 2
    7761 
    7762 [Repeated 1 time(s)]
    7763 
    7764 > color zone #36 near #37 distance 1.9
    7765 
    7766 > color zone #36 near #37 distance 1.8
    7767 
    7768 > color zone #36 near #37 distance 1.7
    7769 
    7770 > volume splitbyzone #36
    7771 
    7772 Opened hOAT1-TFV_IF.mrc 0 as #38.1, grid size 320,320,320, pixel 0.83, shown
    7773 at level 0.00852, step 1, values float32 
    7774 Opened hOAT1-TFV_IF.mrc 1 as #38.2, grid size 320,320,320, pixel 0.83, shown
    7775 at level 0.00852, step 1, values float32 
    7776 Opened hOAT1-TFV_IF.mrc 2 as #38.3, grid size 320,320,320, pixel 0.83, shown
    7777 at level 0.00852, step 1, values float32 
    7778 
    7779 > close #38.1-2
    7780 
    7781 > color #38.3 white models
    7782 
    7783 > color #38.3 #ffffb2ff models
    7784 
    7785 > color #38.3 #ffffb296 models
    7786 
    7787 > color #37 #aaff7fff
    7788 
    7789 > select add #37
    7790 
    7791 4375 atoms, 4481 bonds, 564 residues, 1 model selected 
    7792 
    7793 > color sel byhetero
    7794 
    7795 > save
    7796 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    7797 > includeMaps true
    7798 
    7799 QXcbConnection: XCB error: 3 (BadWindow), sequence: 48690, resource id:
    7800 35657985, major code: 40 (TranslateCoords), minor code: 0 
    7801 
    7802 > hide #!38.3 models
    7803 
    7804 > hide #!38 models
    7805 
    7806 > select subtract #37
    7807 
    7808 Nothing selected 
    7809 
    7810 > show #!34 models
    7811 
    7812 Drag select of 25 atoms, 383 residues, 24 bonds 
    7813 
    7814 > select up
    7815 
    7816 2906 atoms, 2958 bonds, 383 residues, 2 models selected 
    7817 
    7818 > select clear
    7819 
    7820 > select add #37/A:326
    7821 
    7822 5 atoms, 4 bonds, 1 residue, 1 model selected 
    7823 
    7824 > select clear
    7825 
    7826 > hide #!34 models
    7827 
    7828 > select add #37
    7829 
    7830 4375 atoms, 4481 bonds, 564 residues, 1 model selected 
    7831 
    7832 > select subtract #37
    7833 
    7834 Nothing selected 
    7835 
    7836 > save
    7837 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF.pdb
    7838 
    7839 > save
    7840 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF.pdb
    7841 > models #37 relModel #36
    7842 
    7843 QXcbConnection: XCB error: 3 (BadWindow), sequence: 16970, resource id:
    7844 35658005, major code: 40 (TranslateCoords), minor code: 0 
    7845 
    7846 QXcbConnection: XCB error: 3 (BadWindow), sequence: 16981, resource id:
    7847 35657995, major code: 40 (TranslateCoords), minor code: 0 
    7848 
    7849 > open
    7850 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20241127_hOAT1-TFV/outward_j68_3.1A/postprocess.mrc
    7851 
    7852 Opened postprocess.mrc as #39, grid size 320,320,320, pixel 0.83, shown at
    7853 level 0.00436, step 2, values float32 
    7854 
    7855 QXcbConnection: XCB error: 3 (BadWindow), sequence: 18302, resource id:
    7856 35658010, major code: 40 (TranslateCoords), minor code: 0 
    7857 
    7858 > rename #39 hOAT1-TFV_OF.mrc
    7859 
    7860 > volume #39 step 1
    7861 
    7862 > volume #39 level 0.01031
    7863 
    7864 > hide #!39 models
    7865 
    7866 > open
    7867 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF.pdb
    7868 
    7869 Chain information for hOAT1-TFV_OF.pdb #40 
    7870 --- 
    7871 Chain | Description 
    7872 A | No description available 
    7873  
    7874 
    7875 > hide #37 models
    7876 
    7877 > select #40: 320-600
    7878 
    7879 1850 atoms, 1888 bonds, 244 residues, 1 model selected 
    7880 
    7881 > hide sel cartoons
    7882 
    7883 [Repeated 1 time(s)]
    7884 
    7885 > show sel cartoons
    7886 
    7887 > ui tool show Matchmaker
    7888 
    7889 > matchmaker #40 & sel to #18
    7890 
    7891 Parameters 
    7892 --- 
    7893 Chain pairing | bb 
    7894 Alignment algorithm | Needleman-Wunsch 
    7895 Similarity matrix | BLOSUM-62 
    7896 SS fraction | 0.3 
    7897 Gap open (HH/SS/other) | 18/18/6 
    7898 Gap extend | 1 
    7899 SS matrix |  |  | H | S | O 
    7900 ---|---|---|--- 
    7901 H | 6 | -9 | -6 
    7902 S |  | 6 | -6 
    7903 O |  |  | 4 
    7904 Iteration cutoff | 2 
    7905  
    7906 Matchmaker rOAT1-TFV_OF-coot-1_real_space_refined_007.pdb, chain A (#18) with
    7907 hOAT1-TFV_OF.pdb, chain A (#40), sequence alignment score = 866.1 
    7908 RMSD between 164 pruned atom pairs is 0.748 angstroms; (across all 200 pairs:
    7909 7.198) 
    7910  
    7911 
    7912 > matchmaker #40 to #15
    7913 
    7914 Parameters 
    7915 --- 
    7916 Chain pairing | bb 
    7917 Alignment algorithm | Needleman-Wunsch 
    7918 Similarity matrix | BLOSUM-62 
    7919 SS fraction | 0.3 
    7920 Gap open (HH/SS/other) | 18/18/6 
    7921 Gap extend | 1 
    7922 SS matrix |  |  | H | S | O 
    7923 ---|---|---|--- 
    7924 H | 6 | -9 | -6 
    7925 S |  | 6 | -6 
    7926 O |  |  | 4 
    7927 Iteration cutoff | 2 
    7928  
    7929 Matchmaker rOAT1-TFV_IF-coot-3.pdb, chain A (#15) with hOAT1-TFV_OF.pdb, chain
    7930 A (#40), sequence alignment score = 2368.6 
    7931 RMSD between 493 pruned atom pairs is 0.665 angstroms; (across all 500 pairs:
    7932 0.719) 
    7933  
    7934 
    7935 > show #!18 models
    7936 
    7937 > ui mousemode right "translate selected atoms"
    7938 
    7939 > ui mousemode right "rotate selected models"
    7940 
    7941 > view matrix models
    7942 > #40,0.99727,-0.025813,-0.069217,13.221,0.025375,0.99965,-0.0072002,-1.7643,0.069379,0.0054242,0.99758,-8.8122
    7943 
    7944 > undo
    7945 
    7946 > ui mousemode right "move picked models"
    7947 
    7948 > view matrix models #18,1,0,0,0.019269,0,1,0,-0.04277,0,0,1,0.28987
    7949 
    7950 > undo
    7951 
    7952 > ui mousemode right pivot
    7953 
    7954 > ui tool show Matchmaker
    7955 
    7956 > matchmaker #40 & sel to #5 & sel
    7957 
    7958 No 'to' model specified 
    7959 
    7960 > select clear
    7961 
    7962 > hide #!18 models
    7963 
    7964 > show #!18 models
    7965 
    7966 > select #18,40: 320-600
    7967 
    7968 3274 atoms, 3340 bonds, 2 pseudobonds, 433 residues, 3 models selected 
    7969 
    7970 > ui tool show Matchmaker
    7971 
    7972 > matchmaker #40 & sel to #5 & sel
    7973 
    7974 No 'to' model specified 
    7975 
    7976 > matchmaker #40 & sel to #5 & sel
    7977 
    7978 No 'to' model specified 
    7979 
    7980 > matchmaker #40 & sel to #5 & sel
    7981 
    7982 No 'to' model specified 
    7983 
    7984 > ui mousemode right "translate selected atoms"
    7985 
    7986 > select #40: 320-600
    7987 
    7988 1850 atoms, 1888 bonds, 244 residues, 1 model selected 
    7989 
    7990 > hide #!18 models
    7991 
    7992 > show #!18 models
    7993 
    7994 > hide #40 models
    7995 
    7996 > hide #!18 models
    7997 
    7998 > show #40 models
    7999 
    8000 > save
    8001 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF.pdb
    8002 > models #40 relModel #39
    8003 
    8004 QXcbConnection: XCB error: 3 (BadWindow), sequence: 34583, resource id:
    8005 35658147, major code: 40 (TranslateCoords), minor code: 0 
    8006 
    8007 > fitmap #40 inMap #39
    8008 
    8009 Fit molecule hOAT1-TFV_OF.pdb (#40) to map hOAT1-TFV_OF.mrc (#39) using 4375
    8010 atoms 
    8011 average map value = 0.007219, steps = 88 
    8012 shifted from previous position = 0.909 
    8013 rotated from previous position = 8.49 degrees 
    8014 atoms outside contour = 2887, contour level = 0.010308 
    8015  
    8016 Position of hOAT1-TFV_OF.pdb (#40) relative to hOAT1-TFV_OF.mrc (#39)
    8017 coordinates: 
    8018 Matrix rotation and translation 
    8019 0.99019825 -0.07829950 -0.11565728 27.38037598 
    8020 0.07892080 0.99688057 0.00079533 -10.70816731 
    8021 0.11523422 -0.00991530 0.99328886 -13.08861468 
    8022 Axis -0.03831490 -0.82596303 0.56242070 
    8023 Axis point 128.86145300 0.00000000 225.96021530 
    8024 Rotation angle (degrees) 8.03460025 
    8025 Shift along axis 0.43416611 
    8026  
    8027 
    8028 > save
    8029 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF.pdb
    8030 > models #40 relModel #39
    8031 
    8032 > undo
    8033 
    8034 > select clear
    8035 
    8036 > show #!39 models
    8037 
    8038 > fitmap #40 inMap #39
    8039 
    8040 Fit molecule hOAT1-TFV_OF.pdb (#40) to map hOAT1-TFV_OF.mrc (#39) using 4375
    8041 atoms 
    8042 average map value = 0.007218, steps = 28 
    8043 shifted from previous position = 0.0175 
    8044 rotated from previous position = 0.016 degrees 
    8045 atoms outside contour = 2888, contour level = 0.010308 
    8046  
    8047 Position of hOAT1-TFV_OF.pdb (#40) relative to hOAT1-TFV_OF.mrc (#39)
    8048 coordinates: 
    8049 Matrix rotation and translation 
    8050 0.99020256 -0.07845145 -0.11551732 27.36683659 
    8051 0.07909202 0.99686685 0.00096497 -10.76110579 
    8052 0.11507968 -0.01009202 0.99330500 -13.04322773 
    8053 Axis -0.03956067 -0.82505023 0.56367284 
    8054 Axis point 128.67057833 0.00000000 226.14572082 
    8055 Rotation angle (degrees) 8.03322105 
    8056 Shift along axis 0.44368911 
    8057  
    8058 
    8059 > fitmap #40 inMap #39
    8060 
    8061 Fit molecule hOAT1-TFV_OF.pdb (#40) to map hOAT1-TFV_OF.mrc (#39) using 4375
    8062 atoms 
    8063 average map value = 0.007219, steps = 44 
    8064 shifted from previous position = 0.00455 
    8065 rotated from previous position = 0.00258 degrees 
    8066 atoms outside contour = 2889, contour level = 0.010308 
    8067  
    8068 Position of hOAT1-TFV_OF.pdb (#40) relative to hOAT1-TFV_OF.mrc (#39)
    8069 coordinates: 
    8070 Matrix rotation and translation 
    8071 0.99020340 -0.07846932 -0.11549800 27.37049731 
    8072 0.07911379 0.99686509 0.00099928 -10.76639922 
    8073 0.11505751 -0.01012698 0.99330721 -13.03687370 
    8074 Axis -0.03980982 -0.82492871 0.56383314 
    8075 Axis point 128.62890621 0.00000000 226.21984207 
    8076 Rotation angle (degrees) 8.03295687 
    8077 Shift along axis 0.44127588 
    8078  
    8079 
    8080 > select add #40
    8081 
    8082 4375 atoms, 4481 bonds, 564 residues, 1 model selected 
    8083 
    8084 > fitmap #40 inMap #39
    8085 
    8086 Fit molecule hOAT1-TFV_OF.pdb (#40) to map hOAT1-TFV_OF.mrc (#39) using 4375
    8087 atoms 
    8088 average map value = 0.007219, steps = 60 
    8089 shifted from previous position = 2.24 
    8090 rotated from previous position = 0.00666 degrees 
    8091 atoms outside contour = 2889, contour level = 0.010308 
    8092  
    8093 Position of hOAT1-TFV_OF.pdb (#40) relative to hOAT1-TFV_OF.mrc (#39)
    8094 coordinates: 
    8095 Matrix rotation and translation 
    8096 0.99020164 -0.07840067 -0.11555975 25.97288245 
    8097 0.07903810 0.99687116 0.00093711 -9.32824593 
    8098 0.11512471 -0.01006155 0.99330009 -12.03377088 
    8099 Axis -0.03935047 -0.82533103 0.56327634 
    8100 Axis point 116.53468443 0.00000000 214.84157931 
    8101 Rotation angle (degrees) 8.03353574 
    8102 Shift along axis -0.10149276 
    8103  
    8104 
    8105 > show #!17 models
    8106 
    8107 > fitmap #39 inMap #19.3
    8108 
    8109 Fit map hOAT1-TFV_OF.mrc in map rOAT1-TVF_OF.mrc 2 using 37364 points 
    8110 correlation = 0.03002, correlation about mean = -0.02439, overlap = 0.01206 
    8111 steps = 936, shift = 1.08, angle = 13.4 degrees 
    8112  
    8113 Position of hOAT1-TFV_OF.mrc (#39) relative to rOAT1-TVF_OF.mrc 2 (#19.3)
    8114 coordinates: 
    8115 Matrix rotation and translation 
    8116 0.98280665 -0.13043667 -0.13068041 37.39205996 
    8117 0.11063752 0.98266445 -0.14876125 8.18112237 
    8118 0.14781892 0.13174539 0.98020035 -34.01816129 
    8119 Axis 0.60585490 -0.60151939 0.52068635 
    8120 Axis point 0.00000000 261.98069292 24.54762139 
    8121 Rotation angle (degrees) 13.38519605 
    8122 Shift along axis 0.02026683 
    8123  
    8124 
    8125 > fitmap #39 inMap #19.3
    8126 
    8127 Fit map hOAT1-TFV_OF.mrc in map rOAT1-TVF_OF.mrc 2 using 37364 points 
    8128 correlation = 0.03002, correlation about mean = -0.0244, overlap = 0.01206 
    8129 steps = 48, shift = 0.0138, angle = 0.161 degrees 
    8130  
    8131 Position of hOAT1-TFV_OF.mrc (#39) relative to rOAT1-TVF_OF.mrc 2 (#19.3)
    8132 coordinates: 
    8133 Matrix rotation and translation 
    8134 0.98301413 -0.12857767 -0.13096186 37.15798588 
    8135 0.10847145 0.98263409 -0.15054633 8.70610140 
    8136 0.14804449 0.13378355 0.97989019 -34.26954280 
    8137 Axis 0.61337235 -0.60188813 0.51137563 
    8138 Axis point -0.00000000 260.45263984 27.89398858 
    8139 Rotation angle (degrees) 13.40165031 
    8140 Shift along axis 0.02697294 
    8141  
    8142 
    8143 > fitmap #40 inMap #39
    8144 
    8145 Fit molecule hOAT1-TFV_OF.pdb (#40) to map hOAT1-TFV_OF.mrc (#39) using 4375
    8146 atoms 
    8147 average map value = 0.007219, steps = 132 
    8148 shifted from previous position = 0.778 
    8149 rotated from previous position = 13.4 degrees 
    8150 atoms outside contour = 2889, contour level = 0.010308 
    8151  
    8152 Position of hOAT1-TFV_OF.pdb (#40) relative to hOAT1-TFV_OF.mrc (#39)
    8153 coordinates: 
    8154 Matrix rotation and translation 
    8155 0.99020454 -0.07852899 -0.11544767 25.97319443 
    8156 0.07917768 0.99685998 0.00103677 -9.35919916 
    8157 0.11500374 -0.01016749 0.99331302 -12.00484753 
    8158 Axis -0.04009077 -0.82459474 0.56430155 
    8159 Axis point 116.41047661 0.00000000 215.06686153 
    8160 Rotation angle (degrees) 8.03257950 
    8161 Shift along axis -0.09809308 
    8162  
    8163 
    8164 > hide #!17 models
    8165 
    8166 > hide #!39 models
    8167 
    8168 > close #40
    8169 
    8170 > open /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF-
    8171 > coot-1.pdb
    8172 
    8173 Chain information for hOAT1-TFV_OF-coot-1.pdb #40 
    8174 --- 
    8175 Chain | Description 
    8176 A | No description available 
    8177  
    8178 
    8179 > show #!39 models
    8180 
    8181 > color #39 white models
    8182 
    8183 > color #40 white
    8184 
    8185 > hide #!39 models
    8186 
    8187 > select up
    8188 
    8189 2 atoms, 1 bond, 1 residue, 1 model selected 
    8190 
    8191 > color sel red
    8192 
    8193 > select up
    8194 
    8195 31 atoms, 32 bonds, 1 residue, 1 model selected 
    8196 
    8197 > color sel red
    8198 
    8199 > show #!39 models
    8200 
    8201 > color zone #39 near #40 distance 4.98
    8202 
    8203 > color zone #39 near #40 distance 2
    8204 
    8205 [Repeated 1 time(s)]
    8206 
    8207 > volume #39 level 0.01241
    8208 
    8209 > open /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF-
    8210 > coot-2.pdb
    8211 
    8212 Chain information for hOAT1-TFV_OF-coot-2.pdb #41 
    8213 --- 
    8214 Chain | Description 
    8215 A | No description available 
    8216  
    8217 
    8218 > hide #!40 models
    8219 
    8220 > color #41 white
    8221 
    8222 > color zone #39 near #41 distance 2
    8223 
    8224 > select up
    8225 
    8226 2 atoms, 1 bond, 1 residue, 1 model selected 
    8227 
    8228 > select up
    8229 
    8230 31 atoms, 32 bonds, 1 residue, 1 model selected 
    8231 
    8232 > color sel red
    8233 
    8234 > color zone #39 near #41 distance 2
    8235 
    8236 > volume #39 level 0.01056
    8237 
    8238 > color zone #39 near #41 distance 2.1
    8239 
    8240 > color zone #39 near #41 distance 2.2
    8241 
    8242 > color zone #39 near #41 distance 2.3
    8243 
    8244 > color zone #39 near #41 distance 2.4
    8245 
    8246 > color zone #39 near #41 distance 2.5
    8247 
    8248 > color zone #39 near #41 distance 2.6
    8249 
    8250 > color zone #39 near #41 distance 2.7
    8251 
    8252 > color zone #39 near #41 distance 2.8
    8253 
    8254 > color zone #39 near #41 distance 2.9
    8255 
    8256 > color zone #39 near #41 distance 3
    8257 
    8258 > color zone #39 near #41 distance 2.9
    8259 
    8260 > color zone #39 near #41 distance 2.8
    8261 
    8262 > color zone #39 near #41 distance 2.7
    8263 
    8264 > color zone #39 near #41 distance 2.6
    8265 
    8266 > color zone #39 near #41 distance 2.5
    8267 
    8268 > color zone #39 near #41 distance 2.4
    8269 
    8270 > color zone #39 near #41 distance 2.3
    8271 
    8272 > color zone #39 near #41 distance 2.2
    8273 
    8274 > color zone #39 near #41 distance 2.1
    8275 
    8276 > color zone #39 near #41 distance 2
    8277 
    8278 > color zone #39 near #41 distance 1.9
    8279 
    8280 > color zone #39 near #41 distance 2
    8281 
    8282 > color zone #39 near #41 distance 2.1
    8283 
    8284 > color zone #39 near #41 distance 2.2
    8285 
    8286 > color zone #39 near #41 distance 2.3
    8287 
    8288 > color zone #39 near #41 distance 2.4
    8289 
    8290 > color zone #39 near #41 distance 2.5
    8291 
    8292 > volume splitbyzone #39
    8293 
    8294 Opened hOAT1-TFV_OF.mrc 0 as #42.1, grid size 320,320,320, pixel 0.83, shown
    8295 at level 0.0106, step 1, values float32 
    8296 Opened hOAT1-TFV_OF.mrc 1 as #42.2, grid size 320,320,320, pixel 0.83, shown
    8297 at level 0.0106, step 1, values float32 
    8298 Opened hOAT1-TFV_OF.mrc 2 as #42.3, grid size 320,320,320, pixel 0.83, shown
    8299 at level 0.0106, step 1, values float32 
    8300 
    8301 > close #42.1-2
    8302 
    8303 > color #42.3 white models
    8304 
    8305 > color #42.3 #ffffb2ff models
    8306 
    8307 > color #42.3 #ffffb296 models
    8308 
    8309 > volume #42.3 level 0.006989
    8310 
    8311 > select add #41
    8312 
    8313 4375 atoms, 4481 bonds, 1 pseudobond, 564 residues, 2 models selected 
    8314 
    8315 > color #41 #aaffffff
    8316 
    8317 > color #41 blue
    8318 
    8319 > color #41 red
    8320 
    8321 > color #41 #aa00ffff
    8322 
    8323 > color #41 #0055ffff
    8324 
    8325 > color #41 #55557fff
    8326 
    8327 > color #41 #ff557fff
    8328 
    8329 > color #41 #ffaaffff
    8330 
    8331 > color (#!41 & sel) byhetero
    8332 
    8333 > save
    8334 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    8335 > includeMaps true
    8336 
    8337 > show #!34 models
    8338 
    8339 > hide #!41 models
    8340 
    8341 > hide #!42 models
    8342 
    8343 > hide #!42.3 models
    8344 
    8345 > select subtract #41
    8346 
    8347 Nothing selected 
    8348 
    8349 > hide #!34 models
    8350 
    8351 > show #1 models
    8352 
    8353 > show #!3.3 models
    8354 
    8355 > hide #!3.3 models
    8356 
    8357 > hide #!3 models
    8358 
    8359 > hide #1 models
    8360 
    8361 > show #!22.3 models
    8362 
    8363 > show #21 models
    8364 
    8365 > select add #21/A:601@O25
    8366 
    8367 1 atom, 1 bond, 1 residue, 1 model selected 
    8368 
    8369 > select up
    8370 
    8371 3 atoms, 1 bond, 2 residues, 1 model selected 
    8372 
    8373 > view sel
    8374 
    8375 > volume #22.3 level 0.01409
    8376 
    8377 > hide #!22.3 models
    8378 
    8379 > hide #!22 models
    8380 
    8381 > hide #21 models
    8382 
    8383 > show #!22.3 models
    8384 
    8385 > hide #!22.3 models
    8386 
    8387 > hide #!22 models
    8388 
    8389 > show #!23 models
    8390 
    8391 > hide #!23 models
    8392 
    8393 > show #!25.3 models
    8394 
    8395 > show #!24 models
    8396 
    8397 > hide #!25.3 models
    8398 
    8399 > hide #!25 models
    8400 
    8401 > hide #!24 models
    8402 
    8403 > show #1 models
    8404 
    8405 > show #!3.3 models
    8406 
    8407 > hide #!3.3 models
    8408 
    8409 > hide #!3 models
    8410 
    8411 > hide #1 models
    8412 
    8413 > show #!5 models
    8414 
    8415 > show #!6.3 models
    8416 
    8417 > hide #!6.3 models
    8418 
    8419 > hide #!6 models
    8420 
    8421 > hide #!5 models
    8422 
    8423 > show #8 models
    8424 
    8425 > show #!9.3 models
    8426 
    8427 > volume #9.3 level 0.003826
    8428 
    8429 > select #8/A:230
    8430 
    8431 12 atoms, 12 bonds, 1 residue, 1 model selected 
    8432 
    8433 > show sel atoms
    8434 
    8435 > select #8/A:227
    8436 
    8437 4 atoms, 3 bonds, 1 residue, 1 model selected 
    8438 
    8439 > show sel atoms
    8440 
    8441 > select clear
    8442 
    8443 > hide #!9.3 models
    8444 
    8445 > hide #!9 models
    8446 
    8447 > hide #8 models
    8448 
    8449 > show #!12 models
    8450 
    8451 > show #!11.3 models
    8452 
    8453 > color #11.3 #ffffb296 models
    8454 
    8455 > hide #!12 models
    8456 
    8457 > hide #!11.3 models
    8458 
    8459 > hide #!11 models
    8460 
    8461 > show #15 models
    8462 
    8463 > show #!16.3 models
    8464 
    8465 > hide #!16.3 models
    8466 
    8467 > hide #!16 models
    8468 
    8469 > hide #15 models
    8470 
    8471 > show #!18 models
    8472 
    8473 > show #!19.3 models
    8474 
    8475 > hide #!18 models
    8476 
    8477 > hide #!19 models
    8478 
    8479 > hide #!19.3 models
    8480 
    8481 > show #37 models
    8482 
    8483 > show #!38.3 models
    8484 
    8485 > hide #!38.3 models
    8486 
    8487 > hide #!38 models
    8488 
    8489 > hide #37 models
    8490 
    8491 > close #40
    8492 
    8493 > show #!41 models
    8494 
    8495 > show #!42.3 models
    8496 
    8497 > hide #!42.3 models
    8498 
    8499 > hide #!42 models
    8500 
    8501 > hide #!41 models
    8502 
    8503 > show #!26 models
    8504 
    8505 > show #!28.3 models
    8506 
    8507 > select #26/A:230
    8508 
    8509 12 atoms, 12 bonds, 1 residue, 1 model selected 
    8510 
    8511 > show sel atoms
    8512 
    8513 > select #26/A:200
    8514 
    8515 5 atoms, 4 bonds, 1 residue, 1 model selected 
    8516 
    8517 > show sel atoms
    8518 
    8519 > select add #26
    8520 
    8521 3865 atoms, 3947 bonds, 1 pseudobond, 506 residues, 2 models selected 
    8522 
    8523 > color (#!26 & sel) byhetero
    8524 
    8525 > select clear
    8526 
    8527 > select #26/A:223
    8528 
    8529 4 atoms, 3 bonds, 1 residue, 1 model selected 
    8530 
    8531 > show sel atoms
    8532 
    8533 > select #26/A:227
    8534 
    8535 4 atoms, 3 bonds, 1 residue, 1 model selected 
    8536 
    8537 > show sel atoms
    8538 
    8539 > select #26/A:223
    8540 
    8541 4 atoms, 3 bonds, 1 residue, 1 model selected 
    8542 
    8543 > show sel atoms
    8544 
    8545 > select #26/A:200
    8546 
    8547 5 atoms, 4 bonds, 1 residue, 1 model selected 
    8548 
    8549 > show sel atoms
    8550 
    8551 > select #26/A:226
    8552 
    8553 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8554 
    8555 > show sel atoms
    8556 
    8557 > select #26/A:204
    8558 
    8559 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8560 
    8561 > show sel atoms
    8562 
    8563 > select clear
    8564 
    8565 > hide #!28.3 models
    8566 
    8567 > hide #!28 models
    8568 
    8569 > hide #!26 models
    8570 
    8571 > show #!31.3 models
    8572 
    8573 > show #30 models
    8574 
    8575 > select add #30
    8576 
    8577 4327 atoms, 4393 bonds, 591 residues, 1 model selected 
    8578 
    8579 > color sel byhetero
    8580 
    8581 > select clear
    8582 
    8583 > save
    8584 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    8585 > includeMaps true
    8586 
    8587 ——— End of log from Mon Feb 10 17:46:10 2025 ———
    8588 
    8589 opened ChimeraX session 
    8590 
    8591 > hide #!31.3 models
    8592 
    8593 > hide #!31 models
    8594 
    8595 > hide #30 models
    8596 
    8597 > show #!34 models
    8598 
    8599 > show #!35 models
    8600 
    8601 > show #!35.3 models
    8602 
    8603 > volume #35.3 level 0.01175
    8604 
    8605 > select #35.3
    8606 
    8607 2 models selected 
    8608 
    8609 > view sel
    8610 
    8611 > color #34 tan
    8612 
    8613 > ui tool show "Side View"
    8614 
    8615 > select add #34
    8616 
    8617 3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 4 models selected 
    8618 
    8619 > color (#!34 & sel) byhetero
    8620 
    8621 > select clear
    8622 
    8623 > select #34/A:447
    8624 
    8625 9 atoms, 8 bonds, 1 residue, 1 model selected 
    8626 
    8627 > show sel atoms
    8628 
    8629 > select #34/A:507
    8630 
    8631 7 atoms, 6 bonds, 1 residue, 1 model selected 
    8632 
    8633 > show sel atoms
    8634 
    8635 > select clear
    8636 
    8637 > save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
    8638 
    8639 ——— End of log from Tue Mar 11 12:00:09 2025 ———
    8640 
    8641 opened ChimeraX session 
    8642 
    8643 > hide #!35.3 models
    8644 
    8645 > hide #!35 models
    8646 
    8647 > show #!17 models
    8648 
    8649 > color #17 #ffffb2ff models
    8650 
    8651 > color #17 #ffffb280 models
    8652 
    8653 > ui tool show "Side View"
    8654 
    8655 > color #17 #ffffb24d models
    8656 
    8657 > save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
    8658 
    8659 ——— End of log from Thu Apr 10 14:06:06 2025 ———
    8660 
    8661 opened ChimeraX session 
    8662 
    8663 > movie record
    8664 
    8665 > turn y 2 180
    8666 
    8667 > wait 180
    8668 
    8669 > movie encode /Users/dout2/Desktop/movie1.mp4
    8670 
    8671 Movie saved to /Users/dout2/Desktop/movie1.mp4 
    8672  
    8673 
    8674 > select add #34
    8675 
    8676 3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 2 models selected 
    8677 
    8678 > show sel atoms
    8679 
    8680 > select clear
    8681 
    8682 > hide #!34 models
    8683 
    8684 > hide #!17 models
    8685 
    8686 > show #!6 models
    8687 
    8688 > show #1 models
    8689 
    8690 > view
    8691 
    8692 > select #1/A:463
    8693 
    8694 7 atoms, 6 bonds, 1 residue, 1 model selected 
    8695 
    8696 > select #1/A:466
    8697 
    8698 11 atoms, 10 bonds, 1 residue, 1 model selected 
    8699 
    8700 > select #1/A:228
    8701 
    8702 12 atoms, 12 bonds, 1 residue, 1 model selected 
    8703 
    8704 > select #1/A:230
    8705 
    8706 12 atoms, 12 bonds, 1 residue, 1 model selected 
    8707 
    8708 > select #1/A:231
    8709 
    8710 6 atoms, 5 bonds, 1 residue, 1 model selected 
    8711 
    8712 > select #1/A:377
    8713 
    8714 7 atoms, 6 bonds, 1 residue, 1 model selected 
    8715 
    8716 > select #1/A:378
    8717 
    8718 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8719 
    8720 > select #1/A:381
    8721 
    8722 5 atoms, 4 bonds, 1 residue, 1 model selected 
    8723 
    8724 > select #1/A:225
    8725 
    8726 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8727 
    8728 > select #1/A:382
    8729 
    8730 9 atoms, 8 bonds, 1 residue, 1 model selected 
    8731 
    8732 > show sel atoms
    8733 
    8734 > hide #!6 models
    8735 
    8736 > show #!6 models
    8737 
    8738 > hide #1 models
    8739 
    8740 > show #1 models
    8741 
    8742 > select add #1
    8743 
    8744 3905 atoms, 3986 bonds, 515 residues, 1 model selected 
    8745 
    8746 > select subtract #1
    8747 
    8748 Nothing selected 
    8749 
    8750 > hide #1 models
    8751 
    8752 > hide #!6 models
    8753 
    8754 > show #!18 models
    8755 
    8756 > hide #!18 models
    8757 
    8758 > show #1 models
    8759 
    8760 > select #1/A:228
    8761 
    8762 12 atoms, 12 bonds, 1 residue, 1 model selected 
    8763 
    8764 > select #1/A:199
    8765 
    8766 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8767 
    8768 > select #1/A:257
    8769 
    8770 7 atoms, 7 bonds, 1 residue, 1 model selected 
    8771 
    8772 > select #1/A:145
    8773 
    8774 7 atoms, 6 bonds, 1 residue, 1 model selected 
    8775 
    8776 > select #1/A:466
    8777 
    8778 11 atoms, 10 bonds, 1 residue, 1 model selected 
    8779 
    8780 > show sel atoms
    8781 
    8782 > select #1/A:149
    8783 
    8784 5 atoms, 4 bonds, 1 residue, 1 model selected 
    8785 
    8786 > select #1/A:146
    8787 
    8788 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8789 
    8790 > select #1/A:204
    8791 
    8792 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8793 
    8794 > select #1/A:150
    8795 
    8796 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8797 
    8798 > select #1/A:149
    8799 
    8800 5 atoms, 4 bonds, 1 residue, 1 model selected 
    8801 
    8802 > select #1/A:203
    8803 
    8804 5 atoms, 4 bonds, 1 residue, 1 model selected 
    8805 
    8806 > select #1/A:146
    8807 
    8808 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8809 
    8810 > select #1/A:149
    8811 
    8812 5 atoms, 4 bonds, 1 residue, 1 model selected 
    8813 Drag select of 13 residues 
    8814 
    8815 > select #1/A:463
    8816 
    8817 7 atoms, 6 bonds, 1 residue, 1 model selected 
    8818 
    8819 > show sel atoms
    8820 
    8821 > select #1/A:466@CZ
    8822 
    8823 1 atom, 1 residue, 1 model selected 
    8824 
    8825 > select up
    8826 
    8827 11 atoms, 10 bonds, 1 residue, 1 model selected 
    8828 
    8829 > ui tool show Contacts
    8830 
    8831 > contacts sel intraRes true ignoreHiddenModels true select true
    8832 > makePseudobonds false reveal true
    8833 
    8834 26 contacts 
    8835 
    8836 > select clear
    8837 
    8838 > select : 382
    8839 
    8840 126 atoms, 112 bonds, 14 residues, 14 models selected 
    8841 
    8842 > select : 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    8843 
    8844 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    8845 
    8846 > show sel & #1 atoms
    8847 
    8848 > hide #!6 target m
    8849 
    8850 [Repeated 1 time(s)]
    8851 
    8852 > hide #!4 target m
    8853 
    8854 > select add #1
    8855 
    8856 5716 atoms, 5702 bonds, 714 residues, 14 models selected 
    8857 
    8858 > select subtract #1
    8859 
    8860 1811 atoms, 1716 bonds, 199 residues, 13 models selected 
    8861 
    8862 > select add #5
    8863 
    8864 5446 atoms, 5448 bonds, 5 pseudobonds, 670 residues, 14 models selected 
    8865 
    8866 > select subtract #5
    8867 
    8868 1672 atoms, 1584 bonds, 184 residues, 12 models selected 
    8869 
    8870 > select add #8
    8871 
    8872 5445 atoms, 5437 bonds, 691 residues, 12 models selected 
    8873 
    8874 > select subtract #8
    8875 
    8876 1533 atoms, 1452 bonds, 169 residues, 11 models selected 
    8877 
    8878 > select add #12
    8879 
    8880 5186 atoms, 5201 bonds, 5 pseudobonds, 640 residues, 12 models selected 
    8881 
    8882 > select subtract #12
    8883 
    8884 1394 atoms, 1320 bonds, 154 residues, 10 models selected 
    8885 
    8886 > hide #1 models
    8887 
    8888 > show #1 models
    8889 
    8890 > select add #15
    8891 
    8892 5172 atoms, 5186 bonds, 654 residues, 10 models selected 
    8893 
    8894 > select subtract #15
    8895 
    8896 1255 atoms, 1188 bonds, 139 residues, 9 models selected 
    8897 
    8898 > select add #18
    8899 
    8900 4902 atoms, 4932 bonds, 5 pseudobonds, 610 residues, 10 models selected 
    8901 
    8902 > select subtract #18
    8903 
    8904 1116 atoms, 1056 bonds, 124 residues, 8 models selected 
    8905 
    8906 > select add #21
    8907 
    8908 4933 atoms, 4966 bonds, 625 residues, 8 models selected 
    8909 
    8910 > select subtract #21
    8911 
    8912 977 atoms, 924 bonds, 109 residues, 7 models selected 
    8913 
    8914 > select add #24
    8915 
    8916 4628 atoms, 4674 bonds, 5 pseudobonds, 580 residues, 8 models selected 
    8917 
    8918 > select subtract #24
    8919 
    8920 838 atoms, 792 bonds, 94 residues, 6 models selected 
    8921 
    8922 > select add #26
    8923 
    8924 4564 atoms, 4607 bonds, 1 pseudobond, 585 residues, 7 models selected 
    8925 
    8926 > select subtract #26
    8927 
    8928 699 atoms, 660 bonds, 79 residues, 5 models selected 
    8929 
    8930 > select add #30
    8931 
    8932 4885 atoms, 4921 bonds, 653 residues, 5 models selected 
    8933 
    8934 > select subtract #30
    8935 
    8936 558 atoms, 528 bonds, 62 residues, 4 models selected 
    8937 
    8938 > select add #33
    8939 
    8940 4744 atoms, 4789 bonds, 636 residues, 4 models selected 
    8941 
    8942 > select subtract #33
    8943 
    8944 417 atoms, 396 bonds, 45 residues, 3 models selected 
    8945 
    8946 > select add #34
    8947 
    8948 4065 atoms, 4140 bonds, 5 pseudobonds, 517 residues, 4 models selected 
    8949 
    8950 > select subtract #34
    8951 
    8952 278 atoms, 264 bonds, 30 residues, 2 models selected 
    8953 
    8954 > select add #37
    8955 
    8956 4514 atoms, 4613 bonds, 579 residues, 2 models selected 
    8957 
    8958 > select subtract #37
    8959 
    8960 139 atoms, 132 bonds, 15 residues, 1 model selected 
    8961 
    8962 > select add #41
    8963 
    8964 4375 atoms, 4481 bonds, 1 pseudobond, 564 residues, 2 models selected 
    8965 
    8966 > select subtract #41
    8967 
    8968 Nothing selected 
    8969 
    8970 > show #!2 models
    8971 
    8972 > hide #!2 models
    8973 
    8974 > show #!3 models
    8975 
    8976 > show #!3.3 models
    8977 
    8978 > ui tool show "Side View"
    8979 
    8980 > select #1/A:35@CG
    8981 
    8982 1 atom, 1 residue, 1 model selected 
    8983 
    8984 > select : 35
    8985 
    8986 112 atoms, 98 bonds, 14 residues, 14 models selected 
    8987 
    8988 > hide sel & #1 atoms
    8989 
    8990 > select up
    8991 
    8992 2 atoms, 1 bond, 1 residue, 1 model selected 
    8993 
    8994 > select up
    8995 
    8996 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8997 
    8998 > hide sel atoms
    8999 
    9000 > select clear
    9001 
    9002 > select : 35
    9003 
    9004 112 atoms, 98 bonds, 14 residues, 14 models selected 
    9005 
    9006 > show sel & #1 atoms
    9007 
    9008 > select clear
    9009 
    9010 > select : 35
    9011 
    9012 112 atoms, 98 bonds, 14 residues, 14 models selected 
    9013 
    9014 > hide sel & #1 atoms
    9015 
    9016 > save /Users/dout2/Desktop/image1.png supersample 3
    9017 
    9018 > save /Users/dout2/Desktop/rOAT1-AZT_OF_LigandDensity.png supersample 3
    9019 
    9020 > select add #1
    9021 
    9022 4009 atoms, 4077 bonds, 528 residues, 14 models selected 
    9023 
    9024 > select subtract #1
    9025 
    9026 104 atoms, 91 bonds, 13 residues, 13 models selected 
    9027 
    9028 > select add #5
    9029 
    9030 3870 atoms, 3948 bonds, 5 pseudobonds, 498 residues, 14 models selected 
    9031 
    9032 > select subtract #5
    9033 
    9034 96 atoms, 84 bonds, 12 residues, 12 models selected 
    9035 
    9036 > select add #8
    9037 
    9038 4000 atoms, 4062 bonds, 533 residues, 12 models selected 
    9039 
    9040 > select subtract #8
    9041 
    9042 88 atoms, 77 bonds, 11 residues, 11 models selected 
    9043 
    9044 > select add #12
    9045 
    9046 3872 atoms, 3951 bonds, 5 pseudobonds, 496 residues, 12 models selected 
    9047 
    9048 > select subtract #12
    9049 
    9050 80 atoms, 70 bonds, 10 residues, 10 models selected 
    9051 
    9052 > select add #21
    9053 
    9054 4028 atoms, 4105 bonds, 525 residues, 10 models selected 
    9055 
    9056 > select subtract #21
    9057 
    9058 72 atoms, 63 bonds, 9 residues, 9 models selected 
    9059 
    9060 > select add #18
    9061 
    9062 3850 atoms, 3932 bonds, 5 pseudobonds, 494 residues, 10 models selected 
    9063 
    9064 > select subtract #18
    9065 
    9066 64 atoms, 56 bonds, 8 residues, 8 models selected 
    9067 
    9068 > select add #24
    9069 
    9070 3846 atoms, 3931 bonds, 5 pseudobonds, 493 residues, 9 models selected 
    9071 
    9072 > select subtract #24
    9073 
    9074 56 atoms, 49 bonds, 7 residues, 7 models selected 
    9075 
    9076 > select add #26
    9077 
    9078 3913 atoms, 3989 bonds, 1 pseudobond, 512 residues, 8 models selected 
    9079 
    9080 > select subtract #26
    9081 
    9082 48 atoms, 42 bonds, 6 residues, 6 models selected 
    9083 
    9084 > select add #30
    9085 
    9086 4367 atoms, 4428 bonds, 596 residues, 6 models selected 
    9087 
    9088 > select subtract #30
    9089 
    9090 40 atoms, 35 bonds, 5 residues, 5 models selected 
    9091 
    9092 > select add #33
    9093 
    9094 4359 atoms, 4421 bonds, 595 residues, 5 models selected 
    9095 
    9096 > select subtract #33
    9097 
    9098 32 atoms, 28 bonds, 4 residues, 4 models selected 
    9099 
    9100 > select add #34
    9101 
    9102 3811 atoms, 3897 bonds, 5 pseudobonds, 490 residues, 5 models selected 
    9103 
    9104 > select subtract #34
    9105 
    9106 24 atoms, 21 bonds, 3 residues, 3 models selected 
    9107 
    9108 > select add #37
    9109 
    9110 4391 atoms, 4495 bonds, 566 residues, 3 models selected 
    9111 
    9112 > select subtract #37
    9113 
    9114 16 atoms, 14 bonds, 2 residues, 2 models selected 
    9115 
    9116 > select add #41
    9117 
    9118 4383 atoms, 4488 bonds, 1 pseudobond, 565 residues, 3 models selected 
    9119 
    9120 > select subtract #41
    9121 
    9122 8 atoms, 7 bonds, 1 residue, 1 model selected 
    9123 
    9124 > hide #!3.3 models
    9125 
    9126 > hide #!3 models
    9127 
    9128 > hide #1 models
    9129 
    9130 > show #!5 models
    9131 
    9132 > show #!6.3 models
    9133 
    9134 > hide #!6.3 models
    9135 
    9136 > hide #!6 models
    9137 
    9138 > hide #!5 models
    9139 
    9140 > show #8 models
    9141 
    9142 > show #!9 models
    9143 
    9144 > show #!9.3 models
    9145 
    9146 > select : 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    9147 
    9148 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    9149 
    9150 > show sel & #8 atoms
    9151 
    9152 > select: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    9153 
    9154 Unknown command: select:
    9155 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234 
    9156 
    9157 > select : 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    9158 
    9159 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    9160 
    9161 > show sel & #8 atoms
    9162 
    9163 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    9164 
    9165 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    9166 
    9167 > show sel & #8 atoms
    9168 
    9169 > select clear
    9170 
    9171 > volume #9.3 level 0.00516
    9172 
    9173 > save /Users/dout2/Desktop/rOAT1-PBD_IF_LigandDensity.png supersample 3
    9174 
    9175 > hide #!9.3 models
    9176 
    9177 > hide #!9 models
    9178 
    9179 > hide #8 models
    9180 
    9181 > show #15 models
    9182 
    9183 > show #!16 models
    9184 
    9185 > show #!16.3 models
    9186 
    9187 > select #15/A:442
    9188 
    9189 11 atoms, 11 bonds, 1 residue, 1 model selected 
    9190 
    9191 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    9192 
    9193 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    9194 
    9195 > show sel & #15 atoms
    9196 
    9197 > select #1-50: 438
    9198 
    9199 154 atoms, 154 bonds, 14 residues, 14 models selected 
    9200 
    9201 > select clear
    9202 
    9203 > save /Users/dout2/Desktop/rOAT1-TFV_IF_LigandDensity.png supersample 3
    9204 
    9205 > hide #!16.3 models
    9206 
    9207 > hide #!16 models
    9208 
    9209 > hide #15 models
    9210 
    9211 > show #21 models
    9212 
    9213 > show #!22 models
    9214 
    9215 > show #!22.3 models
    9216 
    9217 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    9218 
    9219 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    9220 
    9221 > show sel & #21 atoms
    9222 
    9223 > select clear
    9224 
    9225 > save /Users/dout2/Desktop/rOAT1-AAI_IF_LigandDensity.png supersample 3
    9226 
    9227 > volume #22.3 level 0.0128
    9228 
    9229 > hide #!22.3 models
    9230 
    9231 > hide #!22 models
    9232 
    9233 > hide #21 models
    9234 
    9235 > show #!27 models
    9236 
    9237 > show #!28 models
    9238 
    9239 > hide #!27 models
    9240 
    9241 > show #!26 models
    9242 
    9243 > show #!28.3 models
    9244 
    9245 > volume #28.3 level 0.06828
    9246 
    9247 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    9248 
    9249 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    9250 
    9251 > show sel & #!26 atoms
    9252 
    9253 > select clear
    9254 
    9255 > save /Users/dout2/Desktop/rOAT1-PAH_IF_LigandDensity.png supersample 3
    9256 
    9257 > hide #!28.3 models
    9258 
    9259 > hide #!28 models
    9260 
    9261 > hide #!26 models
    9262 
    9263 > show #30 models
    9264 
    9265 > show #!31 models
    9266 
    9267 > show #!31.3 models
    9268 
    9269 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    9270 
    9271 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    9272 
    9273 > show sel & #30 atoms
    9274 
    9275 > select clear
    9276 
    9277 > save /Users/dout2/Desktop/rOAT1-FBP_IF_LigandDensity.png supersample 3
    9278 
    9279 > hide #!31.3 models
    9280 
    9281 > hide #!31 models
    9282 
    9283 > hide #30 models
    9284 
    9285 > show #37 models
    9286 
    9287 > show #!38 models
    9288 
    9289 > show #!38.3 models
    9290 
    9291 > select clear
    9292 
    9293 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    9294 
    9295 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    9296 
    9297 > show sel & #37 atoms
    9298 
    9299 > select clear
    9300 
    9301 > show #!36 models
    9302 
    9303 > hide #!36 models
    9304 
    9305 > show #!36 models
    9306 
    9307 > hide #!36 models
    9308 
    9309 > volume #38.3 level 0.006101
    9310 
    9311 > volume #38.3 level 0.006864
    9312 
    9313 > save /Users/dout2/Desktop/hOAT1-TFV_IF_LigandDensity.png supersample 3
    9314 
    9315 > hide #!38.3 models
    9316 
    9317 > hide #!38 models
    9318 
    9319 > hide #37 models
    9320 
    9321 > show #!2 models
    9322 
    9323 > hide #!2 models
    9324 
    9325 > show #1 models
    9326 
    9327 > show #!3 models
    9328 
    9329 > show #!3.3 models
    9330 
    9331 > hide #!3.3 models
    9332 
    9333 > hide #!3 models
    9334 
    9335 > hide #1 models
    9336 
    9337 > show #!5 models
    9338 
    9339 > show #!6.3 models
    9340 
    9341 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    9342 
    9343 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    9344 
    9345 > show sel & #!5 atoms
    9346 
    9347 > select clear
    9348 
    9349 > select up
    9350 
    9351 2 atoms, 1 bond, 1 residue, 1 model selected 
    9352 
    9353 > select up
    9354 
    9355 8 atoms, 7 bonds, 1 residue, 1 model selected 
    9356 
    9357 > hide sel atoms
    9358 
    9359 > select clear
    9360 
    9361 [Repeated 1 time(s)]
    9362 
    9363 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    9364 
    9365 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    9366 
    9367 > show sel & #!5 atoms
    9368 
    9369 > select clear
    9370 
    9371 > select up
    9372 
    9373 2 atoms, 1 bond, 1 residue, 1 model selected 
    9374 
    9375 > hide sel atoms
    9376 
    9377 > select up
    9378 
    9379 8 atoms, 7 bonds, 1 residue, 1 model selected 
    9380 
    9381 > hide sel atoms
    9382 
    9383 > select clear
    9384 
    9385 > volume #6.3 level 0.0106
    9386 
    9387 > save /Users/dout2/Desktop/rOAT1-AZT_OF_LigandDensity.png supersample 3
    9388 
    9389 > hide #!5 models
    9390 
    9391 > hide #!6 models
    9392 
    9393 > hide #!6.3 models
    9394 
    9395 > show #!11 models
    9396 
    9397 > show #!12 models
    9398 
    9399 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    9400 
    9401 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    9402 
    9403 > show sel & #!12 atoms
    9404 
    9405 > select clear
    9406 
    9407 > show #!11.3 models
    9408 
    9409 > select clear
    9410 
    9411 > volume #11.3 level 0.009777
    9412 
    9413 > select clear
    9414 
    9415 > show #!10 models
    9416 
    9417 > hide #!10 models
    9418 
    9419 > select clear
    9420 
    9421 > volume #11.3 level 0.01081
    9422 
    9423 > select clear
    9424 
    9425 > show #!10 models
    9426 
    9427 > hide #!10 models
    9428 
    9429 > save /Users/dout2/Desktop/rOAT1-PBD_OF_LigandDensity.png supersample 3
    9430 
    9431 > hide #!12 models
    9432 
    9433 > hide #!11 models
    9434 
    9435 > show #!18 models
    9436 
    9437 > show #!19 models
    9438 
    9439 > show #!19.3 models
    9440 
    9441 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    9442 
    9443 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    9444 
    9445 > show sel & #!18 atoms
    9446 
    9447 > select clear
    9448 
    9449 > save /Users/dout2/Desktop/rOAT1-TFV_OF_LigandDensity.png supersample 3
    9450 
    9451 > hide #!19 models
    9452 
    9453 > hide #!18 models
    9454 
    9455 > show #!24 models
    9456 
    9457 > show #!25 models
    9458 
    9459 > show #!25.3 models
    9460 
    9461 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    9462 
    9463 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    9464 
    9465 > show sel & #!24 atoms
    9466 
    9467 > select clear
    9468 
    9469 > save /Users/dout2/Desktop/rOAT1-AAI_OF_LigandDensity.png supersample 3
    9470 
    9471 > hide #!25 models
    9472 
    9473 > hide #!24 models
    9474 
    9475 > show #!35 models
    9476 
    9477 > show #!34 models
    9478 
    9479 > show #!35.3 models
    9480 
    9481 > hide #!35.3 models
    9482 
    9483 > hide #!35 models
    9484 
    9485 > hide #!34 models
    9486 
    9487 > show #!41 models
    9488 
    9489 > show #!42 models
    9490 
    9491 > show #!42.3 models
    9492 
    9493 > save /Users/dout2/Desktop/rOAT1-AAI_OF_LigandDensity.png supersample 3
    9494 
    9495 > hide #!41 models
    9496 
    9497 > hide #!42 models
    9498 
    9499 > hide #!42.3 models
    9500 
    9501 > show #!25 models
    9502 
    9503 > show #!24 models
    9504 
    9505 > save /Users/dout2/Desktop/rOAT1-AAI_OF_LigandDensity.png supersample 3
    9506 
    9507 > hide #!24 models
    9508 
    9509 > hide #!25 models
    9510 
    9511 > show #!42.3 models
    9512 
    9513 > show #!41 models
    9514 
    9515 > select clear
    9516 
    9517 [Repeated 1 time(s)]
    9518 
    9519 > ui tool show Distances
    9520 
    9521 > select clear
    9522 
    9523 No distances to delete! 
    9524 
    9525 > save /Users/dout2/Desktop/hOAT1-TFV_OF_LigandDensity.png supersample 3
    9526 
    9527 > view
    9528 
    9529 > view orient
    9530 
    9531 > open /Users/dout2/Downloads/20250226_rOAT1-AKG/r3d_j156_2.68A_outward-
    9532 > facing/postprocess.mrc
    9533 
    9534 Opened postprocess.mrc as #40, grid size 320,320,320, pixel 0.83, shown at
    9535 level 0.00432, step 2, values float32 
    9536 
    9537 > volume #40 step 1
    9538 
    9539 > volume #40 level 0.008916
    9540 
    9541 > hide #!41 models
    9542 
    9543 > hide #!40 models
    9544 
    9545 > select add #41
    9546 
    9547 4375 atoms, 4481 bonds, 1 pseudobond, 564 residues, 2 models selected 
    9548 
    9549 > select subtract #41
    9550 
    9551 Nothing selected 
    9552 
    9553 > hide #!42 models
    9554 
    9555 > show #!40 models
    9556 
    9557 > rename #40 rOAT1-AKG_OF.mrc
    9558 
    9559 > open /Users/dout2/Downloads/20250226_rOAT1-AKG/r3d_j156_2.68A_outward-
    9560 > facing/RealSpaceRefine_1/rOAT1-AKG_OF-coot-5_real_space_refined_001.pdb
    9561 
    9562 Chain information for rOAT1-AKG_OF-coot-5_real_space_refined_001.pdb #43 
    9563 --- 
    9564 Chain | Description 
    9565 A | No description available 
    9566  
    9567 
    9568 > select clear
    9569 
    9570 > open /Users/dout2/Downloads/20250226_rOAT1-AKG/r3d_j122_2.63A_outward-
    9571 > occluded/postprocess.mrc
    9572 
    9573 Opened postprocess.mrc as #44, grid size 320,320,320, pixel 0.83, shown at
    9574 level 0.00378, step 2, values float32 
    9575 
    9576 > rename #44 rOAT1-AKG_OOC.mrc
    9577 
    9578 > open /Users/dout2/Downloads/20250226_rOAT1-AKG/r3d_j122_2.63A_outward-
    9579 > occluded/RealSpaceRefine_3/rOAT1-AKG_OF-coot-4_real_space_refined_003.pdb
    9580 
    9581 Chain information for rOAT1-AKG_OF-coot-4_real_space_refined_003.pdb #45 
    9582 --- 
    9583 Chain | Description 
    9584 A | No description available 
    9585  
    9586 
    9587 > rename #45 rOAT1-AKG_OOC-coot-4_real_space_refined_003.pdb
    9588 
    9589 > hide #!43 models
    9590 
    9591 > hide #!40 models
    9592 
    9593 > volume #44 step 1
    9594 
    9595 > volume #44 level 0.01023
    9596 
    9597 > select ::name="AKG"
    9598 
    9599 20 atoms, 18 bonds, 2 residues, 2 models selected 
    9600 
    9601 > view sel
    9602 
    9603 > color #44 #ffffb24d models
    9604 
    9605 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    9606 
    9607 2228 atoms, 2112 bonds, 244 residues, 16 models selected 
    9608 
    9609 > show sel & #!45 atoms
    9610 
    9611 > select clear
    9612 
    9613 > save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
    9614 
    9615 > color #44 #ffffb280 models
    9616 
    9617 > color #44 #ffffb266 models
    9618 
    9619 > color #44 #ffffb24d models
    9620 
    9621 > select clear
    9622 
    9623 > save /Users/dout2/Desktop/hOAT1-AKG_OOC_LigandDensity.png supersample 3
    9624 
    9625 > movie record
    9626 
    9627 > turn y 2 180
    9628 
    9629 > wait 180
    9630 
    9631 > movie encode /Users/dout2/Desktop/movie2.mp4
    9632 
    9633 Movie saved to /Users/dout2/Desktop/movie2.mp4 
    9634  
    9635 
    9636 > movie record
    9637 
    9638 > turn y 2 180
    9639 
    9640 > wait 180
    9641 
    9642 > movie encode /Users/dout2/Desktop/movie3.mp4
    9643 
    9644 Movie saved to /Users/dout2/Desktop/movie3.mp4 
    9645  
    9646 
    9647 > hide #!45 models
    9648 
    9649 > hide #!44 models
    9650 
    9651 > show #!43 models
    9652 
    9653 > show #!40 models
    9654 
    9655 > color #40 #b2b2b24d models
    9656 
    9657 > select clear
    9658 
    9659 > color #40 #ffffb24d models
    9660 
    9661 > select clear
    9662 
    9663 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    9664 
    9665 2228 atoms, 2112 bonds, 244 residues, 16 models selected 
    9666 
    9667 > show sel & #!43 atoms
    9668 
    9669 > select clear
    9670 
    9671 [Repeated 1 time(s)]
    9672 
    9673 > volume #40 level 0.009283
    9674 
    9675 > save /Users/dout2/Desktop/rOAT1-AKG_OF_LigandDensity.png supersample 3
    9676 
    9677 > movie record
    9678 
    9679 > turn y 2 180
    9680 
    9681 > wait 180
    9682 
    9683 > movie encode /Users/dout2/Desktop/movie3.mp4
    9684 
    9685 Movie saved to /Users/dout2/Desktop/movie3.mp4 
    9686  
    9687 
    9688 > volume #40 level 0.01222
    9689 
    9690 > movie record
    9691 
    9692 > turn y 2 180
    9693 
    9694 > wait 180
    9695 
    9696 > movie encode /Users/dout2/Desktop/movie4.mp4
    9697 
    9698 Movie saved to /Users/dout2/Desktop/movie4.mp4 
    9699  
    9700 
    9701 > hide #!43 models
    9702 
    9703 > hide #!40 models
    9704 
    9705 > open /Users/dout2/Downloads/20250328_rOAT1-R466A/r3d_j052_2.71A_outward-
    9706 > occluded/postprocess_rescaled.mrc
    9707 
    9708 Opened postprocess_rescaled.mrc as #46, grid size 480,480,480, pixel 0.553,
    9709 shown at level 0.0038, step 2, values float32 
    9710 
    9711 > open /Users/dout2/Downloads/20250328_rOAT1-R466A/r3d_j052_2.71A_outward-
    9712 > occluded/RealSpaceRefine_1/rOAT1-R466A_OO-coot-2_real_space_refined_001.pdb
    9713 
    9714 Chain information for rOAT1-R466A_OO-coot-2_real_space_refined_001.pdb #47 
    9715 --- 
    9716 Chain | Description 
    9717 A | No description available 
    9718  
    9719 
    9720 > select #46
    9721 
    9722 4 models selected 
    9723 
    9724 > select clear
    9725 
    9726 > view
    9727 
    9728 > volume #46 step 1
    9729 
    9730 > volume #46 level 0.01147
    9731 
    9732 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    9733 
    9734 2367 atoms, 2244 bonds, 259 residues, 17 models selected 
    9735 
    9736 > view sel
    9737 
    9738 > color #46 #b2ffff4d models
    9739 
    9740 > select #46
    9741 
    9742 4 models selected 
    9743 
    9744 > show #!47 atoms
    9745 
    9746 > select clear
    9747 
    9748 > save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
    9749 
    9750 > close #47
    9751 
    9752 > open /Users/dout2/Downloads/20250328_rOAT1-R466A/r3d_j052_2.71A_outward-
    9753 > occluded/RealSpaceRefine_2/rOAT1-R466A_OO-coot-3_real_space_refined_002.pdb
    9754 
    9755 Chain information for rOAT1-R466A_OO-coot-3_real_space_refined_002.pdb #47 
    9756 --- 
    9757 Chain | Description 
    9758 A | No description available 
    9759  
    9760 
    9761 > select add #46
    9762 
    9763 4 models selected 
    9764 
    9765 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    9766 
    9767 2361 atoms, 2238 bonds, 259 residues, 17 models selected 
    9768 
    9769 > show sel & #!47 atoms
    9770 
    9771 > select clear
    9772 
    9773 > select #46
    9774 
    9775 4 models selected 
    9776 
    9777 > select clear
    9778 
    9779 > save /Users/dout2/Desktop/rOAT1-R466A_OF_LigandDensity.png supersample 3
    9780 
    9781 > movie record
    9782 
    9783 > turn y 2 180
    9784 
    9785 > wait 180
    9786 
    9787 > movie encode /Users/dout2/Desktop/movie4.mp4
    9788 
    9789 Movie saved to /Users/dout2/Desktop/movie4.mp4 
    9790  
    9791 
    9792 > hide #!46 models
    9793 
    9794 > show #!46 models
    9795 
    9796 > save /Users/dout2/Desktop/rOAT1-R466A_OF_LigandDensity2.png supersample 3
    9797 
    9798 > movie record
    9799 
    9800 > turn y 2 180
    9801 
    9802 > wait 180
    9803 
    9804 > movie encode /Users/dout2/Desktop/movie4.mp4
    9805 
    9806 Movie saved to /Users/dout2/Desktop/movie4.mp4 
    9807  
    9808 
    9809 > view
    9810 
    9811 > color #46 #b2ffffff models
    9812 
    9813 > color #46 #b2ffffab models
    9814 
    9815 > color #46 #b2ffffff models
    9816 
    9817 > select clear
    9818 
    9819 [Repeated 1 time(s)]
    9820 
    9821 > save /Users/dout2/Desktop/rOAT1-R466A_OF.png supersample 3
    9822 
    9823 > save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
    9824 
    9825 ——— End of log from Thu Apr 10 15:43:35 2025 ———
    9826 
    9827 opened ChimeraX session 
    9828 
    9829 > hide #!47 models
    9830 
    9831 > hide #!46 models
    9832 
    9833 > rename #46 rOAT1-R466A.mrc
    9834 
    9835 > open
    9836 > /Users/dout2/Documents/Manuscripts/rOAT1_2023/cryoEM/rOAT1-apo_20220519_cryoSPARC/J12_2.05A_clip-240/cryosparc_P4_J16__localfilter_240.mrc
    9837 
    9838 Opened cryosparc_P4_J16__localfilter_240.mrc as #48, grid size 240,240,240,
    9839 pixel 0.553, shown at level 0.238, step 1, values float32 
    9840 
    9841 > open
    9842 > /Users/dout2/Documents/Manuscripts/rOAT1_2023/cryoEM/rOAT1-apo_20220519_cryoSPARC/model/rOAT1-apo-
    9843 > coot-4_real_space_refined_004.pdb
    9844 
    9845 Chain information for rOAT1-apo-coot-4_real_space_refined_004.pdb #49 
    9846 --- 
    9847 Chain | Description 
    9848 A | No description available 
    9849  
    9850 
    9851 The cached device pixel ratio value was stale on window expose. Please file a
    9852 QTBUG which explains how to reproduce. 
    9853 
    9854 > rename #48 rOAT1-Apo.mrc
    9855 
    9856 > hide #49 models
    9857 
    9858 > hide #!48 models
    9859 
    9860 > hide #48.1 models
    9861 
    9862 > show #49 models
    9863 
    9864 > save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
    9865 
    9866 > select #49: 382, 353,438,230,442,466
    9867 
    9868 66 atoms, 64 bonds, 6 residues, 1 model selected 
    9869 
    9870 > show sel atoms
    9871 
    9872 > size stickRadius 0.3
    9873 
    9874 Changed 72733 bond radii 
    9875 
    9876 > select add #49
    9877 
    9878 3942 atoms, 3966 bonds, 570 residues, 1 model selected 
    9879 
    9880 > hide sel cartoons
    9881 
    9882 > select clear
    9883 
    9884 Drag select of 10 atoms, 11 bonds 
    9885 Drag select of 6 atoms, 9 bonds 
    9886 Drag select of 8 atoms, 10 bonds 
    9887 Drag select of 4 atoms, 4 bonds 
    9888 
    9889 > select up
    9890 
    9891 36 atoms, 34 bonds, 4 residues, 1 model selected 
    9892 
    9893 > lighting flat
    9894 
    9895 > graphics silhouettes false
    9896 
    9897 > select clear
    9898 
    9899 > select #49: 382, 353,438,230,442,466
    9900 
    9901 66 atoms, 64 bonds, 6 residues, 1 model selected 
    9902 
    9903 > select clear
    9904 
    9905 > select #49: 382, 353,438,230,442,466
    9906 
    9907 66 atoms, 64 bonds, 6 residues, 1 model selected 
    9908 
    9909 > color sel orange
    9910 
    9911 > color sel purple
    9912 
    9913 > color sel hot pink
    9914 
    9915 > size stickRadius 0.5
    9916 
    9917 Changed 72733 bond radii 
    9918 
    9919 > size stickRadius 0.4
    9920 
    9921 Changed 72733 bond radii 
    9922 
    9923 > select clear
    9924 
    9925 > select add #49/A:466@CB
    9926 
    9927 1 atom, 1 residue, 1 model selected 
    9928 
    9929 > select add #49/A:382@NZ
    9930 
    9931 2 atoms, 2 residues, 1 model selected 
    9932 
    9933 > select up
    9934 
    9935 20 atoms, 18 bonds, 2 residues, 1 model selected 
    9936 
    9937 > select #49: 382, 353,438,230,442,466
    9938 
    9939 66 atoms, 64 bonds, 6 residues, 1 model selected 
    9940 
    9941 > color sel lime
    9942 
    9943 > color sel purple
    9944 
    9945 > select clear
    9946 
    9947 > select add #49/A:382@NZ
    9948 
    9949 1 atom, 1 residue, 1 model selected 
    9950 
    9951 > select up
    9952 
    9953 3 atoms, 1 bond, 2 residues, 1 model selected 
    9954 
    9955 > select up
    9956 
    9957 20 atoms, 18 bonds, 2 residues, 1 model selected 
    9958 
    9959 > color sel byhetero
    9960 
    9961 > select #49: 382, 353,438,230,442,466
    9962 
    9963 66 atoms, 64 bonds, 6 residues, 1 model selected 
    9964 
    9965 > color sel purple
    9966 
    9967 > select clear
    9968 
    9969 > select #49/A:382@NZ
    9970 
    9971 1 atom, 1 residue, 1 model selected 
    9972 
    9973 > select add #49/A:466@NH2
    9974 
    9975 2 atoms, 2 residues, 1 model selected 
    9976 
    9977 > select add #49/A:466@NH1
    9978 
    9979 3 atoms, 2 residues, 1 model selected 
    9980 
    9981 > select add #49/A:466@CZ
    9982 
    9983 4 atoms, 2 residues, 1 model selected 
    9984 
    9985 > select add #49/A:466@NE
    9986 
    9987 5 atoms, 2 residues, 1 model selected 
    9988 
    9989 > color sel byhetero
    9990 
    9991 > select clear
    9992 
    9993 > save /Users/dout2/Desktop/rOAT1-Apo_keyresidue.png supersample 3
    9994 > transparentBackground true
    9995 
    9996 > save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
    9997 
    9998 > select #49: 382, 353,438,230,442,466
    9999 
    10000 66 atoms, 64 bonds, 6 residues, 1 model selected 
    10001 
    10002 > ui tool show "Color Actions"
    10003 
    10004 The cached device pixel ratio value was stale on window expose. Please file a
    10005 QTBUG which explains how to reproduce. 
    10006 
    10007 > select #49: 382, 353,438,230,442,466
    10008 
    10009 66 atoms, 64 bonds, 6 residues, 1 model selected 
    10010 
    10011 > hide sel atoms
    10012 
    10013 > select add #49
    10014 
    10015 3942 atoms, 3966 bonds, 570 residues, 1 model selected 
    10016 
    10017 > show sel cartoons
    10018 
    10019 > select clear
    10020 
    10021 > view
    10022 
    10023 > select add #49
    10024 
    10025 3942 atoms, 3966 bonds, 570 residues, 1 model selected 
    10026 
    10027 > color sel gray
    10028 
    10029 > color sel light gray
    10030 
    10031 > color sel dark gray
    10032 
    10033 > surface sel
    10034 
    10035 > select clear
    10036 
    10037 > save /Users/dout2/Desktop/rOAT1-Apo_bg.png supersample 3
    10038 > transparentBackground true
    10039 
    10040 > open /Users/dout2/Downloads/af3/roat1-AKG_model/seed-1_sample-0/model.cif
    10041 
    10042 Summary of feedback from opening
    10043 /Users/dout2/Downloads/af3/roat1-AKG_model/seed-1_sample-0/model.cif 
    10044 --- 
    10045 warning | Unable to fetch template for 'LIG_B': will connect using distance criteria 
    10046  
    10047 Chain information for model.cif #50 
    10048 --- 
    10049 Chain | Description 
    10050 A | . 
    10051  
    10052 
    10053 No chain in structure corresponds to chain ID given in local score info (chain
    10054 'B') 
    10055 
    10056 > hide #!49 models
    10057 
    10058 > rename #50 rOAT1-AKG_IF_af3.cif
    10059 
    10060 > select add #50
    10061 
    10062 4280 atoms, 4381 bonds, 552 residues, 1 model selected 
    10063 
    10064 > select clear
    10065 
    10066 > select #50: 382, 353,438,230,442,466
    10067 
    10068 66 atoms, 64 bonds, 6 residues, 1 model selected 
    10069 
    10070 > show sel atoms
    10071 
    10072 > color sel purple
    10073 
    10074 > size stickRadius 0.4
    10075 
    10076 Changed 77114 bond radii 
    10077 
    10078 > select clear
    10079 
    10080 > select add #50
    10081 
    10082 4280 atoms, 4381 bonds, 552 residues, 1 model selected 
    10083 
    10084 > hide sel cartoons
    10085 
    10086 > select clear
    10087 
    10088 [Repeated 1 time(s)]
    10089 
    10090 > select #50/A:354@CG
    10091 
    10092 1 atom, 1 residue, 1 model selected 
    10093 
    10094 > select up
    10095 
    10096 12 atoms, 12 bonds, 1 residue, 1 model selected 
    10097 
    10098 > hide sel atoms
    10099 
    10100 > select #50/B:1@C4
    10101 
    10102 1 atom, 1 residue, 1 model selected 
    10103 
    10104 > select up
    10105 
    10106 10 atoms, 9 bonds, 1 residue, 1 model selected 
    10107 
    10108 > color sel yellow
    10109 
    10110 > color sel byhetero
    10111 
    10112 > select #50/A:382@NZ
    10113 
    10114 1 atom, 1 residue, 1 model selected 
    10115 
    10116 > select add #50/A:466@NH1
    10117 
    10118 2 atoms, 2 residues, 1 model selected 
    10119 
    10120 > select add #50/A:466@NH2
    10121 
    10122 3 atoms, 2 residues, 1 model selected 
    10123 
    10124 > select add #50/A:466@NE
    10125 
    10126 4 atoms, 2 residues, 1 model selected 
    10127 
    10128 > color sel byhetero
    10129 
    10130 > select clear
    10131 
    10132 > save /Users/dout2/Desktop/rOAT1-AKG_keyresidue.png supersample 3
    10133 > transparentBackground true
    10134 
    10135 > select add #50
    10136 
    10137 4280 atoms, 4381 bonds, 552 residues, 1 model selected 
    10138 
    10139 > hide sel atoms
    10140 
    10141 > show sel cartoons
    10142 
    10143 > surface sel
    10144 
    10145 > color (#!50 & sel) dark gray
    10146 
    10147 > select clear
    10148 
    10149 > save /Users/dout2/Desktop/rOAT1-AKG_bg.png supersample 3
    10150 > transparentBackground true
    10151 
    10152 > save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
    10153 
    10154 > hide #!50 models
    10155 
    10156 > show #!45 models
    10157 
    10158 > show #!44 models
    10159 
    10160 > hide #!44 models
    10161 
    10162 > view
    10163 
    10164 > view orient
    10165 
    10166 > hide #!45 models
    10167 
    10168 > show #!43 models
    10169 
    10170 > show #!45 models
    10171 
    10172 > hide #!45 models
    10173 
    10174 > select add #43
    10175 
    10176 3807 atoms, 3899 bonds, 3 pseudobonds, 492 residues, 2 models selected 
    10177 
    10178 > color (#!43 & sel) dark gray
    10179 
    10180 > surface (#!43 & sel)
    10181 
    10182 > select clear
    10183 
    10184 > save /Users/dout2/Desktop/rOAT1-AKG_OF_bg.png supersample 3
    10185 > transparentBackground true
    10186 
    10187 > hide #43.2 models
    10188 
    10189 > hide #43.1 models
    10190 
    10191 > show #43.1 models
    10192 
    10193 > select #43: 382, 353,438,230,442,466
    10194 
    10195 66 atoms, 64 bonds, 6 residues, 1 model selected 
    10196 
    10197 > select subtract #43.2
    10198 
    10199 1 model selected 
    10200 
    10201 > select add #43
    10202 
    10203 3807 atoms, 3899 bonds, 3 pseudobonds, 492 residues, 2 models selected 
    10204 
    10205 > hide sel cartoons
    10206 
    10207 > select clear
    10208 
    10209 > select #43: 382, 353,438,230,442,466
    10210 
    10211 66 atoms, 64 bonds, 6 residues, 1 model selected 
    10212 
    10213 > select add #43
    10214 
    10215 3807 atoms, 3899 bonds, 3 pseudobonds, 492 residues, 3 models selected 
    10216 
    10217 > hide sel atoms
    10218 
    10219 > select #43: 382, 353,438,230,442,466
    10220 
    10221 66 atoms, 64 bonds, 6 residues, 1 model selected 
    10222 
    10223 > show sel atoms
    10224 
    10225 > select #43: akg
    10226 
    10227 10 atoms, 9 bonds, 1 residue, 1 model selected 
    10228 
    10229 > show sel atoms
    10230 
    10231 > select clear
    10232 
    10233 > select #43/A:601@C2
    10234 
    10235 1 atom, 1 residue, 1 model selected 
    10236 
    10237 > select up
    10238 
    10239 10 atoms, 9 bonds, 1 residue, 1 model selected 
    10240 
    10241 > color sel yellow
    10242 
    10243 > color sel byhetero
    10244 
    10245 > select clear
    10246 
    10247 > select #43/A:466@NH2
    10248 
    10249 1 atom, 1 residue, 1 model selected 
    10250 
    10251 > select add #43/A:466@NH1
    10252 
    10253 2 atoms, 1 residue, 2 models selected 
    10254 
    10255 > select add #43/A:466@NE
    10256 
    10257 3 atoms, 1 residue, 2 models selected 
    10258 
    10259 > select add #43/A:382@NZ
    10260 
    10261 4 atoms, 2 residues, 2 models selected 
    10262 
    10263 > color (#!43 & sel) byhetero
    10264 
    10265 > select clear
    10266 
    10267 > select #43: 382, 353,438,230,442,466
    10268 
    10269 66 atoms, 64 bonds, 6 residues, 1 model selected 
    10270 
    10271 > color (#!43 & sel) purple
    10272 
    10273 > select subtract #43/A:382@NZ
    10274 
    10275 65 atoms, 63 bonds, 6 residues, 2 models selected 
    10276 
    10277 > select subtract #43/A:466@NH2
    10278 
    10279 64 atoms, 62 bonds, 6 residues, 2 models selected 
    10280 
    10281 > select subtract #43/A:466@NH1
    10282 
    10283 63 atoms, 61 bonds, 6 residues, 2 models selected 
    10284 
    10285 > select subtract #43/A:466@CD
    10286 
    10287 62 atoms, 59 bonds, 6 residues, 2 models selected 
    10288 
    10289 > color (#!43 & sel) byhetero
    10290 
    10291 > select #43: 382, 353,438,230,442,466
    10292 
    10293 66 atoms, 64 bonds, 6 residues, 1 model selected 
    10294 
    10295 > color (#!43 & sel) purple
    10296 
    10297 > select subtract #43/A:382@NZ
    10298 
    10299 65 atoms, 63 bonds, 6 residues, 2 models selected 
    10300 
    10301 > select subtract #43/A:466@NH1
    10302 
    10303 64 atoms, 62 bonds, 6 residues, 2 models selected 
    10304 
    10305 > select subtract #43/A:466@NH2
    10306 
    10307 63 atoms, 61 bonds, 6 residues, 2 models selected 
    10308 
    10309 > select clear
    10310 
    10311 > select add #43/A:466@NH2
    10312 
    10313 1 atom, 1 residue, 1 model selected 
    10314 
    10315 > select add #43/A:466@NH1
    10316 
    10317 2 atoms, 1 residue, 2 models selected 
    10318 
    10319 > select add #43/A:382@NZ
    10320 
    10321 3 atoms, 2 residues, 2 models selected 
    10322 
    10323 > color (#!43 & sel) byhetero
    10324 
    10325 > select clear
    10326 
    10327 > save /Users/dout2/Desktop/rOAT1-AKG_OF_residue.png supersample 3
    10328 > transparentBackground true
    10329 
    10330 > save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
    10331 
    10332 > open /Users/dout2/Downloads/af3/roat1-AKG_model/seed-1_sample-1/model.cif
    10333 
    10334 Summary of feedback from opening
    10335 /Users/dout2/Downloads/af3/roat1-AKG_model/seed-1_sample-1/model.cif 
    10336 --- 
    10337 warning | Unable to fetch template for 'LIG_B': will connect using distance criteria 
    10338  
    10339 Chain information for model.cif #51 
    10340 --- 
    10341 Chain | Description 
    10342 A | . 
    10343  
    10344 
    10345 No chain in structure corresponds to chain ID given in local score info (chain
    10346 'B') 
    10347 
    10348 > hide #!43 models
    10349 
    10350 > hide #43.1 models
    10351 
    10352 > view
    10353 
    10354 > rename #51 rOAT1-AKG_IF_af3_model1.cif
    10355 
    10356 > rename #51 rOAT1-AKG_IF_af3_model1-1.cif
    10357 
    10358 > select add #51
    10359 
    10360 4280 atoms, 4381 bonds, 552 residues, 1 model selected 
    10361 
    10362 > color sel dark gray
    10363 
    10364 > surface sel
    10365 
    10366 > select clear
    10367 
    10368 > save /Users/dout2/Desktop/rOAT1-AKG_IF_bg.png supersample 3
    10369 > transparentBackground true
    10370 
    10371 > hide #51.1 models
    10372 
    10373 > select add #51
    10374 
    10375 4280 atoms, 4381 bonds, 552 residues, 1 model selected 
    10376 
    10377 > hide sel atoms
    10378 
    10379 > hide sel cartoons
    10380 
    10381 > select #51: 382, 353,438,230,442,466
    10382 
    10383 66 atoms, 64 bonds, 6 residues, 1 model selected 
    10384 
    10385 > show sel atoms
    10386 
    10387 > color (#!51 & sel) purple
    10388 
    10389 > size stickRadius 0.4
    10390 
    10391 Changed 81495 bond radii 
    10392 
    10393 > select clear
    10394 
    10395 > select #51: AKG
    10396 
    10397 Nothing selected 
    10398 
    10399 > show #!51 atoms
    10400 
    10401 > undo
    10402 
    10403 > select add #51
    10404 
    10405 4280 atoms, 4381 bonds, 552 residues, 1 model selected 
    10406 
    10407 > show sel atoms
    10408 
    10409 > select #51/B:1@C3
    10410 
    10411 1 atom, 1 residue, 1 model selected 
    10412 
    10413 > select up
    10414 
    10415 10 atoms, 9 bonds, 1 residue, 1 model selected 
    10416 
    10417 > select add #51
    10418 
    10419 4280 atoms, 4381 bonds, 552 residues, 1 model selected 
    10420 
    10421 > hide sel atoms
    10422 
    10423 > select #51/B
    10424 
    10425 10 atoms, 9 bonds, 1 residue, 1 model selected 
    10426 
    10427 > show sel atoms
    10428 
    10429 > color sel yellow
    10430 
    10431 > color sel byhetero
    10432 
    10433 > select clear
    10434 
    10435 > select #51: 382, 353,438,230,442,466
    10436 
    10437 66 atoms, 64 bonds, 6 residues, 1 model selected 
    10438 
    10439 > show sel atoms
    10440 
    10441 > select #51/A:382@NZ
    10442 
    10443 1 atom, 1 residue, 1 model selected 
    10444 
    10445 > select add #51/A:466@NH1
    10446 
    10447 2 atoms, 2 residues, 2 models selected 
    10448 
    10449 > select add #51/A:466@NH2
    10450 
    10451 3 atoms, 2 residues, 2 models selected 
    10452 
    10453 > color (#!51 & sel) byhetero
    10454 
    10455 > select #51/A:466@NE
    10456 
    10457 1 atom, 1 residue, 1 model selected 
    10458 
    10459 > color (#!51 & sel) byhetero
    10460 
    10461 > select clear
    10462 
    10463 > save /Users/dout2/Desktop/rOAT1-AKG_IF_residue.png supersample 3
    10464 > transparentBackground true
    10465 
    10466 > close #50
    10467 
    10468 > save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
    10469 
    10470 ——— End of log from Sat Apr 12 21:31:41 2025 ———
    10471 
    10472 opened ChimeraX session 
    10473 
    10474 > hide #!51 models
    10475 
    10476 > show #!2 models
    10477 
    10478 > show #1 models
    10479 
    10480 > view
    10481 
    10482 > lighting simple
    10483 
    10484 > lighting soft
    10485 
    10486 > lighting simple
    10487 
    10488 > hide #!2 models
    10489 
    10490 > select #1: 382, 353,438,230,442,466
    10491 
    10492 66 atoms, 64 bonds, 6 residues, 1 model selected 
    10493 
    10494 > view sel
    10495 
    10496 > cofr sel
    10497 
    10498 > select clear
    10499 
    10500 > show #!2 models
    10501 
    10502 > color #2 #ffffb2ff models
    10503 
    10504 > color #2 #ffffb24f models
    10505 
    10506 > color #2 #ffffb24e models
    10507 
    10508 > color #2 #ffffb24d models
    10509 
    10510 > select clear
    10511 
    10512 [Repeated 1 time(s)]
    10513 
    10514 > color #2 #a5ffb24d models
    10515 
    10516 > color #2 #9effb24d models
    10517 
    10518 > color #2 #9e43b24d models
    10519 
    10520 > color #2 #9effb24d models
    10521 
    10522 > color #2 #9effff4d models
    10523 
    10524 > select clear
    10525 
    10526 > size stickRadius 0.2
    10527 
    10528 Changed 77114 bond radii 
    10529 
    10530 > select clear
    10531 
    10532 > color #2 #942192ff models
    10533 
    10534 > color #2 #9421924d models
    10535 
    10536 > select clear
    10537 
    10538 > color #2 #aa7942ff models
    10539 
    10540 > color #2 #00fdffff models
    10541 
    10542 > color #2 #00fdff4e models
    10543 
    10544 > select clear
    10545 
    10546 > select up
    10547 
    10548 2 atoms, 1 bond, 1 residue, 1 model selected 
    10549 
    10550 > select up
    10551 
    10552 19 atoms, 20 bonds, 1 residue, 1 model selected 
    10553 
    10554 > view sel
    10555 
    10556 > ui tool show "Side View"
    10557 
    10558 > volume #2 level 0.01002
    10559 
    10560 > select clear
    10561 
    10562 > select #1/A:223
    10563 
    10564 4 atoms, 3 bonds, 1 residue, 1 model selected 
    10565 
    10566 > show sel atoms
    10567 
    10568 [Repeated 1 time(s)]
    10569 
    10570 > select #1/A:207
    10571 
    10572 8 atoms, 7 bonds, 1 residue, 1 model selected 
    10573 
    10574 > show sel atoms
    10575 
    10576 > hide #!2 models
    10577 
    10578 > select #1/A:36
    10579 
    10580 7 atoms, 6 bonds, 1 residue, 1 model selected 
    10581 
    10582 > show sel atoms
    10583 
    10584 > show #!2 models
    10585 
    10586 > select clear
    10587 
    10588 > select #1/A:601@C4'
    10589 
    10590 1 atom, 1 residue, 1 model selected 
    10591 
    10592 > select up
    10593 
    10594 19 atoms, 20 bonds, 1 residue, 1 model selected 
    10595 
    10596 > select up
    10597 
    10598 3891 atoms, 3986 bonds, 501 residues, 1 model selected 
    10599 
    10600 > select down
    10601 
    10602 19 atoms, 20 bonds, 1 residue, 1 model selected 
    10603 
    10604 > cofr sel
    10605 
    10606 > movie record
    10607 
    10608 > turn y 2 180
    10609 
    10610 > wait 180
    10611 
    10612 > movie encode /Users/dout2/Desktop/movie1.mp4
    10613 
    10614 Movie saved to /Users/dout2/Desktop/movie1.mp4 
    10615  
    10616 
    10617 > hide #!2 models
    10618 
    10619 > hide #1 models
    10620 
    10621 > select add #1
    10622 
    10623 3905 atoms, 3986 bonds, 515 residues, 1 model selected 
    10624 
    10625 > select subtract #1
    10626 
    10627 Nothing selected 
    10628 
    10629 > show #1 models
    10630 
    10631 > hide #1 models
    10632 
    10633 > show #!5 models
    10634 
    10635 > show #!4 models
    10636 
    10637 > select clear
    10638 
    10639 > volume #4 level 0.01053
    10640 
    10641 > color #4 #fffb00ff models
    10642 
    10643 > color #4 #ffffb2ff models
    10644 
    10645 > color #4 #ffffb24d models
    10646 
    10647 > select #4
    10648 
    10649 4 models selected 
    10650 
    10651 > select clear
    10652 
    10653 > select #1: 382, 353,438,230,442,466,207
    10654 
    10655 74 atoms, 71 bonds, 7 residues, 1 model selected 
    10656 
    10657 > show #!5 atoms
    10658 
    10659 > select add #5
    10660 
    10661 3848 atoms, 3935 bonds, 5 pseudobonds, 493 residues, 3 models selected 
    10662 
    10663 > hide sel & #!5 atoms
    10664 
    10665 > select #5: 382, 353,438,230,442,466,207,601
    10666 
    10667 93 atoms, 91 bonds, 8 residues, 1 model selected 
    10668 
    10669 > show sel atoms
    10670 
    10671 > select clear
    10672 
    10673 > select add #5
    10674 
    10675 3774 atoms, 3864 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    10676 
    10677 > show sel atoms
    10678 
    10679 > select clear
    10680 
    10681 > select #5/A:601@O4
    10682 
    10683 1 atom, 1 residue, 1 model selected 
    10684 
    10685 > select up
    10686 
    10687 19 atoms, 20 bonds, 1 residue, 1 model selected 
    10688 
    10689 > cofr sel
    10690 
    10691 > select #4
    10692 
    10693 4 models selected 
    10694 
    10695 > volume #4 level 0.01089
    10696 
    10697 > volume #4 level 0.01182
    10698 
    10699 > volume #4 level 0.01292
    10700 
    10701 > select clear
    10702 
    10703 > volume #4 level 0.01311
    10704 
    10705 > volume #4 level 0.01274
    10706 
    10707 > volume #4 level 0.01126
    10708 
    10709 > volume #4 level 0.01274
    10710 
    10711 > volume #4 level 0.012
    10712 
    10713 > movie record
    10714 
    10715 > turn y 2 180
    10716 
    10717 > wait 180
    10718 
    10719 > movie encode /Users/dout2/Desktop/movie2.mp4
    10720 
    10721 Movie saved to /Users/dout2/Desktop/movie2.mp4 
    10722  
    10723 
    10724 > movie record
    10725 
    10726 > turn y 2 180
    10727 
    10728 > wait 180
    10729 
    10730 > movie encode /Users/dout2/Desktop/movie3.mp4
    10731 
    10732 Movie saved to /Users/dout2/Desktop/movie3.mp4 
    10733  
    10734 
    10735 > view
    10736 
    10737 > hide #!4 models
    10738 
    10739 > select add #5
    10740 
    10741 3774 atoms, 3864 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    10742 
    10743 > hide sel atoms
    10744 
    10745 > select #5: 382, 353,438,230,442,466,207,601
    10746 
    10747 93 atoms, 91 bonds, 8 residues, 1 model selected 
    10748 
    10749 > show sel atoms
    10750 
    10751 > select clear
    10752 
    10753 > show #!4 models
    10754 
    10755 > hide #!4 models
    10756 
    10757 > hide #!5 models
    10758 
    10759 > show #8 models
    10760 
    10761 > show #!7 models
    10762 
    10763 > hide #8 models
    10764 
    10765 > hide #!7 models
    10766 
    10767 > show #!10 models
    10768 
    10769 > show #!12 models
    10770 
    10771 > color #10 darkgrey models
    10772 
    10773 > color #10 silver models
    10774 
    10775 > color #10 #c0c0c04d models
    10776 
    10777 > select clear
    10778 
    10779 > hide #!12 models
    10780 
    10781 > show #!12 models
    10782 
    10783 > hide #!10 models
    10784 
    10785 > show #!10 models
    10786 
    10787 > save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
    10788 
    10789 > volume #10 level 0.0124
    10790 
    10791 > select up
    10792 
    10793 2 atoms, 1 bond, 1 residue, 1 model selected 
    10794 
    10795 > select up
    10796 
    10797 37 atoms, 37 bonds, 1 residue, 1 model selected 
    10798 
    10799 > select #12: 382, 353,438,230,442,466,207,601
    10800 
    10801 111 atoms, 108 bonds, 8 residues, 1 model selected 
    10802 
    10803 > show sel atoms
    10804 
    10805 > select up
    10806 
    10807 2 atoms, 1 bond, 1 residue, 1 model selected 
    10808 
    10809 > select H
    10810 
    10811 117 atoms, 10 residues, 9 models selected 
    10812 
    10813 > hide sel & #!12 atoms
    10814 
    10815 > select clear
    10816 
    10817 > select #12: 382, 353,438,230,442,466,207,601
    10818 
    10819 111 atoms, 108 bonds, 8 residues, 1 model selected 
    10820 
    10821 > view sel
    10822 
    10823 > cofr sel
    10824 
    10825 > volume #10 level 0.009894
    10826 
    10827 > volume #10 level 0.01073
    10828 
    10829 > select clear
    10830 
    10831 [Repeated 1 time(s)]
    10832 
    10833 > select #12/B:601@C16
    10834 
    10835 1 atom, 1 residue, 1 model selected 
    10836 
    10837 > select up
    10838 
    10839 37 atoms, 37 bonds, 1 residue, 1 model selected 
    10840 
    10841 > view sel
    10842 
    10843 > select clear
    10844 
    10845 > movie record
    10846 
    10847 > turn y 2 180
    10848 
    10849 > wait 180
    10850 
    10851 > movie encode /Users/dout2/Desktop/movie4.mp4
    10852 
    10853 Movie saved to /Users/dout2/Desktop/movie4.mp4 
    10854  
    10855 
    10856 > select #10
    10857 
    10858 4 models selected 
    10859 
    10860 > select clear
    10861 
    10862 > hide #!12 models
    10863 
    10864 > hide #!10 models
    10865 
    10866 > show #8 models
    10867 
    10868 > show #!7 models
    10869 
    10870 > select up
    10871 
    10872 2 atoms, 1 bond, 1 residue, 1 model selected 
    10873 
    10874 > color #7 #ff2f92ff models
    10875 
    10876 > color #7 #ff2f924d models
    10877 
    10878 > select #7
    10879 
    10880 4 models selected 
    10881 
    10882 > select clear
    10883 
    10884 > select #8: 382, 353,438,230,442,466,207,601
    10885 
    10886 93 atoms, 90 bonds, 8 residues, 1 model selected 
    10887 
    10888 > show sel atoms
    10889 
    10890 > select clear
    10891 
    10892 > open
    10893 > /Users/dout2/Documents/Manuscripts/rOAT1_2023/cryoEM/rOAT1-PBD_20230217/cryosparc_P4_J55__localfilter_160.mrc
    10894 
    10895 Opened cryosparc_P4_J55__localfilter_160.mrc as #50, grid size 160,160,160,
    10896 pixel 0.83, shown at level 0.131, step 1, values float32 
    10897 
    10898 > movie record
    10899 
    10900 > turn y 2 180
    10901 
    10902 > wait 180
    10903 
    10904 > movie encode /Users/dout2/Desktop/movie1.mp4
    10905 
    10906 Movie saved to /Users/dout2/Desktop/movie1.mp4 
    10907  
    10908 
    10909 > hide #!7 models
    10910 
    10911 > view
    10912 
    10913 > show #!7 models
    10914 
    10915 > rename #50 rOAT1-PBD_IF.mrc
    10916 
    10917 > select add #50
    10918 
    10919 2 models selected 
    10920 
    10921 > ui mousemode right "translate selected models"
    10922 
    10923 > view matrix models #50,1,0,0,82.163,0,1,0,34.821,0,0,1,72.008
    10924 
    10925 > view matrix models #50,1,0,0,78.322,0,1,0,71.965,0,0,1,68.805
    10926 
    10927 > view matrix models #50,1,0,0,68.336,0,1,0,66.309,0,0,1,66.361
    10928 
    10929 > ui tool show "Fit in Map"
    10930 
    10931 > fitmap #50 inMap #7
    10932 
    10933 Fit map rOAT1-PBD_IF.mrc in map rOAT1-PBD_IF.mrc using 40907 points 
    10934 correlation = 0.9052, correlation about mean = 0.7104, overlap = 318.4 
    10935 steps = 88, shift = 2.7, angle = 7.48 degrees 
    10936  
    10937 Position of rOAT1-PBD_IF.mrc (#50) relative to rOAT1-PBD_IF.mrc (#7)
    10938 coordinates: 
    10939 Matrix rotation and translation 
    10940 0.99182552 0.09586728 -0.08421166 67.85108178 
    10941 -0.09362983 0.99515083 0.03013765 73.24636935 
    10942 0.08669251 -0.02200656 0.99599203 61.03836799 
    10943 Axis -0.20020488 -0.65617735 -0.72756395 
    10944 Axis point 63.93693297 -480.82614561 -0.00000000 
    10945 Rotation angle (degrees) 7.48271681 
    10946 Shift along axis -106.05604184 
    10947  
    10948 
    10949 > hide #!7 models
    10950 
    10951 > color #50 #b2b2b24d models
    10952 
    10953 > select clear
    10954 
    10955 > ui mousemode right translate
    10956 
    10957 > select #8: 382, 353,438,230,442,466,207,601
    10958 
    10959 93 atoms, 90 bonds, 8 residues, 1 model selected 
    10960 
    10961 > view sel
    10962 
    10963 > cofr sel
    10964 
    10965 > volume #50 level 0.2404
    10966 
    10967 > select clear
    10968 
    10969 > select #8: 382, 353,438,230,442,466,207,601
    10970 
    10971 93 atoms, 90 bonds, 8 residues, 1 model selected 
    10972 
    10973 > show sel atoms
    10974 
    10975 > select clear
    10976 
    10977 > volume #50 level 0.2822
    10978 
    10979 > select clear
    10980 
    10981 > movie record
    10982 
    10983 > turn y 2 180
    10984 
    10985 > wait 180
    10986 
    10987 > movie encode /Users/dout2/Desktop/movie2.mp4
    10988 
    10989 Movie saved to /Users/dout2/Desktop/movie2.mp4 
    10990  
    10991 
    10992 > hide #!50 models
    10993 
    10994 > view
    10995 
    10996 > hide #8 models
    10997 
    10998 > show #!20 models
    10999 
    11000 > show #21 models
    11001 
    11002 > color #20 #ffffb2ff models
    11003 
    11004 > color #20 #ffffb24d models
    11005 
    11006 > select clear
    11007 
    11008 > select #21: 382, 353,438,230,442,466,207,601
    11009 
    11010 109 atoms, 109 bonds, 8 residues, 1 model selected 
    11011 
    11012 > show sel atoms
    11013 
    11014 > select clear
    11015 
    11016 > select H
    11017 
    11018 117 atoms, 10 residues, 9 models selected 
    11019 
    11020 > hide sel & #21 atoms
    11021 
    11022 > select clear
    11023 
    11024 > select #21: 382, 353,438,230,442,466,207,601
    11025 
    11026 109 atoms, 109 bonds, 8 residues, 1 model selected 
    11027 
    11028 > view sel
    11029 
    11030 > select clear
    11031 
    11032 > color #20 #ffffb280 models
    11033 
    11034 > select clear
    11035 
    11036 > volume #20 level 0.01329
    11037 
    11038 > select #21/A:602@O24
    11039 
    11040 1 atom, 1 residue, 1 model selected 
    11041 
    11042 > select up
    11043 
    11044 35 atoms, 38 bonds, 1 residue, 1 model selected 
    11045 
    11046 > select clear
    11047 
    11048 > movie record
    11049 
    11050 > turn y 2 180
    11051 
    11052 > wait 180
    11053 
    11054 > movie encode /Users/dout2/Desktop/movie2.mp4
    11055 
    11056 Movie saved to /Users/dout2/Desktop/movie2.mp4 
    11057  
    11058 
    11059 > select #21: 382, 353,438,230,442,466,207,601,602
    11060 
    11061 144 atoms, 147 bonds, 9 residues, 1 model selected 
    11062 
    11063 > select #20
    11064 
    11065 4 models selected 
    11066 
    11067 > select clear
    11068 
    11069 > movie record
    11070 
    11071 > turn y 2 180
    11072 
    11073 > wait 180
    11074 
    11075 > movie encode /Users/dout2/Desktop/movie3.mp4
    11076 
    11077 Movie saved to /Users/dout2/Desktop/movie3.mp4 
    11078  
    11079 
    11080 > hide #!20 models
    11081 
    11082 > view
    11083 
    11084 > hide #21 models
    11085 
    11086 > show #!24 models
    11087 
    11088 > show #!23 models
    11089 
    11090 > color #23 #ffffb2ff models
    11091 
    11092 > select clear
    11093 
    11094 > hide #!23 models
    11095 
    11096 > show #!23 models
    11097 
    11098 > select #24: 382, 353,438,230,442,466,207,601,602
    11099 
    11100 109 atoms, 109 bonds, 8 residues, 1 model selected 
    11101 
    11102 > view sel
    11103 
    11104 > color #23 #ffffb280 models
    11105 
    11106 > select clear
    11107 
    11108 > select #24/A:601@O14
    11109 
    11110 1 atom, 1 residue, 1 model selected 
    11111 
    11112 > select up
    11113 
    11114 35 atoms, 38 bonds, 1 residue, 1 model selected 
    11115 
    11116 > cofr sel
    11117 
    11118 > select #23
    11119 
    11120 4 models selected 
    11121 
    11122 > movie record
    11123 
    11124 > turn y 2 180
    11125 
    11126 > wait 180
    11127 
    11128 > movie encode /Users/dout2/Desktop/movie3.mp4
    11129 
    11130 Movie saved to /Users/dout2/Desktop/movie3.mp4 
    11131  
    11132 
    11133 > select clear
    11134 
    11135 > movie record
    11136 
    11137 > turn y 2 180
    11138 
    11139 > wait 180
    11140 
    11141 > movie encode /Users/dout2/Desktop/movie4.mp4
    11142 
    11143 Movie saved to /Users/dout2/Desktop/movie4.mp4 
    11144  
    11145 
    11146 > save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
    11147 
    11148 ——— End of log from Tue Apr 15 12:09:47 2025 ———
    11149 
    11150 opened ChimeraX session 
    11151 
    11152 > hide #!24 models
    11153 
    11154 > hide #!23 models
    11155 
    11156 > show #!6 models
    11157 
    11158 > show #!5 models
    11159 
    11160 > show #!6.3 models
    11161 
    11162 > show #!4 models
    11163 
    11164 > hide #!6.3 models
    11165 
    11166 > hide #!6 models
    11167 
    11168 > volume #4 level 0.01403
    11169 
    11170 > volume #4 level 0.01126
    11171 
    11172 > hide #!5 models
    11173 
    11174 > hide #!4 models
    11175 
    11176 > show #!2 models
    11177 
    11178 > show #1 models
    11179 
    11180 > show #!5 models
    11181 
    11182 > hide #!5 models
    11183 
    11184 > volume #2 level 0.008618
    11185 
    11186 > hide #!2 models
    11187 
    11188 > hide #1 models
    11189 
    11190 > show #!4 models
    11191 
    11192 > show #!5 models
    11193 
    11194 > hide #!5 models
    11195 
    11196 > hide #!4 models
    11197 
    11198 > show #!2 models
    11199 
    11200 > show #1 models
    11201 
    11202 > hide #1 models
    11203 
    11204 > hide #!2 models
    11205 
    11206 > show #!4 models
    11207 
    11208 > show #!5 models
    11209 
    11210 > hide #!5 models
    11211 
    11212 > hide #!4 models
    11213 
    11214 > show #!2 models
    11215 
    11216 > show #1 models
    11217 
    11218 > open /Volumes/bbc/Lab-
    11219 > Jiang/USERS/dout2/SLC22_MapModel/rOAT1-AZT/IF/rOAT1-AZT_IF-coot-3.pdb
    11220 
    11221 Chain information for rOAT1-AZT_IF-coot-3.pdb #52 
    11222 --- 
    11223 Chain | Description 
    11224 A | No description available 
    11225  
    11226 
    11227 > hide #1 models
    11228 
    11229 > select #1-60: 382, 353,438,230,442,466,207, 234, 227
    11230 
    11231 1734 atoms, 1634 bonds, 180 residues, 20 models selected 
    11232 
    11233 > show sel & #52 atoms
    11234 
    11235 > show #!5 models
    11236 
    11237 > open /Volumes/bbc/Lab-
    11238 > Jiang/USERS/dout2/SLC22_MapModel/rOAT1-AZT/IF/RealSpaceRefine_6/rOAT1-AZT_IF-
    11239 > coot-3_real_space_refined_006.pdb
    11240 
    11241 Chain information for rOAT1-AZT_IF-coot-3_real_space_refined_006.pdb #53 
    11242 --- 
    11243 Chain | Description 
    11244 A | No description available 
    11245  
    11246 
    11247 > hide #52 models
    11248 
    11249 > select add #53
    11250 
    11251 5639 atoms, 5620 bonds, 695 residues, 24 models selected 
    11252 
    11253 > show #53 target m
    11254 
    11255 > select #53
    11256 
    11257 3905 atoms, 3986 bonds, 515 residues, 1 model selected 
    11258 
    11259 > hide #!5 models
    11260 
    11261 > hide #!2 models
    11262 
    11263 > show #!2 models
    11264 
    11265 > close #52
    11266 
    11267 > save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
    11268 
    11269 > save /Users/dout2/Downloads/OAT1_ligand_Colored_domain.cxs includeMaps true
    11270 
    11271 > color #53 tan
    11272 
    11273 > select clear
    11274 
    11275 > select #53/A:601@C2'
    11276 
    11277 1 atom, 1 residue, 1 model selected 
    11278 
    11279 > select up
    11280 
    11281 19 atoms, 20 bonds, 1 residue, 1 model selected 
    11282 
    11283 > color sel byhetero
    11284 
    11285 > select #2
    11286 
    11287 4 models selected 
    11288 
    11289 > select #1-60: 382, 353,438,230,442,466,207, 234, 227
    11290 
    11291 1734 atoms, 1634 bonds, 180 residues, 20 models selected 
    11292 
    11293 > show sel & #53 atoms
    11294 
    11295 > select #53
    11296 
    11297 3905 atoms, 3986 bonds, 515 residues, 1 model selected 
    11298 
    11299 > show #1 target m
    11300 
    11301 > hide #1 models
    11302 
    11303 > hide #53 models
    11304 
    11305 > select subtract #53
    11306 
    11307 Nothing selected 
    11308 
    11309 > hide #!2 models
    11310 
    11311 > show #!4 models
    11312 
    11313 > show #!5 models
    11314 
    11315 > save /Users/dout2/Downloads/OAT1_ligand_Colored_domain.cxs includeMaps true
    11316 
    11317 > show #1 models
    11318 
    11319 > hide #!4 models
    11320 
    11321 > hide #!5 models
    11322 
    11323 > hide #1 models
    11324 
    11325 > show #53 models
    11326 
    11327 > show #!2 models
    11328 
    11329 > select #53:1-317
    11330 
    11331 2371 atoms, 2418 bonds, 313 residues, 1 model selected 
    11332 
    11333 > color sel #a166d1ff
    11334 
    11335 > select #53:318-550
    11336 
    11337 1515 atoms, 1548 bonds, 201 residues, 1 model selected 
    11338 
    11339 > color sel #3ec0c2ff
    11340 
    11341 > select clear
    11342 
    11343 > select add #53
    11344 
    11345 3905 atoms, 3986 bonds, 515 residues, 1 model selected 
    11346 
    11347 > select add #51
    11348 
    11349 8185 atoms, 8367 bonds, 1067 residues, 2 models selected 
    11350 
    11351 > select add #49
    11352 
    11353 12127 atoms, 12333 bonds, 1637 residues, 4 models selected 
    11354 
    11355 > select add #47
    11356 
    11357 15922 atoms, 16217 bonds, 3 pseudobonds, 2132 residues, 7 models selected 
    11358 
    11359 > select #1-53:318-550
    11360 
    11361 31000 atoms, 31598 bonds, 10 pseudobonds, 4147 residues, 25 models selected 
    11362 
    11363 > show #1 models
    11364 
    11365 > hide #!2 models
    11366 
    11367 > color (#1,53 & sel) #3ec0c2ff
    11368 
    11369 > hide #1 models
    11370 
    11371 > show #!5 models
    11372 
    11373 > color (#53#!5 & sel) #3ec0c2ff
    11374 
    11375 > show #8 models
    11376 
    11377 > color (#8,53#!5 & sel) #3ec0c2ff
    11378 
    11379 > show #!12 models
    11380 
    11381 > color (#8,53#!5,12 & sel) #3ec0c2ff
    11382 
    11383 > show #15 models
    11384 
    11385 > color (#8,15,53#!5,12 & sel) #3ec0c2ff
    11386 
    11387 > show #!18 models
    11388 
    11389 > color (#8,15,53#!5,12,18 & sel) #3ec0c2ff
    11390 
    11391 > show #21 models
    11392 
    11393 > color (#8,15,21,53#!5,12,18 & sel) #3ec0c2ff
    11394 
    11395 > show #!24 models
    11396 
    11397 > show #!26 models
    11398 
    11399 > color (#8,15,21,53#!5,12,18,24,26 & sel) #3ec0c2ff
    11400 
    11401 > show #30 models
    11402 
    11403 > show #33 models
    11404 
    11405 > show #!34 models
    11406 
    11407 > show #!24 target m
    11408 
    11409 > show #37 models
    11410 
    11411 > color (#8,15,21,30,33,37,53#!5,12,18,24,26,34 & sel) #3ec0c2ff
    11412 
    11413 > show #!41 models
    11414 
    11415 > show #!43 models
    11416 
    11417 > show #!45 models
    11418 
    11419 > show #!47 models
    11420 
    11421 > show #!49 models
    11422 
    11423 > show #!51 models
    11424 
    11425 > hide #53 models
    11426 
    11427 > show #53 models
    11428 
    11429 > color (#8,15,21,30,33,37,53#!5,12,18,24,26,34,41,43,45,47,49,51 & sel)
    11430 > #3ec0c2ff
    11431 
    11432 > select #1-53:1-317
    11433 
    11434 47755 atoms, 48809 bonds, 17 pseudobonds, 6237 residues, 29 models selected 
    11435 
    11436 > color (#8,15,21,30,33,37,53#!5,12,18,24,26,34,41,43,45,47,49,51 & sel)
    11437 > #a166d1ff
    11438 
    11439 > show #1 models
    11440 
    11441 > color (#1,8,15,21,30,33,37,53#!5,12,18,24,26,34,41,43,45,47,49,51 & sel)
    11442 > #a166d1ff
    11443 
    11444 > save /Users/dout2/Downloads/OAT1_ligand_Colored_domain.cxs includeMaps true
    11445 
    11446 > select #53
    11447 
    11448 3905 atoms, 3986 bonds, 515 residues, 1 model selected 
    11449 
    11450 > show target m
    11451 
    11452 > show
    11453 > #1,5-6,8,12,15,18-19,21,24-26,30-31,33-35,37-38,41,45,47-49,51,53#43.1#!2-4,7,9-11,13-14,16-17,20,22-23,27-29,32,36,39-40,42-44,46,50#!2.1#!3.3#!4.1#!7.1#!9.3#!10.1#!11.3#!13.3#!14.1#!16.3#!17.1#!20.1#!22.3#!23.1#!27.1#!28.3#!29.1#!32.1#!36.1#!39.1#!40.1#!42.3#!43.2#!44.1#!46.1#!50.1#!3.3.1#!9.3.1#!11.3.1#!13.3.1#!16.3.1#!22.3.1#!28.3.1#!42.3.1
    11454 > target m
    11455 
    11456 > select #53
    11457 
    11458 3905 atoms, 3986 bonds, 515 residues, 1 model selected 
    11459 
    11460 > hide target m
    11461 
    11462 > select #53
    11463 
    11464 3905 atoms, 3986 bonds, 515 residues, 1 model selected 
    11465 
    11466 > show #53 models
    11467 
    11468 > select subtract #53
    11469 
    11470 Nothing selected 
    11471 
    11472 > hide #53 models
    11473 
    11474 > show #!5 models
    11475 
    11476 > select #1-60: 382, 353,438,230,442,466,207, 234, 227
    11477 
    11478 1734 atoms, 1634 bonds, 180 residues, 20 models selected 
    11479 
    11480 > show sel & #!5 atoms
    11481 
    11482 > hide sel & #!5 cartoons
    11483 
    11484 > show sel & #!5 cartoons
    11485 
    11486 > show #53 models
    11487 
    11488 > hide #!5 models
    11489 
    11490 > show #1 models
    11491 
    11492 > hide #1 models
    11493 
    11494 > show #!5 models
    11495 
    11496 > hide #!5 models
    11497 
    11498 > hide #53 models
    11499 
    11500 > select add #53
    11501 
    11502 5552 atoms, 5538 bonds, 686 residues, 23 models selected 
    11503 
    11504 > select add #51
    11505 
    11506 9745 atoms, 9837 bonds, 1229 residues, 23 models selected 
    11507 
    11508 > select subtract #51
    11509 
    11510 5465 atoms, 5456 bonds, 677 residues, 22 models selected 
    11511 
    11512 > select subtract #53
    11513 
    11514 1560 atoms, 1470 bonds, 162 residues, 20 models selected 
    11515 
    11516 > select add #53
    11517 
    11518 5465 atoms, 5456 bonds, 677 residues, 21 models selected 
    11519 
    11520 > select subtract #53
    11521 
    11522 1560 atoms, 1470 bonds, 162 residues, 20 models selected 
    11523 
    11524 > select add #49
    11525 
    11526 5415 atoms, 5354 bonds, 723 residues, 20 models selected 
    11527 
    11528 > select subtract #49
    11529 
    11530 1473 atoms, 1388 bonds, 153 residues, 19 models selected 
    11531 
    11532 > select add #47
    11533 
    11534 5187 atoms, 5196 bonds, 3 pseudobonds, 639 residues, 19 models selected 
    11535 
    11536 > select subtract #47
    11537 
    11538 1392 atoms, 1312 bonds, 144 residues, 17 models selected 
    11539 
    11540 > select add #45
    11541 
    11542 5112 atoms, 5129 bonds, 3 pseudobonds, 627 residues, 18 models selected 
    11543 
    11544 > select subtract #45
    11545 
    11546 1305 atoms, 1230 bonds, 135 residues, 16 models selected 
    11547 
    11548 > select add #43
    11549 
    11550 5025 atoms, 5047 bonds, 3 pseudobonds, 618 residues, 17 models selected 
    11551 
    11552 > select subtract #43
    11553 
    11554 1218 atoms, 1148 bonds, 126 residues, 15 models selected 
    11555 
    11556 > select add #41
    11557 
    11558 5506 atoms, 5547 bonds, 1 pseudobond, 681 residues, 15 models selected 
    11559 
    11560 > select subtract #41
    11561 
    11562 1131 atoms, 1066 bonds, 117 residues, 13 models selected 
    11563 
    11564 > select add #37
    11565 
    11566 5419 atoms, 5465 bonds, 672 residues, 13 models selected 
    11567 
    11568 > select subtract #37
    11569 
    11570 1044 atoms, 984 bonds, 108 residues, 12 models selected 
    11571 
    11572 > select add #34
    11573 
    11574 4744 atoms, 4778 bonds, 5 pseudobonds, 586 residues, 13 models selected 
    11575 
    11576 > select subtract #34
    11577 
    11578 957 atoms, 902 bonds, 99 residues, 11 models selected 
    11579 
    11580 > select add #33
    11581 
    11582 5197 atoms, 5213 bonds, 681 residues, 11 models selected 
    11583 
    11584 > select subtract #33
    11585 
    11586 870 atoms, 820 bonds, 90 residues, 10 models selected 
    11587 
    11588 > show #53 models
    11589 
    11590 > select #53: 382, 353,438,230,442,466,207, 234, 227
    11591 
    11592 87 atoms, 82 bonds, 9 residues, 1 model selected 
    11593 
    11594 > hide #53 models
    11595 
    11596 > show #53 models
    11597 
    11598 > select add #53
    11599 
    11600 3905 atoms, 3986 bonds, 515 residues, 1 model selected 
    11601 
    11602 > select subtract #53
    11603 
    11604 Nothing selected 
    11605 
    11606 > show #!2 models
    11607 
    11608 > show #2.1 models
    11609 
    11610 > ui tool show "Color Zone"
    11611 
    11612 > color zone #2 near #53 distance 4.98
    11613 
    11614 > hide #!2 models
    11615 
    11616 > hide #2.1 models
    11617 
    11618 > show #!3.3 models
    11619 
    11620 > select add #3.3
    11621 
    11622 2 models selected 
    11623 
    11624 > select subtract #3.3
    11625 
    11626 Nothing selected 
    11627 
    11628 > select add #3
    11629 
    11630 3 models selected 
    11631 
    11632 > color #3.3 #a166d1ff models
    11633 
    11634 > color #3 #b2b2b2ff models
    11635 
    11636 > show #2.1 models
    11637 
    11638 > hide #!2.1 models
    11639 
    11640 > show #3.3.1 models
    11641 
    11642 > color #3.3.1 #b2b2b280
    11643 
    11644 > select #53/A:346
    11645 
    11646 14 atoms, 15 bonds, 1 residue, 1 model selected 
    11647 
    11648 > color #3.3.1 #b2b2b24d
    11649 
    11650 > select #1-53: 601
    11651 
    11652 417 atoms, 431 bonds, 17 residues, 17 models selected 
    11653 
    11654 > color (#53 & sel) yellow
    11655 
    11656 > color (#53 & sel) byhetero
    11657 
    11658 > color (#53 & sel) hot pink
    11659 
    11660 > ui tool show "Color Actions"
    11661 
    11662 > color sel brown
    11663 
    11664 > color (#53 & sel) byhetero
    11665 
    11666 > color (#53 & sel) hot pink
    11667 
    11668 > color (#53 & sel) byhetero
    11669 
    11670 > ui tool show "Hide Dust"
    11671 
    11672 > surface dust #2 size 4.98
    11673 
    11674 > surface dust #3.3 size 4.98
    11675 
    11676 > surface dust #3.3 size 5.08
    11677 
    11678 > surface dust #3.3 size 5.18
    11679 
    11680 > surface dust #3.3 size 5.28
    11681 
    11682 > surface dust #3.3 size 5.38
    11683 
    11684 > surface dust #3.3 size 5.48
    11685 
    11686 > surface dust #3.3 size 5.58
    11687 
    11688 > surface dust #3.3 size 5.68
    11689 
    11690 > surface dust #3.3 size 5.78
    11691 
    11692 > surface dust #3.3 size 5.88
    11693 
    11694 > surface dust #3.3 size 5.98
    11695 
    11696 > surface dust #3.3 size 6.08
    11697 
    11698 > surface dust #3.3 size 6.18
    11699 
    11700 > surface dust #3.3 size 6.28
    11701 
    11702 > surface dust #3.3 size 6.38
    11703 
    11704 > surface dust #3.3 size 6.48
    11705 
    11706 > surface dust #3.3 size 6.58
    11707 
    11708 > surface dust #3.3 size 6.68
    11709 
    11710 > surface dust #3.3 size 6.78
    11711 
    11712 > surface dust #3.3 size 6.88
    11713 
    11714 > surface dust #3.3 size 6.98
    11715 
    11716 > surface dust #3.3 size 7.08
    11717 
    11718 > surface dust #3.3 size 7.18
    11719 
    11720 > select add #1
    11721 
    11722 4303 atoms, 4397 bonds, 531 residues, 17 models selected 
    11723 
    11724 > select subtract #1
    11725 
    11726 398 atoms, 411 bonds, 16 residues, 16 models selected 
    11727 
    11728 > select add #5
    11729 
    11730 4153 atoms, 4255 bonds, 5 pseudobonds, 501 residues, 17 models selected 
    11731 
    11732 > select subtract #5
    11733 
    11734 379 atoms, 391 bonds, 15 residues, 15 models selected 
    11735 
    11736 > select add #3.3.1
    11737 
    11738 379 atoms, 391 bonds, 15 residues, 17 models selected 
    11739 
    11740 > surface dust #3.3 size 7.28
    11741 
    11742 > surface dust #3.3 size 7.38
    11743 
    11744 > surface dust #3.3 size 7.48
    11745 
    11746 > surface dust #3.3 size 7.38
    11747 
    11748 > surface dust #3.3 size 7.28
    11749 
    11750 > surface dust #3.3 size 2
    11751 
    11752 > surface dust #3.3 size 5
    11753 
    11754 > surface dust #3.3 size 50
    11755 
    11756 > surface dust #3.3 size 1
    11757 
    11758 > surface dust #3.3 size 10
    11759 
    11760 > surface dust #3.3 size 5
    11761 
    11762 > volume #3.3 level 0.008322
    11763 
    11764 > surface dust #3.3 size 3
    11765 
    11766 > volume #3.3 level 0.008386
    11767 
    11768 > select clear
    11769 
    11770 > save /Users/dout2/Downloads/OAT1_ligand_Colored_domain.cxs includeMaps true
    11771 
    11772 > hide #!3 models
    11773 
    11774 > hide #!3.3 models
    11775 
    11776 > hide #3.3.1 models
    11777 
    11778 > show #!2 models
    11779 
    11780 > select add #2
    11781 
    11782 2 models selected 
    11783 
    11784 > show #2.1 models
    11785 
    11786 > hide #53 models
    11787 
    11788 > show #53 models
    11789 
    11790 > color zone #2 near #53 distance 4.98
    11791 
    11792 > hide #!2.1 models
    11793 
    11794 > hide #!2 models
    11795 
    11796 > show #!2 models
    11797 
    11798 > select add #53
    11799 
    11800 3905 atoms, 3986 bonds, 515 residues, 3 models selected 
    11801 
    11802 > show #2.1 models
    11803 
    11804 > color zone #2 near #53 distance 5.08
    11805 
    11806 > color zone #2 near #53 distance 5.18
    11807 
    11808 > color zone #2 near #53 distance 5.28
    11809 
    11810 > color zone #2 near #53 distance 5.38
    11811 
    11812 > color zone #2 near #53 distance 5.48
    11813 
    11814 > color zone #2 near #53 distance 5.58
    11815 
    11816 > color zone #2 near #53 distance 5.68
    11817 
    11818 > color zone #2 near #53 distance 5.58
    11819 
    11820 > color zone #2 near #53 distance 5.48
    11821 
    11822 > color zone #2 near #53 distance 5.38
    11823 
    11824 > color zone #2 near #53 distance 5.28
    11825 
    11826 > color zone #2 near #53 distance 5.18
    11827 
    11828 > color zone #2 near #53 distance 5.08
    11829 
    11830 > color zone #2 near #53 distance 4.98
    11831 
    11832 > color single #2
    11833 
    11834 > color zone #2 near #53 distance 4.98
    11835 
    11836 > select clear
    11837 
    11838 > view
    11839 
    11840 > surface dust #2 size 4.98
    11841 
    11842 > surface dust #2 size 1
    11843 
    11844 > surface dust #2 size 10
    11845 
    11846 > lighting soft
    11847 
    11848 > color zone #2 near #53 distance 2
    11849 
    11850 > select clear
    11851 
    11852 > select add #2
    11853 
    11854 2 models selected 
    11855 No visible atoms or bonds selected 
    11856 
    11857 > hide #53 models
    11858 
    11859 > color #2 #e599004e models
    11860 
    11861 > select clear
    11862 
    11863 > color #2 #e59900ff models
    11864 
    11865 > color zone #2 near #53 distance 5
    11866 
    11867 > color zone #2 near #53 distance 4
    11868 
    11869 > color zone #2 near #53 distance 3.9
    11870 
    11871 > color zone #2 near #53 distance 3.8
    11872 
    11873 > color zone #2 near #53 distance 3.7
    11874 
    11875 > color zone #2 near #53 distance 3.6
    11876 
    11877 > color zone #2 near #53 distance 3.5
    11878 
    11879 > color zone #2 near #53 distance 3.4
    11880 
    11881 > color zone #2 near #53 distance 3.3
    11882 
    11883 > color zone #2 near #53 distance 3.2
    11884 
    11885 > color zone #2 near #53 distance 3.1
    11886 
    11887 > color zone #2 near #53 distance 3
    11888 
    11889 > color zone #2 near #53 distance 3.1
    11890 
    11891 > color zone #2 near #53 distance 3.2
    11892 
    11893 > color zone #2 near #53 distance 3.3
    11894 
    11895 > color zone #2 near #53 distance 3.4
    11896 
    11897 > color zone #2 near #53 distance 3.5
    11898 
    11899 > color zone #2 near #53 distance 3.6
    11900 
    11901 > color zone #2 near #53 distance 3.7
    11902 
    11903 > graphics silhouettes true
    11904 
    11905 > lighting shadows true intensity 0.5
    11906 
    11907 > lighting flat
    11908 
    11909 > color zone #2 near #53 distance 3.8
    11910 
    11911 > color zone #2 near #53 distance 3.9
    11912 
    11913 > color zone #2 near #53 distance 4
    11914 
    11915 > color zone #2 near #53 distance 4.1
    11916 
    11917 > color zone #2 near #53 distance 4.2
    11918 
    11919 > color zone #2 near #53 distance 4.3
    11920 
    11921 > color zone #2 near #53 distance 4.4
    11922 
    11923 > color zone #2 near #53 distance 4.5
    11924 
    11925 > color zone #2 near #53 distance 4.6
    11926 
    11927 > color zone #2 near #53 distance 4.7
    11928 
    11929 > color zone #2 near #53 distance 4.8
    11930 
    11931 > color zone #2 near #53 distance 4.9
    11932 
    11933 > color zone #2 near #53 distance 4.8
    11934 
    11935 > color zone #2 near #53 distance 4.7
    11936 
    11937 > color zone #2 near #53 distance 4.6
    11938 
    11939 > color zone #2 near #53 distance 4.5
    11940 
    11941 > color zone #2 near #53 distance 4.4
    11942 
    11943 > color zone #2 near #53 distance 4.3
    11944 
    11945 > color zone #2 near #53 distance 4.2
    11946 
    11947 > color zone #2 near #53 distance 4.1
    11948 
    11949 > color zone #2 near #53 distance 4
    11950 
    11951 > color zone #2 near #53 distance 3.9
    11952 
    11953 > color zone #2 near #53 distance 3.8
    11954 
    11955 > color zone #2 near #53 distance 3.7
    11956 
    11957 > color zone #2 near #53 distance 3.6
    11958 
    11959 > color zone #2 near #53 distance 3.5
    11960 
    11961 > color zone #2 near #53 distance 3.4
    11962 
    11963 > color zone #2 near #53 distance 3.3
    11964 
    11965 > color zone #2 near #53 distance 3.2
    11966 
    11967 > color zone #2 near #53 distance 3.1
    11968 
    11969 > color zone #2 near #53 distance 3
    11970 
    11971 > color zone #2 near #53 distance 2.9
    11972 
    11973 Drag select of 2 rOAT1-AZT_IF.mrc 
    11974 
    11975 > volume #2 level 0.009345
    11976 
    11977 > color #2 #e5990000 models
    11978 
    11979 > color zone #2 near #53 distance 2.9
    11980 
    11981 > select clear
    11982 
    11983 > color #2 white models
    11984 
    11985 > color zone #2 near #53 distance 2.9
    11986 
    11987 > lighting full
    11988 
    11989 > lighting flat
    11990 
    11991 > lighting full
    11992 
    11993 > lighting soft
    11994 
    11995 > lighting full
    11996 
    11997 > lighting soft
    11998 
    11999 > select clear
    12000 
    12001 > color #2 #ffffff00 models
    12002 
    12003 > color zone #2 near #53 distance 2.9
    12004 
    12005 > select clear
    12006 
    12007 > graphics silhouettes false
    12008 
    12009 > volume #2 level 0.008036
    12010 
    12011 > view
    12012 
    12013 > view orient
    12014 
    12015 > ui tool show "Side View"
    12016 
    12017 > volume #2 level 0.008909
    12018 
    12019 > lighting full
    12020 
    12021 > lighting soft
    12022 
    12023 > lighting flat
    12024 
    12025 > graphics silhouettes false
    12026 
    12027 > lighting soft
    12028 
    12029 > color #2 white models
    12030 
    12031 > color zone #2 near #53 distance 2.9
    12032 
    12033 > color #2.1 #ffffff00
    12034 
    12035 > color zone #2 near #53 distance 2.9
    12036 
    12037 > color #2.1 black
    12038 
    12039 > color zone #2 near #53 distance 2.9
    12040 
    12041 > color #2.1 #fffb00ff
    12042 
    12043 > color zone #2 near #53 distance 2.9
    12044 
    12045 > color #2.1 white
    12046 
    12047 > color #2.1 #ffffff00
    12048 
    12049 > color #2.1 white
    12050 
    12051 > color zone #2 near #53 distance 2.9
    12052 
    12053 > color #2.1 #ffffff00
    12054 
    12055 > color zone #2 near #53 distance 2.9
    12056 
    12057 > select #1-53: 601
    12058 
    12059 417 atoms, 431 bonds, 17 residues, 17 models selected 
    12060 
    12061 > color #2 hot pink
    12062 
    12063 > select #53: 601
    12064 
    12065 19 atoms, 20 bonds, 1 residue, 1 model selected 
    12066 
    12067 > color #2 hot pink
    12068 
    12069 > color zone #2 near #53 distance 2.9
    12070 
    12071 > color #2 white models
    12072 
    12073 > color zone #2 near #53 distance 2.9
    12074 
    12075 > color zone #2 near #53 distance 3
    12076 
    12077 > color zone #2 near #53 distance 3.1
    12078 
    12079 > color zone #2 near #53 distance 3.2
    12080 
    12081 > color zone #2 near #53 distance 3.3
    12082 
    12083 > color zone #2 near #53 distance 3.4
    12084 
    12085 > color zone #2 near #53 distance 3.5
    12086 
    12087 > color zone #2 near #53 distance 3.6
    12088 
    12089 > color zone #2 near #53 distance 3.7
    12090 
    12091 > color zone #2 near #53 distance 3.8
    12092 
    12093 > color zone #2 near #53 distance 3.9
    12094 
    12095 > color zone #2 near #53 distance 4
    12096 
    12097 > surface dust #2 size 4
    12098 
    12099 > color #2.1 #ffffff00
    12100 
    12101 > color zone #2 near #53 distance 4
    12102 
    12103 > color zone #2 near #53 distance 4.1
    12104 
    12105 > color zone #2 near #53 distance 4.2
    12106 
    12107 > color zone #2 near #53 distance 4.3
    12108 
    12109 > color zone #2 near #53 distance 4.4
    12110 
    12111 > color zone #2 near #53 distance 4.5
    12112 
    12113 > color zone #2 near #53 distance 4.6
    12114 
    12115 > color zone #2 near #53 distance 4.7
    12116 
    12117 > color zone #2 near #53 distance 4.8
    12118 
    12119 > color zone #2 near #53 distance 4.9
    12120 
    12121 > color zone #2 near #53 distance 5
    12122 
    12123 > color zone #2 near #53 distance 5.1
    12124 
    12125 > color zone #2 near #53 distance 5.2
    12126 
    12127 > color zone #2 near #53 distance 5.3
    12128 
    12129 > color zone #2 near #53 distance 5.2
    12130 
    12131 > color zone #2 near #53 distance 5.1
    12132 
    12133 > color zone #2 near #53 distance 5
    12134 
    12135 > color #2 #e59900ff models
    12136 
    12137 > color zone #2 near #53 distance 5
    12138 
    12139 > color zone #2 near #53 distance 4.9
    12140 
    12141 > color zone #2 near #53 distance 4.8
    12142 
    12143 > color zone #2 near #53 distance 4.7
    12144 
    12145 > color zone #2 near #53 distance 4.6
    12146 
    12147 > color zone #2 near #53 distance 4.5
    12148 
    12149 > color zone #2 near #53 distance 4.4
    12150 
    12151 > color zone #2 near #53 distance 4.3
    12152 
    12153 > color zone #2 near #53 distance 4.2
    12154 
    12155 > color zone #2 near #53 distance 4.1
    12156 
    12157 > color zone #2 near #53 distance 4
    12158 
    12159 > color zone #2 near #53 distance 3.9
    12160 
    12161 > color zone #2 near #53 distance 3.8
    12162 
    12163 > color zone #2 near #53 distance 3.7
    12164 
    12165 > color zone #2 near #53 distance 3.6
    12166 
    12167 > color zone #2 near #53 distance 3.5
    12168 
    12169 > color zone #2 near #53 distance 3.4
    12170 
    12171 > color zone #2 near #53 distance 3.3
    12172 
    12173 > color zone #2 near #53 distance 3.2
    12174 
    12175 > color zone #2 near #53 distance 3.1
    12176 
    12177 > color zone #2 near #53 distance 3
    12178 
    12179 > surface dust #2 size 1
    12180 
    12181 > surface dust #2 size 10
    12182 
    12183 > volume #2 level 0.009926
    12184 
    12185 > volume #2 level 0.009636
    12186 
    12187 > volume #2 level 0.007891
    12188 
    12189 > volume #2 level 0.006146
    12190 
    12191 > volume #2 level 0.008327
    12192 
    12193 > color zone #2 near #53 distance 3.1
    12194 
    12195 > color zone #2 near #53 distance 3.2
    12196 
    12197 > color zone #2 near #53 distance 3.3
    12198 
    12199 > color zone #2 near #53 distance 3.4
    12200 
    12201 > color zone #2 near #53 distance 3.5
    12202 
    12203 > color zone #2 near #53 distance 3.6
    12204 
    12205 > color zone #2 near #53 distance 3.7
    12206 
    12207 > color zone #2 near #53 distance 3.8
    12208 
    12209 > color zone #2 near #53 distance 3.9
    12210 
    12211 > color zone #2 near #53 distance 4
    12212 
    12213 > color zone #2 near #53 distance 4.1
    12214 
    12215 > color zone #2 near #53 distance 4.2
    12216 
    12217 > color zone #2 near #53 distance 4.1
    12218 
    12219 > color zone #2 near #53 distance 4
    12220 
    12221 > color zone #2 near #53 distance 3.9
    12222 
    12223 > color zone #2 near #53 distance 3.8
    12224 
    12225 > color zone #2 near #53 distance 3.7
    12226 
    12227 > color zone #2 near #53 distance 3.6
    12228 
    12229 > color zone #2 near #53 distance 3.5
    12230 
    12231 > color zone #2 near #53 distance 3.4
    12232 
    12233 > color zone #2 near #53 distance 3.3
    12234 
    12235 > color zone #2 near #53 distance 3.2
    12236 
    12237 > color zone #2 near #53 distance 3.1
    12238 
    12239 > color zone #2 near #53 distance 3
    12240 
    12241 > color zone #2 near #53 distance 2.9
    12242 
    12243 > color zone #2 near #53 distance 2.8
    12244 
    12245 > color zone #2 near #53 distance 2.7
    12246 
    12247 > volume #2 level 0.008036
    12248 
    12249 > hide #!2 models
    12250 
    12251 > hide #2.1 models
    12252 
    12253 > show #53 models
    12254 
    12255 > show #8 models
    12256 
    12257 > show #!49 models
    12258 
    12259 > hide #!49 models
    12260 
    12261 > hide #8 models
    12262 
    12263 > save /Users/dout2/Downloads/OAT1_ligand_Colored_domain.cxs includeMaps true
    12264 
    12265 > hide #53 models
    12266 
    12267 > select add #53
    12268 
    12269 3905 atoms, 3986 bonds, 515 residues, 1 model selected 
    12270 
    12271 > select subtract #53
    12272 
    12273 Nothing selected 
    12274 
    12275 > show #!2 models
    12276 
    12277 > select add #2
    12278 
    12279 2 models selected 
    12280 
    12281 > show #2.1 models
    12282 
    12283 > color zone #2 near #53 distance 2.8
    12284 
    12285 > color zone #2 near #53 distance 2.9
    12286 
    12287 > color zone #2 near #53 distance 3
    12288 
    12289 > color zone #2 near #53 distance 3.1
    12290 
    12291 > select clear
    12292 
    12293 > volume splitbyzone #2
    12294 
    12295 Opened rOAT1-AZT_IF.mrc 0 as #52.1, grid size 320,320,320, pixel 0.83, shown
    12296 at level 0.00804, step 1, values float32 
    12297 Opened rOAT1-AZT_IF.mrc 1 as #52.2, grid size 320,320,320, pixel 0.83, shown
    12298 at level 0.00804, step 1, values float32 
    12299 Opened rOAT1-AZT_IF.mrc 2 as #52.3, grid size 320,320,320, pixel 0.83, shown
    12300 at level 0.00804, step 1, values float32 
    12301 Opened rOAT1-AZT_IF.mrc 3 as #52.4, grid size 320,320,320, pixel 0.83, shown
    12302 at level 0.00804, step 1, values float32 
    12303 Opened rOAT1-AZT_IF.mrc 4 as #52.5, grid size 320,320,320, pixel 0.83, shown
    12304 at level 0.00804, step 1, values float32 
    12305 Opened rOAT1-AZT_IF.mrc 5 as #52.6, grid size 320,320,320, pixel 0.83, shown
    12306 at level 0.00804, step 1, values float32 
    12307 
    12308 > hide #!52.1 models
    12309 
    12310 > show #!52.1 models
    12311 
    12312 > hide #!52.1 models
    12313 
    12314 > hide #!52.2 models
    12315 
    12316 > show #!52.2 models
    12317 
    12318 > show #!52.1 models
    12319 
    12320 > volume #52.1 level 0.0124
    12321 
    12322 > surface dust #52.2 size 4.98
    12323 
    12324 > surface dust #52.1 size 4.98
    12325 
    12326 > volume #52.1 level 0.008531
    12327 
    12328 > hide #!52.6 models
    12329 
    12330 > show #!52.6 models
    12331 
    12332 > hide #!52.5 models
    12333 
    12334 > show #!52.5 models
    12335 
    12336 > show #53 models
    12337 
    12338 > hide #!52 models
    12339 
    12340 > show #!52 models
    12341 
    12342 > hide #!52 models
    12343 
    12344 > select #53: 601
    12345 
    12346 19 atoms, 20 bonds, 1 residue, 1 model selected 
    12347 
    12348 > color sel hot pink
    12349 
    12350 > show #!2 models
    12351 
    12352 > color zone #2 near #53 distance 3.1
    12353 
    12354 > close #52
    12355 
    12356 > volume splitbyzone #2
    12357 
    12358 Opened rOAT1-AZT_IF.mrc 0 as #52.1, grid size 320,320,320, pixel 0.83, shown
    12359 at level 0.00804, step 1, values float32 
    12360 Opened rOAT1-AZT_IF.mrc 1 as #52.2, grid size 320,320,320, pixel 0.83, shown
    12361 at level 0.00804, step 1, values float32 
    12362 Opened rOAT1-AZT_IF.mrc 2 as #52.3, grid size 320,320,320, pixel 0.83, shown
    12363 at level 0.00804, step 1, values float32 
    12364 Opened rOAT1-AZT_IF.mrc 3 as #52.4, grid size 320,320,320, pixel 0.83, shown
    12365 at level 0.00804, step 1, values float32 
    12366 
    12367 > volume #52.1 level 0.01043
    12368 
    12369 > surface dust #52.2 size 4.98
    12370 
    12371 > surface dust #52.1 size 4.98
    12372 
    12373 > surface dust #52.3 size 4.98
    12374 
    12375 > volume #52.3 level 0.009403
    12376 
    12377 > surface dust #52.3 size 4.98
    12378 
    12379 > select clear
    12380 
    12381 > volume #52.1 level 0.008861
    12382 
    12383 > volume #52.1 level 0.009273
    12384 
    12385 > save
    12386 > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-TFV_IF.png
    12387 > width 809 height 738 supersample 3 transparentBackground true
    12388 
    12389 > hide #53 models
    12390 
    12391 > save
    12392 > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-TFV_IF.png
    12393 > width 809 height 738 supersample 3 transparentBackground true
    12394 
    12395 > hide #!52 models
    12396 
    12397 > hide #!52.1 models
    12398 
    12399 > hide #!52.2 models
    12400 
    12401 > hide #!52.3 models
    12402 
    12403 > hide #!52.4 models
    12404 
    12405 > hide #2.1 models
    12406 
    12407 > show #!5 models
    12408 
    12409 > show #!4 models
    12410 
    12411 > show #4.1 models
    12412 
    12413 > color #4 #e59900ff models
    12414 
    12415 > hide #!4 models
    12416 
    12417 > select #5: 601
    12418 
    12419 19 atoms, 20 bonds, 1 residue, 1 model selected 
    12420 
    12421 > color sel hot pink
    12422 
    12423 > save /Users/dout2/Downloads/OAT1_ligand_Colored_domain.cxs includeMaps true
    12424 
    12425 > select clear
    12426 
    12427 > show #!4 models
    12428 
    12429 > color zone #4 near #5 distance 4.98
    12430 
    12431 > color zone #4 near #5 distance 3
    12432 
    12433 > volume #4 level 0.00975
    12434 
    12435 > color zone #4 near #5 distance 2.9
    12436 
    12437 > color zone #4 near #5 distance 2.8
    12438 
    12439 > color zone #4 near #5 distance 2.7
    12440 
    12441 > color zone #4 near #5 distance 2.6
    12442 
    12443 > color zone #4 near #5 distance 2.5
    12444 
    12445 > color zone #4 near #5 distance 2.4
    12446 
    12447 > color zone #4 near #5 distance 2.3
    12448 
    12449 > color zone #4 near #5 distance 2.2
    12450 
    12451 > color zone #4 near #5 distance 2.1
    12452 
    12453 > color zone #4 near #5 distance 2
    12454 
    12455 > color zone #4 near #5 distance 3
    12456 
    12457 > color zone #4 near #5 distance 4
    12458 
    12459 > color zone #4 near #5 distance 3
    12460 
    12461 > color zone #4 near #5 distance 2
    12462 
    12463 > color zone #4 near #5 distance 2.5
    12464 
    12465 > volume splitbyzone #4
    12466 
    12467 Opened rOAT1-AZT_OF.mrc 0 as #54.1, grid size 320,320,320, pixel 0.83, shown
    12468 at level 0.00975, step 1, values float32 
    12469 Opened rOAT1-AZT_OF.mrc 1 as #54.2, grid size 320,320,320, pixel 0.83, shown
    12470 at level 0.00975, step 1, values float32 
    12471 Opened rOAT1-AZT_OF.mrc 2 as #54.3, grid size 320,320,320, pixel 0.83, shown
    12472 at level 0.00975, step 1, values float32 
    12473 Opened rOAT1-AZT_OF.mrc 3 as #54.4, grid size 320,320,320, pixel 0.83, shown
    12474 at level 0.00975, step 1, values float32 
    12475 
    12476 > hide #!5 models
    12477 
    12478 > surface dust #54.1 size 4.98
    12479 
    12480 > surface dust #54.2 size 4.98
    12481 
    12482 > surface dust #54.3 size 4.98
    12483 
    12484 > volume #54.3 level 0.007096
    12485 
    12486 > surface dust #54.4 size 4.98
    12487 
    12488 > surface dust #54.2 size 4.98
    12489 
    12490 > surface dust #54.1 size 4.98
    12491 
    12492 > surface dust #54.4 size 4.98
    12493 
    12494 > surface dust #54.3 size 4.98
    12495 
    12496 > select clear
    12497 
    12498 > volume #54.3 level 0.008865
    12499 
    12500 > hide #!54 models
    12501 
    12502 > show #!5 models
    12503 
    12504 > show #!12 models
    12505 
    12506 > hide #!12 models
    12507 
    12508 > show #!54 models
    12509 
    12510 > hide #!5 models
    12511 
    12512 > surface dust #54.1 size 1
    12513 
    12514 > surface dust #54.1 size 10
    12515 
    12516 > surface dust #54.1 size 8
    12517 
    12518 > surface dust #54.1 size 7
    12519 
    12520 > surface dust #54.1 size 6
    12521 
    12522 > surface dust #54.1 size 5
    12523 
    12524 > surface dust #54.1 size 6
    12525 
    12526 > save
    12527 > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-TFV_OF.png
    12528 > width 809 height 738 supersample 3 transparentBackground true
    12529 
    12530 > hide #!54 models
    12531 
    12532 > show #8 models
    12533 
    12534 > show #!7 models
    12535 
    12536 > show #7.1 models
    12537 
    12538 > color #7 #e59900ff models
    12539 
    12540 > select add #8
    12541 
    12542 3912 atoms, 3985 bonds, 522 residues, 1 model selected 
    12543 
    12544 > select subtract #8
    12545 
    12546 Nothing selected 
    12547 
    12548 > select #8: 601
    12549 
    12550 19 atoms, 19 bonds, 1 residue, 1 model selected 
    12551 
    12552 > color sel hot pink
    12553 
    12554 > select add #8
    12555 
    12556 3912 atoms, 3985 bonds, 522 residues, 1 model selected 
    12557 
    12558 > select subtract #8
    12559 
    12560 Nothing selected 
    12561 
    12562 > color zone #7 near #8 distance 2.5
    12563 
    12564 > volume splitbyzone #7
    12565 
    12566 Opened rOAT1-PBD_IF.mrc 0 as #55.1, grid size 320,320,320, pixel 0.83, shown
    12567 at level 0.0111, step 1, values float32 
    12568 Opened rOAT1-PBD_IF.mrc 1 as #55.2, grid size 320,320,320, pixel 0.83, shown
    12569 at level 0.0111, step 1, values float32 
    12570 Opened rOAT1-PBD_IF.mrc 2 as #55.3, grid size 320,320,320, pixel 0.83, shown
    12571 at level 0.0111, step 1, values float32 
    12572 Opened rOAT1-PBD_IF.mrc 3 as #55.4, grid size 320,320,320, pixel 0.83, shown
    12573 at level 0.0111, step 1, values float32 
    12574 
    12575 > surface dust #55.1 size 4.98
    12576 
    12577 > surface dust #55.2 size 4.98
    12578 
    12579 > surface dust #55.3 size 4.98
    12580 
    12581 > surface dust #55.4 size 4.98
    12582 
    12583 > volume #55.1 level 0.01136
    12584 
    12585 > surface dust #55.4 size 7
    12586 
    12587 > volume #55.1 level 0.01088
    12588 
    12589 > surface dust #55.1 size 4.98
    12590 
    12591 > surface dust #55.1 size 7
    12592 
    12593 > surface dust #55.1 size 8
    12594 
    12595 > volume #55.1 level 0.009811
    12596 
    12597 > save
    12598 > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-PBD_IF.png
    12599 > width 809 height 738 supersample 3 transparentBackground true
    12600 
    12601 > volume #55.1 level 0.009096
    12602 
    12603 > save
    12604 > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-PBD_IF.png
    12605 > width 809 height 738 supersample 3 transparentBackground true
    12606 
    12607 > hide #!55 models
    12608 
    12609 > show #!54 models
    12610 
    12611 > hide #!54 models
    12612 
    12613 > show #!54 models
    12614 
    12615 > hide #!54 models
    12616 
    12617 > hide #8 models
    12618 
    12619 > show #!54 models
    12620 
    12621 > surface dust #54.1 size 6
    12622 
    12623 > volume #54.1 level 0.008735
    12624 
    12625 > volume #54.1 level 0.009565
    12626 
    12627 > save
    12628 > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-TFV_OF.png
    12629 > width 809 height 738 supersample 3 transparentBackground true
    12630 
    12631 > hide #!54 models
    12632 
    12633 > show #!52 models
    12634 
    12635 > show #!52.1 models
    12636 
    12637 > show #!52.2 models
    12638 
    12639 > show #!52.3 models
    12640 
    12641 > show #!52.4 models
    12642 
    12643 > volume #52.1 level 0.007805
    12644 
    12645 > surface dust #50 size 6
    12646 
    12647 > surface dust #52.2 size 6
    12648 
    12649 > surface dust #52.3 size 4.98
    12650 
    12651 > surface dust #52.3 size 6
    12652 
    12653 > surface dust #52.4 size 6
    12654 
    12655 > volume #52.1 level 0.008213
    12656 
    12657 > save
    12658 > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-TFV_IF.png
    12659 > width 809 height 738 supersample 3 transparentBackground true
    12660 
    12661 > hide #8 target m
    12662 
    12663 > hide #!52 models
    12664 
    12665 > show #!10 models
    12666 
    12667 > show #!12 models
    12668 
    12669 > show #10.1 models
    12670 
    12671 > color #10.1 #e599004d
    12672 
    12673 > color #10.1 #e59900ff
    12674 
    12675 > select #12: 601
    12676 
    12677 37 atoms, 37 bonds, 1 residue, 1 model selected 
    12678 
    12679 > color sel hot pink
    12680 
    12681 > select #12: 601
    12682 
    12683 37 atoms, 37 bonds, 1 residue, 1 model selected 
    12684 
    12685 > select clear
    12686 
    12687 > color zone #10 near #12 distance 2.5
    12688 
    12689 > volume #52.1 level 0.009419
    12690 
    12691 > volume #10 level 0.01032
    12692 
    12693 > volume #10 level 0.009917
    12694 
    12695 > color zone #10 near #12 distance 2
    12696 
    12697 > color zone #10 near #12 distance 2.3
    12698 
    12699 > color zone #10 near #12 distance 2.4
    12700 
    12701 > color zone #10 near #12 distance 2.5
    12702 
    12703 > surface dust #10 size 4.98
    12704 
    12705 > volume #10 level 0.01032
    12706 
    12707 > volume #10 level 0.009377
    12708 
    12709 > surface dust #10 size 6
    12710 
    12711 > volume #10 level 0.008296
    12712 
    12713 > surface dust #10 size 7
    12714 
    12715 > surface dust #10 size 8
    12716 
    12717 > volume #10 level 0.009782
    12718 
    12719 > volume #10 level 0.009647
    12720 
    12721 > color zone #10 near #12 distance 2.5
    12722 
    12723 > volume splitbyzone #10
    12724 
    12725 Opened rOAT1-PBD_OF.mrc 0 as #56.1, grid size 320,320,320, pixel 0.83, shown
    12726 at level 0.00965, step 1, values float32 
    12727 Opened rOAT1-PBD_OF.mrc 1 as #56.2, grid size 320,320,320, pixel 0.83, shown
    12728 at level 0.00965, step 1, values float32 
    12729 Opened rOAT1-PBD_OF.mrc 2 as #56.3, grid size 320,320,320, pixel 0.83, shown
    12730 at level 0.00965, step 1, values float32 
    12731 Opened rOAT1-PBD_OF.mrc 3 as #56.4, grid size 320,320,320, pixel 0.83, shown
    12732 at level 0.00965, step 1, values float32 
    12733 
    12734 > hide #10.1 models
    12735 
    12736 > hide #!12 models
    12737 
    12738 > surface dust #56.1 size 8
    12739 
    12740 > surface dust #56.1 size 7
    12741 
    12742 > surface dust #56.1 size 6
    12743 
    12744 > surface dust #56.1 size 5
    12745 
    12746 > surface dust #56.2 size 4.98
    12747 
    12748 > surface dust #56.3 size 4.98
    12749 
    12750 > surface dust #56.4 size 4.98
    12751 
    12752 > save
    12753 > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-PBD_OF.png
    12754 > width 809 height 738 supersample 3 transparentBackground true
    12755 
    12756 > hide #!56 models
    12757 
    12758 > show #15 models
    12759 
    12760 > show #!14 models
    12761 
    12762 > show #14.1 models
    12763 
    12764 > color #14.1 #e59900ff
    12765 
    12766 > volume #14 step 1
    12767 
    12768 > surface dust #14 size 4.98
    12769 
    12770 > volume #14 level 0.006781
    12771 
    12772 > volume #14 level 0.007273
    12773 
    12774 > hide #14.1 models
    12775 
    12776 > show #14.1 models
    12777 
    12778 > select #15: 601
    12779 
    12780 31 atoms, 32 bonds, 1 residue, 1 model selected 
    12781 
    12782 > color sel hot pink
    12783 
    12784 > select clear
    12785 
    12786 > volume #14 level 0.007929
    12787 
    12788 > color zone #14 near #15 distance 4.98
    12789 
    12790 > color zone #14 near #15 distance 2
    12791 
    12792 > color zone #14 near #15 distance 2.5
    12793 
    12794 > select clear
    12795 
    12796 > volume splitbyzone #14
    12797 
    12798 Opened rOAT1-TFV_IF.mrc 0 as #57.1, grid size 320,320,320, pixel 0.83, shown
    12799 at level 0.00793, step 1, values float32 
    12800 Opened rOAT1-TFV_IF.mrc 1 as #57.2, grid size 320,320,320, pixel 0.83, shown
    12801 at level 0.00793, step 1, values float32 
    12802 Opened rOAT1-TFV_IF.mrc 2 as #57.3, grid size 320,320,320, pixel 0.83, shown
    12803 at level 0.00793, step 1, values float32 
    12804 Opened rOAT1-TFV_IF.mrc 3 as #57.4, grid size 320,320,320, pixel 0.83, shown
    12805 at level 0.00793, step 1, values float32 
    12806 
    12807 > hide #15 models
    12808 
    12809 > hide #14.1 models
    12810 
    12811 > surface dust #57.1 size 4.98
    12812 
    12813 > surface dust #57.1 size 6
    12814 
    12815 > surface dust #57.1 size 7
    12816 
    12817 > surface dust #57.1 size 8
    12818 
    12819 > volume #57.1 level 0.008027
    12820 
    12821 > surface dust #57.1 size 8
    12822 
    12823 > surface dust #57.2 size 4.98
    12824 
    12825 > surface dust #57.3 size 4.98
    12826 
    12827 > surface dust #57.4 size 4.98
    12828 
    12829 > select clear
    12830 
    12831 > save
    12832 > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-TFV_IF.png
    12833 > width 809 height 738 supersample 3 transparentBackground true
    12834 
    12835 > hide #!57 models
    12836 
    12837 > show #!18 models
    12838 
    12839 > show #!17 models
    12840 
    12841 > show #17.1 models
    12842 
    12843 > color #17.1 #e599004d
    12844 
    12845 > color #17.1 #e59900ff
    12846 
    12847 > color zone #17 near #18 distance 4.98
    12848 
    12849 > color zone #17 near #18 distance 2
    12850 
    12851 > color zone #17 near #18 distance 2.5
    12852 
    12853 > color zone #17 near #18 distance 3
    12854 
    12855 > color zone #17 near #18 distance 2
    12856 
    12857 > color zone #17 near #18 distance 2.8
    12858 
    12859 > color zone #17 near #18 distance 3
    12860 
    12861 > volume splitbyzone #17
    12862 
    12863 Opened rOAT1-TVF_OF.mrc 0 as #58.1, grid size 320,320,320, pixel 0.83, shown
    12864 at level 0.011, step 1, values float32 
    12865 Opened rOAT1-TVF_OF.mrc 1 as #58.2, grid size 320,320,320, pixel 0.83, shown
    12866 at level 0.011, step 1, values float32 
    12867 Opened rOAT1-TVF_OF.mrc 2 as #58.3, grid size 320,320,320, pixel 0.83, shown
    12868 at level 0.011, step 1, values float32 
    12869 Opened rOAT1-TVF_OF.mrc 3 as #58.4, grid size 320,320,320, pixel 0.83, shown
    12870 at level 0.011, step 1, values float32 
    12871 
    12872 > hide #17.1 models
    12873 
    12874 > hide #!18 models
    12875 
    12876 > close #58
    12877 
    12878 > show #!17 models
    12879 
    12880 > show #!18 models
    12881 
    12882 > show #17.1 models
    12883 
    12884 > select #18: 601
    12885 
    12886 31 atoms, 32 bonds, 1 residue, 1 model selected 
    12887 
    12888 > color sel hot pink
    12889 
    12890 > select clear
    12891 
    12892 > color zone #17 near #18 distance 3
    12893 
    12894 > volume splitbyzone #17
    12895 
    12896 Opened rOAT1-TVF_OF.mrc 0 as #58.1, grid size 320,320,320, pixel 0.83, shown
    12897 at level 0.011, step 1, values float32 
    12898 Opened rOAT1-TVF_OF.mrc 1 as #58.2, grid size 320,320,320, pixel 0.83, shown
    12899 at level 0.011, step 1, values float32 
    12900 Opened rOAT1-TVF_OF.mrc 2 as #58.3, grid size 320,320,320, pixel 0.83, shown
    12901 at level 0.011, step 1, values float32 
    12902 Opened rOAT1-TVF_OF.mrc 3 as #58.4, grid size 320,320,320, pixel 0.83, shown
    12903 at level 0.011, step 1, values float32 
    12904 
    12905 > hide #17.1 models
    12906 
    12907 > hide #!18 models
    12908 
    12909 > surface dust #58.1 size 4.98
    12910 
    12911 > surface dust #58.2 size 4.98
    12912 
    12913 > surface dust #58.3 size 4.98
    12914 
    12915 > surface dust #58.4 size 4.98
    12916 
    12917 > volume #58.2 level 0.004506
    12918 
    12919 > volume #58.1 level 0.008289
    12920 
    12921 > surface dust #58.4 size 7
    12922 
    12923 > surface dust #58.1 size 7
    12924 
    12925 > surface dust #58.1 size 8
    12926 
    12927 > volume #58.1 level 0.008125
    12928 
    12929 > save
    12930 > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-TFV_OF.png
    12931 > width 809 height 738 supersample 3 transparentBackground true
    12932 
    12933 > hide #!58 models
    12934 
    12935 > show #!20 models
    12936 
    12937 > show #21 models
    12938 
    12939 > show #20.1 models
    12940 
    12941 > select #21: 601
    12942 
    12943 35 atoms, 38 bonds, 1 residue, 1 model selected 
    12944 
    12945 > select #21: 601,602
    12946 
    12947 70 atoms, 76 bonds, 2 residues, 1 model selected 
    12948 
    12949 > color sel hot pink
    12950 
    12951 > select clear
    12952 
    12953 > color #20.1 #e5990080
    12954 
    12955 > color #20.1 #e59900ff
    12956 
    12957 > select clear
    12958 
    12959 > color zone #17 near #18 distance 3.01
    12960 
    12961 > color zone #17 near #18 distance 3.02
    12962 
    12963 > color zone #20 near #21 distance 3
    12964 
    12965 > volume #58.1 level 0.007961
    12966 
    12967 > color zone #20 near #21 distance 2
    12968 
    12969 > color zone #20 near #21 distance 2.8
    12970 
    12971 > color zone #20 near #21 distance 2
    12972 
    12973 > color zone #20 near #21 distance 2.7
    12974 
    12975 > volume splitbyzone #20
    12976 
    12977 Opened rOAT1-AAI_IF.mrc 0 as #59.1, grid size 320,320,320, pixel 0.83, shown
    12978 at level 0.0133, step 1, values float32 
    12979 Opened rOAT1-AAI_IF.mrc 1 as #59.2, grid size 320,320,320, pixel 0.83, shown
    12980 at level 0.0133, step 1, values float32 
    12981 Opened rOAT1-AAI_IF.mrc 2 as #59.3, grid size 320,320,320, pixel 0.83, shown
    12982 at level 0.0133, step 1, values float32 
    12983 Opened rOAT1-AAI_IF.mrc 3 as #59.4, grid size 320,320,320, pixel 0.83, shown
    12984 at level 0.0133, step 1, values float32 
    12985 
    12986 > hide #21 models
    12987 
    12988 > hide #20.1 models
    12989 
    12990 > hide #!58.2 models
    12991 
    12992 > hide #!58.3 models
    12993 
    12994 > hide #!58.4 models
    12995 
    12996 > surface dust #59.1 size 4.98
    12997 
    12998 > volume #59.1 level 0.01002
    12999 
    13000 > volume #59.1 level 0.009926
    13001 
    13002 > surface dust #59.2 size 4.98
    13003 
    13004 > select add #59
    13005 
    13006 9 models selected 
    13007 
    13008 > surface dust #59.3 size 4.98
    13009 
    13010 > select clear
    13011 
    13012 > save
    13013 > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-AAI_IF.png
    13014 > width 809 height 738 supersample 3 transparentBackground true
    13015 
    13016 > hide #!59 models
    13017 
    13018 > show #!24 models
    13019 
    13020 > show #!23 models
    13021 
    13022 > show #23.1 models
    13023 
    13024 > select #24: 601,602
    13025 
    13026 35 atoms, 38 bonds, 1 residue, 1 model selected 
    13027 
    13028 > color sel hot pink
    13029 
    13030 > select clear
    13031 
    13032 > color #23.1 #e5990080
    13033 
    13034 > color #23.1 #e59900ff
    13035 
    13036 > select clear
    13037 
    13038 > volume #23 level 0.009882
    13039 
    13040 > color zone #23 near #24 distance 4.98
    13041 
    13042 > color zone #23 near #24 distance 3
    13043 
    13044 > volume splitbyzone #23
    13045 
    13046 Opened rOAT1-AAI_OF.mrc 0 as #60.1, grid size 320,320,320, pixel 0.83, shown
    13047 at level 0.00988, step 1, values float32 
    13048 Opened rOAT1-AAI_OF.mrc 1 as #60.2, grid size 320,320,320, pixel 0.83, shown
    13049 at level 0.00988, step 1, values float32 
    13050 Opened rOAT1-AAI_OF.mrc 2 as #60.3, grid size 320,320,320, pixel 0.83, shown
    13051 at level 0.00988, step 1, values float32 
    13052 Opened rOAT1-AAI_OF.mrc 3 as #60.4, grid size 320,320,320, pixel 0.83, shown
    13053 at level 0.00988, step 1, values float32 
    13054 
    13055 > hide #23.1 models
    13056 
    13057 > hide #!24 models
    13058 
    13059 > select add #60
    13060 
    13061 9 models selected 
    13062 
    13063 > surface dust #59.3 size 4.98
    13064 
    13065 > surface dust #60.1 size 4.98
    13066 
    13067 > surface dust #60.2 size 4.98
    13068 
    13069 > surface dust #60.3 size 4.98
    13070 
    13071 > surface dust #60.4 size 4.98
    13072 
    13073 > select clear
    13074 
    13075 > volume #60.1 level 0.00867
    13076 
    13077 > surface dust #60.4 size 7
    13078 
    13079 > surface dust #60.1 size 4.98
    13080 
    13081 > surface dust #60.1 size 7
    13082 
    13083 > select clear
    13084 
    13085 > surface dust #60.1 size 8
    13086 
    13087 > volume #60.1 level 0.009276
    13088 
    13089 > save
    13090 > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-AAI_OF.png
    13091 > width 809 height 738 supersample 3 transparentBackground true
    13092 
    13093 > hide #!60 models
    13094 
    13095 > show #!36 models
    13096 
    13097 > show #37 models
    13098 
    13099 > select #37: 318-570
    13100 
    13101 1865 atoms, 1903 bonds, 246 residues, 1 model selected 
    13102 
    13103 > color sel #3ec0c2ff
    13104 
    13105 > select clear
    13106 
    13107 > show #36.1 models
    13108 
    13109 > select #37/A:525
    13110 
    13111 7 atoms, 7 bonds, 1 residue, 1 model selected 
    13112 
    13113 > select clear
    13114 
    13115 > select #37: 525-570
    13116 
    13117 316 atoms, 321 bonds, 39 residues, 1 model selected 
    13118 
    13119 > delete atoms sel
    13120 
    13121 > delete bonds sel
    13122 
    13123 > select clear
    13124 
    13125 > save /Users/dout2/Downloads/OAT1_ligand_Colored_domain.cxs includeMaps true
    13126 
    13127 > color #36.1 #e59900ff
    13128 
    13129 > select clear
    13130 
    13131 > select #37: 601-603
    13132 
    13133 31 atoms, 32 bonds, 1 residue, 1 model selected 
    13134 
    13135 > color sel hot pink
    13136 
    13137 > select clear
    13138 
    13139 > color zone #36 near #37 distance 3
    13140 
    13141 > select #36
    13142 
    13143 2 models selected 
    13144 
    13145 > volume splitbyzone #36
    13146 
    13147 Opened hOAT1-TFV_IF.mrc 0 as #61.1, grid size 320,320,320, pixel 0.83, shown
    13148 at level 0.00852, step 1, values float32 
    13149 Opened hOAT1-TFV_IF.mrc 1 as #61.2, grid size 320,320,320, pixel 0.83, shown
    13150 at level 0.00852, step 1, values float32 
    13151 Opened hOAT1-TFV_IF.mrc 2 as #61.3, grid size 320,320,320, pixel 0.83, shown
    13152 at level 0.00852, step 1, values float32 
    13153 Opened hOAT1-TFV_IF.mrc 3 as #61.4, grid size 320,320,320, pixel 0.83, shown
    13154 at level 0.00852, step 1, values float32 
    13155 
    13156 > hide #37 models
    13157 
    13158 > select subtract #36
    13159 
    13160 Nothing selected 
    13161 
    13162 > select add #36
    13163 
    13164 2 models selected 
    13165 
    13166 > select subtract #36
    13167 
    13168 Nothing selected 
    13169 
    13170 > surface dust #61.1 size 4.98
    13171 
    13172 > surface dust #61.2 size 4.98
    13173 
    13174 > surface dust #61.3 size 4.98
    13175 
    13176 > surface dust #61.4 size 4.98
    13177 
    13178 > select clear
    13179 
    13180 > volume #61.1 level 0.009185
    13181 
    13182 > save
    13183 > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/hOAT1-TFV_IF.png
    13184 > width 809 height 738 supersample 3 transparentBackground true
    13185 
    13186 > hide #!61 models
    13187 
    13188 > show #!39 models
    13189 
    13190 > show #!41 models
    13191 
    13192 > select #41: 601-603
    13193 
    13194 31 atoms, 32 bonds, 1 residue, 1 model selected 
    13195 
    13196 > color sel hot pink
    13197 
    13198 > select #41: 525-570
    13199 
    13200 316 atoms, 321 bonds, 39 residues, 1 model selected 
    13201 
    13202 > delete atoms sel
    13203 
    13204 > delete bonds sel
    13205 
    13206 > open /Volumes/bbc/Lab-
    13207 > Jiang/PROJECTS/OAT1/new_structures_20250209/20241127_hOAT1-TFV/outward_j68_3.1A/hOAT1-TFV_OF-
    13208 > coot-5_real_space_refined_007.pdb
    13209 
    13210 Chain information for hOAT1-TFV_OF-coot-5_real_space_refined_007.pdb #62 
    13211 --- 
    13212 Chain | Description 
    13213 A | No description available 
    13214  
    13215 
    13216 > close #41
    13217 
    13218 > select #62: 1-317
    13219 
    13220 2454 atoms, 2519 bonds, 315 residues, 1 model selected 
    13221 
    13222 > select clear
    13223 
    13224 > select #62: 1-317
    13225 
    13226 2454 atoms, 2519 bonds, 315 residues, 1 model selected 
    13227 
    13228 > color sel #a166d1ff
    13229 
    13230 > select #62: 318-570
    13231 
    13232 1503 atoms, 1535 bonds, 200 residues, 1 model selected 
    13233 
    13234 > color sel #3ec0c2ff
    13235 
    13236 > select #62: 601-603
    13237 
    13238 19 atoms, 20 bonds, 1 residue, 1 model selected 
    13239 
    13240 > color sel hot pink
    13241 
    13242 > select clear
    13243 
    13244 > show #!40 models
    13245 
    13246 > hide #!40 models
    13247 
    13248 > show #39.1 models
    13249 
    13250 > ui tool show "Fit in Map"
    13251 
    13252 > fitmap #62 inMap #39
    13253 
    13254 Fit molecule hOAT1-TFV_OF-coot-5_real_space_refined_007.pdb (#62) to map
    13255 hOAT1-TFV_OF.mrc (#39) using 3976 atoms 
    13256 average map value = 0.01786, steps = 124 
    13257 shifted from previous position = 1.62 
    13258 rotated from previous position = 13.4 degrees 
    13259 atoms outside contour = 1104, contour level = 0.010555 
    13260  
    13261 Position of hOAT1-TFV_OF-coot-5_real_space_refined_007.pdb (#62) relative to
    13262 hOAT1-TFV_OF.mrc (#39) coordinates: 
    13263 Matrix rotation and translation 
    13264 0.99999997 0.00013203 0.00020852 -0.03273890 
    13265 -0.00013199 0.99999997 -0.00020384 0.04132497 
    13266 -0.00020855 0.00020382 0.99999996 -0.00751800 
    13267 Axis 0.63678518 0.65147667 -0.41241094 
    13268 Axis point -17.94306109 -0.00000000 185.02377550 
    13269 Rotation angle (degrees) 0.01833990 
    13270 Shift along axis 0.00917511 
    13271  
    13272 Drag select of 39 hOAT1-TFV_OF.mrc 
    13273 
    13274 > select clear
    13275 
    13276 > hide #36.1 models
    13277 
    13278 > color #39.1 #e59900ff
    13279 
    13280 > select clear
    13281 
    13282 > color zone #39 near #62 distance 4.98
    13283 
    13284 > color zone #39 near #62 distance 3
    13285 
    13286 > volume splitbyzone #39
    13287 
    13288 Opened hOAT1-TFV_OF.mrc 0 as #41.1, grid size 320,320,320, pixel 0.83, shown
    13289 at level 0.0106, step 1, values float32 
    13290 Opened hOAT1-TFV_OF.mrc 1 as #41.2, grid size 320,320,320, pixel 0.83, shown
    13291 at level 0.0106, step 1, values float32 
    13292 Opened hOAT1-TFV_OF.mrc 2 as #41.3, grid size 320,320,320, pixel 0.83, shown
    13293 at level 0.0106, step 1, values float32 
    13294 Opened hOAT1-TFV_OF.mrc 3 as #41.4, grid size 320,320,320, pixel 0.83, shown
    13295 at level 0.0106, step 1, values float32 
    13296 
    13297 > hide #39.1 models
    13298 
    13299 > surface dust #41.1 size 4.98
    13300 
    13301 > surface dust #41.2 size 4.98
    13302 
    13303 > surface dust #41.3 size 4.98
    13304 
    13305 > surface dust #41.4 size 4.98
    13306 
    13307 > surface dust #42.3 size 4.98
    13308 
    13309 > surface dust #41.4 size 4.98
    13310 
    13311 > surface dust #41.1 size 4.98
    13312 
    13313 > select clear
    13314 
    13315 > volume #41.1 level 0.01048
    13316 
    13317 > hide #!62 models
    13318 
    13319 > save
    13320 > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/hOAT1-TFV_OF.png
    13321 > width 809 height 738 supersample 3 transparentBackground true
    13322 
    13323 > open /Volumes/bbc/Lab-
    13324 > Jiang/PROJECTS/OAT1/new_structures_20250209/20241127_hOAT1-TFV/inward_j62_3.2A/hOAT1-TVF_IF-
    13325 > coot-3.pdb
    13326 
    13327 Chain information for hOAT1-TVF_IF-coot-3.pdb #63 
    13328 --- 
    13329 Chain | Description 
    13330 A | No description available 
    13331  
    13332 
    13333 > hide #!41 models
    13334 
    13335 > show #!36 models
    13336 
    13337 > show #36.1 models
    13338 
    13339 > ui tool show "Fit in Map"
    13340 
    13341 > fitmap #63 inMap #36
    13342 
    13343 Fit molecule hOAT1-TVF_IF-coot-3.pdb (#63) to map hOAT1-TFV_IF.mrc (#36) using
    13344 3988 atoms 
    13345 average map value = 0.01587, steps = 40 
    13346 shifted from previous position = 0.013 
    13347 rotated from previous position = 0.0468 degrees 
    13348 atoms outside contour = 1071, contour level = 0.008515 
    13349  
    13350 Position of hOAT1-TVF_IF-coot-3.pdb (#63) relative to hOAT1-TFV_IF.mrc (#36)
    13351 coordinates: 
    13352 Matrix rotation and translation 
    13353 0.99999982 0.00052001 0.00028819 -0.09949069 
    13354 -0.00052017 0.99999971 0.00056108 -0.00480012 
    13355 -0.00028790 -0.00056123 0.99999980 0.10326003 
    13356 Axis -0.68640011 0.35233129 -0.63617415 
    13357 Axis point 0.00000000 185.01527828 9.22177002 
    13358 Rotation angle (degrees) 0.04684105 
    13359 Shift along axis 0.00090783 
    13360  
    13361 
    13362 > fitmap #63 inMap #36
    13363 
    13364 Fit molecule hOAT1-TVF_IF-coot-3.pdb (#63) to map hOAT1-TFV_IF.mrc (#36) using
    13365 3988 atoms 
    13366 average map value = 0.01587, steps = 44 
    13367 shifted from previous position = 0.00151 
    13368 rotated from previous position = 0.00338 degrees 
    13369 atoms outside contour = 1071, contour level = 0.008515 
    13370  
    13371 Position of hOAT1-TVF_IF-coot-3.pdb (#63) relative to hOAT1-TFV_IF.mrc (#36)
    13372 coordinates: 
    13373 Matrix rotation and translation 
    13374 0.99999984 0.00047947 0.00028576 -0.09335598 
    13375 -0.00047961 0.99999975 0.00051832 -0.00591563 
    13376 -0.00028551 -0.00051846 0.99999982 0.09657995 
    13377 Axis -0.68052069 0.37496589 -0.62951741 
    13378 Axis point 0.00000000 186.90180615 11.87456849 
    13379 Rotation angle (degrees) 0.04364555 
    13380 Shift along axis 0.00051376 
    13381  
    13382 
    13383 > close #37
    13384 
    13385 > fitmap #63 inMap #36
    13386 
    13387 Fit molecule hOAT1-TVF_IF-coot-3.pdb (#63) to map hOAT1-TFV_IF.mrc (#36) using
    13388 3988 atoms 
    13389 average map value = 0.01587, steps = 40 
    13390 shifted from previous position = 0.00938 
    13391 rotated from previous position = 0.00367 degrees 
    13392 atoms outside contour = 1072, contour level = 0.008515 
    13393  
    13394 Position of hOAT1-TVF_IF-coot-3.pdb (#63) relative to hOAT1-TFV_IF.mrc (#36)
    13395 coordinates: 
    13396 Matrix rotation and translation 
    13397 0.99999986 0.00047777 0.00024709 -0.09234265 
    13398 -0.00047791 0.99999972 0.00056927 -0.01315730 
    13399 -0.00024682 -0.00056939 0.99999981 0.10649613 
    13400 Axis -0.72689618 0.31530566 -0.61008548 
    13401 Axis point 0.00000000 184.88987693 22.09640694 
    13402 Rotation angle (degrees) 0.04487577 
    13403 Shift along axis -0.00199679 
    13404  
    13405 
    13406 > color zone #36 near #63 distance 3
    13407 
    13408 > select add #63
    13409 
    13410 3988 atoms, 4085 bonds, 1 pseudobond, 517 residues, 2 models selected 
    13411 
    13412 > select #63: 601-603
    13413 
    13414 19 atoms, 20 bonds, 1 residue, 1 model selected 
    13415 
    13416 > color sel hot pink
    13417 
    13418 > select #63: 1-317
    13419 
    13420 2471 atoms, 2537 bonds, 316 residues, 1 model selected 
    13421 
    13422 > color sel #a166d1ff
    13423 
    13424 > select #63: 318-570
    13425 
    13426 1498 atoms, 1528 bonds, 200 residues, 1 model selected 
    13427 
    13428 > color sel #3ec0c2ff
    13429 
    13430 > hide #!63 models
    13431 
    13432 > show #!63 models
    13433 
    13434 > color zone #36 near #63 distance 3
    13435 
    13436 > volume splitbyzone #36
    13437 
    13438 Opened hOAT1-TFV_IF.mrc 0 as #37.1, grid size 320,320,320, pixel 0.83, shown
    13439 at level 0.00852, step 1, values float32 
    13440 Opened hOAT1-TFV_IF.mrc 1 as #37.2, grid size 320,320,320, pixel 0.83, shown
    13441 at level 0.00852, step 1, values float32 
    13442 Opened hOAT1-TFV_IF.mrc 2 as #37.3, grid size 320,320,320, pixel 0.83, shown
    13443 at level 0.00852, step 1, values float32 
    13444 Opened hOAT1-TFV_IF.mrc 3 as #37.4, grid size 320,320,320, pixel 0.83, shown
    13445 at level 0.00852, step 1, values float32 
    13446 
    13447 > close #61
    13448 
    13449 > hide #!63 models
    13450 
    13451 > select add #63
    13452 
    13453 3988 atoms, 4085 bonds, 1 pseudobond, 517 residues, 2 models selected 
    13454 
    13455 > select subtract #63
    13456 
    13457 Nothing selected 
    13458 
    13459 > surface dust #37.1 size 4.98
    13460 
    13461 > surface dust #37.2 size 4.98
    13462 
    13463 > surface dust #37.3 size 4.98
    13464 
    13465 > surface dust #37.4 size 4.98
    13466 
    13467 > surface dust #38.3 size 4.98
    13468 
    13469 > volume #37.1 level 0.009315
    13470 
    13471 > save
    13472 > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/hOAT1-TFV_IF.png
    13473 > width 809 height 738 supersample 3 transparentBackground true
    13474 
    13475 > hide #!41.1 models
    13476 
    13477 > hide #36.1 models
    13478 
    13479 > hide #!37 models
    13480 
    13481 > show #!40 models
    13482 
    13483 > show #40.1 models
    13484 
    13485 > show #!43 models
    13486 
    13487 > select add #43
    13488 
    13489 3807 atoms, 3899 bonds, 3 pseudobonds, 492 residues, 2 models selected 
    13490 
    13491 > show sel cartoons
    13492 
    13493 > color #40 #e599004d models
    13494 
    13495 > color #40 #e59900ff models
    13496 
    13497 > select #43: 601-603
    13498 
    13499 10 atoms, 9 bonds, 1 residue, 1 model selected 
    13500 
    13501 > color sel hot pink
    13502 
    13503 > select clear
    13504 
    13505 > select #43: 1-317
    13506 
    13507 2332 atoms, 2392 bonds, 2 pseudobonds, 297 residues, 2 models selected 
    13508 
    13509 > color (#!43 & sel) #a166d1ff
    13510 
    13511 > select #43: 318-570
    13512 
    13513 1465 atoms, 1498 bonds, 194 residues, 1 model selected 
    13514 
    13515 > color (#!43 & sel) #3ec0c2ff
    13516 
    13517 > select clear
    13518 
    13519 > color zone #40 near #43 distance 3
    13520 
    13521 > color zone #40 near #43 distance 2
    13522 
    13523 > color zone #40 near #43 distance 2.8
    13524 
    13525 > volume splitbyzone #40
    13526 
    13527 Opened rOAT1-AKG_OF.mrc 0 as #61.1, grid size 320,320,320, pixel 0.83, shown
    13528 at level 0.0122, step 1, values float32 
    13529 Opened rOAT1-AKG_OF.mrc 1 as #61.2, grid size 320,320,320, pixel 0.83, shown
    13530 at level 0.0122, step 1, values float32 
    13531 Opened rOAT1-AKG_OF.mrc 2 as #61.3, grid size 320,320,320, pixel 0.83, shown
    13532 at level 0.0122, step 1, values float32 
    13533 Opened rOAT1-AKG_OF.mrc 3 as #61.4, grid size 320,320,320, pixel 0.83, shown
    13534 at level 0.0122, step 1, values float32 
    13535 
    13536 > hide #!43 models
    13537 
    13538 > surface dust #61.1 size 4.98
    13539 
    13540 > surface dust #61.2 size 4.98
    13541 
    13542 > surface dust #61.3 size 4.98
    13543 
    13544 > surface dust #61.4 size 4.98
    13545 
    13546 > volume #37.1 level 0.007221
    13547 
    13548 > volume #61.1 level 0.01166
    13549 
    13550 > save
    13551 > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-AKG_OF.png
    13552 > width 809 height 738 supersample 3 transparentBackground true
    13553 
    13554 > hide #!61 models
    13555 
    13556 > show #!44 models
    13557 
    13558 > show #!45 models
    13559 
    13560 > select #45: 601-603
    13561 
    13562 10 atoms, 9 bonds, 1 residue, 1 model selected 
    13563 
    13564 > color sel hot pink
    13565 
    13566 > select clear
    13567 
    13568 > show #!43 models
    13569 
    13570 > hide #!43 models
    13571 
    13572 > show #44.1 models
    13573 
    13574 > color #44.1 #e599004d
    13575 
    13576 > color #44.1 #e59900ff
    13577 
    13578 > color zone #44 near #45 distance 2.8
    13579 
    13580 > volume splitbyzone #44
    13581 
    13582 Opened rOAT1-AKG_OOC.mrc 0 as #64.1, grid size 320,320,320, pixel 0.83, shown
    13583 at level 0.0102, step 1, values float32 
    13584 Opened rOAT1-AKG_OOC.mrc 1 as #64.2, grid size 320,320,320, pixel 0.83, shown
    13585 at level 0.0102, step 1, values float32 
    13586 Opened rOAT1-AKG_OOC.mrc 2 as #64.3, grid size 320,320,320, pixel 0.83, shown
    13587 at level 0.0102, step 1, values float32 
    13588 Opened rOAT1-AKG_OOC.mrc 3 as #64.4, grid size 320,320,320, pixel 0.83, shown
    13589 at level 0.0102, step 1, values float32 
    13590 
    13591 > hide #44.1 models
    13592 
    13593 > hide #!45 models
    13594 
    13595 > surface dust #64.1 size 4.98
    13596 
    13597 > surface dust #64.2 size 4.98
    13598 
    13599 > surface dust #64.3 size 4.98
    13600 
    13601 > surface dust #64.4 size 4.98
    13602 
    13603 > volume #64.1 level 0.01073
    13604 
    13605 > save
    13606 > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-AKG_OO.png
    13607 > width 809 height 738 supersample 3 transparentBackground true
    13608 
    13609 > hide #!64 models
    13610 
    13611 > show #!47 models
    13612 
    13613 > show #!46 models
    13614 
    13615 > show #46.1 models
    13616 
    13617 > color #46.1 #e59900ff
    13618 
    13619 > select clear
    13620 
    13621 > color zone #46 near #47 distance 2.8
    13622 
    13623 > volume splitbyzone #46
    13624 
    13625 Opened rOAT1-R466A.mrc 0 as #65.1, grid size 480,480,480, pixel 0.553, shown
    13626 at level 0.0115, step 1, values float32 
    13627 Opened rOAT1-R466A.mrc 1 as #65.2, grid size 480,480,480, pixel 0.553, shown
    13628 at level 0.0115, step 1, values float32 
    13629 Opened rOAT1-R466A.mrc 2 as #65.3, grid size 480,480,480, pixel 0.553, shown
    13630 at level 0.0115, step 1, values float32 
    13631 
    13632 > hide #46.1 models
    13633 
    13634 > hide #!47 models
    13635 
    13636 > surface dust #65.1 size 3.32
    13637 
    13638 > surface dust #65.2 size 3.32
    13639 
    13640 > surface dust #65.3 size 3.32
    13641 
    13642 > select clear
    13643 
    13644 > volume #65.1 level 0.0121
    13645 
    13646 > surface dust #65.3 size 6
    13647 
    13648 > volume #65.1 level 0.009936
    13649 
    13650 > surface dust #65.1 size 6
    13651 
    13652 > surface dust #65.1 size 7
    13653 
    13654 > volume #65.1 level 0.008672
    13655 
    13656 > surface dust #65.1 size 8
    13657 
    13658 > volume #65.1 level 0.008943
    13659 
    13660 > save
    13661 > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-R466A_OO.png
    13662 > width 809 height 738 supersample 3 transparentBackground true
    13663 
    13664 > hide #!65 models
    13665 
    13666 > show #!59 models
    13667 
    13668 > volume #59.2 level 0.008094
    13669 
    13670 > volume #59.3 level 0.006974
    13671 
    13672 > volume #59.2 level 0.00901
    13673 
    13674 > select ~sel & ##selected
    13675 
    13676 Nothing selected 
    13677 
    13678 > save
    13679 > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-AAI_IF.png
    13680 > width 809 height 738 supersample 3 transparentBackground true
    13681 
    13682 > volume #59.3 level 0.0102
    13683 
    13684 > save
    13685 > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-AAI_IF.png
    13686 > width 809 height 738 supersample 3 transparentBackground true
    13687 
    13688 > save /Users/dout2/Downloads/OAT1_ligand_Colored_domain.cxs includeMaps true
    13689 
    13690 > hide #!59 models
    13691 
    13692 > show #!58 models
    13693 
    13694 > hide #!58 models
    13695 
    13696 > show #!34 models
    13697 
    13698 > show #!35 models
    13699 
    13700 > show #!35.3 models
    13701 
    13702 > color #35 #b2b2b2ff models
    13703 
    13704 > select add #35
    13705 
    13706 3 models selected 
    13707 
    13708 > select add #34
    13709 
    13710 3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 5 models selected 
    13711 
    13712 > hide sel atoms
    13713 
    13714 > color #35 #b2b2b2ff models
    13715 
    13716 > color #35.3 #b2b2b2ff models
    13717 
    13718 > hide #!34 models
    13719 
    13720 > select subtract #34
    13721 
    13722 3 models selected 
    13723 
    13724 > select subtract #35
    13725 
    13726 Nothing selected 
    13727 
    13728 > select add #35
    13729 
    13730 3 models selected 
    13731 
    13732 > view sel
    13733 
    13734 No displayed objects specified. 
    13735 
    13736 > hide #!35 models
    13737 
    13738 > show #!35 models
    13739 
    13740 > hide #!35 models
    13741 
    13742 > hide #!35.3 models
    13743 
    13744 > select subtract #35.3
    13745 
    13746 1 model selected 
    13747 
    13748 > select add #35
    13749 
    13750 3 models selected 
    13751 
    13752 > select subtract #35
    13753 
    13754 Nothing selected 
    13755 
    13756 > show #!34 models
    13757 
    13758 > show #!17 models
    13759 
    13760 > show #17.1 models
    13761 
    13762 > hide #17.1 models
    13763 
    13764 > hide #!17 models
    13765 
    13766 > select ::name="CL"
    13767 
    13768 5 atoms, 5 residues, 5 models selected 
    13769 
    13770 > show sel & #!34 atoms
    13771 
    13772 > select #34/B:1@CL
    13773 
    13774 1 atom, 1 residue, 1 model selected 
    13775 
    13776 > color sel lime
    13777 
    13778 > select clear
    13779 
    13780 > select #34/B:1@CL
    13781 
    13782 1 atom, 1 residue, 1 model selected 
    13783 
    13784 > select add #34
    13785 
    13786 3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 2 models selected 
    13787 
    13788 > show #!19 models
    13789 
    13790 > show #!19.3 models
    13791 
    13792 > hide #!19.3 models
    13793 
    13794 > hide #!19 models
    13795 
    13796 > show #!17 models
    13797 
    13798 > show #17.1 models
    13799 
    13800 > color zone #17 near #34 distance 3.02
    13801 
    13802 > volume splitbyzone #17
    13803 
    13804 Opened rOAT1-TVF_OF.mrc 0 as #66.1, grid size 320,320,320, pixel 0.83, shown
    13805 at level 0.011, step 1, values float32 
    13806 Opened rOAT1-TVF_OF.mrc 1 as #66.2, grid size 320,320,320, pixel 0.83, shown
    13807 at level 0.011, step 1, values float32 
    13808 Opened rOAT1-TVF_OF.mrc 2 as #66.3, grid size 320,320,320, pixel 0.83, shown
    13809 at level 0.011, step 1, values float32 
    13810 Opened rOAT1-TVF_OF.mrc 3 as #66.4, grid size 320,320,320, pixel 0.83, shown
    13811 at level 0.011, step 1, values float32 
    13812 Opened rOAT1-TVF_OF.mrc 4 as #66.5, grid size 320,320,320, pixel 0.83, shown
    13813 at level 0.011, step 1, values float32 
    13814 
    13815 > select clear
    13816 
    13817 > show #!17 models
    13818 
    13819 > hide #!66 models
    13820 
    13821 > show #!66 models
    13822 
    13823 > hide #!66 models
    13824 
    13825 > show #33 models
    13826 
    13827 > hide #33 models
    13828 
    13829 > color #17 #b2b2b2ff models
    13830 
    13831 > select clear
    13832 
    13833 > hide #!17 models
    13834 
    13835 > select #34/B
    13836 
    13837 1 atom, 1 residue, 1 model selected 
    13838 
    13839 > select ::name="HOH"
    13840 
    13841 240 atoms, 240 residues, 10 models selected 
    13842 
    13843 > show #!34 atoms
    13844 
    13845 > select #34: h2o
    13846 
    13847 Nothing selected 
    13848 
    13849 > select add #34
    13850 
    13851 3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 2 models selected 
    13852 
    13853 > hide sel atoms
    13854 
    13855 > select #34/B
    13856 
    13857 1 atom, 1 residue, 1 model selected 
    13858 
    13859 > open /Volumes/bbc/Lab-
    13860 > Jiang/PROJECTS/OAT1/new_structures_20250209/20240831_rOAT1-TFV/outward_j170_2.7A/rOAT1-TFV_OF-
    13861 > coot-4_real_space_refined_009.pdb
    13862 
    13863 Chain information for rOAT1-TFV_OF-coot-4_real_space_refined_009.pdb #67 
    13864 --- 
    13865 Chain | Description 
    13866 A | No description available 
    13867  
    13868 
    13869 > rename #67 rOAT1-TFV-Cl_OF-coot-4_real_space_refined_009.pdb
    13870 
    13871 > select add #67
    13872 
    13873 3829 atoms, 3910 bonds, 3 pseudobonds, 505 residues, 3 models selected 
    13874 
    13875 > show sel atoms
    13876 
    13877 > select #67/B:1@CL
    13878 
    13879 1 atom, 1 residue, 1 model selected 
    13880 
    13881 > style sel ball
    13882 
    13883 Changed 1 atom style 
    13884 
    13885 > hide #!34 models
    13886 
    13887 > select #67:1-317
    13888 
    13889 2344 atoms, 2392 bonds, 2 pseudobonds, 309 residues, 2 models selected 
    13890 
    13891 > color (#!67 & sel) #a166d1ff
    13892 
    13893 > select #67:318-570
    13894 
    13895 1465 atoms, 1498 bonds, 194 residues, 1 model selected 
    13896 
    13897 > color sel #3dc0c2ff
    13898 
    13899 > select #67/B:1@CL
    13900 
    13901 1 atom, 1 residue, 1 model selected 
    13902 
    13903 > select clear
    13904 
    13905 > select #67/B:1@CL
    13906 
    13907 1 atom, 1 residue, 1 model selected 
    13908 
    13909 > color sel lime
    13910 
    13911 > select #67/D:4@O
    13912 
    13913 1 atom, 1 residue, 1 model selected 
    13914 
    13915 > select clear
    13916 
    13917 > select #67/D:4@O
    13918 
    13919 1 atom, 1 residue, 1 model selected 
    13920 
    13921 > color sel red
    13922 
    13923 > select clear
    13924 
    13925 > show #!17 models
    13926 
    13927 > color zone #17 near #67 distance 3.02
    13928 
    13929 Drag select of 17 rOAT1-TVF_OF.mrc , 3 residues, 2 bonds 
    13930 
    13931 > select clear
    13932 
    13933 > hide #17.1 models
    13934 
    13935 > hide #!17 models
    13936 
    13937 > hide #!66.1 models
    13938 
    13939 > show #!47 models
    13940 
    13941 > show #!46 models
    13942 
    13943 > hide #!67 models
    13944 
    13945 > select #47/B
    13946 
    13947 1 atom, 1 residue, 1 model selected 
    13948 
    13949 > show sel atoms
    13950 
    13951 > show #46.1 models
    13952 
    13953 > select #47/B
    13954 
    13955 1 atom, 1 residue, 1 model selected 
    13956 
    13957 > color sel lime
    13958 
    13959 > style sel ball
    13960 
    13961 Changed 1 atom style 
    13962 
    13963 > hide #!46 models
    13964 
    13965 > hide #46.1 models
    13966 
    13967 > hide #!47 models
    13968 
    13969 > select add #47
    13970 
    13971 3795 atoms, 3884 bonds, 3 pseudobonds, 495 residues, 2 models selected 
    13972 
    13973 > select subtract #47
    13974 
    13975 Nothing selected 
    13976 
    13977 > show #!67 models
    13978 
    13979 > select add #67
    13980 
    13981 3828 atoms, 3910 bonds, 3 pseudobonds, 504 residues, 2 models selected 
    13982 
    13983 > show #!17 models
    13984 
    13985 > show #17.1 models
    13986 
    13987 > volume splitbyzone #17
    13988 
    13989 Opened rOAT1-TVF_OF.mrc 0 as #68.1, grid size 320,320,320, pixel 0.83, shown
    13990 at level 0.011, step 1, values float32 
    13991 Opened rOAT1-TVF_OF.mrc 1 as #68.2, grid size 320,320,320, pixel 0.83, shown
    13992 at level 0.011, step 1, values float32 
    13993 Opened rOAT1-TVF_OF.mrc 2 as #68.3, grid size 320,320,320, pixel 0.83, shown
    13994 at level 0.011, step 1, values float32 
    13995 Opened rOAT1-TVF_OF.mrc 3 as #68.4, grid size 320,320,320, pixel 0.83, shown
    13996 at level 0.011, step 1, values float32 
    13997 Opened rOAT1-TVF_OF.mrc 4 as #68.5, grid size 320,320,320, pixel 0.83, shown
    13998 at level 0.011, step 1, values float32 
    13999 Opened rOAT1-TVF_OF.mrc 5 as #68.6, grid size 320,320,320, pixel 0.83, shown
    14000 at level 0.011, step 1, values float32 
    14001 Opened rOAT1-TVF_OF.mrc 6 as #68.7, grid size 320,320,320, pixel 0.83, shown
    14002 at level 0.011, step 1, values float32 
    14003 Opened rOAT1-TVF_OF.mrc 7 as #68.8, grid size 320,320,320, pixel 0.83, shown
    14004 at level 0.011, step 1, values float32 
    14005 Opened rOAT1-TVF_OF.mrc 8 as #68.9, grid size 320,320,320, pixel 0.83, shown
    14006 at level 0.011, step 1, values float32 
    14007 
    14008 > hide #!68.9 models
    14009 
    14010 > hide #!68.7 models
    14011 
    14012 > hide #!68.6 models
    14013 
    14014 > hide #!68.5 models
    14015 
    14016 > hide #!68.4 models
    14017 
    14018 > hide #!68.3 models
    14019 
    14020 > hide #!68.2 models
    14021 
    14022 > hide #!68.1 models
    14023 
    14024 > color #68.8 #b2b2b2ff models
    14025 
    14026 > color #68.8 #b2b2b276 models
    14027 
    14028 > color #68.8 #b2b2b249 models
    14029 
    14030 > color #68.8 #b2b2b24c models
    14031 
    14032 > select clear
    14033 
    14034 > select add #67
    14035 
    14036 3828 atoms, 3910 bonds, 3 pseudobonds, 504 residues, 2 models selected 
    14037 
    14038 > hide sel cartoons
    14039 
    14040 > hide sel atoms
    14041 
    14042 > select #67/B
    14043 
    14044 1 atom, 1 residue, 1 model selected 
    14045 
    14046 > show sel atoms
    14047 
    14048 > select clear
    14049 
    14050 > save
    14051 > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-TFV-
    14052 > Cl_OF.png width 809 height 738 supersample 3 transparentBackground true
    14053 
    14054 > hide #!67 models
    14055 
    14056 > hide #!68 models
    14057 
    14058 > show #!19 models
    14059 
    14060 > show #!19.3 models
    14061 
    14062 > show #!18 models
    14063 
    14064 > color #19.3 #b2b2b29f models
    14065 
    14066 > close #19
    14067 
    14068 > show #!68 models
    14069 
    14070 > show #!68.1 models
    14071 
    14072 > hide #!68.1 models
    14073 
    14074 > show #!68.7 models
    14075 
    14076 > close #68
    14077 
    14078 > select add #67
    14079 
    14080 3828 atoms, 3910 bonds, 3 pseudobonds, 504 residues, 2 models selected 
    14081 
    14082 > show #!67 models
    14083 
    14084 > hide #!18 models
    14085 
    14086 > hide #17.1 models
    14087 
    14088 > show sel cartoons
    14089 
    14090 > show sel atoms
    14091 
    14092 > select up
    14093 
    14094 2 atoms, 1 bond, 1 residue, 1 model selected 
    14095 
    14096 > select up
    14097 
    14098 19 atoms, 20 bonds, 1 residue, 1 model selected 
    14099 
    14100 > color sel hot pink
    14101 
    14102 > select clear
    14103 
    14104 > color zone #17 near #67 distance 3.02
    14105 
    14106 > show #!66 models
    14107 
    14108 > select add #66
    14109 
    14110 11 models selected 
    14111 
    14112 > close #66
    14113 
    14114 > show #!35 models
    14115 
    14116 > close #35
    14117 
    14118 > show #!17 models
    14119 
    14120 > show #17.1 models
    14121 
    14122 > color zone #17 near #67 distance 3.02
    14123 
    14124 > volume splitbyzone #17
    14125 
    14126 Opened rOAT1-TVF_OF.mrc 0 as #19.1, grid size 320,320,320, pixel 0.83, shown
    14127 at level 0.011, step 1, values float32 
    14128 Opened rOAT1-TVF_OF.mrc 1 as #19.2, grid size 320,320,320, pixel 0.83, shown
    14129 at level 0.011, step 1, values float32 
    14130 Opened rOAT1-TVF_OF.mrc 2 as #19.3, grid size 320,320,320, pixel 0.83, shown
    14131 at level 0.011, step 1, values float32 
    14132 Opened rOAT1-TVF_OF.mrc 3 as #19.4, grid size 320,320,320, pixel 0.83, shown
    14133 at level 0.011, step 1, values float32 
    14134 Opened rOAT1-TVF_OF.mrc 4 as #19.5, grid size 320,320,320, pixel 0.83, shown
    14135 at level 0.011, step 1, values float32 
    14136 Opened rOAT1-TVF_OF.mrc 5 as #19.6, grid size 320,320,320, pixel 0.83, shown
    14137 at level 0.011, step 1, values float32 
    14138 
    14139 > hide #!19.2 models
    14140 
    14141 > hide #!19.1 models
    14142 
    14143 > hide #!19.3 models
    14144 
    14145 > hide #!19.6 models
    14146 
    14147 > show #!19.6 models
    14148 
    14149 > hide #!19.6 models
    14150 
    14151 > select add #67
    14152 
    14153 3828 atoms, 3910 bonds, 3 pseudobonds, 504 residues, 2 models selected 
    14154 
    14155 > hide sel atoms
    14156 
    14157 > hide sel cartoons
    14158 
    14159 > select #67:601
    14160 
    14161 19 atoms, 20 bonds, 1 residue, 1 model selected 
    14162 
    14163 > show sel atoms
    14164 
    14165 > color #67 #b2b2b2ff
    14166 
    14167 > color #19.4 #b2b2b2ff models
    14168 
    14169 > color #19.4 #b2b2b280 models
    14170 
    14171 > select #67:601
    14172 
    14173 19 atoms, 20 bonds, 1 residue, 1 model selected 
    14174 
    14175 > color sel lime
    14176 
    14177 > color sel hot pink
    14178 
    14179 > color sel byhetero
    14180 
    14181 > select clear
    14182 
    14183 > save
    14184 > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-TFV_OF-
    14185 > TFV.png width 809 height 738 supersample 3 transparentBackground true
    14186 
    14187 > color #19.4 #b2b2b29b models
    14188 
    14189 > color #19.4 #b2b2b29a models
    14190 
    14191 > color #19.4 #b2b2b280 models
    14192 
    14193 > select clear
    14194 
    14195 > lighting shadows true intensity 0.5
    14196 
    14197 > lighting shadows false
    14198 
    14199 > lighting flat
    14200 
    14201 > graphics silhouettes false
    14202 
    14203 > graphics silhouettes true
    14204 
    14205 > select clear
    14206 
    14207 > lighting flat
    14208 
    14209 > lighting simple
    14210 
    14211 > lighting soft
    14212 
    14213 > lighting flat
    14214 
    14215 > lighting full
    14216 
    14217 > lighting flat
    14218 
    14219 > lighting shadows true intensity 0.5
    14220 
    14221 > lighting shadows false
    14222 
    14223 > lighting flat
    14224 
    14225 > graphics silhouettes false
    14226 
    14227 > lighting flat
    14228 
    14229 > select clear
    14230 
    14231 > save
    14232 > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-TFV_OF-
    14233 > TFV.png width 809 height 738 supersample 3 transparentBackground true
    14234 
    14235 > color #19.4 black models
    14236 
    14237 > color #19.4 #00000008 models
    14238 
    14239 > color #19.4 #0000000a models
    14240 
    14241 > color #19.4 transparent models
    14242 
    14243 > lighting shadows true intensity 0.5
    14244 
    14245 > lighting shadows false
    14246 
    14247 > lighting flat
    14248 
    14249 > graphics silhouettes false
    14250 
    14251 > graphics silhouettes true
    14252 
    14253 > select clear
    14254 
    14255 > color #19.4 #929292ff models
    14256 
    14257 > color #19.4 #797979ff models
    14258 
    14259 > color #19.4 #79797980 models
    14260 
    14261 > color #19.4 silver models
    14262 
    14263 > color #19.4 #c0c0c080 models
    14264 
    14265 > lighting flat
    14266 
    14267 > lighting shadows true intensity 0.5
    14268 
    14269 > lighting flat
    14270 
    14271 > graphics silhouettes false
    14272 
    14273 > lighting flat
    14274 
    14275 > color #19.4 #929292ff models
    14276 
    14277 > color #19.4 #9292927e models
    14278 
    14279 > color #19.4 darkgrey models
    14280 
    14281 > color #19.4 silver models
    14282 
    14283 > select clear
    14284 
    14285 > volume #19.4 level 0.009812
    14286 
    14287 > surface dust #19.4 size 4.98
    14288 
    14289 > volume #19.4 level 0.008153
    14290 
    14291 > save
    14292 > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-TFV_OF-
    14293 > TFV.png width 809 height 738 supersample 3 transparentBackground true
    14294 
    14295 > volume #19.4 level 0.005723
    14296 
    14297 > surface dust #19.4 size 8
    14298 
    14299 > volume #19.4 level 0.007027
    14300 
    14301 > surface dust #19.4 size 8
    14302 
    14303 > volume #19.4 level 0.007797
    14304 
    14305 > surface dust #19.4 size 8
    14306 
    14307 > save
    14308 > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-TFV_OF-
    14309 > TFV.png width 809 height 738 supersample 3 transparentBackground true
    14310 
    14311 > hide #!19 models
    14312 
    14313 > hide #!19.4 models
    14314 
    14315 > hide #!19.5 models
    14316 
    14317 > show #!58 models
    14318 
    14319 > hide #!58 models
    14320 
    14321 > show #!58 models
    14322 
    14323 > close #58
    14324 
    14325 > show #!57 models
    14326 
    14327 > hide #!57.1 models
    14328 
    14329 > hide #!57.2 models
    14330 
    14331 > hide #!57.3 models
    14332 
    14333 > show #!57.1 models
    14334 
    14335 > show #!57.2 models
    14336 
    14337 > show #!57.3 models
    14338 
    14339 > hide #!57.2 models
    14340 
    14341 > hide #!57.1 models
    14342 
    14343 > hide #!57.3 models
    14344 
    14345 > show #15 models
    14346 
    14347 > hide #15 models
    14348 
    14349 > show #15 models
    14350 
    14351 > hide #15 models
    14352 
    14353 > select #67/A:601@C08
    14354 
    14355 1 atom, 1 residue, 1 model selected 
    14356 
    14357 > select up
    14358 
    14359 19 atoms, 20 bonds, 1 residue, 1 model selected 
    14360 
    14361 > hide #!67 models
    14362 
    14363 > hide #67.1 models
    14364 
    14365 > select add #67
    14366 
    14367 3828 atoms, 3910 bonds, 3 pseudobonds, 504 residues, 2 models selected 
    14368 
    14369 > select subtract #67
    14370 
    14371 Nothing selected 
    14372 
    14373 > select #15:601
    14374 
    14375 31 atoms, 32 bonds, 1 residue, 1 model selected 
    14376 
    14377 > select clear
    14378 
    14379 > color #57.4 #ff69b481 models
    14380 
    14381 > color #57.4 #ff69b480 models
    14382 
    14383 > select #15:601
    14384 
    14385 31 atoms, 32 bonds, 1 residue, 1 model selected 
    14386 
    14387 > show #15 models
    14388 
    14389 > select add #15
    14390 
    14391 3917 atoms, 3998 bonds, 515 residues, 1 model selected 
    14392 
    14393 > hide sel atoms
    14394 
    14395 > hide sel cartoons
    14396 
    14397 > select #15:601
    14398 
    14399 31 atoms, 32 bonds, 1 residue, 1 model selected 
    14400 
    14401 > show sel atoms
    14402 
    14403 > hide #17.1 models
    14404 
    14405 > volume #57.4 level 0.006742
    14406 
    14407 > select #15:601
    14408 
    14409 31 atoms, 32 bonds, 1 residue, 1 model selected 
    14410 
    14411 > color sel hot pink
    14412 
    14413 > color sel byhetero
    14414 
    14415 > select clear
    14416 
    14417 > select H
    14418 
    14419 93 atoms, 8 residues, 7 models selected 
    14420 
    14421 > hide sel & #15 atoms
    14422 
    14423 > color #57.4 #b2b2b280 models
    14424 
    14425 > volume #57.4 level 0.007863
    14426 
    14427 > volume #57.4 level 0.007995
    14428 
    14429 > volume #57.4 level 0.007863
    14430 
    14431 > volume #57.4 level 0.007995
    14432 
    14433 > volume #57.4 level 0.007797
    14434 
    14435 > save
    14436 > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-TFV_IF-
    14437 > TFV.png width 809 height 738 supersample 3 transparentBackground true
    14438 
    14439 > show #!63 models
    14440 
    14441 > hide #!57.4 models
    14442 
    14443 > hide #!57 models
    14444 
    14445 > hide #15 models
    14446 
    14447 > select add #15
    14448 
    14449 3998 atoms, 3998 bonds, 522 residues, 7 models selected 
    14450 
    14451 > select subtract #15
    14452 
    14453 81 atoms, 7 residues, 6 models selected 
    14454 
    14455 > select add #18
    14456 
    14457 3855 atoms, 3876 bonds, 5 pseudobonds, 492 residues, 7 models selected 
    14458 
    14459 > select subtract #18
    14460 
    14461 69 atoms, 6 residues, 5 models selected 
    14462 
    14463 > hide #!63 models
    14464 
    14465 > hide #63.1 models
    14466 
    14467 > open /Volumes/bbc/Lab-
    14468 > Jiang/PROJECTS/OAT1/new_structures_20250209/20240831_rOAT1-TFV/inward_j152_2.7A/rOAT1-TFV_IF-
    14469 > coot-1_real_space_refined_001_real_space_refined_002.pdb
    14470 
    14471 Chain information for rOAT1-TFV_IF-
    14472 coot-1_real_space_refined_001_real_space_refined_002.pdb #35 
    14473 --- 
    14474 Chain | Description 
    14475 A | No description available 
    14476  
    14477 
    14478 > show #!57.4 models
    14479 
    14480 > select #35:601
    14481 
    14482 19 atoms, 20 bonds, 1 residue, 1 model selected 
    14483 
    14484 > color sel hot pink
    14485 
    14486 > color sel byhetero
    14487 
    14488 > select clear
    14489 
    14490 > select add #35
    14491 
    14492 3905 atoms, 3986 bonds, 515 residues, 1 model selected 
    14493 
    14494 > hide sel cartoons
    14495 
    14496 > hide sel atoms
    14497 
    14498 > select #35:601
    14499 
    14500 19 atoms, 20 bonds, 1 residue, 1 model selected 
    14501 
    14502 > show sel atoms
    14503 
    14504 > select clear
    14505 
    14506 > save
    14507 > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-TFV_IF-
    14508 > TFV.png width 809 height 738 supersample 3 transparentBackground true
    14509 
    14510 > hide #35 models
    14511 
    14512 > hide #!57.4 models
    14513 
    14514 > show #!59 models
    14515 
    14516 > hide #!59.3 models
    14517 
    14518 > hide #!59.2 models
    14519 
    14520 > hide #!59.1 models
    14521 
    14522 > show #21 models
    14523 
    14524 > select #21: 601-603
    14525 
    14526 70 atoms, 76 bonds, 2 residues, 1 model selected 
    14527 
    14528 > color sel forest green
    14529 
    14530 > color sel byhetero
    14531 
    14532 > color sel orange
    14533 
    14534 > color sel byhetero
    14535 
    14536 > select add #21
    14537 
    14538 3956 atoms, 4042 bonds, 516 residues, 1 model selected 
    14539 
    14540 > hide sel cartoons
    14541 
    14542 > hide sel atoms
    14543 
    14544 > select #21: 601-603
    14545 
    14546 70 atoms, 76 bonds, 2 residues, 1 model selected 
    14547 
    14548 > show sel atoms
    14549 
    14550 > select H
    14551 
    14552 93 atoms, 8 residues, 7 models selected 
    14553 
    14554 > hide sel & #21 atoms
    14555 
    14556 > color #59.4 #b2b2b2ff models
    14557 
    14558 > color #59.4 #b2b2b200 models
    14559 
    14560 > color #59.4 #b2b2b280 models
    14561 
    14562 > surface dust #59.4 size 4.98
    14563 
    14564 > volume #59.4 level 0.01251
    14565 
    14566 > select clear
    14567 
    14568 > save
    14569 > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-AAI_IF-
    14570 > AAI.png width 809 height 738 supersample 3 transparentBackground true
    14571 
    14572 > save /Users/dout2/Downloads/OAT1_ligand_Colored_domain.cxs includeMaps true
    14573 
    14574 > select #21: 601-603
    14575 
    14576 70 atoms, 76 bonds, 2 residues, 1 model selected 
    14577 
    14578 > color sel light sea green
    14579 
    14580 > color sel byhetero
    14581 
    14582 > color sel cornflower blue
    14583 
    14584 > color sel byhetero
    14585 
    14586 > color sel magenta
    14587 
    14588 > color sel byhetero
    14589 
    14590 > color sel forest green
    14591 
    14592 > color sel byhetero
    14593 
    14594 > color sel cornflower blue
    14595 
    14596 > color sel byhetero
    14597 
    14598 > ui tool show "Color Actions"
    14599 
    14600 > color sel olive
    14601 
    14602 > color sel byhetero
    14603 
    14604 > select clear
    14605 
    14606 > save
    14607 > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-AAI_IF-
    14608 > AAI.png width 809 height 738 supersample 3 transparentBackground true
    14609 
    14610 
    14611 ===== Log before crash end =====
    14612 
    14613 Log:
    14614 UCSF ChimeraX version: 1.8 (2024-06-10) 
    14615 © 2016-2024 Regents of the University of California. All rights reserved. 
    14616 
    14617 > open /Users/dout2/Downloads/OAT1_ligand_Colored_domain.cxs
    14618 
    14619 Opened rOAT1-AZT_IF.mrc as #2, grid size 320,320,320, pixel 0.83, shown at
    14620 step 1, values float32 
    14621 Opened rOAT1-AZT_IF.mrc 2 as #3.3, grid size 320,320,320, pixel 0.83, shown at
    14622 step 1, values float32 
    14623 Opened rOAT1-AZT_OF.mrc as #4, grid size 320,320,320, pixel 0.83, shown at
    14624 level 0.00975, step 1, values float32 
    14625 Opened rOAT1-AZT_OF.mrc 2 as #6.3, grid size 320,320,320, pixel 0.83, shown at
    14626 step 1, values float32 
    14627 Opened rOAT1-PBD_IF.mrc as #7, grid size 320,320,320, pixel 0.83, shown at
    14628 level 0.0111, step 1, values float32 
    14629 Opened rOAT1-PBD_IF.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at
    14630 step 1, values float32 
    14631 Opened rOAT1-PBD_OF.mrc as #10, grid size 320,320,320, pixel 0.83, shown at
    14632 step 1, values float32 
    14633 Opened rOAT1-PBD_OF.mrc 2 as #11.3, grid size 320,320,320, pixel 0.83, shown
    14634 at step 1, values float32 
    14635 Opened rOAT1-PBD_OF.mrc 2 as #13.3, grid size 320,320,320, pixel 0.83, shown
    14636 at step 1, values float32 
    14637 Opened rOAT1-TFV_IF.mrc as #14, grid size 320,320,320, pixel 0.83, shown at
    14638 step 1, values float32 
    14639 Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
    14640 at step 1, values float32 
    14641 Opened rOAT1-TVF_OF.mrc as #17, grid size 320,320,320, pixel 0.83, shown at
    14642 step 1, values float32 
    14643 Opened rOAT1-AAI_IF.mrc as #20, grid size 320,320,320, pixel 0.83, shown at
    14644 step 1, values float32 
    14645 Opened rOAT1-AAI_IF.mrc 2 as #22.3, grid size 320,320,320, pixel 0.83, shown
    14646 at step 1, values float32 
    14647 Opened rOAT1-AAI_OF.mrc as #23, grid size 320,320,320, pixel 0.83, shown at
    14648 step 1, values float32 
    14649 Opened rOAT1-AAI_OF.mrc 2 as #25.3, grid size 320,320,320, pixel 0.83, shown
    14650 at step 1, values float32 
    14651 Opened rOAT1-PAH.mrc as #27, grid size 160,160,160, pixel 0.83, shown at step
    14652 1, values float32 
    14653 Opened rOAT1-PAH.mrc 2 as #28.3, grid size 160,160,160, pixel 0.83, shown at
    14654 step 1, values float32 
    14655 Opened rOAT1-FBP.mrc as #29, grid size 320,320,320, pixel 0.83, shown at step
    14656 1, values float32 
    14657 Opened rOAT1-FBP.mrc 2 as #31.3, grid size 320,320,320, pixel 0.83, shown at
    14658 step 1, values float32 
    14659 Opened rOAT1-CFM.mrc as #32, grid size 320,320,320, pixel 0.83, shown at step
    14660 1, values float32 
    14661 Opened hOAT1-TFV_IF.mrc as #36, grid size 320,320,320, pixel 0.83, shown at
    14662 step 1, values float32 
    14663 Opened hOAT1-TFV_IF.mrc 2 as #38.3, grid size 320,320,320, pixel 0.83, shown
    14664 at step 1, values float32 
    14665 Opened hOAT1-TFV_OF.mrc as #39, grid size 320,320,320, pixel 0.83, shown at
    14666 step 1, values float32 
    14667 Opened hOAT1-TFV_OF.mrc 2 as #42.3, grid size 320,320,320, pixel 0.83, shown
    14668 at step 1, values float32 
    14669 Opened rOAT1-AKG_OF.mrc as #40, grid size 320,320,320, pixel 0.83, shown at
    14670 level 0.0122, step 1, values float32 
    14671 Opened rOAT1-AKG_OOC.mrc as #44, grid size 320,320,320, pixel 0.83, shown at
    14672 step 1, values float32 
    14673 Opened rOAT1-R466A.mrc as #46, grid size 480,480,480, pixel 0.553, shown at
    14674 step 1, values float32 
    14675 Opened rOAT1-Apo.mrc as #48, grid size 240,240,240, pixel 0.553, shown at step
    14676 1, values float32 
    14677 Opened rOAT1-PBD_IF.mrc as #50, grid size 160,160,160, pixel 0.83, shown at
    14678 step 1, values float32 
    14679 Opened rOAT1-AZT_IF.mrc 0 as #52.1, grid size 320,320,320, pixel 0.83, shown
    14680 at level 0.00942, step 1, values float32 
    14681 Opened rOAT1-AZT_IF.mrc 1 as #52.2, grid size 320,320,320, pixel 0.83, shown
    14682 at level 0.00804, step 1, values float32 
    14683 Opened rOAT1-AZT_IF.mrc 2 as #52.3, grid size 320,320,320, pixel 0.83, shown
    14684 at level 0.0094, step 1, values float32 
    14685 Opened rOAT1-AZT_IF.mrc 3 as #52.4, grid size 320,320,320, pixel 0.83, shown
    14686 at level 0.00804, step 1, values float32 
    14687 Opened rOAT1-AZT_OF.mrc 0 as #54.1, grid size 320,320,320, pixel 0.83, shown
    14688 at level 0.00957, step 1, values float32 
    14689 Opened rOAT1-AZT_OF.mrc 1 as #54.2, grid size 320,320,320, pixel 0.83, shown
    14690 at level 0.00975, step 1, values float32 
    14691 Opened rOAT1-AZT_OF.mrc 2 as #54.3, grid size 320,320,320, pixel 0.83, shown
    14692 at level 0.00887, step 1, values float32 
    14693 Opened rOAT1-AZT_OF.mrc 3 as #54.4, grid size 320,320,320, pixel 0.83, shown
    14694 at level 0.00975, step 1, values float32 
    14695 Opened rOAT1-PBD_IF.mrc 0 as #55.1, grid size 320,320,320, pixel 0.83, shown
    14696 at level 0.0091, step 1, values float32 
    14697 Opened rOAT1-PBD_IF.mrc 1 as #55.2, grid size 320,320,320, pixel 0.83, shown
    14698 at level 0.0111, step 1, values float32 
    14699 Opened rOAT1-PBD_IF.mrc 2 as #55.3, grid size 320,320,320, pixel 0.83, shown
    14700 at level 0.0111, step 1, values float32 
    14701 Opened rOAT1-PBD_IF.mrc 3 as #55.4, grid size 320,320,320, pixel 0.83, shown
    14702 at level 0.0111, step 1, values float32 
    14703 Opened rOAT1-PBD_OF.mrc 0 as #56.1, grid size 320,320,320, pixel 0.83, shown
    14704 at level 0.00965, step 1, values float32 
    14705 Opened rOAT1-PBD_OF.mrc 1 as #56.2, grid size 320,320,320, pixel 0.83, shown
    14706 at level 0.00965, step 1, values float32 
    14707 Opened rOAT1-PBD_OF.mrc 2 as #56.3, grid size 320,320,320, pixel 0.83, shown
    14708 at level 0.00965, step 1, values float32 
    14709 Opened rOAT1-PBD_OF.mrc 3 as #56.4, grid size 320,320,320, pixel 0.83, shown
    14710 at level 0.00965, step 1, values float32 
    14711 Opened rOAT1-TFV_IF.mrc 0 as #57.1, grid size 320,320,320, pixel 0.83, shown
    14712 at level 0.00803, step 1, values float32 
    14713 Opened rOAT1-TFV_IF.mrc 1 as #57.2, grid size 320,320,320, pixel 0.83, shown
    14714 at level 0.00793, step 1, values float32 
    14715 Opened rOAT1-TFV_IF.mrc 2 as #57.3, grid size 320,320,320, pixel 0.83, shown
    14716 at level 0.00793, step 1, values float32 
    14717 Opened rOAT1-TFV_IF.mrc 3 as #57.4, grid size 320,320,320, pixel 0.83, shown
    14718 at level 0.0078, step 1, values float32 
    14719 Opened rOAT1-AAI_IF.mrc 0 as #59.1, grid size 320,320,320, pixel 0.83, shown
    14720 at level 0.00993, step 1, values float32 
    14721 Opened rOAT1-AAI_IF.mrc 1 as #59.2, grid size 320,320,320, pixel 0.83, shown
    14722 at level 0.00901, step 1, values float32 
    14723 Opened rOAT1-AAI_IF.mrc 2 as #59.3, grid size 320,320,320, pixel 0.83, shown
    14724 at level 0.0102, step 1, values float32 
    14725 Opened rOAT1-AAI_IF.mrc 3 as #59.4, grid size 320,320,320, pixel 0.83, shown
    14726 at level 0.0125, step 1, values float32 
    14727 Opened rOAT1-AAI_OF.mrc 0 as #60.1, grid size 320,320,320, pixel 0.83, shown
    14728 at level 0.00928, step 1, values float32 
    14729 Opened rOAT1-AAI_OF.mrc 1 as #60.2, grid size 320,320,320, pixel 0.83, shown
    14730 at level 0.00988, step 1, values float32 
    14731 Opened rOAT1-AAI_OF.mrc 2 as #60.3, grid size 320,320,320, pixel 0.83, shown
    14732 at level 0.00988, step 1, values float32 
    14733 Opened rOAT1-AAI_OF.mrc 3 as #60.4, grid size 320,320,320, pixel 0.83, shown
    14734 at level 0.00988, step 1, values float32 
    14735 Opened hOAT1-TFV_OF.mrc 0 as #41.1, grid size 320,320,320, pixel 0.83, shown
    14736 at level 0.0105, step 1, values float32 
    14737 Opened hOAT1-TFV_OF.mrc 1 as #41.2, grid size 320,320,320, pixel 0.83, shown
    14738 at level 0.0106, step 1, values float32 
    14739 Opened hOAT1-TFV_OF.mrc 2 as #41.3, grid size 320,320,320, pixel 0.83, shown
    14740 at level 0.0106, step 1, values float32 
    14741 Opened hOAT1-TFV_OF.mrc 3 as #41.4, grid size 320,320,320, pixel 0.83, shown
    14742 at level 0.0106, step 1, values float32 
    14743 Opened hOAT1-TFV_IF.mrc 0 as #37.1, grid size 320,320,320, pixel 0.83, shown
    14744 at level 0.00722, step 1, values float32 
    14745 Opened hOAT1-TFV_IF.mrc 1 as #37.2, grid size 320,320,320, pixel 0.83, shown
    14746 at level 0.00852, step 1, values float32 
    14747 Opened hOAT1-TFV_IF.mrc 2 as #37.3, grid size 320,320,320, pixel 0.83, shown
    14748 at level 0.00852, step 1, values float32 
    14749 Opened hOAT1-TFV_IF.mrc 3 as #37.4, grid size 320,320,320, pixel 0.83, shown
    14750 at level 0.00852, step 1, values float32 
    14751 Opened rOAT1-AKG_OF.mrc 0 as #61.1, grid size 320,320,320, pixel 0.83, shown
    14752 at level 0.0117, step 1, values float32 
    14753 Opened rOAT1-AKG_OF.mrc 1 as #61.2, grid size 320,320,320, pixel 0.83, shown
    14754 at level 0.0122, step 1, values float32 
    14755 Opened rOAT1-AKG_OF.mrc 2 as #61.3, grid size 320,320,320, pixel 0.83, shown
    14756 at level 0.0122, step 1, values float32 
    14757 Opened rOAT1-AKG_OF.mrc 3 as #61.4, grid size 320,320,320, pixel 0.83, shown
    14758 at level 0.0122, step 1, values float32 
    14759 Opened rOAT1-AKG_OOC.mrc 0 as #64.1, grid size 320,320,320, pixel 0.83, shown
    14760 at level 0.0107, step 1, values float32 
    14761 Opened rOAT1-AKG_OOC.mrc 1 as #64.2, grid size 320,320,320, pixel 0.83, shown
    14762 at level 0.0102, step 1, values float32 
    14763 Opened rOAT1-AKG_OOC.mrc 2 as #64.3, grid size 320,320,320, pixel 0.83, shown
    14764 at level 0.0102, step 1, values float32 
    14765 Opened rOAT1-AKG_OOC.mrc 3 as #64.4, grid size 320,320,320, pixel 0.83, shown
    14766 at level 0.0102, step 1, values float32 
    14767 Opened rOAT1-R466A.mrc 0 as #65.1, grid size 480,480,480, pixel 0.553, shown
    14768 at level 0.00894, step 1, values float32 
    14769 Opened rOAT1-R466A.mrc 1 as #65.2, grid size 480,480,480, pixel 0.553, shown
    14770 at level 0.0115, step 1, values float32 
    14771 Opened rOAT1-R466A.mrc 2 as #65.3, grid size 480,480,480, pixel 0.553, shown
    14772 at level 0.0115, step 1, values float32 
    14773 Opened rOAT1-TVF_OF.mrc 0 as #19.1, grid size 320,320,320, pixel 0.83, shown
    14774 at level 0.011, step 1, values float32 
    14775 Opened rOAT1-TVF_OF.mrc 1 as #19.2, grid size 320,320,320, pixel 0.83, shown
    14776 at level 0.011, step 1, values float32 
    14777 Opened rOAT1-TVF_OF.mrc 2 as #19.3, grid size 320,320,320, pixel 0.83, shown
    14778 at level 0.011, step 1, values float32 
    14779 Opened rOAT1-TVF_OF.mrc 3 as #19.4, grid size 320,320,320, pixel 0.83, shown
    14780 at level 0.0078, step 1, values float32 
    14781 Opened rOAT1-TVF_OF.mrc 4 as #19.5, grid size 320,320,320, pixel 0.83, shown
    14782 at level 0.011, step 1, values float32 
    14783 Opened rOAT1-TVF_OF.mrc 5 as #19.6, grid size 320,320,320, pixel 0.83, shown
    14784 at level 0.011, step 1, values float32 
    14785 Log from Sun Apr 20 23:23:04 2025UCSF ChimeraX version: 1.8 (2024-06-10) 
    14786 © 2016-2024 Regents of the University of California. All rights reserved. 
    14787 
    14788 > open /Users/dout2/Downloads/OAT1_ligand_density.cxs
    14789 
    14790 Opened rOAT1-AZT_IF.mrc as #2, grid size 320,320,320, pixel 0.83, shown at
    14791 level 0.01, step 1, values float32 
    14792 Opened rOAT1-AZT_IF.mrc 2 as #3.3, grid size 320,320,320, pixel 0.83, shown at
    14793 level 0.00807, step 1, values float32 
    14794 Opened rOAT1-AZT_OF.mrc as #4, grid size 320,320,320, pixel 0.83, shown at
    14795 level 0.012, step 1, values float32 
    14796 Opened rOAT1-AZT_OF.mrc 2 as #6.3, grid size 320,320,320, pixel 0.83, shown at
    14797 level 0.0106, step 1, values float32 
    14798 Opened rOAT1-PBD_IF.mrc as #7, grid size 320,320,320, pixel 0.83, shown at
    14799 level 0.0111, step 1, values float32 
    14800 Opened rOAT1-PBD_IF.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at
    14801 level 0.00516, step 1, values float32 
    14802 Opened rOAT1-PBD_OF.mrc as #10, grid size 320,320,320, pixel 0.83, shown at
    14803 level 0.0107, step 1, values float32 
    14804 Opened rOAT1-PBD_OF.mrc 2 as #11.3, grid size 320,320,320, pixel 0.83, shown
    14805 at level 0.0108, step 1, values float32 
    14806 Opened rOAT1-PBD_OF.mrc 2 as #13.3, grid size 320,320,320, pixel 0.83, shown
    14807 at level 0.00806, step 1, values float32 
    14808 Opened rOAT1-TFV_IF.mrc as #14, grid size 320,320,320, pixel 0.83, shown at
    14809 level 0.00563, step 2, values float32 
    14810 Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
    14811 at level 0.00563, step 1, values float32 
    14812 Opened rOAT1-TVF_OF.mrc as #17, grid size 320,320,320, pixel 0.83, shown at
    14813 level 0.011, step 1, values float32 
    14814 Opened rOAT1-TVF_OF.mrc 2 as #19.3, grid size 320,320,320, pixel 0.83, shown
    14815 at level 0.011, step 1, values float32 
    14816 Opened rOAT1-AAI_IF.mrc as #20, grid size 320,320,320, pixel 0.83, shown at
    14817 level 0.0133, step 1, values float32 
    14818 Opened rOAT1-AAI_IF.mrc 2 as #22.3, grid size 320,320,320, pixel 0.83, shown
    14819 at level 0.0128, step 1, values float32 
    14820 Opened rOAT1-AAI_OF.mrc as #23, grid size 320,320,320, pixel 0.83, shown at
    14821 level 0.0168, step 1, values float32 
    14822 Opened rOAT1-AAI_OF.mrc 2 as #25.3, grid size 320,320,320, pixel 0.83, shown
    14823 at level 0.0168, step 1, values float32 
    14824 Opened rOAT1-PAH.mrc as #27, grid size 160,160,160, pixel 0.83, shown at level
    14825 0.121, step 1, values float32 
    14826 Opened rOAT1-PAH.mrc 2 as #28.3, grid size 160,160,160, pixel 0.83, shown at
    14827 level 0.0683, step 1, values float32 
    14828 Opened rOAT1-FBP.mrc as #29, grid size 320,320,320, pixel 0.83, shown at level
    14829 0.0104, step 1, values float32 
    14830 Opened rOAT1-FBP.mrc 2 as #31.3, grid size 320,320,320, pixel 0.83, shown at
    14831 level 0.0038, step 1, values float32 
    14832 Opened rOAT1-CFM.mrc as #32, grid size 320,320,320, pixel 0.83, shown at level
    14833 0.0119, step 1, values float32 
    14834 Opened rOAT1-TVF-Cl_OF.mrc 2 as #35.3, grid size 320,320,320, pixel 0.83,
    14835 shown at level 0.0118, step 1, values float32 
    14836 Opened hOAT1-TFV_IF.mrc as #36, grid size 320,320,320, pixel 0.83, shown at
    14837 level 0.00852, step 1, values float32 
    14838 Opened hOAT1-TFV_IF.mrc 2 as #38.3, grid size 320,320,320, pixel 0.83, shown
    14839 at level 0.00686, step 1, values float32 
    14840 Opened hOAT1-TFV_OF.mrc as #39, grid size 320,320,320, pixel 0.83, shown at
    14841 level 0.0106, step 1, values float32 
    14842 Opened hOAT1-TFV_OF.mrc 2 as #42.3, grid size 320,320,320, pixel 0.83, shown
    14843 at level 0.00699, step 1, values float32 
    14844 Opened rOAT1-AKG_OF.mrc as #40, grid size 320,320,320, pixel 0.83, shown at
    14845 level 0.0122, step 1, values float32 
    14846 Opened rOAT1-AKG_OOC.mrc as #44, grid size 320,320,320, pixel 0.83, shown at
    14847 level 0.0102, step 1, values float32 
    14848 Opened rOAT1-R466A.mrc as #46, grid size 480,480,480, pixel 0.553, shown at
    14849 level 0.0115, step 1, values float32 
    14850 Opened rOAT1-Apo.mrc as #48, grid size 240,240,240, pixel 0.553, shown at step
    14851 1, values float32 
    14852 Opened rOAT1-PBD_IF.mrc as #50, grid size 160,160,160, pixel 0.83, shown at
    14853 level 0.282, step 1, values float32 
    14854 Log from Tue Apr 15 12:09:47 2025UCSF ChimeraX version: 1.8 (2024-06-10) 
    14855 © 2016-2024 Regents of the University of California. All rights reserved. 
    14856 
    14857 > open /Users/dout2/Downloads/OAT1_ligand_density.cxs
    14858 
    14859 Opened rOAT1-AZT_IF.mrc as #2, grid size 320,320,320, pixel 0.83, shown at
    14860 level 0.0151, step 1, values float32 
    14861 Opened rOAT1-AZT_IF.mrc 2 as #3.3, grid size 320,320,320, pixel 0.83, shown at
    14862 level 0.00807, step 1, values float32 
    14863 Opened rOAT1-AZT_OF.mrc as #4, grid size 320,320,320, pixel 0.83, shown at
    14864 level 0.0137, step 1, values float32 
    14865 Opened rOAT1-AZT_OF.mrc 2 as #6.3, grid size 320,320,320, pixel 0.83, shown at
    14866 level 0.0106, step 1, values float32 
    14867 Opened rOAT1-PBD_IF.mrc as #7, grid size 320,320,320, pixel 0.83, shown at
    14868 level 0.0111, step 1, values float32 
    14869 Opened rOAT1-PBD_IF.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at
    14870 level 0.00516, step 1, values float32 
    14871 Opened rOAT1-PBD_OF.mrc as #10, grid size 320,320,320, pixel 0.83, shown at
    14872 level 0.00806, step 1, values float32 
    14873 Opened rOAT1-PBD_OF.mrc 2 as #11.3, grid size 320,320,320, pixel 0.83, shown
    14874 at level 0.0108, step 1, values float32 
    14875 Opened rOAT1-PBD_OF.mrc 2 as #13.3, grid size 320,320,320, pixel 0.83, shown
    14876 at level 0.00806, step 1, values float32 
    14877 Opened rOAT1-TFV_IF.mrc as #14, grid size 320,320,320, pixel 0.83, shown at
    14878 level 0.00563, step 2, values float32 
    14879 Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
    14880 at level 0.00563, step 1, values float32 
    14881 Opened rOAT1-TVF_OF.mrc as #17, grid size 320,320,320, pixel 0.83, shown at
    14882 level 0.011, step 1, values float32 
    14883 Opened rOAT1-TVF_OF.mrc 2 as #19.3, grid size 320,320,320, pixel 0.83, shown
    14884 at level 0.011, step 1, values float32 
    14885 Opened rOAT1-AAI_IF.mrc as #20, grid size 320,320,320, pixel 0.83, shown at
    14886 level 0.0194, step 1, values float32 
    14887 Opened rOAT1-AAI_IF.mrc 2 as #22.3, grid size 320,320,320, pixel 0.83, shown
    14888 at level 0.0128, step 1, values float32 
    14889 Opened rOAT1-AAI_OF.mrc as #23, grid size 320,320,320, pixel 0.83, shown at
    14890 level 0.0168, step 1, values float32 
    14891 Opened rOAT1-AAI_OF.mrc 2 as #25.3, grid size 320,320,320, pixel 0.83, shown
    14892 at level 0.0168, step 1, values float32 
    14893 Opened rOAT1-PAH.mrc as #27, grid size 160,160,160, pixel 0.83, shown at level
    14894 0.121, step 1, values float32 
    14895 Opened rOAT1-PAH.mrc 2 as #28.3, grid size 160,160,160, pixel 0.83, shown at
    14896 level 0.0683, step 1, values float32 
    14897 Opened rOAT1-FBP.mrc as #29, grid size 320,320,320, pixel 0.83, shown at level
    14898 0.0104, step 1, values float32 
    14899 Opened rOAT1-FBP.mrc 2 as #31.3, grid size 320,320,320, pixel 0.83, shown at
    14900 level 0.0038, step 1, values float32 
    14901 Opened rOAT1-CFM.mrc as #32, grid size 320,320,320, pixel 0.83, shown at level
    14902 0.0119, step 1, values float32 
    14903 Opened rOAT1-TVF-Cl_OF.mrc 2 as #35.3, grid size 320,320,320, pixel 0.83,
    14904 shown at level 0.0118, step 1, values float32 
    14905 Opened hOAT1-TFV_IF.mrc as #36, grid size 320,320,320, pixel 0.83, shown at
    14906 level 0.00852, step 1, values float32 
    14907 Opened hOAT1-TFV_IF.mrc 2 as #38.3, grid size 320,320,320, pixel 0.83, shown
    14908 at level 0.00686, step 1, values float32 
    14909 Opened hOAT1-TFV_OF.mrc as #39, grid size 320,320,320, pixel 0.83, shown at
    14910 level 0.0106, step 1, values float32 
    14911 Opened hOAT1-TFV_OF.mrc 2 as #42.3, grid size 320,320,320, pixel 0.83, shown
    14912 at level 0.00699, step 1, values float32 
    14913 Opened rOAT1-AKG_OF.mrc as #40, grid size 320,320,320, pixel 0.83, shown at
    14914 level 0.0122, step 1, values float32 
    14915 Opened rOAT1-AKG_OOC.mrc as #44, grid size 320,320,320, pixel 0.83, shown at
    14916 level 0.0102, step 1, values float32 
    14917 Opened rOAT1-R466A.mrc as #46, grid size 480,480,480, pixel 0.553, shown at
    14918 level 0.0115, step 1, values float32 
    14919 Opened rOAT1-Apo.mrc as #48, grid size 240,240,240, pixel 0.553, shown at step
    14920 1, values float32 
    14921 Log from Sat Apr 12 21:31:41 2025UCSF ChimeraX version: 1.8 (2024-06-10) 
    14922 © 2016-2024 Regents of the University of California. All rights reserved. 
    14923 
    14924 > open /Users/dout2/Downloads/OAT1_ligand_density.cxs
    14925 
    14926 Opened rOAT1-AZT_IF.mrc as #2, grid size 320,320,320, pixel 0.83, shown at
    14927 level 0.0151, step 1, values float32 
    14928 Opened rOAT1-AZT_IF.mrc 2 as #3.3, grid size 320,320,320, pixel 0.83, shown at
    14929 level 0.00807, step 1, values float32 
    14930 Opened rOAT1-AZT_OF.mrc as #4, grid size 320,320,320, pixel 0.83, shown at
    14931 level 0.0137, step 1, values float32 
    14932 Opened rOAT1-AZT_OF.mrc 2 as #6.3, grid size 320,320,320, pixel 0.83, shown at
    14933 level 0.0106, step 1, values float32 
    14934 Opened rOAT1-PBD_IF.mrc as #7, grid size 320,320,320, pixel 0.83, shown at
    14935 level 0.0111, step 1, values float32 
    14936 Opened rOAT1-PBD_IF.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at
    14937 level 0.00516, step 1, values float32 
    14938 Opened rOAT1-PBD_OF.mrc as #10, grid size 320,320,320, pixel 0.83, shown at
    14939 level 0.00806, step 1, values float32 
    14940 Opened rOAT1-PBD_OF.mrc 2 as #11.3, grid size 320,320,320, pixel 0.83, shown
    14941 at level 0.0108, step 1, values float32 
    14942 Opened rOAT1-PBD_OF.mrc 2 as #13.3, grid size 320,320,320, pixel 0.83, shown
    14943 at level 0.00806, step 1, values float32 
    14944 Opened rOAT1-TFV_IF.mrc as #14, grid size 320,320,320, pixel 0.83, shown at
    14945 level 0.00563, step 2, values float32 
    14946 Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
    14947 at level 0.00563, step 1, values float32 
    14948 Opened rOAT1-TVF_OF.mrc as #17, grid size 320,320,320, pixel 0.83, shown at
    14949 level 0.011, step 1, values float32 
    14950 Opened rOAT1-TVF_OF.mrc 2 as #19.3, grid size 320,320,320, pixel 0.83, shown
    14951 at level 0.011, step 1, values float32 
    14952 Opened rOAT1-AAI_IF.mrc as #20, grid size 320,320,320, pixel 0.83, shown at
    14953 level 0.0194, step 1, values float32 
    14954 Opened rOAT1-AAI_IF.mrc 2 as #22.3, grid size 320,320,320, pixel 0.83, shown
    14955 at level 0.0128, step 1, values float32 
    14956 Opened rOAT1-AAI_OF.mrc as #23, grid size 320,320,320, pixel 0.83, shown at
    14957 level 0.0168, step 1, values float32 
    14958 Opened rOAT1-AAI_OF.mrc 2 as #25.3, grid size 320,320,320, pixel 0.83, shown
    14959 at level 0.0168, step 1, values float32 
    14960 Opened rOAT1-PAH.mrc as #27, grid size 160,160,160, pixel 0.83, shown at level
    14961 0.121, step 1, values float32 
    14962 Opened rOAT1-PAH.mrc 2 as #28.3, grid size 160,160,160, pixel 0.83, shown at
    14963 level 0.0683, step 1, values float32 
    14964 Opened rOAT1-FBP.mrc as #29, grid size 320,320,320, pixel 0.83, shown at level
    14965 0.0104, step 1, values float32 
    14966 Opened rOAT1-FBP.mrc 2 as #31.3, grid size 320,320,320, pixel 0.83, shown at
    14967 level 0.0038, step 1, values float32 
    14968 Opened rOAT1-CFM.mrc as #32, grid size 320,320,320, pixel 0.83, shown at level
    14969 0.0119, step 1, values float32 
    14970 Opened rOAT1-TVF-Cl_OF.mrc 2 as #35.3, grid size 320,320,320, pixel 0.83,
    14971 shown at level 0.0118, step 1, values float32 
    14972 Opened hOAT1-TFV_IF.mrc as #36, grid size 320,320,320, pixel 0.83, shown at
    14973 level 0.00852, step 1, values float32 
    14974 Opened hOAT1-TFV_IF.mrc 2 as #38.3, grid size 320,320,320, pixel 0.83, shown
    14975 at level 0.00686, step 1, values float32 
    14976 Opened hOAT1-TFV_OF.mrc as #39, grid size 320,320,320, pixel 0.83, shown at
    14977 level 0.0106, step 1, values float32 
    14978 Opened hOAT1-TFV_OF.mrc 2 as #42.3, grid size 320,320,320, pixel 0.83, shown
    14979 at level 0.00699, step 1, values float32 
    14980 Opened rOAT1-AKG_OF.mrc as #40, grid size 320,320,320, pixel 0.83, shown at
    14981 level 0.0122, step 1, values float32 
    14982 Opened rOAT1-AKG_OOC.mrc as #44, grid size 320,320,320, pixel 0.83, shown at
    14983 level 0.0102, step 1, values float32 
    14984 Opened postprocess_rescaled.mrc as #46, grid size 480,480,480, pixel 0.553,
    14985 shown at level 0.0115, step 1, values float32 
    14986 Log from Thu Apr 10 15:43:35 2025UCSF ChimeraX version: 1.8 (2024-06-10) 
    14987 © 2016-2024 Regents of the University of California. All rights reserved. 
    14988 
    14989 > open /Users/dout2/Downloads/OAT1_ligand_density.cxs format session
    14990 
    14991 Opened rOAT1-AZT_IF.mrc as #2, grid size 320,320,320, pixel 0.83, shown at
    14992 level 0.0151, step 1, values float32 
    14993 Opened rOAT1-AZT_IF.mrc 2 as #3.3, grid size 320,320,320, pixel 0.83, shown at
    14994 level 0.00807, step 1, values float32 
    14995 Opened rOAT1-AZT_OF.mrc as #4, grid size 320,320,320, pixel 0.83, shown at
    14996 level 0.0137, step 1, values float32 
    14997 Opened rOAT1-AZT_OF.mrc 2 as #6.3, grid size 320,320,320, pixel 0.83, shown at
    14998 level 0.0116, step 1, values float32 
    14999 Opened rOAT1-PBD_IF.mrc as #7, grid size 320,320,320, pixel 0.83, shown at
    15000 level 0.0111, step 1, values float32 
    15001 Opened rOAT1-PBD_IF.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at
    15002 level 0.00383, step 1, values float32 
    15003 Opened rOAT1-PBD_OF.mrc as #10, grid size 320,320,320, pixel 0.83, shown at
    15004 level 0.00806, step 1, values float32 
    15005 Opened rOAT1-PBD_OF.mrc 2 as #11.3, grid size 320,320,320, pixel 0.83, shown
    15006 at level 0.00806, step 1, values float32 
    15007 Opened rOAT1-PBD_OF.mrc 2 as #13.3, grid size 320,320,320, pixel 0.83, shown
    15008 at level 0.00806, step 1, values float32 
    15009 Opened rOAT1-TFV_IF.mrc as #14, grid size 320,320,320, pixel 0.83, shown at
    15010 level 0.00563, step 2, values float32 
    15011 Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
    15012 at level 0.00563, step 1, values float32 
    15013 Opened rOAT1-TVF_OF.mrc as #17, grid size 320,320,320, pixel 0.83, shown at
    15014 level 0.011, step 1, values float32 
    15015 Opened rOAT1-TVF_OF.mrc 2 as #19.3, grid size 320,320,320, pixel 0.83, shown
    15016 at level 0.011, step 1, values float32 
    15017 Opened rOAT1-AAI_IF.mrc as #20, grid size 320,320,320, pixel 0.83, shown at
    15018 level 0.0194, step 1, values float32 
    15019 Opened rOAT1-AAI_IF.mrc 2 as #22.3, grid size 320,320,320, pixel 0.83, shown
    15020 at level 0.0141, step 1, values float32 
    15021 Opened rOAT1-AAI_OF.mrc as #23, grid size 320,320,320, pixel 0.83, shown at
    15022 level 0.0168, step 1, values float32 
    15023 Opened rOAT1-AAI_OF.mrc 2 as #25.3, grid size 320,320,320, pixel 0.83, shown
    15024 at level 0.0168, step 1, values float32 
    15025 Opened rOAT1-PAH.mrc as #27, grid size 160,160,160, pixel 0.83, shown at level
    15026 0.121, step 1, values float32 
    15027 Opened rOAT1-PAH.mrc 2 as #28.3, grid size 160,160,160, pixel 0.83, shown at
    15028 level 0.0546, step 1, values float32 
    15029 Opened rOAT1-FBP.mrc as #29, grid size 320,320,320, pixel 0.83, shown at level
    15030 0.0104, step 1, values float32 
    15031 Opened rOAT1-FBP.mrc 2 as #31.3, grid size 320,320,320, pixel 0.83, shown at
    15032 level 0.0038, step 1, values float32 
    15033 Opened rOAT1-CFM.mrc as #32, grid size 320,320,320, pixel 0.83, shown at level
    15034 0.0119, step 1, values float32 
    15035 Opened rOAT1-TVF-Cl_OF.mrc 2 as #35.3, grid size 320,320,320, pixel 0.83,
    15036 shown at level 0.0118, step 1, values float32 
    15037 Opened hOAT1-TFV_IF.mrc as #36, grid size 320,320,320, pixel 0.83, shown at
    15038 level 0.00852, step 1, values float32 
    15039 Opened hOAT1-TFV_IF.mrc 2 as #38.3, grid size 320,320,320, pixel 0.83, shown
    15040 at level 0.00852, step 1, values float32 
    15041 Opened hOAT1-TFV_OF.mrc as #39, grid size 320,320,320, pixel 0.83, shown at
    15042 level 0.0106, step 1, values float32 
    15043 Opened hOAT1-TFV_OF.mrc 2 as #42.3, grid size 320,320,320, pixel 0.83, shown
    15044 at level 0.00699, step 1, values float32 
    15045 Log from Thu Apr 10 14:06:06 2025UCSF ChimeraX version: 1.8 (2024-06-10) 
    15046 © 2016-2024 Regents of the University of California. All rights reserved. 
    15047 
    15048 > open /Users/dout2/Downloads/OAT1_ligand_density.cxs
    15049 
    15050 Opened rOAT1-AZT_IF.mrc as #2, grid size 320,320,320, pixel 0.83, shown at
    15051 level 0.0151, step 1, values float32 
    15052 Opened rOAT1-AZT_IF.mrc 2 as #3.3, grid size 320,320,320, pixel 0.83, shown at
    15053 level 0.00807, step 1, values float32 
    15054 Opened rOAT1-AZT_OF.mrc as #4, grid size 320,320,320, pixel 0.83, shown at
    15055 level 0.0137, step 1, values float32 
    15056 Opened rOAT1-AZT_OF.mrc 2 as #6.3, grid size 320,320,320, pixel 0.83, shown at
    15057 level 0.0116, step 1, values float32 
    15058 Opened rOAT1-PBD_IF.mrc as #7, grid size 320,320,320, pixel 0.83, shown at
    15059 level 0.0111, step 1, values float32 
    15060 Opened rOAT1-PBD_IF.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at
    15061 level 0.00383, step 1, values float32 
    15062 Opened rOAT1-PBD_OF.mrc as #10, grid size 320,320,320, pixel 0.83, shown at
    15063 level 0.00806, step 1, values float32 
    15064 Opened rOAT1-PBD_OF.mrc 2 as #11.3, grid size 320,320,320, pixel 0.83, shown
    15065 at level 0.00806, step 1, values float32 
    15066 Opened rOAT1-PBD_OF.mrc 2 as #13.3, grid size 320,320,320, pixel 0.83, shown
    15067 at level 0.00806, step 1, values float32 
    15068 Opened rOAT1-TFV_IF.mrc as #14, grid size 320,320,320, pixel 0.83, shown at
    15069 level 0.00563, step 2, values float32 
    15070 Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
    15071 at level 0.00563, step 1, values float32 
    15072 Opened rOAT1-TVF_OF.mrc as #17, grid size 320,320,320, pixel 0.83, shown at
    15073 level 0.011, step 1, values float32 
    15074 Opened rOAT1-TVF_OF.mrc 2 as #19.3, grid size 320,320,320, pixel 0.83, shown
    15075 at level 0.011, step 1, values float32 
    15076 Opened rOAT1-AAI_IF.mrc as #20, grid size 320,320,320, pixel 0.83, shown at
    15077 level 0.0194, step 1, values float32 
    15078 Opened rOAT1-AAI_IF.mrc 2 as #22.3, grid size 320,320,320, pixel 0.83, shown
    15079 at level 0.0141, step 1, values float32 
    15080 Opened rOAT1-AAI_OF.mrc as #23, grid size 320,320,320, pixel 0.83, shown at
    15081 level 0.0168, step 1, values float32 
    15082 Opened rOAT1-AAI_OF.mrc 2 as #25.3, grid size 320,320,320, pixel 0.83, shown
    15083 at level 0.0168, step 1, values float32 
    15084 Opened rOAT1-PAH.mrc as #27, grid size 160,160,160, pixel 0.83, shown at level
    15085 0.121, step 1, values float32 
    15086 Opened rOAT1-PAH.mrc 2 as #28.3, grid size 160,160,160, pixel 0.83, shown at
    15087 level 0.0546, step 1, values float32 
    15088 Opened rOAT1-FBP.mrc as #29, grid size 320,320,320, pixel 0.83, shown at level
    15089 0.0104, step 1, values float32 
    15090 Opened rOAT1-FBP.mrc 2 as #31.3, grid size 320,320,320, pixel 0.83, shown at
    15091 level 0.0038, step 1, values float32 
    15092 Opened rOAT1-CFM.mrc as #32, grid size 320,320,320, pixel 0.83, shown at level
    15093 0.0119, step 1, values float32 
    15094 Opened rOAT1-TVF-Cl_OF.mrc 2 as #35.3, grid size 320,320,320, pixel 0.83,
    15095 shown at level 0.0118, step 1, values float32 
    15096 Opened hOAT1-TFV_IF.mrc as #36, grid size 320,320,320, pixel 0.83, shown at
    15097 level 0.00852, step 1, values float32 
    15098 Opened hOAT1-TFV_IF.mrc 2 as #38.3, grid size 320,320,320, pixel 0.83, shown
    15099 at level 0.00852, step 1, values float32 
    15100 Opened hOAT1-TFV_OF.mrc as #39, grid size 320,320,320, pixel 0.83, shown at
    15101 level 0.0106, step 1, values float32 
    15102 Opened hOAT1-TFV_OF.mrc 2 as #42.3, grid size 320,320,320, pixel 0.83, shown
    15103 at level 0.00699, step 1, values float32 
    15104 Log from Tue Mar 11 12:00:09 2025UCSF ChimeraX version: 1.8 (2024-06-10) 
    15105 © 2016-2024 Regents of the University of California. All rights reserved. 
    15106 
    15107 > open /Users/dout2/Downloads/OAT1_ligand_density.cxs
    15108 
    15109 Opened rOAT1-AZT_IF.mrc as #2, grid size 320,320,320, pixel 0.83, shown at
    15110 level 0.0151, step 1, values float32 
    15111 Opened rOAT1-AZT_IF.mrc 2 as #3.3, grid size 320,320,320, pixel 0.83, shown at
    15112 level 0.00807, step 1, values float32 
    15113 Opened rOAT1-AZT_OF.mrc as #4, grid size 320,320,320, pixel 0.83, shown at
    15114 level 0.0137, step 1, values float32 
    15115 Opened rOAT1-AZT_OF.mrc 2 as #6.3, grid size 320,320,320, pixel 0.83, shown at
    15116 level 0.0116, step 1, values float32 
    15117 Opened rOAT1-PBD_IF.mrc as #7, grid size 320,320,320, pixel 0.83, shown at
    15118 level 0.0111, step 1, values float32 
    15119 Opened rOAT1-PBD_IF.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at
    15120 level 0.00383, step 1, values float32 
    15121 Opened rOAT1-PBD_OF.mrc as #10, grid size 320,320,320, pixel 0.83, shown at
    15122 level 0.00806, step 1, values float32 
    15123 Opened rOAT1-PBD_OF.mrc 2 as #11.3, grid size 320,320,320, pixel 0.83, shown
    15124 at level 0.00806, step 1, values float32 
    15125 Opened rOAT1-PBD_OF.mrc 2 as #13.3, grid size 320,320,320, pixel 0.83, shown
    15126 at level 0.00806, step 1, values float32 
    15127 Opened rOAT1-TFV_IF.mrc as #14, grid size 320,320,320, pixel 0.83, shown at
    15128 level 0.00563, step 2, values float32 
    15129 Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
    15130 at level 0.00563, step 1, values float32 
    15131 Opened rOAT1-TVF_OF.mrc as #17, grid size 320,320,320, pixel 0.83, shown at
    15132 level 0.011, step 1, values float32 
    15133 Opened rOAT1-TVF_OF.mrc 2 as #19.3, grid size 320,320,320, pixel 0.83, shown
    15134 at level 0.011, step 1, values float32 
    15135 Opened rOAT1-AAI_IF.mrc as #20, grid size 320,320,320, pixel 0.83, shown at
    15136 level 0.0194, step 1, values float32 
    15137 Opened rOAT1-AAI_IF.mrc 2 as #22.3, grid size 320,320,320, pixel 0.83, shown
    15138 at level 0.0141, step 1, values float32 
    15139 Opened rOAT1-AAI_OF.mrc as #23, grid size 320,320,320, pixel 0.83, shown at
    15140 level 0.0168, step 1, values float32 
    15141 Opened rOAT1-AAI_OF.mrc 2 as #25.3, grid size 320,320,320, pixel 0.83, shown
    15142 at level 0.0168, step 1, values float32 
    15143 Opened rOAT1-PAH.mrc as #27, grid size 160,160,160, pixel 0.83, shown at level
    15144 0.121, step 1, values float32 
    15145 Opened rOAT1-PAH.mrc 2 as #28.3, grid size 160,160,160, pixel 0.83, shown at
    15146 level 0.0546, step 1, values float32 
    15147 Opened rOAT1-FBP.mrc as #29, grid size 320,320,320, pixel 0.83, shown at level
    15148 0.0104, step 1, values float32 
    15149 Opened rOAT1-FBP.mrc 2 as #31.3, grid size 320,320,320, pixel 0.83, shown at
    15150 level 0.0038, step 1, values float32 
    15151 Opened rOAT1-CFM.mrc as #32, grid size 320,320,320, pixel 0.83, shown at level
    15152 0.0119, step 1, values float32 
    15153 Opened rOAT1-TVF-Cl_OF.mrc 2 as #35.3, grid size 320,320,320, pixel 0.83,
    15154 shown at step 1, values float32 
    15155 Opened hOAT1-TFV_IF.mrc as #36, grid size 320,320,320, pixel 0.83, shown at
    15156 level 0.00852, step 1, values float32 
    15157 Opened hOAT1-TFV_IF.mrc 2 as #38.3, grid size 320,320,320, pixel 0.83, shown
    15158 at level 0.00852, step 1, values float32 
    15159 Opened hOAT1-TFV_OF.mrc as #39, grid size 320,320,320, pixel 0.83, shown at
    15160 level 0.0106, step 1, values float32 
    15161 Opened hOAT1-TFV_OF.mrc 2 as #42.3, grid size 320,320,320, pixel 0.83, shown
    15162 at level 0.00699, step 1, values float32 
    15163 Log from Mon Feb 10 17:46:10 2025UCSF ChimeraX version: 1.7.1 (2024-01-23) 
    15164 © 2016-2023 Regents of the University of California. All rights reserved. 
    15165 
    15166 > open
    15167 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/Analysis.cxs
    15168 
    15169 Opened relion_locres_filtered.mrc as #3, grid size 320,320,320, pixel 0.83,
    15170 shown at level 0.00928, step 1, values float32 
    15171 Log from Wed Dec 11 13:28:04 2024UCSF ChimeraX version: 1.7.1 (2024-01-23) 
    15172 © 2016-2023 Regents of the University of California. All rights reserved. 
    15173 
    15174 > open
    15175 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/Analysis.cxs
    15176 > format session
    15177 
    15178 Opened relion_locres_filtered.mrc as #3, grid size 320,320,320, pixel 0.83,
    15179 shown at level 0.00928, step 1, values float32 
    15180 Log from Tue Dec 10 11:33:02 2024 Startup Messages 
    15181 --- 
    15182 warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr bundle with that from OME-Zarr bundle 
    15183 Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with
    15184 that from NMRSTAR bundle 
    15185  
    15186 UCSF ChimeraX version: 1.7.1 (2024-01-23) 
    15187 © 2016-2023 Regents of the University of California. All rights reserved. 
    15188 How to cite UCSF ChimeraX 
    15189 
    15190 > open
    15191 > "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/RealSpaceRefine_2/
    15192 > hOCT1-VB1_3_real_space_refined_002.pdb"
    15193 
    15194 Chain information for hOCT1-VB1_3_real_space_refined_002.pdb #1 
    15195 --- 
    15196 Chain | Description 
    15197 A | No description available 
    15198  
    15199 
    15200 QXcbConnection: XCB error: 3 (BadWindow), sequence: 1650, resource id:
    15201 35652789, major code: 40 (TranslateCoords), minor code: 0 
    15202 
    15203 > select ::name="VIB"
    15204 
    15205 18 atoms, 19 bonds, 1 residue, 1 model selected 
    15206 
    15207 > delete atoms sel
    15208 
    15209 > delete bonds sel
    15210 
    15211 > save
    15212 > "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/RealSpaceRefine_2/
    15213 > hOCT1-noVB1.pdb" relModel #1
    15214 
    15215 QXcbConnection: XCB error: 3 (BadWindow), sequence: 7992, resource id:
    15216 35652794, major code: 40 (TranslateCoords), minor code: 0 
    15217 
    15218 > close session
    15219 
    15220 > open
    15221 > "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/RealSpaceRefine_2/
    15222 > hOCT1-noVB1.pdb"
    15223 
    15224 Chain information for hOCT1-noVB1.pdb #1 
    15225 --- 
    15226 Chain | Description 
    15227 A | No description available 
    15228  
    15229 
    15230 > open
    15231 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/ligand.pdbqt
    15232 
    15233 Summary of feedback from opening
    15234 /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/ligand.pdbqt 
    15235 --- 
    15236 warnings | Ignored bad PDB record found on line 1 
    15237 REMARK SMILES Cc1ncc(C[n+]2csc(CCO)c2C)c(N)n1 
    15238  
    15239 Ignored bad PDB record found on line 2 
    15240 REMARK SMILES IDX 15 1 14 2 10 3 9 4 8 5 7 6 11 7 12 8 13 9 6 11 5 12 4 13 
    15241  
    15242 Ignored bad PDB record found on line 3 
    15243 REMARK SMILES IDX 16 14 3 15 18 16 2 17 1 18 17 19 
    15244  
    15245 Ignored bad PDB record found on line 4 
    15246 REMARK H PARENT 13 10 17 20 17 21 
    15247  
    15248 Ignored bad PDB record found on line 5 
    15249 REMARK Flexibility Score: inf 
    15250  
    15251 15 messages similar to the above omitted 
    15252  
    15253 Opened ligand.pdbqt containing 1 structures (21 atoms, 22 bonds) 
    15254 
    15255 > open
    15256 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/ligand.pdbqt
    15257 
    15258 Summary of feedback from opening
    15259 /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/ligand.pdbqt 
    15260 --- 
    15261 warnings | Ignored bad PDB record found on line 1 
    15262 REMARK SMILES Cc1ncc(C[n+]2csc(CCO)c2C)c(N)n1 
    15263  
    15264 Ignored bad PDB record found on line 2 
    15265 REMARK SMILES IDX 15 1 14 2 10 3 9 4 8 5 7 6 11 7 12 8 13 9 6 11 5 12 4 13 
    15266  
    15267 Ignored bad PDB record found on line 3 
    15268 REMARK SMILES IDX 16 14 3 15 18 16 2 17 1 18 17 19 
    15269  
    15270 Ignored bad PDB record found on line 4 
    15271 REMARK H PARENT 13 10 17 20 17 21 
    15272  
    15273 Ignored bad PDB record found on line 5 
    15274 REMARK Flexibility Score: inf 
    15275  
    15276 15 messages similar to the above omitted 
    15277  
    15278 Opened ligand.pdbqt containing 1 structures (21 atoms, 22 bonds) 
    15279 
    15280 QXcbConnection: XCB error: 3 (BadWindow), sequence: 6676, resource id:
    15281 35652851, major code: 40 (TranslateCoords), minor code: 0 
    15282 
    15283 > hide #3 models
    15284 
    15285 > show #3 models
    15286 
    15287 > hide #3 models
    15288 
    15289 > close #2-3
    15290 
    15291 > open
    15292 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/vina_dock.pdbqt
    15293 
    15294 Summary of feedback from opening
    15295 /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/vina_dock.pdbqt 
    15296 --- 
    15297 warnings | Ignored bad PDB record found on line 2 
    15298 REMARK VINA RESULT: -6.139 0.000 0.000 
    15299  
    15300 Ignored bad PDB record found on line 3 
    15301 REMARK INTER + INTRA: -8.396 
    15302  
    15303 Ignored bad PDB record found on line 4 
    15304 REMARK INTER: -7.934 
    15305  
    15306 Ignored bad PDB record found on line 5 
    15307 REMARK INTRA: -0.463 
    15308  
    15309 Ignored bad PDB record found on line 6 
    15310 REMARK UNBOUND: -0.463 
    15311  
    15312 495 messages similar to the above omitted 
    15313  
    15314 Opened vina_dock.pdbqt containing 20 structures (420 atoms, 440 bonds) 
    15315 
    15316 > viewdockx #2.1-20
    15317 
    15318 > set bgColor white
    15319 
    15320 > select #2.9/?:1@@serial_number=16
    15321 
    15322 1 atom, 1 residue, 1 model selected 
    15323 
    15324 > select up
    15325 
    15326 21 atoms, 22 bonds, 1 residue, 1 model selected 
    15327 
    15328 > view sel
    15329 
    15330 > open
    15331 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/job320/note.txt
    15332 
    15333 Unrecognized file suffix '.txt' 
    15334 
    15335 > open
    15336 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/job320/relion_locres_filtered.mrc
    15337 
    15338 Opened relion_locres_filtered.mrc as #3, grid size 320,320,320, pixel 0.83,
    15339 shown at level 0.00146, step 2, values float32 
    15340 
    15341 > color #3 #b2b2b296 models
    15342 
    15343 > volume #3 step 1
    15344 
    15345 > ui tool show "Side View"
    15346 
    15347 > volume #3 level 0.01472
    15348 
    15349 > select add #1
    15350 
    15351 3482 atoms, 3578 bonds, 1 pseudobond, 448 residues, 3 models selected 
    15352 
    15353 > show sel atoms
    15354 
    15355 JS console(viewdockx_table.js:133:error): Uncaught TypeError: Cannot read
    15356 properties of undefined (reading 'id') 
    15357 
    15358 > hide #2.1-20 models
    15359 
    15360 > show #2.1 models
    15361 
    15362 > select clear
    15363 
    15364 > volume #3 level 0.01037
    15365 
    15366 > show #2.2 models
    15367 
    15368 > show #2.3 models
    15369 
    15370 > hide #2.2 models
    15371 
    15372 > hide #2.1 models
    15373 
    15374 > volume #3 level 0.009064
    15375 
    15376 > volume #3 level 0.009281
    15377 
    15378 > hide #2.3 models
    15379 
    15380 > show #2.4 models
    15381 
    15382 > hide #2.4 models
    15383 
    15384 > show #2.5 models
    15385 
    15386 > close #1
    15387 
    15388 > open
    15389 > "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/RealSpaceRefine_2/
    15390 > hOCT1-noVB1.pdb"
    15391 
    15392 Chain information for hOCT1-noVB1.pdb #1 
    15393 --- 
    15394 Chain | Description 
    15395 A | No description available 
    15396  
    15397 
    15398 > select add #1
    15399 
    15400 3461 atoms, 3556 bonds, 1 pseudobond, 447 residues, 2 models selected 
    15401 
    15402 > show sel atoms
    15403 
    15404 > select clear
    15405 
    15406 > hide #2.5 models
    15407 
    15408 > show #2.6 models
    15409 
    15410 > hide #2.6 models
    15411 
    15412 > show #2.7 models
    15413 
    15414 > hide #2.7 models
    15415 
    15416 > show #2.8 models
    15417 
    15418 > hide #2.8 models
    15419 
    15420 > show #2.9 models
    15421 
    15422 > hide #2.9 models
    15423 
    15424 > show #2.10 models
    15425 
    15426 > hide #2.10 models
    15427 
    15428 > show #2.10 models
    15429 
    15430 > hide #2.10 models
    15431 
    15432 > show #2.11 models
    15433 
    15434 > hide #2.11 models
    15435 
    15436 > show #2.12 models
    15437 
    15438 > save
    15439 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/Analysis.cxs
    15440 > includeMaps true
    15441 
    15442 > lighting soft
    15443 
    15444 > lighting simple
    15445 
    15446 > color #3 #b2b2b264 models
    15447 
    15448 > hide #2.12 models
    15449 
    15450 > show #2.13 models
    15451 
    15452 > hide #2.13 models
    15453 
    15454 > show #2.14 models
    15455 
    15456 > hide #2.14 models
    15457 
    15458 > show #2.15 models
    15459 
    15460 > hide #2.15 models
    15461 
    15462 > show #2.15 models
    15463 
    15464 > hide #2.15 models
    15465 
    15466 > show #2.16 models
    15467 
    15468 > hide #2.16 models
    15469 
    15470 > show #2.17 models
    15471 
    15472 > hide #2.17 models
    15473 
    15474 > show #2.18 models
    15475 
    15476 > hide #2.18 models
    15477 
    15478 > show #2.19 models
    15479 
    15480 > hide #2.19 models
    15481 
    15482 > show #2.20 models
    15483 
    15484 > hide #2.20 models
    15485 
    15486 > show #2.19 models
    15487 
    15488 > hide #2.19 models
    15489 
    15490 > show #2.20 models
    15491 
    15492 > hide #2.20 models
    15493 
    15494 > show #2.1 models
    15495 
    15496 > hide #2.1 models
    15497 
    15498 > show #2.2 models
    15499 
    15500 > hide #2.2 models
    15501 
    15502 > show #2.1 models
    15503 
    15504 > hide #2.1 models
    15505 
    15506 > show #2.2 models
    15507 
    15508 > hide #2.2 models
    15509 
    15510 > show #2.3 models
    15511 
    15512 > hide #2.3 models
    15513 
    15514 > show #2.3 models
    15515 
    15516 > hide #2.3 models
    15517 
    15518 > show #2.4 models
    15519 
    15520 > hide #2.4 models
    15521 
    15522 > show #2.5 models
    15523 
    15524 > hide #2.5 models
    15525 
    15526 > show #2.6 models
    15527 
    15528 > hide #2.6 models
    15529 
    15530 > show #2.7 models
    15531 
    15532 > hide #2.7 models
    15533 
    15534 > show #2.7 models
    15535 
    15536 > hide #2.7 models
    15537 
    15538 > show #2.8 models
    15539 
    15540 > hide #2.8 models
    15541 
    15542 > show #2.9 models
    15543 
    15544 > hide #2.9 models
    15545 
    15546 > show #2.10 models
    15547 
    15548 > select down
    15549 
    15550 Nothing selected 
    15551 
    15552 > hide #2.10 models
    15553 
    15554 > show #2.10 models
    15555 
    15556 > hide #2.10 models
    15557 
    15558 > show #2.11 models
    15559 
    15560 > hide #2.11 models
    15561 
    15562 > show #2.12 models
    15563 
    15564 > hide #2.12 models
    15565 
    15566 > show #2.13 models
    15567 
    15568 > hide #2.13 models
    15569 
    15570 > show #2.14 models
    15571 
    15572 > hide #2.14 models
    15573 
    15574 > show #2.15 models
    15575 
    15576 > hide #2.15 models
    15577 
    15578 > show #2.15 models
    15579 
    15580 > hide #2.15 models
    15581 
    15582 > show #2.15 models
    15583 
    15584 > hide #2.15 models
    15585 
    15586 > show #2.16 models
    15587 
    15588 > hide #2.16 models
    15589 
    15590 > show #2.16 models
    15591 
    15592 > hide #2.16 models
    15593 
    15594 > show #2.17 models
    15595 
    15596 > hide #2.17 models
    15597 
    15598 > show #2.17 models
    15599 
    15600 > hide #2.17 models
    15601 
    15602 > show #2.18 models
    15603 
    15604 > hide #2.18 models
    15605 
    15606 > show #2.19 models
    15607 
    15608 > hide #2.19 models
    15609 
    15610 > show #2.20 models
    15611 
    15612 > volume #3 level 0.01124
    15613 
    15614 > hide #2.20 models
    15615 
    15616 > show #2.20 models
    15617 
    15618 > hide #2.20 models
    15619 
    15620 > show #2.20 models
    15621 
    15622 > hide #2.20 models
    15623 
    15624 > show #2.19 models
    15625 
    15626 > hide #2.19 models
    15627 
    15628 > show #2.18 models
    15629 
    15630 > hide #2.18 models
    15631 
    15632 > show #2.19 models
    15633 
    15634 > hide #2.19 models
    15635 
    15636 > show #2.18 models
    15637 
    15638 > volume #3 level 0.008629
    15639 
    15640 > hide #2.18 models
    15641 
    15642 > show #2.18 models
    15643 
    15644 > hide #2.18 models
    15645 
    15646 > show #2.17 models
    15647 
    15648 > hide #2.17 models
    15649 
    15650 > show #2.16 models
    15651 
    15652 > hide #2.16 models
    15653 
    15654 > show #2.15 models
    15655 
    15656 > hide #2.15 models
    15657 
    15658 > show #2.14 models
    15659 
    15660 > hide #2.14 models
    15661 
    15662 > show #2.13 models
    15663 
    15664 > hide #2.13 models
    15665 
    15666 > show #2.12 models
    15667 
    15668 > hide #2.12 models
    15669 
    15670 > show #2.11 models
    15671 
    15672 > hide #2.11 models
    15673 
    15674 > show #2.10 models
    15675 
    15676 > hide #2.10 models
    15677 
    15678 > show #2.1 models
    15679 
    15680 > hide #2.1 models
    15681 
    15682 > show #2.1 models
    15683 
    15684 > hide #2.1 models
    15685 
    15686 > show #2.2 models
    15687 
    15688 > hide #2.2 models
    15689 
    15690 > show #2.3 models
    15691 
    15692 > hide #2.3 models
    15693 
    15694 > show #2.4 models
    15695 
    15696 > hide #2.4 models
    15697 
    15698 > show #2.5 models
    15699 
    15700 > hide #2.5 models
    15701 
    15702 > show #2.6 models
    15703 
    15704 > hide #2.6 models
    15705 
    15706 > show #2.7 models
    15707 
    15708 > hide #2.7 models
    15709 
    15710 > show #2.8 models
    15711 
    15712 > hide #2.8 models
    15713 
    15714 > show #2.9 models
    15715 
    15716 > hide #2.9 models
    15717 
    15718 > show #2.9 models
    15719 
    15720 > hide #2.9 models
    15721 
    15722 > show #2.9 models
    15723 
    15724 > hide #2.9 models
    15725 
    15726 > show #2.10 models
    15727 
    15728 > hide #2.10 models
    15729 
    15730 > show #2.11 models
    15731 
    15732 > hide #2.11 models
    15733 
    15734 > show #2.12 models
    15735 
    15736 > hide #2.12 models
    15737 
    15738 > show #2.13 models
    15739 
    15740 > hide #2.13 models
    15741 
    15742 > show #2.12 models
    15743 
    15744 > hide #2.12 models
    15745 
    15746 > show #2.1 models
    15747 
    15748 > hide #2.1 models
    15749 
    15750 > show #2.2 models
    15751 
    15752 > hide #2.2 models
    15753 
    15754 > show #2.3 models
    15755 
    15756 > hide #2.3 models
    15757 
    15758 > show #2.4 models
    15759 
    15760 > hide #2.4 models
    15761 
    15762 > show #2.5 models
    15763 
    15764 > hide #2.5 models
    15765 
    15766 > show #2.6 models
    15767 
    15768 > hide #2.6 models
    15769 
    15770 > show #2.7 models
    15771 
    15772 > hide #2.7 models
    15773 
    15774 > show #2.8 models
    15775 
    15776 > hide #2.8 models
    15777 
    15778 > show #2.8 models
    15779 
    15780 > hide #2.8 models
    15781 
    15782 > show #2.9 models
    15783 
    15784 > hide #2.9 models
    15785 
    15786 > show #2.10 models
    15787 
    15788 > hide #2.10 models
    15789 
    15790 > show #2.11 models
    15791 
    15792 > hide #2.11 models
    15793 
    15794 > show #2.12 models
    15795 
    15796 > hide #2.12 models
    15797 
    15798 > show #2.1 models
    15799 
    15800 > save
    15801 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/Analysis.cxs
    15802 > includeMaps true
    15803 
    15804 QXcbConnection: XCB error: 3 (BadWindow), sequence: 35492, resource id:
    15805 35652978, major code: 40 (TranslateCoords), minor code: 0 
    15806 
    15807 > volume #3 level 0.009281
    15808 
    15809 > hide #2.1 models
    15810 
    15811 > show #2.2 models
    15812 
    15813 > hide #2.2 models
    15814 
    15815 > show #2.3 models
    15816 
    15817 > hide #2.3 models
    15818 
    15819 > show #2.4 models
    15820 
    15821 > show #2.5 models
    15822 
    15823 > hide #2.4 models
    15824 
    15825 > hide #2.5 models
    15826 
    15827 > show #2.18 models
    15828 
    15829 > hide #2.18 models
    15830 
    15831 > show #2.18 models
    15832 
    15833 > hide #2.18 models
    15834 
    15835 > show #2.17 models
    15836 
    15837 > hide #2.17 models
    15838 
    15839 > show #2.16 models
    15840 
    15841 > hide #2.16 models
    15842 
    15843 > show #2.15 models
    15844 
    15845 > hide #2.15 models
    15846 
    15847 > show #2.14 models
    15848 
    15849 > hide #2.14 models
    15850 
    15851 > show #2.13 models
    15852 
    15853 > hide #2.13 models
    15854 
    15855 > show #2.12 models
    15856 
    15857 > hide #2.12 models
    15858 
    15859 > show #2.12 models
    15860 
    15861 > hide #2.12 models
    15862 
    15863 > save
    15864 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/Analysis.cxs
    15865 > includeMaps true
    15866 
    15867 QXcbConnection: XCB error: 3 (BadWindow), sequence: 32670, resource id:
    15868 35652988, major code: 40 (TranslateCoords), minor code: 0 
    15869 
    15870 ——— End of log from Tue Dec 10 11:33:02 2024 ———
    15871 
    15872 opened ChimeraX session 
    15873 JS console(:1:error): Uncaught ReferenceError: vdxtable is not defined 
    15874 JS console(:1:error): Uncaught ReferenceError: vdxtable is not defined 
    15875 
    15876 > save
    15877 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/Analysis.cxs
    15878 > includeMaps true
    15879 
    15880 QXcbConnection: XCB error: 3 (BadWindow), sequence: 7404, resource id:
    15881 35653140, major code: 40 (TranslateCoords), minor code: 0 
    15882 
    15883 QXcbConnection: XCB error: 3 (BadWindow), sequence: 7416, resource id:
    15884 35653135, major code: 40 (TranslateCoords), minor code: 0 
    15885 
    15886 > show #2.11 models
    15887 
    15888 > hide #2.11 models
    15889 
    15890 > show #2.12 models
    15891 
    15892 > hide #2.12 models
    15893 
    15894 > save
    15895 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/Analysis.cxs
    15896 > includeMaps true
    15897 
    15898 QXcbConnection: XCB error: 3 (BadWindow), sequence: 60442, resource id:
    15899 35653379, major code: 40 (TranslateCoords), minor code: 0 
    15900 
    15901 ——— End of log from Wed Dec 11 13:28:04 2024 ———
    15902 
    15903 opened ChimeraX session 
    15904 JS console(:1:error): Uncaught ReferenceError: vdxtable is not defined 
    15905 JS console(:1:error): Uncaught ReferenceError: vdxtable is not defined 
    15906 
    15907 > show #2.11 models
    15908 
    15909 > show #2.12 models
    15910 
    15911 > hide #2.11 models
    15912 
    15913 > open
    15914 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/RealSpaceRefine_7/hOCT1VB1007.pdb
    15915 
    15916 Chain information for hOCT1VB1007.pdb #4 
    15917 --- 
    15918 Chain | Description 
    15919 A | No description available 
    15920  
    15921 
    15922 > open
    15923 > "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/RealSpaceRefine_8/
    15924 > hOCT1-VB_Dock2_real_space_refined_008.pdb"
    15925 
    15926 Chain information for hOCT1-VB_Dock2_real_space_refined_008.pdb #5 
    15927 --- 
    15928 Chain | Description 
    15929 A | No description available 
    15930  
    15931 
    15932 QXcbConnection: XCB error: 3 (BadWindow), sequence: 17659, resource id:
    15933 35653657, major code: 40 (TranslateCoords), minor code: 0 
    15934 
    15935 > close session
    15936 
    15937 > open
    15938 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_20220303_cryoSPARC/J149_2.26A_clip-240/P3_J149_fsc_iteration_010_after_fsc_mask_auto_tightening.pdf
    15939 
    15940 QXcbConnection: XCB error: 3 (BadWindow), sequence: 50929, resource id:
    15941 35654568, major code: 40 (TranslateCoords), minor code: 0 
    15942 
    15943 > open
    15944 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_20220303_cryoSPARC/J149_2.26A_clip-240/cryosparc_P3_J154__localfilter_240.mrc
    15945 
    15946 Opened cryosparc_P3_J154__localfilter_240.mrc as #1, grid size 240,240,240,
    15947 pixel 0.553, shown at level 0.207, step 1, values float32 
    15948 
    15949 > open
    15950 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_20220303_cryoSPARC/J149_2.26A_clip-240/cryosparc_P3_J154__localfilter_240_VB1.mrc
    15951 
    15952 Opened cryosparc_P3_J154__localfilter_240_VB1.mrc as #2, grid size
    15953 240,240,240, pixel 0.553, shown at level 0.000117, step 1, values float32 
    15954 
    15955 > volume #2 level 0.3318
    15956 
    15957 Drag select of 2 cryosparc_P3_J154__localfilter_240_VB1.mrc 
    15958 
    15959 > view orient
    15960 
    15961 > select clear
    15962 
    15963 > open
    15964 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_Model/mOCT1-VB1_RSF_014_VB1.pdb
    15965 
    15966 Summary of feedback from opening
    15967 /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_Model/mOCT1-VB1_RSF_014_VB1.pdb 
    15968 --- 
    15969 warnings | Cannot find LINK/SSBOND residue CYS (50 ) 
    15970 Cannot find LINK/SSBOND residue CYS (62 ) 
    15971 Cannot find LINK/SSBOND residue CYS (89 ) 
    15972  
    15973 
    15974 > open
    15975 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_Model/RealSpaceRefine_6/mOCT1-VB1-coot-11_real_space_refined_006.pdb
    15976 
    15977 Chain information for mOCT1-VB1-coot-11_real_space_refined_006.pdb #4 
    15978 --- 
    15979 Chain | Description 
    15980 A | No description available 
    15981  
    15982 
    15983 > open
    15984 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_Model/mOCT1-VB1_real_space_refined_014.pdb
    15985 
    15986 Chain information for mOCT1-VB1_real_space_refined_014.pdb #5 
    15987 --- 
    15988 Chain | Description 
    15989 A | No description available 
    15990  
    15991 
    15992 > close #3#4
    15993 
    15994 > volume #2 color #ffffb296
    15995 
    15996 > volume #2 color #ffffb2c8
    15997 
    15998 > volume #2 level 0.4304
    15999 
    16000 > volume #2 level 0.3677
    16001 
    16002 > select /A:601@C15
    16003 
    16004 1 atom, 1 residue, 1 model selected 
    16005 
    16006 > select up
    16007 
    16008 18 atoms, 19 bonds, 1 residue, 1 model selected 
    16009 
    16010 > view sel
    16011 
    16012 > select clear
    16013 
    16014 > open
    16015 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-ABC_Model/mOCT1-ABC_real_space_refined_009.pdb
    16016 
    16017 Chain information for mOCT1-ABC_real_space_refined_009.pdb #3 
    16018 --- 
    16019 Chain | Description 
    16020 A | No description available 
    16021  
    16022 
    16023 > open
    16024 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-ABC_20220411_cryoSPARC/J142_2.25A_clip-240/cryosparc_P3_J150__localfilter_240.mrc
    16025 
    16026 Opened cryosparc_P3_J150__localfilter_240.mrc as #4, grid size 240,240,240,
    16027 pixel 0.553, shown at level 0.229, step 1, values float32 
    16028 
    16029 > volume #4 level 0.7041
    16030 
    16031 > hide #!2 models
    16032 
    16033 > hide #!3 models
    16034 
    16035 > hide #!5 models
    16036 
    16037 > show #!3 models
    16038 
    16039 > select ::name="ABC"
    16040 
    16041 42 atoms, 48 bonds, 2 residues, 1 model selected 
    16042 
    16043 > view sel
    16044 
    16045 > volume #4 level 0.5273
    16046 
    16047 > hide #!4 models
    16048 
    16049 > show #!4 models
    16050 
    16051 > show #!1 models
    16052 
    16053 > hide #!3 models
    16054 
    16055 > save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
    16056 > density.cxs" includeMaps true
    16057 
    16058 QXcbConnection: XCB error: 3 (BadWindow), sequence: 57982, resource id:
    16059 35654641, major code: 40 (TranslateCoords), minor code: 0 
    16060 
    16061 > hide #!1 models
    16062 
    16063 > rename #1 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    16064 
    16065 > rename #2 mOCT1-VB1_cryosparc_P3_J154__localfilter_240_VB1.mrc
    16066 
    16067 > rename #4 mOCT1-ABC_cryosparc_P3_J150__localfilter_240.mrc
    16068 
    16069 > show #!3 models
    16070 
    16071 > select clear
    16072 
    16073 > hide #!4 models
    16074 
    16075 > select ::name="ABC"
    16076 
    16077 42 atoms, 48 bonds, 2 residues, 1 model selected 
    16078 
    16079 > select add #3
    16080 
    16081 3550 atoms, 3613 bonds, 1 pseudobond, 490 residues, 2 models selected 
    16082 
    16083 > color (#!3 & sel) white
    16084 
    16085 > select clear
    16086 
    16087 > select ::name="ABC"
    16088 
    16089 42 atoms, 48 bonds, 2 residues, 1 model selected 
    16090 
    16091 > color sel red
    16092 
    16093 > show #!4 models
    16094 
    16095 > ui tool show "Color Zone"
    16096 
    16097 > color zone #4 near #3 distance 3.32
    16098 
    16099 > volume splitbyzone #4
    16100 
    16101 Opened mOCT1-ABC_cryosparc_P3_J150__localfilter_240.mrc 0 as #6.1, grid size
    16102 240,240,240, pixel 0.553, shown at level 0.527, step 1, values float32 
    16103 Opened mOCT1-ABC_cryosparc_P3_J150__localfilter_240.mrc 1 as #6.2, grid size
    16104 240,240,240, pixel 0.553, shown at level 0.527, step 1, values float32 
    16105 Opened mOCT1-ABC_cryosparc_P3_J150__localfilter_240.mrc 2 as #6.3, grid size
    16106 240,240,240, pixel 0.553, shown at level 0.527, step 1, values float32 
    16107 
    16108 > hide #!3 models
    16109 
    16110 > select add #3
    16111 
    16112 3550 atoms, 3613 bonds, 1 pseudobond, 490 residues, 2 models selected 
    16113 
    16114 > select subtract #3
    16115 
    16116 Nothing selected 
    16117 
    16118 > hide #!6.1 models
    16119 
    16120 > hide #!6.3 models
    16121 
    16122 > show #!6.3 models
    16123 
    16124 > hide #!6.2 models
    16125 
    16126 > close #6.1-2
    16127 
    16128 > save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
    16129 > density.cxs" includeMaps true
    16130 
    16131 QXcbConnection: XCB error: 3 (BadWindow), sequence: 18121, resource id:
    16132 35654647, major code: 40 (TranslateCoords), minor code: 0 
    16133 
    16134 > show #!3 models
    16135 
    16136 > color #3 #fffffbff
    16137 
    16138 > color #3 #ddddaaff
    16139 
    16140 > color #3 #dda0deff
    16141 
    16142 > color #3 plum
    16143 
    16144 > select add #3
    16145 
    16146 3550 atoms, 3613 bonds, 1 pseudobond, 490 residues, 2 models selected 
    16147 
    16148 > color (#!3 & sel) byhetero
    16149 
    16150 > color #6.3 #ddddaaff models
    16151 
    16152 > color #6.3 plum models
    16153 
    16154 > color #6.3 #ffffb2ff models
    16155 
    16156 Drag select of 6.3 mOCT1-ABC_cryosparc_P3_J150__localfilter_240.mrc 2 , 5
    16157 atoms, 5 residues, 5 bonds 
    16158 
    16159 > select clear
    16160 
    16161 > color #6.3 #ffffb2c8 models
    16162 
    16163 > select ::name="ABC"
    16164 
    16165 42 atoms, 48 bonds, 2 residues, 1 model selected 
    16166 
    16167 > view sel
    16168 
    16169 > select #3/A:234
    16170 
    16171 11 atoms, 10 bonds, 1 residue, 1 model selected 
    16172 
    16173 > color #6.3 #ffffb296 models
    16174 
    16175 > show #!2 models
    16176 
    16177 > hide #!2 models
    16178 
    16179 > show #!2 models
    16180 
    16181 > hide #!3 models
    16182 
    16183 > hide #!6 models
    16184 
    16185 > hide #!6.3 models
    16186 
    16187 > show #!4 models
    16188 
    16189 > hide #!4 models
    16190 
    16191 > show #!5 models
    16192 
    16193 > show #!3 models
    16194 
    16195 > hide #!3 models
    16196 
    16197 > select #5/A:36
    16198 
    16199 12 atoms, 12 bonds, 1 residue, 1 model selected 
    16200 
    16201 > show sel atoms
    16202 
    16203 > hide #!5 models
    16204 
    16205 > hide #!2 models
    16206 
    16207 > show #!1 models
    16208 
    16209 > view
    16210 
    16211 > save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
    16212 > density.cxs" includeMaps true
    16213 
    16214 QXcbConnection: XCB error: 3 (BadWindow), sequence: 5156, resource id:
    16215 35654673, major code: 40 (TranslateCoords), minor code: 0 
    16216 
    16217 > open
    16218 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-3TC_20240411/job207/relion_locres_filtered.mrc
    16219 
    16220 Opened relion_locres_filtered.mrc as #7, grid size 320,320,320, pixel 0.83,
    16221 shown at level 0.00144, step 2, values float32 
    16222 
    16223 > volume #7 level 0.01204
    16224 
    16225 > select add #7
    16226 
    16227 12 atoms, 12 bonds, 1 residue, 3 models selected 
    16228 
    16229 > select add #5
    16230 
    16231 3526 atoms, 3584 bonds, 1 pseudobond, 489 residues, 4 models selected 
    16232 
    16233 > select subtract #5
    16234 
    16235 2 models selected 
    16236 
    16237 > ui mousemode right "translate selected models"
    16238 
    16239 > view matrix models #7,1,0,0,-67.025,0,1,0,-62.171,0,0,1,-62.016
    16240 
    16241 > view matrix models #7,1,0,0,-65.422,0,1,0,-60.829,0,0,1,-69.057
    16242 
    16243 > ui mousemode right "rotate selected models"
    16244 
    16245 > view matrix models
    16246 > #7,-0.44906,0.62428,0.63923,-47.882,-0.83076,-0.55508,-0.041522,263.31,0.32891,-0.5497,0.76789,-6.0495
    16247 
    16248 > ui mousemode right "translate selected models"
    16249 
    16250 > view matrix models
    16251 > #7,-0.44906,0.62428,0.63923,-43.112,-0.83076,-0.55508,-0.041522,259.52,0.32891,-0.5497,0.76789,-3.3226
    16252 
    16253 > view matrix models
    16254 > #7,-0.44906,0.62428,0.63923,-46.691,-0.83076,-0.55508,-0.041522,257.64,0.32891,-0.5497,0.76789,-5.4256
    16255 
    16256 > view matrix models
    16257 > #7,-0.44906,0.62428,0.63923,-43.086,-0.83076,-0.55508,-0.041522,254.57,0.32891,-0.5497,0.76789,-5.2175
    16258 
    16259 > ui tool show "Fit in Map"
    16260 
    16261 > fitmap #7 inMap #1
    16262 
    16263 Fit map relion_locres_filtered.mrc in map
    16264 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc using 3812 points 
    16265 correlation = 0.2373, correlation about mean = 0.07089, overlap = 11.07 
    16266 steps = 116, shift = 1.21, angle = 8.84 degrees 
    16267  
    16268 Position of relion_locres_filtered.mrc (#7) relative to
    16269 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    16270 Matrix rotation and translation 
    16271 -0.36461695 0.73265397 0.57469351 -59.14787422 
    16272 -0.87490183 -0.48082660 0.05790126 236.29988230 
    16273 0.31874951 -0.48168862 0.81631784 -18.80617873 
    16274 Axis -0.31464704 0.14924672 -0.93740208 
    16275 Axis point 41.71559551 127.71968026 0.00000000 
    16276 Rotation angle (degrees) 120.96824033 
    16277 Shift along axis 71.50663710 
    16278  
    16279 
    16280 > rename #7 mOCT1-3TC
    16281 
    16282 > select clear
    16283 
    16284 [Repeated 1 time(s)]
    16285 
    16286 > rename #7 mOCT1-3TC.mrc
    16287 
    16288 > open
    16289 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-3TC_Model/RealSpaceRefine_6/mOCT1-3TC-
    16290 > coot-14_real_space_refined_006.pdb
    16291 
    16292 Chain information for mOCT1-3TC-coot-14_real_space_refined_006.pdb #8 
    16293 --- 
    16294 Chain | Description 
    16295 A | No description available 
    16296  
    16297 
    16298 > ui tool show Matchmaker
    16299 
    16300 > matchmaker #!8 to #5
    16301 
    16302 Parameters 
    16303 --- 
    16304 Chain pairing | bb 
    16305 Alignment algorithm | Needleman-Wunsch 
    16306 Similarity matrix | BLOSUM-62 
    16307 SS fraction | 0.3 
    16308 Gap open (HH/SS/other) | 18/18/6 
    16309 Gap extend | 1 
    16310 SS matrix |  |  | H | S | O 
    16311 ---|---|---|--- 
    16312 H | 6 | -9 | -6 
    16313 S |  | 6 | -6 
    16314 O |  |  | 4 
    16315 Iteration cutoff | 2 
    16316  
    16317 Matchmaker mOCT1-VB1_real_space_refined_014.pdb, chain A (#5) with mOCT1-3TC-
    16318 coot-14_real_space_refined_006.pdb, chain A (#8), sequence alignment score =
    16319 2352.2 
    16320 RMSD between 450 pruned atom pairs is 0.409 angstroms; (across all 450 pairs:
    16321 0.409) 
    16322  
    16323 
    16324 > hide #!1 models
    16325 
    16326 > hide #!7 models
    16327 
    16328 > show #!1 models
    16329 
    16330 > hide #!8 models
    16331 
    16332 > show #!7 models
    16333 
    16334 > select add #7
    16335 
    16336 2 models selected 
    16337 
    16338 > ui mousemode right "rotate selected models"
    16339 
    16340 > view matrix models
    16341 > #7,0.49719,-0.57211,-0.6523,173.98,0.80196,0.58997,0.093813,-133.23,0.33116,-0.56976,0.75214,0.34956
    16342 
    16343 > ui mousemode right "translate selected models"
    16344 
    16345 > view matrix models
    16346 > #7,0.49719,-0.57211,-0.6523,164.87,0.80196,0.58997,0.093813,-137.47,0.33116,-0.56976,0.75214,-2.3096
    16347 
    16348 > fitmap #7 inMap #1
    16349 
    16350 Fit map mOCT1-3TC.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    16351 using 3812 points 
    16352 correlation = 0.9181, correlation about mean = 0.7496, overlap = 65.08 
    16353 steps = 160, shift = 6.4, angle = 20.1 degrees 
    16354  
    16355 Position of mOCT1-3TC.mrc (#7) relative to
    16356 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    16357 Matrix rotation and translation 
    16358 0.27009123 -0.75134279 -0.60210857 210.67160095 
    16359 0.83888334 0.49056205 -0.23584655 -78.20606144 
    16360 0.47257322 -0.44139877 0.76278546 -39.17036140 
    16361 Axis -0.10648785 -0.55674686 0.82382842 
    16362 Axis point 169.78551241 113.86943556 0.00000000 
    16363 Rotation angle (degrees) 74.82789173 
    16364 Shift along axis -11.16264322 
    16365  
    16366 
    16367 > fitmap #8 inMap #7
    16368 
    16369 Fit molecule mOCT1-3TC-coot-14_real_space_refined_006.pdb (#8) to map
    16370 mOCT1-3TC.mrc (#7) using 7048 atoms 
    16371 average map value = 0.01706, steps = 60 
    16372 shifted from previous position = 0.0823 
    16373 rotated from previous position = 0.357 degrees 
    16374 atoms outside contour = 4146, contour level = 0.012041 
    16375  
    16376 Position of mOCT1-3TC-coot-14_real_space_refined_006.pdb (#8) relative to
    16377 mOCT1-3TC.mrc (#7) coordinates: 
    16378 Matrix rotation and translation 
    16379 0.99999991 -0.00005602 -0.00043067 0.07339565 
    16380 0.00005621 0.99999991 0.00043709 -0.06044298 
    16381 0.00043064 -0.00043712 0.99999982 0.02180230 
    16382 Axis -0.70938425 -0.69891365 0.09106970 
    16383 Axis point 0.00000000 51.44490735 150.82453668 
    16384 Rotation angle (degrees) 0.03530433 
    16385 Shift along axis -0.00783577 
    16386  
    16387 
    16388 > show #!8 models
    16389 
    16390 > hide #!8 models
    16391 
    16392 > select subtract #7
    16393 
    16394 Nothing selected 
    16395 
    16396 > hide #!1 models
    16397 
    16398 > show #!8 models
    16399 
    16400 > select ::name="3TC"
    16401 
    16402 26 atoms, 27 bonds, 1 residue, 1 model selected 
    16403 
    16404 > select add #8
    16405 
    16406 7048 atoms, 7109 bonds, 1 pseudobond, 486 residues, 2 models selected 
    16407 
    16408 > color (#!8 & sel) white
    16409 
    16410 > select ::name="3TC"
    16411 
    16412 26 atoms, 27 bonds, 1 residue, 1 model selected 
    16413 
    16414 > color sel red
    16415 
    16416 > view sel
    16417 
    16418 > volume #7 step 1
    16419 
    16420 > color zone #7 near #8 distance 4.98
    16421 
    16422 > volume splitbyzone #7
    16423 
    16424 Opened mOCT1-3TC.mrc 0 as #9.1, grid size 320,320,320, pixel 0.83, shown at
    16425 level 0.012, step 1, values float32 
    16426 Opened mOCT1-3TC.mrc 1 as #9.2, grid size 320,320,320, pixel 0.83, shown at
    16427 level 0.012, step 1, values float32 
    16428 Opened mOCT1-3TC.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at
    16429 level 0.012, step 1, values float32 
    16430 
    16431 > close #9.2
    16432 
    16433 > close #9.1
    16434 
    16435 > color #9.3 white models
    16436 
    16437 > color #9.3 #ffffb2ff models
    16438 
    16439 > color #9.3 #ffffb296 models
    16440 
    16441 > select #8/A:447
    16442 
    16443 19 atoms, 18 bonds, 1 residue, 1 model selected 
    16444 
    16445 > select add #8
    16446 
    16447 7048 atoms, 7109 bonds, 1 pseudobond, 486 residues, 2 models selected 
    16448 
    16449 > color #8 #bb22ffff
    16450 
    16451 > color #8 #b2fffbff
    16452 
    16453 > color #8 #b2ffb2ff
    16454 
    16455 > color (#!8 & sel) byhetero
    16456 
    16457 > select clear
    16458 
    16459 [Repeated 1 time(s)]
    16460 
    16461 > save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
    16462 > density.cxs" includeMaps true
    16463 
    16464 > hide #!9.3 models
    16465 
    16466 > hide #!9 models
    16467 
    16468 > hide #!8 models
    16469 
    16470 > open
    16471 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-AZT_20240413/job307/relion_locres_filtered_flipz.mrc
    16472 
    16473 Opened relion_locres_filtered_flipz.mrc as #10, grid size 320,320,320, pixel
    16474 0.83, shown at level 0.00125, step 2, values float32 
    16475 
    16476 > show #!1 models
    16477 
    16478 > view
    16479 
    16480 > volume #1 level 0.3063
    16481 
    16482 > volume #10 step 1
    16483 
    16484 > volume #10 level 0.01019
    16485 
    16486 > rename #10 mOCT1-AZT.mrc
    16487 
    16488 > select add #10
    16489 
    16490 2 models selected 
    16491 
    16492 > view matrix models #10,1,0,0,-48.383,0,1,0,-77.671,0,0,1,-67.093
    16493 
    16494 > view matrix models #10,1,0,0,-54.836,0,1,0,-59.483,0,0,1,-63.826
    16495 
    16496 > ui mousemode right "rotate selected models"
    16497 
    16498 > view matrix models
    16499 > #10,0.55307,0.83192,0.044939,-108.96,-0.78881,0.54024,-0.29312,148.24,-0.26813,0.12666,0.95502,-37.718
    16500 
    16501 > ui mousemode right "translate selected models"
    16502 
    16503 > view matrix models
    16504 > #10,0.55307,0.83192,0.044939,-120.39,-0.78881,0.54024,-0.29312,136.85,-0.26813,0.12666,0.95502,-39.969
    16505 
    16506 > view matrix models
    16507 > #10,0.55307,0.83192,0.044939,-121.53,-0.78881,0.54024,-0.29312,137.41,-0.26813,0.12666,0.95502,-39.609
    16508 
    16509 > fitmap #10 inMap #1
    16510 
    16511 Fit map mOCT1-AZT.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    16512 using 33175 points 
    16513 correlation = 0.9169, correlation about mean = 0.7611, overlap = 495.2 
    16514 steps = 172, shift = 3.01, angle = 24.4 degrees 
    16515  
    16516 Position of mOCT1-AZT.mrc (#10) relative to
    16517 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    16518 Matrix rotation and translation 
    16519 0.17958596 0.98366820 0.01207312 -89.49221412 
    16520 -0.89232990 0.16805236 -0.41893408 218.60375344 
    16521 -0.41412105 0.06446147 0.90793639 -7.62218964 
    16522 Axis 0.24369569 0.21485858 -0.94575272 
    16523 Axis point 81.50821029 166.97786454 0.00000000 
    16524 Rotation angle (degrees) 82.65824965 
    16525 Shift along axis 32.36873253 
    16526  
    16527 
    16528 > view
    16529 
    16530 > view orient
    16531 
    16532 > ui tool show "Side View"
    16533 
    16534 > open
    16535 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-AZT_Model/RealSpaceRefine_4/mOCT1-AZT_14_real_space_refined_004.pdb
    16536 
    16537 Chain information for mOCT1-AZT_14_real_space_refined_004.pdb #11 
    16538 --- 
    16539 Chain | Description 
    16540 A | No description available 
    16541  
    16542 
    16543 > ui tool show Matchmaker
    16544 
    16545 > matchmaker #!11 to #5
    16546 
    16547 Parameters 
    16548 --- 
    16549 Chain pairing | bb 
    16550 Alignment algorithm | Needleman-Wunsch 
    16551 Similarity matrix | BLOSUM-62 
    16552 SS fraction | 0.3 
    16553 Gap open (HH/SS/other) | 18/18/6 
    16554 Gap extend | 1 
    16555 SS matrix |  |  | H | S | O 
    16556 ---|---|---|--- 
    16557 H | 6 | -9 | -6 
    16558 S |  | 6 | -6 
    16559 O |  |  | 4 
    16560 Iteration cutoff | 2 
    16561  
    16562 Matchmaker mOCT1-VB1_real_space_refined_014.pdb, chain A (#5) with
    16563 mOCT1-AZT_14_real_space_refined_004.pdb, chain A (#11), sequence alignment
    16564 score = 2367.3 
    16565 RMSD between 449 pruned atom pairs is 0.415 angstroms; (across all 449 pairs:
    16566 0.415) 
    16567  
    16568 
    16569 > fitmap #11 inMap #10
    16570 
    16571 Fit molecule mOCT1-AZT_14_real_space_refined_004.pdb (#11) to map
    16572 mOCT1-AZT.mrc (#10) using 7017 atoms 
    16573 average map value = 0.01592, steps = 48 
    16574 shifted from previous position = 0.0651 
    16575 rotated from previous position = 0.278 degrees 
    16576 atoms outside contour = 3029, contour level = 0.010186 
    16577  
    16578 Position of mOCT1-AZT_14_real_space_refined_004.pdb (#11) relative to
    16579 mOCT1-AZT.mrc (#10) coordinates: 
    16580 Matrix rotation and translation 
    16581 -0.89530533 -0.39092164 -0.21356179 331.89133766 
    16582 0.43778783 -0.68362766 -0.58394781 243.21431714 
    16583 0.08228108 -0.61630634 0.78319622 99.39179726 
    16584 Axis -0.03674901 -0.33598352 0.94115067 
    16585 Axis point 137.92729950 180.24940846 0.00000000 
    16586 Rotation angle (degrees) 153.87927506 
    16587 Shift along axis -0.37002346 
    16588  
    16589 
    16590 > hide #!1 models
    16591 
    16592 > select ::name="AZZ"
    16593 
    16594 19 atoms, 20 bonds, 1 residue, 1 model selected 
    16595 
    16596 > hide #!10 models
    16597 
    16598 > select add #11
    16599 
    16600 7017 atoms, 7080 bonds, 1 pseudobond, 483 residues, 2 models selected 
    16601 
    16602 > select subtract #11
    16603 
    16604 Nothing selected 
    16605 
    16606 > select add #11
    16607 
    16608 7017 atoms, 7080 bonds, 1 pseudobond, 483 residues, 2 models selected 
    16609 
    16610 > color (#!11 & sel) white
    16611 
    16612 > color #11 #aaaaffff
    16613 
    16614 > color (#!11 & sel) white
    16615 
    16616 > select ::name="AZZ"
    16617 
    16618 19 atoms, 20 bonds, 1 residue, 1 model selected 
    16619 
    16620 > color sel red
    16621 
    16622 > color zone #10 near #11 distance 4.98
    16623 
    16624 > show #!10 models
    16625 
    16626 > volume splitbyzone #10
    16627 
    16628 Opened mOCT1-AZT.mrc 0 as #12.1, grid size 320,320,320, pixel 0.83, shown at
    16629 level 0.0102, step 1, values float32 
    16630 Opened mOCT1-AZT.mrc 1 as #12.2, grid size 320,320,320, pixel 0.83, shown at
    16631 level 0.0102, step 1, values float32 
    16632 Opened mOCT1-AZT.mrc 2 as #12.3, grid size 320,320,320, pixel 0.83, shown at
    16633 level 0.0102, step 1, values float32 
    16634 
    16635 > close #12.2
    16636 
    16637 > close #12.1
    16638 
    16639 > color #12.3 #ff0000fe models
    16640 
    16641 > color #12.3 #ff000096 models
    16642 
    16643 > color #12.3 #ffffff96 models
    16644 
    16645 > color #12.3 #ffffb296 models
    16646 
    16647 > color #11 #aaffffff
    16648 
    16649 > color #11 #aaaaffff
    16650 
    16651 > select add #11
    16652 
    16653 7017 atoms, 7080 bonds, 1 pseudobond, 483 residues, 2 models selected 
    16654 
    16655 > color (#!11 & sel) byhetero
    16656 
    16657 > select clear
    16658 
    16659 > show #!3 models
    16660 
    16661 > hide #!3 models
    16662 
    16663 > save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
    16664 > density.cxs" includeMaps true
    16665 
    16666 > hide #!12.3 models
    16667 
    16668 > hide #!12 models
    16669 
    16670 > hide #!11 models
    16671 
    16672 > show #!1 models
    16673 
    16674 > open
    16675 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-MTF_20240702/job350/postprocess.mrc
    16676 
    16677 Opened postprocess.mrc as #13, grid size 320,320,320, pixel 0.83, shown at
    16678 level 0.00595, step 2, values float32 
    16679 
    16680 > volume #13 step 1
    16681 
    16682 > volume #13 level 0.02012
    16683 
    16684 > select add #13
    16685 
    16686 2 models selected 
    16687 
    16688 > view matrix models #13,1,0,0,-56.643,0,1,0,-72.238,0,0,1,-68.565
    16689 
    16690 > ui mousemode right "rotate selected models"
    16691 
    16692 > view matrix models
    16693 > #13,0.02465,-0.61986,0.78433,49.618,-0.43145,0.70114,0.56768,-50.105,-0.9018,-0.35239,-0.25015,252.26
    16694 
    16695 > ui mousemode right "translate selected models"
    16696 
    16697 > view matrix models
    16698 > #13,0.02465,-0.61986,0.78433,42.91,-0.43145,0.70114,0.56768,-47.812,-0.9018,-0.35239,-0.25015,260.75
    16699 
    16700 > view matrix models
    16701 > #13,0.02465,-0.61986,0.78433,45.137,-0.43145,0.70114,0.56768,-48.218,-0.9018,-0.35239,-0.25015,267.86
    16702 
    16703 > rename #13 mOCT1-MTF.mrc
    16704 
    16705 > open
    16706 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-MTF_20240603/RealSpaceRefine_3/mOCT1_MTF-
    16707 > coot-9_real_space_refined_003.pdb
    16708 
    16709 Chain information for mOCT1_MTF-coot-9_real_space_refined_003.pdb #14 
    16710 --- 
    16711 Chain | Description 
    16712 A | No description available 
    16713  
    16714 
    16715 > fitmap #13 inMap #1
    16716 
    16717 Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    16718 using 17817 points 
    16719 correlation = 0.2983, correlation about mean = 0.07385, overlap = 82.29 
    16720 steps = 200, shift = 2.4, angle = 7.61 degrees 
    16721  
    16722 Position of mOCT1-MTF.mrc (#13) relative to
    16723 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    16724 Matrix rotation and translation 
    16725 -0.05771312 -0.64461025 0.76232987 59.74942259 
    16726 -0.34050237 0.73052504 0.59193860 -66.21901607 
    16727 -0.93847075 -0.22541250 -0.26165220 256.68697920 
    16728 Axis -0.42762978 0.88984156 0.15910615 
    16729 Axis point 123.33045199 0.00000000 117.21732044 
    16730 Rotation angle (degrees) 107.12276965 
    16731 Shift along axis -43.63458901 
    16732  
    16733 
    16734 > select subtract #13
    16735 
    16736 Nothing selected 
    16737 
    16738 > select add #13
    16739 
    16740 2 models selected 
    16741 
    16742 > ui mousemode right "rotate selected models"
    16743 
    16744 > view matrix models
    16745 > #13,0.50114,0.40107,-0.76681,42.081,-0.045209,-0.87277,-0.48604,255.79,-0.86419,0.27824,-0.41924,198.29
    16746 
    16747 > ui mousemode right "translate selected models"
    16748 
    16749 > view matrix models
    16750 > #13,0.50114,0.40107,-0.76681,41.903,-0.045209,-0.87277,-0.48604,247.49,-0.86419,0.27824,-0.41924,198.18
    16751 
    16752 > view matrix models
    16753 > #13,0.50114,0.40107,-0.76681,53.046,-0.045209,-0.87277,-0.48604,251.12,-0.86419,0.27824,-0.41924,198.38
    16754 
    16755 > fitmap #13 inMap #1
    16756 
    16757 Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    16758 using 17817 points 
    16759 correlation = 0.2273, correlation about mean = 0.06656, overlap = 59.06 
    16760 steps = 120, shift = 2.59, angle = 4.72 degrees 
    16761  
    16762 Position of mOCT1-MTF.mrc (#13) relative to
    16763 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    16764 Matrix rotation and translation 
    16765 0.43566959 0.38627366 -0.81300964 69.55864121 
    16766 -0.07375796 -0.88487887 -0.45994473 251.91510217 
    16767 -0.89707959 0.26034986 -0.35702406 194.41028021 
    16768 Axis 0.83873143 0.09789343 -0.53567385 
    16769 Axis point 0.00000000 97.27212052 153.57991582 
    16770 Rotation angle (degrees) 154.57081238 
    16771 Shift along axis -21.13865268 
    16772  
    16773 
    16774 > view matrix models
    16775 > #13,0.43567,0.38627,-0.81301,67.4,-0.073758,-0.88488,-0.45994,259.27,-0.89708,0.26035,-0.35702,197.15
    16776 
    16777 > ui mousemode right "rotate selected models"
    16778 
    16779 > view matrix models
    16780 > #13,0.3307,0.47313,-0.81657,68.962,0.20831,-0.88051,-0.42581,219.2,-0.92046,-0.029281,-0.38974,244.12
    16781 
    16782 > view matrix models
    16783 > #13,0.3796,0.48184,-0.78977,58.246,0.18592,-0.87598,-0.44507,223.83,-0.90628,0.022112,-0.42211,239.42
    16784 
    16785 > ui mousemode right "translate selected models"
    16786 
    16787 > view matrix models
    16788 > #13,0.3796,0.48184,-0.78977,53.846,0.18592,-0.87598,-0.44507,217.81,-0.90628,0.022112,-0.42211,235.11
    16789 
    16790 > fitmap #13 inMap #1
    16791 
    16792 Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    16793 using 17817 points 
    16794 correlation = 0.2652, correlation about mean = 0.06679, overlap = 73.72 
    16795 steps = 92, shift = 1.81, angle = 5.01 degrees 
    16796  
    16797 Position of mOCT1-MTF.mrc (#13) relative to
    16798 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    16799 Matrix rotation and translation 
    16800 0.31415893 0.53789144 -0.78228958 53.81386032 
    16801 0.19698588 -0.84300825 -0.50053338 220.95415625 
    16802 -0.92870918 0.00314703 -0.37079559 234.49017112 
    16803 Axis 0.80514260 0.23405449 -0.54494394 
    16804 Axis point 0.00000000 81.07236056 158.23174632 
    16805 Rotation angle (degrees) 161.77257653 
    16806 Shift along axis -32.74085292 
    16807  
    16808 
    16809 > view matrix models
    16810 > #13,0.31416,0.53789,-0.78229,60.198,0.19699,-0.84301,-0.50053,217.39,-0.92871,0.003147,-0.3708,234.22
    16811 
    16812 > fitmap #13 inMap #1
    16813 
    16814 Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    16815 using 17817 points 
    16816 correlation = 0.2449, correlation about mean = 0.05515, overlap = 65.5 
    16817 steps = 80, shift = 1.45, angle = 5.73 degrees 
    16818  
    16819 Position of mOCT1-MTF.mrc (#13) relative to
    16820 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    16821 Matrix rotation and translation 
    16822 0.28419679 0.60053681 -0.74738728 50.81854511 
    16823 0.27816291 -0.79764719 -0.53514891 205.19579930 
    16824 -0.91752798 -0.05580782 -0.39373584 245.12613641 
    16825 Axis 0.79598780 0.28253351 -0.53533003 
    16826 Axis point 0.00000000 71.54715698 160.41463451 
    16827 Rotation angle (degrees) 162.47642045 
    16828 Shift along axis -32.79775064 
    16829  
    16830 
    16831 > view matrix models
    16832 > #13,0.2842,0.60054,-0.74739,49.177,0.27816,-0.79765,-0.53515,206.5,-0.91753,-0.055808,-0.39374,243.99
    16833 
    16834 > fitmap #13 inMap #1
    16835 
    16836 Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    16837 using 17817 points 
    16838 correlation = 0.3559, correlation about mean = 0.151, overlap = 107.2 
    16839 steps = 88, shift = 2.33, angle = 2.34 degrees 
    16840  
    16841 Position of mOCT1-MTF.mrc (#13) relative to
    16842 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    16843 Matrix rotation and translation 
    16844 0.29378487 0.57675594 -0.76226180 52.65591556 
    16845 0.29516509 -0.81321822 -0.50155130 203.18767751 
    16846 -0.90915787 -0.07764488 -0.40914943 245.95334709 
    16847 Axis 0.80029578 0.27732609 -0.53161726 
    16848 Axis point 0.00000000 73.19686532 158.33534093 
    16849 Rotation angle (degrees) 164.64234082 
    16850 Shift along axis -32.26349399 
    16851  
    16852 
    16853 > view matrix models
    16854 > #13,0.29378,0.57676,-0.76226,50.19,0.29517,-0.81322,-0.50155,203.5,-0.90916,-0.077645,-0.40915,251.78
    16855 
    16856 > fitmap #13 inMap #1
    16857 
    16858 Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    16859 using 17817 points 
    16860 correlation = 0.9033, correlation about mean = 0.6277, overlap = 419.6 
    16861 steps = 52, shift = 1.52, angle = 1.92 degrees 
    16862  
    16863 Position of mOCT1-MTF.mrc (#13) relative to
    16864 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    16865 Matrix rotation and translation 
    16866 0.29574252 0.60146473 -0.74214321 45.38180479 
    16867 0.29484975 -0.79643687 -0.52796964 204.44935424 
    16868 -0.90862533 -0.06267767 -0.41288198 249.74597785 
    16869 Axis 0.80005949 0.28626242 -0.52721784 
    16870 Axis point 0.00000000 72.71544700 159.79227740 
    16871 Rotation angle (degrees) 163.09499009 
    16872 Shift along axis -36.83622428 
    16873  
    16874 
    16875 > ui tool show Matchmaker
    16876 
    16877 > matchmaker #!14 to #5
    16878 
    16879 Parameters 
    16880 --- 
    16881 Chain pairing | bb 
    16882 Alignment algorithm | Needleman-Wunsch 
    16883 Similarity matrix | BLOSUM-62 
    16884 SS fraction | 0.3 
    16885 Gap open (HH/SS/other) | 18/18/6 
    16886 Gap extend | 1 
    16887 SS matrix |  |  | H | S | O 
    16888 ---|---|---|--- 
    16889 H | 6 | -9 | -6 
    16890 S |  | 6 | -6 
    16891 O |  |  | 4 
    16892 Iteration cutoff | 2 
    16893  
    16894 Matchmaker mOCT1-VB1_real_space_refined_014.pdb, chain A (#5) with mOCT1_MTF-
    16895 coot-9_real_space_refined_003.pdb, chain A (#14), sequence alignment score =
    16896 2355.8 
    16897 RMSD between 450 pruned atom pairs is 0.377 angstroms; (across all 450 pairs:
    16898 0.377) 
    16899  
    16900 
    16901 > select add #14
    16902 
    16903 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 4 models selected 
    16904 
    16905 > select subtract #13
    16906 
    16907 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected 
    16908 
    16909 > hide #!1 models
    16910 
    16911 > save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
    16912 > density.cxs" includeMaps true
    16913 
    16914 QXcbConnection: XCB error: 3 (BadWindow), sequence: 5891, resource id:
    16915 35654810, major code: 40 (TranslateCoords), minor code: 0 
    16916 
    16917 > color #14 #95cacdff
    16918 
    16919 > select ::name="MF8"
    16920 
    16921 22 atoms, 21 bonds, 1 residue, 1 model selected 
    16922 
    16923 > select add #14
    16924 
    16925 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected 
    16926 
    16927 > select subtract #14
    16928 
    16929 Nothing selected 
    16930 
    16931 > select add #14
    16932 
    16933 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected 
    16934 
    16935 > color (#!14 & sel) white
    16936 
    16937 > select ::name="MF8"
    16938 
    16939 22 atoms, 21 bonds, 1 residue, 1 model selected 
    16940 
    16941 > color sel red
    16942 
    16943 > color zone #10 near #11 distance 4.98
    16944 
    16945 > color zone #13 near #14 distance 4.98
    16946 
    16947 > hide #!14 models
    16948 
    16949 > show #!14 models
    16950 
    16951 > volume #13 level 0.0238
    16952 
    16953 > volume #13 level 0.02122
    16954 
    16955 > volume #13 level 0.01423
    16956 
    16957 > volume splitbyzone #13
    16958 
    16959 Opened mOCT1-MTF.mrc 0 as #15.1, grid size 320,320,320, pixel 0.83, shown at
    16960 level 0.0142, step 1, values float32 
    16961 Opened mOCT1-MTF.mrc 1 as #15.2, grid size 320,320,320, pixel 0.83, shown at
    16962 level 0.0142, step 1, values float32 
    16963 Opened mOCT1-MTF.mrc 2 as #15.3, grid size 320,320,320, pixel 0.83, shown at
    16964 level 0.0142, step 1, values float32 
    16965 
    16966 > close #15.1
    16967 
    16968 > close #15.2
    16969 
    16970 > volume #15.3 level 0.009273
    16971 
    16972 > volume #15.3 level 0.01703
    16973 
    16974 > close #15#15.3
    16975 
    16976 > select add #14
    16977 
    16978 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected 
    16979 
    16980 > show #!13 models
    16981 
    16982 > color zone #13 near #14 distance 4.88
    16983 
    16984 > color zone #13 near #14 distance 4.78
    16985 
    16986 > color zone #13 near #14 distance 4.68
    16987 
    16988 > color zone #13 near #14 distance 4.58
    16989 
    16990 > color zone #13 near #14 distance 4.48
    16991 
    16992 > color zone #13 near #14 distance 4.38
    16993 
    16994 > color zone #13 near #14 distance 4.28
    16995 
    16996 > color zone #13 near #14 distance 4.18
    16997 
    16998 > color zone #13 near #14 distance 4.08
    16999 
    17000 > color zone #13 near #14 distance 3.98
    17001 
    17002 > color zone #13 near #14 distance 3.88
    17003 
    17004 > color zone #13 near #14 distance 3.78
    17005 
    17006 > color zone #13 near #14 distance 3.68
    17007 
    17008 > color zone #13 near #14 distance 3.58
    17009 
    17010 > color zone #13 near #14 distance 3.48
    17011 
    17012 > color zone #13 near #14 distance 3.38
    17013 
    17014 [Repeated 1 time(s)]
    17015 
    17016 > volume splitbyzone #13
    17017 
    17018 Opened mOCT1-MTF.mrc 0 as #15.1, grid size 320,320,320, pixel 0.83, shown at
    17019 level 0.0142, step 1, values float32 
    17020 Opened mOCT1-MTF.mrc 1 as #15.2, grid size 320,320,320, pixel 0.83, shown at
    17021 level 0.0142, step 1, values float32 
    17022 Opened mOCT1-MTF.mrc 2 as #15.3, grid size 320,320,320, pixel 0.83, shown at
    17023 level 0.0142, step 1, values float32 
    17024 
    17025 > close #15.1-2
    17026 
    17027 > volume #15.3 level 0.009634
    17028 
    17029 > color zone #13 near #14 distance 3.28
    17030 
    17031 > color zone #13 near #14 distance 3.18
    17032 
    17033 > color zone #13 near #14 distance 3.08
    17034 
    17035 > close #15#15.3
    17036 
    17037 > show #!13 models
    17038 
    17039 > select add #13
    17040 
    17041 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 4 models selected 
    17042 
    17043 > select subtract #13
    17044 
    17045 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected 
    17046 
    17047 > color zone #13 near #14 distance 2.98
    17048 
    17049 > color zone #13 near #14 distance 2.88
    17050 
    17051 > color zone #13 near #14 distance 2.78
    17052 
    17053 > color zone #13 near #14 distance 2.68
    17054 
    17055 > color zone #13 near #14 distance 2.58
    17056 
    17057 > color zone #13 near #14 distance 2.48
    17058 
    17059 > volume #13 level 0.01681
    17060 
    17061 > fitmap #14 inMap #13
    17062 
    17063 Fit molecule mOCT1_MTF-coot-9_real_space_refined_003.pdb (#14) to map
    17064 mOCT1-MTF.mrc (#13) using 7044 atoms 
    17065 average map value = 0.01572, steps = 48 
    17066 shifted from previous position = 0.0765 
    17067 rotated from previous position = 0.266 degrees 
    17068 atoms outside contour = 4386, contour level = 0.016807 
    17069  
    17070 Position of mOCT1_MTF-coot-9_real_space_refined_003.pdb (#14) relative to
    17071 mOCT1-MTF.mrc (#13) coordinates: 
    17072 Matrix rotation and translation 
    17073 0.99946408 0.01781074 -0.02746495 0.87693504 
    17074 -0.01720783 0.99960910 0.02203450 -1.16466203 
    17075 0.02784666 -0.02155008 0.99937988 -1.14535630 
    17076 Axis -0.55418255 -0.70329295 -0.44526478 
    17077 Axis point 28.72708736 -0.00000000 48.38067452 
    17078 Rotation angle (degrees) 2.25364092 
    17079 Shift along axis 0.84310332 
    17080  
    17081 
    17082 > color zone #13 near #14 distance 2.48
    17083 
    17084 [Repeated 1 time(s)]
    17085 
    17086 > color single #13
    17087 
    17088 > color zone #13 near #14 distance 2.48
    17089 
    17090 > color zone #13 near #14 distance 2.38
    17091 
    17092 > color zone #13 near #14 distance 2.28
    17093 
    17094 > color zone #13 near #14 distance 2.18
    17095 
    17096 > color zone #13 near #14 distance 2.08
    17097 
    17098 > color zone #13 near #14 distance 1.98
    17099 
    17100 > color zone #13 near #14 distance 1.88
    17101 
    17102 > color zone #13 near #14 distance 1.78
    17103 
    17104 > color zone #13 near #14 distance 1.68
    17105 
    17106 > color zone #13 near #14 distance 1.58
    17107 
    17108 > color zone #13 near #14 distance 1.48
    17109 
    17110 > color zone #13 near #14 distance 1.38
    17111 
    17112 > color zone #13 near #14 distance 1.48
    17113 
    17114 > color zone #13 near #14 distance 1.58
    17115 
    17116 > color zone #13 near #14 distance 1.68
    17117 
    17118 > color zone #13 near #14 distance 1.78
    17119 
    17120 > color zone #13 near #14 distance 1.88
    17121 
    17122 > color zone #13 near #14 distance 1.98
    17123 
    17124 > volume #13 level 0.01957
    17125 
    17126 > color zone #13 near #14 distance 1.98
    17127 
    17128 > volume splitbyzone #13
    17129 
    17130 Opened mOCT1-MTF.mrc 0 as #15.1, grid size 320,320,320, pixel 0.83, shown at
    17131 level 0.0196, step 1, values float32 
    17132 Opened mOCT1-MTF.mrc 1 as #15.2, grid size 320,320,320, pixel 0.83, shown at
    17133 level 0.0196, step 1, values float32 
    17134 Opened mOCT1-MTF.mrc 2 as #15.3, grid size 320,320,320, pixel 0.83, shown at
    17135 level 0.0196, step 1, values float32 
    17136 
    17137 > close #15.1-2
    17138 
    17139 > color #15.3 yellow models
    17140 
    17141 > color #15.3 white models
    17142 
    17143 > color #15.3 #ffffb2ff models
    17144 
    17145 > color #15.3 #ffffb296 models
    17146 
    17147 > volume #15.3 level 0.01524
    17148 
    17149 > volume #15.3 level 0.0119
    17150 
    17151 > select subtract #14
    17152 
    17153 Nothing selected 
    17154 
    17155 > select add #14
    17156 
    17157 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected 
    17158 
    17159 > color #14 #55dd44ff
    17160 
    17161 > color #14 #5d42cdff
    17162 
    17163 > color #14 #5858cdff
    17164 
    17165 > color #14 #7d76cdff
    17166 
    17167 > color #14 #9d7bcdff
    17168 
    17169 > color #14 #cd75baff
    17170 
    17171 > color #14 #9381cdff
    17172 
    17173 > color (#!14 & sel) byhetero
    17174 
    17175 > select clear
    17176 
    17177 > save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
    17178 > density.cxs" includeMaps true
    17179 
    17180 > hide #!15.3 models
    17181 
    17182 > hide #!15 models
    17183 
    17184 > hide #!14 models
    17185 
    17186 > show #!1 models
    17187 
    17188 > open
    17189 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/job321/relion_locres_filtered.mrc
    17190 
    17191 Opened relion_locres_filtered.mrc as #16, grid size 320,320,320, pixel 0.83,
    17192 shown at level 0.00147, step 2, values float32 
    17193 
    17194 > volume #13 level 0.01846
    17195 
    17196 > volume #16 step 1
    17197 
    17198 > volume #16 level 0.01137
    17199 
    17200 > select add #16
    17201 
    17202 2 models selected 
    17203 
    17204 > ui mousemode right "rotate selected models"
    17205 
    17206 > view matrix models
    17207 > #16,0.91726,-0.046522,0.39555,-35.801,-0.13266,0.90075,0.41357,-25.02,-0.37554,-0.43183,0.82006,127.4
    17208 
    17209 > view matrix models
    17210 > #16,0.97308,0.0084656,-0.23031,32.94,-0.035652,0.99283,-0.11414,20.659,0.2277,0.11927,0.9664,-40.203
    17211 
    17212 > view matrix models
    17213 > #16,0.95291,-0.013325,0.30296,-32.366,-0.094841,0.93583,0.33946,-24.554,-0.28805,-0.35221,0.89049,96.605
    17214 
    17215 > view matrix models
    17216 > #16,0.68405,0.72927,0.015283,-53.826,0.65561,-0.6055,-0.45117,179.02,-0.31977,0.31864,-0.89231,251.74
    17217 
    17218 > view matrix models
    17219 > #16,-0.14871,0.82898,-0.53915,114.85,0.43367,-0.43531,-0.78894,230.9,-0.88872,-0.35114,-0.29476,331.38
    17220 
    17221 > view matrix models
    17222 > #16,-0.59154,0.6904,-0.41646,173.56,0.69281,0.17103,-0.70054,108.52,-0.41243,-0.70292,-0.57948,352.16
    17223 
    17224 > ui mousemode right "translate selected models"
    17225 
    17226 > view matrix models
    17227 > #16,-0.59154,0.6904,-0.41646,98.473,0.69281,0.17103,-0.70054,82.195,-0.41243,-0.70292,-0.57948,295.09
    17228 
    17229 > view matrix models
    17230 > #16,-0.59154,0.6904,-0.41646,115.7,0.69281,0.17103,-0.70054,51.467,-0.41243,-0.70292,-0.57948,297.87
    17231 
    17232 > view matrix models
    17233 > #16,-0.59154,0.6904,-0.41646,109.24,0.69281,0.17103,-0.70054,49.803,-0.41243,-0.70292,-0.57948,297.08
    17234 
    17235 > view matrix models
    17236 > #16,-0.59154,0.6904,-0.41646,112.5,0.69281,0.17103,-0.70054,41.909,-0.41243,-0.70292,-0.57948,292.69
    17237 
    17238 > ui mousemode right "rotate selected models"
    17239 
    17240 > view matrix models
    17241 > #16,-0.52634,0.62911,-0.57201,132.47,0.46428,-0.35094,-0.81319,152.81,-0.71233,-0.69359,-0.10737,267.76
    17242 
    17243 > view matrix models
    17244 > #16,-0.56071,0.74447,-0.36245,94.475,0.40226,-0.13769,-0.90511,145.91,-0.72373,-0.6533,-0.22227,279.35
    17245 
    17246 > ui mousemode right "translate selected models"
    17247 
    17248 > view matrix models
    17249 > #16,-0.56071,0.74447,-0.36245,91.988,0.40226,-0.13769,-0.90511,152.84,-0.72373,-0.6533,-0.22227,276.37
    17250 
    17251 > ui mousemode right "rotate selected models"
    17252 
    17253 > view matrix models
    17254 > #16,-0.69312,0.68147,-0.23491,100.24,0.41746,0.11382,-0.90154,118.42,-0.58764,-0.72294,-0.36338,286.3
    17255 
    17256 > rename #16 hOCT1-VB1.mrc
    17257 
    17258 > fitmap #16 inMap #1
    17259 
    17260 Fit map hOCT1-VB1.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    17261 using 29501 points 
    17262 correlation = 0.336, correlation about mean = 0.1558, overlap = 114.4 
    17263 steps = 148, shift = 3.34, angle = 5.64 degrees 
    17264  
    17265 Position of hOCT1-VB1.mrc (#16) relative to
    17266 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    17267 Matrix rotation and translation 
    17268 -0.66774800 0.66848229 -0.32748134 111.59775010 
    17269 0.47076725 0.03845367 -0.88141903 115.78397104 
    17270 -0.57662015 -0.74273329 -0.34037693 282.67572866 
    17271 Axis 0.39969377 0.71802066 -0.56981683 
    17272 Axis point 39.62225841 0.00000000 179.67701786 
    17273 Rotation angle (degrees) 170.00920250 
    17274 Shift along axis -33.33317846 
    17275  
    17276 
    17277 > ui mousemode right "translate selected models"
    17278 
    17279 > view matrix models
    17280 > #16,-0.66775,0.66848,-0.32748,111.72,0.47077,0.038454,-0.88142,115.95,-0.57662,-0.74273,-0.34038,288.9
    17281 
    17282 > fitmap #16 inMap #1
    17283 
    17284 Fit map hOCT1-VB1.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    17285 using 29501 points 
    17286 correlation = 0.7772, correlation about mean = 0.5328, overlap = 352.7 
    17287 steps = 60, shift = 1.34, angle = 1.92 degrees 
    17288  
    17289 Position of hOCT1-VB1.mrc (#16) relative to
    17290 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    17291 Matrix rotation and translation 
    17292 -0.68896253 0.65809895 -0.30370448 111.90845021 
    17293 0.45027206 0.06027049 -0.89085495 116.65862228 
    17294 -0.56796628 -0.75051532 -0.33784768 287.44343290 
    17295 Axis 0.38522072 0.72537689 -0.57046767 
    17296 Axis point 41.86637964 0.00000000 181.62562393 
    17297 Rotation angle (degrees) 169.50470225 
    17298 Shift along axis -36.24626372 
    17299  
    17300 
    17301 > view matrix models
    17302 > #16,-0.68896,0.6581,-0.3037,110.15,0.45027,0.06027,-0.89085,119.19,-0.56797,-0.75052,-0.33785,287.46
    17303 
    17304 > fitmap #16 inMap #1
    17305 
    17306 Fit map hOCT1-VB1.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    17307 using 29501 points 
    17308 correlation = 0.7772, correlation about mean = 0.5327, overlap = 352.7 
    17309 steps = 72, shift = 3.09, angle = 0.0182 degrees 
    17310  
    17311 Position of hOCT1-VB1.mrc (#16) relative to
    17312 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    17313 Matrix rotation and translation 
    17314 -0.68902052 0.65795875 -0.30387662 111.96278841 
    17315 0.45022908 0.06002731 -0.89089309 116.69902951 
    17316 -0.56793001 -0.75065771 -0.33759222 287.41226501 
    17317 Axis 0.38519550 0.72529614 -0.57058737 
    17318 Axis point 41.87016659 0.00000000 181.64241189 
    17319 Rotation angle (degrees) 169.51189271 
    17320 Shift along axis -36.22489055 
    17321  
    17322 
    17323 > fitmap #16 inMap #1
    17324 
    17325 Fit map hOCT1-VB1.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
    17326 using 29501 points 
    17327 correlation = 0.7772, correlation about mean = 0.5328, overlap = 352.7 
    17328 steps = 36, shift = 0.00448, angle = 0.00722 degrees 
    17329  
    17330 Position of hOCT1-VB1.mrc (#16) relative to
    17331 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: 
    17332 Matrix rotation and translation 
    17333 -0.68898476 0.65802671 -0.30381055 111.93916561 
    17334 0.45024501 0.06010903 -0.89087953 116.68451889 
    17335 -0.56796077 -0.75059160 -0.33768744 287.42460080 
    17336 Axis 0.38521270 0.72532270 -0.57054198 
    17337 Axis point 41.86758112 0.00000000 181.63640339 
    17338 Rotation angle (degrees) 169.50839167 
    17339 Shift along axis -36.23348002 
    17340  
    17341 
    17342 > open
    17343 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/RealSpaceRefine_10/hOCT1-VB_Dock2_real_space_refined_010.pdb
    17344 
    17345 Chain information for hOCT1-VB_Dock2_real_space_refined_010.pdb #17 
    17346 --- 
    17347 Chain | Description 
    17348 A | No description available 
    17349  
    17350 
    17351 > ui tool show Matchmaker
    17352 
    17353 > matchmaker #!17 to #5
    17354 
    17355 Parameters 
    17356 --- 
    17357 Chain pairing | bb 
    17358 Alignment algorithm | Needleman-Wunsch 
    17359 Similarity matrix | BLOSUM-62 
    17360 SS fraction | 0.3 
    17361 Gap open (HH/SS/other) | 18/18/6 
    17362 Gap extend | 1 
    17363 SS matrix |  |  | H | S | O 
    17364 ---|---|---|--- 
    17365 H | 6 | -9 | -6 
    17366 S |  | 6 | -6 
    17367 O |  |  | 4 
    17368 Iteration cutoff | 2 
    17369  
    17370 Matchmaker mOCT1-VB1_real_space_refined_014.pdb, chain A (#5) with
    17371 hOCT1-VB_Dock2_real_space_refined_010.pdb, chain A (#17), sequence alignment
    17372 score = 1980 
    17373 RMSD between 416 pruned atom pairs is 0.792 angstroms; (across all 446 pairs:
    17374 1.346) 
    17375  
    17376 
    17377 > fitmap #17 inMap #16
    17378 
    17379 Fit molecule hOCT1-VB_Dock2_real_space_refined_010.pdb (#17) to map
    17380 hOCT1-VB1.mrc (#16) using 3479 atoms 
    17381 average map value = 0.02025, steps = 64 
    17382 shifted from previous position = 0.153 
    17383 rotated from previous position = 0.521 degrees 
    17384 atoms outside contour = 1063, contour level = 0.011373 
    17385  
    17386 Position of hOCT1-VB_Dock2_real_space_refined_010.pdb (#17) relative to
    17387 hOCT1-VB1.mrc (#16) coordinates: 
    17388 Matrix rotation and translation 
    17389 0.99999651 0.00186028 0.00187897 -0.40239474 
    17390 -0.00185675 0.99999652 -0.00187607 0.55801929 
    17391 -0.00188246 0.00187257 0.99999648 0.09469763 
    17392 Axis 0.57831092 0.58028383 -0.57343453 
    17393 Axis point 61.09212114 0.00000000 225.59585813 
    17394 Rotation angle (degrees) 0.18569746 
    17395 Shift along axis 0.03679741 
    17396  
    17397 
    17398 > fitmap #17 inMap #16
    17399 
    17400 Fit molecule hOCT1-VB_Dock2_real_space_refined_010.pdb (#17) to map
    17401 hOCT1-VB1.mrc (#16) using 3479 atoms 
    17402 average map value = 0.02025, steps = 28 
    17403 shifted from previous position = 0.0153 
    17404 rotated from previous position = 0.0146 degrees 
    17405 atoms outside contour = 1064, contour level = 0.011373 
    17406  
    17407 Position of hOCT1-VB_Dock2_real_space_refined_010.pdb (#17) relative to
    17408 hOCT1-VB1.mrc (#16) coordinates: 
    17409 Matrix rotation and translation 
    17410 0.99999599 0.00211002 0.00188874 -0.43726655 
    17411 -0.00210638 0.99999592 -0.00192887 0.59237860 
    17412 -0.00189280 0.00192488 0.99999636 0.07510223 
    17413 Axis 0.56254941 0.55200867 -0.61548727 
    17414 Axis point 271.69369003 217.02489508 0.00000000 
    17415 Rotation angle (degrees) 0.19625280 
    17416 Shift along axis 0.03478962 
    17417  
    17418 
    17419 > hide #!1 models
    17420 
    17421 > select add #17
    17422 
    17423 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 4 models selected 
    17424 
    17425 > select subtract #16
    17426 
    17427 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 2 models selected 
    17428 
    17429 > color (#!17 & sel) white
    17430 
    17431 > select clear
    17432 
    17433 > select ::name="VIB"
    17434 
    17435 18 atoms, 19 bonds, 1 residue, 1 model selected 
    17436 
    17437 > color sel red
    17438 
    17439 > color zone #16 near #17 distance 4.98
    17440 
    17441 > color zone #16 near #17 distance 4.88
    17442 
    17443 > color zone #16 near #17 distance 4.78
    17444 
    17445 > color zone #16 near #17 distance 4.68
    17446 
    17447 > color zone #16 near #17 distance 4.58
    17448 
    17449 > color zone #16 near #17 distance 4.48
    17450 
    17451 > color zone #16 near #17 distance 4.38
    17452 
    17453 > color zone #16 near #17 distance 4.28
    17454 
    17455 > color zone #16 near #17 distance 4.18
    17456 
    17457 > color zone #16 near #17 distance 4.08
    17458 
    17459 > color zone #16 near #17 distance 3.98
    17460 
    17461 > color zone #16 near #17 distance 3.88
    17462 
    17463 > color zone #16 near #17 distance 3.78
    17464 
    17465 > color zone #16 near #17 distance 3.68
    17466 
    17467 > color zone #16 near #17 distance 3.58
    17468 
    17469 > color zone #16 near #17 distance 3.48
    17470 
    17471 > color zone #16 near #17 distance 3.38
    17472 
    17473 > color zone #16 near #17 distance 3.28
    17474 
    17475 > color sel white
    17476 
    17477 > select ::name="VIB"
    17478 
    17479 18 atoms, 19 bonds, 1 residue, 1 model selected 
    17480 
    17481 > color sel red
    17482 
    17483 > select add #16
    17484 
    17485 18 atoms, 19 bonds, 1 residue, 3 models selected 
    17486 
    17487 > select add #17
    17488 
    17489 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 4 models selected 
    17490 
    17491 > select subtract #17
    17492 
    17493 2 models selected 
    17494 
    17495 > color #16.1 white
    17496 
    17497 > color zone #16 near #17 distance 3.28
    17498 
    17499 > color zone #16 near #17 distance 3.18
    17500 
    17501 > color zone #16 near #17 distance 3.08
    17502 
    17503 > color zone #16 near #17 distance 2.98
    17504 
    17505 > color zone #16 near #17 distance 2.88
    17506 
    17507 > color zone #16 near #17 distance 2.98
    17508 
    17509 > color zone #16 near #17 distance 3.08
    17510 
    17511 > color zone #16 near #17 distance 3.18
    17512 
    17513 > color zone #16 near #17 distance 3.28
    17514 
    17515 > color zone #16 near #17 distance 3.38
    17516 
    17517 [Repeated 1 time(s)]
    17518 
    17519 > volume splitbyzone #16
    17520 
    17521 Opened hOCT1-VB1.mrc 0 as #18.1, grid size 320,320,320, pixel 0.83, shown at
    17522 level 0.0114, step 1, values float32 
    17523 Opened hOCT1-VB1.mrc 1 as #18.2, grid size 320,320,320, pixel 0.83, shown at
    17524 level 0.0114, step 1, values float32 
    17525 Opened hOCT1-VB1.mrc 2 as #18.3, grid size 320,320,320, pixel 0.83, shown at
    17526 level 0.0114, step 1, values float32 
    17527 
    17528 > close #18.1-2
    17529 
    17530 > color #18.3 yellow models
    17531 
    17532 > color #18.3 white models
    17533 
    17534 > color #18.3 #ffffb2ff models
    17535 
    17536 > color #18.3 #ffffb296 models
    17537 
    17538 > select add #17
    17539 
    17540 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 4 models selected 
    17541 
    17542 > select subtract #16
    17543 
    17544 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 2 models selected 
    17545 
    17546 > color #17 #6622bbff
    17547 
    17548 > color #17 #62be40ff
    17549 
    17550 > color (#!17 & sel) byhetero
    17551 
    17552 Drag select of 1 atoms, 1 bonds 
    17553 
    17554 > volume #18.3 level 0.006511
    17555 
    17556 > volume #18.3 level 0.01112
    17557 
    17558 > close #18#18.3
    17559 
    17560 > select add #17
    17561 
    17562 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 2 models selected 
    17563 
    17564 > color (#!17 & sel) white
    17565 
    17566 > select ::name="VIB"
    17567 
    17568 18 atoms, 19 bonds, 1 residue, 1 model selected 
    17569 
    17570 > color sel red
    17571 
    17572 > show #!16 models
    17573 
    17574 > color zone #16 near #17 distance 3.28
    17575 
    17576 > color zone #16 near #17 distance 3.18
    17577 
    17578 > color zone #16 near #17 distance 3.08
    17579 
    17580 > color zone #16 near #17 distance 2.98
    17581 
    17582 > color zone #16 near #17 distance 2.88
    17583 
    17584 > color zone #16 near #17 distance 2.78
    17585 
    17586 > color zone #16 near #17 distance 2.68
    17587 
    17588 > color zone #16 near #17 distance 2.58
    17589 
    17590 > color zone #16 near #17 distance 2.48
    17591 
    17592 > color zone #16 near #17 distance 2.38
    17593 
    17594 > color zone #16 near #17 distance 2.28
    17595 
    17596 > color zone #16 near #17 distance 2.18
    17597 
    17598 > color zone #16 near #17 distance 2.08
    17599 
    17600 > color zone #16 near #17 distance 1.98
    17601 
    17602 > color zone #16 near #17 distance 1.88
    17603 
    17604 > color zone #16 near #17 distance 1.78
    17605 
    17606 > color zone #16 near #17 distance 1.68
    17607 
    17608 > color zone #16 near #17 distance 1.78
    17609 
    17610 > color zone #16 near #17 distance 1.88
    17611 
    17612 > color zone #16 near #17 distance 1.98
    17613 
    17614 > color zone #16 near #17 distance 2.08
    17615 
    17616 > volume splitbyzone #16
    17617 
    17618 Opened hOCT1-VB1.mrc 0 as #18.1, grid size 320,320,320, pixel 0.83, shown at
    17619 level 0.0114, step 1, values float32 
    17620 Opened hOCT1-VB1.mrc 1 as #18.2, grid size 320,320,320, pixel 0.83, shown at
    17621 level 0.0114, step 1, values float32 
    17622 Opened hOCT1-VB1.mrc 2 as #18.3, grid size 320,320,320, pixel 0.83, shown at
    17623 level 0.0114, step 1, values float32 
    17624 
    17625 > close #18.1-2
    17626 
    17627 > color #18.3 white models
    17628 
    17629 > color #18.3 #ffffb2ff models
    17630 
    17631 > select add #18.3
    17632 
    17633 18 atoms, 19 bonds, 1 residue, 3 models selected 
    17634 
    17635 > color #18.3 #ffffb296 models
    17636 
    17637 > select subtract #18.3
    17638 
    17639 18 atoms, 19 bonds, 1 residue, 1 model selected 
    17640 
    17641 > select add #17
    17642 
    17643 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 2 models selected 
    17644 
    17645 > select subtract #17
    17646 
    17647 Nothing selected 
    17648 
    17649 > select add #17
    17650 
    17651 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 2 models selected 
    17652 
    17653 > color #17 #6622bbff
    17654 
    17655 > color #17 #62be40ff
    17656 
    17657 > color (#!17 & sel) byhetero
    17658 
    17659 > view
    17660 
    17661 > hide #!18.3 models
    17662 
    17663 > hide #!18 models
    17664 
    17665 > hide #!17 models
    17666 
    17667 > select subtract #17
    17668 
    17669 Nothing selected 
    17670 
    17671 > show #!1 models
    17672 
    17673 > open
    17674 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241004Krios_hOCT1-AZT/job154/postprocess_masked.mrc
    17675 
    17676 Opened postprocess_masked.mrc as #19, grid size 320,320,320, pixel 0.83, shown
    17677 at level 2.83e-06, step 2, values float32 
    17678 
    17679 > volume #19 step 1
    17680 
    17681 > volume #19 level 0.0131
    17682 
    17683 > select add #19
    17684 
    17685 2 models selected 
    17686 
    17687 > ui mousemode right "rotate selected models"
    17688 
    17689 > view matrix models
    17690 > #19,-0.93986,0.28611,-0.18654,253.04,-0.10485,-0.76147,-0.63967,340.05,-0.32506,-0.58164,0.74567,158.04
    17691 
    17692 > ui mousemode right "translate selected models"
    17693 
    17694 > view matrix models
    17695 > #19,-0.93986,0.28611,-0.18654,175.89,-0.10485,-0.76147,-0.63967,293,-0.32506,-0.58164,0.74567,91.801
    17696 
    17697 > view matrix models
    17698 > #19,-0.93986,0.28611,-0.18654,185.27,-0.10485,-0.76147,-0.63967,269.77,-0.32506,-0.58164,0.74567,91.027
    17699 
    17700 > view matrix models
    17701 > #19,-0.93986,0.28611,-0.18654,178.6,-0.10485,-0.76147,-0.63967,268.3,-0.32506,-0.58164,0.74567,89.593
    17702 
    17703 > rename #19 hOCT1-AZT.mrc
    17704 
    17705 > fitmap #19 inMap #16
    17706 
    17707 Fit map hOCT1-AZT.mrc in map hOCT1-VB1.mrc using 23475 points 
    17708 correlation = 0.9652, correlation about mean = 0.8232, overlap = 14.07 
    17709 steps = 112, shift = 2.59, angle = 19.3 degrees 
    17710  
    17711 Position of hOCT1-AZT.mrc (#19) relative to hOCT1-VB1.mrc (#16) coordinates: 
    17712 Matrix rotation and translation 
    17713 0.86934918 -0.02079803 -0.49376051 87.20318527 
    17714 -0.45396874 0.36123943 -0.81450504 253.58267245 
    17715 0.19530587 0.93224113 0.30460154 -57.13169181 
    17716 Axis 0.90642923 -0.35757337 -0.22478286 
    17717 Axis point 0.00000000 185.25380563 166.58335969 
    17718 Rotation angle (degrees) 74.47879004 
    17719 Shift along axis 1.21133072 
    17720  
    17721 
    17722 > open
    17723 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241004Krios_hOCT1-AZT/RealSpaceRefine_6/hOCT1_AZT-
    17724 > coot-2_real_space_refined_006.pdb
    17725 
    17726 Chain information for hOCT1_AZT-coot-2_real_space_refined_006.pdb #20 
    17727 --- 
    17728 Chain | Description 
    17729 A | No description available 
    17730  
    17731 
    17732 > ui tool show Matchmaker
    17733 
    17734 > matchmaker #!20 to #5
    17735 
    17736 Parameters 
    17737 --- 
    17738 Chain pairing | bb 
    17739 Alignment algorithm | Needleman-Wunsch 
    17740 Similarity matrix | BLOSUM-62 
    17741 SS fraction | 0.3 
    17742 Gap open (HH/SS/other) | 18/18/6 
    17743 Gap extend | 1 
    17744 SS matrix |  |  | H | S | O 
    17745 ---|---|---|--- 
    17746 H | 6 | -9 | -6 
    17747 S |  | 6 | -6 
    17748 O |  |  | 4 
    17749 Iteration cutoff | 2 
    17750  
    17751 Matchmaker mOCT1-VB1_real_space_refined_014.pdb, chain A (#5) with hOCT1_AZT-
    17752 coot-2_real_space_refined_006.pdb, chain A (#20), sequence alignment score =
    17753 1978 
    17754 RMSD between 414 pruned atom pairs is 0.849 angstroms; (across all 446 pairs:
    17755 1.482) 
    17756  
    17757 
    17758 > hide #!1 models
    17759 
    17760 > color #19 white models
    17761 
    17762 > select add #20
    17763 
    17764 3578 atoms, 3672 bonds, 1 pseudobond, 463 residues, 4 models selected 
    17765 
    17766 > color #20 white
    17767 
    17768 > hide #!19 models
    17769 
    17770 > select subtract #19
    17771 
    17772 3578 atoms, 3672 bonds, 1 pseudobond, 463 residues, 2 models selected 
    17773 
    17774 > select up
    17775 
    17776 2 atoms, 1 bond, 1 residue, 1 model selected 
    17777 
    17778 > select up
    17779 
    17780 19 atoms, 20 bonds, 1 residue, 1 model selected 
    17781 
    17782 > color sel red
    17783 
    17784 > color zone #19 near #20 distance 4.98
    17785 
    17786 > show #!19 models
    17787 
    17788 > select add #19
    17789 
    17790 19 atoms, 20 bonds, 1 residue, 3 models selected 
    17791 
    17792 > select subtract #19
    17793 
    17794 19 atoms, 20 bonds, 1 residue, 1 model selected 
    17795 
    17796 > color zone #19 near #20 distance 4.88
    17797 
    17798 > color zone #19 near #20 distance 4.78
    17799 
    17800 > color zone #19 near #20 distance 4.68
    17801 
    17802 > color zone #19 near #20 distance 4.58
    17803 
    17804 > color zone #19 near #20 distance 4.48
    17805 
    17806 > color zone #19 near #20 distance 4.38
    17807 
    17808 > color zone #19 near #20 distance 4.28
    17809 
    17810 > color zone #19 near #20 distance 4.18
    17811 
    17812 > color zone #19 near #20 distance 4.08
    17813 
    17814 > color zone #19 near #20 distance 3.98
    17815 
    17816 > color zone #19 near #20 distance 3.88
    17817 
    17818 > color zone #19 near #20 distance 3.78
    17819 
    17820 > color zone #19 near #20 distance 3.68
    17821 
    17822 > color zone #19 near #20 distance 3.58
    17823 
    17824 > color zone #19 near #20 distance 3.48
    17825 
    17826 > volume #19 level 0.01039
    17827 
    17828 > color zone #19 near #20 distance 3.38
    17829 
    17830 > color zone #19 near #20 distance 3.28
    17831 
    17832 > color zone #19 near #20 distance 3.18
    17833 
    17834 > color zone #19 near #20 distance 3.08
    17835 
    17836 > color zone #19 near #20 distance 2.98
    17837 
    17838 > color zone #19 near #20 distance 2.88
    17839 
    17840 > color zone #19 near #20 distance 2.78
    17841 
    17842 > color zone #19 near #20 distance 2.68
    17843 
    17844 > color zone #19 near #20 distance 2.58
    17845 
    17846 > color zone #19 near #20 distance 2.48
    17847 
    17848 > color zone #19 near #20 distance 2.38
    17849 
    17850 > color zone #19 near #20 distance 2.28
    17851 
    17852 > color zone #19 near #20 distance 2.18
    17853 
    17854 > color zone #19 near #20 distance 2.08
    17855 
    17856 > color zone #19 near #20 distance 1.98
    17857 
    17858 > color zone #19 near #20 distance 1.88
    17859 
    17860 > color zone #19 near #20 distance 1.78
    17861 
    17862 > color zone #19 near #20 distance 1.88
    17863 
    17864 > color zone #19 near #20 distance 1.98
    17865 
    17866 > color zone #19 near #20 distance 2.08
    17867 
    17868 [Repeated 1 time(s)]
    17869 
    17870 > volume splitbyzone #19
    17871 
    17872 Opened hOCT1-AZT.mrc 0 as #21.1, grid size 320,320,320, pixel 0.83, shown at
    17873 level 0.0104, step 1, values float32 
    17874 Opened hOCT1-AZT.mrc 1 as #21.2, grid size 320,320,320, pixel 0.83, shown at
    17875 level 0.0104, step 1, values float32 
    17876 Opened hOCT1-AZT.mrc 2 as #21.3, grid size 320,320,320, pixel 0.83, shown at
    17877 level 0.0104, step 1, values float32 
    17878 
    17879 > close #21.1-2
    17880 
    17881 > select add #20
    17882 
    17883 3578 atoms, 3672 bonds, 1 pseudobond, 463 residues, 2 models selected 
    17884 
    17885 > select subtract #20
    17886 
    17887 Nothing selected 
    17888 
    17889 > select add #20
    17890 
    17891 3578 atoms, 3672 bonds, 1 pseudobond, 463 residues, 2 models selected 
    17892 
    17893 > color #20 #773333ff
    17894 
    17895 > color #20 #733551ff
    17896 
    17897 > color (#!20 & sel) byhetero
    17898 
    17899 > select clear
    17900 
    17901 > color #21.3 #ff000096 models
    17902 
    17903 > color #21.3 #ffffff96 models
    17904 
    17905 > color #21.3 #ffffb296 models
    17906 
    17907 > volume #21.3 level 0.008896
    17908 
    17909 > hide #!21.3 models
    17910 
    17911 > hide #!21 models
    17912 
    17913 > hide #!20 models
    17914 
    17915 > save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
    17916 > density.cxs" includeMaps true
    17917 
    17918 QXcbConnection: XCB error: 3 (BadWindow), sequence: 59019, resource id:
    17919 35654939, major code: 40 (TranslateCoords), minor code: 0 
    17920 
    17921 > show #!3 models
    17922 
    17923 > show #!6.3 models
    17924 
    17925 > select ::name="ABC"
    17926 
    17927 42 atoms, 48 bonds, 2 residues, 1 model selected 
    17928 
    17929 > view sel
    17930 
    17931 > select clear
    17932 
    17933 > hide #!6.3 models
    17934 
    17935 > hide #!6 models
    17936 
    17937 > hide #!3 models
    17938 
    17939 > show #!2 models
    17940 
    17941 > show #!5 models
    17942 
    17943 > hide #!5 models
    17944 
    17945 > hide #!2 models
    17946 
    17947 > show #!8 models
    17948 
    17949 > show #!9.3 models
    17950 
    17951 > hide #!9.3 models
    17952 
    17953 > hide #!9 models
    17954 
    17955 > hide #!8 models
    17956 
    17957 > show #!11 models
    17958 
    17959 > show #!12.3 models
    17960 
    17961 > hide #!12.3 models
    17962 
    17963 > hide #!12 models
    17964 
    17965 > hide #!11 models
    17966 
    17967 > show #!14 models
    17968 
    17969 > show #!15 models
    17970 
    17971 > hide #!15 models
    17972 
    17973 > show #!15.3 models
    17974 
    17975 > hide #!14 models
    17976 
    17977 > hide #!15 models
    17978 
    17979 > hide #!15.3 models
    17980 
    17981 > show #!17 models
    17982 
    17983 > show #!18.3 models
    17984 
    17985 > hide #!18.3 models
    17986 
    17987 > hide #!18 models
    17988 
    17989 > hide #!17 models
    17990 
    17991 > show #!20 models
    17992 
    17993 > show #!21.3 models
    17994 
    17995 > save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
    17996 > density.cxs" includeMaps true
    17997 
    17998 > save
    17999 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1_structures_ligand_density.cxs
    18000 > includeMaps true
    18001 
    18002 [Repeated 1 time(s)]
    18003 
    18004 > close session
    18005 
    18006 > open
    18007 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AZT_20240729/0-coot-
    18008 > history.scm
    18009 
    18010 Unrecognized file suffix '.scm' 
    18011 
    18012 > open
    18013 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AZT_20240729/RealSpaceRefine_2/rOAT1-AZT_coot-4_real_space_refined_002.cif
    18014 
    18015 Summary of feedback from opening
    18016 /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AZT_20240729/RealSpaceRefine_2/rOAT1-AZT_coot-4_real_space_refined_002.cif 
    18017 --- 
    18018 warnings | Skipping chem_comp category: Missing column 'type' near line 187 
    18019 Missing entity information. Treating each chain as a separate entity. 
    18020 Bad residue range for struct_conf "3" near line 98 
    18021 Bad residue range for struct_conf "4" near line 99 
    18022 Bad residue range for struct_conf "5" near line 100 
    18023 Bad residue range for struct_conf "6" near line 101 
    18024 Bad residue range for struct_conf "7" near line 102 
    18025 15 messages similar to the above omitted 
    18026 Invalid sheet range for struct_sheet_range "2 1" near line 183 
    18027 Invalid sheet range for struct_sheet_range "3 1" near line 184 
    18028 Invalid sheet range for struct_sheet_range "4 1" near line 186 
    18029 Missing or incomplete sequence information. Inferred polymer connectivity. 
    18030 Skipping chem_comp category: Missing column 'type' near line 4361 
    18031  
    18032 Chain information for rOAT1-AZT_coot-4_real_space_refined_002.cif #1 
    18033 --- 
    18034 Chain | Description 
    18035 A | No description available 
    18036  
    18037 
    18038 > close session
    18039 
    18040 > open
    18041 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AZT_20240729/RealSpaceRefine_2/rOAT1-AZT_coot-4_real_space_refined_002.pdb
    18042 
    18043 Chain information for rOAT1-AZT_coot-4_real_space_refined_002.pdb #1 
    18044 --- 
    18045 Chain | Description 
    18046 A | No description available 
    18047  
    18048 
    18049 QXcbConnection: XCB error: 3 (BadWindow), sequence: 10568, resource id:
    18050 35655077, major code: 40 (TranslateCoords), minor code: 0 
    18051 
    18052 > open
    18053 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/inward_j156_2.7A/postprocess.mrc
    18054 
    18055 Opened postprocess.mrc as #2, grid size 320,320,320, pixel 0.83, shown at
    18056 level 0.00421, step 2, values float32 
    18057 
    18058 > rename #2 rOAT1-AZT.mrc
    18059 
    18060 > volume #2 step 1
    18061 
    18062 > volume #2 level 0.01415
    18063 
    18064 > save
    18065 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    18066 > includeMaps true
    18067 
    18068 > select add #1
    18069 
    18070 3905 atoms, 3986 bonds, 515 residues, 1 model selected 
    18071 
    18072 > ui mousemode right "rotate selected models"
    18073 
    18074 > view matrix models
    18075 > #1,-0.81264,-0.025153,-0.58222,300.85,0.24435,0.8923,-0.37961,31.685,0.52906,-0.45075,-0.71897,210.07
    18076 
    18077 > ui mousemode right "translate selected models"
    18078 
    18079 > view matrix models
    18080 > #1,-0.81264,-0.025153,-0.58222,320.11,0.24435,0.8923,-0.37961,31.387,0.52906,-0.45075,-0.71897,214.5
    18081 
    18082 > ui mousemode right "rotate selected models"
    18083 
    18084 > view matrix models
    18085 > #1,-0.62181,-0.74054,-0.25487,347.35,-0.028985,0.34697,-0.93743,205.98,0.78263,-0.57551,-0.23722,138.33
    18086 
    18087 > ui mousemode right "translate selected models"
    18088 
    18089 > view matrix models
    18090 > #1,-0.62181,-0.74054,-0.25487,344.94,-0.028985,0.34697,-0.93743,211.72,0.78263,-0.57551,-0.23722,135.34
    18091 
    18092 > view matrix models
    18093 > #1,-0.62181,-0.74054,-0.25487,347.37,-0.028985,0.34697,-0.93743,211.37,0.78263,-0.57551,-0.23722,136.41
    18094 
    18095 > ui tool show "Fit in Map"
    18096 
    18097 > fitmap #1 inMap #2
    18098 
    18099 Fit molecule rOAT1-AZT_coot-4_real_space_refined_002.pdb (#1) to map
    18100 rOAT1-AZT.mrc (#2) using 3905 atoms 
    18101 average map value = 0.01965, steps = 108 
    18102 shifted from previous position = 2.32 
    18103 rotated from previous position = 12.8 degrees 
    18104 atoms outside contour = 1436, contour level = 0.014154 
    18105  
    18106 Position of rOAT1-AZT_coot-4_real_space_refined_002.pdb (#1) relative to
    18107 rOAT1-AZT.mrc (#2) coordinates: 
    18108 Matrix rotation and translation 
    18109 -0.62427498 -0.78041245 -0.03517318 323.27181278 
    18110 -0.15760640 0.16991691 -0.97277359 257.26632447 
    18111 0.76514114 -0.60173470 -0.22907287 142.60270901 
    18112 Axis 0.34360458 -0.74113973 0.57675627 
    18113 Axis point 193.37147122 0.00000000 235.15956508 
    18114 Rotation angle (degrees) 147.32171525 
    18115 Shift along axis 2.65438788 
    18116  
    18117 
    18118 > select subtract #1
    18119 
    18120 Nothing selected 
    18121 
    18122 > select add #1
    18123 
    18124 3905 atoms, 3986 bonds, 515 residues, 1 model selected 
    18125 
    18126 > color sel white
    18127 
    18128 > select ::name="AZZ"
    18129 
    18130 19 atoms, 20 bonds, 1 residue, 1 model selected 
    18131 
    18132 > color sel red
    18133 
    18134 > ui tool show "Color Zone"
    18135 
    18136 > color zone #2 near #1 distance 4.98
    18137 
    18138 > volume #2 level 0.0105
    18139 
    18140 > color zone #2 near #1 distance 4.88
    18141 
    18142 > color zone #2 near #1 distance 4.78
    18143 
    18144 > color zone #2 near #1 distance 4.68
    18145 
    18146 > color zone #2 near #1 distance 4.58
    18147 
    18148 > color zone #2 near #1 distance 4.48
    18149 
    18150 > color zone #2 near #1 distance 4.38
    18151 
    18152 > color zone #2 near #1 distance 4.28
    18153 
    18154 > color zone #2 near #1 distance 4.18
    18155 
    18156 > color zone #2 near #1 distance 4.08
    18157 
    18158 > color zone #2 near #1 distance 3.98
    18159 
    18160 > color zone #2 near #1 distance 3.88
    18161 
    18162 > color zone #2 near #1 distance 3.78
    18163 
    18164 > color zone #2 near #1 distance 3.68
    18165 
    18166 > color zone #2 near #1 distance 3.58
    18167 
    18168 > color zone #2 near #1 distance 3.48
    18169 
    18170 > color zone #2 near #1 distance 3.38
    18171 
    18172 > color zone #2 near #1 distance 3.28
    18173 
    18174 > color zone #2 near #1 distance 3.18
    18175 
    18176 > color zone #2 near #1 distance 3.08
    18177 
    18178 > color zone #2 near #1 distance 2.98
    18179 
    18180 > color zone #2 near #1 distance 2.88
    18181 
    18182 > color zone #2 near #1 distance 2.78
    18183 
    18184 > color zone #2 near #1 distance 2.68
    18185 
    18186 > color zone #2 near #1 distance 2.58
    18187 
    18188 > color zone #2 near #1 distance 2.48
    18189 
    18190 > color zone #2 near #1 distance 2.38
    18191 
    18192 > color zone #2 near #1 distance 2.28
    18193 
    18194 > color zone #2 near #1 distance 2.18
    18195 
    18196 > color zone #2 near #1 distance 2.08
    18197 
    18198 > color zone #2 near #1 distance 1.98
    18199 
    18200 > color zone #2 near #1 distance 1.88
    18201 
    18202 > color zone #2 near #1 distance 1.78
    18203 
    18204 > volume #2 level 0.008069
    18205 
    18206 > volume splitbyzone #2
    18207 
    18208 Opened rOAT1-AZT.mrc 0 as #3.1, grid size 320,320,320, pixel 0.83, shown at
    18209 level 0.00807, step 1, values float32 
    18210 Opened rOAT1-AZT.mrc 1 as #3.2, grid size 320,320,320, pixel 0.83, shown at
    18211 level 0.00807, step 1, values float32 
    18212 Opened rOAT1-AZT.mrc 2 as #3.3, grid size 320,320,320, pixel 0.83, shown at
    18213 level 0.00807, step 1, values float32 
    18214 
    18215 > close #3.1-2
    18216 
    18217 > color #3.3 white models
    18218 
    18219 > color #3.3 #ffffb2ff models
    18220 
    18221 > select add #1
    18222 
    18223 3905 atoms, 3986 bonds, 515 residues, 1 model selected 
    18224 
    18225 > color #1 #dd22bbff
    18226 
    18227 > color #1 tan
    18228 
    18229 > color sel byhetero
    18230 
    18231 > color #3.3 #ffffb296 models
    18232 
    18233 > save
    18234 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    18235 > includeMaps true
    18236 
    18237 QXcbConnection: XCB error: 3 (BadWindow), sequence: 355, resource id:
    18238 35655128, major code: 40 (TranslateCoords), minor code: 0 
    18239 
    18240 QXcbConnection: XCB error: 3 (BadWindow), sequence: 366, resource id:
    18241 35655123, major code: 40 (TranslateCoords), minor code: 0 
    18242 
    18243 > save
    18244 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    18245 > includeMaps true
    18246 
    18247 QXcbConnection: XCB error: 3 (BadWindow), sequence: 14345, resource id:
    18248 35655133, major code: 40 (TranslateCoords), minor code: 0 
    18249 
    18250 > rename #1 rOAT1-AZT_IF.pdb
    18251 
    18252 > rename #2 rOAT1-AZT_IF.mrc
    18253 
    18254 > rename #3 "rOAT1-AZT_IF.mrc split"
    18255 
    18256 > rename #3.3 "rOAT1-AZT_IF.mrc 2"
    18257 
    18258 > save
    18259 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    18260 > includeMaps true
    18261 
    18262 QXcbConnection: XCB error: 3 (BadWindow), sequence: 23455, resource id:
    18263 35655148, major code: 40 (TranslateCoords), minor code: 0 
    18264 
    18265 > open
    18266 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/outward_j170_2.7A/run_class001.mrc
    18267 
    18268 Opened run_class001.mrc as #4, grid size 320,320,320, pixel 0.83, shown at
    18269 level 0.00134, step 2, values float32 
    18270 
    18271 > close #4
    18272 
    18273 > open
    18274 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/outward_j170_2.7A/postprocess.mrc
    18275 
    18276 Opened postprocess.mrc as #4, grid size 320,320,320, pixel 0.83, shown at
    18277 level 0.00459, step 2, values float32 
    18278 
    18279 > volume #4 step 1
    18280 
    18281 > volume #4 level 0.01366
    18282 
    18283 > rename #4 rOAT1-AZT_OF.mrc
    18284 
    18285 > open
    18286 > /home/dout2/isilon/PROJECTS/OAT1/cryoEM/rOAT1-PBD_LMNG_combined_20230419_20230217_OF/rOAT1-PBD_OF-
    18287 > coot-7_real_space_refined_008.pdb
    18288 
    18289 Chain information for rOAT1-PBD_OF-coot-7_real_space_refined_008.pdb #5 
    18290 --- 
    18291 Chain | Description 
    18292 A | No description available 
    18293  
    18294 
    18295 > select subtract #1
    18296 
    18297 Nothing selected 
    18298 
    18299 > select add #5
    18300 
    18301 3792 atoms, 3881 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    18302 
    18303 > hide #!3 models
    18304 
    18305 > hide #!3.3 models
    18306 
    18307 > hide #1 models
    18308 
    18309 > view matrix models #5,1,0,0,68.569,0,1,0,64.41,0,0,1,67.632
    18310 
    18311 > view matrix models #5,1,0,0,67.083,0,1,0,66.14,0,0,1,66.95
    18312 
    18313 > fitmap #5 inMap #4
    18314 
    18315 Fit molecule rOAT1-PBD_OF-coot-7_real_space_refined_008.pdb (#5) to map
    18316 rOAT1-AZT_OF.mrc (#4) using 3792 atoms 
    18317 average map value = 0.01938, steps = 84 
    18318 shifted from previous position = 0.803 
    18319 rotated from previous position = 4.35 degrees 
    18320 atoms outside contour = 1323, contour level = 0.013659 
    18321  
    18322 Position of rOAT1-PBD_OF-coot-7_real_space_refined_008.pdb (#5) relative to
    18323 rOAT1-AZT_OF.mrc (#4) coordinates: 
    18324 Matrix rotation and translation 
    18325 0.99822969 -0.04531644 -0.03852150 72.45731875 
    18326 0.04345449 0.99790785 -0.04787105 67.21065914 
    18327 0.04061025 0.04611237 0.99811044 61.32293455 
    18328 Axis 0.62004547 -0.52206316 0.58565662 
    18329 Axis point 0.00000000 -669.59173064 1932.22009801 
    18330 Rotation angle (degrees) 4.34647273 
    18331 Shift along axis 45.75280586 
    18332  
    18333 
    18334 > save
    18335 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/outward_j170_2.7A/rOAT1-AZT_OF.pdb
    18336 > models #5 relModel #4
    18337 
    18338 > save
    18339 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/inward_j156_2.7A/rOAT1-AZT_IF.pdb
    18340 > models #1
    18341 
    18342 > close #5
    18343 
    18344 > open
    18345 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/outward_j170_2.7A/postprocess.mrc
    18346 
    18347 Opened rOAT1-AZT_OF.mrc as #5, grid size 320,320,320, pixel 0.83, shown at
    18348 level 0.00459, step 2, values float32 
    18349 
    18350 > close #5
    18351 
    18352 > open
    18353 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/outward_j170_2.7A/rOAT1-AZT_OF-
    18354 > coot-0_real_space_refined_003.pdb
    18355 
    18356 Chain information for rOAT1-AZT_OF-coot-0_real_space_refined_003.pdb #5 
    18357 --- 
    18358 Chain | Description 
    18359 A | No description available 
    18360  
    18361 
    18362 > select add #4
    18363 
    18364 2 models selected 
    18365 
    18366 > select subtract #4
    18367 
    18368 Nothing selected 
    18369 
    18370 > select add #5
    18371 
    18372 3774 atoms, 3864 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    18373 
    18374 > select clear
    18375 
    18376 > select add #5
    18377 
    18378 3774 atoms, 3864 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    18379 
    18380 > color #5 white
    18381 
    18382 > color #4 white models
    18383 
    18384 > color #2 white models
    18385 
    18386 > select #5/A:601@O4
    18387 
    18388 1 atom, 1 residue, 1 model selected 
    18389 
    18390 > select up
    18391 
    18392 19 atoms, 20 bonds, 1 residue, 1 model selected 
    18393 
    18394 > color sel red
    18395 
    18396 > color zone #4 near #5 distance 4.98
    18397 
    18398 > color zone #4 near #5 distance 4.88
    18399 
    18400 > color zone #4 near #5 distance 4.78
    18401 
    18402 > color zone #4 near #5 distance 4.68
    18403 
    18404 > color zone #4 near #5 distance 4.58
    18405 
    18406 > color zone #4 near #5 distance 4.48
    18407 
    18408 > color zone #4 near #5 distance 4.38
    18409 
    18410 > color zone #4 near #5 distance 4.28
    18411 
    18412 > color zone #4 near #5 distance 4.18
    18413 
    18414 > color zone #4 near #5 distance 4.08
    18415 
    18416 > color zone #4 near #5 distance 3.98
    18417 
    18418 > color zone #4 near #5 distance 3.88
    18419 
    18420 > color zone #4 near #5 distance 3.78
    18421 
    18422 > color zone #4 near #5 distance 3.68
    18423 
    18424 > color zone #4 near #5 distance 3.58
    18425 
    18426 > color zone #4 near #5 distance 3.48
    18427 
    18428 > color zone #4 near #5 distance 3.38
    18429 
    18430 > color zone #4 near #5 distance 3.28
    18431 
    18432 > color zone #4 near #5 distance 3.18
    18433 
    18434 > color zone #4 near #5 distance 3.08
    18435 
    18436 > color zone #4 near #5 distance 2.98
    18437 
    18438 > color zone #4 near #5 distance 2.88
    18439 
    18440 > color zone #4 near #5 distance 2.78
    18441 
    18442 > color zone #4 near #5 distance 2.68
    18443 
    18444 > color zone #4 near #5 distance 2.58
    18445 
    18446 > color zone #4 near #5 distance 2.48
    18447 
    18448 > color zone #4 near #5 distance 2.38
    18449 
    18450 > color zone #4 near #5 distance 2.28
    18451 
    18452 > color zone #4 near #5 distance 2.18
    18453 
    18454 > color zone #4 near #5 distance 2.08
    18455 
    18456 > color zone #4 near #5 distance 1.98
    18457 
    18458 > color zone #4 near #5 distance 1.88
    18459 
    18460 > color zone #4 near #5 distance 1.78
    18461 
    18462 > color zone #4 near #5 distance 1.68
    18463 
    18464 > color zone #4 near #5 distance 1.58
    18465 
    18466 > color zone #4 near #5 distance 1.48
    18467 
    18468 > color zone #4 near #5 distance 1.58
    18469 
    18470 > color zone #4 near #5 distance 1.68
    18471 
    18472 > color zone #4 near #5 distance 1.78
    18473 
    18474 > color zone #4 near #5 distance 1.88
    18475 
    18476 > volume splitbyzone #4
    18477 
    18478 Opened rOAT1-AZT_OF.mrc 0 as #6.1, grid size 320,320,320, pixel 0.83, shown at
    18479 level 0.0137, step 1, values float32 
    18480 Opened rOAT1-AZT_OF.mrc 1 as #6.2, grid size 320,320,320, pixel 0.83, shown at
    18481 level 0.0137, step 1, values float32 
    18482 Opened rOAT1-AZT_OF.mrc 2 as #6.3, grid size 320,320,320, pixel 0.83, shown at
    18483 level 0.0137, step 1, values float32 
    18484 
    18485 > close #6.1-2
    18486 
    18487 > volume #6.3 level 0.0116
    18488 
    18489 > select add #5
    18490 
    18491 3774 atoms, 3864 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    18492 
    18493 > select subtract #5
    18494 
    18495 Nothing selected 
    18496 
    18497 > color #6.3 yellow models
    18498 
    18499 > color #6.3 white models
    18500 
    18501 > color #6.3 #ffffb2ff models
    18502 
    18503 > select add #5
    18504 
    18505 3774 atoms, 3864 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    18506 
    18507 > color #5 #ffaa88ff
    18508 
    18509 > color #5 salmon
    18510 
    18511 > color (#!5 & sel) byhetero
    18512 
    18513 > color #6.3 #ffffb296 models
    18514 
    18515 > select clear
    18516 
    18517 > save
    18518 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    18519 > includeMaps true
    18520 
    18521 > show #!2 models
    18522 
    18523 > hide #!5 models
    18524 
    18525 > hide #!6 models
    18526 
    18527 > hide #!6.3 models
    18528 
    18529 > volume #2 level 0.01456
    18530 
    18531 > color #2 #a5a5a5ff models
    18532 
    18533 > open
    18534 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20230419_rOAT1-PBD/inward_j261_2.6A/postprocess.mrc
    18535 
    18536 Opened postprocess.mrc as #7, grid size 320,320,320, pixel 0.83, shown at
    18537 level 0.00408, step 2, values float32 
    18538 
    18539 > rename #7 rOAT1-PBD_IF.mrc
    18540 
    18541 > volume #2 level 0.01983
    18542 
    18543 > volume #2 level 0.0151
    18544 
    18545 > hide #!7 models
    18546 
    18547 > volume #7 level 0.01185
    18548 
    18549 > volume #7 step 1
    18550 
    18551 > volume #7 level 0.01094
    18552 
    18553 > hide #!2 models
    18554 
    18555 > open
    18556 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20230419_rOAT1-PBD/inward_j261_2.6A/rOAT1-PBD-
    18557 > coot-6.pdb
    18558 
    18559 Chain information for rOAT1-PBD-coot-6.pdb #8 
    18560 --- 
    18561 Chain | Description 
    18562 A | No description available 
    18563  
    18564 
    18565 > select add #8
    18566 
    18567 3912 atoms, 3985 bonds, 522 residues, 1 model selected 
    18568 
    18569 > ui mousemode right "translate selected models"
    18570 
    18571 > view matrix models #8,1,0,0,55.004,0,1,0,73.737,0,0,1,58.702
    18572 
    18573 > view matrix models #8,1,0,0,66.378,0,1,0,64.897,0,0,1,63.973
    18574 
    18575 > fitmap #8 inMap #7
    18576 
    18577 Fit molecule rOAT1-PBD-coot-6.pdb (#8) to map rOAT1-PBD_IF.mrc (#7) using 3912
    18578 atoms 
    18579 average map value = 0.02737, steps = 56 
    18580 shifted from previous position = 2.6 
    18581 rotated from previous position = 0.396 degrees 
    18582 atoms outside contour = 571, contour level = 0.010939 
    18583  
    18584 Position of rOAT1-PBD-coot-6.pdb (#8) relative to rOAT1-PBD_IF.mrc (#7)
    18585 coordinates: 
    18586 Matrix rotation and translation 
    18587 0.99998387 0.00531886 -0.00199304 66.36205660 
    18588 -0.00532668 0.99997806 -0.00393867 67.06308709 
    18589 0.00197205 0.00394922 0.99999026 65.65327743 
    18590 Axis 0.57034742 -0.28670293 -0.76974363 
    18591 Axis point 10937.66555565 -15865.74627304 0.00000000 
    18592 Rotation angle (degrees) 0.39620277 
    18593 Shift along axis -31.91394767 
    18594  
    18595 
    18596 > rename #8 rOAT1-PBD_IF.pdb
    18597 
    18598 > save
    18599 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    18600 > includeMaps true
    18601 
    18602 QXcbConnection: XCB error: 3 (BadWindow), sequence: 51376, resource id:
    18603 35655645, major code: 40 (TranslateCoords), minor code: 0 
    18604 
    18605 QXcbConnection: XCB error: 3 (BadWindow), sequence: 51388, resource id:
    18606 35655640, major code: 40 (TranslateCoords), minor code: 0 
    18607 
    18608 > color #8 white
    18609 
    18610 > hide #!7 models
    18611 
    18612 > select up
    18613 
    18614 2 atoms, 1 bond, 1 residue, 1 model selected 
    18615 
    18616 > select up
    18617 
    18618 19 atoms, 19 bonds, 1 residue, 1 model selected 
    18619 
    18620 > color sel red
    18621 
    18622 > show #!7 models
    18623 
    18624 > color zone #7 near #8 distance 4.98
    18625 
    18626 > color zone #7 near #8 distance 4.88
    18627 
    18628 > color zone #7 near #8 distance 4.78
    18629 
    18630 > color zone #7 near #8 distance 4.68
    18631 
    18632 > color zone #7 near #8 distance 4.58
    18633 
    18634 > color zone #7 near #8 distance 4.48
    18635 
    18636 > color zone #7 near #8 distance 4.38
    18637 
    18638 > color zone #7 near #8 distance 4.28
    18639 
    18640 > color zone #7 near #8 distance 4.18
    18641 
    18642 > color zone #7 near #8 distance 4.08
    18643 
    18644 > color zone #7 near #8 distance 3.98
    18645 
    18646 > color zone #7 near #8 distance 3.88
    18647 
    18648 > color zone #7 near #8 distance 3.78
    18649 
    18650 > color zone #7 near #8 distance 3.68
    18651 
    18652 > volume #7 level 0.02515
    18653 
    18654 > volume #7 level 0.01677
    18655 
    18656 > volume #7 level 0.0124
    18657 
    18658 > volume #7 level 0.01476
    18659 
    18660 > color zone #7 near #8 distance 3.58
    18661 
    18662 > color zone #7 near #8 distance 3.48
    18663 
    18664 > color zone #7 near #8 distance 3.38
    18665 
    18666 > color zone #7 near #8 distance 3.28
    18667 
    18668 > color zone #7 near #8 distance 3.18
    18669 
    18670 > color zone #7 near #8 distance 3.08
    18671 
    18672 > color zone #7 near #8 distance 2.98
    18673 
    18674 > color zone #7 near #8 distance 2.88
    18675 
    18676 > color zone #7 near #8 distance 2.78
    18677 
    18678 > color zone #7 near #8 distance 2.68
    18679 
    18680 > color zone #7 near #8 distance 2.58
    18681 
    18682 > color zone #7 near #8 distance 2.48
    18683 
    18684 > color zone #7 near #8 distance 2.38
    18685 
    18686 > color zone #7 near #8 distance 2.28
    18687 
    18688 > volume #7 level 0.01112
    18689 
    18690 > color zone #7 near #8 distance 2.18
    18691 
    18692 > color zone #7 near #8 distance 2.08
    18693 
    18694 > color zone #7 near #8 distance 1.98
    18695 
    18696 > color zone #7 near #8 distance 1.88
    18697 
    18698 > color zone #7 near #8 distance 1.98
    18699 
    18700 > color zone #7 near #8 distance 2.08
    18701 
    18702 > volume splitbyzone #7
    18703 
    18704 Opened rOAT1-PBD_IF.mrc 0 as #9.1, grid size 320,320,320, pixel 0.83, shown at
    18705 level 0.0111, step 1, values float32 
    18706 Opened rOAT1-PBD_IF.mrc 1 as #9.2, grid size 320,320,320, pixel 0.83, shown at
    18707 level 0.0111, step 1, values float32 
    18708 Opened rOAT1-PBD_IF.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at
    18709 level 0.0111, step 1, values float32 
    18710 
    18711 > close #9.1-2
    18712 
    18713 > color #9.3 #ff000096 models
    18714 
    18715 > color #9.3 #ffff0096 models
    18716 
    18717 > color #9.3 #ffffff96 models
    18718 
    18719 > color #9.3 #ffffb296 models
    18720 
    18721 > select add #8
    18722 
    18723 3912 atoms, 3985 bonds, 522 residues, 1 model selected 
    18724 
    18725 > color #8 #ffffddff
    18726 
    18727 > color #8 gold
    18728 
    18729 > select clear
    18730 
    18731 > select add #8
    18732 
    18733 3912 atoms, 3985 bonds, 522 residues, 1 model selected 
    18734 
    18735 > color sel byhetero
    18736 
    18737 > select clear
    18738 
    18739 > save
    18740 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    18741 > includeMaps true
    18742 
    18743 QXcbConnection: XCB error: 3 (BadWindow), sequence: 19133, resource id:
    18744 35655670, major code: 40 (TranslateCoords), minor code: 0 
    18745 
    18746 > open
    18747 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20230419_rOAT1-PBD/outward_j272_3.0A/postprocess.mrc
    18748 
    18749 Opened postprocess.mrc as #10, grid size 320,320,320, pixel 0.83, shown at
    18750 level 0.00409, step 2, values float32 
    18751 
    18752 QXcbConnection: XCB error: 3 (BadWindow), sequence: 23804, resource id:
    18753 35655680, major code: 40 (TranslateCoords), minor code: 0 
    18754 
    18755 > open
    18756 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20230419_rOAT1-PBD/outward_j272_3.0A/rOAT1-PBD_OF-
    18757 > coot-0.pdb
    18758 
    18759 Chain information for rOAT1-PBD_OF-coot-0.pdb #11 
    18760 --- 
    18761 Chain | Description 
    18762 A | No description available 
    18763  
    18764 
    18765 > hide #!9 models
    18766 
    18767 > hide #8 models
    18768 
    18769 > rename #10 rOAT1-PBD_OF
    18770 
    18771 > rename #10 rOAT1-PBD_OF.mrc
    18772 
    18773 > show #!2 models
    18774 
    18775 > volume #10 level 0.004712
    18776 
    18777 > volume #10 step 1
    18778 
    18779 > volume #10 level 0.01128
    18780 
    18781 > hide #!2 models
    18782 
    18783 > select add #11
    18784 
    18785 3872 atoms, 3966 bonds, 500 residues, 1 model selected 
    18786 
    18787 > view matrix models #11,1,0,0,65.11,0,1,0,69.986,0,0,1,61.035
    18788 
    18789 > view matrix models #11,1,0,0,68.61,0,1,0,68.058,0,0,1,65.073
    18790 
    18791 > view matrix models #11,1,0,0,67.516,0,1,0,68.105,0,0,1,67.386
    18792 
    18793 > fitmap #11 inMap #10
    18794 
    18795 Fit molecule rOAT1-PBD_OF-coot-0.pdb (#11) to map rOAT1-PBD_OF.mrc (#10) using
    18796 3872 atoms 
    18797 average map value = 0.01531, steps = 56 
    18798 shifted from previous position = 2.42 
    18799 rotated from previous position = 0.764 degrees 
    18800 atoms outside contour = 1505, contour level = 0.011277 
    18801  
    18802 Position of rOAT1-PBD_OF-coot-0.pdb (#11) relative to rOAT1-PBD_OF.mrc (#10)
    18803 coordinates: 
    18804 Matrix rotation and translation 
    18805 0.99995211 0.00939248 0.00274947 65.65298070 
    18806 -0.00936721 0.99991506 -0.00906240 67.47749964 
    18807 -0.00283436 0.00903621 0.99995516 65.83404461 
    18808 Axis 0.67891074 0.20945939 -0.70370943 
    18809 Axis point 6981.74049553 -6059.62250131 0.00000000 
    18810 Rotation angle (degrees) 0.76372650 
    18811 Shift along axis 12.37827175 
    18812  
    18813 
    18814 > show sel atoms
    18815 
    18816 > hide #!10 models
    18817 
    18818 > show #!10 models
    18819 
    18820 > open
    18821 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-PBD_LMNG_combined_20230419_20230217_OF/rOAT1-PBD_OF-
    18822 > coot-7_real_space_refined_008.pdb
    18823 
    18824 Chain information for rOAT1-PBD_OF-coot-7_real_space_refined_008.pdb #12 
    18825 --- 
    18826 Chain | Description 
    18827 A | No description available 
    18828  
    18829 
    18830 > ui tool show Matchmaker
    18831 
    18832 > matchmaker #!12 to #11
    18833 
    18834 Parameters 
    18835 --- 
    18836 Chain pairing | bb 
    18837 Alignment algorithm | Needleman-Wunsch 
    18838 Similarity matrix | BLOSUM-62 
    18839 SS fraction | 0.3 
    18840 Gap open (HH/SS/other) | 18/18/6 
    18841 Gap extend | 1 
    18842 SS matrix |  |  | H | S | O 
    18843 ---|---|---|--- 
    18844 H | 6 | -9 | -6 
    18845 S |  | 6 | -6 
    18846 O |  |  | 4 
    18847 Iteration cutoff | 2 
    18848  
    18849 Matchmaker rOAT1-PBD_OF-coot-0.pdb, chain A (#11) with rOAT1-PBD_OF-
    18850 coot-7_real_space_refined_008.pdb, chain A (#12), sequence alignment score =
    18851 2423.1 
    18852 RMSD between 470 pruned atom pairs is 0.696 angstroms; (across all 485 pairs:
    18853 1.080) 
    18854  
    18855 
    18856 > hide #11 models
    18857 
    18858 > select subtract #11
    18859 
    18860 Nothing selected 
    18861 
    18862 > show #11 models
    18863 
    18864 > hide #!12 models
    18865 
    18866 > hide #!10 models
    18867 
    18868 > show #!12 models
    18869 
    18870 > close #11
    18871 
    18872 > color #12 #bb4455ff
    18873 
    18874 > color #12 #b4503bff
    18875 
    18876 QXcbConnection: XCB error: 3 (BadWindow), sequence: 15705, resource id:
    18877 35655708, major code: 40 (TranslateCoords), minor code: 0 
    18878 
    18879 > show #!10 models
    18880 
    18881 > save
    18882 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    18883 > includeMaps true
    18884 
    18885 QXcbConnection: XCB error: 3 (BadWindow), sequence: 19760, resource id:
    18886 35655718, major code: 40 (TranslateCoords), minor code: 0 
    18887 
    18888 QXcbConnection: XCB error: 3 (BadWindow), sequence: 19772, resource id:
    18889 35655713, major code: 40 (TranslateCoords), minor code: 0 
    18890 
    18891 > color #10 #ffb2ff96 models
    18892 
    18893 > volume #10 level 0.009218
    18894 
    18895 > volume #10 level 0.008059
    18896 
    18897 > color #10 #ffb2ffff models
    18898 
    18899 > select add #12
    18900 
    18901 3792 atoms, 3881 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    18902 
    18903 > hide #!10 models
    18904 
    18905 > color #12 white
    18906 
    18907 > select clear
    18908 
    18909 > select #12/B:601@C11
    18910 
    18911 1 atom, 1 residue, 1 model selected 
    18912 
    18913 > select up
    18914 
    18915 37 atoms, 37 bonds, 1 residue, 1 model selected 
    18916 
    18917 > color sel red
    18918 
    18919 > color #10 white models
    18920 
    18921 > select add #10
    18922 
    18923 37 atoms, 37 bonds, 1 residue, 3 models selected 
    18924 
    18925 > select subtract #10
    18926 
    18927 37 atoms, 37 bonds, 1 residue, 1 model selected 
    18928 
    18929 > show #!10 models
    18930 
    18931 > color zone #10 near #12 distance 2
    18932 
    18933 > color zone #10 near #12 distance 1.9
    18934 
    18935 > color zone #10 near #12 distance 1.8
    18936 
    18937 > color zone #10 near #12 distance 1.7
    18938 
    18939 > color zone #10 near #12 distance 1.8
    18940 
    18941 > color zone #10 near #12 distance 1.9
    18942 
    18943 > color zone #10 near #12 distance 2
    18944 
    18945 [Repeated 1 time(s)]
    18946 
    18947 > volume splitbyzone #10
    18948 
    18949 Opened rOAT1-PBD_OF.mrc 0 as #11.1, grid size 320,320,320, pixel 0.83, shown
    18950 at level 0.00806, step 1, values float32 
    18951 Opened rOAT1-PBD_OF.mrc 1 as #11.2, grid size 320,320,320, pixel 0.83, shown
    18952 at level 0.00806, step 1, values float32 
    18953 Opened rOAT1-PBD_OF.mrc 2 as #11.3, grid size 320,320,320, pixel 0.83, shown
    18954 at level 0.00806, step 1, values float32 
    18955 
    18956 > volume splitbyzone #10
    18957 
    18958 Opened rOAT1-PBD_OF.mrc 0 as #13.1, grid size 320,320,320, pixel 0.83, shown
    18959 at level 0.00806, step 1, values float32 
    18960 Opened rOAT1-PBD_OF.mrc 1 as #13.2, grid size 320,320,320, pixel 0.83, shown
    18961 at level 0.00806, step 1, values float32 
    18962 Opened rOAT1-PBD_OF.mrc 2 as #13.3, grid size 320,320,320, pixel 0.83, shown
    18963 at level 0.00806, step 1, values float32 
    18964 
    18965 > close #11.1-2
    18966 
    18967 > hide #!12 models
    18968 
    18969 > hide #!11.3 models
    18970 
    18971 > hide #!11 models
    18972 
    18973 > select add #12
    18974 
    18975 3792 atoms, 3881 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    18976 
    18977 > select subtract #12
    18978 
    18979 Nothing selected 
    18980 
    18981 > close #13.1-2
    18982 
    18983 > show #!12 models
    18984 
    18985 > color #11.3 white models
    18986 
    18987 > color #11.3 #ffffb2ff models
    18988 
    18989 > color #13.3 white models
    18990 
    18991 > color #13.3 #ffffb2ff models
    18992 
    18993 > select add #12
    18994 
    18995 3792 atoms, 3881 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    18996 
    18997 > color #12 #bb4455ff
    18998 
    18999 > color #12 #b4503bff
    19000 
    19001 > color (#!12 & sel) byhetero
    19002 
    19003 > select #12/A:440
    19004 
    19005 6 atoms, 5 bonds, 1 residue, 1 model selected 
    19006 
    19007 > select add #12
    19008 
    19009 3792 atoms, 3881 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    19010 
    19011 > select subtract #12
    19012 
    19013 Nothing selected 
    19014 
    19015 > save
    19016 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    19017 > includeMaps true
    19018 
    19019 > hide #!13 models
    19020 
    19021 > hide #!13.3 models
    19022 
    19023 > hide #!12 models
    19024 
    19025 > open
    19026 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240831_rOAT1-TFV/inward_j152_2.7A/postprocess.mrc
    19027 
    19028 Opened postprocess.mrc as #14, grid size 320,320,320, pixel 0.83, shown at
    19029 level 0.00408, step 2, values float32 
    19030 
    19031 QXcbConnection: XCB error: 3 (BadWindow), sequence: 27239, resource id:
    19032 35655778, major code: 40 (TranslateCoords), minor code: 0 
    19033 
    19034 > show #!2 models
    19035 
    19036 > hide #!2 models
    19037 
    19038 > rename #14 rOAT1-TFV_IF.mrc
    19039 
    19040 > show #1 models
    19041 
    19042 > hide #!14 models
    19043 
    19044 > save
    19045 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/IF/rOAT1-TFV_IF.pdb
    19046 > models #1 relModel #14
    19047 
    19048 > open
    19049 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/RealSpaceRefine_5/rOAT1-TFV_IF-
    19050 > coot-2_real_space_refined_005.pdb
    19051 
    19052 Chain information for rOAT1-TFV_IF-coot-2_real_space_refined_005.pdb #15 
    19053 --- 
    19054 Chain | Description 
    19055 A | No description available 
    19056  
    19057 
    19058 > hide #1 models
    19059 
    19060 > show #!14 models
    19061 
    19062 > color #15 white
    19063 
    19064 > color #14 white models
    19065 
    19066 > select ::name="TFV"
    19067 
    19068 31 atoms, 32 bonds, 1 residue, 1 model selected 
    19069 
    19070 > color sel red
    19071 
    19072 > color zone #14 near #15 distance 4.68
    19073 
    19074 > color zone #14 near #15 distance 4.58
    19075 
    19076 > color zone #14 near #15 distance 4.48
    19077 
    19078 > color zone #14 near #15 distance 4.38
    19079 
    19080 > color zone #14 near #15 distance 4.28
    19081 
    19082 > color zone #14 near #15 distance 4.18
    19083 
    19084 > color zone #14 near #15 distance 4.08
    19085 
    19086 > color zone #14 near #15 distance 3.98
    19087 
    19088 > color zone #14 near #15 distance 3.88
    19089 
    19090 > color zone #14 near #15 distance 3.78
    19091 
    19092 > color zone #14 near #15 distance 3.68
    19093 
    19094 > color zone #14 near #15 distance 3.58
    19095 
    19096 > color zone #14 near #15 distance 3.48
    19097 
    19098 > color zone #14 near #15 distance 3.38
    19099 
    19100 > color zone #14 near #15 distance 3.28
    19101 
    19102 > color zone #14 near #15 distance 3.18
    19103 
    19104 > color zone #14 near #15 distance 3.08
    19105 
    19106 > color zone #14 near #15 distance 2.98
    19107 
    19108 > color zone #14 near #15 distance 2.88
    19109 
    19110 > color zone #14 near #15 distance 2.78
    19111 
    19112 > color zone #14 near #15 distance 2.68
    19113 
    19114 > volume #14 level 0.007613
    19115 
    19116 > color zone #14 near #15 distance 2.78
    19117 
    19118 > color zone #14 near #15 distance 2.88
    19119 
    19120 > color zone #14 near #15 distance 2.98
    19121 
    19122 > color zone #14 near #15 distance 2.88
    19123 
    19124 > color zone #14 near #15 distance 2.78
    19125 
    19126 > color zone #14 near #15 distance 2.68
    19127 
    19128 > color zone #14 near #15 distance 2.58
    19129 
    19130 > color zone #14 near #15 distance 2.48
    19131 
    19132 > color zone #14 near #15 distance 2.38
    19133 
    19134 > volume #14 level 0.005915
    19135 
    19136 > volume #14 level 0.005632
    19137 
    19138 > volume splitbyzone #14
    19139 
    19140 Opened rOAT1-TFV_IF.mrc 0 as #16.1, grid size 320,320,320, pixel 0.83, shown
    19141 at level 0.00563, step 1, values float32 
    19142 Opened rOAT1-TFV_IF.mrc 1 as #16.2, grid size 320,320,320, pixel 0.83, shown
    19143 at level 0.00563, step 1, values float32 
    19144 Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
    19145 at level 0.00563, step 1, values float32 
    19146 
    19147 > close #16.1-2
    19148 
    19149 > color zone #14 near #15 distance 2.09
    19150 
    19151 > close #16#16.3
    19152 
    19153 > show #!14 models
    19154 
    19155 > color zone #14 near #15 distance 1.99
    19156 
    19157 > color zone #14 near #15 distance 2.09
    19158 
    19159 > color zone #14 near #15 distance 2.19
    19160 
    19161 > color zone #14 near #15 distance 2.29
    19162 
    19163 > color zone #14 near #15 distance 2.39
    19164 
    19165 > color zone #14 near #15 distance 2.29
    19166 
    19167 > volume splitbyzone #14
    19168 
    19169 Opened rOAT1-TFV_IF.mrc 0 as #16.1, grid size 320,320,320, pixel 0.83, shown
    19170 at level 0.00563, step 1, values float32 
    19171 Opened rOAT1-TFV_IF.mrc 1 as #16.2, grid size 320,320,320, pixel 0.83, shown
    19172 at level 0.00563, step 1, values float32 
    19173 Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
    19174 at level 0.00563, step 1, values float32 
    19175 
    19176 > close #16.1-2
    19177 
    19178 > select add #15
    19179 
    19180 3917 atoms, 3998 bonds, 515 residues, 1 model selected 
    19181 
    19182 > color #16.3 #ff5500ff models
    19183 
    19184 > color #16.3 #aa0000ff models
    19185 
    19186 > color #16.3 #ff5500ff models
    19187 
    19188 > color #16.3 #ff557fff models
    19189 
    19190 > color #15 #ff557fff
    19191 
    19192 > color #16.3 white models
    19193 
    19194 > color #16.3 #ffffb2ff models
    19195 
    19196 > color #16.3 #ffffb296 models
    19197 
    19198 > open
    19199 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/IF/rOAT1-TFV_IF-
    19200 > coot-3.pdb
    19201 
    19202 Chain information for rOAT1-TFV_IF-coot-3.pdb #17 
    19203 --- 
    19204 Chain | Description 
    19205 A | No description available 
    19206  
    19207 
    19208 > close #17#16#16.3
    19209 
    19210 > close #15
    19211 
    19212 > open
    19213 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/IF/rOAT1-TFV_IF-
    19214 > coot-3.pdb
    19215 
    19216 Chain information for rOAT1-TFV_IF-coot-3.pdb #15 
    19217 --- 
    19218 Chain | Description 
    19219 A | No description available 
    19220  
    19221 
    19222 QXcbConnection: XCB error: 3 (BadWindow), sequence: 28850, resource id:
    19223 35656402, major code: 40 (TranslateCoords), minor code: 0 
    19224 
    19225 > show #!14 models
    19226 
    19227 > select add #15
    19228 
    19229 3917 atoms, 3998 bonds, 515 residues, 1 model selected 
    19230 
    19231 > select subtract #15
    19232 
    19233 Nothing selected 
    19234 
    19235 > select add #15
    19236 
    19237 3917 atoms, 3998 bonds, 515 residues, 1 model selected 
    19238 
    19239 > color #15 white
    19240 
    19241 > color zone #14 near #15 distance 2.29
    19242 
    19243 > select ::name="TFV"
    19244 
    19245 31 atoms, 32 bonds, 1 residue, 1 model selected 
    19246 
    19247 > color sel red
    19248 
    19249 > color zone #14 near #15 distance 2.29
    19250 
    19251 > color zone #14 near #15 distance 2.19
    19252 
    19253 > color zone #14 near #15 distance 2.09
    19254 
    19255 > color zone #14 near #15 distance 1.99
    19256 
    19257 > color zone #14 near #15 distance 1.89
    19258 
    19259 > color zone #14 near #15 distance 1.79
    19260 
    19261 > color zone #14 near #15 distance 1.69
    19262 
    19263 > color zone #14 near #15 distance 1.59
    19264 
    19265 > color zone #14 near #15 distance 1.49
    19266 
    19267 > color zone #14 near #15 distance 1.39
    19268 
    19269 > color zone #14 near #15 distance 1.29
    19270 
    19271 > color zone #14 near #15 distance 1.19
    19272 
    19273 > color zone #14 near #15 distance 1.09
    19274 
    19275 > color zone #14 near #15 distance 1.19
    19276 
    19277 > color zone #14 near #15 distance 1.29
    19278 
    19279 > color zone #14 near #15 distance 1.39
    19280 
    19281 > color zone #14 near #15 distance 1.49
    19282 
    19283 > color zone #14 near #15 distance 1.59
    19284 
    19285 > color zone #14 near #15 distance 1.69
    19286 
    19287 > color zone #14 near #15 distance 1.79
    19288 
    19289 > color zone #14 near #15 distance 1.89
    19290 
    19291 > color zone #14 near #15 distance 1.99
    19292 
    19293 > color zone #14 near #15 distance 2.09
    19294 
    19295 [Repeated 1 time(s)]
    19296 
    19297 > volume splitbyzone #14
    19298 
    19299 Opened rOAT1-TFV_IF.mrc 0 as #16.1, grid size 320,320,320, pixel 0.83, shown
    19300 at level 0.00563, step 1, values float32 
    19301 Opened rOAT1-TFV_IF.mrc 1 as #16.2, grid size 320,320,320, pixel 0.83, shown
    19302 at level 0.00563, step 1, values float32 
    19303 Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
    19304 at level 0.00563, step 1, values float32 
    19305 
    19306 > close #16.1-2
    19307 
    19308 > color #16.3 white models
    19309 
    19310 > color #16.3 #ffffb2ff models
    19311 
    19312 > color #16.3 #ffffb296 models
    19313 
    19314 > color #15 #ff5500ff
    19315 
    19316 > color #15 #ff557fff
    19317 
    19318 > select add #15
    19319 
    19320 3917 atoms, 3998 bonds, 515 residues, 1 model selected 
    19321 
    19322 > color sel byhetero
    19323 
    19324 > select clear
    19325 
    19326 > save
    19327 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    19328 > includeMaps true
    19329 
    19330 > open
    19331 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240831_rOAT1-TFV/outward_j170_2.7A/postprocess.mrc
    19332 
    19333 Opened postprocess.mrc as #17, grid size 320,320,320, pixel 0.83, shown at
    19334 level 0.00401, step 2, values float32 
    19335 
    19336 > rename #17 rOAT1-TVF_OF.mrc
    19337 
    19338 > hide #15 models
    19339 
    19340 > hide #!16 models
    19341 
    19342 > show #8 models
    19343 
    19344 > hide #8 models
    19345 
    19346 > show #!11.3 models
    19347 
    19348 > hide #!11 models
    19349 
    19350 > hide #!11.3 models
    19351 
    19352 > show #!12 models
    19353 
    19354 > volume #17 step 1
    19355 
    19356 > volume #17 level 0.01305
    19357 
    19358 > save
    19359 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240831_rOAT1-TFV/outward_j170_2.7A/rOAT1-TFV_OF.pdb
    19360 > models #12 relModel #17
    19361 
    19362 > hide #!16.3 models
    19363 
    19364 > hide #!12 models
    19365 
    19366 > open
    19367 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240831_rOAT1-TFV/outward_j170_2.7A/rOAT1-TFV_OF.pdb
    19368 
    19369 Chain information for rOAT1-TFV_OF.pdb #18 
    19370 --- 
    19371 Chain | Description 
    19372 A | No description available 
    19373  
    19374 
    19375 > save
    19376 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    19377 > includeMaps true
    19378 
    19379 > close #18
    19380 
    19381 > open
    19382 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/RealSpaceRefine_7/rOAT1-TFV_OF-
    19383 > coot-1_real_space_refined_007.pdb
    19384 
    19385 Chain information for rOAT1-TFV_OF-coot-1_real_space_refined_007.pdb #18 
    19386 --- 
    19387 Chain | Description 
    19388 A | No description available 
    19389  
    19390 
    19391 > select add #18
    19392 
    19393 3786 atoms, 3876 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    19394 
    19395 > color #18 white
    19396 
    19397 > color #17 white models
    19398 
    19399 > select #18/A:601@H131
    19400 
    19401 1 atom, 1 residue, 1 model selected 
    19402 
    19403 > select up
    19404 
    19405 31 atoms, 32 bonds, 1 residue, 1 model selected 
    19406 
    19407 > color sel red
    19408 
    19409 > volume #17 level 0.011
    19410 
    19411 > color zone #17 near #18 distance 4.98
    19412 
    19413 > color zone #17 near #18 distance 4.88
    19414 
    19415 > color zone #17 near #18 distance 4.78
    19416 
    19417 > color zone #17 near #18 distance 4.68
    19418 
    19419 > color zone #17 near #18 distance 4.58
    19420 
    19421 > color zone #17 near #18 distance 4.48
    19422 
    19423 > color zone #17 near #18 distance 4.38
    19424 
    19425 > color zone #17 near #18 distance 4.28
    19426 
    19427 > color zone #17 near #18 distance 4.18
    19428 
    19429 > color zone #17 near #18 distance 4.08
    19430 
    19431 > color zone #17 near #18 distance 3.98
    19432 
    19433 > color zone #17 near #18 distance 3.88
    19434 
    19435 > color zone #17 near #18 distance 3.78
    19436 
    19437 > color zone #17 near #18 distance 3.68
    19438 
    19439 > color zone #17 near #18 distance 3.58
    19440 
    19441 > color zone #17 near #18 distance 3.48
    19442 
    19443 > color zone #17 near #18 distance 3.38
    19444 
    19445 > color zone #17 near #18 distance 3.28
    19446 
    19447 > color zone #17 near #18 distance 3.18
    19448 
    19449 > color zone #17 near #18 distance 3.08
    19450 
    19451 > color zone #17 near #18 distance 2.98
    19452 
    19453 > volume splitbyzone #17
    19454 
    19455 Opened rOAT1-TVF_OF.mrc 0 as #19.1, grid size 320,320,320, pixel 0.83, shown
    19456 at level 0.011, step 1, values float32 
    19457 Opened rOAT1-TVF_OF.mrc 1 as #19.2, grid size 320,320,320, pixel 0.83, shown
    19458 at level 0.011, step 1, values float32 
    19459 Opened rOAT1-TVF_OF.mrc 2 as #19.3, grid size 320,320,320, pixel 0.83, shown
    19460 at level 0.011, step 1, values float32 
    19461 
    19462 > close #19.1-2
    19463 
    19464 > color #19.3 white models
    19465 
    19466 > color #19.3 #ffffb2ff models
    19467 
    19468 > select add #18
    19469 
    19470 3786 atoms, 3876 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    19471 
    19472 > color #18 #337744ff
    19473 
    19474 > color #18 #374c02ff
    19475 
    19476 > color (#!18 & sel) byhetero
    19477 
    19478 > select clear
    19479 
    19480 > color #19.3 #ffffb296 models
    19481 
    19482 > save
    19483 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    19484 > includeMaps true
    19485 
    19486 > open
    19487 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20250129_rOAT1-AAI/inward_j112_2.6A/postprocess.mrc
    19488 
    19489 Opened postprocess.mrc as #20, grid size 320,320,320, pixel 0.83, shown at
    19490 level 0.00494, step 2, values float32 
    19491 
    19492 > volume #20 step 1
    19493 
    19494 > hide #!19 models
    19495 
    19496 > hide #!18 models
    19497 
    19498 > rename #20 rOAT1-AAI_IF.mrc
    19499 
    19500 > volume #20 level 0.0194
    19501 
    19502 QXcbConnection: XCB error: 3 (BadWindow), sequence: 35473, resource id:
    19503 35656688, major code: 40 (TranslateCoords), minor code: 0 
    19504 
    19505 > show #!2 models
    19506 
    19507 > hide #!2 models
    19508 
    19509 > show #1 models
    19510 
    19511 > save
    19512 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/IF/rOAT1-AAI_IF.pdb
    19513 > models #1 relModel #20
    19514 
    19515 > hide #1 models
    19516 
    19517 > open
    19518 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/IF/rOAT1-AAI_IF.pdb
    19519 
    19520 Chain information for rOAT1-AAI_IF.pdb #21 
    19521 --- 
    19522 Chain | Description 
    19523 A | No description available 
    19524  
    19525 
    19526 > close #21
    19527 
    19528 > open
    19529 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/RealSpaceRefine_1/rOAT1-AAI_IF_real_space_refined_001.pdb
    19530 
    19531 Chain information for rOAT1-AAI_IF_real_space_refined_001.pdb #21 
    19532 --- 
    19533 Chain | Description 
    19534 A | No description available 
    19535  
    19536 
    19537 QXcbConnection: XCB error: 3 (BadWindow), sequence: 12758, resource id:
    19538 35656914, major code: 40 (TranslateCoords), minor code: 0 
    19539 
    19540 > close #21
    19541 
    19542 > open
    19543 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/RealSpaceRefine_3/rOAT1-AAI_IF-
    19544 > coot-1_real_space_refined_003_initial.geo
    19545 
    19546 Unrecognized file suffix '.geo' 
    19547 
    19548 > open
    19549 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/RealSpaceRefine_3/rOAT1-AAI_IF-
    19550 > coot-1_real_space_refined_003.pdb
    19551 
    19552 Chain information for rOAT1-AAI_IF-coot-1_real_space_refined_003.pdb #21 
    19553 --- 
    19554 Chain | Description 
    19555 A | No description available 
    19556  
    19557 
    19558 QXcbConnection: XCB error: 3 (BadWindow), sequence: 49188, resource id:
    19559 35657106, major code: 40 (TranslateCoords), minor code: 0 
    19560 
    19561 > select add #21
    19562 
    19563 3956 atoms, 4042 bonds, 516 residues, 1 model selected 
    19564 
    19565 > color #21 white
    19566 
    19567 > color #20 white models
    19568 
    19569 > select clear
    19570 
    19571 > select #21/A:602@O24
    19572 
    19573 1 atom, 1 residue, 1 model selected 
    19574 
    19575 > select up
    19576 
    19577 35 atoms, 38 bonds, 1 residue, 1 model selected 
    19578 
    19579 > select #21/A:601@O20
    19580 
    19581 1 atom, 1 residue, 1 model selected 
    19582 
    19583 > select add #21/A:602@C23
    19584 
    19585 2 atoms, 2 residues, 1 model selected 
    19586 
    19587 > select up
    19588 
    19589 70 atoms, 76 bonds, 2 residues, 1 model selected 
    19590 
    19591 > color sel red
    19592 
    19593 > color zone #20 near #21 distance 4.98
    19594 
    19595 > color zone #20 near #21 distance 4.88
    19596 
    19597 > color zone #20 near #21 distance 4.78
    19598 
    19599 > color zone #20 near #21 distance 4.68
    19600 
    19601 > color zone #20 near #21 distance 4.58
    19602 
    19603 > color zone #20 near #21 distance 4.48
    19604 
    19605 > color zone #20 near #21 distance 4.38
    19606 
    19607 > color zone #20 near #21 distance 4.28
    19608 
    19609 > color zone #20 near #21 distance 4.18
    19610 
    19611 > color zone #20 near #21 distance 4.08
    19612 
    19613 > color zone #20 near #21 distance 3.98
    19614 
    19615 > color zone #20 near #21 distance 3.88
    19616 
    19617 > color zone #20 near #21 distance 3.78
    19618 
    19619 > color zone #20 near #21 distance 3.68
    19620 
    19621 > color zone #20 near #21 distance 3.58
    19622 
    19623 > color zone #20 near #21 distance 3.48
    19624 
    19625 > color zone #20 near #21 distance 3.38
    19626 
    19627 > color zone #20 near #21 distance 3.28
    19628 
    19629 > color zone #20 near #21 distance 3.18
    19630 
    19631 > color zone #20 near #21 distance 3.08
    19632 
    19633 > color zone #20 near #21 distance 2.98
    19634 
    19635 > color zone #20 near #21 distance 2.88
    19636 
    19637 > volume splitbyzone #20
    19638 
    19639 Opened rOAT1-AAI_IF.mrc 0 as #22.1, grid size 320,320,320, pixel 0.83, shown
    19640 at level 0.0194, step 1, values float32 
    19641 Opened rOAT1-AAI_IF.mrc 1 as #22.2, grid size 320,320,320, pixel 0.83, shown
    19642 at level 0.0194, step 1, values float32 
    19643 Opened rOAT1-AAI_IF.mrc 2 as #22.3, grid size 320,320,320, pixel 0.83, shown
    19644 at level 0.0194, step 1, values float32 
    19645 
    19646 > close #22.1-2
    19647 
    19648 > color #22.3 yellow models
    19649 
    19650 > color #22.3 white models
    19651 
    19652 > color #22.3 #ffffb2ff models
    19653 
    19654 > color #22.3 #ffffb296 models
    19655 
    19656 > select add #21
    19657 
    19658 3956 atoms, 4042 bonds, 516 residues, 1 model selected 
    19659 
    19660 > color #21 #668855ff
    19661 
    19662 > color #21 #685d73ff
    19663 
    19664 > color sel byhetero
    19665 
    19666 > select clear
    19667 
    19668 [Repeated 1 time(s)]
    19669 
    19670 > save
    19671 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    19672 > includeMaps true
    19673 
    19674 QXcbConnection: XCB error: 3 (BadWindow), sequence: 7603, resource id:
    19675 35657141, major code: 40 (TranslateCoords), minor code: 0 
    19676 
    19677 QXcbConnection: XCB error: 3 (BadWindow), sequence: 7615, resource id:
    19678 35657136, major code: 40 (TranslateCoords), minor code: 0 
    19679 
    19680 > hide #!22.3 models
    19681 
    19682 > hide #!22 models
    19683 
    19684 > hide #21 models
    19685 
    19686 > open
    19687 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20250129_rOAT1-AAI/outward_j122_2.5A/postprocess.mrc
    19688 
    19689 Opened postprocess.mrc as #23, grid size 320,320,320, pixel 0.83, shown at
    19690 level 0.00494, step 2, values float32 
    19691 
    19692 > volume #23 level 0.01307
    19693 
    19694 > volume #23 step 1
    19695 
    19696 > volume #23 level 0.01684
    19697 
    19698 > show #1 models
    19699 
    19700 > hide #1 models
    19701 
    19702 > show #!5 models
    19703 
    19704 > rename #23 rOAT1-AAI_OF.mrc
    19705 
    19706 > save
    19707 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20250129_rOAT1-AAI/outward_j122_2.5A/rOAT1-AAI_OF.pdb
    19708 > models #5 relModel #23
    19709 
    19710 > open
    19711 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/RealSpaceRefine_4/rOAT1-AAI_OF-
    19712 > coot-1_real_space_refined_004.pdb
    19713 
    19714 Chain information for rOAT1-AAI_OF-coot-1_real_space_refined_004.pdb #24 
    19715 --- 
    19716 Chain | Description 
    19717 A | No description available 
    19718  
    19719 
    19720 > color #23 white models
    19721 
    19722 > color #24 white
    19723 
    19724 > hide #!5 models
    19725 
    19726 > select add #24/A:601@O24
    19727 
    19728 1 atom, 1 residue, 1 model selected 
    19729 
    19730 > select add #24/A:230@OH
    19731 
    19732 2 atoms, 2 residues, 1 model selected 
    19733 
    19734 > select clear
    19735 
    19736 > select add #24/A:601@O24
    19737 
    19738 1 atom, 1 residue, 1 model selected 
    19739 
    19740 > select up
    19741 
    19742 35 atoms, 38 bonds, 1 residue, 1 model selected 
    19743 
    19744 > color sel red
    19745 
    19746 > color zone #23 near #24 distance 4.98
    19747 
    19748 > volume splitbyzone #23
    19749 
    19750 Opened rOAT1-AAI_OF.mrc 0 as #25.1, grid size 320,320,320, pixel 0.83, shown
    19751 at level 0.0168, step 1, values float32 
    19752 Opened rOAT1-AAI_OF.mrc 1 as #25.2, grid size 320,320,320, pixel 0.83, shown
    19753 at level 0.0168, step 1, values float32 
    19754 Opened rOAT1-AAI_OF.mrc 2 as #25.3, grid size 320,320,320, pixel 0.83, shown
    19755 at level 0.0168, step 1, values float32 
    19756 
    19757 > close #25.1-2
    19758 
    19759 > select add #24
    19760 
    19761 3790 atoms, 3882 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    19762 
    19763 > select subtract #24
    19764 
    19765 Nothing selected 
    19766 
    19767 > color #25.3 white models
    19768 
    19769 > color #25.3 #ffffb2ff models
    19770 
    19771 > select add #24
    19772 
    19773 3790 atoms, 3882 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    19774 
    19775 > color #24 #1177ccff
    19776 
    19777 > color #24 #17c127ff
    19778 
    19779 > color (#!24 & sel) byhetero
    19780 
    19781 > select #24/A:438@CE2
    19782 
    19783 1 atom, 1 residue, 1 model selected 
    19784 Drag select of 1 atoms, 1 bonds 
    19785 
    19786 > select clear
    19787 
    19788 > color #25.3 #ffffb296 models
    19789 
    19790 > select clear
    19791 
    19792 > save
    19793 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    19794 > includeMaps true
    19795 
    19796 > open
    19797 > /home/dout2/isilon/PROJECTS/OAT1/cryoEM/rOAT1-PAH_20220730_20230218/rOAT1-PAH-
    19798 > coot-7_real_space_refined_007.pdb
    19799 
    19800 Chain information for rOAT1-PAH-coot-7_real_space_refined_007.pdb #26 
    19801 --- 
    19802 Chain | Description 
    19803 A | No description available 
    19804  
    19805 
    19806 QXcbConnection: XCB error: 3 (BadWindow), sequence: 7338, resource id:
    19807 35657291, major code: 40 (TranslateCoords), minor code: 0 
    19808 
    19809 > open
    19810 > /home/dout2/isilon/PROJECTS/OAT1/cryoEM/rOAT1-PAH_20220730_20230218/cryosparc_P4_J89__localfilter_160.mrc
    19811 
    19812 Opened cryosparc_P4_J89__localfilter_160.mrc as #27, grid size 160,160,160,
    19813 pixel 0.83, shown at level 0.134, step 1, values float32 
    19814 
    19815 > hide #!24 models
    19816 
    19817 > hide #!25.3 models
    19818 
    19819 > hide #!25 models
    19820 
    19821 > view
    19822 
    19823 > show #!2 models
    19824 
    19825 > select add #26
    19826 
    19827 3865 atoms, 3947 bonds, 1 pseudobond, 506 residues, 2 models selected 
    19828 
    19829 > select add #27
    19830 
    19831 3865 atoms, 3947 bonds, 1 pseudobond, 506 residues, 4 models selected 
    19832 
    19833 > view matrix models
    19834 > #26,1,0,0,55.434,0,1,0,82.728,0,0,1,62.865,#27,1,0,0,55.434,0,1,0,82.728,0,0,1,62.865
    19835 
    19836 > view matrix models
    19837 > #26,1,0,0,67.067,0,1,0,66.938,0,0,1,64.563,#27,1,0,0,67.067,0,1,0,66.938,0,0,1,64.563
    19838 
    19839 > rename #27 rOAT1-PAH
    19840 
    19841 > rename #27 rOAT1-PAH.mrc
    19842 
    19843 > view
    19844 
    19845 > fitmap #26 inMap #27
    19846 
    19847 Fit molecule rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) to map
    19848 rOAT1-PAH.mrc (#27) using 3865 atoms 
    19849 average map value = 0.3441, steps = 44 
    19850 shifted from previous position = 0.0131 
    19851 rotated from previous position = 0.0158 degrees 
    19852 atoms outside contour = 699, contour level = 0.13428 
    19853  
    19854 Position of rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) relative to
    19855 rOAT1-PAH.mrc (#27) coordinates: 
    19856 Matrix rotation and translation 
    19857 0.99999996 -0.00021122 0.00016567 0.00535685 
    19858 0.00021123 0.99999998 -0.00006568 0.00053709 
    19859 -0.00016566 0.00006571 0.99999998 -0.00148379 
    19860 Axis 0.23771757 0.59945172 0.76429575 
    19861 Axis point -1.23064203 24.84299856 0.00000000 
    19862 Rotation angle (degrees) 0.01583428 
    19863 Shift along axis 0.00046132 
    19864  
    19865 
    19866 > hide #!2 models
    19867 
    19868 > color #27 white models
    19869 
    19870 > color #26 white
    19871 
    19872 > hide #!26 models
    19873 
    19874 > select subtract #27
    19875 
    19876 3865 atoms, 3947 bonds, 1 pseudobond, 506 residues, 2 models selected 
    19877 
    19878 > select subtract #26
    19879 
    19880 Nothing selected 
    19881 
    19882 > hide #!27 models
    19883 
    19884 > show #!26 models
    19885 
    19886 > select #26/B:601@C07
    19887 
    19888 1 atom, 1 residue, 1 model selected 
    19889 
    19890 > select up
    19891 
    19892 23 atoms, 23 bonds, 1 residue, 1 model selected 
    19893 
    19894 > color sel red
    19895 
    19896 > show #!27 models
    19897 
    19898 > color zone #27 near #26 distance 4.98
    19899 
    19900 > color zone #27 near #26 distance 4.88
    19901 
    19902 > color zone #27 near #26 distance 4.78
    19903 
    19904 > color zone #27 near #26 distance 4.68
    19905 
    19906 > color zone #27 near #26 distance 4.58
    19907 
    19908 > color zone #27 near #26 distance 4.48
    19909 
    19910 > color zone #27 near #26 distance 4.38
    19911 
    19912 > color zone #27 near #26 distance 4.28
    19913 
    19914 > color zone #27 near #26 distance 4.18
    19915 
    19916 > color zone #27 near #26 distance 4.08
    19917 
    19918 > color zone #27 near #26 distance 3.98
    19919 
    19920 > color zone #27 near #26 distance 3.88
    19921 
    19922 > color zone #27 near #26 distance 3.78
    19923 
    19924 > color zone #27 near #26 distance 3.68
    19925 
    19926 > color zone #27 near #26 distance 3.58
    19927 
    19928 > color zone #27 near #26 distance 3.48
    19929 
    19930 > color zone #27 near #26 distance 3.38
    19931 
    19932 > color zone #27 near #26 distance 3.28
    19933 
    19934 > color zone #27 near #26 distance 3.18
    19935 
    19936 > color zone #27 near #26 distance 3.08
    19937 
    19938 > color zone #27 near #26 distance 2.98
    19939 
    19940 > color zone #27 near #26 distance 2.88
    19941 
    19942 > color zone #27 near #26 distance 2.78
    19943 
    19944 > color zone #27 near #26 distance 2.68
    19945 
    19946 > color zone #27 near #26 distance 2.58
    19947 
    19948 > color zone #27 near #26 distance 2.48
    19949 
    19950 > color zone #27 near #26 distance 2.38
    19951 
    19952 > color zone #27 near #26 distance 2.28
    19953 
    19954 > volume #27 level 0.1207
    19955 
    19956 > color zone #27 near #26 distance 2.18
    19957 
    19958 > color zone #27 near #26 distance 2.08
    19959 
    19960 > hide #!27 models
    19961 
    19962 > show #!27 models
    19963 
    19964 > fitmap #26 inMap #27
    19965 
    19966 Fit molecule rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) to map
    19967 rOAT1-PAH.mrc (#27) using 3865 atoms 
    19968 average map value = 0.3441, steps = 44 
    19969 shifted from previous position = 0.00509 
    19970 rotated from previous position = 0.0145 degrees 
    19971 atoms outside contour = 605, contour level = 0.12073 
    19972  
    19973 Position of rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) relative to
    19974 rOAT1-PAH.mrc (#27) coordinates: 
    19975 Matrix rotation and translation 
    19976 1.00000000 -0.00003177 0.00004592 0.00408484 
    19977 0.00003177 1.00000000 0.00006809 -0.00110606 
    19978 -0.00004592 -0.00006809 1.00000000 0.00040828 
    19979 Axis -0.77323345 0.52146975 0.36080373 
    19980 Axis point 0.00000000 25.00840435 -11.23310139 
    19981 Rotation angle (degrees) 0.00504562 
    19982 Shift along axis -0.00358800 
    19983  
    19984 
    19985 > fitmap #26 inMap #27
    19986 
    19987 Fit molecule rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) to map
    19988 rOAT1-PAH.mrc (#27) using 3865 atoms 
    19989 average map value = 0.3441, steps = 40 
    19990 shifted from previous position = 0.0153 
    19991 rotated from previous position = 0.0197 degrees 
    19992 atoms outside contour = 607, contour level = 0.12073 
    19993  
    19994 Position of rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) relative to
    19995 rOAT1-PAH.mrc (#27) coordinates: 
    19996 Matrix rotation and translation 
    19997 0.99999998 -0.00017402 -0.00004728 0.01145050 
    19998 0.00017401 0.99999996 -0.00023139 -0.00012574 
    19999 0.00004732 0.00023138 0.99999997 -0.01696563 
    20000 Axis 0.78875519 -0.16123857 0.59318410 
    20001 Axis point 0.00000000 70.72803400 -1.26127659 
    20002 Rotation angle (degrees) 0.01680827 
    20003 Shift along axis -0.00101183 
    20004  
    20005 
    20006 > volume splitbyzone #27
    20007 
    20008 Opened rOAT1-PAH.mrc 0 as #28.1, grid size 160,160,160, pixel 0.83, shown at
    20009 level 0.121, step 1, values float32 
    20010 Opened rOAT1-PAH.mrc 1 as #28.2, grid size 160,160,160, pixel 0.83, shown at
    20011 level 0.121, step 1, values float32 
    20012 Opened rOAT1-PAH.mrc 2 as #28.3, grid size 160,160,160, pixel 0.83, shown at
    20013 level 0.121, step 1, values float32 
    20014 
    20015 > close #28.1-2
    20016 
    20017 > volume #28.3 level 0.05463
    20018 
    20019 > color #28.3 white models
    20020 
    20021 > color #28.3 #ffffb2ff models
    20022 
    20023 > color #28.3 #ffffb296 models
    20024 
    20025 > select add #26
    20026 
    20027 3865 atoms, 3947 bonds, 1 pseudobond, 506 residues, 2 models selected 
    20028 
    20029 > color #26 #bf3434ff
    20030 
    20031 > select subtract #26
    20032 
    20033 Nothing selected 
    20034 
    20035 > hide #!26 models
    20036 
    20037 > hide #!28 models
    20038 
    20039 > hide #!28.3 models
    20040 
    20041 > show #!28 models
    20042 
    20043 > show #!28.3 models
    20044 
    20045 > hide #!28 models
    20046 
    20047 > show #!28 models
    20048 
    20049 > show #!26 models
    20050 
    20051 > save
    20052 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    20053 > includeMaps true
    20054 
    20055 QXcbConnection: XCB error: 3 (BadWindow), sequence: 59852, resource id:
    20056 35657337, major code: 40 (TranslateCoords), minor code: 0 
    20057 
    20058 > hide #!26 models
    20059 
    20060 > hide #!28 models
    20061 
    20062 > hide #!28.3 models
    20063 
    20064 > open
    20065 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20220525_rOAT1-FBP/inward_j46_2.8A/postprocess.mrc
    20066 
    20067 Opened postprocess.mrc as #29, grid size 320,320,320, pixel 0.83, shown at
    20068 level 0.0068, step 2, values float32 
    20069 
    20070 > open
    20071 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-FBP_model/rOAT1-FBP_Model04_RSR_004.pdb
    20072 
    20073 Chain information for rOAT1-FBP_Model04_RSR_004.pdb #30 
    20074 --- 
    20075 Chain | Description 
    20076 A | No description available 
    20077  
    20078 
    20079 > show #!2 models
    20080 
    20081 > volume #29 step 1
    20082 
    20083 > volume #29 level 0.01695
    20084 
    20085 > select add #30
    20086 
    20087 4327 atoms, 4393 bonds, 591 residues, 1 model selected 
    20088 
    20089 > view matrix models #30,1,0,0,75.395,0,1,0,59.328,0,0,1,65.467
    20090 
    20091 > view matrix models #30,1,0,0,69.37,0,1,0,69.752,0,0,1,66.8
    20092 
    20093 > view matrix models #30,1,0,0,64.899,0,1,0,72.303,0,0,1,66.211
    20094 
    20095 > view matrix models #30,1,0,0,67.675,0,1,0,68.154,0,0,1,64.823
    20096 
    20097 > rename #29 rOAT1-FBP.mrc
    20098 
    20099 > fitmap #30 inMap #29
    20100 
    20101 Fit molecule rOAT1-FBP_Model04_RSR_004.pdb (#30) to map rOAT1-FBP.mrc (#29)
    20102 using 4327 atoms 
    20103 average map value = 0.02366, steps = 64 
    20104 shifted from previous position = 2.15 
    20105 rotated from previous position = 1.57 degrees 
    20106 atoms outside contour = 1497, contour level = 0.016951 
    20107  
    20108 Position of rOAT1-FBP_Model04_RSR_004.pdb (#30) relative to rOAT1-FBP.mrc
    20109 (#29) coordinates: 
    20110 Matrix rotation and translation 
    20111 0.99965949 -0.01809184 -0.01880406 69.16631575 
    20112 0.01825291 0.99979787 0.00842953 64.90387685 
    20113 0.01864775 -0.00876989 0.99978765 65.39100171 
    20114 Axis -0.31300664 -0.68157330 0.66142625 
    20115 Axis point -4271.01743380 0.00000000 3378.83285764 
    20116 Rotation angle (degrees) 1.57437238 
    20117 Shift along axis -22.63494048 
    20118  
    20119 
    20120 > fitmap #29 inMap #28.3
    20121 
    20122 Fit map rOAT1-FBP.mrc in map rOAT1-PAH.mrc 2 using 25401 points 
    20123 correlation = 0.04397, correlation about mean = 0.03331, overlap = 0.1449 
    20124 steps = 2000, shift = 8.88, angle = 34.9 degrees 
    20125  
    20126 Position of rOAT1-FBP.mrc (#29) relative to rOAT1-PAH.mrc 2 (#28.3)
    20127 coordinates: 
    20128 Matrix rotation and translation 
    20129 0.83021101 -0.04922054 -0.55527201 36.70411652 
    20130 0.13130357 0.98533433 0.10897540 -101.23145590 
    20131 0.54176475 -0.16338178 0.82449824 -98.97434819 
    20132 Axis -0.23793623 -0.95839145 0.15770918 
    20133 Axis point 214.13564799 0.00000000 31.76591481 
    20134 Rotation angle (degrees) 34.91302477 
    20135 Shift along axis 72.67695975 
    20136  
    20137 
    20138 > fitmap #29 inMap #28.3
    20139 
    20140 Fit map rOAT1-FBP.mrc in map rOAT1-PAH.mrc 2 using 25401 points 
    20141 correlation = 0.06352, correlation about mean = 0.0448, overlap = 0.3215 
    20142 steps = 1976, shift = 9.79, angle = 47.5 degrees 
    20143  
    20144 Position of rOAT1-FBP.mrc (#29) relative to rOAT1-PAH.mrc 2 (#28.3)
    20145 coordinates: 
    20146 Matrix rotation and translation 
    20147 0.44591506 0.03168285 -0.89451437 128.47676238 
    20148 -0.42572042 0.88660402 -0.18081879 31.25418163 
    20149 0.78735118 0.46144286 0.40883812 -156.17744024 
    20150 Axis 0.34576253 -0.90543486 -0.24624374 
    20151 Axis point 186.53313716 0.00000000 6.98625710 
    20152 Rotation angle (degrees) 68.24252592 
    20153 Shift along axis 54.58154231 
    20154  
    20155 
    20156 > fitmap #29 inMap #2
    20157 
    20158 Fit map rOAT1-FBP.mrc in map rOAT1-AZT_IF.mrc using 25401 points 
    20159 correlation = 0.2561, correlation about mean = 0.04268, overlap = 2.051 
    20160 steps = 232, shift = 3.32, angle = 8.56 degrees 
    20161  
    20162 Position of rOAT1-FBP.mrc (#29) relative to rOAT1-AZT_IF.mrc (#2) coordinates: 
    20163 Matrix rotation and translation 
    20164 0.54964589 -0.00012465 -0.83539774 175.75622877 
    20165 -0.44507129 0.84621907 -0.29295875 119.06565669 
    20166 0.70696602 0.53283512 0.46506536 -99.09845418 
    20167 Axis 0.45744920 -0.85439368 -0.24647856 
    20168 Axis point 210.95352936 0.00000000 94.96801349 
    20169 Rotation angle (degrees) 64.50291620 
    20170 Shift along axis 3.09624573 
    20171  
    20172 
    20173 > select add #29
    20174 
    20175 4327 atoms, 4393 bonds, 591 residues, 3 models selected 
    20176 
    20177 > hide #!2 models
    20178 
    20179 > show #!2 models
    20180 
    20181 > hide #!2 models
    20182 
    20183 > show #!27 models
    20184 
    20185 > view matrix models
    20186 > #29,0.54965,-0.00012465,-0.8354,176.85,-0.44507,0.84622,-0.29296,120.37,0.70697,0.53284,0.46507,-99.177,#30,0.99966,-0.018092,-0.018804,70.259,0.018253,0.9998,0.0084295,66.206,0.018648,-0.0087699,0.99979,65.312
    20187 
    20188 > select subtract #30
    20189 
    20190 2 models selected 
    20191 
    20192 > ui mousemode right "rotate selected models"
    20193 
    20194 > view matrix models
    20195 > #29,0.93603,-0.13155,0.32642,-36.684,0.29946,0.78494,-0.54239,70.054,-0.18487,0.60545,0.77412,-40.4
    20196 
    20197 > view matrix models
    20198 > #29,0.99097,-0.1328,0.018694,4.0787,0.13411,0.98118,-0.13891,3.4116,0.00010362,0.14016,0.99013,-37.407
    20199 
    20200 > ui mousemode right "translate selected models"
    20201 
    20202 > view matrix models
    20203 > #29,0.99097,-0.1328,0.018694,17.811,0.13411,0.98118,-0.13891,8.06,0.00010362,0.14016,0.99013,-17.751
    20204 
    20205 > view matrix models
    20206 > #29,0.99097,-0.1328,0.018694,18.852,0.13411,0.98118,-0.13891,3.5023,0.00010362,0.14016,0.99013,-19.331
    20207 
    20208 > fitmap #29 inMap #2
    20209 
    20210 Fit map rOAT1-FBP.mrc in map rOAT1-AZT_IF.mrc using 25401 points 
    20211 correlation = 0.937, correlation about mean = 0.7119, overlap = 14.98 
    20212 steps = 260, shift = 2.93, angle = 16.7 degrees 
    20213  
    20214 Position of rOAT1-FBP.mrc (#29) relative to rOAT1-AZT_IF.mrc (#2) coordinates: 
    20215 Matrix rotation and translation 
    20216 0.99338416 0.10541244 -0.04556454 -5.89234048 
    20217 -0.10461957 0.99432199 0.01945563 14.33237930 
    20218 0.04735669 -0.01455997 0.99877192 -4.89753719 
    20219 Axis -0.14650897 -0.40022199 -0.90463113 
    20220 Axis point 131.78683646 64.78395429 0.00000000 
    20221 Rotation angle (degrees) 6.66633138 
    20222 Shift along axis -0.44238796 
    20223  
    20224 
    20225 > fitmap #30 inMap #29
    20226 
    20227 Fit molecule rOAT1-FBP_Model04_RSR_004.pdb (#30) to map rOAT1-FBP.mrc (#29)
    20228 using 4327 atoms 
    20229 average map value = 0.02366, steps = 84 
    20230 shifted from previous position = 1.18 
    20231 rotated from previous position = 6.66 degrees 
    20232 atoms outside contour = 1496, contour level = 0.016951 
    20233  
    20234 Position of rOAT1-FBP_Model04_RSR_004.pdb (#30) relative to rOAT1-FBP.mrc
    20235 (#29) coordinates: 
    20236 Matrix rotation and translation 
    20237 0.99966027 -0.01808767 -0.01876641 69.16021058 
    20238 0.01824668 0.99979876 0.00833662 64.90031908 
    20239 0.01861185 -0.00867622 0.99978914 65.39198117 
    20240 Axis -0.31026139 -0.68166338 0.66262576 
    20241 Axis point -4271.35731029 0.00000000 3392.84555643 
    20242 Rotation angle (degrees) 1.57107230 
    20243 Shift along axis -22.36750269 
    20244  
    20245 
    20246 > select subtract #29
    20247 
    20248 Nothing selected 
    20249 
    20250 > hide #!27 models
    20251 
    20252 > color #29 white models
    20253 
    20254 > color #30 white
    20255 
    20256 > select ::name="FBP"
    20257 
    20258 18 atoms, 19 bonds, 1 residue, 1 model selected 
    20259 
    20260 > color sel red
    20261 
    20262 > color zone #29 near #30 distance 4.98
    20263 
    20264 > volume #29 level 0.01043
    20265 
    20266 > volume splitbyzone #29
    20267 
    20268 Opened rOAT1-FBP.mrc 0 as #31.1, grid size 320,320,320, pixel 0.83, shown at
    20269 level 0.0104, step 1, values float32 
    20270 Opened rOAT1-FBP.mrc 1 as #31.2, grid size 320,320,320, pixel 0.83, shown at
    20271 level 0.0104, step 1, values float32 
    20272 Opened rOAT1-FBP.mrc 2 as #31.3, grid size 320,320,320, pixel 0.83, shown at
    20273 level 0.0104, step 1, values float32 
    20274 
    20275 > close #31.1-2
    20276 
    20277 > volume #31.3 level 0.002491
    20278 
    20279 > volume #31.3 level 0.005476
    20280 
    20281 > close #31#31.3
    20282 
    20283 > show #!29 models
    20284 
    20285 > color zone #29 near #30 distance 2
    20286 
    20287 [Repeated 1 time(s)]
    20288 
    20289 > volume splitbyzone #29
    20290 
    20291 Opened rOAT1-FBP.mrc 0 as #31.1, grid size 320,320,320, pixel 0.83, shown at
    20292 level 0.0104, step 1, values float32 
    20293 Opened rOAT1-FBP.mrc 1 as #31.2, grid size 320,320,320, pixel 0.83, shown at
    20294 level 0.0104, step 1, values float32 
    20295 Opened rOAT1-FBP.mrc 2 as #31.3, grid size 320,320,320, pixel 0.83, shown at
    20296 level 0.0104, step 1, values float32 
    20297 
    20298 > close #31.1-2
    20299 
    20300 > volume #31.3 level 0.003802
    20301 
    20302 > color #31.3 white models
    20303 
    20304 > color #31.3 #ffffb2ff models
    20305 
    20306 > color #31.3 #ffffb20f models
    20307 
    20308 > color #31.3 #ffffb296 models
    20309 
    20310 > select add #30
    20311 
    20312 4327 atoms, 4393 bonds, 591 residues, 1 model selected 
    20313 
    20314 > color #30 #889944ff
    20315 
    20316 > color #30 #894a08ff
    20317 
    20318 > save
    20319 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    20320 > includeMaps true
    20321 
    20322 > hide #!31.3 models
    20323 
    20324 > hide #!31 models
    20325 
    20326 > select subtract #30
    20327 
    20328 Nothing selected 
    20329 
    20330 > hide #30 models
    20331 
    20332 > show #!2 models
    20333 
    20334 > open
    20335 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20220609_rOAT1-CFM/inward_j194_2.7A/postprocess.mrc
    20336 
    20337 Opened postprocess.mrc as #32, grid size 320,320,320, pixel 0.83, shown at
    20338 level 0.00396, step 2, values float32 
    20339 
    20340 QXcbConnection: XCB error: 3 (BadWindow), sequence: 4668, resource id:
    20341 35657387, major code: 40 (TranslateCoords), minor code: 0 
    20342 
    20343 > volume #32 step 1
    20344 
    20345 > volume #32 level 0.01186
    20346 
    20347 > rename #32 rOAT1-CFM.mrc
    20348 
    20349 > fitmap #31.3 inMap #32
    20350 
    20351 Fit map rOAT1-FBP.mrc 2 in map rOAT1-CFM.mrc using 186 points 
    20352 correlation = 0.7788, correlation about mean = 0.1794, overlap = 0.008643 
    20353 steps = 80, shift = 1.06, angle = 39.7 degrees 
    20354  
    20355 Position of rOAT1-FBP.mrc 2 (#31.3) relative to rOAT1-CFM.mrc (#32)
    20356 coordinates: 
    20357 Matrix rotation and translation 
    20358 0.74404465 0.65679786 0.12253212 -67.09990326 
    20359 -0.66239846 0.70118044 0.26376935 89.56606533 
    20360 0.08732602 -0.27742126 0.95677145 29.93219993 
    20361 Axis -0.37942983 0.02468307 -0.92489121 
    20362 Axis point 75.79903236 131.70903838 0.00000000 
    20363 Rotation angle (degrees) 45.49284979 
    20364 Shift along axis -0.01355792 
    20365  
    20366 
    20367 > fitmap #31.3 inMap #2
    20368 
    20369 Fit map rOAT1-FBP.mrc 2 in map rOAT1-AZT_IF.mrc using 186 points 
    20370 correlation = 0.8514, correlation about mean = 0.3895, overlap = 0.01295 
    20371 steps = 76, shift = 0.987, angle = 35 degrees 
    20372  
    20373 Position of rOAT1-FBP.mrc 2 (#31.3) relative to rOAT1-AZT_IF.mrc (#2)
    20374 coordinates: 
    20375 Matrix rotation and translation 
    20376 0.98357109 0.17790518 -0.03062105 -15.98050765 
    20377 -0.17592201 0.98266732 0.05844983 19.75924781 
    20378 0.04048883 -0.05210265 0.99782061 1.12732183 
    20379 Axis -0.29288928 -0.18839308 -0.93740275 
    20380 Axis point 102.41456930 99.44616144 0.00000000 
    20381 Rotation angle (degrees) 10.87852675 
    20382 Shift along axis -0.09874061 
    20383  
    20384 
    20385 > fitmap #32 inMap #2
    20386 
    20387 Fit map rOAT1-CFM.mrc in map rOAT1-AZT_IF.mrc using 30016 points 
    20388 correlation = 0.9542, correlation about mean = 0.7898, overlap = 13.57 
    20389 steps = 72, shift = 2.43, angle = 7.06 degrees 
    20390  
    20391 Position of rOAT1-CFM.mrc (#32) relative to rOAT1-AZT_IF.mrc (#2) coordinates: 
    20392 Matrix rotation and translation 
    20393 0.99240829 0.11776796 -0.03544703 -8.88787383 
    20394 -0.11778889 0.99303752 0.00150464 18.44106769 
    20395 0.03537743 0.00268205 0.99937042 -5.69387210 
    20396 Axis 0.00478670 -0.28793162 -0.95763901 
    20397 Axis point 151.76616064 85.25679566 0.00000000 
    20398 Rotation angle (degrees) 7.06459913 
    20399 Shift along axis 0.10036409 
    20400  
    20401 
    20402 > save
    20403 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-CFM/rOAT1-CFM_IF.pdb
    20404 > models #30 relModel #32
    20405 
    20406 > open
    20407 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-CFM/rOAT1-CFM_IF.pdb
    20408 
    20409 Chain information for rOAT1-CFM_IF.pdb #33 
    20410 --- 
    20411 Chain | Description 
    20412 A | No description available 
    20413  
    20414 
    20415 > color #33 #ffff7fff
    20416 
    20417 > color #33 #55aaffff
    20418 
    20419 > select add #33
    20420 
    20421 4327 atoms, 4393 bonds, 591 residues, 1 model selected 
    20422 
    20423 > view matrix models #33,1,0,0,-3.2206,0,1,0,10.827,0,0,1,-3.1224
    20424 
    20425 > view matrix models #33,1,0,0,-4.4307,0,1,0,11.668,0,0,1,-3.5924
    20426 
    20427 > view matrix models #33,1,0,0,-4.3326,0,1,0,9.3726,0,0,1,-2.8036
    20428 
    20429 > fitmap #33 inMap #32
    20430 
    20431 Fit molecule rOAT1-CFM_IF.pdb (#33) to map rOAT1-CFM.mrc (#32) using 4327
    20432 atoms 
    20433 average map value = 0.0191, steps = 80 
    20434 shifted from previous position = 1.1 
    20435 rotated from previous position = 7.12 degrees 
    20436 atoms outside contour = 1362, contour level = 0.01186 
    20437  
    20438 Position of rOAT1-CFM_IF.pdb (#33) relative to rOAT1-CFM.mrc (#32)
    20439 coordinates: 
    20440 Matrix rotation and translation 
    20441 0.99999299 -0.00023005 -0.00373680 -4.70643521 
    20442 0.00021365 0.99999035 -0.00438786 8.58155234 
    20443 0.00373777 0.00438703 0.99998339 -3.97966882 
    20444 Axis 0.76069466 -0.64796926 0.03846397 
    20445 Axis point 0.00000000 827.85989235 581.48051316 
    20446 Rotation angle (degrees) 0.33046593 
    20447 Shift along axis -9.29381608 
    20448  
    20449 
    20450 > save /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-CFM/rOAT1-CFM.pdb
    20451 > models #33 relModel #32
    20452 
    20453 QXcbConnection: XCB error: 3 (BadWindow), sequence: 60371, resource id:
    20454 35657459, major code: 40 (TranslateCoords), minor code: 0 
    20455 
    20456 > hide #33 models
    20457 
    20458 > hide #!32 models
    20459 
    20460 > select subtract #33
    20461 
    20462 Nothing selected 
    20463 
    20464 > show #!17 models
    20465 
    20466 > hide #!17 models
    20467 
    20468 > show #!17 models
    20469 
    20470 > hide #!2 models
    20471 
    20472 > open
    20473 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/RealSpaceRefine_7/rOAT1-TFV-
    20474 > Cl_OF-coot-2.pdb
    20475 
    20476 Chain information for rOAT1-TFV-Cl_OF-coot-2.pdb #34 
    20477 --- 
    20478 Chain | Description 
    20479 A | No description available 
    20480  
    20481 
    20482 > select ::name="CL"
    20483 
    20484 1 atom, 1 residue, 1 model selected 
    20485 
    20486 > hide #!17 models
    20487 
    20488 > show sel atoms
    20489 
    20490 > show #!17 models
    20491 
    20492 > style sel stick
    20493 
    20494 Changed 1 atom style 
    20495 
    20496 > color zone #17 near #34 distance 2.98
    20497 
    20498 > select add #34
    20499 
    20500 3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 2 models selected 
    20501 
    20502 > color #34 white
    20503 
    20504 > color zone #17 near #34 distance 2.98
    20505 
    20506 > select ::name="CL"
    20507 
    20508 1 atom, 1 residue, 1 model selected 
    20509 
    20510 > color sel red
    20511 
    20512 > color zone #17 near #34 distance 2.98
    20513 
    20514 > volume splitbyzone #17
    20515 
    20516 Opened rOAT1-TVF_OF.mrc 0 as #35.1, grid size 320,320,320, pixel 0.83, shown
    20517 at level 0.011, step 1, values float32 
    20518 Opened rOAT1-TVF_OF.mrc 1 as #35.2, grid size 320,320,320, pixel 0.83, shown
    20519 at level 0.011, step 1, values float32 
    20520 Opened rOAT1-TVF_OF.mrc 2 as #35.3, grid size 320,320,320, pixel 0.83, shown
    20521 at level 0.011, step 1, values float32 
    20522 
    20523 > rename #35 "rOAT1-TVF-Cl_OF.mrc split"
    20524 
    20525 > close #35.1-2
    20526 
    20527 > rename #35.3 "rOAT1-TVF-Cl_OF.mrc 2"
    20528 
    20529 > hide #!35.3 models
    20530 
    20531 > select #34/B:1@CL
    20532 
    20533 1 atom, 1 residue, 1 model selected 
    20534 
    20535 > ui tool show Contacts
    20536 
    20537 > contacts sel interModel false ignoreHiddenModels true select true
    20538 
    20539 6 contacts 
    20540 
    20541 > ui tool show Contacts
    20542 
    20543 > contacts sel intraRes true ignoreHiddenModels true select true
    20544 
    20545 15 contacts 
    20546 
    20547 > show sel atoms
    20548 
    20549 > color #34 yellow
    20550 
    20551 > show sel atoms
    20552 
    20553 > close #36
    20554 
    20555 > select add #34
    20556 
    20557 3787 atoms, 3876 bonds, 11 pseudobonds, 487 residues, 3 models selected 
    20558 
    20559 > color #34 white
    20560 
    20561 > hide sel atoms
    20562 
    20563 > select ::name="CL"
    20564 
    20565 1 atom, 1 residue, 1 model selected 
    20566 
    20567 > show sel atoms
    20568 
    20569 > hide #35.3.1 models
    20570 
    20571 > show #35.3.1 models
    20572 
    20573 > close #34.2
    20574 
    20575 > hide #!35.3 models
    20576 
    20577 > hide #35.3.1 models
    20578 
    20579 > hide #!35 models
    20580 
    20581 > hide #34.1 models
    20582 
    20583 > select #34/B:1@CL
    20584 
    20585 1 atom, 1 residue, 1 model selected 
    20586 
    20587 > select #34/A:216
    20588 
    20589 8 atoms, 7 bonds, 1 residue, 1 model selected 
    20590 
    20591 > show sel atoms
    20592 
    20593 > select #34/A:511
    20594 
    20595 7 atoms, 7 bonds, 1 residue, 1 model selected 
    20596 
    20597 > show sel atoms
    20598 
    20599 > select #34: 219
    20600 
    20601 11 atoms, 10 bonds, 1 residue, 1 model selected 
    20602 
    20603 > show sel atoms
    20604 
    20605 > select #34: 273
    20606 
    20607 11 atoms, 10 bonds, 1 residue, 1 model selected 
    20608 
    20609 > show sel atoms
    20610 
    20611 > select #34/A:4
    20612 
    20613 8 atoms, 7 bonds, 1 residue, 1 model selected 
    20614 
    20615 > show sel atoms
    20616 
    20617 > select add #34/A:511
    20618 
    20619 15 atoms, 14 bonds, 2 residues, 1 model selected 
    20620 
    20621 > show sel atoms
    20622 
    20623 > select add #34/A:512
    20624 
    20625 23 atoms, 21 bonds, 3 residues, 1 model selected 
    20626 
    20627 > show sel atoms
    20628 
    20629 > select #34/B:1@CL
    20630 
    20631 1 atom, 1 residue, 1 model selected 
    20632 
    20633 > color sel lime
    20634 
    20635 > color #35.3.1 white
    20636 
    20637 > color #35.3.1 #ffffb2ff
    20638 
    20639 > color #35.3.1 #ffffb296
    20640 
    20641 > select #34/B:1@CL
    20642 
    20643 1 atom, 1 residue, 1 model selected 
    20644 
    20645 > select add #34
    20646 
    20647 3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 2 models selected 
    20648 
    20649 > color #34 #374c02ff
    20650 
    20651 > select #34/B:1@CL
    20652 
    20653 1 atom, 1 residue, 1 model selected 
    20654 
    20655 > color sel lime
    20656 
    20657 > select add #34
    20658 
    20659 3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 2 models selected 
    20660 
    20661 > color (#!34 & sel) byhetero
    20662 
    20663 > select #34/A:2
    20664 
    20665 5 atoms, 4 bonds, 1 residue, 1 model selected 
    20666 
    20667 > show sel atoms
    20668 
    20669 > select #34/A:3
    20670 
    20671 11 atoms, 11 bonds, 1 residue, 1 model selected 
    20672 
    20673 > show sel atoms
    20674 
    20675 > select add #34/A:215
    20676 
    20677 18 atoms, 18 bonds, 2 residues, 1 model selected 
    20678 
    20679 > show sel atoms
    20680 
    20681 > select #34/B:1@CL
    20682 
    20683 1 atom, 1 residue, 1 model selected 
    20684 
    20685 > show #35.3.1 models
    20686 
    20687 > view sel
    20688 
    20689 > hide #35.3.1 models
    20690 
    20691 > hide #!35.3 models
    20692 
    20693 > hide #!35 models
    20694 
    20695 > hide #!34 models
    20696 
    20697 > select add #34
    20698 
    20699 3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 2 models selected 
    20700 
    20701 > select subtract #34
    20702 
    20703 Nothing selected 
    20704 
    20705 > show #1 models
    20706 
    20707 > view
    20708 
    20709 > hide #1 models
    20710 
    20711 > show #21 models
    20712 
    20713 > select add #21/A:602@C12
    20714 
    20715 1 atom, 1 residue, 1 model selected 
    20716 
    20717 > select up
    20718 
    20719 3 atoms, 1 bond, 2 residues, 1 model selected 
    20720 
    20721 > select up
    20722 
    20723 44 atoms, 46 bonds, 2 residues, 1 model selected 
    20724 
    20725 > select clear
    20726 
    20727 > select #21/A:602@O14
    20728 
    20729 1 atom, 1 residue, 1 model selected 
    20730 
    20731 > select add #21/A:601@C04
    20732 
    20733 2 atoms, 2 residues, 1 model selected 
    20734 
    20735 > select up
    20736 
    20737 70 atoms, 76 bonds, 2 residues, 1 model selected 
    20738 
    20739 > view sel
    20740 
    20741 > show #!22.3 models
    20742 
    20743 > hide #!22.3 models
    20744 
    20745 > hide #!22 models
    20746 
    20747 > hide #21 models
    20748 
    20749 > select add #21
    20750 
    20751 3956 atoms, 4042 bonds, 516 residues, 1 model selected 
    20752 
    20753 > select subtract #21
    20754 
    20755 Nothing selected 
    20756 
    20757 > save
    20758 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    20759 > includeMaps true
    20760 
    20761 QXcbConnection: XCB error: 3 (BadWindow), sequence: 40781, resource id:
    20762 35657669, major code: 40 (TranslateCoords), minor code: 0 
    20763 
    20764 > open
    20765 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20241127_hOAT1-TFV/inward_j62_3.2A/postprocess.mrc
    20766 
    20767 Opened postprocess.mrc as #36, grid size 320,320,320, pixel 0.83, shown at
    20768 level 0.00418, step 2, values float32 
    20769 
    20770 > open
    20771 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20241127_hOAT1-TFV/inward_j62_3.2A/hOAT1_AF-Q4U2R8-F1-model_v4.pdb
    20772 
    20773 hOAT1_AF-Q4U2R8-F1-model_v4.pdb title: 
    20774 Alphafold monomer V2.0 prediction for solute carrier family 22 member 6
    20775 (Q4U2R8) [more info...] 
    20776  
    20777 Chain information for hOAT1_AF-Q4U2R8-F1-model_v4.pdb #37 
    20778 --- 
    20779 Chain | Description | UniProt 
    20780 A | solute carrier family 22 member 6 | S22A6_HUMAN 1-563 
    20781  
    20782 
    20783 > rename #36 hOAT1-TFV.mrc
    20784 
    20785 > volume #36 step 1
    20786 
    20787 > volume #36 level 0.008515
    20788 
    20789 > rename #37 hOAT1-TFV_IF.pdb
    20790 
    20791 > view
    20792 
    20793 > show #!2 models
    20794 
    20795 > hide #!2 models
    20796 
    20797 > ui tool show Matchmaker
    20798 
    20799 > matchmaker #37 to #1
    20800 
    20801 Parameters 
    20802 --- 
    20803 Chain pairing | bb 
    20804 Alignment algorithm | Needleman-Wunsch 
    20805 Similarity matrix | BLOSUM-62 
    20806 SS fraction | 0.3 
    20807 Gap open (HH/SS/other) | 18/18/6 
    20808 Gap extend | 1 
    20809 SS matrix |  |  | H | S | O 
    20810 ---|---|---|--- 
    20811 H | 6 | -9 | -6 
    20812 S |  | 6 | -6 
    20813 O |  |  | 4 
    20814 Iteration cutoff | 2 
    20815  
    20816 Matchmaker rOAT1-AZT_IF.pdb, chain A (#1) with hOAT1-TFV_IF.pdb, chain A
    20817 (#37), sequence alignment score = 2359.6 
    20818 RMSD between 490 pruned atom pairs is 0.806 angstroms; (across all 500 pairs:
    20819 0.862) 
    20820  
    20821 
    20822 > matchmaker #37 to #1
    20823 
    20824 Parameters 
    20825 --- 
    20826 Chain pairing | bb 
    20827 Alignment algorithm | Needleman-Wunsch 
    20828 Similarity matrix | BLOSUM-62 
    20829 SS fraction | 0.3 
    20830 Gap open (HH/SS/other) | 18/18/6 
    20831 Gap extend | 1 
    20832 SS matrix |  |  | H | S | O 
    20833 ---|---|---|--- 
    20834 H | 6 | -9 | -6 
    20835 S |  | 6 | -6 
    20836 O |  |  | 4 
    20837 Iteration cutoff | 2 
    20838  
    20839 Matchmaker rOAT1-AZT_IF.pdb, chain A (#1) with hOAT1-TFV_IF.pdb, chain A
    20840 (#37), sequence alignment score = 2359.6 
    20841 RMSD between 490 pruned atom pairs is 0.806 angstroms; (across all 500 pairs:
    20842 0.862) 
    20843  
    20844 
    20845 > save
    20846 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20241127_hOAT1-TFV/inward_j62_3.2A/hOAT1-TVF_IF.pdb
    20847 > models #37 relModel #36
    20848 
    20849 > rename #36 hOAT1-TFV_IF.mrc
    20850 
    20851 > hide #37 models
    20852 
    20853 > hide #!36 models
    20854 
    20855 > open
    20856 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20241127_hOAT1-TFV/inward_j62_3.2A/hOAT1_AF-Q4U2R8-F1-model_v4.pdb
    20857 
    20858 hOAT1_AF-Q4U2R8-F1-model_v4.pdb title: 
    20859 Alphafold monomer V2.0 prediction for solute carrier family 22 member 6
    20860 (Q4U2R8) [more info...] 
    20861  
    20862 Chain information for hOAT1_AF-Q4U2R8-F1-model_v4.pdb #38 
    20863 --- 
    20864 Chain | Description | UniProt 
    20865 A | solute carrier family 22 member 6 | S22A6_HUMAN 1-563 
    20866  
    20867 
    20868 > close #38
    20869 
    20870 > close #37
    20871 
    20872 > open
    20873 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/RealSpaceRefine_2/hOAT1-TVF_IF-
    20874 > coot-1_real_space_refined_002.pdb
    20875 
    20876 Chain information for hOAT1-TVF_IF-coot-1_real_space_refined_002.pdb #37 
    20877 --- 
    20878 Chain | Description 
    20879 A | No description available 
    20880  
    20881 
    20882 > show #!36 models
    20883 
    20884 > color #36 white models
    20885 
    20886 > color #37 white
    20887 
    20888 > hide #!36 models
    20889 
    20890 > select up
    20891 
    20892 2 atoms, 1 bond, 1 residue, 1 model selected 
    20893 
    20894 > select #37/A:601@C08
    20895 
    20896 1 atom, 1 residue, 1 model selected 
    20897 
    20898 > select up
    20899 
    20900 31 atoms, 32 bonds, 1 residue, 1 model selected 
    20901 
    20902 > color sel red
    20903 
    20904 > show #!36 models
    20905 
    20906 > color zone #36 near #37 distance 4.98
    20907 
    20908 > color zone #36 near #37 distance 2
    20909 
    20910 [Repeated 1 time(s)]
    20911 
    20912 > color zone #36 near #37 distance 1.9
    20913 
    20914 > color zone #36 near #37 distance 1.8
    20915 
    20916 > color zone #36 near #37 distance 1.7
    20917 
    20918 > volume splitbyzone #36
    20919 
    20920 Opened hOAT1-TFV_IF.mrc 0 as #38.1, grid size 320,320,320, pixel 0.83, shown
    20921 at level 0.00852, step 1, values float32 
    20922 Opened hOAT1-TFV_IF.mrc 1 as #38.2, grid size 320,320,320, pixel 0.83, shown
    20923 at level 0.00852, step 1, values float32 
    20924 Opened hOAT1-TFV_IF.mrc 2 as #38.3, grid size 320,320,320, pixel 0.83, shown
    20925 at level 0.00852, step 1, values float32 
    20926 
    20927 > close #38.1-2
    20928 
    20929 > color #38.3 white models
    20930 
    20931 > color #38.3 #ffffb2ff models
    20932 
    20933 > color #38.3 #ffffb296 models
    20934 
    20935 > color #37 #aaff7fff
    20936 
    20937 > select add #37
    20938 
    20939 4375 atoms, 4481 bonds, 564 residues, 1 model selected 
    20940 
    20941 > color sel byhetero
    20942 
    20943 > save
    20944 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    20945 > includeMaps true
    20946 
    20947 QXcbConnection: XCB error: 3 (BadWindow), sequence: 48690, resource id:
    20948 35657985, major code: 40 (TranslateCoords), minor code: 0 
    20949 
    20950 > hide #!38.3 models
    20951 
    20952 > hide #!38 models
    20953 
    20954 > select subtract #37
    20955 
    20956 Nothing selected 
    20957 
    20958 > show #!34 models
    20959 
    20960 Drag select of 25 atoms, 383 residues, 24 bonds 
    20961 
    20962 > select up
    20963 
    20964 2906 atoms, 2958 bonds, 383 residues, 2 models selected 
    20965 
    20966 > select clear
    20967 
    20968 > select add #37/A:326
    20969 
    20970 5 atoms, 4 bonds, 1 residue, 1 model selected 
    20971 
    20972 > select clear
    20973 
    20974 > hide #!34 models
    20975 
    20976 > select add #37
    20977 
    20978 4375 atoms, 4481 bonds, 564 residues, 1 model selected 
    20979 
    20980 > select subtract #37
    20981 
    20982 Nothing selected 
    20983 
    20984 > save
    20985 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF.pdb
    20986 
    20987 > save
    20988 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF.pdb
    20989 > models #37 relModel #36
    20990 
    20991 QXcbConnection: XCB error: 3 (BadWindow), sequence: 16970, resource id:
    20992 35658005, major code: 40 (TranslateCoords), minor code: 0 
    20993 
    20994 QXcbConnection: XCB error: 3 (BadWindow), sequence: 16981, resource id:
    20995 35657995, major code: 40 (TranslateCoords), minor code: 0 
    20996 
    20997 > open
    20998 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20241127_hOAT1-TFV/outward_j68_3.1A/postprocess.mrc
    20999 
    21000 Opened postprocess.mrc as #39, grid size 320,320,320, pixel 0.83, shown at
    21001 level 0.00436, step 2, values float32 
    21002 
    21003 QXcbConnection: XCB error: 3 (BadWindow), sequence: 18302, resource id:
    21004 35658010, major code: 40 (TranslateCoords), minor code: 0 
    21005 
    21006 > rename #39 hOAT1-TFV_OF.mrc
    21007 
    21008 > volume #39 step 1
    21009 
    21010 > volume #39 level 0.01031
    21011 
    21012 > hide #!39 models
    21013 
    21014 > open
    21015 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF.pdb
    21016 
    21017 Chain information for hOAT1-TFV_OF.pdb #40 
    21018 --- 
    21019 Chain | Description 
    21020 A | No description available 
    21021  
    21022 
    21023 > hide #37 models
    21024 
    21025 > select #40: 320-600
    21026 
    21027 1850 atoms, 1888 bonds, 244 residues, 1 model selected 
    21028 
    21029 > hide sel cartoons
    21030 
    21031 [Repeated 1 time(s)]
    21032 
    21033 > show sel cartoons
    21034 
    21035 > ui tool show Matchmaker
    21036 
    21037 > matchmaker #40 & sel to #18
    21038 
    21039 Parameters 
    21040 --- 
    21041 Chain pairing | bb 
    21042 Alignment algorithm | Needleman-Wunsch 
    21043 Similarity matrix | BLOSUM-62 
    21044 SS fraction | 0.3 
    21045 Gap open (HH/SS/other) | 18/18/6 
    21046 Gap extend | 1 
    21047 SS matrix |  |  | H | S | O 
    21048 ---|---|---|--- 
    21049 H | 6 | -9 | -6 
    21050 S |  | 6 | -6 
    21051 O |  |  | 4 
    21052 Iteration cutoff | 2 
    21053  
    21054 Matchmaker rOAT1-TFV_OF-coot-1_real_space_refined_007.pdb, chain A (#18) with
    21055 hOAT1-TFV_OF.pdb, chain A (#40), sequence alignment score = 866.1 
    21056 RMSD between 164 pruned atom pairs is 0.748 angstroms; (across all 200 pairs:
    21057 7.198) 
    21058  
    21059 
    21060 > matchmaker #40 to #15
    21061 
    21062 Parameters 
    21063 --- 
    21064 Chain pairing | bb 
    21065 Alignment algorithm | Needleman-Wunsch 
    21066 Similarity matrix | BLOSUM-62 
    21067 SS fraction | 0.3 
    21068 Gap open (HH/SS/other) | 18/18/6 
    21069 Gap extend | 1 
    21070 SS matrix |  |  | H | S | O 
    21071 ---|---|---|--- 
    21072 H | 6 | -9 | -6 
    21073 S |  | 6 | -6 
    21074 O |  |  | 4 
    21075 Iteration cutoff | 2 
    21076  
    21077 Matchmaker rOAT1-TFV_IF-coot-3.pdb, chain A (#15) with hOAT1-TFV_OF.pdb, chain
    21078 A (#40), sequence alignment score = 2368.6 
    21079 RMSD between 493 pruned atom pairs is 0.665 angstroms; (across all 500 pairs:
    21080 0.719) 
    21081  
    21082 
    21083 > show #!18 models
    21084 
    21085 > ui mousemode right "translate selected atoms"
    21086 
    21087 > ui mousemode right "rotate selected models"
    21088 
    21089 > view matrix models
    21090 > #40,0.99727,-0.025813,-0.069217,13.221,0.025375,0.99965,-0.0072002,-1.7643,0.069379,0.0054242,0.99758,-8.8122
    21091 
    21092 > undo
    21093 
    21094 > ui mousemode right "move picked models"
    21095 
    21096 > view matrix models #18,1,0,0,0.019269,0,1,0,-0.04277,0,0,1,0.28987
    21097 
    21098 > undo
    21099 
    21100 > ui mousemode right pivot
    21101 
    21102 > ui tool show Matchmaker
    21103 
    21104 > matchmaker #40 & sel to #5 & sel
    21105 
    21106 No 'to' model specified 
    21107 
    21108 > select clear
    21109 
    21110 > hide #!18 models
    21111 
    21112 > show #!18 models
    21113 
    21114 > select #18,40: 320-600
    21115 
    21116 3274 atoms, 3340 bonds, 2 pseudobonds, 433 residues, 3 models selected 
    21117 
    21118 > ui tool show Matchmaker
    21119 
    21120 > matchmaker #40 & sel to #5 & sel
    21121 
    21122 No 'to' model specified 
    21123 
    21124 > matchmaker #40 & sel to #5 & sel
    21125 
    21126 No 'to' model specified 
    21127 
    21128 > matchmaker #40 & sel to #5 & sel
    21129 
    21130 No 'to' model specified 
    21131 
    21132 > ui mousemode right "translate selected atoms"
    21133 
    21134 > select #40: 320-600
    21135 
    21136 1850 atoms, 1888 bonds, 244 residues, 1 model selected 
    21137 
    21138 > hide #!18 models
    21139 
    21140 > show #!18 models
    21141 
    21142 > hide #40 models
    21143 
    21144 > hide #!18 models
    21145 
    21146 > show #40 models
    21147 
    21148 > save
    21149 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF.pdb
    21150 > models #40 relModel #39
    21151 
    21152 QXcbConnection: XCB error: 3 (BadWindow), sequence: 34583, resource id:
    21153 35658147, major code: 40 (TranslateCoords), minor code: 0 
    21154 
    21155 > fitmap #40 inMap #39
    21156 
    21157 Fit molecule hOAT1-TFV_OF.pdb (#40) to map hOAT1-TFV_OF.mrc (#39) using 4375
    21158 atoms 
    21159 average map value = 0.007219, steps = 88 
    21160 shifted from previous position = 0.909 
    21161 rotated from previous position = 8.49 degrees 
    21162 atoms outside contour = 2887, contour level = 0.010308 
    21163  
    21164 Position of hOAT1-TFV_OF.pdb (#40) relative to hOAT1-TFV_OF.mrc (#39)
    21165 coordinates: 
    21166 Matrix rotation and translation 
    21167 0.99019825 -0.07829950 -0.11565728 27.38037598 
    21168 0.07892080 0.99688057 0.00079533 -10.70816731 
    21169 0.11523422 -0.00991530 0.99328886 -13.08861468 
    21170 Axis -0.03831490 -0.82596303 0.56242070 
    21171 Axis point 128.86145300 0.00000000 225.96021530 
    21172 Rotation angle (degrees) 8.03460025 
    21173 Shift along axis 0.43416611 
    21174  
    21175 
    21176 > save
    21177 > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF.pdb
    21178 > models #40 relModel #39
    21179 
    21180 > undo
    21181 
    21182 > select clear
    21183 
    21184 > show #!39 models
    21185 
    21186 > fitmap #40 inMap #39
    21187 
    21188 Fit molecule hOAT1-TFV_OF.pdb (#40) to map hOAT1-TFV_OF.mrc (#39) using 4375
    21189 atoms 
    21190 average map value = 0.007218, steps = 28 
    21191 shifted from previous position = 0.0175 
    21192 rotated from previous position = 0.016 degrees 
    21193 atoms outside contour = 2888, contour level = 0.010308 
    21194  
    21195 Position of hOAT1-TFV_OF.pdb (#40) relative to hOAT1-TFV_OF.mrc (#39)
    21196 coordinates: 
    21197 Matrix rotation and translation 
    21198 0.99020256 -0.07845145 -0.11551732 27.36683659 
    21199 0.07909202 0.99686685 0.00096497 -10.76110579 
    21200 0.11507968 -0.01009202 0.99330500 -13.04322773 
    21201 Axis -0.03956067 -0.82505023 0.56367284 
    21202 Axis point 128.67057833 0.00000000 226.14572082 
    21203 Rotation angle (degrees) 8.03322105 
    21204 Shift along axis 0.44368911 
    21205  
    21206 
    21207 > fitmap #40 inMap #39
    21208 
    21209 Fit molecule hOAT1-TFV_OF.pdb (#40) to map hOAT1-TFV_OF.mrc (#39) using 4375
    21210 atoms 
    21211 average map value = 0.007219, steps = 44 
    21212 shifted from previous position = 0.00455 
    21213 rotated from previous position = 0.00258 degrees 
    21214 atoms outside contour = 2889, contour level = 0.010308 
    21215  
    21216 Position of hOAT1-TFV_OF.pdb (#40) relative to hOAT1-TFV_OF.mrc (#39)
    21217 coordinates: 
    21218 Matrix rotation and translation 
    21219 0.99020340 -0.07846932 -0.11549800 27.37049731 
    21220 0.07911379 0.99686509 0.00099928 -10.76639922 
    21221 0.11505751 -0.01012698 0.99330721 -13.03687370 
    21222 Axis -0.03980982 -0.82492871 0.56383314 
    21223 Axis point 128.62890621 0.00000000 226.21984207 
    21224 Rotation angle (degrees) 8.03295687 
    21225 Shift along axis 0.44127588 
    21226  
    21227 
    21228 > select add #40
    21229 
    21230 4375 atoms, 4481 bonds, 564 residues, 1 model selected 
    21231 
    21232 > fitmap #40 inMap #39
    21233 
    21234 Fit molecule hOAT1-TFV_OF.pdb (#40) to map hOAT1-TFV_OF.mrc (#39) using 4375
    21235 atoms 
    21236 average map value = 0.007219, steps = 60 
    21237 shifted from previous position = 2.24 
    21238 rotated from previous position = 0.00666 degrees 
    21239 atoms outside contour = 2889, contour level = 0.010308 
    21240  
    21241 Position of hOAT1-TFV_OF.pdb (#40) relative to hOAT1-TFV_OF.mrc (#39)
    21242 coordinates: 
    21243 Matrix rotation and translation 
    21244 0.99020164 -0.07840067 -0.11555975 25.97288245 
    21245 0.07903810 0.99687116 0.00093711 -9.32824593 
    21246 0.11512471 -0.01006155 0.99330009 -12.03377088 
    21247 Axis -0.03935047 -0.82533103 0.56327634 
    21248 Axis point 116.53468443 0.00000000 214.84157931 
    21249 Rotation angle (degrees) 8.03353574 
    21250 Shift along axis -0.10149276 
    21251  
    21252 
    21253 > show #!17 models
    21254 
    21255 > fitmap #39 inMap #19.3
    21256 
    21257 Fit map hOAT1-TFV_OF.mrc in map rOAT1-TVF_OF.mrc 2 using 37364 points 
    21258 correlation = 0.03002, correlation about mean = -0.02439, overlap = 0.01206 
    21259 steps = 936, shift = 1.08, angle = 13.4 degrees 
    21260  
    21261 Position of hOAT1-TFV_OF.mrc (#39) relative to rOAT1-TVF_OF.mrc 2 (#19.3)
    21262 coordinates: 
    21263 Matrix rotation and translation 
    21264 0.98280665 -0.13043667 -0.13068041 37.39205996 
    21265 0.11063752 0.98266445 -0.14876125 8.18112237 
    21266 0.14781892 0.13174539 0.98020035 -34.01816129 
    21267 Axis 0.60585490 -0.60151939 0.52068635 
    21268 Axis point 0.00000000 261.98069292 24.54762139 
    21269 Rotation angle (degrees) 13.38519605 
    21270 Shift along axis 0.02026683 
    21271  
    21272 
    21273 > fitmap #39 inMap #19.3
    21274 
    21275 Fit map hOAT1-TFV_OF.mrc in map rOAT1-TVF_OF.mrc 2 using 37364 points 
    21276 correlation = 0.03002, correlation about mean = -0.0244, overlap = 0.01206 
    21277 steps = 48, shift = 0.0138, angle = 0.161 degrees 
    21278  
    21279 Position of hOAT1-TFV_OF.mrc (#39) relative to rOAT1-TVF_OF.mrc 2 (#19.3)
    21280 coordinates: 
    21281 Matrix rotation and translation 
    21282 0.98301413 -0.12857767 -0.13096186 37.15798588 
    21283 0.10847145 0.98263409 -0.15054633 8.70610140 
    21284 0.14804449 0.13378355 0.97989019 -34.26954280 
    21285 Axis 0.61337235 -0.60188813 0.51137563 
    21286 Axis point -0.00000000 260.45263984 27.89398858 
    21287 Rotation angle (degrees) 13.40165031 
    21288 Shift along axis 0.02697294 
    21289  
    21290 
    21291 > fitmap #40 inMap #39
    21292 
    21293 Fit molecule hOAT1-TFV_OF.pdb (#40) to map hOAT1-TFV_OF.mrc (#39) using 4375
    21294 atoms 
    21295 average map value = 0.007219, steps = 132 
    21296 shifted from previous position = 0.778 
    21297 rotated from previous position = 13.4 degrees 
    21298 atoms outside contour = 2889, contour level = 0.010308 
    21299  
    21300 Position of hOAT1-TFV_OF.pdb (#40) relative to hOAT1-TFV_OF.mrc (#39)
    21301 coordinates: 
    21302 Matrix rotation and translation 
    21303 0.99020454 -0.07852899 -0.11544767 25.97319443 
    21304 0.07917768 0.99685998 0.00103677 -9.35919916 
    21305 0.11500374 -0.01016749 0.99331302 -12.00484753 
    21306 Axis -0.04009077 -0.82459474 0.56430155 
    21307 Axis point 116.41047661 0.00000000 215.06686153 
    21308 Rotation angle (degrees) 8.03257950 
    21309 Shift along axis -0.09809308 
    21310  
    21311 
    21312 > hide #!17 models
    21313 
    21314 > hide #!39 models
    21315 
    21316 > close #40
    21317 
    21318 > open /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF-
    21319 > coot-1.pdb
    21320 
    21321 Chain information for hOAT1-TFV_OF-coot-1.pdb #40 
    21322 --- 
    21323 Chain | Description 
    21324 A | No description available 
    21325  
    21326 
    21327 > show #!39 models
    21328 
    21329 > color #39 white models
    21330 
    21331 > color #40 white
    21332 
    21333 > hide #!39 models
    21334 
    21335 > select up
    21336 
    21337 2 atoms, 1 bond, 1 residue, 1 model selected 
    21338 
    21339 > color sel red
    21340 
    21341 > select up
    21342 
    21343 31 atoms, 32 bonds, 1 residue, 1 model selected 
    21344 
    21345 > color sel red
    21346 
    21347 > show #!39 models
    21348 
    21349 > color zone #39 near #40 distance 4.98
    21350 
    21351 > color zone #39 near #40 distance 2
    21352 
    21353 [Repeated 1 time(s)]
    21354 
    21355 > volume #39 level 0.01241
    21356 
    21357 > open /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF-
    21358 > coot-2.pdb
    21359 
    21360 Chain information for hOAT1-TFV_OF-coot-2.pdb #41 
    21361 --- 
    21362 Chain | Description 
    21363 A | No description available 
    21364  
    21365 
    21366 > hide #!40 models
    21367 
    21368 > color #41 white
    21369 
    21370 > color zone #39 near #41 distance 2
    21371 
    21372 > select up
    21373 
    21374 2 atoms, 1 bond, 1 residue, 1 model selected 
    21375 
    21376 > select up
    21377 
    21378 31 atoms, 32 bonds, 1 residue, 1 model selected 
    21379 
    21380 > color sel red
    21381 
    21382 > color zone #39 near #41 distance 2
    21383 
    21384 > volume #39 level 0.01056
    21385 
    21386 > color zone #39 near #41 distance 2.1
    21387 
    21388 > color zone #39 near #41 distance 2.2
    21389 
    21390 > color zone #39 near #41 distance 2.3
    21391 
    21392 > color zone #39 near #41 distance 2.4
    21393 
    21394 > color zone #39 near #41 distance 2.5
    21395 
    21396 > color zone #39 near #41 distance 2.6
    21397 
    21398 > color zone #39 near #41 distance 2.7
    21399 
    21400 > color zone #39 near #41 distance 2.8
    21401 
    21402 > color zone #39 near #41 distance 2.9
    21403 
    21404 > color zone #39 near #41 distance 3
    21405 
    21406 > color zone #39 near #41 distance 2.9
    21407 
    21408 > color zone #39 near #41 distance 2.8
    21409 
    21410 > color zone #39 near #41 distance 2.7
    21411 
    21412 > color zone #39 near #41 distance 2.6
    21413 
    21414 > color zone #39 near #41 distance 2.5
    21415 
    21416 > color zone #39 near #41 distance 2.4
    21417 
    21418 > color zone #39 near #41 distance 2.3
    21419 
    21420 > color zone #39 near #41 distance 2.2
    21421 
    21422 > color zone #39 near #41 distance 2.1
    21423 
    21424 > color zone #39 near #41 distance 2
    21425 
    21426 > color zone #39 near #41 distance 1.9
    21427 
    21428 > color zone #39 near #41 distance 2
    21429 
    21430 > color zone #39 near #41 distance 2.1
    21431 
    21432 > color zone #39 near #41 distance 2.2
    21433 
    21434 > color zone #39 near #41 distance 2.3
    21435 
    21436 > color zone #39 near #41 distance 2.4
    21437 
    21438 > color zone #39 near #41 distance 2.5
    21439 
    21440 > volume splitbyzone #39
    21441 
    21442 Opened hOAT1-TFV_OF.mrc 0 as #42.1, grid size 320,320,320, pixel 0.83, shown
    21443 at level 0.0106, step 1, values float32 
    21444 Opened hOAT1-TFV_OF.mrc 1 as #42.2, grid size 320,320,320, pixel 0.83, shown
    21445 at level 0.0106, step 1, values float32 
    21446 Opened hOAT1-TFV_OF.mrc 2 as #42.3, grid size 320,320,320, pixel 0.83, shown
    21447 at level 0.0106, step 1, values float32 
    21448 
    21449 > close #42.1-2
    21450 
    21451 > color #42.3 white models
    21452 
    21453 > color #42.3 #ffffb2ff models
    21454 
    21455 > color #42.3 #ffffb296 models
    21456 
    21457 > volume #42.3 level 0.006989
    21458 
    21459 > select add #41
    21460 
    21461 4375 atoms, 4481 bonds, 1 pseudobond, 564 residues, 2 models selected 
    21462 
    21463 > color #41 #aaffffff
    21464 
    21465 > color #41 blue
    21466 
    21467 > color #41 red
    21468 
    21469 > color #41 #aa00ffff
    21470 
    21471 > color #41 #0055ffff
    21472 
    21473 > color #41 #55557fff
    21474 
    21475 > color #41 #ff557fff
    21476 
    21477 > color #41 #ffaaffff
    21478 
    21479 > color (#!41 & sel) byhetero
    21480 
    21481 > save
    21482 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    21483 > includeMaps true
    21484 
    21485 > show #!34 models
    21486 
    21487 > hide #!41 models
    21488 
    21489 > hide #!42 models
    21490 
    21491 > hide #!42.3 models
    21492 
    21493 > select subtract #41
    21494 
    21495 Nothing selected 
    21496 
    21497 > hide #!34 models
    21498 
    21499 > show #1 models
    21500 
    21501 > show #!3.3 models
    21502 
    21503 > hide #!3.3 models
    21504 
    21505 > hide #!3 models
    21506 
    21507 > hide #1 models
    21508 
    21509 > show #!22.3 models
    21510 
    21511 > show #21 models
    21512 
    21513 > select add #21/A:601@O25
    21514 
    21515 1 atom, 1 bond, 1 residue, 1 model selected 
    21516 
    21517 > select up
    21518 
    21519 3 atoms, 1 bond, 2 residues, 1 model selected 
    21520 
    21521 > view sel
    21522 
    21523 > volume #22.3 level 0.01409
    21524 
    21525 > hide #!22.3 models
    21526 
    21527 > hide #!22 models
    21528 
    21529 > hide #21 models
    21530 
    21531 > show #!22.3 models
    21532 
    21533 > hide #!22.3 models
    21534 
    21535 > hide #!22 models
    21536 
    21537 > show #!23 models
    21538 
    21539 > hide #!23 models
    21540 
    21541 > show #!25.3 models
    21542 
    21543 > show #!24 models
    21544 
    21545 > hide #!25.3 models
    21546 
    21547 > hide #!25 models
    21548 
    21549 > hide #!24 models
    21550 
    21551 > show #1 models
    21552 
    21553 > show #!3.3 models
    21554 
    21555 > hide #!3.3 models
    21556 
    21557 > hide #!3 models
    21558 
    21559 > hide #1 models
    21560 
    21561 > show #!5 models
    21562 
    21563 > show #!6.3 models
    21564 
    21565 > hide #!6.3 models
    21566 
    21567 > hide #!6 models
    21568 
    21569 > hide #!5 models
    21570 
    21571 > show #8 models
    21572 
    21573 > show #!9.3 models
    21574 
    21575 > volume #9.3 level 0.003826
    21576 
    21577 > select #8/A:230
    21578 
    21579 12 atoms, 12 bonds, 1 residue, 1 model selected 
    21580 
    21581 > show sel atoms
    21582 
    21583 > select #8/A:227
    21584 
    21585 4 atoms, 3 bonds, 1 residue, 1 model selected 
    21586 
    21587 > show sel atoms
    21588 
    21589 > select clear
    21590 
    21591 > hide #!9.3 models
    21592 
    21593 > hide #!9 models
    21594 
    21595 > hide #8 models
    21596 
    21597 > show #!12 models
    21598 
    21599 > show #!11.3 models
    21600 
    21601 > color #11.3 #ffffb296 models
    21602 
    21603 > hide #!12 models
    21604 
    21605 > hide #!11.3 models
    21606 
    21607 > hide #!11 models
    21608 
    21609 > show #15 models
    21610 
    21611 > show #!16.3 models
    21612 
    21613 > hide #!16.3 models
    21614 
    21615 > hide #!16 models
    21616 
    21617 > hide #15 models
    21618 
    21619 > show #!18 models
    21620 
    21621 > show #!19.3 models
    21622 
    21623 > hide #!18 models
    21624 
    21625 > hide #!19 models
    21626 
    21627 > hide #!19.3 models
    21628 
    21629 > show #37 models
    21630 
    21631 > show #!38.3 models
    21632 
    21633 > hide #!38.3 models
    21634 
    21635 > hide #!38 models
    21636 
    21637 > hide #37 models
    21638 
    21639 > close #40
    21640 
    21641 > show #!41 models
    21642 
    21643 > show #!42.3 models
    21644 
    21645 > hide #!42.3 models
    21646 
    21647 > hide #!42 models
    21648 
    21649 > hide #!41 models
    21650 
    21651 > show #!26 models
    21652 
    21653 > show #!28.3 models
    21654 
    21655 > select #26/A:230
    21656 
    21657 12 atoms, 12 bonds, 1 residue, 1 model selected 
    21658 
    21659 > show sel atoms
    21660 
    21661 > select #26/A:200
    21662 
    21663 5 atoms, 4 bonds, 1 residue, 1 model selected 
    21664 
    21665 > show sel atoms
    21666 
    21667 > select add #26
    21668 
    21669 3865 atoms, 3947 bonds, 1 pseudobond, 506 residues, 2 models selected 
    21670 
    21671 > color (#!26 & sel) byhetero
    21672 
    21673 > select clear
    21674 
    21675 > select #26/A:223
    21676 
    21677 4 atoms, 3 bonds, 1 residue, 1 model selected 
    21678 
    21679 > show sel atoms
    21680 
    21681 > select #26/A:227
    21682 
    21683 4 atoms, 3 bonds, 1 residue, 1 model selected 
    21684 
    21685 > show sel atoms
    21686 
    21687 > select #26/A:223
    21688 
    21689 4 atoms, 3 bonds, 1 residue, 1 model selected 
    21690 
    21691 > show sel atoms
    21692 
    21693 > select #26/A:200
    21694 
    21695 5 atoms, 4 bonds, 1 residue, 1 model selected 
    21696 
    21697 > show sel atoms
    21698 
    21699 > select #26/A:226
    21700 
    21701 8 atoms, 7 bonds, 1 residue, 1 model selected 
    21702 
    21703 > show sel atoms
    21704 
    21705 > select #26/A:204
    21706 
    21707 8 atoms, 7 bonds, 1 residue, 1 model selected 
    21708 
    21709 > show sel atoms
    21710 
    21711 > select clear
    21712 
    21713 > hide #!28.3 models
    21714 
    21715 > hide #!28 models
    21716 
    21717 > hide #!26 models
    21718 
    21719 > show #!31.3 models
    21720 
    21721 > show #30 models
    21722 
    21723 > select add #30
    21724 
    21725 4327 atoms, 4393 bonds, 591 residues, 1 model selected 
    21726 
    21727 > color sel byhetero
    21728 
    21729 > select clear
    21730 
    21731 > save
    21732 > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
    21733 > includeMaps true
    21734 
    21735 ——— End of log from Mon Feb 10 17:46:10 2025 ———
    21736 
    21737 opened ChimeraX session 
    21738 
    21739 > hide #!31.3 models
    21740 
    21741 > hide #!31 models
    21742 
    21743 > hide #30 models
    21744 
    21745 > show #!34 models
    21746 
    21747 > show #!35 models
    21748 
    21749 > show #!35.3 models
    21750 
    21751 > volume #35.3 level 0.01175
    21752 
    21753 > select #35.3
    21754 
    21755 2 models selected 
    21756 
    21757 > view sel
    21758 
    21759 > color #34 tan
    21760 
    21761 > ui tool show "Side View"
    21762 
    21763 > select add #34
    21764 
    21765 3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 4 models selected 
    21766 
    21767 > color (#!34 & sel) byhetero
    21768 
    21769 > select clear
    21770 
    21771 > select #34/A:447
    21772 
    21773 9 atoms, 8 bonds, 1 residue, 1 model selected 
    21774 
    21775 > show sel atoms
    21776 
    21777 > select #34/A:507
    21778 
    21779 7 atoms, 6 bonds, 1 residue, 1 model selected 
    21780 
    21781 > show sel atoms
    21782 
    21783 > select clear
    21784 
    21785 > save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
    21786 
    21787 ——— End of log from Tue Mar 11 12:00:09 2025 ———
    21788 
    21789 opened ChimeraX session 
    21790 
    21791 > hide #!35.3 models
    21792 
    21793 > hide #!35 models
    21794 
    21795 > show #!17 models
    21796 
    21797 > color #17 #ffffb2ff models
    21798 
    21799 > color #17 #ffffb280 models
    21800 
    21801 > ui tool show "Side View"
    21802 
    21803 > color #17 #ffffb24d models
    21804 
    21805 > save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
    21806 
    21807 ——— End of log from Thu Apr 10 14:06:06 2025 ———
    21808 
    21809 opened ChimeraX session 
    21810 
    21811 > movie record
    21812 
    21813 > turn y 2 180
    21814 
    21815 > wait 180
    21816 
    21817 > movie encode /Users/dout2/Desktop/movie1.mp4
    21818 
    21819 Movie saved to /Users/dout2/Desktop/movie1.mp4 
    21820  
    21821 
    21822 > select add #34
    21823 
    21824 3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 2 models selected 
    21825 
    21826 > show sel atoms
    21827 
    21828 > select clear
    21829 
    21830 > hide #!34 models
    21831 
    21832 > hide #!17 models
    21833 
    21834 > show #!6 models
    21835 
    21836 > show #1 models
    21837 
    21838 > view
    21839 
    21840 > select #1/A:463
    21841 
    21842 7 atoms, 6 bonds, 1 residue, 1 model selected 
    21843 
    21844 > select #1/A:466
    21845 
    21846 11 atoms, 10 bonds, 1 residue, 1 model selected 
    21847 
    21848 > select #1/A:228
    21849 
    21850 12 atoms, 12 bonds, 1 residue, 1 model selected 
    21851 
    21852 > select #1/A:230
    21853 
    21854 12 atoms, 12 bonds, 1 residue, 1 model selected 
    21855 
    21856 > select #1/A:231
    21857 
    21858 6 atoms, 5 bonds, 1 residue, 1 model selected 
    21859 
    21860 > select #1/A:377
    21861 
    21862 7 atoms, 6 bonds, 1 residue, 1 model selected 
    21863 
    21864 > select #1/A:378
    21865 
    21866 8 atoms, 7 bonds, 1 residue, 1 model selected 
    21867 
    21868 > select #1/A:381
    21869 
    21870 5 atoms, 4 bonds, 1 residue, 1 model selected 
    21871 
    21872 > select #1/A:225
    21873 
    21874 8 atoms, 7 bonds, 1 residue, 1 model selected 
    21875 
    21876 > select #1/A:382
    21877 
    21878 9 atoms, 8 bonds, 1 residue, 1 model selected 
    21879 
    21880 > show sel atoms
    21881 
    21882 > hide #!6 models
    21883 
    21884 > show #!6 models
    21885 
    21886 > hide #1 models
    21887 
    21888 > show #1 models
    21889 
    21890 > select add #1
    21891 
    21892 3905 atoms, 3986 bonds, 515 residues, 1 model selected 
    21893 
    21894 > select subtract #1
    21895 
    21896 Nothing selected 
    21897 
    21898 > hide #1 models
    21899 
    21900 > hide #!6 models
    21901 
    21902 > show #!18 models
    21903 
    21904 > hide #!18 models
    21905 
    21906 > show #1 models
    21907 
    21908 > select #1/A:228
    21909 
    21910 12 atoms, 12 bonds, 1 residue, 1 model selected 
    21911 
    21912 > select #1/A:199
    21913 
    21914 8 atoms, 7 bonds, 1 residue, 1 model selected 
    21915 
    21916 > select #1/A:257
    21917 
    21918 7 atoms, 7 bonds, 1 residue, 1 model selected 
    21919 
    21920 > select #1/A:145
    21921 
    21922 7 atoms, 6 bonds, 1 residue, 1 model selected 
    21923 
    21924 > select #1/A:466
    21925 
    21926 11 atoms, 10 bonds, 1 residue, 1 model selected 
    21927 
    21928 > show sel atoms
    21929 
    21930 > select #1/A:149
    21931 
    21932 5 atoms, 4 bonds, 1 residue, 1 model selected 
    21933 
    21934 > select #1/A:146
    21935 
    21936 8 atoms, 7 bonds, 1 residue, 1 model selected 
    21937 
    21938 > select #1/A:204
    21939 
    21940 8 atoms, 7 bonds, 1 residue, 1 model selected 
    21941 
    21942 > select #1/A:150
    21943 
    21944 8 atoms, 7 bonds, 1 residue, 1 model selected 
    21945 
    21946 > select #1/A:149
    21947 
    21948 5 atoms, 4 bonds, 1 residue, 1 model selected 
    21949 
    21950 > select #1/A:203
    21951 
    21952 5 atoms, 4 bonds, 1 residue, 1 model selected 
    21953 
    21954 > select #1/A:146
    21955 
    21956 8 atoms, 7 bonds, 1 residue, 1 model selected 
    21957 
    21958 > select #1/A:149
    21959 
    21960 5 atoms, 4 bonds, 1 residue, 1 model selected 
    21961 Drag select of 13 residues 
    21962 
    21963 > select #1/A:463
    21964 
    21965 7 atoms, 6 bonds, 1 residue, 1 model selected 
    21966 
    21967 > show sel atoms
    21968 
    21969 > select #1/A:466@CZ
    21970 
    21971 1 atom, 1 residue, 1 model selected 
    21972 
    21973 > select up
    21974 
    21975 11 atoms, 10 bonds, 1 residue, 1 model selected 
    21976 
    21977 > ui tool show Contacts
    21978 
    21979 > contacts sel intraRes true ignoreHiddenModels true select true
    21980 > makePseudobonds false reveal true
    21981 
    21982 26 contacts 
    21983 
    21984 > select clear
    21985 
    21986 > select : 382
    21987 
    21988 126 atoms, 112 bonds, 14 residues, 14 models selected 
    21989 
    21990 > select : 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    21991 
    21992 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    21993 
    21994 > show sel & #1 atoms
    21995 
    21996 > hide #!6 target m
    21997 
    21998 [Repeated 1 time(s)]
    21999 
    22000 > hide #!4 target m
    22001 
    22002 > select add #1
    22003 
    22004 5716 atoms, 5702 bonds, 714 residues, 14 models selected 
    22005 
    22006 > select subtract #1
    22007 
    22008 1811 atoms, 1716 bonds, 199 residues, 13 models selected 
    22009 
    22010 > select add #5
    22011 
    22012 5446 atoms, 5448 bonds, 5 pseudobonds, 670 residues, 14 models selected 
    22013 
    22014 > select subtract #5
    22015 
    22016 1672 atoms, 1584 bonds, 184 residues, 12 models selected 
    22017 
    22018 > select add #8
    22019 
    22020 5445 atoms, 5437 bonds, 691 residues, 12 models selected 
    22021 
    22022 > select subtract #8
    22023 
    22024 1533 atoms, 1452 bonds, 169 residues, 11 models selected 
    22025 
    22026 > select add #12
    22027 
    22028 5186 atoms, 5201 bonds, 5 pseudobonds, 640 residues, 12 models selected 
    22029 
    22030 > select subtract #12
    22031 
    22032 1394 atoms, 1320 bonds, 154 residues, 10 models selected 
    22033 
    22034 > hide #1 models
    22035 
    22036 > show #1 models
    22037 
    22038 > select add #15
    22039 
    22040 5172 atoms, 5186 bonds, 654 residues, 10 models selected 
    22041 
    22042 > select subtract #15
    22043 
    22044 1255 atoms, 1188 bonds, 139 residues, 9 models selected 
    22045 
    22046 > select add #18
    22047 
    22048 4902 atoms, 4932 bonds, 5 pseudobonds, 610 residues, 10 models selected 
    22049 
    22050 > select subtract #18
    22051 
    22052 1116 atoms, 1056 bonds, 124 residues, 8 models selected 
    22053 
    22054 > select add #21
    22055 
    22056 4933 atoms, 4966 bonds, 625 residues, 8 models selected 
    22057 
    22058 > select subtract #21
    22059 
    22060 977 atoms, 924 bonds, 109 residues, 7 models selected 
    22061 
    22062 > select add #24
    22063 
    22064 4628 atoms, 4674 bonds, 5 pseudobonds, 580 residues, 8 models selected 
    22065 
    22066 > select subtract #24
    22067 
    22068 838 atoms, 792 bonds, 94 residues, 6 models selected 
    22069 
    22070 > select add #26
    22071 
    22072 4564 atoms, 4607 bonds, 1 pseudobond, 585 residues, 7 models selected 
    22073 
    22074 > select subtract #26
    22075 
    22076 699 atoms, 660 bonds, 79 residues, 5 models selected 
    22077 
    22078 > select add #30
    22079 
    22080 4885 atoms, 4921 bonds, 653 residues, 5 models selected 
    22081 
    22082 > select subtract #30
    22083 
    22084 558 atoms, 528 bonds, 62 residues, 4 models selected 
    22085 
    22086 > select add #33
    22087 
    22088 4744 atoms, 4789 bonds, 636 residues, 4 models selected 
    22089 
    22090 > select subtract #33
    22091 
    22092 417 atoms, 396 bonds, 45 residues, 3 models selected 
    22093 
    22094 > select add #34
    22095 
    22096 4065 atoms, 4140 bonds, 5 pseudobonds, 517 residues, 4 models selected 
    22097 
    22098 > select subtract #34
    22099 
    22100 278 atoms, 264 bonds, 30 residues, 2 models selected 
    22101 
    22102 > select add #37
    22103 
    22104 4514 atoms, 4613 bonds, 579 residues, 2 models selected 
    22105 
    22106 > select subtract #37
    22107 
    22108 139 atoms, 132 bonds, 15 residues, 1 model selected 
    22109 
    22110 > select add #41
    22111 
    22112 4375 atoms, 4481 bonds, 1 pseudobond, 564 residues, 2 models selected 
    22113 
    22114 > select subtract #41
    22115 
    22116 Nothing selected 
    22117 
    22118 > show #!2 models
    22119 
    22120 > hide #!2 models
    22121 
    22122 > show #!3 models
    22123 
    22124 > show #!3.3 models
    22125 
    22126 > ui tool show "Side View"
    22127 
    22128 > select #1/A:35@CG
    22129 
    22130 1 atom, 1 residue, 1 model selected 
    22131 
    22132 > select : 35
    22133 
    22134 112 atoms, 98 bonds, 14 residues, 14 models selected 
    22135 
    22136 > hide sel & #1 atoms
    22137 
    22138 > select up
    22139 
    22140 2 atoms, 1 bond, 1 residue, 1 model selected 
    22141 
    22142 > select up
    22143 
    22144 8 atoms, 7 bonds, 1 residue, 1 model selected 
    22145 
    22146 > hide sel atoms
    22147 
    22148 > select clear
    22149 
    22150 > select : 35
    22151 
    22152 112 atoms, 98 bonds, 14 residues, 14 models selected 
    22153 
    22154 > show sel & #1 atoms
    22155 
    22156 > select clear
    22157 
    22158 > select : 35
    22159 
    22160 112 atoms, 98 bonds, 14 residues, 14 models selected 
    22161 
    22162 > hide sel & #1 atoms
    22163 
    22164 > save /Users/dout2/Desktop/image1.png supersample 3
    22165 
    22166 > save /Users/dout2/Desktop/rOAT1-AZT_OF_LigandDensity.png supersample 3
    22167 
    22168 > select add #1
    22169 
    22170 4009 atoms, 4077 bonds, 528 residues, 14 models selected 
    22171 
    22172 > select subtract #1
    22173 
    22174 104 atoms, 91 bonds, 13 residues, 13 models selected 
    22175 
    22176 > select add #5
    22177 
    22178 3870 atoms, 3948 bonds, 5 pseudobonds, 498 residues, 14 models selected 
    22179 
    22180 > select subtract #5
    22181 
    22182 96 atoms, 84 bonds, 12 residues, 12 models selected 
    22183 
    22184 > select add #8
    22185 
    22186 4000 atoms, 4062 bonds, 533 residues, 12 models selected 
    22187 
    22188 > select subtract #8
    22189 
    22190 88 atoms, 77 bonds, 11 residues, 11 models selected 
    22191 
    22192 > select add #12
    22193 
    22194 3872 atoms, 3951 bonds, 5 pseudobonds, 496 residues, 12 models selected 
    22195 
    22196 > select subtract #12
    22197 
    22198 80 atoms, 70 bonds, 10 residues, 10 models selected 
    22199 
    22200 > select add #21
    22201 
    22202 4028 atoms, 4105 bonds, 525 residues, 10 models selected 
    22203 
    22204 > select subtract #21
    22205 
    22206 72 atoms, 63 bonds, 9 residues, 9 models selected 
    22207 
    22208 > select add #18
    22209 
    22210 3850 atoms, 3932 bonds, 5 pseudobonds, 494 residues, 10 models selected 
    22211 
    22212 > select subtract #18
    22213 
    22214 64 atoms, 56 bonds, 8 residues, 8 models selected 
    22215 
    22216 > select add #24
    22217 
    22218 3846 atoms, 3931 bonds, 5 pseudobonds, 493 residues, 9 models selected 
    22219 
    22220 > select subtract #24
    22221 
    22222 56 atoms, 49 bonds, 7 residues, 7 models selected 
    22223 
    22224 > select add #26
    22225 
    22226 3913 atoms, 3989 bonds, 1 pseudobond, 512 residues, 8 models selected 
    22227 
    22228 > select subtract #26
    22229 
    22230 48 atoms, 42 bonds, 6 residues, 6 models selected 
    22231 
    22232 > select add #30
    22233 
    22234 4367 atoms, 4428 bonds, 596 residues, 6 models selected 
    22235 
    22236 > select subtract #30
    22237 
    22238 40 atoms, 35 bonds, 5 residues, 5 models selected 
    22239 
    22240 > select add #33
    22241 
    22242 4359 atoms, 4421 bonds, 595 residues, 5 models selected 
    22243 
    22244 > select subtract #33
    22245 
    22246 32 atoms, 28 bonds, 4 residues, 4 models selected 
    22247 
    22248 > select add #34
    22249 
    22250 3811 atoms, 3897 bonds, 5 pseudobonds, 490 residues, 5 models selected 
    22251 
    22252 > select subtract #34
    22253 
    22254 24 atoms, 21 bonds, 3 residues, 3 models selected 
    22255 
    22256 > select add #37
    22257 
    22258 4391 atoms, 4495 bonds, 566 residues, 3 models selected 
    22259 
    22260 > select subtract #37
    22261 
    22262 16 atoms, 14 bonds, 2 residues, 2 models selected 
    22263 
    22264 > select add #41
    22265 
    22266 4383 atoms, 4488 bonds, 1 pseudobond, 565 residues, 3 models selected 
    22267 
    22268 > select subtract #41
    22269 
    22270 8 atoms, 7 bonds, 1 residue, 1 model selected 
    22271 
    22272 > hide #!3.3 models
    22273 
    22274 > hide #!3 models
    22275 
    22276 > hide #1 models
    22277 
    22278 > show #!5 models
    22279 
    22280 > show #!6.3 models
    22281 
    22282 > hide #!6.3 models
    22283 
    22284 > hide #!6 models
    22285 
    22286 > hide #!5 models
    22287 
    22288 > show #8 models
    22289 
    22290 > show #!9 models
    22291 
    22292 > show #!9.3 models
    22293 
    22294 > select : 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    22295 
    22296 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    22297 
    22298 > show sel & #8 atoms
    22299 
    22300 > select: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    22301 
    22302 Unknown command: select:
    22303 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234 
    22304 
    22305 > select : 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    22306 
    22307 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    22308 
    22309 > show sel & #8 atoms
    22310 
    22311 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    22312 
    22313 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    22314 
    22315 > show sel & #8 atoms
    22316 
    22317 > select clear
    22318 
    22319 > volume #9.3 level 0.00516
    22320 
    22321 > save /Users/dout2/Desktop/rOAT1-PBD_IF_LigandDensity.png supersample 3
    22322 
    22323 > hide #!9.3 models
    22324 
    22325 > hide #!9 models
    22326 
    22327 > hide #8 models
    22328 
    22329 > show #15 models
    22330 
    22331 > show #!16 models
    22332 
    22333 > show #!16.3 models
    22334 
    22335 > select #15/A:442
    22336 
    22337 11 atoms, 11 bonds, 1 residue, 1 model selected 
    22338 
    22339 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    22340 
    22341 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    22342 
    22343 > show sel & #15 atoms
    22344 
    22345 > select #1-50: 438
    22346 
    22347 154 atoms, 154 bonds, 14 residues, 14 models selected 
    22348 
    22349 > select clear
    22350 
    22351 > save /Users/dout2/Desktop/rOAT1-TFV_IF_LigandDensity.png supersample 3
    22352 
    22353 > hide #!16.3 models
    22354 
    22355 > hide #!16 models
    22356 
    22357 > hide #15 models
    22358 
    22359 > show #21 models
    22360 
    22361 > show #!22 models
    22362 
    22363 > show #!22.3 models
    22364 
    22365 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    22366 
    22367 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    22368 
    22369 > show sel & #21 atoms
    22370 
    22371 > select clear
    22372 
    22373 > save /Users/dout2/Desktop/rOAT1-AAI_IF_LigandDensity.png supersample 3
    22374 
    22375 > volume #22.3 level 0.0128
    22376 
    22377 > hide #!22.3 models
    22378 
    22379 > hide #!22 models
    22380 
    22381 > hide #21 models
    22382 
    22383 > show #!27 models
    22384 
    22385 > show #!28 models
    22386 
    22387 > hide #!27 models
    22388 
    22389 > show #!26 models
    22390 
    22391 > show #!28.3 models
    22392 
    22393 > volume #28.3 level 0.06828
    22394 
    22395 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    22396 
    22397 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    22398 
    22399 > show sel & #!26 atoms
    22400 
    22401 > select clear
    22402 
    22403 > save /Users/dout2/Desktop/rOAT1-PAH_IF_LigandDensity.png supersample 3
    22404 
    22405 > hide #!28.3 models
    22406 
    22407 > hide #!28 models
    22408 
    22409 > hide #!26 models
    22410 
    22411 > show #30 models
    22412 
    22413 > show #!31 models
    22414 
    22415 > show #!31.3 models
    22416 
    22417 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    22418 
    22419 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    22420 
    22421 > show sel & #30 atoms
    22422 
    22423 > select clear
    22424 
    22425 > save /Users/dout2/Desktop/rOAT1-FBP_IF_LigandDensity.png supersample 3
    22426 
    22427 > hide #!31.3 models
    22428 
    22429 > hide #!31 models
    22430 
    22431 > hide #30 models
    22432 
    22433 > show #37 models
    22434 
    22435 > show #!38 models
    22436 
    22437 > show #!38.3 models
    22438 
    22439 > select clear
    22440 
    22441 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    22442 
    22443 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    22444 
    22445 > show sel & #37 atoms
    22446 
    22447 > select clear
    22448 
    22449 > show #!36 models
    22450 
    22451 > hide #!36 models
    22452 
    22453 > show #!36 models
    22454 
    22455 > hide #!36 models
    22456 
    22457 > volume #38.3 level 0.006101
    22458 
    22459 > volume #38.3 level 0.006864
    22460 
    22461 > save /Users/dout2/Desktop/hOAT1-TFV_IF_LigandDensity.png supersample 3
    22462 
    22463 > hide #!38.3 models
    22464 
    22465 > hide #!38 models
    22466 
    22467 > hide #37 models
    22468 
    22469 > show #!2 models
    22470 
    22471 > hide #!2 models
    22472 
    22473 > show #1 models
    22474 
    22475 > show #!3 models
    22476 
    22477 > show #!3.3 models
    22478 
    22479 > hide #!3.3 models
    22480 
    22481 > hide #!3 models
    22482 
    22483 > hide #1 models
    22484 
    22485 > show #!5 models
    22486 
    22487 > show #!6.3 models
    22488 
    22489 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    22490 
    22491 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    22492 
    22493 > show sel & #!5 atoms
    22494 
    22495 > select clear
    22496 
    22497 > select up
    22498 
    22499 2 atoms, 1 bond, 1 residue, 1 model selected 
    22500 
    22501 > select up
    22502 
    22503 8 atoms, 7 bonds, 1 residue, 1 model selected 
    22504 
    22505 > hide sel atoms
    22506 
    22507 > select clear
    22508 
    22509 [Repeated 1 time(s)]
    22510 
    22511 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    22512 
    22513 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    22514 
    22515 > show sel & #!5 atoms
    22516 
    22517 > select clear
    22518 
    22519 > select up
    22520 
    22521 2 atoms, 1 bond, 1 residue, 1 model selected 
    22522 
    22523 > hide sel atoms
    22524 
    22525 > select up
    22526 
    22527 8 atoms, 7 bonds, 1 residue, 1 model selected 
    22528 
    22529 > hide sel atoms
    22530 
    22531 > select clear
    22532 
    22533 > volume #6.3 level 0.0106
    22534 
    22535 > save /Users/dout2/Desktop/rOAT1-AZT_OF_LigandDensity.png supersample 3
    22536 
    22537 > hide #!5 models
    22538 
    22539 > hide #!6 models
    22540 
    22541 > hide #!6.3 models
    22542 
    22543 > show #!11 models
    22544 
    22545 > show #!12 models
    22546 
    22547 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    22548 
    22549 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    22550 
    22551 > show sel & #!12 atoms
    22552 
    22553 > select clear
    22554 
    22555 > show #!11.3 models
    22556 
    22557 > select clear
    22558 
    22559 > volume #11.3 level 0.009777
    22560 
    22561 > select clear
    22562 
    22563 > show #!10 models
    22564 
    22565 > hide #!10 models
    22566 
    22567 > select clear
    22568 
    22569 > volume #11.3 level 0.01081
    22570 
    22571 > select clear
    22572 
    22573 > show #!10 models
    22574 
    22575 > hide #!10 models
    22576 
    22577 > save /Users/dout2/Desktop/rOAT1-PBD_OF_LigandDensity.png supersample 3
    22578 
    22579 > hide #!12 models
    22580 
    22581 > hide #!11 models
    22582 
    22583 > show #!18 models
    22584 
    22585 > show #!19 models
    22586 
    22587 > show #!19.3 models
    22588 
    22589 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    22590 
    22591 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    22592 
    22593 > show sel & #!18 atoms
    22594 
    22595 > select clear
    22596 
    22597 > save /Users/dout2/Desktop/rOAT1-TFV_OF_LigandDensity.png supersample 3
    22598 
    22599 > hide #!19 models
    22600 
    22601 > hide #!18 models
    22602 
    22603 > show #!24 models
    22604 
    22605 > show #!25 models
    22606 
    22607 > show #!25.3 models
    22608 
    22609 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    22610 
    22611 1950 atoms, 1848 bonds, 214 residues, 14 models selected 
    22612 
    22613 > show sel & #!24 atoms
    22614 
    22615 > select clear
    22616 
    22617 > save /Users/dout2/Desktop/rOAT1-AAI_OF_LigandDensity.png supersample 3
    22618 
    22619 > hide #!25 models
    22620 
    22621 > hide #!24 models
    22622 
    22623 > show #!35 models
    22624 
    22625 > show #!34 models
    22626 
    22627 > show #!35.3 models
    22628 
    22629 > hide #!35.3 models
    22630 
    22631 > hide #!35 models
    22632 
    22633 > hide #!34 models
    22634 
    22635 > show #!41 models
    22636 
    22637 > show #!42 models
    22638 
    22639 > show #!42.3 models
    22640 
    22641 > save /Users/dout2/Desktop/rOAT1-AAI_OF_LigandDensity.png supersample 3
    22642 
    22643 > hide #!41 models
    22644 
    22645 > hide #!42 models
    22646 
    22647 > hide #!42.3 models
    22648 
    22649 > show #!25 models
    22650 
    22651 > show #!24 models
    22652 
    22653 > save /Users/dout2/Desktop/rOAT1-AAI_OF_LigandDensity.png supersample 3
    22654 
    22655 > hide #!24 models
    22656 
    22657 > hide #!25 models
    22658 
    22659 > show #!42.3 models
    22660 
    22661 > show #!41 models
    22662 
    22663 > select clear
    22664 
    22665 [Repeated 1 time(s)]
    22666 
    22667 > ui tool show Distances
    22668 
    22669 > select clear
    22670 
    22671 No distances to delete! 
    22672 
    22673 > save /Users/dout2/Desktop/hOAT1-TFV_OF_LigandDensity.png supersample 3
    22674 
    22675 > view
    22676 
    22677 > view orient
    22678 
    22679 > open /Users/dout2/Downloads/20250226_rOAT1-AKG/r3d_j156_2.68A_outward-
    22680 > facing/postprocess.mrc
    22681 
    22682 Opened postprocess.mrc as #40, grid size 320,320,320, pixel 0.83, shown at
    22683 level 0.00432, step 2, values float32 
    22684 
    22685 > volume #40 step 1
    22686 
    22687 > volume #40 level 0.008916
    22688 
    22689 > hide #!41 models
    22690 
    22691 > hide #!40 models
    22692 
    22693 > select add #41
    22694 
    22695 4375 atoms, 4481 bonds, 1 pseudobond, 564 residues, 2 models selected 
    22696 
    22697 > select subtract #41
    22698 
    22699 Nothing selected 
    22700 
    22701 > hide #!42 models
    22702 
    22703 > show #!40 models
    22704 
    22705 > rename #40 rOAT1-AKG_OF.mrc
    22706 
    22707 > open /Users/dout2/Downloads/20250226_rOAT1-AKG/r3d_j156_2.68A_outward-
    22708 > facing/RealSpaceRefine_1/rOAT1-AKG_OF-coot-5_real_space_refined_001.pdb
    22709 
    22710 Chain information for rOAT1-AKG_OF-coot-5_real_space_refined_001.pdb #43 
    22711 --- 
    22712 Chain | Description 
    22713 A | No description available 
    22714  
    22715 
    22716 > select clear
    22717 
    22718 > open /Users/dout2/Downloads/20250226_rOAT1-AKG/r3d_j122_2.63A_outward-
    22719 > occluded/postprocess.mrc
    22720 
    22721 Opened postprocess.mrc as #44, grid size 320,320,320, pixel 0.83, shown at
    22722 level 0.00378, step 2, values float32 
    22723 
    22724 > rename #44 rOAT1-AKG_OOC.mrc
    22725 
    22726 > open /Users/dout2/Downloads/20250226_rOAT1-AKG/r3d_j122_2.63A_outward-
    22727 > occluded/RealSpaceRefine_3/rOAT1-AKG_OF-coot-4_real_space_refined_003.pdb
    22728 
    22729 Chain information for rOAT1-AKG_OF-coot-4_real_space_refined_003.pdb #45 
    22730 --- 
    22731 Chain | Description 
    22732 A | No description available 
    22733  
    22734 
    22735 > rename #45 rOAT1-AKG_OOC-coot-4_real_space_refined_003.pdb
    22736 
    22737 > hide #!43 models
    22738 
    22739 > hide #!40 models
    22740 
    22741 > volume #44 step 1
    22742 
    22743 > volume #44 level 0.01023
    22744 
    22745 > select ::name="AKG"
    22746 
    22747 20 atoms, 18 bonds, 2 residues, 2 models selected 
    22748 
    22749 > view sel
    22750 
    22751 > color #44 #ffffb24d models
    22752 
    22753 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    22754 
    22755 2228 atoms, 2112 bonds, 244 residues, 16 models selected 
    22756 
    22757 > show sel & #!45 atoms
    22758 
    22759 > select clear
    22760 
    22761 > save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
    22762 
    22763 > color #44 #ffffb280 models
    22764 
    22765 > color #44 #ffffb266 models
    22766 
    22767 > color #44 #ffffb24d models
    22768 
    22769 > select clear
    22770 
    22771 > save /Users/dout2/Desktop/hOAT1-AKG_OOC_LigandDensity.png supersample 3
    22772 
    22773 > movie record
    22774 
    22775 > turn y 2 180
    22776 
    22777 > wait 180
    22778 
    22779 > movie encode /Users/dout2/Desktop/movie2.mp4
    22780 
    22781 Movie saved to /Users/dout2/Desktop/movie2.mp4 
    22782  
    22783 
    22784 > movie record
    22785 
    22786 > turn y 2 180
    22787 
    22788 > wait 180
    22789 
    22790 > movie encode /Users/dout2/Desktop/movie3.mp4
    22791 
    22792 Movie saved to /Users/dout2/Desktop/movie3.mp4 
    22793  
    22794 
    22795 > hide #!45 models
    22796 
    22797 > hide #!44 models
    22798 
    22799 > show #!43 models
    22800 
    22801 > show #!40 models
    22802 
    22803 > color #40 #b2b2b24d models
    22804 
    22805 > select clear
    22806 
    22807 > color #40 #ffffb24d models
    22808 
    22809 > select clear
    22810 
    22811 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    22812 
    22813 2228 atoms, 2112 bonds, 244 residues, 16 models selected 
    22814 
    22815 > show sel & #!43 atoms
    22816 
    22817 > select clear
    22818 
    22819 [Repeated 1 time(s)]
    22820 
    22821 > volume #40 level 0.009283
    22822 
    22823 > save /Users/dout2/Desktop/rOAT1-AKG_OF_LigandDensity.png supersample 3
    22824 
    22825 > movie record
    22826 
    22827 > turn y 2 180
    22828 
    22829 > wait 180
    22830 
    22831 > movie encode /Users/dout2/Desktop/movie3.mp4
    22832 
    22833 Movie saved to /Users/dout2/Desktop/movie3.mp4 
    22834  
    22835 
    22836 > volume #40 level 0.01222
    22837 
    22838 > movie record
    22839 
    22840 > turn y 2 180
    22841 
    22842 > wait 180
    22843 
    22844 > movie encode /Users/dout2/Desktop/movie4.mp4
    22845 
    22846 Movie saved to /Users/dout2/Desktop/movie4.mp4 
    22847  
    22848 
    22849 > hide #!43 models
    22850 
    22851 > hide #!40 models
    22852 
    22853 > open /Users/dout2/Downloads/20250328_rOAT1-R466A/r3d_j052_2.71A_outward-
    22854 > occluded/postprocess_rescaled.mrc
    22855 
    22856 Opened postprocess_rescaled.mrc as #46, grid size 480,480,480, pixel 0.553,
    22857 shown at level 0.0038, step 2, values float32 
    22858 
    22859 > open /Users/dout2/Downloads/20250328_rOAT1-R466A/r3d_j052_2.71A_outward-
    22860 > occluded/RealSpaceRefine_1/rOAT1-R466A_OO-coot-2_real_space_refined_001.pdb
    22861 
    22862 Chain information for rOAT1-R466A_OO-coot-2_real_space_refined_001.pdb #47 
    22863 --- 
    22864 Chain | Description 
    22865 A | No description available 
    22866  
    22867 
    22868 > select #46
    22869 
    22870 4 models selected 
    22871 
    22872 > select clear
    22873 
    22874 > view
    22875 
    22876 > volume #46 step 1
    22877 
    22878 > volume #46 level 0.01147
    22879 
    22880 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    22881 
    22882 2367 atoms, 2244 bonds, 259 residues, 17 models selected 
    22883 
    22884 > view sel
    22885 
    22886 > color #46 #b2ffff4d models
    22887 
    22888 > select #46
    22889 
    22890 4 models selected 
    22891 
    22892 > show #!47 atoms
    22893 
    22894 > select clear
    22895 
    22896 > save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
    22897 
    22898 > close #47
    22899 
    22900 > open /Users/dout2/Downloads/20250328_rOAT1-R466A/r3d_j052_2.71A_outward-
    22901 > occluded/RealSpaceRefine_2/rOAT1-R466A_OO-coot-3_real_space_refined_002.pdb
    22902 
    22903 Chain information for rOAT1-R466A_OO-coot-3_real_space_refined_002.pdb #47 
    22904 --- 
    22905 Chain | Description 
    22906 A | No description available 
    22907  
    22908 
    22909 > select add #46
    22910 
    22911 4 models selected 
    22912 
    22913 > select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
    22914 
    22915 2361 atoms, 2238 bonds, 259 residues, 17 models selected 
    22916 
    22917 > show sel & #!47 atoms
    22918 
    22919 > select clear
    22920 
    22921 > select #46
    22922 
    22923 4 models selected 
    22924 
    22925 > select clear
    22926 
    22927 > save /Users/dout2/Desktop/rOAT1-R466A_OF_LigandDensity.png supersample 3
    22928 
    22929 > movie record
    22930 
    22931 > turn y 2 180
    22932 
    22933 > wait 180
    22934 
    22935 > movie encode /Users/dout2/Desktop/movie4.mp4
    22936 
    22937 Movie saved to /Users/dout2/Desktop/movie4.mp4 
    22938  
    22939 
    22940 > hide #!46 models
    22941 
    22942 > show #!46 models
    22943 
    22944 > save /Users/dout2/Desktop/rOAT1-R466A_OF_LigandDensity2.png supersample 3
    22945 
    22946 > movie record
    22947 
    22948 > turn y 2 180
    22949 
    22950 > wait 180
    22951 
    22952 > movie encode /Users/dout2/Desktop/movie4.mp4
    22953 
    22954 Movie saved to /Users/dout2/Desktop/movie4.mp4 
    22955  
    22956 
    22957 > view
    22958 
    22959 > color #46 #b2ffffff models
    22960 
    22961 > color #46 #b2ffffab models
    22962 
    22963 > color #46 #b2ffffff models
    22964 
    22965 > select clear
    22966 
    22967 [Repeated 1 time(s)]
    22968 
    22969 > save /Users/dout2/Desktop/rOAT1-R466A_OF.png supersample 3
    22970 
    22971 > save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
    22972 
    22973 ——— End of log from Thu Apr 10 15:43:35 2025 ———
    22974 
    22975 opened ChimeraX session 
    22976 
    22977 > hide #!47 models
    22978 
    22979 > hide #!46 models
    22980 
    22981 > rename #46 rOAT1-R466A.mrc
    22982 
    22983 > open
    22984 > /Users/dout2/Documents/Manuscripts/rOAT1_2023/cryoEM/rOAT1-apo_20220519_cryoSPARC/J12_2.05A_clip-240/cryosparc_P4_J16__localfilter_240.mrc
    22985 
    22986 Opened cryosparc_P4_J16__localfilter_240.mrc as #48, grid size 240,240,240,
    22987 pixel 0.553, shown at level 0.238, step 1, values float32 
    22988 
    22989 > open
    22990 > /Users/dout2/Documents/Manuscripts/rOAT1_2023/cryoEM/rOAT1-apo_20220519_cryoSPARC/model/rOAT1-apo-
    22991 > coot-4_real_space_refined_004.pdb
    22992 
    22993 Chain information for rOAT1-apo-coot-4_real_space_refined_004.pdb #49 
    22994 --- 
    22995 Chain | Description 
    22996 A | No description available 
    22997  
    22998 
    22999 The cached device pixel ratio value was stale on window expose. Please file a
    23000 QTBUG which explains how to reproduce. 
    23001 
    23002 > rename #48 rOAT1-Apo.mrc
    23003 
    23004 > hide #49 models
    23005 
    23006 > hide #!48 models
    23007 
    23008 > hide #48.1 models
    23009 
    23010 > show #49 models
    23011 
    23012 > save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
    23013 
    23014 > select #49: 382, 353,438,230,442,466
    23015 
    23016 66 atoms, 64 bonds, 6 residues, 1 model selected 
    23017 
    23018 > show sel atoms
    23019 
    23020 > size stickRadius 0.3
    23021 
    23022 Changed 72733 bond radii 
    23023 
    23024 > select add #49
    23025 
    23026 3942 atoms, 3966 bonds, 570 residues, 1 model selected 
    23027 
    23028 > hide sel cartoons
    23029 
    23030 > select clear
    23031 
    23032 Drag select of 10 atoms, 11 bonds 
    23033 Drag select of 6 atoms, 9 bonds 
    23034 Drag select of 8 atoms, 10 bonds 
    23035 Drag select of 4 atoms, 4 bonds 
    23036 
    23037 > select up
    23038 
    23039 36 atoms, 34 bonds, 4 residues, 1 model selected 
    23040 
    23041 > lighting flat
    23042 
    23043 > graphics silhouettes false
    23044 
    23045 > select clear
    23046 
    23047 > select #49: 382, 353,438,230,442,466
    23048 
    23049 66 atoms, 64 bonds, 6 residues, 1 model selected 
    23050 
    23051 > select clear
    23052 
    23053 > select #49: 382, 353,438,230,442,466
    23054 
    23055 66 atoms, 64 bonds, 6 residues, 1 model selected 
    23056 
    23057 > color sel orange
    23058 
    23059 > color sel purple
    23060 
    23061 > color sel hot pink
    23062 
    23063 > size stickRadius 0.5
    23064 
    23065 Changed 72733 bond radii 
    23066 
    23067 > size stickRadius 0.4
    23068 
    23069 Changed 72733 bond radii 
    23070 
    23071 > select clear
    23072 
    23073 > select add #49/A:466@CB
    23074 
    23075 1 atom, 1 residue, 1 model selected 
    23076 
    23077 > select add #49/A:382@NZ
    23078 
    23079 2 atoms, 2 residues, 1 model selected 
    23080 
    23081 > select up
    23082 
    23083 20 atoms, 18 bonds, 2 residues, 1 model selected 
    23084 
    23085 > select #49: 382, 353,438,230,442,466
    23086 
    23087 66 atoms, 64 bonds, 6 residues, 1 model selected 
    23088 
    23089 > color sel lime
    23090 
    23091 > color sel purple
    23092 
    23093 > select clear
    23094 
    23095 > select add #49/A:382@NZ
    23096 
    23097 1 atom, 1 residue, 1 model selected 
    23098 
    23099 > select up
    23100 
    23101 3 atoms, 1 bond, 2 residues, 1 model selected 
    23102 
    23103 > select up
    23104 
    23105 20 atoms, 18 bonds, 2 residues, 1 model selected 
    23106 
    23107 > color sel byhetero
    23108 
    23109 > select #49: 382, 353,438,230,442,466
    23110 
    23111 66 atoms, 64 bonds, 6 residues, 1 model selected 
    23112 
    23113 > color sel purple
    23114 
    23115 > select clear
    23116 
    23117 > select #49/A:382@NZ
    23118 
    23119 1 atom, 1 residue, 1 model selected 
    23120 
    23121 > select add #49/A:466@NH2
    23122 
    23123 2 atoms, 2 residues, 1 model selected 
    23124 
    23125 > select add #49/A:466@NH1
    23126 
    23127 3 atoms, 2 residues, 1 model selected 
    23128 
    23129 > select add #49/A:466@CZ
    23130 
    23131 4 atoms, 2 residues, 1 model selected 
    23132 
    23133 > select add #49/A:466@NE
    23134 
    23135 5 atoms, 2 residues, 1 model selected 
    23136 
    23137 > color sel byhetero
    23138 
    23139 > select clear
    23140 
    23141 > save /Users/dout2/Desktop/rOAT1-Apo_keyresidue.png supersample 3
    23142 > transparentBackground true
    23143 
    23144 > save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
    23145 
    23146 > select #49: 382, 353,438,230,442,466
    23147 
    23148 66 atoms, 64 bonds, 6 residues, 1 model selected 
    23149 
    23150 > ui tool show "Color Actions"
    23151 
    23152 The cached device pixel ratio value was stale on window expose. Please file a
    23153 QTBUG which explains how to reproduce. 
    23154 
    23155 > select #49: 382, 353,438,230,442,466
    23156 
    23157 66 atoms, 64 bonds, 6 residues, 1 model selected 
    23158 
    23159 > hide sel atoms
    23160 
    23161 > select add #49
    23162 
    23163 3942 atoms, 3966 bonds, 570 residues, 1 model selected 
    23164 
    23165 > show sel cartoons
    23166 
    23167 > select clear
    23168 
    23169 > view
    23170 
    23171 > select add #49
    23172 
    23173 3942 atoms, 3966 bonds, 570 residues, 1 model selected 
    23174 
    23175 > color sel gray
    23176 
    23177 > color sel light gray
    23178 
    23179 > color sel dark gray
    23180 
    23181 > surface sel
    23182 
    23183 > select clear
    23184 
    23185 > save /Users/dout2/Desktop/rOAT1-Apo_bg.png supersample 3
    23186 > transparentBackground true
    23187 
    23188 > open /Users/dout2/Downloads/af3/roat1-AKG_model/seed-1_sample-0/model.cif
    23189 
    23190 Summary of feedback from opening
    23191 /Users/dout2/Downloads/af3/roat1-AKG_model/seed-1_sample-0/model.cif 
    23192 --- 
    23193 warning | Unable to fetch template for 'LIG_B': will connect using distance criteria 
    23194  
    23195 Chain information for model.cif #50 
    23196 --- 
    23197 Chain | Description 
    23198 A | . 
    23199  
    23200 
    23201 No chain in structure corresponds to chain ID given in local score info (chain
    23202 'B') 
    23203 
    23204 > hide #!49 models
    23205 
    23206 > rename #50 rOAT1-AKG_IF_af3.cif
    23207 
    23208 > select add #50
    23209 
    23210 4280 atoms, 4381 bonds, 552 residues, 1 model selected 
    23211 
    23212 > select clear
    23213 
    23214 > select #50: 382, 353,438,230,442,466
    23215 
    23216 66 atoms, 64 bonds, 6 residues, 1 model selected 
    23217 
    23218 > show sel atoms
    23219 
    23220 > color sel purple
    23221 
    23222 > size stickRadius 0.4
    23223 
    23224 Changed 77114 bond radii 
    23225 
    23226 > select clear
    23227 
    23228 > select add #50
    23229 
    23230 4280 atoms, 4381 bonds, 552 residues, 1 model selected 
    23231 
    23232 > hide sel cartoons
    23233 
    23234 > select clear
    23235 
    23236 [Repeated 1 time(s)]
    23237 
    23238 > select #50/A:354@CG
    23239 
    23240 1 atom, 1 residue, 1 model selected 
    23241 
    23242 > select up
    23243 
    23244 12 atoms, 12 bonds, 1 residue, 1 model selected 
    23245 
    23246 > hide sel atoms
    23247 
    23248 > select #50/B:1@C4
    23249 
    23250 1 atom, 1 residue, 1 model selected 
    23251 
    23252 > select up
    23253 
    23254 10 atoms, 9 bonds, 1 residue, 1 model selected 
    23255 
    23256 > color sel yellow
    23257 
    23258 > color sel byhetero
    23259 
    23260 > select #50/A:382@NZ
    23261 
    23262 1 atom, 1 residue, 1 model selected 
    23263 
    23264 > select add #50/A:466@NH1
    23265 
    23266 2 atoms, 2 residues, 1 model selected 
    23267 
    23268 > select add #50/A:466@NH2
    23269 
    23270 3 atoms, 2 residues, 1 model selected 
    23271 
    23272 > select add #50/A:466@NE
    23273 
    23274 4 atoms, 2 residues, 1 model selected 
    23275 
    23276 > color sel byhetero
    23277 
    23278 > select clear
    23279 
    23280 > save /Users/dout2/Desktop/rOAT1-AKG_keyresidue.png supersample 3
    23281 > transparentBackground true
    23282 
    23283 > select add #50
    23284 
    23285 4280 atoms, 4381 bonds, 552 residues, 1 model selected 
    23286 
    23287 > hide sel atoms
    23288 
    23289 > show sel cartoons
    23290 
    23291 > surface sel
    23292 
    23293 > color (#!50 & sel) dark gray
    23294 
    23295 > select clear
    23296 
    23297 > save /Users/dout2/Desktop/rOAT1-AKG_bg.png supersample 3
    23298 > transparentBackground true
    23299 
    23300 > save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
    23301 
    23302 > hide #!50 models
    23303 
    23304 > show #!45 models
    23305 
    23306 > show #!44 models
    23307 
    23308 > hide #!44 models
    23309 
    23310 > view
    23311 
    23312 > view orient
    23313 
    23314 > hide #!45 models
    23315 
    23316 > show #!43 models
    23317 
    23318 > show #!45 models
    23319 
    23320 > hide #!45 models
    23321 
    23322 > select add #43
    23323 
    23324 3807 atoms, 3899 bonds, 3 pseudobonds, 492 residues, 2 models selected 
    23325 
    23326 > color (#!43 & sel) dark gray
    23327 
    23328 > surface (#!43 & sel)
    23329 
    23330 > select clear
    23331 
    23332 > save /Users/dout2/Desktop/rOAT1-AKG_OF_bg.png supersample 3
    23333 > transparentBackground true
    23334 
    23335 > hide #43.2 models
    23336 
    23337 > hide #43.1 models
    23338 
    23339 > show #43.1 models
    23340 
    23341 > select #43: 382, 353,438,230,442,466
    23342 
    23343 66 atoms, 64 bonds, 6 residues, 1 model selected 
    23344 
    23345 > select subtract #43.2
    23346 
    23347 1 model selected 
    23348 
    23349 > select add #43
    23350 
    23351 3807 atoms, 3899 bonds, 3 pseudobonds, 492 residues, 2 models selected 
    23352 
    23353 > hide sel cartoons
    23354 
    23355 > select clear
    23356 
    23357 > select #43: 382, 353,438,230,442,466
    23358 
    23359 66 atoms, 64 bonds, 6 residues, 1 model selected 
    23360 
    23361 > select add #43
    23362 
    23363 3807 atoms, 3899 bonds, 3 pseudobonds, 492 residues, 3 models selected 
    23364 
    23365 > hide sel atoms
    23366 
    23367 > select #43: 382, 353,438,230,442,466
    23368 
    23369 66 atoms, 64 bonds, 6 residues, 1 model selected 
    23370 
    23371 > show sel atoms
    23372 
    23373 > select #43: akg
    23374 
    23375 10 atoms, 9 bonds, 1 residue, 1 model selected 
    23376 
    23377 > show sel atoms
    23378 
    23379 > select clear
    23380 
    23381 > select #43/A:601@C2
    23382 
    23383 1 atom, 1 residue, 1 model selected 
    23384 
    23385 > select up
    23386 
    23387 10 atoms, 9 bonds, 1 residue, 1 model selected 
    23388 
    23389 > color sel yellow
    23390 
    23391 > color sel byhetero
    23392 
    23393 > select clear
    23394 
    23395 > select #43/A:466@NH2
    23396 
    23397 1 atom, 1 residue, 1 model selected 
    23398 
    23399 > select add #43/A:466@NH1
    23400 
    23401 2 atoms, 1 residue, 2 models selected 
    23402 
    23403 > select add #43/A:466@NE
    23404 
    23405 3 atoms, 1 residue, 2 models selected 
    23406 
    23407 > select add #43/A:382@NZ
    23408 
    23409 4 atoms, 2 residues, 2 models selected 
    23410 
    23411 > color (#!43 & sel) byhetero
    23412 
    23413 > select clear
    23414 
    23415 > select #43: 382, 353,438,230,442,466
    23416 
    23417 66 atoms, 64 bonds, 6 residues, 1 model selected 
    23418 
    23419 > color (#!43 & sel) purple
    23420 
    23421 > select subtract #43/A:382@NZ
    23422 
    23423 65 atoms, 63 bonds, 6 residues, 2 models selected 
    23424 
    23425 > select subtract #43/A:466@NH2
    23426 
    23427 64 atoms, 62 bonds, 6 residues, 2 models selected 
    23428 
    23429 > select subtract #43/A:466@NH1
    23430 
    23431 63 atoms, 61 bonds, 6 residues, 2 models selected 
    23432 
    23433 > select subtract #43/A:466@CD
    23434 
    23435 62 atoms, 59 bonds, 6 residues, 2 models selected 
    23436 
    23437 > color (#!43 & sel) byhetero
    23438 
    23439 > select #43: 382, 353,438,230,442,466
    23440 
    23441 66 atoms, 64 bonds, 6 residues, 1 model selected 
    23442 
    23443 > color (#!43 & sel) purple
    23444 
    23445 > select subtract #43/A:382@NZ
    23446 
    23447 65 atoms, 63 bonds, 6 residues, 2 models selected 
    23448 
    23449 > select subtract #43/A:466@NH1
    23450 
    23451 64 atoms, 62 bonds, 6 residues, 2 models selected 
    23452 
    23453 > select subtract #43/A:466@NH2
    23454 
    23455 63 atoms, 61 bonds, 6 residues, 2 models selected 
    23456 
    23457 > select clear
    23458 
    23459 > select add #43/A:466@NH2
    23460 
    23461 1 atom, 1 residue, 1 model selected 
    23462 
    23463 > select add #43/A:466@NH1
    23464 
    23465 2 atoms, 1 residue, 2 models selected 
    23466 
    23467 > select add #43/A:382@NZ
    23468 
    23469 3 atoms, 2 residues, 2 models selected 
    23470 
    23471 > color (#!43 & sel) byhetero
    23472 
    23473 > select clear
    23474 
    23475 > save /Users/dout2/Desktop/rOAT1-AKG_OF_residue.png supersample 3
    23476 > transparentBackground true
    23477 
    23478 > save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
    23479 
    23480 > open /Users/dout2/Downloads/af3/roat1-AKG_model/seed-1_sample-1/model.cif
    23481 
    23482 Summary of feedback from opening
    23483 /Users/dout2/Downloads/af3/roat1-AKG_model/seed-1_sample-1/model.cif 
    23484 --- 
    23485 warning | Unable to fetch template for 'LIG_B': will connect using distance criteria 
    23486  
    23487 Chain information for model.cif #51 
    23488 --- 
    23489 Chain | Description 
    23490 A | . 
    23491  
    23492 
    23493 No chain in structure corresponds to chain ID given in local score info (chain
    23494 'B') 
    23495 
    23496 > hide #!43 models
    23497 
    23498 > hide #43.1 models
    23499 
    23500 > view
    23501 
    23502 > rename #51 rOAT1-AKG_IF_af3_model1.cif
    23503 
    23504 > rename #51 rOAT1-AKG_IF_af3_model1-1.cif
    23505 
    23506 > select add #51
    23507 
    23508 4280 atoms, 4381 bonds, 552 residues, 1 model selected 
    23509 
    23510 > color sel dark gray
    23511 
    23512 > surface sel
    23513 
    23514 > select clear
    23515 
    23516 > save /Users/dout2/Desktop/rOAT1-AKG_IF_bg.png supersample 3
    23517 > transparentBackground true
    23518 
    23519 > hide #51.1 models
    23520 
    23521 > select add #51
    23522 
    23523 4280 atoms, 4381 bonds, 552 residues, 1 model selected 
    23524 
    23525 > hide sel atoms
    23526 
    23527 > hide sel cartoons
    23528 
    23529 > select #51: 382, 353,438,230,442,466
    23530 
    23531 66 atoms, 64 bonds, 6 residues, 1 model selected 
    23532 
    23533 > show sel atoms
    23534 
    23535 > color (#!51 & sel) purple
    23536 
    23537 > size stickRadius 0.4
    23538 
    23539 Changed 81495 bond radii 
    23540 
    23541 > select clear
    23542 
    23543 > select #51: AKG
    23544 
    23545 Nothing selected 
    23546 
    23547 > show #!51 atoms
    23548 
    23549 > undo
    23550 
    23551 > select add #51
    23552 
    23553 4280 atoms, 4381 bonds, 552 residues, 1 model selected 
    23554 
    23555 > show sel atoms
    23556 
    23557 > select #51/B:1@C3
    23558 
    23559 1 atom, 1 residue, 1 model selected 
    23560 
    23561 > select up
    23562 
    23563 10 atoms, 9 bonds, 1 residue, 1 model selected 
    23564 
    23565 > select add #51
    23566 
    23567 4280 atoms, 4381 bonds, 552 residues, 1 model selected 
    23568 
    23569 > hide sel atoms
    23570 
    23571 > select #51/B
    23572 
    23573 10 atoms, 9 bonds, 1 residue, 1 model selected 
    23574 
    23575 > show sel atoms
    23576 
    23577 > color sel yellow
    23578 
    23579 > color sel byhetero
    23580 
    23581 > select clear
    23582 
    23583 > select #51: 382, 353,438,230,442,466
    23584 
    23585 66 atoms, 64 bonds, 6 residues, 1 model selected 
    23586 
    23587 > show sel atoms
    23588 
    23589 > select #51/A:382@NZ
    23590 
    23591 1 atom, 1 residue, 1 model selected 
    23592 
    23593 > select add #51/A:466@NH1
    23594 
    23595 2 atoms, 2 residues, 2 models selected 
    23596 
    23597 > select add #51/A:466@NH2
    23598 
    23599 3 atoms, 2 residues, 2 models selected 
    23600 
    23601 > color (#!51 & sel) byhetero
    23602 
    23603 > select #51/A:466@NE
    23604 
    23605 1 atom, 1 residue, 1 model selected 
    23606 
    23607 > color (#!51 & sel) byhetero
    23608 
    23609 > select clear
    23610 
    23611 > save /Users/dout2/Desktop/rOAT1-AKG_IF_residue.png supersample 3
    23612 > transparentBackground true
    23613 
    23614 > close #50
    23615 
    23616 > save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
    23617 
    23618 ——— End of log from Sat Apr 12 21:31:41 2025 ———
    23619 
    23620 opened ChimeraX session 
    23621 
    23622 > hide #!51 models
    23623 
    23624 > show #!2 models
    23625 
    23626 > show #1 models
    23627 
    23628 > view
    23629 
    23630 > lighting simple
    23631 
    23632 > lighting soft
    23633 
    23634 > lighting simple
    23635 
    23636 > hide #!2 models
    23637 
    23638 > select #1: 382, 353,438,230,442,466
    23639 
    23640 66 atoms, 64 bonds, 6 residues, 1 model selected 
    23641 
    23642 > view sel
    23643 
    23644 > cofr sel
    23645 
    23646 > select clear
    23647 
    23648 > show #!2 models
    23649 
    23650 > color #2 #ffffb2ff models
    23651 
    23652 > color #2 #ffffb24f models
    23653 
    23654 > color #2 #ffffb24e models
    23655 
    23656 > color #2 #ffffb24d models
    23657 
    23658 > select clear
    23659 
    23660 [Repeated 1 time(s)]
    23661 
    23662 > color #2 #a5ffb24d models
    23663 
    23664 > color #2 #9effb24d models
    23665 
    23666 > color #2 #9e43b24d models
    23667 
    23668 > color #2 #9effb24d models
    23669 
    23670 > color #2 #9effff4d models
    23671 
    23672 > select clear
    23673 
    23674 > size stickRadius 0.2
    23675 
    23676 Changed 77114 bond radii 
    23677 
    23678 > select clear
    23679 
    23680 > color #2 #942192ff models
    23681 
    23682 > color #2 #9421924d models
    23683 
    23684 > select clear
    23685 
    23686 > color #2 #aa7942ff models
    23687 
    23688 > color #2 #00fdffff models
    23689 
    23690 > color #2 #00fdff4e models
    23691 
    23692 > select clear
    23693 
    23694 > select up
    23695 
    23696 2 atoms, 1 bond, 1 residue, 1 model selected 
    23697 
    23698 > select up
    23699 
    23700 19 atoms, 20 bonds, 1 residue, 1 model selected 
    23701 
    23702 > view sel
    23703 
    23704 > ui tool show "Side View"
    23705 
    23706 > volume #2 level 0.01002
    23707 
    23708 > select clear
    23709 
    23710 > select #1/A:223
    23711 
    23712 4 atoms, 3 bonds, 1 residue, 1 model selected 
    23713 
    23714 > show sel atoms
    23715 
    23716 [Repeated 1 time(s)]
    23717 
    23718 > select #1/A:207
    23719 
    23720 8 atoms, 7 bonds, 1 residue, 1 model selected 
    23721 
    23722 > show sel atoms
    23723 
    23724 > hide #!2 models
    23725 
    23726 > select #1/A:36
    23727 
    23728 7 atoms, 6 bonds, 1 residue, 1 model selected 
    23729 
    23730 > show sel atoms
    23731 
    23732 > show #!2 models
    23733 
    23734 > select clear
    23735 
    23736 > select #1/A:601@C4'
    23737 
    23738 1 atom, 1 residue, 1 model selected 
    23739 
    23740 > select up
    23741 
    23742 19 atoms, 20 bonds, 1 residue, 1 model selected 
    23743 
    23744 > select up
    23745 
    23746 3891 atoms, 3986 bonds, 501 residues, 1 model selected 
    23747 
    23748 > select down
    23749 
    23750 19 atoms, 20 bonds, 1 residue, 1 model selected 
    23751 
    23752 > cofr sel
    23753 
    23754 > movie record
    23755 
    23756 > turn y 2 180
    23757 
    23758 > wait 180
    23759 
    23760 > movie encode /Users/dout2/Desktop/movie1.mp4
    23761 
    23762 Movie saved to /Users/dout2/Desktop/movie1.mp4 
    23763  
    23764 
    23765 > hide #!2 models
    23766 
    23767 > hide #1 models
    23768 
    23769 > select add #1
    23770 
    23771 3905 atoms, 3986 bonds, 515 residues, 1 model selected 
    23772 
    23773 > select subtract #1
    23774 
    23775 Nothing selected 
    23776 
    23777 > show #1 models
    23778 
    23779 > hide #1 models
    23780 
    23781 > show #!5 models
    23782 
    23783 > show #!4 models
    23784 
    23785 > select clear
    23786 
    23787 > volume #4 level 0.01053
    23788 
    23789 > color #4 #fffb00ff models
    23790 
    23791 > color #4 #ffffb2ff models
    23792 
    23793 > color #4 #ffffb24d models
    23794 
    23795 > select #4
    23796 
    23797 4 models selected 
    23798 
    23799 > select clear
    23800 
    23801 > select #1: 382, 353,438,230,442,466,207
    23802 
    23803 74 atoms, 71 bonds, 7 residues, 1 model selected 
    23804 
    23805 > show #!5 atoms
    23806 
    23807 > select add #5
    23808 
    23809 3848 atoms, 3935 bonds, 5 pseudobonds, 493 residues, 3 models selected 
    23810 
    23811 > hide sel & #!5 atoms
    23812 
    23813 > select #5: 382, 353,438,230,442,466,207,601
    23814 
    23815 93 atoms, 91 bonds, 8 residues, 1 model selected 
    23816 
    23817 > show sel atoms
    23818 
    23819 > select clear
    23820 
    23821 > select add #5
    23822 
    23823 3774 atoms, 3864 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    23824 
    23825 > show sel atoms
    23826 
    23827 > select clear
    23828 
    23829 > select #5/A:601@O4
    23830 
    23831 1 atom, 1 residue, 1 model selected 
    23832 
    23833 > select up
    23834 
    23835 19 atoms, 20 bonds, 1 residue, 1 model selected 
    23836 
    23837 > cofr sel
    23838 
    23839 > select #4
    23840 
    23841 4 models selected 
    23842 
    23843 > volume #4 level 0.01089
    23844 
    23845 > volume #4 level 0.01182
    23846 
    23847 > volume #4 level 0.01292
    23848 
    23849 > select clear
    23850 
    23851 > volume #4 level 0.01311
    23852 
    23853 > volume #4 level 0.01274
    23854 
    23855 > volume #4 level 0.01126
    23856 
    23857 > volume #4 level 0.01274
    23858 
    23859 > volume #4 level 0.012
    23860 
    23861 > movie record
    23862 
    23863 > turn y 2 180
    23864 
    23865 > wait 180
    23866 
    23867 > movie encode /Users/dout2/Desktop/movie2.mp4
    23868 
    23869 Movie saved to /Users/dout2/Desktop/movie2.mp4 
    23870  
    23871 
    23872 > movie record
    23873 
    23874 > turn y 2 180
    23875 
    23876 > wait 180
    23877 
    23878 > movie encode /Users/dout2/Desktop/movie3.mp4
    23879 
    23880 Movie saved to /Users/dout2/Desktop/movie3.mp4 
    23881  
    23882 
    23883 > view
    23884 
    23885 > hide #!4 models
    23886 
    23887 > select add #5
    23888 
    23889 3774 atoms, 3864 bonds, 5 pseudobonds, 486 residues, 2 models selected 
    23890 
    23891 > hide sel atoms
    23892 
    23893 > select #5: 382, 353,438,230,442,466,207,601
    23894 
    23895 93 atoms, 91 bonds, 8 residues, 1 model selected 
    23896 
    23897 > show sel atoms
    23898 
    23899 > select clear
    23900 
    23901 > show #!4 models
    23902 
    23903 > hide #!4 models
    23904 
    23905 > hide #!5 models
    23906 
    23907 > show #8 models
    23908 
    23909 > show #!7 models
    23910 
    23911 > hide #8 models
    23912 
    23913 > hide #!7 models
    23914 
    23915 > show #!10 models
    23916 
    23917 > show #!12 models
    23918 
    23919 > color #10 darkgrey models
    23920 
    23921 > color #10 silver models
    23922 
    23923 > color #10 #c0c0c04d models
    23924 
    23925 > select clear
    23926 
    23927 > hide #!12 models
    23928 
    23929 > show #!12 models
    23930 
    23931 > hide #!10 models
    23932 
    23933 > show #!10 models
    23934 
    23935 > save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
    23936 
    23937 > volume #10 level 0.0124
    23938 
    23939 > select up
    23940 
    23941 2 atoms, 1 bond, 1 residue, 1 model selected 
    23942 
    23943 > select up
    23944 
    23945 37 atoms, 37 bonds, 1 residue, 1 model selected 
    23946 
    23947 > select #12: 382, 353,438,230,442,466,207,601
    23948 
    23949 111 atoms, 108 bonds, 8 residues, 1 model selected 
    23950 
    23951 > show sel atoms
    23952 
    23953 > select up
    23954 
    23955 2 atoms, 1 bond, 1 residue, 1 model selected 
    23956 
    23957 > select H
    23958 
    23959 117 atoms, 10 residues, 9 models selected 
    23960 
    23961 > hide sel & #!12 atoms
    23962 
    23963 > select clear
    23964 
    23965 > select #12: 382, 353,438,230,442,466,207,601
    23966 
    23967 111 atoms, 108 bonds, 8 residues, 1 model selected 
    23968 
    23969 > view sel
    23970 
    23971 > cofr sel
    23972 
    23973 > volume #10 level 0.009894
    23974 
    23975 > volume #10 level 0.01073
    23976 
    23977 > select clear
    23978 
    23979 [Repeated 1 time(s)]
    23980 
    23981 > select #12/B:601@C16
    23982 
    23983 1 atom, 1 residue, 1 model selected 
    23984 
    23985 > select up
    23986 
    23987 37 atoms, 37 bonds, 1 residue, 1 model selected 
    23988 
    23989 > view sel
    23990 
    23991 > select clear
    23992 
    23993 > movie record
    23994 
    23995 > turn y 2 180
    23996 
    23997 > wait 180
    23998 
    23999 > movie encode /Users/dout2/Desktop/movie4.mp4
    24000 
    24001 Movie saved to /Users/dout2/Desktop/movie4.mp4 
    24002  
    24003 
    24004 > select #10
    24005 
    24006 4 models selected 
    24007 
    24008 > select clear
    24009 
    24010 > hide #!12 models
    24011 
    24012 > hide #!10 models
    24013 
    24014 > show #8 models
    24015 
    24016 > show #!7 models
    24017 
    24018 > select up
    24019 
    24020 2 atoms, 1 bond, 1 residue, 1 model selected 
    24021 
    24022 > color #7 #ff2f92ff models
    24023 
    24024 > color #7 #ff2f924d models
    24025 
    24026 > select #7
    24027 
    24028 4 models selected 
    24029 
    24030 > select clear
    24031 
    24032 > select #8: 382, 353,438,230,442,466,207,601
    24033 
    24034 93 atoms, 90 bonds, 8 residues, 1 model selected 
    24035 
    24036 > show sel atoms
    24037 
    24038 > select clear
    24039 
    24040 > open
    24041 > /Users/dout2/Documents/Manuscripts/rOAT1_2023/cryoEM/rOAT1-PBD_20230217/cryosparc_P4_J55__localfilter_160.mrc
    24042 
    24043 Opened cryosparc_P4_J55__localfilter_160.mrc as #50, grid size 160,160,160,
    24044 pixel 0.83, shown at level 0.131, step 1, values float32 
    24045 
    24046 > movie record
    24047 
    24048 > turn y 2 180
    24049 
    24050 > wait 180
    24051 
    24052 > movie encode /Users/dout2/Desktop/movie1.mp4
    24053 
    24054 Movie saved to /Users/dout2/Desktop/movie1.mp4 
    24055  
    24056 
    24057 > hide #!7 models
    24058 
    24059 > view
    24060 
    24061 > show #!7 models
    24062 
    24063 > rename #50 rOAT1-PBD_IF.mrc
    24064 
    24065 > select add #50
    24066 
    24067 2 models selected 
    24068 
    24069 > ui mousemode right "translate selected models"
    24070 
    24071 > view matrix models #50,1,0,0,82.163,0,1,0,34.821,0,0,1,72.008
    24072 
    24073 > view matrix models #50,1,0,0,78.322,0,1,0,71.965,0,0,1,68.805
    24074 
    24075 > view matrix models #50,1,0,0,68.336,0,1,0,66.309,0,0,1,66.361
    24076 
    24077 > ui tool show "Fit in Map"
    24078 
    24079 > fitmap #50 inMap #7
    24080 
    24081 Fit map rOAT1-PBD_IF.mrc in map rOAT1-PBD_IF.mrc using 40907 points 
    24082 correlation = 0.9052, correlation about mean = 0.7104, overlap = 318.4 
    24083 steps = 88, shift = 2.7, angle = 7.48 degrees 
    24084  
    24085 Position of rOAT1-PBD_IF.mrc (#50) relative to rOAT1-PBD_IF.mrc (#7)
    24086 coordinates: 
    24087 Matrix rotation and translation 
    24088 0.99182552 0.09586728 -0.08421166 67.85108178 
    24089 -0.09362983 0.99515083 0.03013765 73.24636935 
    24090 0.08669251 -0.02200656 0.99599203 61.03836799 
    24091 Axis -0.20020488 -0.65617735 -0.72756395 
    24092 Axis point 63.93693297 -480.82614561 -0.00000000 
    24093 Rotation angle (degrees) 7.48271681 
    24094 Shift along axis -106.05604184 
    24095  
    24096 
    24097 > hide #!7 models
    24098 
    24099 > color #50 #b2b2b24d models
    24100 
    24101 > select clear
    24102 
    24103 > ui mousemode right translate
    24104 
    24105 > select #8: 382, 353,438,230,442,466,207,601
    24106 
    24107 93 atoms, 90 bonds, 8 residues, 1 model selected 
    24108 
    24109 > view sel
    24110 
    24111 > cofr sel
    24112 
    24113 > volume #50 level 0.2404
    24114 
    24115 > select clear
    24116 
    24117 > select #8: 382, 353,438,230,442,466,207,601
    24118 
    24119 93 atoms, 90 bonds, 8 residues, 1 model selected 
    24120 
    24121 > show sel atoms
    24122 
    24123 > select clear
    24124 
    24125 > volume #50 level 0.2822
    24126 
    24127 > select clear
    24128 
    24129 > movie record
    24130 
    24131 > turn y 2 180
    24132 
    24133 > wait 180
    24134 
    24135 > movie encode /Users/dout2/Desktop/movie2.mp4
    24136 
    24137 Movie saved to /Users/dout2/Desktop/movie2.mp4 
    24138  
    24139 
    24140 > hide #!50 models
    24141 
    24142 > view
    24143 
    24144 > hide #8 models
    24145 
    24146 > show #!20 models
    24147 
    24148 > show #21 models
    24149 
    24150 > color #20 #ffffb2ff models
    24151 
    24152 > color #20 #ffffb24d models
    24153 
    24154 > select clear
    24155 
    24156 > select #21: 382, 353,438,230,442,466,207,601
    24157 
    24158 109 atoms, 109 bonds, 8 residues, 1 model selected 
    24159 
    24160 > show sel atoms
    24161 
    24162 > select clear
    24163 
    24164 > select H
    24165 
    24166 117 atoms, 10 residues, 9 models selected 
    24167 
    24168 > hide sel & #21 atoms
    24169 
    24170 > select clear
    24171 
    24172 > select #21: 382, 353,438,230,442,466,207,601
    24173 
    24174 109 atoms, 109 bonds, 8 residues, 1 model selected 
    24175 
    24176 > view sel
    24177 
    24178 > select clear
    24179 
    24180 > color #20 #ffffb280 models
    24181 
    24182 > select clear
    24183 
    24184 > volume #20 level 0.01329
    24185 
    24186 > select #21/A:602@O24
    24187 
    24188 1 atom, 1 residue, 1 model selected 
    24189 
    24190 > select up
    24191 
    24192 35 atoms, 38 bonds, 1 residue, 1 model selected 
    24193 
    24194 > select clear
    24195 
    24196 > movie record
    24197 
    24198 > turn y 2 180
    24199 
    24200 > wait 180
    24201 
    24202 > movie encode /Users/dout2/Desktop/movie2.mp4
    24203 
    24204 Movie saved to /Users/dout2/Desktop/movie2.mp4 
    24205  
    24206 
    24207 > select #21: 382, 353,438,230,442,466,207,601,602
    24208 
    24209 144 atoms, 147 bonds, 9 residues, 1 model selected 
    24210 
    24211 > select #20
    24212 
    24213 4 models selected 
    24214 
    24215 > select clear
    24216 
    24217 > movie record
    24218 
    24219 > turn y 2 180
    24220 
    24221 > wait 180
    24222 
    24223 > movie encode /Users/dout2/Desktop/movie3.mp4
    24224 
    24225 Movie saved to /Users/dout2/Desktop/movie3.mp4 
    24226  
    24227 
    24228 > hide #!20 models
    24229 
    24230 > view
    24231 
    24232 > hide #21 models
    24233 
    24234 > show #!24 models
    24235 
    24236 > show #!23 models
    24237 
    24238 > color #23 #ffffb2ff models
    24239 
    24240 > select clear
    24241 
    24242 > hide #!23 models
    24243 
    24244 > show #!23 models
    24245 
    24246 > select #24: 382, 353,438,230,442,466,207,601,602
    24247 
    24248 109 atoms, 109 bonds, 8 residues, 1 model selected 
    24249 
    24250 > view sel
    24251 
    24252 > color #23 #ffffb280 models
    24253 
    24254 > select clear
    24255 
    24256 > select #24/A:601@O14
    24257 
    24258 1 atom, 1 residue, 1 model selected 
    24259 
    24260 > select up
    24261 
    24262 35 atoms, 38 bonds, 1 residue, 1 model selected 
    24263 
    24264 > cofr sel
    24265 
    24266 > select #23
    24267 
    24268 4 models selected 
    24269 
    24270 > movie record
    24271 
    24272 > turn y 2 180
    24273 
    24274 > wait 180
    24275 
    24276 > movie encode /Users/dout2/Desktop/movie3.mp4
    24277 
    24278 Movie saved to /Users/dout2/Desktop/movie3.mp4 
    24279  
    24280 
    24281 > select clear
    24282 
    24283 > movie record
    24284 
    24285 > turn y 2 180
    24286 
    24287 > wait 180
    24288 
    24289 > movie encode /Users/dout2/Desktop/movie4.mp4
    24290 
    24291 Movie saved to /Users/dout2/Desktop/movie4.mp4 
    24292  
    24293 
    24294 > save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
    24295 
    24296 ——— End of log from Tue Apr 15 12:09:47 2025 ———
    24297 
    24298 opened ChimeraX session 
    24299 
    24300 > hide #!24 models
    24301 
    24302 > hide #!23 models
    24303 
    24304 > show #!6 models
    24305 
    24306 > show #!5 models
    24307 
    24308 > show #!6.3 models
    24309 
    24310 > show #!4 models
    24311 
    24312 > hide #!6.3 models
    24313 
    24314 > hide #!6 models
    24315 
    24316 > volume #4 level 0.01403
    24317 
    24318 > volume #4 level 0.01126
    24319 
    24320 > hide #!5 models
    24321 
    24322 > hide #!4 models
    24323 
    24324 > show #!2 models
    24325 
    24326 > show #1 models
    24327 
    24328 > show #!5 models
    24329 
    24330 > hide #!5 models
    24331 
    24332 > volume #2 level 0.008618
    24333 
    24334 > hide #!2 models
    24335 
    24336 > hide #1 models
    24337 
    24338 > show #!4 models
    24339 
    24340 > show #!5 models
    24341 
    24342 > hide #!5 models
    24343 
    24344 > hide #!4 models
    24345 
    24346 > show #!2 models
    24347 
    24348 > show #1 models
    24349 
    24350 > hide #1 models
    24351 
    24352 > hide #!2 models
    24353 
    24354 > show #!4 models
    24355 
    24356 > show #!5 models
    24357 
    24358 > hide #!5 models
    24359 
    24360 > hide #!4 models
    24361 
    24362 > show #!2 models
    24363 
    24364 > show #1 models
    24365 
    24366 > open /Volumes/bbc/Lab-
    24367 > Jiang/USERS/dout2/SLC22_MapModel/rOAT1-AZT/IF/rOAT1-AZT_IF-coot-3.pdb
    24368 
    24369 Chain information for rOAT1-AZT_IF-coot-3.pdb #52 
    24370 --- 
    24371 Chain | Description 
    24372 A | No description available 
    24373  
    24374 
    24375 > hide #1 models
    24376 
    24377 > select #1-60: 382, 353,438,230,442,466,207, 234, 227
    24378 
    24379 1734 atoms, 1634 bonds, 180 residues, 20 models selected 
    24380 
    24381 > show sel & #52 atoms
    24382 
    24383 > show #!5 models
    24384 
    24385 > open /Volumes/bbc/Lab-
    24386 > Jiang/USERS/dout2/SLC22_MapModel/rOAT1-AZT/IF/RealSpaceRefine_6/rOAT1-AZT_IF-
    24387 > coot-3_real_space_refined_006.pdb
    24388 
    24389 Chain information for rOAT1-AZT_IF-coot-3_real_space_refined_006.pdb #53 
    24390 --- 
    24391 Chain | Description 
    24392 A | No description available 
    24393  
    24394 
    24395 > hide #52 models
    24396 
    24397 > select add #53
    24398 
    24399 5639 atoms, 5620 bonds, 695 residues, 24 models selected 
    24400 
    24401 > show #53 target m
    24402 
    24403 > select #53
    24404 
    24405 3905 atoms, 3986 bonds, 515 residues, 1 model selected 
    24406 
    24407 > hide #!5 models
    24408 
    24409 > hide #!2 models
    24410 
    24411 > show #!2 models
    24412 
    24413 > close #52
    24414 
    24415 > save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
    24416 
    24417 > save /Users/dout2/Downloads/OAT1_ligand_Colored_domain.cxs includeMaps true
    24418 
    24419 > color #53 tan
    24420 
    24421 > select clear
    24422 
    24423 > select #53/A:601@C2'
    24424 
    24425 1 atom, 1 residue, 1 model selected 
    24426 
    24427 > select up
    24428 
    24429 19 atoms, 20 bonds, 1 residue, 1 model selected 
    24430 
    24431 > color sel byhetero
    24432 
    24433 > select #2
    24434 
    24435 4 models selected 
    24436 
    24437 > select #1-60: 382, 353,438,230,442,466,207, 234, 227
    24438 
    24439 1734 atoms, 1634 bonds, 180 residues, 20 models selected 
    24440 
    24441 > show sel & #53 atoms
    24442 
    24443 > select #53
    24444 
    24445 3905 atoms, 3986 bonds, 515 residues, 1 model selected 
    24446 
    24447 > show #1 target m
    24448 
    24449 > hide #1 models
    24450 
    24451 > hide #53 models
    24452 
    24453 > select subtract #53
    24454 
    24455 Nothing selected 
    24456 
    24457 > hide #!2 models
    24458 
    24459 > show #!4 models
    24460 
    24461 > show #!5 models
    24462 
    24463 > save /Users/dout2/Downloads/OAT1_ligand_Colored_domain.cxs includeMaps true
    24464 
    24465 > show #1 models
    24466 
    24467 > hide #!4 models
    24468 
    24469 > hide #!5 models
    24470 
    24471 > hide #1 models
    24472 
    24473 > show #53 models
    24474 
    24475 > show #!2 models
    24476 
    24477 > select #53:1-317
    24478 
    24479 2371 atoms, 2418 bonds, 313 residues, 1 model selected 
    24480 
    24481 > color sel #a166d1ff
    24482 
    24483 > select #53:318-550
    24484 
    24485 1515 atoms, 1548 bonds, 201 residues, 1 model selected 
    24486 
    24487 > color sel #3ec0c2ff
    24488 
    24489 > select clear
    24490 
    24491 > select add #53
    24492 
    24493 3905 atoms, 3986 bonds, 515 residues, 1 model selected 
    24494 
    24495 > select add #51
    24496 
    24497 8185 atoms, 8367 bonds, 1067 residues, 2 models selected 
    24498 
    24499 > select add #49
    24500 
    24501 12127 atoms, 12333 bonds, 1637 residues, 4 models selected 
    24502 
    24503 > select add #47
    24504 
    24505 15922 atoms, 16217 bonds, 3 pseudobonds, 2132 residues, 7 models selected 
    24506 
    24507 > select #1-53:318-550
    24508 
    24509 31000 atoms, 31598 bonds, 10 pseudobonds, 4147 residues, 25 models selected 
    24510 
    24511 > show #1 models
    24512 
    24513 > hide #!2 models
    24514 
    24515 > color (#1,53 & sel) #3ec0c2ff
    24516 
    24517 [Repeated 1 time(s)]
    24518 
    24519 > hide #1 models
    24520 
    24521 > show #!5 models
    24522 
    24523 > color (#53#!5 & sel) #3ec0c2ff
    24524 
    24525 [Repeated 1 time(s)]
    24526 
    24527 > show #8 models
    24528 
    24529 > color (#8,53#!5 & sel) #3ec0c2ff
    24530 
    24531 [Repeated 1 time(s)]
    24532 
    24533 > show #!12 models
    24534 
    24535 > color (#8,53#!5,12 & sel) #3ec0c2ff
    24536 
    24537 [Repeated 1 time(s)]
    24538 
    24539 > show #15 models
    24540 
    24541 > color (#8,15,53#!5,12 & sel) #3ec0c2ff
    24542 
    24543 [Repeated 1 time(s)]
    24544 
    24545 > show #!18 models
    24546 
    24547 > color (#8,15,53#!5,12,18 & sel) #3ec0c2ff
    24548 
    24549 [Repeated 1 time(s)]
    24550 
    24551 > show #21 models
    24552 
    24553 > color (#8,15,21,53#!5,12,18 & sel) #3ec0c2ff
    24554 
    24555 [Repeated 1 time(s)]
    24556 
    24557 > show #!24 models
    24558 
    24559 > show #!26 models
    24560 
    24561 > color (#8,15,21,53#!5,12,18,24,26 & sel) #3ec0c2ff
    24562 
    24563 [Repeated 1 time(s)]
    24564 
    24565 > show #30 models
    24566 
    24567 > show #33 models
    24568 
    24569 > show #!34 models
    24570 
    24571 > show #!24 target m
    24572 
    24573 > show #37 models
    24574 
    24575 > color (#8,15,21,30,33,37,53#!5,12,18,24,26,34 & sel) #3ec0c2ff
    24576 
    24577 [Repeated 1 time(s)]
    24578 
    24579 > show #!41 models
    24580 
    24581 > show #!43 models
    24582 
    24583 > show #!45 models
    24584 
    24585 > show #!47 models
    24586 
    24587 > show #!49 models
    24588 
    24589 > show #!51 models
    24590 
    24591 > hide #53 models
    24592 
    24593 > show #53 models
    24594 
    24595 > color (#8,15,21,30,33,37,53#!5,12,18,24,26,34,41,43,45,47,49,51 & sel)
    24596 > #3ec0c2ff
    24597 
    24598 [Repeated 1 time(s)]
    24599 
    24600 > select #1-53:1-317
    24601 
    24602 47755 atoms, 48809 bonds, 17 pseudobonds, 6237 residues, 29 models selected 
    24603 
    24604 > color (#8,15,21,30,33,37,53#!5,12,18,24,26,34,41,43,45,47,49,51 & sel)
    24605 > #a166d1ff
    24606 
    24607 > show #1 models
    24608 
    24609 > color (#1,8,15,21,30,33,37,53#!5,12,18,24,26,34,41,43,45,47,49,51 & sel)
    24610 > #a166d1ff
    24611 
    24612 [Repeated 1 time(s)]
    24613 
    24614 > save /Users/dout2/Downloads/OAT1_ligand_Colored_domain.cxs includeMaps true
    24615 
    24616 > select #53
    24617 
    24618 3905 atoms, 3986 bonds, 515 residues, 1 model selected 
    24619 
    24620 > show target m
    24621 
    24622 > show
    24623 > #1,5-6,8,12,15,18-19,21,24-26,30-31,33-35,37-38,41,45,47-49,51,53#43.1#!2-4,7,9-11,13-14,16-17,20,22-23,27-29,32,36,39-40,42-44,46,50#!2.1#!3.3#!4.1#!7.1#!9.3#!10.1#!11.3#!13.3#!14.1#!16.3#!17.1#!20.1#!22.3#!23.1#!27.1#!28.3#!29.1#!32.1#!36.1#!39.1#!40.1#!42.3#!43.2#!44.1#!46.1#!50.1#!3.3.1#!9.3.1#!11.3.1#!13.3.1#!16.3.1#!22.3.1#!28.3.1#!42.3.1
    24624 > target m
    24625 
    24626 > select #53
    24627 
    24628 3905 atoms, 3986 bonds, 515 residues, 1 model selected 
    24629 
    24630 > hide target m
    24631 
    24632 > select #53
    24633 
    24634 3905 atoms, 3986 bonds, 515 residues, 1 model selected 
    24635 
    24636 > show #53 models
    24637 
    24638 > select subtract #53
    24639 
    24640 Nothing selected 
    24641 
    24642 > hide #53 models
    24643 
    24644 > show #!5 models
    24645 
    24646 > select #1-60: 382, 353,438,230,442,466,207, 234, 227
    24647 
    24648 1734 atoms, 1634 bonds, 180 residues, 20 models selected 
    24649 
    24650 > show sel & #!5 atoms
    24651 
    24652 > hide sel & #!5 cartoons
    24653 
    24654 > show sel & #!5 cartoons
    24655 
    24656 > show #53 models
    24657 
    24658 > hide #!5 models
    24659 
    24660 > show #1 models
    24661 
    24662 > hide #1 models
    24663 
    24664 > show #!5 models
    24665 
    24666 > hide #!5 models
    24667 
    24668 > hide #53 models
    24669 
    24670 > select add #53
    24671 
    24672 5552 atoms, 5538 bonds, 686 residues, 23 models selected 
    24673 
    24674 > select add #51
    24675 
    24676 9745 atoms, 9837 bonds, 1229 residues, 23 models selected 
    24677 
    24678 > select subtract #51
    24679 
    24680 5465 atoms, 5456 bonds, 677 residues, 22 models selected 
    24681 
    24682 > select subtract #53
    24683 
    24684 1560 atoms, 1470 bonds, 162 residues, 20 models selected 
    24685 
    24686 > select add #53
    24687 
    24688 5465 atoms, 5456 bonds, 677 residues, 21 models selected 
    24689 
    24690 > select subtract #53
    24691 
    24692 1560 atoms, 1470 bonds, 162 residues, 20 models selected 
    24693 
    24694 > select add #49
    24695 
    24696 5415 atoms, 5354 bonds, 723 residues, 20 models selected 
    24697 
    24698 > select subtract #49
    24699 
    24700 1473 atoms, 1388 bonds, 153 residues, 19 models selected 
    24701 
    24702 > select add #47
    24703 
    24704 5187 atoms, 5196 bonds, 3 pseudobonds, 639 residues, 19 models selected 
    24705 
    24706 > select subtract #47
    24707 
    24708 1392 atoms, 1312 bonds, 144 residues, 17 models selected 
    24709 
    24710 > select add #45
    24711 
    24712 5112 atoms, 5129 bonds, 3 pseudobonds, 627 residues, 18 models selected 
    24713 
    24714 > select subtract #45
    24715 
    24716 1305 atoms, 1230 bonds, 135 residues, 16 models selected 
    24717 
    24718 > select add #43
    24719 
    24720 5025 atoms, 5047 bonds, 3 pseudobonds, 618 residues, 17 models selected 
    24721 
    24722 > select subtract #43
    24723 
    24724 1218 atoms, 1148 bonds, 126 residues, 15 models selected 
    24725 
    24726 > select add #41
    24727 
    24728 5506 atoms, 5547 bonds, 1 pseudobond, 681 residues, 15 models selected 
    24729 
    24730 > select subtract #41
    24731 
    24732 1131 atoms, 1066 bonds, 117 residues, 13 models selected 
    24733 
    24734 > select add #37
    24735 
    24736 5419 atoms, 5465 bonds, 672 residues, 13 models selected 
    24737 
    24738 > select subtract #37
    24739 
    24740 1044 atoms, 984 bonds, 108 residues, 12 models selected 
    24741 
    24742 > select add #34
    24743 
    24744 4744 atoms, 4778 bonds, 5 pseudobonds, 586 residues, 13 models selected 
    24745 
    24746 > select subtract #34
    24747 
    24748 957 atoms, 902 bonds, 99 residues, 11 models selected 
    24749 
    24750 > select add #33
    24751 
    24752 5197 atoms, 5213 bonds, 681 residues, 11 models selected 
    24753 
    24754 > select subtract #33
    24755 
    24756 870 atoms, 820 bonds, 90 residues, 10 models selected 
    24757 
    24758 > show #53 models
    24759 
    24760 > select #53: 382, 353,438,230,442,466,207, 234, 227
    24761 
    24762 87 atoms, 82 bonds, 9 residues, 1 model selected 
    24763 
    24764 > hide #53 models
    24765 
    24766 > show #53 models
    24767 
    24768 > select add #53
    24769 
    24770 3905 atoms, 3986 bonds, 515 residues, 1 model selected 
    24771 
    24772 > select subtract #53
    24773 
    24774 Nothing selected 
    24775 
    24776 > show #!2 models
    24777 
    24778 > show #2.1 models
    24779 
    24780 > ui tool show "Color Zone"
    24781 
    24782 > color zone #2 near #53 distance 4.98
    24783 
    24784 > hide #!2 models
    24785 
    24786 > hide #2.1 models
    24787 
    24788 > show #!3.3 models
    24789 
    24790 > select add #3.3
    24791 
    24792 2 models selected 
    24793 
    24794 > select subtract #3.3
    24795 
    24796 Nothing selected 
    24797 
    24798 > select add #3
    24799 
    24800 3 models selected 
    24801 
    24802 > color #3.3 #a166d1ff models
    24803 
    24804 > color #3 #b2b2b2ff models
    24805 
    24806 > show #2.1 models
    24807 
    24808 > hide #!2.1 models
    24809 
    24810 > show #3.3.1 models
    24811 
    24812 > color #3.3.1 #b2b2b280
    24813 
    24814 > select #53/A:346
    24815 
    24816 14 atoms, 15 bonds, 1 residue, 1 model selected 
    24817 
    24818 > color #3.3.1 #b2b2b24d
    24819 
    24820 > select #1-53: 601
    24821 
    24822 417 atoms, 431 bonds, 17 residues, 17 models selected 
    24823 
    24824 > color (#53 & sel) yellow
    24825 
    24826 > color (#53 & sel) byhetero
    24827 
    24828 > color (#53 & sel) hot pink
    24829 
    24830 > ui tool show "Color Actions"
    24831 
    24832 > color sel brown
    24833 
    24834 [Repeated 1 time(s)]
    24835 
    24836 > color (#53 & sel) byhetero
    24837 
    24838 > color (#53 & sel) hot pink
    24839 
    24840 > color (#53 & sel) byhetero
    24841 
    24842 > ui tool show "Hide Dust"
    24843 
    24844 > surface dust #2 size 4.98
    24845 
    24846 [Repeated 1 time(s)]
    24847 
    24848 > surface dust #3.3 size 4.98
    24849 
    24850 > surface dust #3.3 size 5.08
    24851 
    24852 [Repeated 1 time(s)]
    24853 
    24854 > surface dust #3.3 size 5.18
    24855 
    24856 > surface dust #3.3 size 5.28
    24857 
    24858 > surface dust #3.3 size 5.38
    24859 
    24860 > surface dust #3.3 size 5.48
    24861 
    24862 > surface dust #3.3 size 5.58
    24863 
    24864 > surface dust #3.3 size 5.68
    24865 
    24866 > surface dust #3.3 size 5.78
    24867 
    24868 > surface dust #3.3 size 5.88
    24869 
    24870 > surface dust #3.3 size 5.98
    24871 
    24872 > surface dust #3.3 size 6.08
    24873 
    24874 > surface dust #3.3 size 6.18
    24875 
    24876 > surface dust #3.3 size 6.28
    24877 
    24878 > surface dust #3.3 size 6.38
    24879 
    24880 > surface dust #3.3 size 6.48
    24881 
    24882 > surface dust #3.3 size 6.58
    24883 
    24884 > surface dust #3.3 size 6.68
    24885 
    24886 > surface dust #3.3 size 6.78
    24887 
    24888 > surface dust #3.3 size 6.88
    24889 
    24890 > surface dust #3.3 size 6.98
    24891 
    24892 > surface dust #3.3 size 7.08
    24893 
    24894 > surface dust #3.3 size 7.18
    24895 
    24896 [Repeated 1 time(s)]
    24897 
    24898 > select add #1
    24899 
    24900 4303 atoms, 4397 bonds, 531 residues, 17 models selected 
    24901 
    24902 > select subtract #1
    24903 
    24904 398 atoms, 411 bonds, 16 residues, 16 models selected 
    24905 
    24906 > select add #5
    24907 
    24908 4153 atoms, 4255 bonds, 5 pseudobonds, 501 residues, 17 models selected 
    24909 
    24910 > select subtract #5
    24911 
    24912 379 atoms, 391 bonds, 15 residues, 15 models selected 
    24913 
    24914 > select add #3.3.1
    24915 
    24916 379 atoms, 391 bonds, 15 residues, 17 models selected 
    24917 
    24918 > surface dust #3.3 size 7.28
    24919 
    24920 > surface dust #3.3 size 7.38
    24921 
    24922 > surface dust #3.3 size 7.48
    24923 
    24924 > surface dust #3.3 size 7.38
    24925 
    24926 > surface dust #3.3 size 7.28
    24927 
    24928 > surface dust #3.3 size 2
    24929 
    24930 [Repeated 1 time(s)]
    24931 
    24932 > surface dust #3.3 size 5
    24933 
    24934 > surface dust #3.3 size 50
    24935 
    24936 > surface dust #3.3 size 1
    24937 
    24938 > surface dust #3.3 size 10
    24939 
    24940 > surface dust #3.3 size 5
    24941 
    24942 > volume #3.3 level 0.008322
    24943 
    24944 > surface dust #3.3 size 3
    24945 
    24946 [Repeated 1 time(s)]
    24947 
    24948 > volume #3.3 level 0.008386
    24949 
    24950 > select clear
    24951 
    24952 > save /Users/dout2/Downloads/OAT1_ligand_Colored_domain.cxs includeMaps true
    24953 
    24954 > hide #!3 models
    24955 
    24956 > hide #!3.3 models
    24957 
    24958 > hide #3.3.1 models
    24959 
    24960 > show #!2 models
    24961 
    24962 > select add #2
    24963 
    24964 2 models selected 
    24965 
    24966 > show #2.1 models
    24967 
    24968 > hide #53 models
    24969 
    24970 > show #53 models
    24971 
    24972 > color zone #2 near #53 distance 4.98
    24973 
    24974 > hide #!2.1 models
    24975 
    24976 > hide #!2 models
    24977 
    24978 > show #!2 models
    24979 
    24980 > select add #53
    24981 
    24982 3905 atoms, 3986 bonds, 515 residues, 3 models selected 
    24983 
    24984 > show #2.1 models
    24985 
    24986 > color zone #2 near #53 distance 5.08
    24987 
    24988 > color zone #2 near #53 distance 5.18
    24989 
    24990 > color zone #2 near #53 distance 5.28
    24991 
    24992 > color zone #2 near #53 distance 5.38
    24993 
    24994 > color zone #2 near #53 distance 5.48
    24995 
    24996 > color zone #2 near #53 distance 5.58
    24997 
    24998 > color zone #2 near #53 distance 5.68
    24999 
    25000 > color zone #2 near #53 distance 5.58
    25001 
    25002 > color zone #2 near #53 distance 5.48
    25003 
    25004 > color zone #2 near #53 distance 5.38
    25005 
    25006 > color zone #2 near #53 distance 5.28
    25007 
    25008 > color zone #2 near #53 distance 5.18
    25009 
    25010 > color zone #2 near #53 distance 5.08
    25011 
    25012 > color zone #2 near #53 distance 4.98
    25013 
    25014 [Repeated 1 time(s)]
    25015 
    25016 > color single #2
    25017 
    25018 > color zone #2 near #53 distance 4.98
    25019 
    25020 > select clear
    25021 
    25022 > view
    25023 
    25024 > surface dust #2 size 4.98
    25025 
    25026 > surface dust #2 size 1
    25027 
    25028 > surface dust #2 size 10
    25029 
    25030 [Repeated 1 time(s)]
    25031 
    25032 > lighting soft
    25033 
    25034 > color zone #2 near #53 distance 2
    25035 
    25036 [Repeated 1 time(s)]
    25037 
    25038 > select clear
    25039 
    25040 > select add #2
    25041 
    25042 2 models selected 
    25043 No visible atoms or bonds selected 
    25044 [Repeated 2 time(s)]
    25045 
    25046 > hide #53 models
    25047 
    25048 > color #2 #e599004e models
    25049 
    25050 > select clear
    25051 
    25052 > color #2 #e59900ff models
    25053 
    25054 > color zone #2 near #53 distance 5
    25055 
    25056 > color zone #2 near #53 distance 4
    25057 
    25058 [Repeated 1 time(s)]
    25059 
    25060 > color zone #2 near #53 distance 3.9
    25061 
    25062 > color zone #2 near #53 distance 3.8
    25063 
    25064 > color zone #2 near #53 distance 3.7
    25065 
    25066 > color zone #2 near #53 distance 3.6
    25067 
    25068 > color zone #2 near #53 distance 3.5
    25069 
    25070 > color zone #2 near #53 distance 3.4
    25071 
    25072 > color zone #2 near #53 distance 3.3
    25073 
    25074 > color zone #2 near #53 distance 3.2
    25075 
    25076 > color zone #2 near #53 distance 3.1
    25077 
    25078 > color zone #2 near #53 distance 3
    25079 
    25080 > color zone #2 near #53 distance 3.1
    25081 
    25082 > color zone #2 near #53 distance 3.2
    25083 
    25084 > color zone #2 near #53 distance 3.3
    25085 
    25086 > color zone #2 near #53 distance 3.4
    25087 
    25088 > color zone #2 near #53 distance 3.5
    25089 
    25090 > color zone #2 near #53 distance 3.6
    25091 
    25092 > color zone #2 near #53 distance 3.7
    25093 
    25094 > graphics silhouettes true
    25095 
    25096 > lighting shadows true intensity 0.5
    25097 
    25098 > lighting flat
    25099 
    25100 > color zone #2 near #53 distance 3.8
    25101 
    25102 > color zone #2 near #53 distance 3.9
    25103 
    25104 > color zone #2 near #53 distance 4
    25105 
    25106 > color zone #2 near #53 distance 4.1
    25107 
    25108 > color zone #2 near #53 distance 4.2
    25109 
    25110 > color zone #2 near #53 distance 4.3
    25111 
    25112 > color zone #2 near #53 distance 4.4
    25113 
    25114 > color zone #2 near #53 distance 4.5
    25115 
    25116 > color zone #2 near #53 distance 4.6
    25117 
    25118 > color zone #2 near #53 distance 4.7
    25119 
    25120 > color zone #2 near #53 distance 4.8
    25121 
    25122 > color zone #2 near #53 distance 4.9
    25123 
    25124 > color zone #2 near #53 distance 4.8
    25125 
    25126 > color zone #2 near #53 distance 4.7
    25127 
    25128 > color zone #2 near #53 distance 4.6
    25129 
    25130 > color zone #2 near #53 distance 4.5
    25131 
    25132 > color zone #2 near #53 distance 4.4
    25133 
    25134 > color zone #2 near #53 distance 4.3
    25135 
    25136 > color zone #2 near #53 distance 4.2
    25137 
    25138 > color zone #2 near #53 distance 4.1
    25139 
    25140 > color zone #2 near #53 distance 4
    25141 
    25142 > color zone #2 near #53 distance 3.9
    25143 
    25144 > color zone #2 near #53 distance 3.8
    25145 
    25146 > color zone #2 near #53 distance 3.7
    25147 
    25148 > color zone #2 near #53 distance 3.6
    25149 
    25150 > color zone #2 near #53 distance 3.5
    25151 
    25152 > color zone #2 near #53 distance 3.4
    25153 
    25154 > color zone #2 near #53 distance 3.3
    25155 
    25156 > color zone #2 near #53 distance 3.2
    25157 
    25158 > color zone #2 near #53 distance 3.1
    25159 
    25160 > color zone #2 near #53 distance 3
    25161 
    25162 > color zone #2 near #53 distance 2.9
    25163 
    25164 Drag select of 2 rOAT1-AZT_IF.mrc 
    25165 
    25166 > volume #2 level 0.009345
    25167 
    25168 > color #2 #e5990000 models
    25169 
    25170 > color zone #2 near #53 distance 2.9
    25171 
    25172 > select clear
    25173 
    25174 > color #2 white models
    25175 
    25176 > color zone #2 near #53 distance 2.9
    25177 
    25178 > lighting full
    25179 
    25180 > lighting flat
    25181 
    25182 > lighting full
    25183 
    25184 > lighting soft
    25185 
    25186 > lighting full
    25187 
    25188 [Repeated 2 time(s)]
    25189 
    25190 > lighting soft
    25191 
    25192 > select clear
    25193 
    25194 > color #2 #ffffff00 models
    25195 
    25196 > color zone #2 near #53 distance 2.9
    25197 
    25198 > select clear
    25199 
    25200 > graphics silhouettes false
    25201 
    25202 > volume #2 level 0.008036
    25203 
    25204 > view
    25205 
    25206 > view orient
    25207 
    25208 > ui tool show "Side View"
    25209 
    25210 > volume #2 level 0.008909
    25211 
    25212 > lighting full
    25213 
    25214 > lighting soft
    25215 
    25216 > lighting flat
    25217 
    25218 > graphics silhouettes false
    25219 
    25220 > lighting soft
    25221 
    25222 > color #2 white models
    25223 
    25224 > color zone #2 near #53 distance 2.9
    25225 
    25226 > color #2.1 #ffffff00
    25227 
    25228 > color zone #2 near #53 distance 2.9
    25229 
    25230 > color #2.1 black
    25231 
    25232 > color zone #2 near #53 distance 2.9
    25233 
    25234 > color #2.1 #fffb00ff
    25235 
    25236 > color zone #2 near #53 distance 2.9
    25237 
    25238 > color #2.1 white
    25239 
    25240 > color #2.1 #ffffff00
    25241 
    25242 > color #2.1 white
    25243 
    25244 > color zone #2 near #53 distance 2.9
    25245 
    25246 > color #2.1 #ffffff00
    25247 
    25248 > color zone #2 near #53 distance 2.9
    25249 
    25250 > select #1-53: 601
    25251 
    25252 417 atoms, 431 bonds, 17 residues, 17 models selected 
    25253 
    25254 > color #2 hot pink
    25255 
    25256 > select #53: 601
    25257 
    25258 19 atoms, 20 bonds, 1 residue, 1 model selected 
    25259 
    25260 > color #2 hot pink
    25261 
    25262 > color zone #2 near #53 distance 2.9
    25263 
    25264 > color #2 white models
    25265 
    25266 > color zone #2 near #53 distance 2.9
    25267 
    25268 > color zone #2 near #53 distance 3
    25269 
    25270 > color zone #2 near #53 distance 3.1
    25271 
    25272 > color zone #2 near #53 distance 3.2
    25273 
    25274 > color zone #2 near #53 distance 3.3
    25275 
    25276 > color zone #2 near #53 distance 3.4
    25277 
    25278 > color zone #2 near #53 distance 3.5
    25279 
    25280 > color zone #2 near #53 distance 3.6
    25281 
    25282 > color zone #2 near #53 distance 3.7
    25283 
    25284 > color zone #2 near #53 distance 3.8
    25285 
    25286 > color zone #2 near #53 distance 3.9
    25287 
    25288 > color zone #2 near #53 distance 4
    25289 
    25290 > surface dust #2 size 4
    25291 
    25292 [Repeated 1 time(s)]
    25293 
    25294 > color #2.1 #ffffff00
    25295 
    25296 > color zone #2 near #53 distance 4
    25297 
    25298 > color zone #2 near #53 distance 4.1
    25299 
    25300 > color zone #2 near #53 distance 4.2
    25301 
    25302 > color zone #2 near #53 distance 4.3
    25303 
    25304 > color zone #2 near #53 distance 4.4
    25305 
    25306 > color zone #2 near #53 distance 4.5
    25307 
    25308 > color zone #2 near #53 distance 4.6
    25309 
    25310 > color zone #2 near #53 distance 4.7
    25311 
    25312 > color zone #2 near #53 distance 4.8
    25313 
    25314 > color zone #2 near #53 distance 4.9
    25315 
    25316 > color zone #2 near #53 distance 5
    25317 
    25318 > color zone #2 near #53 distance 5.1
    25319 
    25320 > color zone #2 near #53 distance 5.2
    25321 
    25322 > color zone #2 near #53 distance 5.3
    25323 
    25324 > color zone #2 near #53 distance 5.2
    25325 
    25326 > color zone #2 near #53 distance 5.1
    25327 
    25328 > color zone #2 near #53 distance 5
    25329 
    25330 > color #2 #e59900ff models
    25331 
    25332 > color zone #2 near #53 distance 5
    25333 
    25334 > color zone #2 near #53 distance 4.9
    25335 
    25336 > color zone #2 near #53 distance 4.8
    25337 
    25338 > color zone #2 near #53 distance 4.7
    25339 
    25340 > color zone #2 near #53 distance 4.6
    25341 
    25342 > color zone #2 near #53 distance 4.5
    25343 
    25344 > color zone #2 near #53 distance 4.4
    25345 
    25346 > color zone #2 near #53 distance 4.3
    25347 
    25348 > color zone #2 near #53 distance 4.2
    25349 
    25350 > color zone #2 near #53 distance 4.1
    25351 
    25352 > color zone #2 near #53 distance 4
    25353 
    25354 > color zone #2 near #53 distance 3.9
    25355 
    25356 > color zone #2 near #53 distance 3.8
    25357 
    25358 > color zone #2 near #53 distance 3.7
    25359 
    25360 > color zone #2 near #53 distance 3.6
    25361 
    25362 > color zone #2 near #53 distance 3.5
    25363 
    25364 > color zone #2 near #53 distance 3.4
    25365 
    25366 > color zone #2 near #53 distance 3.3
    25367 
    25368 > color zone #2 near #53 distance 3.2
    25369 
    25370 > color zone #2 near #53 distance 3.1
    25371 
    25372 > color zone #2 near #53 distance 3
    25373 
    25374 > surface dust #2 size 1
    25375 
    25376 > surface dust #2 size 10
    25377 
    25378 [Repeated 1 time(s)]
    25379 
    25380 > volume #2 level 0.009926
    25381 
    25382 > volume #2 level 0.009636
    25383 
    25384 > volume #2 level 0.007891
    25385 
    25386 > volume #2 level 0.006146
    25387 
    25388 > volume #2 level 0.008327
    25389 
    25390 > color zone #2 near #53 distance 3.1
    25391 
    25392 > color zone #2 near #53 distance 3.2
    25393 
    25394 > color zone #2 near #53 distance 3.3
    25395 
    25396 > color zone #2 near #53 distance 3.4
    25397 
    25398 > color zone #2 near #53 distance 3.5
    25399 
    25400 > color zone #2 near #53 distance 3.6
    25401 
    25402 > color zone #2 near #53 distance 3.7
    25403 
    25404 > color zone #2 near #53 distance 3.8
    25405 
    25406 > color zone #2 near #53 distance 3.9
    25407 
    25408 > color zone #2 near #53 distance 4
    25409 
    25410 > color zone #2 near #53 distance 4.1
    25411 
    25412 > color zone #2 near #53 distance 4.2
    25413 
    25414 > color zone #2 near #53 distance 4.1
    25415 
    25416 > color zone #2 near #53 distance 4
    25417 
    25418 > color zone #2 near #53 distance 3.9
    25419 
    25420 > color zone #2 near #53 distance 3.8
    25421 
    25422 > color zone #2 near #53 distance 3.7
    25423 
    25424 > color zone #2 near #53 distance 3.6
    25425 
    25426 > color zone #2 near #53 distance 3.5
    25427 
    25428 > color zone #2 near #53 distance 3.4
    25429 
    25430 > color zone #2 near #53 distance 3.3
    25431 
    25432 > color zone #2 near #53 distance 3.2
    25433 
    25434 > color zone #2 near #53 distance 3.1
    25435 
    25436 > color zone #2 near #53 distance 3
    25437 
    25438 > color zone #2 near #53 distance 2.9
    25439 
    25440 > color zone #2 near #53 distance 2.8
    25441 
    25442 > color zone #2 near #53 distance 2.7
    25443 
    25444 > volume #2 level 0.008036
    25445 
    25446 > hide #!2 models
    25447 
    25448 > hide #2.1 models
    25449 
    25450 > show #53 models
    25451 
    25452 > show #8 models
    25453 
    25454 > show #!49 models
    25455 
    25456 > hide #!49 models
    25457 
    25458 > hide #8 models
    25459 
    25460 > save /Users/dout2/Downloads/OAT1_ligand_Colored_domain.cxs includeMaps true
    25461 
    25462 > hide #53 models
    25463 
    25464 > select add #53
    25465 
    25466 3905 atoms, 3986 bonds, 515 residues, 1 model selected 
    25467 
    25468 > select subtract #53
    25469 
    25470 Nothing selected 
    25471 
    25472 > show #!2 models
    25473 
    25474 > select add #2
    25475 
    25476 2 models selected 
    25477 
    25478 > show #2.1 models
    25479 
    25480 > color zone #2 near #53 distance 2.8
    25481 
    25482 > color zone #2 near #53 distance 2.9
    25483 
    25484 > color zone #2 near #53 distance 3
    25485 
    25486 > color zone #2 near #53 distance 3.1
    25487 
    25488 > select clear
    25489 
    25490 > volume splitbyzone #2
    25491 
    25492 Opened rOAT1-AZT_IF.mrc 0 as #52.1, grid size 320,320,320, pixel 0.83, shown
    25493 at level 0.00804, step 1, values float32 
    25494 Opened rOAT1-AZT_IF.mrc 1 as #52.2, grid size 320,320,320, pixel 0.83, shown
    25495 at level 0.00804, step 1, values float32 
    25496 Opened rOAT1-AZT_IF.mrc 2 as #52.3, grid size 320,320,320, pixel 0.83, shown
    25497 at level 0.00804, step 1, values float32 
    25498 Opened rOAT1-AZT_IF.mrc 3 as #52.4, grid size 320,320,320, pixel 0.83, shown
    25499 at level 0.00804, step 1, values float32 
    25500 Opened rOAT1-AZT_IF.mrc 4 as #52.5, grid size 320,320,320, pixel 0.83, shown
    25501 at level 0.00804, step 1, values float32 
    25502 Opened rOAT1-AZT_IF.mrc 5 as #52.6, grid size 320,320,320, pixel 0.83, shown
    25503 at level 0.00804, step 1, values float32 
    25504 
    25505 > hide #!52.1 models
    25506 
    25507 > show #!52.1 models
    25508 
    25509 > hide #!52.1 models
    25510 
    25511 > hide #!52.2 models
    25512 
    25513 > show #!52.2 models
    25514 
    25515 > show #!52.1 models
    25516 
    25517 > volume #52.1 level 0.0124
    25518 
    25519 > surface dust #52.2 size 4.98
    25520 
    25521 > surface dust #52.1 size 4.98
    25522 
    25523 > volume #52.1 level 0.008531
    25524 
    25525 > hide #!52.6 models
    25526 
    25527 > show #!52.6 models
    25528 
    25529 > hide #!52.5 models
    25530 
    25531 > show #!52.5 models
    25532 
    25533 > show #53 models
    25534 
    25535 > hide #!52 models
    25536 
    25537 > show #!52 models
    25538 
    25539 > hide #!52 models
    25540 
    25541 > select #53: 601
    25542 
    25543 19 atoms, 20 bonds, 1 residue, 1 model selected 
    25544 
    25545 > color sel hot pink
    25546 
    25547 > show #!2 models
    25548 
    25549 > color zone #2 near #53 distance 3.1
    25550 
    25551 [Repeated 1 time(s)]
    25552 
    25553 > close #52
    25554 
    25555 > volume splitbyzone #2
    25556 
    25557 Opened rOAT1-AZT_IF.mrc 0 as #52.1, grid size 320,320,320, pixel 0.83, shown
    25558 at level 0.00804, step 1, values float32 
    25559 Opened rOAT1-AZT_IF.mrc 1 as #52.2, grid size 320,320,320, pixel 0.83, shown
    25560 at level 0.00804, step 1, values float32 
    25561 Opened rOAT1-AZT_IF.mrc 2 as #52.3, grid size 320,320,320, pixel 0.83, shown
    25562 at level 0.00804, step 1, values float32 
    25563 Opened rOAT1-AZT_IF.mrc 3 as #52.4, grid size 320,320,320, pixel 0.83, shown
    25564 at level 0.00804, step 1, values float32 
    25565 
    25566 > volume #52.1 level 0.01043
    25567 
    25568 > surface dust #52.2 size 4.98
    25569 
    25570 > surface dust #52.1 size 4.98
    25571 
    25572 > surface dust #52.3 size 4.98
    25573 
    25574 [Repeated 1 time(s)]
    25575 
    25576 > volume #52.3 level 0.009403
    25577 
    25578 > surface dust #52.3 size 4.98
    25579 
    25580 > select clear
    25581 
    25582 > volume #52.1 level 0.008861
    25583 
    25584 > volume #52.1 level 0.009273
    25585 
    25586 > save
    25587 > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-TFV_IF.png
    25588 > width 809 height 738 supersample 3 transparentBackground true
    25589 
    25590 > hide #53 models
    25591 
    25592 > save
    25593 > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-TFV_IF.png
    25594 > width 809 height 738 supersample 3 transparentBackground true
    25595 
    25596 > hide #!52 models
    25597 
    25598 > hide #!52.1 models
    25599 
    25600 > hide #!52.2 models
    25601 
    25602 > hide #!52.3 models
    25603 
    25604 > hide #!52.4 models
    25605 
    25606 > hide #2.1 models
    25607 
    25608 > show #!5 models
    25609 
    25610 > show #!4 models
    25611 
    25612 > show #4.1 models
    25613 
    25614 > color #4 #e59900ff models
    25615 
    25616 > hide #!4 models
    25617 
    25618 > select #5: 601
    25619 
    25620 19 atoms, 20 bonds, 1 residue, 1 model selected 
    25621 
    25622 > color sel hot pink
    25623 
    25624 > save /Users/dout2/Downloads/OAT1_ligand_Colored_domain.cxs includeMaps true
    25625 
    25626 > select clear
    25627 
    25628 > show #!4 models
    25629 
    25630 > color zone #4 near #5 distance 4.98
    25631 
    25632 > color zone #4 near #5 distance 3
    25633 
    25634 [Repeated 1 time(s)]
    25635 
    25636 > volume #4 level 0.00975
    25637 
    25638 > color zone #4 near #5 distance 2.9
    25639 
    25640 > color zone #4 near #5 distance 2.8
    25641 
    25642 > color zone #4 near #5 distance 2.7
    25643 
    25644 > color zone #4 near #5 distance 2.6
    25645 
    25646 > color zone #4 near #5 distance 2.5
    25647 
    25648 > color zone #4 near #5 distance 2.4
    25649 
    25650 > color zone #4 near #5 distance 2.3
    25651 
    25652 > color zone #4 near #5 distance 2.2
    25653 
    25654 > color zone #4 near #5 distance 2.1
    25655 
    25656 > color zone #4 near #5 distance 2
    25657 
    25658 > color zone #4 near #5 distance 3
    25659 
    25660 > color zone #4 near #5 distance 4
    25661 
    25662 > color zone #4 near #5 distance 3
    25663 
    25664 > color zone #4 near #5 distance 2
    25665 
    25666 > color zone #4 near #5 distance 2.5
    25667 
    25668 [Repeated 1 time(s)]
    25669 
    25670 > volume splitbyzone #4
    25671 
    25672 Opened rOAT1-AZT_OF.mrc 0 as #54.1, grid size 320,320,320, pixel 0.83, shown
    25673 at level 0.00975, step 1, values float32 
    25674 Opened rOAT1-AZT_OF.mrc 1 as #54.2, grid size 320,320,320, pixel 0.83, shown
    25675 at level 0.00975, step 1, values float32 
    25676 Opened rOAT1-AZT_OF.mrc 2 as #54.3, grid size 320,320,320, pixel 0.83, shown
    25677 at level 0.00975, step 1, values float32 
    25678 Opened rOAT1-AZT_OF.mrc 3 as #54.4, grid size 320,320,320, pixel 0.83, shown
    25679 at level 0.00975, step 1, values float32 
    25680 
    25681 > hide #!5 models
    25682 
    25683 > surface dust #54.1 size 4.98
    25684 
    25685 [Repeated 1 time(s)]
    25686 
    25687 > surface dust #54.2 size 4.98
    25688 
    25689 > surface dust #54.3 size 4.98
    25690 
    25691 > volume #54.3 level 0.007096
    25692 
    25693 > surface dust #54.4 size 4.98
    25694 
    25695 > surface dust #54.2 size 4.98
    25696 
    25697 > surface dust #54.1 size 4.98
    25698 
    25699 > surface dust #54.4 size 4.98
    25700 
    25701 > surface dust #54.3 size 4.98
    25702 
    25703 > select clear
    25704 
    25705 > volume #54.3 level 0.008865
    25706 
    25707 > hide #!54 models
    25708 
    25709 > show #!5 models
    25710 
    25711 > show #!12 models
    25712 
    25713 > hide #!12 models
    25714 
    25715 > show #!54 models
    25716 
    25717 > hide #!5 models
    25718 
    25719 > surface dust #54.1 size 1
    25720 
    25721 > surface dust #54.1 size 10
    25722 
    25723 > surface dust #54.1 size 8
    25724 
    25725 > surface dust #54.1 size 7
    25726 
    25727 > surface dust #54.1 size 6
    25728 
    25729 > surface dust #54.1 size 5
    25730 
    25731 > surface dust #54.1 size 6
    25732 
    25733 > save
    25734 > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-TFV_OF.png
    25735 > width 809 height 738 supersample 3 transparentBackground true
    25736 
    25737 > hide #!54 models
    25738 
    25739 > show #8 models
    25740 
    25741 > show #!7 models
    25742 
    25743 > show #7.1 models
    25744 
    25745 > color #7 #e59900ff models
    25746 
    25747 > select add #8
    25748 
    25749 3912 atoms, 3985 bonds, 522 residues, 1 model selected 
     1300[deleted to fit within ticket limits]
     1301
    257501302
    257511303> select subtract #8