Changes between Initial Version and Version 1 of Ticket #20294


Ignore:
Timestamp:
May 8, 2026, 12:00:53 PM (4 days ago)
Author:
Tom Goddard
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #20294

    • Property Component Unassigned → Sequence
    • Property Owner set to Eric Pettersen
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → assigned
    • Property Summary ChimeraX bug report submission → Crash trying to render GUI with hundreds of sequence viewers

  • Ticket #20294 – Description

    initial v1  
    28272827Shift along axis 55.44158488 
    28282828 
    2829 
    2830 > view matrix models
    2831 > #1,-0.34306,0.064653,-0.93709,202.25,-0.15112,-0.98843,-0.012871,197.23,-0.92708,0.1372,0.34886,143.06
    2832 
    2833 > view matrix models
    2834 > #1,0.89084,0.24868,-0.38022,79.922,0.1402,-0.94652,-0.29059,192.22,-0.43215,0.20556,-0.87806,178.59
    2835 
    2836 > view matrix models
    2837 > #1,0.98069,0.15076,0.12459,50.828,0.17789,-0.95233,-0.24786,187.69,0.081282,0.26523,-0.96075,146.99
    2838 
    2839 > transparency #2 50
    2840 
    2841 > view matrix models
    2842 > #1,0.29239,0.037619,0.95556,53.368,0.22932,-0.97283,-0.03187,173.11,0.9284,0.22844,-0.29308,56.382
    2843 
    2844 > view matrix models
    2845 > #1,-0.29179,0.14333,0.94568,84.773,0.13863,-0.97193,0.19008,165.94,0.94638,0.18656,0.26373,25.435
    2846 
    2847 > fitmap #1 inMap #2
    2848 
    2849 Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
    2850 using 2975 atoms 
    2851 average map value = 0.05731, steps = 92 
    2852 shifted from previous position = 3.83 
    2853 rotated from previous position = 8.94 degrees 
    2854 atoms outside contour = 1851, contour level = 0.066523 
    2855  
    2856 Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
    2857 coordinates: 
    2858 Matrix rotation and translation 
    2859 -0.32142151 0.28922900 0.90168442 78.62508488 
    2860 0.10483022 -0.93549119 0.33744164 157.26649378 
    2861 0.94111574 0.20298478 0.27036706 21.13366302 
    2862 Axis -0.58056816 -0.17025957 -0.79621121 
    2863 Axis point 36.79057462 75.39561878 -0.00000000 
    2864 Rotation angle (degrees) 173.35036530 
    2865 Shift along axis -89.25020548 
    2866  
    2867 
    2868 > fitmap #1 inMap #2
    2869 
    2870 Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
    2871 using 2975 atoms 
    2872 average map value = 0.05731, steps = 76 
    2873 shifted from previous position = 0.0143 
    2874 rotated from previous position = 0.0108 degrees 
    2875 atoms outside contour = 1850, contour level = 0.066523 
    2876  
    2877 Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
    2878 coordinates: 
    2879 Matrix rotation and translation 
    2880 -0.32139468 0.28930309 0.90167022 78.61286146 
    2881 0.10496741 -0.93543603 0.33755190 157.24594170 
    2882 0.94110961 0.20313337 0.27027676 21.11828838 
    2883 Axis -0.58058094 -0.17034675 -0.79618324 
    2884 Axis point 36.78722862 75.38632197 0.00000000 
    2885 Rotation angle (degrees) 173.35241654 
    2886 Shift along axis -89.24149146 
    2887  
    2888 
    2889 > view matrix models
    2890 > #1,0.48423,0.47971,0.73171,25.463,0.23276,-0.87679,0.42079,140.68,0.84341,-0.033442,-0.53622,88.647
    2891 
    2892 > fitmap #1 inMap #2
    2893 
    2894 Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
    2895 using 2975 atoms 
    2896 average map value = 0.05854, steps = 96 
    2897 shifted from previous position = 2.57 
    2898 rotated from previous position = 9.29 degrees 
    2899 atoms outside contour = 1796, contour level = 0.066523 
    2900  
    2901 Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
    2902 coordinates: 
    2903 Matrix rotation and translation 
    2904 0.39156198 0.46621567 0.79329828 28.63896931 
    2905 0.32834063 -0.87617582 0.35285743 137.96501568 
    2906 0.85957643 0.12230650 -0.49615469 78.33453532 
    2907 Axis -0.83325343 -0.23954143 -0.49830575 
    2908 Axis point 0.00000000 66.13906102 25.80824474 
    2909 Rotation angle (degrees) 172.04797842 
    2910 Shift along axis -95.94640636 
    2911  
    2912 
    2913 > fitmap #1 inMap #2
    2914 
    2915 Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
    2916 using 2975 atoms 
    2917 average map value = 0.05854, steps = 72 
    2918 shifted from previous position = 0.00208 
    2919 rotated from previous position = 0.0113 degrees 
    2920 atoms outside contour = 1796, contour level = 0.066523 
    2921  
    2922 Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
    2923 coordinates: 
    2924 Matrix rotation and translation 
    2925 0.39171342 0.46612484 0.79327690 28.63726861 
    2926 0.32836586 -0.87622221 0.35271873 137.97292978 
    2927 0.85949779 0.12232039 -0.49628748 78.34647546 
    2928 Axis -0.83330036 -0.23950649 -0.49824406 
    2929 Axis point 0.00000000 66.14388335 25.81952433 
    2930 Rotation angle (degrees) 172.05372561 
    2931 Shift along axis -95.94452502 
    2932  
    2933 
    2934 > view matrix models
    2935 > #1,0.76487,0.62103,0.17117,31.524,0.60943,-0.78369,0.12011,127.91,0.20873,0.012451,-0.97789,154.56
    2936 
    2937 > fitmap #1 inMap #2
    2938 
    2939 Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
    2940 using 2975 atoms 
    2941 average map value = 0.05756, steps = 152 
    2942 shifted from previous position = 4.36 
    2943 rotated from previous position = 22.9 degrees 
    2944 atoms outside contour = 1854, contour level = 0.066523 
    2945  
    2946 Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
    2947 coordinates: 
    2948 Matrix rotation and translation 
    2949 0.91851505 0.27415782 0.28489928 35.47934780 
    2950 0.28051968 -0.95965858 0.01908170 161.02943922 
    2951 0.27863743 0.06239303 -0.95836751 146.25557472 
    2952 Axis 0.97941439 0.14160128 0.14386290 
    2953 Axis point 0.00000000 77.18823065 71.36819300 
    2954 Rotation angle (degrees) 178.73303939 
    2955 Shift along axis 78.59170916 
    2956  
    2957 
    2958 > view matrix models
    2959 > #1,0.70928,0.23412,0.66491,29.192,0.22662,-0.9689,0.099416,160.36,0.6675,0.080168,-0.74028,107.68
    2960 
    2961 > view matrix models
    2962 > #1,0.38932,0.16756,0.90573,39.677,0.11688,-0.98435,0.13187,166.42,0.91366,0.054523,-0.40281,73.929
    2963 
    2964 > view matrix models
    2965 > #1,0.33533,0.23749,0.91168,38.512,0.22246,-0.9603,0.16833,156.1,0.91546,0.14637,-0.37485,66.587
    2966 
    2967 > view matrix models
    2968 > #1,0.33533,0.23749,0.91168,38.861,0.22246,-0.9603,0.16833,151.64,0.91546,0.14637,-0.37485,67.054
    2969 
    2970 > view matrix models
    2971 > #1,0.34573,0.097318,0.93327,45.492,0.021529,-0.99517,0.095797,170.8,0.93809,-0.013027,-0.34615,73.665
    2972 
    2973 > fitmap #1 inMap #2
    2974 
    2975 Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
    2976 using 2975 atoms 
    2977 average map value = 0.05854, steps = 136 
    2978 shifted from previous position = 9.44 
    2979 rotated from previous position = 25.1 degrees 
    2980 atoms outside contour = 1797, contour level = 0.066523 
    2981  
    2982 Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
    2983 coordinates: 
    2984 Matrix rotation and translation 
    2985 0.39128073 0.46623746 0.79342424 28.64047706 
    2986 0.32828593 -0.87615611 0.35295725 137.95838588 
    2987 0.85972538 0.12236464 -0.49588220 78.32133865 
    2988 Axis -0.83316813 -0.23955669 -0.49844103 
    2989 Axis point 0.00000000 66.13417831 25.79650241 
    2990 Rotation angle (degrees) 172.04571172 
    2991 Shift along axis -95.94975542 
    2992  
    2993 
    2994 > view matrix models
    2995 > #1,0.39128,0.46624,0.79342,25.073,0.32829,-0.87616,0.35296,137.6,0.85973,0.12236,-0.49588,78.077
    2996 
    2997 > view matrix models
    2998 > #1,-0.056102,0.1979,0.97862,59.23,0.073542,-0.97668,0.20173,168.77,0.99571,0.083287,0.04024,40.63
    2999 
    3000 > view matrix models
    3001 > #1,-0.064697,0.19676,0.97831,59.866,-0.033318,-0.98025,0.19495,176.2,0.99735,-0.019983,0.069975,45.097
    3002 
    3003 > view matrix models
    3004 > #1,-0.064697,0.19676,0.97831,60.856,-0.033318,-0.98025,0.19495,173.38,0.99735,-0.019983,0.069975,44.14
    3005 
    3006 > view matrix models
    3007 > #1,-0.064697,0.19676,0.97831,62.425,-0.033318,-0.98025,0.19495,171.85,0.99735,-0.019983,0.069975,46.927
    3008 
    3009 > view matrix models
    3010 > #1,0.048374,0.23427,0.97097,53.348,-0.027021,-0.97144,0.23574,168.54,0.99846,-0.037639,-0.040662,54.362
    3011 
    3012 > fitmap #1 inMap #2
    3013 
    3014 Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
    3015 using 2975 atoms 
    3016 average map value = 0.05548, steps = 116 
    3017 shifted from previous position = 2.18 
    3018 rotated from previous position = 10.2 degrees 
    3019 atoms outside contour = 1897, contour level = 0.066523 
    3020  
    3021 Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
    3022 coordinates: 
    3023 Matrix rotation and translation 
    3024 0.15476290 0.36480201 0.91813285 40.06056626 
    3025 0.00453943 -0.92958252 0.36858613 155.48377322 
    3026 0.98794121 -0.05287566 -0.14552088 61.55028255 
    3027 Axis -0.75418435 -0.12491849 -0.64467149 
    3028 Axis point 0.00000000 74.79947560 0.01397902 
    3029 Rotation angle (degrees) 163.77466905 
    3030 Shift along axis -89.31556288 
    3031  
    3032 
    3033 > view matrix models
    3034 > #1,0.15476,0.3648,0.91813,43.614,0.0045394,-0.92958,0.36859,155.22,0.98794,-0.052876,-0.14552,59.521
    3035 
    3036 > view matrix models
    3037 > #1,-0.2078,0.33394,0.9194,68.56,-0.052237,-0.94237,0.33048,161.84,0.97677,0.020648,0.21327,34.9
    3038 
    3039 > view matrix models
    3040 > #1,-0.21574,0.16972,0.96159,76.632,-0.13117,-0.98089,0.1437,180.08,0.9676,-0.095125,0.23388,41.35
    3041 
    3042 > fitmap #1 inMap #2
    3043 
    3044 Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
    3045 using 2975 atoms 
    3046 average map value = 0.05783, steps = 140 
    3047 shifted from previous position = 8.76 
    3048 rotated from previous position = 14.8 degrees 
    3049 atoms outside contour = 1859, contour level = 0.066523 
    3050  
    3051 Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
    3052 coordinates: 
    3053 Matrix rotation and translation 
    3054 -0.45352763 0.10818223 0.88465208 99.24914335 
    3055 -0.11633057 -0.99129935 0.06158562 193.39501529 
    3056 0.88361750 -0.07498130 0.46216655 30.32738546 
    3057 Axis -0.51968455 0.00393692 -0.85434915 
    3058 Axis point 47.88058461 94.47454852 0.00000000 
    3059 Rotation angle (degrees) 172.44984306 
    3060 Shift along axis -76.72704192 
    3061  
    3062 
    3063 > view matrix models
    3064 > #1,-0.44996,0.138,0.88232,97.338,-0.1451,-0.98616,0.080249,193.83,0.88118,-0.091912,0.46376,31.423
    3065 
    3066 > view matrix models
    3067 > #1,-0.44996,0.138,0.88232,96.943,-0.1451,-0.98616,0.080249,180.07,0.88118,-0.091912,0.46376,31.456
    3068 
    3069 > fitmap #1 inMap #2
    3070 
    3071 Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
    3072 using 2975 atoms 
    3073 average map value = 0.05816, steps = 144 
    3074 shifted from previous position = 5.29 
    3075 rotated from previous position = 25.5 degrees 
    3076 atoms outside contour = 1860, contour level = 0.066523 
    3077  
    3078 Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
    3079 coordinates: 
    3080 Matrix rotation and translation 
    3081 -0.76791109 0.07342342 0.63633447 137.05037337 
    3082 0.02287887 -0.98963117 0.14179815 171.02871657 
    3083 0.64014773 0.12344698 0.75826890 16.52925526 
    3084 Axis -0.34041716 -0.07073658 -0.93760999 
    3085 Axis point 66.71618726 84.08739228 0.00000000 
    3086 Rotation angle (degrees) 178.45546636 
    3087 Shift along axis -74.25028018 
    3088  
    3089 
    3090 > volume flip #2 axis z
    3091 
    3092 Opened cryosparc_P371_J880_003_volume_map.mrc z flip as #3, grid size
    3093 300,300,300, pixel 0.867, shown at step 1, values float32 
    3094 
    3095 > fitmap #1 inMap #2
    3096 
    3097 Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
    3098 using 2975 atoms 
    3099 average map value = 0.05816, steps = 44 
    3100 shifted from previous position = 0.00304 
    3101 rotated from previous position = 0.0131 degrees 
    3102 atoms outside contour = 1859, contour level = 0.066523 
    3103  
    3104 Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
    3105 coordinates: 
    3106 Matrix rotation and translation 
    3107 -0.76779231 0.07330789 0.63649111 137.03880955 
    3108 0.02299050 -0.98964048 0.14171507 171.02535003 
    3109 0.64028619 0.12344099 0.75815296 16.52599590 
    3110 Axis -0.34050650 -0.07071503 -0.93757917 
    3111 Axis point 66.70481841 84.08969330 0.00000000 
    3112 Rotation angle (degrees) 178.46235923 
    3113 Shift along axis -74.25109879 
    3114  
    3115 
    3116 > view matrix models
    3117 > #1,-0.52389,0.12388,0.84273,106.41,0.091727,-0.97541,0.20041,162.36,0.84683,0.18229,0.49964,14.777
    3118 
    3119 > select add #3
    3120 
    3121 2975 atoms, 2968 bonds, 437 residues, 3 models selected 
    3122 
    3123 > select subtract #3
    3124 
    3125 2975 atoms, 2968 bonds, 437 residues, 1 model selected 
    3126 
    3127 > view matrix models
    3128 > #1,-0.52389,0.12388,0.84273,105.24,0.091727,-0.97541,0.20041,169.49,0.84683,0.18229,0.49964,54.589
    3129 
    3130 > view matrix models
    3131 > #1,-0.52389,0.12388,0.84273,103,0.091727,-0.97541,0.20041,168.04,0.84683,0.18229,0.49964,53.744
    3132 
    3133 > fitmap #1 inMap #2
    3134 
    3135 Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
    3136 using 2975 atoms 
    3137 average map value = 0.05198, steps = 396 
    3138 shifted from previous position = 26.6 
    3139 rotated from previous position = 41.8 degrees 
    3140 atoms outside contour = 2024, contour level = 0.066523 
    3141  
    3142 Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
    3143 coordinates: 
    3144 Matrix rotation and translation 
    3145 -0.40282969 0.31103532 0.86080501 84.94134983 
    3146 0.59685966 -0.62373813 0.50468732 103.56065454 
    3147 0.69389249 0.71708282 0.06561581 32.32204409 
    3148 Axis 0.54006522 0.42441412 0.72677522 
    3149 Axis point 26.67261820 43.96459459 0.00000000 
    3150 Rotation angle (degrees) 168.65952926 
    3151 Shift along axis 113.31733317 
    3152  
    3153 
    3154 > view matrix models
    3155 > #1,-0.43926,0.065153,0.89599,100.22,0.59516,-0.72598,0.34457,119.21,0.67293,0.68462,0.28012,23.176
    3156 
    3157 > view matrix models
    3158 > #1,-0.43926,0.065153,0.89599,90.909,0.59516,-0.72598,0.34457,101.79,0.67293,0.68462,0.28012,39.972
    3159 
    3160 > view matrix models
    3161 > #1,-0.86466,-0.41381,0.28483,182.78,0.49939,-0.76955,0.39798,107.46,0.054503,0.48636,0.87206,57.135
    3162 
    3163 > view matrix models
    3164 > #1,-0.41714,-0.50359,-0.75657,220.21,0.34751,-0.85757,0.37922,123.61,-0.83978,-0.10473,0.53273,169.98
    3165 
    3166 > view matrix models
    3167 > #1,0.75417,0.076431,-0.65222,104.02,0.19721,-0.97372,0.11393,155.7,-0.62637,-0.21455,-0.74942,237.56
    3168 
    3169 > view matrix models
    3170 > #1,0.59893,0.091914,-0.79551,121.31,0.19286,-0.98071,0.031893,161.17,-0.77723,-0.17253,-0.6051,236.24
    3171 
    3172 > view matrix models
    3173 > #1,0.59893,0.091914,-0.79551,120.05,0.19286,-0.98071,0.031893,163.86,-0.77723,-0.17253,-0.6051,238.3
    3174 
    3175 > view matrix models
    3176 > #1,0.60587,0.10394,-0.78874,118.48,0.22025,-0.97459,0.040753,161.22,-0.76446,-0.19841,-0.61337,239.55
    3177 
    3178 > view matrix models
    3179 > #1,0.60587,0.10394,-0.78874,137.03,0.22025,-0.97459,0.040753,164.86,-0.76446,-0.19841,-0.61337,244.11
    3180 
    3181 > fitmap #1 inMap #2
    3182 
    3183 Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
    3184 using 2975 atoms 
    3185 average map value = 0.05241, steps = 240 
    3186 shifted from previous position = 27.2 
    3187 rotated from previous position = 10.6 degrees 
    3188 atoms outside contour = 2020, contour level = 0.066523 
    3189  
    3190 Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
    3191 coordinates: 
    3192 Matrix rotation and translation 
    3193 0.57403834 -0.00393553 -0.81881897 142.71357757 
    3194 0.04701479 -0.99818033 0.03775763 187.83819388 
    3195 -0.81747758 -0.06017093 -0.57280875 212.09998405 
    3196 Axis -0.88704943 -0.01215043 0.46151455 
    3197 Axis point 0.00000000 96.46648529 140.25698861 
    3198 Rotation angle (degrees) 176.83571969 
    3199 Shift along axis -30.98908429 
    3200  
    3201 
    3202 > view matrix models
    3203 > #1,0.50366,0.028512,-0.86343,147.82,0.16923,-0.98335,0.066244,177.48,-0.84716,-0.17948,-0.5001,217.05
    3204 
    3205 > view matrix models
    3206 > #1,0.50366,0.028512,-0.86343,159.38,0.16923,-0.98335,0.066244,163.53,-0.84716,-0.17948,-0.5001,218.36
    3207 
    3208 > view matrix models
    3209 > #1,0.77888,-0.021397,-0.6268,131.11,0.011385,-0.99877,0.048242,175.59,-0.62706,-0.044711,-0.77768,212.22
    3210 
    3211 > view matrix models
    3212 > #1,0.80541,-0.036391,-0.5916,128.29,-0.023432,-0.99929,0.029569,178.93,-0.59225,-0.0099531,-0.80569,209.51
    3213 
    3214 > view matrix models
    3215 > #1,0.80541,-0.036391,-0.5916,124.59,-0.023432,-0.99929,0.029569,182.08,-0.59225,-0.0099531,-0.80569,208.91
    3216 
    3217 > fitmap #1 inMap #2
    3218 
    3219 Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
    3220 using 2975 atoms 
    3221 average map value = 0.06114, steps = 180 
    3222 shifted from previous position = 15 
    3223 rotated from previous position = 14.2 degrees 
    3224 atoms outside contour = 1746, contour level = 0.066523 
    3225  
    3226 Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
    3227 coordinates: 
    3228 Matrix rotation and translation 
    3229 0.85347860 0.03851228 -0.51970287 104.90951223 
    3230 -0.07623353 -0.97731057 -0.19761705 201.13931543 
    3231 -0.51552180 0.20828070 -0.83117774 180.17182734 
    3232 Axis 0.96224006 -0.00991186 -0.27202175 
    3233 Axis point 0.00000000 90.37179533 116.08940430 
    3234 Rotation angle (degrees) 167.82414204 
    3235 Shift along axis 49.94381521 
    3236  
    3237 
    3238 > view matrix models
    3239 > #1,0.85348,0.038512,-0.5197,94.645,-0.076234,-0.97731,-0.19762,192.73,-0.51552,0.20828,-0.83118,215.52
    3240 
    3241 > fitmap #1 inMap #2
    3242 
    3243 Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
    3244 using 2975 atoms 
    3245 average map value = 0.04998, steps = 228 
    3246 shifted from previous position = 24.7 
    3247 rotated from previous position = 22.8 degrees 
    3248 atoms outside contour = 2007, contour level = 0.066523 
    3249  
    3250 Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
    3251 coordinates: 
    3252 Matrix rotation and translation 
    3253 0.83373907 0.05761081 -0.54914494 106.68752994 
    3254 -0.27258804 -0.82195371 -0.50008786 229.20333513 
    3255 -0.48018219 0.56663312 -0.66959090 165.21182517 
    3256 Axis 0.95346344 -0.06164073 -0.29514047 
    3257 Axis point 0.00000000 89.71271679 136.26536856 
    3258 Rotation angle (degrees) 145.98619039 
    3259 Shift along axis 38.83370161 
    3260  
    3261 
    3262 > view matrix models
    3263 > #1,0.85957,-0.051768,-0.50839,109.34,-0.30914,-0.84485,-0.43665,229.25,-0.40691,0.5325,-0.74221,166.84
    3264 
    3265 > view matrix models
    3266 > #1,0.85957,-0.051768,-0.50839,105.72,-0.30914,-0.84485,-0.43665,214.62,-0.40691,0.5325,-0.74221,185.48
    3267 
    3268 > view matrix models
    3269 > #1,0.90687,0.19702,-0.37252,79.626,0.12723,-0.97073,-0.20369,180.91,-0.40175,0.13732,-0.90539,218.74
    3270 
    3271 > view matrix models
    3272 > #1,0.67914,0.18357,0.71068,32.037,0.24568,-0.96923,0.015585,160.52,0.69167,0.16401,-0.70334,135.59
    3273 
    3274 > view matrix models
    3275 > #1,0.17493,0.05579,0.983,56.185,0.11322,-0.99291,0.036205,169.22,0.97805,0.10496,-0.18,90.508
    3276 
    3277 > view matrix models
    3278 > #1,0.77968,0.065182,0.62277,37.951,0.11391,-0.99274,-0.038712,173.52,0.61572,0.10113,-0.78145,148.81
    3279 
    3280 > view matrix models
    3281 > #1,0.92537,0.30742,-0.22176,62.951,0.27327,-0.94648,-0.17175,168.25,-0.26269,0.09833,-0.95986,215.41
    3282 
    3283 > view matrix models
    3284 > #1,0.70434,0.40439,-0.58342,92.157,0.29038,-0.9141,-0.28304,171.65,-0.64776,0.02994,-0.76126,232.61
    3285 
    3286 > view matrix models
    3287 > #1,0.63232,0.36591,-0.68285,104.88,0.25844,-0.93057,-0.25933,173.32,-0.73033,-0.012492,-0.68298,235.92
    3288 
    3289 > view matrix models
    3290 > #1,0.63232,0.36591,-0.68285,105.28,0.25844,-0.93057,-0.25933,173.87,-0.73033,-0.012492,-0.68298,234.43
    3291 
    3292 > view matrix models
    3293 > #1,0.62644,0.35038,-0.69628,107.38,0.25038,-0.93639,-0.24594,173.97,-0.73816,-0.020267,-0.67432,234.9
    3294 
    3295 > fitmap #1 inMap #2
    3296 
    3297 Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
    3298 using 2975 atoms 
    3299 average map value = 0.04135, steps = 172 
    3300 shifted from previous position = 17.5 
    3301 rotated from previous position = 15.7 degrees 
    3302 atoms outside contour = 2209, contour level = 0.066523 
    3303  
    3304 Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
    3305 coordinates: 
    3306 Matrix rotation and translation 
    3307 0.64106806 0.54805599 -0.53727682 84.29416786 
    3308 0.45670740 -0.83502441 -0.30684294 171.83349628 
    3309 -0.61680637 -0.04867109 -0.78560870 224.33733641 
    3310 Axis 0.90532451 0.27888420 -0.32032972 
    3311 Axis point 0.00000000 63.39099370 133.30398496 
    3312 Rotation angle (degrees) 171.80252826 
    3313 Shift along axis 52.37330856 
    3314  
    3315 
    3316 > volume #3 level 0.08411
    3317 
    3318 > view matrix models
    3319 > #1,0.89403,0.11377,0.43333,38.242,0.12475,-0.99218,0.0031177,184.59,0.43029,0.051272,-0.90123,158.14
    3320 
    3321 > view matrix models
    3322 > #1,-0.18632,0.03739,0.98178,79.976,-0.079477,-0.99657,0.02287,196.75,0.97927,-0.073767,0.18865,67.401
    3323 
    3324 > view matrix models
    3325 > #1,-0.90953,0.27518,-0.3115,186.77,-0.18965,-0.94164,-0.2781,217.91,-0.36985,-0.19387,0.90864,118.99
    3326 
    3327 > view matrix models
    3328 > #1,0.24398,0.16972,-0.95481,156.97,0.38319,-0.92132,-0.065848,167.79,-0.89086,-0.34981,-0.28982,231.39
    3329 
    3330 > view matrix models
    3331 > #1,0.42166,0.25626,-0.86979,135.42,0.41641,-0.90683,-0.065311,164.75,-0.80549,-0.33465,-0.48908,236.59
    3332 
    3333 > view matrix models
    3334 > #1,0.47933,0.24843,-0.84174,130.58,0.4184,-0.90778,-0.029658,162.61,-0.77148,-0.33797,-0.53907,237.53
    3335 
    3336 > ui mousemode right "translate selected models"
    3337 
    3338 > view matrix models
    3339 > #1,0.47933,0.24843,-0.84174,128.8,0.4184,-0.90778,-0.029658,153.85,-0.77148,-0.33797,-0.53907,247.51
    3340 
    3341 > fitmap #1 inMap #3
    3342 
    3343 Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc z flip
    3344 (#3) using 2975 atoms 
    3345 average map value = 0.05446, steps = 68 
    3346 shifted from previous position = 3.18 
    3347 rotated from previous position = 7.84 degrees 
    3348 atoms outside contour = 2178, contour level = 0.08411 
    3349  
    3350 Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc z
    3351 flip (#3) coordinates: 
    3352 Matrix rotation and translation 
    3353 0.52841759 0.14565472 -0.83639676 133.99651702 
    3354 0.41790523 -0.90217777 0.10691341 147.19357847 
    3355 -0.73900613 -0.40602951 -0.53759648 249.57659595 
    3356 Axis -0.87112860 -0.16539807 0.46236180 
    3357 Axis point 0.00000000 83.46704951 147.99690601 
    3358 Rotation angle (degrees) 162.87766715 
    3359 Shift along axis -25.67904816 
    3360  
    3361 
    3362 > view matrix models
    3363 > #1,0.228,0.04128,-0.97279,167.46,0.36006,-0.93185,0.04485,156.3,-0.90464,-0.36049,-0.22733,239.34
    3364 
    3365 > view matrix models
    3366 > #1,0.228,0.04128,-0.97279,168.72,0.36006,-0.93185,0.04485,153.1,-0.90464,-0.36049,-0.22733,238.66
    3367 
    3368 > fitmap #1 inMap #3
    3369 
    3370 Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc z flip
    3371 (#3) using 2975 atoms 
    3372 average map value = 0.08066, steps = 176 
    3373 shifted from previous position = 5.39 
    3374 rotated from previous position = 39.4 degrees 
    3375 atoms outside contour = 1661, contour level = 0.08411 
    3376  
    3377 Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc z
    3378 flip (#3) coordinates: 
    3379 Matrix rotation and translation 
    3380 -0.38244590 0.10991711 -0.91741668 203.00581119 
    3381 0.07750617 -0.98558322 -0.15039445 183.86146589 
    3382 -0.92072141 -0.12862319 0.36841301 193.39522834 
    3383 Axis 0.55561740 0.08433916 -0.82714945 
    3384 Axis point 167.56182272 100.48395710 0.00000000 
    3385 Rotation angle (degrees) 178.87739199 
    3386 Shift along axis -31.66647401 
    3387  
    3388 
    3389 > save /Users/apple/Downloads/csparc.cxs includeMaps true
    3390 
    3391 > select subtract #1
    3392 
    3393 Nothing selected 
    3394 
    3395 > select add #3
    3396 
    3397 2 models selected 
    3398 
    3399 > save /Users/apple/Downloads/flipped_J880.mrc models #3
    3400 
    3401 > open /Users/apple/Downloads/3C11_Fab_D_1292144377_model-annotate_P1_HL-
    3402 > coot-0.pdb /Users/apple/Downloads/1ezx_moved-coot-0.pdb
    3403 
    3404 Summary of feedback from opening
    3405 /Users/apple/Downloads/3C11_Fab_D_1292144377_model-annotate_P1_HL-coot-0.pdb 
    3406 --- 
    3407 warnings | Start residue of secondary structure not found: HELIX 8 AA8 THR I 28 TYR I 32 5 5 
    3408 Start residue of secondary structure not found: HELIX 9 AA9 ASN I 73 LYS I 75
    3409 5 3 
    3410 Start residue of secondary structure not found: HELIX 10 AB1 LYS I 83 THR I 87
    3411 5 5 
    3412 Start residue of secondary structure not found: HELIX 11 AB2 SER I 156 SER I
    3413 158 5 3 
    3414 Start residue of secondary structure not found: HELIX 12 AB3 PRO I 200 SER I
    3415 203 5 4 
    3416 49 messages similar to the above omitted 
    3417 Cannot find LINK/SSBOND residue CYS (22 ) 
    3418 Cannot find LINK/SSBOND residue CYS (128 ) 
    3419 Cannot find LINK/SSBOND residue CYS (140 ) 
    3420 Cannot find LINK/SSBOND residue CYS (24 ) 
    3421 Cannot find LINK/SSBOND residue CYS (135 ) 
    3422  
    3423 3C11_Fab_D_1292144377_model-annotate_P1_HL-coot-0.pdb title: 
    3424 Fab fragment of an antibody that recognises all conformations of
    3425 α-1-antitrypsin [more info...] 
    3426  
    3427 Chain information for 3C11_Fab_D_1292144377_model-annotate_P1_HL-coot-0.pdb #4 
    3428 --- 
    3429 Chain | Description 
    3430 H | fab 3C11 heavy chain 
    3431 L | fab 3C11 light chain 
    3432  
    3433 128 atoms have alternate locations. Control/examine alternate locations with
    3434 Altloc Explorer [start tool...] or the altlocs command. 
    3435 Chain information for 1ezx_moved-coot-0.pdb #5 
    3436 --- 
    3437 Chain | Description 
    3438 A | No description available 
    3439 B | No description available 
    3440  
    3441 Computing secondary structure 
    3442 
    3443 > hide #!1 models
    3444 
    3445 > show #!1 models
    3446 
    3447 > hide #!1 models
    3448 
    3449 > show #!1 models
    3450 
    3451 > hide #!1 models
    3452 
    3453 > show #!1 models
    3454 
    3455 > hide #!1 models
    3456 
    3457 > show #!1 models
    3458 
    3459 > hide #!1 models
    3460 
    3461 > save /Users/apple/Downloads/csparc.cxs includeMaps true
    3462 
    3463 > open /Users/apple/Downloads/3C11_Fab_D_1292144377_model-annotate_P1_HL.pdb
    3464 
    3465 Summary of feedback from opening
    3466 /Users/apple/Downloads/3C11_Fab_D_1292144377_model-annotate_P1_HL.pdb 
    3467 --- 
    3468 warnings | Start residue of secondary structure not found: HELIX 8 AA8 THR I 28 TYR I 32 5 5 
    3469 Start residue of secondary structure not found: HELIX 9 AA9 ASN I 73 LYS I 75
    3470 5 3 
    3471 Start residue of secondary structure not found: HELIX 10 AB1 LYS I 83 THR I 87
    3472 5 5 
    3473 Start residue of secondary structure not found: HELIX 11 AB2 SER I 156 SER I
    3474 158 5 3 
    3475 Start residue of secondary structure not found: HELIX 12 AB3 PRO I 200 SER I
    3476 203 5 4 
    3477 49 messages similar to the above omitted 
    3478 Cannot find LINK/SSBOND residue CYS (22 ) 
    3479 Cannot find LINK/SSBOND residue CYS (128 ) 
    3480 Cannot find LINK/SSBOND residue CYS (140 ) 
    3481 Cannot find LINK/SSBOND residue CYS (24 ) 
    3482 Cannot find LINK/SSBOND residue CYS (135 ) 
    3483  
    3484 3C11_Fab_D_1292144377_model-annotate_P1_HL.pdb title: 
    3485 Fab fragment of an antibody that recognises all conformations of
    3486 α-1-antitrypsin [more info...] 
    3487  
    3488 Chain information for 3C11_Fab_D_1292144377_model-annotate_P1_HL.pdb #6 
    3489 --- 
    3490 Chain | Description 
    3491 H | fab 3C11 heavy chain 
    3492 L | fab 3C11 light chain 
    3493  
    3494 128 atoms have alternate locations. Control/examine alternate locations with
    3495 Altloc Explorer [start tool...] or the altlocs command. 
    3496 
    3497 > mmaker #6 to #4
    3498 
    3499 Computing secondary structure 
    3500 [Repeated 1 time(s)]  Parameters 
    3501 --- 
    3502 Chain pairing | bb 
    3503 Alignment algorithm | Needleman-Wunsch 
    3504 Similarity matrix | BLOSUM-62 
    3505 SS fraction | 0.3 
    3506 Gap open (HH/SS/other) | 18/18/6 
    3507 Gap extend | 1 
    3508 SS matrix |  |  | H | S | O 
    3509 ---|---|---|--- 
    3510 H | 6 | -9 | -6 
    3511 S |  | 6 | -6 
    3512 O |  |  | 4 
    3513 Iteration cutoff | 2 
    3514  
    3515 Matchmaker 3C11_Fab_D_1292144377_model-annotate_P1_HL-coot-0.pdb, chain L (#4)
    3516 with 3C11_Fab_D_1292144377_model-annotate_P1_HL.pdb, chain L (#6), sequence
    3517 alignment score = 1108.5 
    3518 RMSD between 208 pruned atom pairs is 0.000 angstroms; (across all 208 pairs:
    3519 0.000) 
    3520  
    3521 
    3522 > hide #!4 models
    3523 
    3524 > save /Users/apple/Downloads/csparc.cxs includeMaps true
    3525 
    3526 > open /Users/apple/Downloads/cryosparc_P371_J891_003_volume_map.mrc
    3527 
    3528 Opened cryosparc_P371_J891_003_volume_map.mrc as #7, grid size 300,300,300,
    3529 pixel 0.867, shown at level 0.0162, step 2, values float32 
    3530 
    3531 > volume #7 level 0.0734
    3532 
    3533 > select subtract #3
    3534 
    3535 Nothing selected 
    3536 
    3537 > hide #5 models
    3538 
    3539 > hide #!6 models
    3540 
    3541 > volume #7 level 0.05238
    3542 
    3543 > hide #!7 models
    3544 
    3545 > show #!6 models
    3546 
    3547 > show #5 models
    3548 
    3549 > show #!3 models
    3550 
    3551 > show #!7 models
    3552 
    3553 > hide #!7 models
    3554 
    3555 > open "/Users/apple/Downloads/cryosparc_P371_J882_005_volume_map (1).mrc"
    3556 
    3557 Opened cryosparc_P371_J882_005_volume_map (1).mrc as #8, grid size
    3558 300,300,300, pixel 0.867, shown at level 0.0235, step 2, values float32 
    3559 
    3560 > hide #5 models
    3561 
    3562 > hide #!6 models
    3563 
    3564 > volume #8 level 0.0555
    3565 
    3566 > volume flip #8 axis z
    3567 
    3568 Opened cryosparc_P371_J882_005_volume_map (1).mrc z flip as #9, grid size
    3569 300,300,300, pixel 0.867, shown at step 1, values float32 
    3570 
    3571 > volume #9 level 0.06023
    3572 
    3573 > show #!1 models
    3574 
    3575 > hide #!1 models
    3576 
    3577 > show #5 models
    3578 
    3579 > hide #5 models
    3580 
    3581 > volume copy #5
    3582 
    3583 > show #5 models
    3584 
    3585 > hide #5 models
    3586 
    3587 > show #!1 models
    3588 
    3589 > transparency #8 50
    3590 
    3591 > transparency #9 50
    3592 
    3593 > show #!4 models
    3594 
    3595 > hide #!4 models
    3596 
    3597 > show #!6 models
    3598 
    3599 > close #8
    3600 
    3601 > show #!7 models
    3602 
    3603 > hide #!7 models
    3604 
    3605 > show #!4 models
    3606 
    3607 > hide #!4 models
    3608 
    3609 > show #!3 models
    3610 
    3611 > hide #!3 models
    3612 
    3613 > show #!3 models
    3614 
    3615 > hide #!9 models
    3616 
    3617 > show #!9 models
    3618 
    3619 > hide #!9 models
    3620 
    3621 > show #!9 models
    3622 
    3623 > hide #!9 models
    3624 
    3625 > show #!9 models
    3626 
    3627 > open /Users/apple/Downloads/cryosparc_P371_J881_class_08_00006_volume.mrc
    3628 
    3629 Opened cryosparc_P371_J881_class_08_00006_volume.mrc as #8, grid size
    3630 180,180,180, pixel 1.44, shown at level 0.0542, step 1, values float32 
    3631 
    3632 > volume #8 level 0.122
    3633 
    3634 > volume flip #8 axis z
    3635 
    3636 Opened cryosparc_P371_J881_class_08_00006_volume.mrc z flip as #10, grid size
    3637 180,180,180, pixel 1.44, shown at step 1, values float32 
    3638 
    3639 > select down
    3640 
    3641 Nothing selected 
    3642 
    3643 > select down
    3644 
    3645 Nothing selected 
    3646 
    3647 > transparency #8 50
    3648 
    3649 > transparency #10 50
    3650 
    3651 > hide #!10 models
    3652 
    3653 > show #!9 models
    3654 
    3655 > hide #!9 models
    3656 
    3657 > show #!8 models
    3658 
    3659 > hide #!8 models
    3660 
    3661 > close #8
    3662 
    3663 > show #!7 models
    3664 
    3665 > hide #!7 models
    3666 
    3667 > close #7
    3668 
    3669 > save /Users/apple/Downloads/csparc.cxs includeMaps true
    3670 
    3671 ——— End of log from Tue Nov 25 15:20:48 2025 ———
    3672 
    3673 opened ChimeraX session 
    3674 
    3675 > show #!3 models
    3676 
    3677 > open 5A0C fromDatabase pdb format mmcif
    3678 
    3679 5a0c title: 
    3680 Crystal Structure of human neutrophil elastase in complex with a
    3681 dihydropyrimidone inhibitor [more info...] 
    3682  
    3683 Chain information for 5a0c #7 
    3684 --- 
    3685 Chain | Description | UniProt 
    3686 A B | NEUTROPHIL ELASTASE | ELNE_HUMAN 16-252 
    3687  
    3688 Non-standard residues in 5a0c #7 
    3689 --- 
    3690 FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose;
    3691 L-fucose; fucose) 
    3692 JJV — (6S)-6-(4-cyano-2-methylsulfonyl-
    3693 phenyl)-4-methyl-2-oxidanylidene-3-[3-(trifluoromethyl)phenyl]-1,6-dihydropyrimidine-5-carbonitrile 
    3694 MES — 2-(N-morpholino)-ethanesulfonic acid 
    3695 NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
    3696 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
    3697 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) 
    3698 XPE — 3,6,9,12,15,18,21,24,27-nonaoxanonacosane-1,29-diol (decaethylene
    3699 glycol) 
    3700  
    3701 5a0c mmCIF Assemblies 
    3702 --- 
    3703 1| author_and_software_defined_assembly 
    3704 2| author_and_software_defined_assembly 
    3705  
    3706 
    3707 > hide #!1 models
    3708 
    3709 > show #!1 models
    3710 
    3711 > open 1ezx fromDatabase pdb format mmcif
    3712 
    3713 1ezx title: 
    3714 Crystal structure of A serpin:protease complex [more info...] 
    3715  
    3716 Chain information for 1ezx #8 
    3717 --- 
    3718 Chain | Description | UniProt 
    3719 A | ALPHA-1-ANTITRYPSIN | A1AT_HUMAN 24-358 
    3720 B | ALPHA-1-ANTITRYPSIN | A1AT_HUMAN 359-394 
    3721 C | TRYPSIN | TRY1_BOVIN 42-245 
    3722  
    3723 
    3724 > select #8/A
    3725 
    3726 2686 atoms, 2674 bonds, 398 residues, 1 model selected 
    3727 
    3728 > mmaker #8 to #1
    3729 
    3730 Computing secondary structure 
    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 1ezx, chain A (#1) with 1ezx, chain A (#8), sequence alignment
    3747 score = 1734 
    3748 RMSD between 335 pruned atom pairs is 0.000 angstroms; (across all 335 pairs:
    3749 0.000) 
    3750  
    3751 
    3752 > select #7/B, C, D, E, F
    3753 
    3754 1965 atoms, 1848 bonds, 391 residues, 1 model selected 
    3755 
    3756 > delete #7/B, C, D, E, F
    3757 
    3758 > mmaker #7 to #8
    3759 
    3760 Computing secondary structure 
    3761 [Repeated 1 time(s)]  Parameters 
    3762 --- 
    3763 Chain pairing | bb 
    3764 Alignment algorithm | Needleman-Wunsch 
    3765 Similarity matrix | BLOSUM-62 
    3766 SS fraction | 0.3 
    3767 Gap open (HH/SS/other) | 18/18/6 
    3768 Gap extend | 1 
    3769 SS matrix |  |  | H | S | O 
    3770 ---|---|---|--- 
    3771 H | 6 | -9 | -6 
    3772 S |  | 6 | -6 
    3773 O |  |  | 4 
    3774 Iteration cutoff | 2 
    3775  
    3776 Matchmaker 1ezx, chain C (#8) with 5a0c, chain A (#7), sequence alignment
    3777 score = 241.2 
    3778 RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
    3779 3.073) 
    3780  
    3781 
    3782 > hide #7#!1,6,8 atoms
    3783 
    3784 > save /Users/apple/Downloads/csparc.cxs includeMaps true
    3785 
    3786 > open /Users/apple/Downloads/cryosparc_P371_J916_map.mrc
    3787 
    3788 Opened cryosparc_P371_J916_map.mrc as #11, grid size 300,300,300, pixel 0.867,
    3789 shown at level 0.0238, step 2, values float32 
    3790 
    3791 > volume flip #11 axis z
    3792 
    3793 Opened cryosparc_P371_J916_map.mrc z flip as #12, grid size 300,300,300, pixel
    3794 0.867, shown at step 1, values float32 
    3795 
    3796 > volume #12 level 0.06229
    3797 
    3798 > transparency #12 50
    3799 
    3800 > hide #!1 models
    3801 
    3802 > show #!1 models
    3803 
    3804 > hide #!3 models
    3805 
    3806 > show #!3 models
    3807 
    3808 > hide #!6 models
    3809 
    3810 > show #!6 models
    3811 
    3812 > hide #!8 models
    3813 
    3814 > show #!8 models
    3815 
    3816 > hide #!1 models
    3817 
    3818 > show #!1 models
    3819 
    3820 > hide #!1 models
    3821 
    3822 > hide #7 models
    3823 
    3824 > show #7 models
    3825 
    3826 > hide #!8 models
    3827 
    3828 > ui tool show "Fit in Map"
    3829 
    3830 > fitmap #7 inMap #12
    3831 
    3832 Fit molecule 5a0c (#7) to map cryosparc_P371_J916_map.mrc z flip (#12) using
    3833 1883 atoms 
    3834 average map value = 0.05726, steps = 204 
    3835 shifted from previous position = 18.9 
    3836 rotated from previous position = 30.2 degrees 
    3837 atoms outside contour = 1095, contour level = 0.06229 
    3838  
    3839 Position of 5a0c (#7) relative to cryosparc_P371_J916_map.mrc z flip (#12)
    3840 coordinates: 
    3841 Matrix rotation and translation 
    3842 -0.89591156 -0.08748371 -0.43553310 147.09781032 
    3843 0.42229009 -0.47204043 -0.77385329 138.97672191 
    3844 -0.13788968 -0.87722542 0.45984998 149.26233444 
    3845 Axis -0.17249142 -0.49666131 0.85063168 
    3846 Axis point 74.69777418 126.82872456 0.00000000 
    3847 Rotation angle (degrees) 162.56376196 
    3848 Shift along axis 32.56979814 
    3849  
    3850 
    3851 > show #!1 models
    3852 
    3853 > hide #7 models
    3854 
    3855 > show #7 models
    3856 
    3857 > volume #11 level 0.05033
    3858 
    3859 > volume #12 level 0.08057
    3860 
    3861 > open /Users/apple/Downloads/cryosparc_P371_J919_class_00_final_volume.mrc
    3862 
    3863 Opened cryosparc_P371_J919_class_00_final_volume.mrc as #13, grid size
    3864 128,128,128, pixel 2.03, shown at level 0.08, step 1, values float32 
    3865 
    3866 > transparency #18 50
    3867 
    3868 > transparency #13 50
    3869 
    3870 > hide #!13 models
    3871 
    3872 > hide #7 models
    3873 
    3874 > hide #!6 models
    3875 
    3876 > hide #!3 models
    3877 
    3878 > show #!3 models
    3879 
    3880 > hide #!3 models
    3881 
    3882 > show #!3 models
    3883 
    3884 > hide #!12 models
    3885 
    3886 > show #!12 models
    3887 
    3888 > hide #!12 models
    3889 
    3890 > show #!12 models
    3891 
    3892 > hide #!12 models
    3893 
    3894 > hide #!1 models
    3895 
    3896 > show #7 models
    3897 
    3898 > show #!8 models
    3899 
    3900 > hide #!8 models
    3901 
    3902 > show #!1 models
    3903 
    3904 > show #!13 models
    3905 
    3906 > show #!4 models
    3907 
    3908 > hide #!4 models
    3909 
    3910 > show #5 models
    3911 
    3912 > hide #5 models
    3913 
    3914 > show #!6 models
    3915 
    3916 > hide #!6 models
    3917 
    3918 > save /Users/apple/Downloads/csparc.cxs includeMaps true
    3919 
    3920 ——— End of log from Fri Nov 28 18:17:17 2025 ———
    3921 
    3922 opened ChimeraX session 
    3923 
    3924 > hide #!13 models
    3925 
    3926 > open /Users/apple/Downloads/cryosparc_P371_J937_003_volume_map.mrc
    3927 
    3928 Opened cryosparc_P371_J937_003_volume_map.mrc as #14, grid size 300,300,300,
    3929 pixel 0.867, shown at level 0.0245, step 2, values float32 
    3930 
    3931 > volume flip #14 axis z
    3932 
    3933 Opened cryosparc_P371_J937_003_volume_map.mrc z flip as #15, grid size
    3934 300,300,300, pixel 0.867, shown at step 1, values float32 
    3935 
    3936 > hide #!15 models
    3937 
    3938 > hide #!1 models
    3939 
    3940 > show #!1 models
    3941 
    3942 > combine #1 close false
    3943 
    3944 > hide #!1 models
    3945 
    3946 > show #!6 models
    3947 
    3948 > combine #6 close false
    3949 
    3950 > combine #7 close false
    3951 
    3952 > hide #7 models
    3953 
    3954 > hide #!6 models
    3955 
    3956 > hide #!3 models
    3957 
    3958 > show #!15 models
    3959 
    3960 > transparency #15 50
    3961 
    3962 > volume #15 level 0.07742
    3963 
    3964 > hide #!17 models
    3965 
    3966 > hide #18 models
    3967 
    3968 > hide #!16 models
    3969 
    3970 > show #!16 models
    3971 
    3972 > show #!17 models
    3973 
    3974 > show #18 models
    3975 
    3976 > select add #16
    3977 
    3978 2975 atoms, 2968 bonds, 437 residues, 1 model selected 
    3979 
    3980 > ui mousemode right "translate selected models"
    3981 
    3982 > view matrix models
    3983 > #16,-0.38245,0.10992,-0.91742,194.95,0.077506,-0.98558,-0.15039,187,-0.92072,-0.12862,0.36841,167.53
    3984 
    3985 > view matrix models
    3986 > #16,-0.38245,0.10992,-0.91742,191.4,0.077506,-0.98558,-0.15039,187.17,-0.92072,-0.12862,0.36841,156.11
    3987 
    3988 > view matrix models
    3989 > #16,-0.014922,0.064965,-0.99778,175.36,0.069994,-0.99537,-0.065855,183.33,-0.99744,-0.070821,0.010305,178.28
    3990 
    3991 > hide #!17 models
    3992 
    3993 > view matrix models
    3994 > #16,-0.014922,0.064965,-0.99778,182.37,0.069994,-0.99537,-0.065855,183.4,-0.99744,-0.070821,0.010305,175.03
    3995 
    3996 > view matrix models
    3997 > #16,0.94124,0.016979,-0.33731,85.904,0.1062,-0.96295,0.24788,160.88,-0.32061,-0.26914,-0.90817,197.31
    3998 
    3999 > view matrix models
    4000 > #16,0.6158,0.19853,0.76248,31.693,-0.013436,-0.96495,0.26209,167.81,0.78779,-0.17164,-0.59155,102.23
    4001 
    4002 > view matrix models
    4003 > #16,-0.056736,0.045988,0.99733,70.269,-0.1345,-0.99018,0.038008,190.1,0.98929,-0.13198,0.062364,48.953
    4004 
    4005 > view matrix models
    4006 > #16,-0.056736,0.045988,0.99733,68.694,-0.1345,-0.99018,0.038008,189.37,0.98929,-0.13198,0.062364,47.206
    4007 
    4008 > ui tool show "Fit in Map"
    4009 
    4010 > fitmap #16 inMap #15
    4011 
    4012 Fit molecule copy of 1ezx (#16) to map cryosparc_P371_J937_003_volume_map.mrc
    4013 z flip (#15) using 2975 atoms 
    4014 average map value = 0.08682, steps = 136 
    4015 shifted from previous position = 1.54 
    4016 rotated from previous position = 27.4 degrees 
    4017 atoms outside contour = 1268, contour level = 0.077423 
    4018  
    4019 Position of copy of 1ezx (#16) relative to
    4020 cryosparc_P371_J937_003_volume_map.mrc z flip (#15) coordinates: 
    4021 Matrix rotation and translation 
    4022 0.36221471 -0.11330418 0.92518250 57.47272519 
    4023 -0.01922981 -0.99328137 -0.11411544 191.48317940 
    4024 0.93189630 0.02354321 -0.36195994 67.99746912 
    4025 Axis 0.82495481 -0.04023415 0.56376482 
    4026 Axis point 0.00000000 96.53522281 19.29015841 
    4027 Rotation angle (degrees) 175.21401689 
    4028 Shift along axis 78.04281848 
    4029  
    4030 
    4031 > show #!17 models
    4032 
    4033 > select subtract #16
    4034 
    4035 Nothing selected 
    4036 
    4037 > select add #17
    4038 
    4039 3190 atoms, 3270 bonds, 2 pseudobonds, 422 residues, 3 models selected 
    4040 
    4041 > view matrix models
    4042 > #17,-0.14524,0.98625,-0.078838,137.46,-0.95305,-0.11806,0.27883,132.77,0.26569,0.11563,0.9571,127.09
    4043 
    4044 > view matrix models
    4045 > #17,0.35108,0.87998,0.31997,116.61,0.41428,-0.45244,0.78973,93.952,0.83971,-0.14471,-0.5234,164.49
    4046 
    4047 > view matrix models
    4048 > #17,0.54911,0.70874,-0.44291,137.73,0.78853,-0.61496,-0.0064507,113,-0.27694,-0.3457,-0.89655,196.5
    4049 
    4050 > view matrix models
    4051 > #17,0.54911,0.70874,-0.44291,134.48,0.78853,-0.61496,-0.0064507,113.87,-0.27694,-0.3457,-0.89655,190.34
    4052 
    4053 > view matrix models
    4054 > #17,0.9378,-0.11961,-0.32592,126.95,-0.057609,-0.97937,0.19367,123.71,-0.34236,-0.16285,-0.92535,191.74
    4055 
    4056 > view matrix models
    4057 > #17,0.3628,-0.93186,-0.0012508,129.72,-0.91856,-0.35785,0.16792,137.38,-0.15693,-0.059774,-0.9858,190.03
    4058 
    4059 > view matrix models
    4060 > #17,-0.40726,-0.90893,0.089337,140.28,-0.91297,0.40784,-0.012447,140.22,-0.025122,-0.086631,-0.99592,188.13
    4061 
    4062 > view matrix models
    4063 > #17,-0.40726,-0.90893,0.089337,140.76,-0.91297,0.40784,-0.012447,134.78,-0.025122,-0.086631,-0.99592,187.94
    4064 
    4065 > view matrix models
    4066 > #17,-0.073903,-0.92576,-0.37083,149.44,-0.76049,-0.18823,0.62147,114.32,-0.64513,0.32794,-0.69012,187.71
    4067 
    4068 > view matrix models
    4069 > #17,-0.013726,-0.97437,-0.22454,143.96,-0.96969,-0.041822,0.24075,129.42,-0.24397,0.22104,-0.94426,189.05
    4070 
    4071 > view matrix models
    4072 > #17,-0.13546,-0.99065,0.016086,138.59,-0.95193,0.13463,0.27516,127.4,-0.27475,0.02196,-0.96126,190.84
    4073 
    4074 > view matrix models
    4075 > #17,-0.13546,-0.99065,0.016086,134.75,-0.95193,0.13463,0.27516,129.71,-0.27475,0.02196,-0.96126,190.41
    4076 
    4077 > view matrix models
    4078 > #17,-0.13546,-0.99065,0.016086,134.74,-0.95193,0.13463,0.27516,129.59,-0.27475,0.02196,-0.96126,189.59
    4079 
    4080 > fitmap #17 inMap #15
    4081 
    4082 Fit molecule copy of 3C11_Fab_D_1292144377_model-annotate_P1_HL.pdb (#17) to
    4083 map cryosparc_P371_J937_003_volume_map.mrc z flip (#15) using 3190 atoms 
    4084 average map value = 0.08611, steps = 92 
    4085 shifted from previous position = 1.81 
    4086 rotated from previous position = 13.7 degrees 
    4087 atoms outside contour = 1360, contour level = 0.077423 
    4088  
    4089 Position of copy of 3C11_Fab_D_1292144377_model-annotate_P1_HL.pdb (#17)
    4090 relative to cryosparc_P371_J937_003_volume_map.mrc z flip (#15) coordinates: 
    4091 Matrix rotation and translation 
    4092 0.06326154 -0.99140205 0.11454237 128.16146514 
    4093 -0.92943347 -0.01671960 0.36861077 128.17971107 
    4094 -0.36352637 -0.12977839 -0.92249995 190.93357303 
    4095 Axis -0.71877784 0.68947168 0.08937122 
    4096 Axis point 0.00000000 149.17005870 88.62629203 
    4097 Rotation angle (degrees) 159.71487953 
    4098 Shift along axis 13.32062667 
    4099  
    4100 
    4101 > select subtract #17
    4102 
    4103 Nothing selected 
    4104 
    4105 > select add #18
    4106 
    4107 1883 atoms, 1745 bonds, 394 residues, 1 model selected 
    4108 
    4109 > view matrix models
    4110 > #18,-0.26486,0.8524,-0.45085,130.11,0.42774,-0.31518,-0.84718,156.88,-0.86423,-0.41723,-0.28112,157.69
    4111 
    4112 > view matrix models
    4113 > #18,-0.26486,0.8524,-0.45085,127.04,0.42774,-0.31518,-0.84718,159.13,-0.86423,-0.41723,-0.28112,133.82
    4114 
    4115 > view matrix models
    4116 > #18,0.36105,0.83492,0.4154,114.71,0.60304,0.13074,-0.78692,152.96,-0.71132,0.53462,-0.45629,125.04
    4117 
    4118 > show #!8 models
    4119 
    4120 > select up
    4121 
    4122 26260 atoms, 26186 bonds, 3972 residues, 27 models selected 
    4123 
    4124 > select up
    4125 
    4126 26260 atoms, 26186 bonds, 3972 residues, 27 models selected 
    4127 
    4128 > select down
    4129 
    4130 1883 atoms, 1745 bonds, 394 residues, 1 model selected 
    4131 
    4132 > select down
    4133 
    4134 1883 atoms, 1745 bonds, 394 residues, 1 model selected 
    4135 
    4136 > combine #8 close false
    4137 
    4138 > hide #!8 models
    4139 
    4140 > select subtract #18
    4141 
    4142 Nothing selected 
    4143 
    4144 > mmaker #19 to #16
    4145 
    4146 Parameters 
    4147 --- 
    4148 Chain pairing | bb 
    4149 Alignment algorithm | Needleman-Wunsch 
    4150 Similarity matrix | BLOSUM-62 
    4151 SS fraction | 0.3 
    4152 Gap open (HH/SS/other) | 18/18/6 
    4153 Gap extend | 1 
    4154 SS matrix |  |  | H | S | O 
    4155 ---|---|---|--- 
    4156 H | 6 | -9 | -6 
    4157 S |  | 6 | -6 
    4158 O |  |  | 4 
    4159 Iteration cutoff | 2 
    4160  
    4161 Matchmaker copy of 1ezx, chain A (#16) with copy of 1ezx, chain A (#19),
    4162 sequence alignment score = 1734 
    4163 RMSD between 335 pruned atom pairs is 0.000 angstroms; (across all 335 pairs:
    4164 0.000) 
    4165  
    4166 
    4167 > hide #!16 models
    4168 
    4169 > show #!16 models
    4170 
    4171 > mmaker #18 to #19
    4172 
    4173 Parameters 
    4174 --- 
    4175 Chain pairing | bb 
    4176 Alignment algorithm | Needleman-Wunsch 
    4177 Similarity matrix | BLOSUM-62 
    4178 SS fraction | 0.3 
    4179 Gap open (HH/SS/other) | 18/18/6 
    4180 Gap extend | 1 
    4181 SS matrix |  |  | H | S | O 
    4182 ---|---|---|--- 
    4183 H | 6 | -9 | -6 
    4184 S |  | 6 | -6 
    4185 O |  |  | 4 
    4186 Iteration cutoff | 2 
    4187  
    4188 Matchmaker copy of 1ezx, chain C (#19) with copy of 5a0c, chain A (#18),
    4189 sequence alignment score = 241.2 
    4190 RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
    4191 3.073) 
    4192  
    4193 
    4194 > hide #!19 models
    4195 
    4196 > show #!19 models
    4197 
    4198 > hide #18 models
    4199 
    4200 > show #18 models
    4201 
    4202 > hide #!15 models
    4203 
    4204 > show #!15 models
    4205 
    4206 > volume #15 level 0.06266
    4207 
    4208 > combine #18 close false
    4209 
    4210 > hide #!19 models
    4211 
    4212 > hide #18 models
    4213 
    4214 > select add #20
    4215 
    4216 1883 atoms, 1745 bonds, 394 residues, 1 model selected 
    4217 
    4218 > view matrix models
    4219 > #20,0.93703,-0.32924,0.11649,110.54,-0.085791,-0.54033,-0.83707,168.71,0.33854,0.77436,-0.53456,110.95
    4220 
    4221 > fitmap #20 inMap #15
    4222 
    4223 Fit molecule copy of copy of 5a0c (#20) to map
    4224 cryosparc_P371_J937_003_volume_map.mrc z flip (#15) using 1883 atoms 
    4225 average map value = 0.05371, steps = 112 
    4226 shifted from previous position = 3.05 
    4227 rotated from previous position = 21.1 degrees 
    4228 atoms outside contour = 1163, contour level = 0.062657 
    4229  
    4230 Position of copy of copy of 5a0c (#20) relative to
    4231 cryosparc_P371_J937_003_volume_map.mrc z flip (#15) coordinates: 
    4232 Matrix rotation and translation 
    4233 0.82283210 -0.54792418 -0.15075286 115.81404414 
    4234 -0.42467040 -0.41658213 -0.80381240 174.25196583 
    4235 0.37762731 0.72542292 -0.57546433 108.00195017 
    4236 Axis 0.94244068 -0.32563135 0.07595913 
    4237 Axis point 0.00000000 79.04749924 102.02767242 
    4238 Rotation angle (degrees) 125.77524387 
    4239 Shift along axis 60.60969773 
    4240  
    4241 
    4242 > volume #15 level 0.07496
    4243 
    4244 > volume #15 level 0.102
    4245 
    4246 > fitmap #20 inMap #15
    4247 
    4248 Fit molecule copy of copy of 5a0c (#20) to map
    4249 cryosparc_P371_J937_003_volume_map.mrc z flip (#15) using 1883 atoms 
    4250 average map value = 0.05371, steps = 40 
    4251 shifted from previous position = 0.00581 
    4252 rotated from previous position = 0.0038 degrees 
    4253 atoms outside contour = 1822, contour level = 0.10203 
    4254  
    4255 Position of copy of copy of 5a0c (#20) relative to
    4256 cryosparc_P371_J937_003_volume_map.mrc z flip (#15) coordinates: 
    4257 Matrix rotation and translation 
    4258 0.82283660 -0.54793499 -0.15068899 115.81020155 
    4259 -0.42463523 -0.41661833 -0.80381222 174.25584664 
    4260 0.37765705 0.72539397 -0.57548131 108.00286277 
    4261 Axis 0.94244310 -0.32561736 0.07598910 
    4262 Axis point 0.00000000 79.04924478 102.02529443 
    4263 Rotation angle (degrees) 125.77696296 
    4264 Shift along axis 60.61083741 
    4265  
    4266 
    4267 > volume #15 level 0.08481
    4268 
    4269 > select #20/Ser195
    4270 
    4271 Nothing selected 
    4272 
    4273 > ui tool show "Show Sequence Viewer"
    4274 
    4275 > sequence chain #7/A #18/A #20/A
    4276 
    4277 Alignment identifier is 1 
    4278 
    4279 > select #7/A:157 #18/A:157 #20/A:157
    4280 
    4281 18 atoms, 15 bonds, 3 residues, 3 models selected 
    4282 
    4283 > select #7/A:157 #18/A:157 #20/A:157
    4284 
    4285 18 atoms, 15 bonds, 3 residues, 3 models selected 
    4286 NEUTROPHIL ELASTASE [ID: 1] region 3 chains [138] RMSD: 42.465 
    4287  
    4288 
    4289 > show #18 models
    4290 
    4291 > hide #20 models
    4292 
    4293 > select #7/A:157 #18/A:157 #20/A:157
    4294 
    4295 18 atoms, 15 bonds, 3 residues, 3 models selected 
    4296 
    4297 > select #7/A:157 #18/A:157 #20/A:157
    4298 
    4299 18 atoms, 15 bonds, 3 residues, 3 models selected 
    4300 NEUTROPHIL ELASTASE [ID: 1] region 3 chains [138] RMSD: 42.465 
    4301  
    4302 
    4303 > select #7/A:195 #18/A:195 #20/A:195
    4304 
    4305 15 atoms, 12 bonds, 3 residues, 3 models selected 
    4306 
    4307 > select #7/A:195 #18/A:195 #20/A:195
    4308 
    4309 15 atoms, 12 bonds, 3 residues, 3 models selected 
    4310 NEUTROPHIL ELASTASE [ID: 1] region 3 chains [166] RMSD: 29.400 
    4311  
    4312 
    4313 > show #!19 models
    4314 
    4315 > hide #!15 models
    4316 
    4317 > select #7/A:195 #18/A:195 #20/A:195
    4318 
    4319 15 atoms, 12 bonds, 3 residues, 3 models selected 
    4320 
    4321 > select #7/A:195 #18/A:195 #20/A:195
    4322 
    4323 15 atoms, 12 bonds, 3 residues, 3 models selected 
    4324 
    4325 > select #7/A:195-198 #18/A:195-198 #20/A:195-198
    4326 
    4327 66 atoms, 63 bonds, 12 residues, 3 models selected 
    4328 NEUTROPHIL ELASTASE [ID: 1] region 3 chains [166-169] RMSD: 25.331 
    4329  
    4330 
    4331 > select #7/A:196 #18/A:196 #20/A:196
    4332 
    4333 12 atoms, 9 bonds, 3 residues, 3 models selected 
    4334 
    4335 > select #7/A:195-196 #18/A:195-196 #20/A:195-196
    4336 
    4337 27 atoms, 24 bonds, 6 residues, 3 models selected 
    4338 NEUTROPHIL ELASTASE [ID: 1] region 3 chains [166-167] RMSD: 26.853 
    4339  
    4340 
    4341 > hide #18 models
    4342 
    4343 > ui tool show "Show Sequence Viewer"
    4344 
    4345 > sequence chain #8/C #19/C
    4346 
    4347 Alignment identifier is 2 
    4348 
    4349 > select #7/A:202 #18/A:202 #20/A:202
    4350 
    4351 18 atoms, 15 bonds, 3 residues, 3 models selected 
    4352 
    4353 > select #7/A:202 #18/A:202 #20/A:202
    4354 
    4355 18 atoms, 15 bonds, 3 residues, 3 models selected 
    4356 NEUTROPHIL ELASTASE [ID: 1] region 3 chains [173] RMSD: 20.338 
    4357  
    4358 
    4359 > show #18 models
    4360 
    4361 > hide #!19 models
    4362 
    4363 > show #20 models
    4364 
    4365 > hide #18 models
    4366 
    4367 > show #!15 models
    4368 
    4369 > fitmap #20 inMap #15
    4370 
    4371 Fit molecule copy of copy of 5a0c (#20) to map
    4372 cryosparc_P371_J937_003_volume_map.mrc z flip (#15) using 1883 atoms 
    4373 average map value = 0.05371, steps = 44 
    4374 shifted from previous position = 0.00953 
    4375 rotated from previous position = 0.0167 degrees 
    4376 atoms outside contour = 1647, contour level = 0.084806 
    4377  
    4378 Position of copy of copy of 5a0c (#20) relative to
    4379 cryosparc_P371_J937_003_volume_map.mrc z flip (#15) coordinates: 
    4380 Matrix rotation and translation 
    4381 0.82274117 -0.54810241 -0.15060115 115.80769501 
    4382 -0.42459237 -0.41645168 -0.80392121 174.26154718 
    4383 0.37791306 0.72536318 -0.57535204 108.00158372 
    4384 Axis 0.94240739 -0.32569200 0.07611192 
    4385 Axis point 0.00000000 79.05386504 102.02910751 
    4386 Rotation angle (degrees) 125.76988347 
    4387 Shift along axis 60.60264436 
    4388  
    4389 
    4390 > save /Users/apple/Downloads/csparc.cxs
    4391 
    4392 > show #!19 models
    4393 
    4394 > hide #20 models
    4395 
    4396 > show #20 models
    4397 
    4398 > hide #!19 models
    4399 
    4400 > save /Users/apple/Downloads/csparc.cxs includeMaps true
    4401 
    4402 > open /Users/apple/Downloads/cryosparc_P371_J936_volume_map.mrc
    4403 
    4404 Opened cryosparc_P371_J936_volume_map.mrc as #21, grid size 300,300,300, pixel
    4405 0.867, shown at level 0.0323, step 2, values float32 
    4406 
    4407 > volume #21 level 0.05076
    4408 
    4409 > volume flip #21 axis z
    4410 
    4411 Opened cryosparc_P371_J936_volume_map.mrc z flip as #22, grid size
    4412 300,300,300, pixel 0.867, shown at step 1, values float32 
    4413 
    4414 > transparency #22 50
    4415 
    4416 > volume #22 level 0.08397
    4417 
    4418 > hide #!15 models
    4419 
    4420 > hide #!22 models
    4421 
    4422 > show #!22 models
    4423 
    4424 > volume #22 level 0.09518
    4425 
    4426 > select add #21
    4427 
    4428 18 atoms, 15 bonds, 3 residues, 5 models selected 
    4429 
    4430 > select subtract #21
    4431 
    4432 18 atoms, 15 bonds, 3 residues, 3 models selected 
    4433 
    4434 > close #21-22
    4435 
    4436 > show #!15 models
    4437 
    4438 > volume #15 level 0.06828
    4439 
    4440 > show #!19 models
    4441 
    4442 > hide #!19 models
    4443 
    4444 > show #!19 models
    4445 
    4446 > select up
    4447 
    4448 309 atoms, 309 bonds, 45 residues, 3 models selected 
    4449 
    4450 > select up
    4451 
    4452 4908 atoms, 5010 bonds, 654 residues, 3 models selected 
    4453 
    4454 > select down
    4455 
    4456 309 atoms, 309 bonds, 45 residues, 3 models selected 
    4457 
    4458 > select down
    4459 
    4460 18 atoms, 15 bonds, 3 residues, 3 models selected 
    4461 
    4462 > mmaker #20 to #19
    4463 
    4464 Parameters 
    4465 --- 
    4466 Chain pairing | bb 
    4467 Alignment algorithm | Needleman-Wunsch 
    4468 Similarity matrix | BLOSUM-62 
    4469 SS fraction | 0.3 
    4470 Gap open (HH/SS/other) | 18/18/6 
    4471 Gap extend | 1 
    4472 SS matrix |  |  | H | S | O 
    4473 ---|---|---|--- 
    4474 H | 6 | -9 | -6 
    4475 S |  | 6 | -6 
    4476 O |  |  | 4 
    4477 Iteration cutoff | 2 
    4478  
    4479 Matchmaker copy of 1ezx, chain C (#19) with copy of copy of 5a0c, chain A
    4480 (#20), sequence alignment score = 241.2 
    4481 RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
    4482 3.073) 
    4483  
    4484 
    4485 > fitmap #20 inMap #15
    4486 
    4487 Fit molecule copy of copy of 5a0c (#20) to map
    4488 cryosparc_P371_J937_003_volume_map.mrc z flip (#15) using 1883 atoms 
    4489 average map value = 0.05371, steps = 112 
    4490 shifted from previous position = 3.64 
    4491 rotated from previous position = 21.1 degrees 
    4492 atoms outside contour = 1322, contour level = 0.068282 
    4493  
    4494 Position of copy of copy of 5a0c (#20) relative to
    4495 cryosparc_P371_J937_003_volume_map.mrc z flip (#15) coordinates: 
    4496 Matrix rotation and translation 
    4497 0.82286685 -0.54787123 -0.15075561 115.81112827 
    4498 -0.42466982 -0.41665469 -0.80377510 174.25405615 
    4499 0.37755223 0.72542124 -0.57551571 108.00346093 
    4500 Axis 0.94245398 -0.32559967 0.07592986 
    4501 Axis point 0.00000000 79.04723098 102.02619388 
    4502 Rotation angle (degrees) 125.77839312 
    4503 Shift along axis 60.61028363 
    4504  
    4505 
    4506 > hide #!19 models
    4507 
    4508 > show #18 models
    4509 
    4510 > hide #18 models
    4511 
    4512 > color #20 #ff9cd5ff
    4513 
    4514 > open /Users/apple/Downloads/cryosparc_P371_J948_003_volume_map.mrc
    4515 
    4516 Opened cryosparc_P371_J948_003_volume_map.mrc as #21, grid size 300,300,300,
    4517 pixel 0.867, shown at level 0.0208, step 2, values float32 
    4518 
    4519 > volume flip #21 axis z
    4520 
    4521 Opened cryosparc_P371_J948_003_volume_map.mrc z flip as #22, grid size
    4522 300,300,300, pixel 0.867, shown at step 1, values float32 
    4523 
    4524 > select add #22
    4525 
    4526 18 atoms, 15 bonds, 3 residues, 5 models selected 
    4527 
    4528 > select subtract #22
    4529 
    4530 18 atoms, 15 bonds, 3 residues, 3 models selected 
    4531 
    4532 > hide #20 models
    4533 
    4534 > show #20 models
    4535 
    4536 > hide #20 models
    4537 
    4538 > show #20 models
    4539 
    4540 > hide #20 models
    4541 
    4542 > hide #!17 models
    4543 
    4544 > hide #!16 models
    4545 
    4546 > select add #18
    4547 
    4548 1895 atoms, 1755 bonds, 396 residues, 3 models selected 
    4549 
    4550 > select subtract #18
    4551 
    4552 12 atoms, 10 bonds, 2 residues, 2 models selected 
    4553 
    4554 > select add #20
    4555 
    4556 1889 atoms, 1750 bonds, 395 residues, 2 models selected 
    4557 
    4558 > select subtract #20
    4559 
    4560 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4561 
    4562 > select add #7
    4563 
    4564 1883 atoms, 1745 bonds, 394 residues, 1 model selected 
    4565 
    4566 > select subtract #7
    4567 
    4568 Nothing selected 
    4569 
    4570 > volume #22 level 0.07591
    4571 
    4572 > select down
    4573 
    4574 Nothing selected 
    4575 
    4576 > combine #16 close false
    4577 
    4578 > combine #17 close false
    4579 
    4580 > combine #118 close false
    4581 
    4582 No structures specified 
    4583 
    4584 > combine #18 close false
    4585 
    4586 > combine #19 close false
    4587 
    4588 > transparency #22 50
    4589 
    4590 > hide #!26 models
    4591 
    4592 > hide #25 models
    4593 
    4594 > hide #!24 models
    4595 
    4596 > select add #23
    4597 
    4598 2975 atoms, 2968 bonds, 437 residues, 1 model selected 
    4599 
    4600 > view matrix models
    4601 > #23,0.36221,-0.1133,0.92518,56.114,-0.01923,-0.99328,-0.11412,190.58,0.9319,0.023543,-0.36196,109.58
    4602 
    4603 > view matrix models
    4604 > #23,0.36479,-0.4655,-0.80637,178.05,-0.26782,-0.88191,0.38795,170.47,-0.89174,0.074435,-0.44638,227.76
    4605 
    4606 > view matrix models
    4607 > #23,0.44719,-0.25874,-0.8562,163.07,-0.021132,-0.96003,0.27908,165.82,-0.89419,-0.10671,-0.43478,238.29
    4608 
    4609 > fitmap #23 inMap #22
    4610 
    4611 Fit molecule copy of copy of 1ezx (#23) to map
    4612 cryosparc_P371_J948_003_volume_map.mrc z flip (#22) using 2975 atoms 
    4613 average map value = 0.09755, steps = 212 
    4614 shifted from previous position = 6.95 
    4615 rotated from previous position = 52.1 degrees 
    4616 atoms outside contour = 1049, contour level = 0.075909 
    4617  
    4618 Position of copy of copy of 1ezx (#23) relative to
    4619 cryosparc_P371_J948_003_volume_map.mrc z flip (#22) coordinates: 
    4620 Matrix rotation and translation 
    4621 -0.35370767 0.06701706 -0.93295209 204.77529060 
    4622 0.13164154 -0.98393545 -0.12058828 178.13445921 
    4623 -0.92604610 -0.16546825 0.33920329 197.74865607 
    4624 Axis -0.56822714 -0.08743693 0.81821311 
    4625 Axis point 168.87143840 102.30996261 0.00000000 
    4626 Rotation angle (degrees) 177.73673097 
    4627 Shift along axis 29.86613558 
    4628  
    4629 
    4630 > show #!24 models
    4631 
    4632 > select subtract #23
    4633 
    4634 Nothing selected 
    4635 
    4636 > select add #24
    4637 
    4638 3190 atoms, 3270 bonds, 2 pseudobonds, 422 residues, 3 models selected 
    4639 
    4640 > view matrix models
    4641 > #24,0.063262,-0.9914,0.11454,130.74,-0.92943,-0.01672,0.36861,129.85,-0.36353,-0.12978,-0.9225,142.93
    4642 
    4643 > view matrix models
    4644 > #24,-0.096416,0.97724,-0.18895,136.05,-0.93565,-0.024237,0.35209,130.5,0.33949,0.21074,0.9167,71.599
    4645 
    4646 > fitmap #24 inMap #22
    4647 
    4648 Fit molecule copy of copy of 3C11_Fab_D_1292144377_model-annotate_P1_HL.pdb
    4649 (#24) to map cryosparc_P371_J948_003_volume_map.mrc z flip (#22) using 3190
    4650 atoms 
    4651 average map value = 0.0891, steps = 132 
    4652 shifted from previous position = 5.66 
    4653 rotated from previous position = 8.17 degrees 
    4654 atoms outside contour = 1367, contour level = 0.075909 
    4655  
    4656 Position of copy of copy of 3C11_Fab_D_1292144377_model-annotate_P1_HL.pdb
    4657 (#24) relative to cryosparc_P371_J948_003_volume_map.mrc z flip (#22)
    4658 coordinates: 
    4659 Matrix rotation and translation 
    4660 -0.11543452 0.98844688 -0.09822239 132.09657369 
    4661 -0.96240593 -0.08681878 0.25736612 135.79332431 
    4662 0.24586519 0.12423874 0.96130902 66.63288452 
    4663 Axis -0.06705205 -0.17330603 -0.98258284 
    4664 Axis point 117.34974721 5.42399614 0.00000000 
    4665 Rotation angle (degrees) 96.91935179 
    4666 Shift along axis -97.86347693 
    4667  
    4668 
    4669 > select subtract #24
    4670 
    4671 Nothing selected 
    4672 
    4673 > show #25 models
    4674 
    4675 > hide #25 models
    4676 
    4677 > show #!26 models
    4678 
    4679 > mmaker #26 to #23
    4680 
    4681 Parameters 
    4682 --- 
    4683 Chain pairing | bb 
    4684 Alignment algorithm | Needleman-Wunsch 
    4685 Similarity matrix | BLOSUM-62 
    4686 SS fraction | 0.3 
    4687 Gap open (HH/SS/other) | 18/18/6 
    4688 Gap extend | 1 
    4689 SS matrix |  |  | H | S | O 
    4690 ---|---|---|--- 
    4691 H | 6 | -9 | -6 
    4692 S |  | 6 | -6 
    4693 O |  |  | 4 
    4694 Iteration cutoff | 2 
    4695  
    4696 Matchmaker copy of copy of 1ezx, chain A (#23) with copy of copy of 1ezx,
    4697 chain A (#26), sequence alignment score = 1734 
    4698 RMSD between 335 pruned atom pairs is 0.000 angstroms; (across all 335 pairs:
    4699 0.000) 
    4700  
    4701 
    4702 > hide #!24 models
    4703 
    4704 > show #!24 models
    4705 
    4706 > hide #!23 models
    4707 
    4708 > show #25 models
    4709 
    4710 > mmaker #25 to #26
    4711 
    4712 Parameters 
    4713 --- 
    4714 Chain pairing | bb 
    4715 Alignment algorithm | Needleman-Wunsch 
    4716 Similarity matrix | BLOSUM-62 
    4717 SS fraction | 0.3 
    4718 Gap open (HH/SS/other) | 18/18/6 
    4719 Gap extend | 1 
    4720 SS matrix |  |  | H | S | O 
    4721 ---|---|---|--- 
    4722 H | 6 | -9 | -6 
    4723 S |  | 6 | -6 
    4724 O |  |  | 4 
    4725 Iteration cutoff | 2 
    4726  
    4727 Matchmaker copy of copy of 1ezx, chain C (#26) with copy of copy of 5a0c,
    4728 chain A (#25), sequence alignment score = 241.2 
    4729 RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
    4730 3.073) 
    4731  
    4732 
    4733 > hide #!26 models
    4734 
    4735 > fitmap #25 inMap #22
    4736 
    4737 Fit molecule copy of copy of 5a0c (#25) to map
    4738 cryosparc_P371_J948_003_volume_map.mrc z flip (#22) using 1883 atoms 
    4739 average map value = 0.05123, steps = 108 
    4740 shifted from previous position = 4.84 
    4741 rotated from previous position = 10.8 degrees 
    4742 atoms outside contour = 1517, contour level = 0.075909 
    4743  
    4744 Position of copy of copy of 5a0c (#25) relative to
    4745 cryosparc_P371_J948_003_volume_map.mrc z flip (#22) coordinates: 
    4746 Matrix rotation and translation 
    4747 -0.96845122 0.24832236 -0.02093422 151.81572996 
    4748 -0.06074205 -0.31669183 -0.94658158 164.61638030 
    4749 -0.24168707 -0.91544650 0.32178420 153.13479473 
    4750 Axis 0.08170221 0.57928205 -0.81102223 
    4751 Axis point 93.94357397 127.91849703 0.00000000 
    4752 Rotation angle (degrees) 169.01569846 
    4753 Shift along axis -16.43272779 
    4754  
    4755 
    4756 > select add #25
    4757 
    4758 1883 atoms, 1745 bonds, 394 residues, 1 model selected 
    4759 
    4760 > view matrix models
    4761 > #25,-0.77469,0.63129,-0.036468,145.91,-0.26885,-0.38101,-0.88462,168.48,-0.57235,-0.6755,0.46489,156.84
    4762 
    4763 > select subtract #25
    4764 
    4765 Nothing selected 
    4766 
    4767 > show #!26 models
    4768 
    4769 > hide #!24 models
    4770 
    4771 > show #!24 models
    4772 
    4773 > hide #25 models
    4774 
    4775 > mmaker #25 to #26
    4776 
    4777 Parameters 
    4778 --- 
    4779 Chain pairing | bb 
    4780 Alignment algorithm | Needleman-Wunsch 
    4781 Similarity matrix | BLOSUM-62 
    4782 SS fraction | 0.3 
    4783 Gap open (HH/SS/other) | 18/18/6 
    4784 Gap extend | 1 
    4785 SS matrix |  |  | H | S | O 
    4786 ---|---|---|--- 
    4787 H | 6 | -9 | -6 
    4788 S |  | 6 | -6 
    4789 O |  |  | 4 
    4790 Iteration cutoff | 2 
    4791  
    4792 Matchmaker copy of copy of 1ezx, chain C (#26) with copy of copy of 5a0c,
    4793 chain A (#25), sequence alignment score = 241.2 
    4794 RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
    4795 3.073) 
    4796  
    4797 
    4798 > hide #!26 models
    4799 
    4800 > show #25 models
    4801 
    4802 > show #!26 models
    4803 
    4804 > mmaker #25 to #26
    4805 
    4806 Parameters 
    4807 --- 
    4808 Chain pairing | bb 
    4809 Alignment algorithm | Needleman-Wunsch 
    4810 Similarity matrix | BLOSUM-62 
    4811 SS fraction | 0.3 
    4812 Gap open (HH/SS/other) | 18/18/6 
    4813 Gap extend | 1 
    4814 SS matrix |  |  | H | S | O 
    4815 ---|---|---|--- 
    4816 H | 6 | -9 | -6 
    4817 S |  | 6 | -6 
    4818 O |  |  | 4 
    4819 Iteration cutoff | 2 
    4820  
    4821 Matchmaker copy of copy of 1ezx, chain C (#26) with copy of copy of 5a0c,
    4822 chain A (#25), sequence alignment score = 241.2 
    4823 RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
    4824 3.073) 
    4825  
    4826 
    4827 > show #!23 models
    4828 
    4829 > hide #!23 models
    4830 
    4831 > hide #!26 models
    4832 
    4833 > hide #25 models
    4834 
    4835 > show #!26 models
    4836 
    4837 > hide #!26 models
    4838 
    4839 > show #25 models
    4840 
    4841 > hide #25 models
    4842 
    4843 > show #25 models
    4844 
    4845 > show #!26 models
    4846 
    4847 > select add #25
    4848 
    4849 1883 atoms, 1745 bonds, 394 residues, 1 model selected 
    4850 
    4851 > view matrix models
    4852 > #25,-0.9367,0.31111,-0.16061,148.23,0.0082594,-0.43896,-0.89847,161.81,-0.35002,-0.84292,0.40861,148.72
    4853 
    4854 > mmaker #25 to #26
    4855 
    4856 Parameters 
    4857 --- 
    4858 Chain pairing | bb 
    4859 Alignment algorithm | Needleman-Wunsch 
    4860 Similarity matrix | BLOSUM-62 
    4861 SS fraction | 0.3 
    4862 Gap open (HH/SS/other) | 18/18/6 
    4863 Gap extend | 1 
    4864 SS matrix |  |  | H | S | O 
    4865 ---|---|---|--- 
    4866 H | 6 | -9 | -6 
    4867 S |  | 6 | -6 
    4868 O |  |  | 4 
    4869 Iteration cutoff | 2 
    4870  
    4871 Matchmaker copy of copy of 1ezx, chain C (#26) with copy of copy of 5a0c,
    4872 chain A (#25), sequence alignment score = 241.2 
    4873 RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
    4874 3.073) 
    4875  
    4876 
    4877 > hide #!22 models
    4878 
    4879 > hide #!26 models
    4880 
    4881 > select subtract #25
    4882 
    4883 Nothing selected 
    4884 
    4885 > show #!22 models
    4886 
    4887 > hide #!22 models
    4888 
    4889 > show #!26 models
    4890 
    4891 > hide #25 models
    4892 
    4893 > show #25 models
    4894 
    4895 > hide #25 models
    4896 
    4897 > show #25 models
    4898 
    4899 > select add #25
    4900 
    4901 1883 atoms, 1745 bonds, 394 residues, 1 model selected 
    4902 
    4903 > view matrix models
    4904 > #25,-0.9367,0.31111,-0.16061,148.98,0.0082594,-0.43896,-0.89847,185.49,-0.35002,-0.84292,0.40861,135.78
    4905 
    4906 > view matrix models
    4907 > #25,-0.94082,0.30916,-0.13882,149.02,0.0018899,-0.40484,-0.91439,185.4,-0.33889,-0.86054,0.3803,135.77
    4908 
    4909 > view matrix models
    4910 > #25,-0.94082,0.30916,-0.13882,149.87,0.0018899,-0.40484,-0.91439,185.44,-0.33889,-0.86054,0.3803,134.62
    4911 
    4912 > view matrix models
    4913 > #25,0.61831,0.086644,0.78114,122.91,0.644,0.51386,-0.56675,167.46,-0.45051,0.85348,0.26193,124.99
    4914 
    4915 > view matrix models
    4916 > #25,0.68702,0.1216,0.7164,121.63,0.51681,0.61128,-0.59937,169.03,-0.5108,0.78202,0.35712,126.32
    4917 
    4918 > view matrix models
    4919 > #25,-0.95703,-0.21929,0.18975,153.1,-0.15891,-0.15078,-0.97571,186.56,0.24258,-0.96394,0.10945,125.96
    4920 
    4921 > select #8/C:202 #19/C:202
    4922 
    4923 12 atoms, 10 bonds, 2 residues, 2 models selected 
    4924 
    4925 > select #8/C:202 #19/C:202
    4926 
    4927 12 atoms, 10 bonds, 2 residues, 2 models selected 
    4928 TRYPSIN [ID: 2] region 2 chains [204] RMSD: 14.654 
    4929  
    4930 
    4931 > select #8/C:195 #19/C:195
    4932 
    4933 12 atoms, 10 bonds, 2 residues, 2 models selected 
    4934 
    4935 > select #8/C:195 #19/C:195
    4936 
    4937 12 atoms, 10 bonds, 2 residues, 2 models selected 
    4938 TRYPSIN [ID: 2] region 2 chains [197] RMSD: 26.141 
    4939  
    4940 
    4941 > select #7/A:202 #18/A:202 #20/A:202
    4942 
    4943 18 atoms, 15 bonds, 3 residues, 3 models selected 
    4944 
    4945 > select #7/A:202 #18/A:202 #20/A:202
    4946 
    4947 18 atoms, 15 bonds, 3 residues, 3 models selected 
    4948 NEUTROPHIL ELASTASE [ID: 1] region 3 chains [173] RMSD: 20.338 
    4949  
    4950 
    4951 > show #20 models
    4952 
    4953 > hide #20 models
    4954 
    4955 > select #25/A Ser 202
    4956 
    4957 Expected a keyword 
    4958 
    4959 > select #25/A:Ser 202
    4960 
    4961 Expected a keyword 
    4962 
    4963 > select #25/A:Ser202
    4964 
    4965 Nothing selected 
    4966 
    4967 > select #25: 202.A
    4968 
    4969 Expected an objects specifier or a keyword 
    4970 
    4971 > select #25/A: 202
    4972 
    4973 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4974 
    4975 > select add #25
    4976 
    4977 1883 atoms, 1745 bonds, 394 residues, 1 model selected 
    4978 
    4979 > select subtract #25
    4980 
    4981 Nothing selected 
    4982 
    4983 > select add #25
    4984 
    4985 1883 atoms, 1745 bonds, 394 residues, 1 model selected 
    4986 
    4987 > hide #!26 models
    4988 
    4989 > show #!22 models
    4990 
    4991 > show #!21 models
    4992 
    4993 > hide #!21 models
    4994 
    4995 > show #!23 models
    4996 
    4997 > view matrix models
    4998 > #25,-0.95703,-0.21929,0.18975,145.87,-0.15891,-0.15078,-0.97571,168.63,0.24258,-0.96394,0.10945,142.99
    4999 
    5000 > view matrix models
    5001 > #25,-0.92453,-0.26838,-0.2706,146.59,0.26503,0.057502,-0.96252,159.94,0.27389,-0.96159,0.017967,142.62
    5002 
    5003 > select #25/A: 202
    5004 
    5005 6 atoms, 5 bonds, 1 residue, 1 model selected 
    5006 
    5007 > fitmap #25 inMap #22
    5008 
    5009 Fit molecule copy of copy of 5a0c (#25) to map
    5010 cryosparc_P371_J948_003_volume_map.mrc z flip (#22) using 1883 atoms 
    5011 average map value = 0.05191, steps = 80 
    5012 shifted from previous position = 6.32 
    5013 rotated from previous position = 2.92 degrees 
    5014 atoms outside contour = 1497, contour level = 0.075909 
    5015  
    5016 Position of copy of copy of 5a0c (#25) relative to
    5017 cryosparc_P371_J948_003_volume_map.mrc z flip (#22) coordinates: 
    5018 Matrix rotation and translation 
    5019 -0.92706110 -0.29700612 -0.22879047 151.40778359 
    5020 0.22401549 0.05050483 -0.97327608 156.79876717 
    5021 0.30062397 -0.95353900 0.01971291 143.82999540 
    5022 Axis 0.02656202 -0.71248224 0.70118722 
    5023 Axis point 58.53175465 0.00000000 169.56684388 
    5024 Rotation angle (degrees) 158.19010570 
    5025 Shift along axis -6.84288466 
    5026  
    5027 
    5028 > hide #!22 models
    5029 
    5030 > show #!22 models
    5031 
    5032 > view
    5033 
    5034 > ui mousemode right "tape measure"
    5035 
    5036 > marker segment #27 position 135.4,127.7,167.7 toPosition 124.3,129.1,64.78
    5037 > color yellow radius 0.2167 label 103.5 labelHeight 10.35 labelColor yellow
    5038 
    5039 > marker segment #27 position 125.5,89.39,147.8 toPosition 125.6,178.4,143.9
    5040 > color yellow radius 0.2167 label 89.07 labelHeight 8.907 labelColor yellow
    5041 
    5042 > close #27
    5043 
    5044 > save /Users/apple/Downloads/csparc.cxs includeMaps true
    5045 
    5046 > open 1oph fromDatabase pdb format mmcif
    5047 
    5048 1oph title: 
    5049 Non-covalent complex between α-1-π-pittsburgh and S195A trypsin [more info...] 
    5050  
    5051 Chain information for 1oph #27 
    5052 --- 
    5053 Chain | Description | UniProt 
    5054 A | Alpha-1-antitrypsin precursor | A1AT_HUMAN 1-394 
    5055 B | Trypsinogen, cationic precursor | TRY1_BOVIN -4-245 
    5056  
    5057 1oph mmCIF Assemblies 
    5058 --- 
    5059 1| author_and_software_defined_assembly 
    5060 2| software_defined_assembly 
    5061  
    5062 
    5063 > select #27/A
    5064 
    5065 3121 atoms, 2980 bonds, 578 residues, 1 model selected 
    5066 
    5067 > delete #27/A
    5068 
    5069 > mmaker #27 to #26
    5070 
    5071 Computing secondary structure 
    5072 Parameters 
    5073 --- 
    5074 Chain pairing | bb 
    5075 Alignment algorithm | Needleman-Wunsch 
    5076 Similarity matrix | BLOSUM-62 
    5077 SS fraction | 0.3 
    5078 Gap open (HH/SS/other) | 18/18/6 
    5079 Gap extend | 1 
    5080 SS matrix |  |  | H | S | O 
    5081 ---|---|---|--- 
    5082 H | 6 | -9 | -6 
    5083 S |  | 6 | -6 
    5084 O |  |  | 4 
    5085 Iteration cutoff | 2 
    5086  
    5087 Matchmaker copy of copy of 1ezx, chain C (#26) with 1oph, chain B (#27),
    5088 sequence alignment score = 997.3 
    5089 RMSD between 122 pruned atom pairs is 0.798 angstroms; (across all 140 pairs:
    5090 2.232) 
    5091  
    5092 
    5093 > show #!26 models
    5094 
    5095 > hide #25 models
    5096 
    5097 > hide #!26 models
    5098 
    5099 > select add #27
    5100 
    5101 1798 atoms, 1661 bonds, 397 residues, 1 model selected 
    5102 
    5103 > ui mousemode right "translate selected models"
    5104 
    5105 > ui mousemode right "rotate selected models"
    5106 
    5107 > view matrix models
    5108 > #27,-0.045437,0.97583,0.21376,84.546,-0.056484,-0.21614,0.97473,106.46,0.99737,0.032215,0.06494,111.78
    5109 
    5110 > view matrix models
    5111 > #27,-0.045437,0.97583,0.21376,84.655,-0.056484,-0.21614,0.97473,107.21,0.99737,0.032215,0.06494,111.79
    5112 
    5113 > view matrix models
    5114 > #27,-0.028766,0.99015,0.13706,88.816,-0.25704,-0.13983,0.95623,110.79,0.96597,-0.0077222,0.25853,101.15
    5115 
    5116 > hide #27 models
    5117 
    5118 > show #25 models
    5119 
    5120 > show #27 models
    5121 
    5122 > hide #25 models
    5123 
    5124 > fitmap #27 inMap #22
    5125 
    5126 Fit molecule 1oph (#27) to map cryosparc_P371_J948_003_volume_map.mrc z flip
    5127 (#22) using 1798 atoms 
    5128 average map value = 0.05191, steps = 140 
    5129 shifted from previous position = 5.08 
    5130 rotated from previous position = 28.4 degrees 
    5131 atoms outside contour = 1427, contour level = 0.075909 
    5132  
    5133 Position of 1oph (#27) relative to cryosparc_P371_J948_003_volume_map.mrc z
    5134 flip (#22) coordinates: 
    5135 Matrix rotation and translation 
    5136 0.00693020 0.97101511 -0.23891762 117.08280460 
    5137 0.05673053 0.23815679 0.96956846 87.39953806 
    5138 0.99836547 -0.02027323 -0.05343572 123.84959279 
    5139 Axis -0.54108517 -0.67634607 -0.49978278 
    5140 Axis point 8.31144747 0.00000000 37.97716599 
    5141 Rotation angle (degrees) 113.83939914 
    5142 Shift along axis -184.36199747 
    5143  
    5144 
    5145 > ui tool show "Show Sequence Viewer"
    5146 
    5147 > sequence chain #27/B
    5148 
    5149 Alignment identifier is 27/B 
    5150 
    5151 > select #27/B:195
    5152 
    5153 5 atoms, 4 bonds, 1 residue, 1 model selected 
    5154 
    5155 > select #27/B:195
    5156 
    5157 5 atoms, 4 bonds, 1 residue, 1 model selected 
    5158 
    5159 > hide #27 models
    5160 
    5161 > select add #27
    5162 
    5163 1798 atoms, 1661 bonds, 397 residues, 1 model selected 
    5164 
    5165 > show #25 models
    5166 
    5167 > show #!26 models
    5168 
    5169 > hide #25 models
    5170 
    5171 > hide #!26 models
    5172 
    5173 > show #!26 models
    5174 
    5175 > select up
    5176 
    5177 45957 atoms, 45539 bonds, 7200 residues, 38 models selected 
    5178 
    5179 > select up
    5180 
    5181 45957 atoms, 45539 bonds, 7200 residues, 38 models selected 
    5182 
    5183 > select down
    5184 
    5185 1798 atoms, 1661 bonds, 397 residues, 1 model selected 
    5186 
    5187 > select down
    5188 
    5189 1798 atoms, 1661 bonds, 397 residues, 1 model selected 
    5190 
    5191 > select down
    5192 
    5193 1798 atoms, 1661 bonds, 397 residues, 1 model selected 
    5194 
    5195 > select #25/A: 202
    5196 
    5197 6 atoms, 5 bonds, 1 residue, 1 model selected 
    5198 
    5199 > show #25 models
    5200 
    5201 > hide #25 models
    5202 
    5203 > select add #25
    5204 
    5205 1883 atoms, 1745 bonds, 394 residues, 1 model selected 
    5206 
    5207 > select #26/B: 195
    5208 
    5209 Nothing selected 
    5210 
    5211 > select #26/A: 195
    5212 
    5213 9 atoms, 8 bonds, 1 residue, 1 model selected 
    5214 
    5215 > hide #!22 models
    5216 
    5217 > select #26/C: 195
    5218 
    5219 6 atoms, 5 bonds, 1 residue, 1 model selected 
    5220 
    5221 > style sel ball
    5222 
    5223 Changed 6 atom styles 
    5224 
    5225 > show sel atoms
    5226 
    5227 > show #25 models
    5228 
    5229 > hide #!26 models
    5230 
    5231 > select #25/A: 202
    5232 
    5233 6 atoms, 5 bonds, 1 residue, 1 model selected 
    5234 
    5235 > show sel atoms
    5236 
    5237 > style sel ball
    5238 
    5239 Changed 6 atom styles 
    5240 
    5241 > style sel sphere
    5242 
    5243 Changed 6 atom styles 
    5244 
    5245 > style sel ball
    5246 
    5247 Changed 6 atom styles 
    5248 
    5249 > select add #25
    5250 
    5251 1883 atoms, 1745 bonds, 394 residues, 1 model selected 
    5252 
    5253 > select subtract #25
    5254 
    5255 Nothing selected 
    5256 
    5257 > select #23/A: 358
    5258 
    5259 8 atoms, 7 bonds, 1 residue, 1 model selected 
    5260 
    5261 > show sel atoms
    5262 
    5263 > style sel sphere
    5264 
    5265 Changed 8 atom styles 
    5266 
    5267 > style sel stick
    5268 
    5269 Changed 8 atom styles 
    5270 
    5271 > style sel ball
    5272 
    5273 Changed 8 atom styles 
    5274 
    5275 > rainbow sel
    5276 
    5277 > style sel ball
    5278 
    5279 Changed 8 atom styles 
    5280 
    5281 > rainbow sel
    5282 
    5283 > select add #23
    5284 
    5285 2975 atoms, 2968 bonds, 437 residues, 1 model selected 
    5286 
    5287 > select subtract #23
    5288 
    5289 Nothing selected 
    5290 
    5291 > show #!22 models
    5292 
    5293 > hide #25 models
    5294 
    5295 > show #!26 models
    5296 
    5297 > hide #!26 models
    5298 
    5299 > show #25 models
    5300 
    5301 > hide #25 models
    5302 
    5303 > volume #22 level 0.09375
    5304 
    5305 > show #25 models
    5306 
    5307 > hide #25 models
    5308 
    5309 > show #!26 models
    5310 
    5311 > hide #!26 models
    5312 
    5313 > show #25 models
    5314 
    5315 > hide #25 models
    5316 
    5317 > open /Users/apple/Downloads/cryosparc_P371_J950_050_class_averages.mrc
    5318 
    5319 Opened cryosparc_P371_J950_050_class_averages.mrc as #28, grid size
    5320 256,256,200, pixel 1.02,1.02,1.02, shown at level 0.251, step 1, values
    5321 float32 
    5322 
    5323 > close #28
    5324 
    5325 > show #25 models
    5326 
    5327 > select #25/A: 358
    5328 
    5329 Nothing selected 
    5330 
    5331 > select #25/A: 202
    5332 
    5333 6 atoms, 5 bonds, 1 residue, 1 model selected 
    5334 
    5335 > show #!26 models
    5336 
    5337 > hide #!26 models
    5338 
    5339 > hide #25 models
    5340 
    5341 > hide #!24 models
    5342 
    5343 > hide #!23 models
    5344 
    5345 > show #!26 models
    5346 
    5347 > hide #!22 models
    5348 
    5349 > show #!22 models
    5350 
    5351 > show #25 models
    5352 
    5353 > hide #25 models
    5354 
    5355 > hide #!26 models
    5356 
    5357 > show #25 models
    5358 
    5359 > show #!23 models
    5360 
    5361 > ui mousemode right "mark center"
    5362 
    5363 > marker #28 position 123.2,156.9,145.8 color yellow radius 1
    5364 
    5365 > marker #28 position 123.8,156.1,145.9 color yellow radius 1
    5366 
    5367 > marker #28 position 124.3,155.3,145.5 color yellow radius 1
    5368 
    5369 > marker #28 position 125.1,154.7,145.3 color yellow radius 1
    5370 
    5371 > marker #28 position 133.4,155.3,146.7 color yellow radius 1
    5372 
    5373 > close #28
    5374 
    5375 > marker #28 position 138.7,150.2,141.7 color yellow radius 1
    5376 
    5377 > ui mousemode right "translate selected models"
    5378 
    5379 > view matrix models #28,1,0,0,-3.5551,0,1,0,1.3867,0,0,1,-2.5059
    5380 
    5381 > view matrix models #28,1,0,0,-9.6384,0,1,0,2.0334,0,0,1,1.97
    5382 
    5383 > view matrix models #28,1,0,0,-10.982,0,1,0,2.5507,0,0,1,3.0554
    5384 
    5385 > view matrix models #28,1,0,0,-10.831,0,1,0,1.6826,0,0,1,8.0306
    5386 
    5387 > view matrix models #28,1,0,0,-9.3846,0,1,0,2.9816,0,0,1,8.0266
    5388 
    5389 > view matrix models #28,1,0,0,-8.1692,0,1,0,2.6506,0,0,1,8.3086
    5390 
    5391 > save /Users/apple/Downloads/csparc.cxs includeMaps true
    5392 
    5393 ——— End of log from Wed Dec 10 00:50:43 2025 ———
    5394 
    5395 opened ChimeraX session 
    5396 
    5397 > open /Users/apple/Downloads/cryosparc_P371_J1081_flex_map.mrc
    5398 
    5399 Opened cryosparc_P371_J1081_flex_map.mrc as #29, grid size 300,300,300, pixel
    5400 0.867, shown at level 0.000695, step 2, values float32 
    5401 
    5402 > open /Users/apple/Downloads/cryosparc_P371_J1081_noflex_map.mrc
    5403 
    5404 Opened cryosparc_P371_J1081_noflex_map.mrc as #30, grid size 300,300,300,
    5405 pixel 0.867, shown at level 0.000724, step 2, values float32 
    5406 
    5407 > select subtract #28
    5408 
    5409 Nothing selected 
    5410 
    5411 > hide #28 models
    5412 
    5413 > hide #25 models
    5414 
    5415 > hide #!23 models
    5416 
    5417 > hide #!22 models
    5418 
    5419 > volume #29 level 0.002147
    5420 
    5421 > volume #30 level 0.002175
    5422 
    5423 > volume #29 level 0.003511
    5424 
    5425 > transparency #29 50
    5426 
    5427 > combine #23 close false
    5428 
    5429 > select #31
    5430 
    5431 2975 atoms, 2968 bonds, 437 residues, 1 model selected 
    5432 
    5433 > ui mousemode right "translate selected models"
    5434 
    5435 > view matrix models
    5436 > #31,0.50304,0.85251,0.14206,39.723,-0.75321,0.51304,-0.41165,160.2,-0.42382,0.10008,0.9002,116.9
    5437 
    5438 > view matrix models
    5439 > #31,-0.21174,-0.30564,-0.9283,218.18,-0.38185,0.90021,-0.2093,101.13,0.89964,0.31016,-0.30733,89.797
    5440 
    5441 > view matrix models
    5442 > #31,-0.21174,-0.30564,-0.9283,229.13,-0.38185,0.90021,-0.2093,126.74,0.89964,0.31016,-0.30733,63.57
    5443 
    5444 > view matrix models
    5445 > #31,-0.62266,-0.60519,-0.49602,248.5,-0.47185,0.79608,-0.37898,148.7,0.62422,-0.0019301,-0.78124,127.72
    5446 
    5447 > view matrix models
    5448 > #31,-0.0049269,-0.1605,-0.98702,210.49,-0.17098,0.97264,-0.15731,105.85,0.98526,0.16799,-0.032234,50.793
    5449 
    5450 > view matrix models
    5451 > #31,-0.0049269,-0.1605,-0.98702,193.82,-0.17098,0.97264,-0.15731,100.89,0.98526,0.16799,-0.032234,45.314
    5452 
    5453 > ui tool show "Fit to Segments"
    5454 
    5455 > ui tool show "Fit in Map"
    5456 
    5457 > fitmap #31 inMap #29
    5458 
    5459 Fit molecule copy of copy of copy of 1ezx (#31) to map
    5460 cryosparc_P371_J1081_flex_map.mrc (#29) using 2975 atoms 
    5461 average map value = 0.00359, steps = 168 
    5462 shifted from previous position = 8.5 
    5463 rotated from previous position = 22.8 degrees 
    5464 atoms outside contour = 1538, contour level = 0.003511 
    5465  
    5466 Position of copy of copy of copy of 1ezx (#31) relative to
    5467 cryosparc_P371_J1081_flex_map.mrc (#29) coordinates: 
    5468 Matrix rotation and translation 
    5469 -0.34543281 0.02159528 -0.93819498 206.18704506 
    5470 -0.19036417 0.97733785 0.09258621 89.05596314 
    5471 0.91893289 0.21058103 -0.33349359 58.61087565 
    5472 Axis 0.06300096 -0.99157607 -0.11317149 
    5473 Axis point 88.67581154 0.00000000 98.10599897 
    5474 Rotation angle (degrees) 110.53590433 
    5475 Shift along axis -81.94885947 
    5476  
    5477 
    5478 > combine #26 close false
    5479 
    5480 > mmaker #32 to #31
    5481 
    5482 Parameters 
    5483 --- 
    5484 Chain pairing | bb 
    5485 Alignment algorithm | Needleman-Wunsch 
    5486 Similarity matrix | BLOSUM-62 
    5487 SS fraction | 0.3 
    5488 Gap open (HH/SS/other) | 18/18/6 
    5489 Gap extend | 1 
    5490 SS matrix |  |  | H | S | O 
    5491 ---|---|---|--- 
    5492 H | 6 | -9 | -6 
    5493 S |  | 6 | -6 
    5494 O |  |  | 4 
    5495 Iteration cutoff | 2 
    5496  
    5497 Matchmaker copy of copy of copy of 1ezx, chain A (#31) with copy of copy of
    5498 copy of 1ezx, chain A (#32), sequence alignment score = 1734 
    5499 RMSD between 335 pruned atom pairs is 0.000 angstroms; (across all 335 pairs:
    5500 0.000) 
    5501  
    5502 
    5503 > volume #29 level 0.003107
    5504 
    5505 > hide #!32 models
    5506 
    5507 > show #!32 models
    5508 
    5509 > mmaker #27 to #32
    5510 
    5511 Parameters 
    5512 --- 
    5513 Chain pairing | bb 
    5514 Alignment algorithm | Needleman-Wunsch 
    5515 Similarity matrix | BLOSUM-62 
    5516 SS fraction | 0.3 
    5517 Gap open (HH/SS/other) | 18/18/6 
    5518 Gap extend | 1 
    5519 SS matrix |  |  | H | S | O 
    5520 ---|---|---|--- 
    5521 H | 6 | -9 | -6 
    5522 S |  | 6 | -6 
    5523 O |  |  | 4 
    5524 Iteration cutoff | 2 
    5525  
    5526 Matchmaker copy of copy of copy of 1ezx, chain C (#32) with 1oph, chain B
    5527 (#27), sequence alignment score = 997.3 
    5528 RMSD between 122 pruned atom pairs is 0.798 angstroms; (across all 140 pairs:
    5529 2.232) 
    5530  
    5531 
    5532 > show #27 models
    5533 
    5534 > select subtract #31
    5535 
    5536 Nothing selected 
    5537 
    5538 > hide #!32 models
    5539 
    5540 > fitmap #27 inMap #29
    5541 
    5542 Fit molecule 1oph (#27) to map cryosparc_P371_J1081_flex_map.mrc (#29) using
    5543 1798 atoms 
    5544 average map value = 0.001969, steps = 84 
    5545 shifted from previous position = 3.54 
    5546 rotated from previous position = 2.5 degrees 
    5547 atoms outside contour = 1466, contour level = 0.003107 
    5548  
    5549 Position of 1oph (#27) relative to cryosparc_P371_J1081_flex_map.mrc (#29)
    5550 coordinates: 
    5551 Matrix rotation and translation 
    5552 0.01488540 0.98783365 0.15480023 90.39787129 
    5553 0.09394517 0.15275083 -0.98378935 155.00101390 
    5554 -0.99546609 0.02918683 -0.09052845 143.69933185 
    5555 Axis 0.57090422 0.64827970 -0.50378746 
    5556 Axis point 63.02718238 0.00000000 111.05539948 
    5557 Rotation angle (degrees) 117.48046157 
    5558 Shift along axis 79.69861501 
    5559  
    5560 
    5561 > select #27/A: 195
    5562 
    5563 Nothing selected 
    5564 
    5565 > select #27/B: 195
    5566 
    5567 5 atoms, 4 bonds, 1 residue, 1 model selected 
    5568 
    5569 > show sel atoms
    5570 
    5571 > style sel ball
    5572 
    5573 Changed 5 atom styles 
    5574 
    5575 > rainbow sel
    5576 
    5577 > color sel red
    5578 
    5579 > select add #27
    5580 
    5581 1798 atoms, 1661 bonds, 397 residues, 1 model selected 
    5582 
    5583 > select subtract #27
    5584 
    5585 Nothing selected 
    5586 
    5587 > select add #27
    5588 
    5589 1798 atoms, 1661 bonds, 397 residues, 1 model selected 
    5590 
    5591 > view matrix models
    5592 > #27,0.014885,0.98783,0.1548,88.407,0.093945,0.15275,-0.98379,156.95,-0.99547,0.029187,-0.090528,145.09
    5593 
    5594 > view matrix models
    5595 > #27,0.50068,0.52374,0.68922,56.841,0.53814,0.43533,-0.72173,119.4,-0.67804,0.73225,-0.063887,112.1
    5596 
    5597 > view matrix models
    5598 > #27,0.50068,0.52374,0.68922,56.703,0.53814,0.43533,-0.72173,120.1,-0.67804,0.73225,-0.063887,108.86
    5599 
    5600 > fitmap #27 inMap #29
    5601 
    5602 Fit molecule 1oph (#27) to map cryosparc_P371_J1081_flex_map.mrc (#29) using
    5603 1798 atoms 
    5604 average map value = 0.002206, steps = 72 
    5605 shifted from previous position = 3.25 
    5606 rotated from previous position = 11.5 degrees 
    5607 atoms outside contour = 1384, contour level = 0.003107 
    5608  
    5609 Position of 1oph (#27) relative to cryosparc_P371_J1081_flex_map.mrc (#29)
    5610 coordinates: 
    5611 Matrix rotation and translation 
    5612 0.43383501 0.41278377 0.80087249 57.23345510 
    5613 0.54433424 0.58824117 -0.59805732 104.34070071 
    5614 -0.71797452 0.69540053 0.03050727 103.99925252 
    5615 Axis 0.64695257 0.75968612 0.06579798 
    5616 Axis point 48.98630646 0.00000000 62.63708921 
    5617 Rotation angle (degrees) 88.49342140 
    5618 Shift along axis 123.13645375 
    5619  
    5620 
    5621 > mmaker #27 to #32
    5622 
    5623 Parameters 
    5624 --- 
    5625 Chain pairing | bb 
    5626 Alignment algorithm | Needleman-Wunsch 
    5627 Similarity matrix | BLOSUM-62 
    5628 SS fraction | 0.3 
    5629 Gap open (HH/SS/other) | 18/18/6 
    5630 Gap extend | 1 
    5631 SS matrix |  |  | H | S | O 
    5632 ---|---|---|--- 
    5633 H | 6 | -9 | -6 
    5634 S |  | 6 | -6 
    5635 O |  |  | 4 
    5636 Iteration cutoff | 2 
    5637  
    5638 Matchmaker copy of copy of copy of 1ezx, chain C (#32) with 1oph, chain B
    5639 (#27), sequence alignment score = 997.3 
    5640 RMSD between 122 pruned atom pairs is 0.798 angstroms; (across all 140 pairs:
    5641 2.232) 
    5642  
    5643 
    5644 > hide #27 models
    5645 
    5646 > show #!32 models
    5647 
    5648 > hide #!31 models
    5649 
    5650 > volume #29 level 0.002349
    5651 
    5652 > show #27 models
    5653 
    5654 > color #27 #dbd548ff
    5655 
    5656 > select subtract #27
    5657 
    5658 Nothing selected 
    5659 
    5660 > select add #27
    5661 
    5662 1798 atoms, 1661 bonds, 397 residues, 1 model selected 
    5663 
    5664 > select subtract #27
    5665 
    5666 Nothing selected 
    5667 
    5668 > select add #32
    5669 
    5670 3984 atoms, 3982 bonds, 5 pseudobonds, 592 residues, 3 models selected 
    5671 
    5672 > hide #!32 models
    5673 
    5674 > hide #27 models
    5675 
    5676 > show #28 models
    5677 
    5678 > hide #28 models
    5679 
    5680 > show #27 models
    5681 
    5682 > select subtract #32
    5683 
    5684 Nothing selected 
    5685 
    5686 > select add #27
    5687 
    5688 1798 atoms, 1661 bonds, 397 residues, 1 model selected 
    5689 
    5690 > view matrix models
    5691 > #27,-0.014536,0.98302,0.18291,86.474,0.10897,0.18339,-0.97698,152.94,-0.99394,0.00573,-0.10979,145.21
    5692 
    5693 > view matrix models
    5694 > #27,-0.094668,0.98683,0.13115,91.714,0.12875,0.14277,-0.98135,154.1,-0.98715,-0.076017,-0.14057,149.8
    5695 
    5696 > view matrix models
    5697 > #27,-0.094668,0.98683,0.13115,93.34,0.12875,0.14277,-0.98135,151.17,-0.98715,-0.076017,-0.14057,149.26
    5698 
    5699 > view matrix models
    5700 > #27,-0.22979,0.97316,0.012679,104.9,0.38456,0.10276,-0.91736,142.04,-0.89404,-0.20593,-0.39785,168.25
    5701 
    5702 > view matrix models
    5703 > #27,-0.22979,0.97316,0.012679,104.93,0.38456,0.10276,-0.91736,141.75,-0.89404,-0.20593,-0.39785,167.14
    5704 
    5705 > view matrix models
    5706 > #27,-0.22979,0.97316,0.012679,104.2,0.38456,0.10276,-0.91736,144.37,-0.89404,-0.20593,-0.39785,166.13
    5707 
    5708 > hide #27 models
    5709 
    5710 > show #27 models
    5711 
    5712 > hide #27 models
    5713 
    5714 > show #27 models
    5715 
    5716 > view matrix models
    5717 > #27,-0.49784,0.70316,-0.50765,154.01,0.28651,-0.41914,-0.86153,160.52,-0.81858,-0.57435,0.0072046,149.92
    5718 
    5719 > view matrix models
    5720 > #27,-0.29847,0.7881,-0.53834,148.31,0.35815,-0.43034,-0.82857,156.97,-0.88467,-0.44011,-0.15381,157.66
    5721 
    5722 > view matrix models
    5723 > #27,-0.24543,0.58716,-0.77137,169.05,0.40215,-0.66234,-0.63212,150.71,-0.88207,-0.46535,-0.073571,153.15
    5724 
    5725 > view matrix models
    5726 > #27,-0.18594,0.44822,-0.87437,179.01,0.44471,-0.75513,-0.48167,142.87,-0.87616,-0.4784,-0.058915,152.48
    5727 
    5728 > view matrix models
    5729 > #27,0.22752,0.8665,-0.44432,126.63,0.092657,-0.47348,-0.87592,168.02,-0.96935,0.15812,-0.18801,142.01
    5730 
    5731 > view matrix models
    5732 > #27,0.50128,0.79078,-0.35126,116.34,0.31994,-0.54657,-0.77389,158.19,-0.80396,0.27556,-0.52699,156.35
    5733 
    5734 > view matrix models
    5735 > #27,0.70079,0.62982,-0.335,115.76,0.20665,-0.62869,-0.74969,162.11,-0.68278,0.45615,-0.57073,150.23
    5736 
    5737 > view matrix models
    5738 > #27,0.70079,0.62982,-0.335,118.94,0.20665,-0.62869,-0.74969,162.08,-0.68278,0.45615,-0.57073,148.91
    5739 
    5740 > view matrix models
    5741 > #27,-0.4262,0.53806,-0.72722,175.4,-0.24981,-0.84263,-0.47705,162.45,-0.86946,-0.021651,0.49354,99.401
    5742 
    5743 > view matrix models
    5744 > #27,-0.4262,0.53806,-0.72722,174.48,-0.24981,-0.84263,-0.47705,159.2,-0.86946,-0.021651,0.49354,98.413
    5745 
    5746 > hide #27 models
    5747 
    5748 > select subtract #27
    5749 
    5750 Nothing selected 
    5751 
    5752 > hide #!29 models
    5753 
    5754 > show #!30 models
    5755 
    5756 > show #!29 models
    5757 
    5758 > hide #!29 models
    5759 
    5760 > transparency #30 50
    5761 
    5762 > show #!29 models
    5763 
    5764 > hide #!29 models
    5765 
    5766 > volume #30 level 0.002739
    5767 
    5768 > show #!24 models
    5769 
    5770 > hide #!24 models
    5771 
    5772 > show #!6 models
    5773 
    5774 > hide #!6 models
    5775 
    5776 > combine #6 close false
    5777 
    5778 > select add #33
    5779 
    5780 3190 atoms, 3270 bonds, 2 pseudobonds, 422 residues, 3 models selected 
    5781 
    5782 > view matrix models
    5783 > #33,-0.12378,0.83325,-0.53886,145.44,-0.98558,-0.040107,0.16437,137.25,0.11535,0.55143,0.8262,70.943
    5784 
    5785 > view matrix models
    5786 > #33,-0.12378,0.83325,-0.53886,121.31,-0.98558,-0.040107,0.16437,137.63,0.11535,0.55143,0.8262,134.88
    5787 
    5788 > view matrix models
    5789 > #33,0.096483,0.85305,0.51282,84.33,-0.9177,-0.12324,0.37767,130.03,0.38537,-0.50706,0.77096,135.66
    5790 
    5791 > view matrix models
    5792 > #33,0.64301,0.74737,-0.16726,96.505,-0.76213,0.64595,-0.043654,137.8,0.075414,0.15554,0.98495,132
    5793 
    5794 > view matrix models
    5795 > #33,0.64301,0.74737,-0.16726,99.153,-0.76213,0.64595,-0.043654,141.43,0.075414,0.15554,0.98495,123.21
    5796 
    5797 > view matrix models
    5798 > #33,0.53757,0.81725,-0.20763,102.02,-0.84165,0.53507,-0.073018,144.14,0.051423,0.214,0.97548,123.72
    5799 
    5800 > view matrix models
    5801 > #33,0.56724,0.791,-0.22925,102.27,-0.77653,0.60643,0.17101,135.07,0.2743,0.081017,0.95823,120.83
    5802 
    5803 > view matrix models
    5804 > #33,0.56724,0.791,-0.22925,126.45,-0.77653,0.60643,0.17101,136.72,0.2743,0.081017,0.95823,121.23
    5805 
    5806 > view matrix models
    5807 > #33,0.56724,0.791,-0.22925,77.167,-0.77653,0.60643,0.17101,133.67,0.2743,0.081017,0.95823,119.95
    5808 
    5809 > view matrix models
    5810 > #33,0.74297,0.64514,-0.17831,73.008,0.66921,-0.71089,0.21633,111.62,0.012799,-0.28005,-0.9599,186.09
    5811 
    5812 > view matrix models
    5813 > #33,0.09813,0.99411,-0.046082,78.903,0.94172,-0.077789,0.32727,101.1,0.32175,-0.075511,-0.94381,179.45
    5814 
    5815 > view matrix models
    5816 > #33,0.09813,0.99411,-0.046082,125.57,0.94172,-0.077789,0.32727,97.242,0.32175,-0.075511,-0.94381,182.15
    5817 
    5818 > view matrix models
    5819 > #33,0.09813,0.99411,-0.046082,123.79,0.94172,-0.077789,0.32727,98.857,0.32175,-0.075511,-0.94381,179.28
    5820 
    5821 > view matrix models
    5822 > #33,0.09813,0.99411,-0.046082,130.36,0.94172,-0.077789,0.32727,110.04,0.32175,-0.075511,-0.94381,181.04
    5823 
    5824 > view matrix models
    5825 > #33,0.18807,0.98065,-0.054404,129.09,0.97234,-0.17809,0.15115,115.39,0.13853,-0.081324,-0.98701,185.63
    5826 
    5827 > view matrix models
    5828 > #33,0.12584,0.98709,-0.099091,131.56,0.99196,-0.12652,-0.00060121,119.63,-0.01313,-0.098219,-0.99508,188.6
    5829 
    5830 > view matrix models
    5831 > #33,0.12584,0.98709,-0.099091,132.15,0.99196,-0.12652,-0.00060121,116.48,-0.01313,-0.098219,-0.99508,193.2
    5832 
    5833 > fitmap #33 inMap #29
    5834 
    5835 Fit molecule copy of 3C11_Fab_D_1292144377_model-annotate_P1_HL.pdb (#33) to
    5836 map cryosparc_P371_J1081_flex_map.mrc (#29) using 3190 atoms 
    5837 average map value = 0.003475, steps = 104 
    5838 shifted from previous position = 6.47 
    5839 rotated from previous position = 18.9 degrees 
    5840 atoms outside contour = 969, contour level = 0.0023495 
    5841  
    5842 Position of copy of 3C11_Fab_D_1292144377_model-annotate_P1_HL.pdb (#33)
    5843 relative to cryosparc_P371_J1081_flex_map.mrc (#29) coordinates: 
    5844 Matrix rotation and translation 
    5845 -0.15475687 0.98403031 -0.08794666 131.65046804 
    5846 0.97076802 0.13493018 -0.19850246 120.81278809 
    5847 -0.18346579 -0.11609543 -0.97614657 191.47093637 
    5848 Axis 0.64964584 0.75301343 -0.10455170 
    5849 Axis point 18.09163929 0.00000000 103.49035885 
    5850 Rotation angle (degrees) 176.36359820 
    5851 Shift along axis 156.48121953 
    5852  
    5853 
    5854 > select subtract #33
    5855 
    5856 Nothing selected 
    5857 
    5858 > color #33 #dbda64ff
    5859 
    5860 > show #!30 models
    5861 
    5862 > hide #!29 models
    5863 
    5864 > hide #!30 models
    5865 
    5866 > hide #!33 models
    5867 
    5868 > open /Users/apple/Downloads/cryosparc_P371_J973_003_volume_map.mrc
    5869 
    5870 Opened cryosparc_P371_J973_003_volume_map.mrc as #34, grid size 300,300,300,
    5871 pixel 0.867, shown at level 0.0274, step 2, values float32 
    5872 
    5873 > volume #34 level 0.05742
    5874 
    5875 > transparency #34 50
    5876 
    5877 > show #27 models
    5878 
    5879 > volume flip #34 axis z
    5880 
    5881 Opened cryosparc_P371_J973_003_volume_map.mrc z flip as #35, grid size
    5882 300,300,300, pixel 0.867, shown at step 1, values float32 
    5883 
    5884 > select add #27
    5885 
    5886 1798 atoms, 1661 bonds, 397 residues, 1 model selected 
    5887 
    5888 > view matrix models
    5889 > #27,-0.4262,0.53806,-0.72722,176.2,-0.24981,-0.84263,-0.47705,165.62,-0.86946,-0.021651,0.49354,102.24
    5890 
    5891 > view matrix models
    5892 > #27,-0.4262,0.53806,-0.72722,178.78,-0.24981,-0.84263,-0.47705,174.86,-0.86946,-0.021651,0.49354,105.39
    5893 
    5894 > view matrix models
    5895 > #27,-0.4262,0.53806,-0.72722,181.47,-0.24981,-0.84263,-0.47705,184.66,-0.86946,-0.021651,0.49354,109.78
    5896 
    5897 > view matrix models
    5898 > #27,-0.4262,0.53806,-0.72722,190.87,-0.24981,-0.84263,-0.47705,217.94,-0.86946,-0.021651,0.49354,118.99
    5899 
    5900 > view matrix models
    5901 > #27,-0.3858,0.47048,-0.7936,196.51,0.046117,-0.84929,-0.52592,214.13,-0.92143,-0.2395,0.30596,139.88
    5902 
    5903 > view matrix models
    5904 > #27,-0.66587,0.4077,0.62482,112.13,-0.39323,0.51992,-0.75832,194.48,-0.63402,-0.75064,-0.18588,182.26
    5905 
    5906 > view matrix models
    5907 > #27,-0.68529,0.37699,0.6231,113.74,-0.37744,0.54787,-0.74658,192.39,-0.62283,-0.74681,-0.23315,184.97
    5908 
    5909 > view matrix models
    5910 > #27,-0.64501,-0.54498,0.53568,149.28,-0.48286,0.83399,0.26704,118.72,-0.59228,-0.086414,-0.80108,199.55
    5911 
    5912 > view matrix models
    5913 > #27,-0.64501,-0.54498,0.53568,147.06,-0.48286,0.83399,0.26704,118.55,-0.59228,-0.086414,-0.80108,205.77
    5914 
    5915 > view matrix models
    5916 > #27,-0.98854,-0.0066051,-0.15082,182.67,-0.13987,0.41609,0.8985,82.549,0.056821,0.9093,-0.41224,131.06
    5917 
    5918 > view matrix models
    5919 > #27,-0.98854,-0.0066051,-0.15082,167.04,-0.13987,0.41609,0.8985,91.832,0.056821,0.9093,-0.41224,120.45
    5920 
    5921 > view matrix models
    5922 > #27,-0.98854,-0.0066051,-0.15082,170.38,-0.13987,0.41609,0.8985,89.105,0.056821,0.9093,-0.41224,122.96
    5923 
    5924 > view matrix models
    5925 > #27,-0.98854,-0.0066051,-0.15082,170.42,-0.13987,0.41609,0.8985,90.399,0.056821,0.9093,-0.41224,133.48
    5926 
    5927 > volume #35 level 0.043
    5928 
    5929 > open /Users/apple/Downloads/cryosparc_P371_J937_003_volume_map.mrc
    5930 
    5931 Opened cryosparc_P371_J937_003_volume_map.mrc as #36, grid size 300,300,300,
    5932 pixel 0.867, shown at level 0.0245, step 2, values float32 
    5933 
    5934 > volume #36 level 0.06028
    5935 
    5936 > hide #27 models
    5937 
    5938 > select subtract #27
    5939 
    5940 Nothing selected 
    5941 
    5942 > volume flip #36 axis z
    5943 
    5944 Opened cryosparc_P371_J937_003_volume_map.mrc z flip as #37, grid size
    5945 300,300,300, pixel 0.867, shown at step 1, values float32 
    5946 
    5947 > transparency #37 50
    5948 
    5949 > show #!31 models
    5950 
    5951 > select add #31
    5952 
    5953 2975 atoms, 2968 bonds, 437 residues, 1 model selected 
    5954 
    5955 > view matrix models
    5956 > #31,0.39135,-0.20933,0.89611,66.667,-0.16444,-0.97402,-0.15572,220.86,0.90543,-0.086415,-0.41561,82.36
    5957 
    5958 > view matrix models
    5959 > #31,-0.095994,-0.17972,0.97902,91.144,-0.11035,-0.97558,-0.18991,219.49,0.98925,-0.12627,0.073818,51.003
    5960 
    5961 > view matrix models
    5962 > #31,-0.095994,-0.17972,0.97902,86.989,-0.11035,-0.97558,-0.18991,196.02,0.98925,-0.12627,0.073818,43.81
    5963 
    5964 > view matrix models
    5965 > #31,-0.14959,-0.29832,0.94267,99.755,-0.024842,-0.95196,-0.3052,195.83,0.98844,-0.069073,0.13499,36.818
    5966 
    5967 > view matrix models
    5968 > #31,-0.14959,-0.29832,0.94267,100.18,-0.024842,-0.95196,-0.3052,202.18,0.98844,-0.069073,0.13499,38.064
    5969 
    5970 > fitmap #31 inMap #37
    5971 
    5972 Fit molecule copy of copy of copy of 1ezx (#31) to map
    5973 cryosparc_P371_J937_003_volume_map.mrc z flip (#37) using 2975 atoms 
    5974 average map value = 0.08682, steps = 132 
    5975 shifted from previous position = 2.02 
    5976 rotated from previous position = 31.6 degrees 
    5977 atoms outside contour = 867, contour level = 0.06028 
    5978  
    5979 Position of copy of copy of copy of 1ezx (#31) relative to
    5980 cryosparc_P371_J937_003_volume_map.mrc z flip (#37) coordinates: 
    5981 Matrix rotation and translation 
    5982 0.36233036 -0.11333577 0.92513335 57.46362679 
    5983 -0.01935243 -0.99328021 -0.11410485 191.49517202 
    5984 0.93184880 0.02344008 -0.36208890 68.00033796 
    5985 Axis 0.82499051 -0.04027910 0.56370937 
    5986 Axis point 0.00000000 96.54263836 19.29334389 
    5987 Rotation angle (degrees) 175.21818737 
    5988 Shift along axis 78.02612084 
    5989  
    5990 
    5991 > mmaker #32 to #31
    5992 
    5993 Parameters 
    5994 --- 
    5995 Chain pairing | bb 
    5996 Alignment algorithm | Needleman-Wunsch 
    5997 Similarity matrix | BLOSUM-62 
    5998 SS fraction | 0.3 
    5999 Gap open (HH/SS/other) | 18/18/6 
    6000 Gap extend | 1 
    6001 SS matrix |  |  | H | S | O 
    6002 ---|---|---|--- 
    6003 H | 6 | -9 | -6 
    6004 S |  | 6 | -6 
    6005 O |  |  | 4 
    6006 Iteration cutoff | 2 
    6007  
    6008 Matchmaker copy of copy of copy of 1ezx, chain A (#31) with copy of copy of
    6009 copy of 1ezx, chain A (#32), sequence alignment score = 1734 
    6010 RMSD between 335 pruned atom pairs is 0.000 angstroms; (across all 335 pairs:
    6011 0.000) 
    6012  
    6013 
    6014 > show #!32 models
    6015 
    6016 > select subtract #31
    6017 
    6018 Nothing selected 
    6019 
    6020 > hide #!32 models
    6021 
    6022 > transparency #37 30
    6023 
    6024 > transparency #37 65
    6025 
    6026 > show #!32 models
    6027 
    6028 > show #27 models
    6029 
    6030 > mmaker #27 to #32
    6031 
    6032 Parameters 
    6033 --- 
    6034 Chain pairing | bb 
    6035 Alignment algorithm | Needleman-Wunsch 
    6036 Similarity matrix | BLOSUM-62 
    6037 SS fraction | 0.3 
    6038 Gap open (HH/SS/other) | 18/18/6 
    6039 Gap extend | 1 
    6040 SS matrix |  |  | H | S | O 
    6041 ---|---|---|--- 
    6042 H | 6 | -9 | -6 
    6043 S |  | 6 | -6 
    6044 O |  |  | 4 
    6045 Iteration cutoff | 2 
    6046  
    6047 Matchmaker copy of copy of copy of 1ezx, chain C (#32) with 1oph, chain B
    6048 (#27), sequence alignment score = 997.3 
    6049 RMSD between 122 pruned atom pairs is 0.798 angstroms; (across all 140 pairs:
    6050 2.232) 
    6051  
    6052 
    6053 > hide #!32 models
    6054 
    6055 > select #27/B: 195
    6056 
    6057 5 atoms, 4 bonds, 1 residue, 1 model selected 
    6058 
    6059 > color sel red
    6060 
    6061 > select add #27
    6062 
    6063 1798 atoms, 1661 bonds, 397 residues, 1 model selected 
    6064 
    6065 > select subtract #27
    6066 
    6067 Nothing selected 
    6068 
    6069 > select add #27
    6070 
    6071 1798 atoms, 1661 bonds, 397 residues, 1 model selected 
    6072 
    6073 > view matrix models
    6074 > #27,0.0036574,-0.99591,-0.090234,167.1,0.079873,-0.089656,0.99276,103.86,-0.9968,-0.010838,0.079218,136.78
    6075 
    6076 > view matrix models
    6077 > #27,0.0036574,-0.99591,-0.090234,167.32,0.079873,-0.089656,0.99276,103.5,-0.9968,-0.010838,0.079218,136.17
    6078 
    6079 > view matrix models
    6080 > #27,0.0036574,-0.99591,-0.090234,167.31,0.079873,-0.089656,0.99276,103.59,-0.9968,-0.010838,0.079218,135.71
    6081 
    6082 > view matrix models
    6083 > #27,-0.286,-0.74268,-0.6055,199.85,-0.56632,-0.37872,0.73202,146.21,-0.77297,0.55227,-0.31228,137.19
    6084 
    6085 > view matrix models
    6086 > #27,-0.286,-0.74268,-0.6055,200.26,-0.56632,-0.37872,0.73202,145.27,-0.77297,0.55227,-0.31228,137.56
    6087 
    6088 > view matrix models
    6089 > #27,-0.11735,-0.92157,-0.37006,186.61,-0.43047,-0.2886,0.85522,130.83,-0.89494,0.25966,-0.36284,153.64
    6090 
    6091 > view matrix models
    6092 > #27,-0.11735,-0.92157,-0.37006,187.37,-0.43047,-0.2886,0.85522,129.56,-0.89494,0.25966,-0.36284,153.71
    6093 
    6094 > fitmap #27 inMap #37
    6095 
    6096 Fit molecule 1oph (#27) to map cryosparc_P371_J937_003_volume_map.mrc z flip
    6097 (#37) using 1798 atoms 
    6098 average map value = 0.0548, steps = 128 
    6099 shifted from previous position = 3.42 
    6100 rotated from previous position = 38.8 degrees 
    6101 atoms outside contour = 1047, contour level = 0.06028 
    6102  
    6103 Position of 1oph (#27) relative to cryosparc_P371_J937_003_volume_map.mrc z
    6104 flip (#37) coordinates: 
    6105 Matrix rotation and translation 
    6106 -0.45346895 -0.89029021 0.04182410 166.01007315 
    6107 -0.59816316 0.33879139 0.72623772 117.01111106 
    6108 -0.66073198 0.30430862 -0.68617018 166.01554475 
    6109 Axis -0.48496079 0.80751043 0.33576770 
    6110 Axis point 138.35331070 0.00000000 30.35915407 
    6111 Rotation angle (degrees) 154.21383871 
    6112 Shift along axis 69.72197468 
    6113  
    6114 
    6115 > view matrix models
    6116 > #27,-0.92301,-0.085578,-0.37515,178.08,-0.38272,0.30509,0.87204,103.27,0.039826,0.94847,-0.31435,102.9
    6117 
    6118 > view matrix models
    6119 > #27,-0.92301,-0.085578,-0.37515,178.04,-0.38272,0.30509,0.87204,107.02,0.039826,0.94847,-0.31435,104.53
    6120 
    6121 > view matrix models
    6122 > #27,-0.8652,-0.36102,-0.348,184.03,-0.41726,0.13347,0.89893,111.83,-0.27809,0.92296,-0.26611,109.99
    6123 
    6124 > view matrix models
    6125 > #27,-0.8652,-0.36102,-0.348,184.08,-0.41726,0.13347,0.89893,110,-0.27809,0.92296,-0.26611,108.82
    6126 
    6127 > view matrix models
    6128 > #27,-0.74437,-0.58007,-0.33081,187.3,-0.42416,0.028093,0.90515,113.28,-0.51575,0.81408,-0.26695,118.33
    6129 
    6130 > fitmap #27 inMap #37
    6131 
    6132 Fit molecule 1oph (#27) to map cryosparc_P371_J937_003_volume_map.mrc z flip
    6133 (#37) using 1798 atoms 
    6134 average map value = 0.05355, steps = 84 
    6135 shifted from previous position = 0.767 
    6136 rotated from previous position = 14.4 degrees 
    6137 atoms outside contour = 1098, contour level = 0.06028 
    6138  
    6139 Position of 1oph (#27) relative to cryosparc_P371_J937_003_volume_map.mrc z
    6140 flip (#37) coordinates: 
    6141 Matrix rotation and translation 
    6142 -0.61577270 -0.75165872 -0.23629043 184.50519497 
    6143 -0.34375795 -0.01355748 0.93896042 110.78003691 
    6144 -0.70898128 0.65941290 -0.25004033 128.04401792 
    6145 Axis -0.40864695 0.69098691 0.59627574 
    6146 Axis point 135.45180710 0.00000000 -11.35956716 
    6147 Rotation angle (degrees) 159.99876589 
    6148 Shift along axis 77.49961288 
    6149  
    6150 
    6151 > hide #!31 models
    6152 
    6153 > close #34-37
    6154 
    6155 > hide #27 models
    6156 
    6157 > select subtract #27
    6158 
    6159 Nothing selected 
    6160 
    6161 > save /Users/apple/Downloads/csparc.cxs includeMaps true
    6162 
    6163  
    6164 You deleted or moved a volume file that is still open in ChimeraX. 
    6165  
    6166 /Users/apple/Downloads/cryosparc_P371_J1081_noflex_map.mrc 
    6167  
    6168 To allow fast initial display of volume data ChimeraX does not read all data
    6169 from the file when it is first opened, and will later read more data when
    6170 needed. ChimeraX got an error trying to read the above file. 
    6171 [Repeated 1 time(s)]
    6172 
    6173 > close #29-30
    6174 
    6175 > save /Users/apple/Downloads/csparc.cxs includeMaps true
    6176 
    6177 ——— End of log from Wed Dec 31 02:28:23 2025 ———
    6178 
    6179 opened ChimeraX session 
    6180 
    6181 > open /Users/apple/Downloads/J1122.mrc
    6182 
    6183 Opened J1122.mrc as #29, grid size 300,300,300, pixel 0.867, shown at level
    6184 0.0211, step 2, values float32 
    6185 
    6186 > volume #29 level 0.06448
    6187 
    6188 > transparency #29 50
    6189 
    6190 > show #!31 models
    6191 
    6192 > hide #!31 models
    6193 
    6194 > show #!32 models
    6195 
    6196 > select add #32
    6197 
    6198 3984 atoms, 3982 bonds, 5 pseudobonds, 592 residues, 3 models selected 
    6199 
    6200 > ui mousemode right "translate selected models"
    6201 
    6202 > view matrix models
    6203 > #32,-0.4387,-0.32363,-0.83834,223.29,0.093735,-0.94429,0.31548,159.1,-0.89373,0.059819,0.44459,173.61
    6204 
    6205 > view matrix models
    6206 > #32,-0.051177,-0.06552,-0.99654,192.53,-0.071281,-0.99506,0.069084,187.1,-0.99614,0.074569,0.046254,202.65
    6207 
    6208 > view matrix models
    6209 > #32,-0.051177,-0.06552,-0.99654,191.33,-0.071281,-0.99506,0.069084,184.14,-0.99614,0.074569,0.046254,203.41
    6210 
    6211 > view matrix models
    6212 > #32,0.026039,-0.29812,-0.95417,195.35,0.13022,-0.94535,0.29892,154.62,-0.99114,-0.13204,0.014206,215.34
    6213 
    6214 > view matrix models
    6215 > #32,0.026039,-0.29812,-0.95417,195.13,0.13022,-0.94535,0.29892,154.52,-0.99114,-0.13204,0.014206,218.61
    6216 
    6217 > view matrix models
    6218 > #32,0.32421,-0.1599,-0.93237,166.33,0.029424,-0.98343,0.17889,170.24,-0.94553,-0.085432,-0.31413,231.84
    6219 
    6220 > ui tool show "Fit in Map"
    6221 
    6222 > fitmap #32 inMap #29
    6223 
    6224 Fit molecule copy of copy of copy of 1ezx (#32) to map J1122.mrc (#29) using
    6225 3984 atoms 
    6226 average map value = 0.08314, steps = 224 
    6227 shifted from previous position = 4.3 
    6228 rotated from previous position = 41.5 degrees 
    6229 atoms outside contour = 1668, contour level = 0.06448 
    6230  
    6231 Position of copy of copy of copy of 1ezx (#32) relative to J1122.mrc (#29)
    6232 coordinates: 
    6233 Matrix rotation and translation 
    6234 -0.34900889 0.03003688 -0.93663792 206.58097603 
    6235 0.14034902 -0.98653802 -0.08393380 177.23372304 
    6236 -0.92655003 -0.16074986 0.34009489 197.98573410 
    6237 Axis -0.56984891 -0.07483556 0.81833481 
    6238 Axis point 168.52294892 102.29267921 0.00000000 
    6239 Rotation angle (degrees) 176.13531334 
    6240 Shift along axis 31.03528983 
    6241  
    6242 
    6243 > volume #29 level 0.07099
    6244 
    6245 > surface dust #29 size 8.67
    6246 
    6247 > select subtract #32
    6248 
    6249 Nothing selected 
    6250 
    6251 > open cryosparc_P371_J1130_component_001/J1130_component_001_frame_???.mrc
    6252 > vseries true
    6253 
    6254 Opened map series J1130_component_001_frame_000.mrc as #30, 20 images, grid
    6255 size 300,300,300, pixel 0.867, shown at level 0.033, step 2, values float32 
    6256 
    6257 > volume #30.1 level 0.04835
    6258 
    6259 > surface dust #29 size 8.67
    6260 
    6261 > surface dust #30.1 size 8.67
    6262 
    6263 > transparency #30 50
    6264 
    6265 > volume #30.7 level 0.06047
    6266 
    6267 > open /Users/apple/Downloads/J1134.mrc
    6268 
    6269 Opened J1134.mrc as #34, grid size 300,300,300, pixel 0.867, shown at level
    6270 0.0252, step 2, values float32 
    6271 
    6272 > transparency #31 50
    6273 
    6274 > volume #34 level 0.04544
    6275 
    6276 > transparency #31450
    6277 
    6278 Missing or invalid "percent" argument: Expected a number 
    6279 
    6280 > transparency #34 50
    6281 
    6282 > hide #!32 models
    6283 
    6284 > show #!34 models
    6285 
    6286 > volume #34 level 0.05837
    6287 
    6288 > hide #!30 models
    6289 
    6290 > show #!30 models
    6291 
    6292 > hide #!29 models
    6293 
    6294 > show #!32 models
    6295 
    6296 > show #!29 models
    6297 
    6298 > hide #!34 models
    6299 
    6300 > hide #!30 models
    6301 
    6302 > show #!34 models
    6303 
    6304 > hide #!29 models
    6305 
    6306 > volume #34 level 0.0685
    6307 
    6308 > mmaker #27 to #32
    6309 
    6310 Parameters 
    6311 --- 
    6312 Chain pairing | bb 
    6313 Alignment algorithm | Needleman-Wunsch 
    6314 Similarity matrix | BLOSUM-62 
    6315 SS fraction | 0.3 
    6316 Gap open (HH/SS/other) | 18/18/6 
    6317 Gap extend | 1 
    6318 SS matrix |  |  | H | S | O 
    6319 ---|---|---|--- 
    6320 H | 6 | -9 | -6 
    6321 S |  | 6 | -6 
    6322 O |  |  | 4 
    6323 Iteration cutoff | 2 
    6324  
    6325 Matchmaker copy of copy of copy of 1ezx, chain C (#32) with 1oph, chain B
    6326 (#27), sequence alignment score = 997.3 
    6327 RMSD between 122 pruned atom pairs is 0.798 angstroms; (across all 140 pairs:
    6328 2.232) 
    6329  
    6330 
    6331 > show #27 models
    6332 
    6333 > hide #!32 models
    6334 
    6335 > hide #27 models
    6336 
    6337 > show #!29 models
    6338 
    6339 > hide #!34 models
    6340 
    6341 > show #!23 models
    6342 
    6343 > hide #!29 models
    6344 
    6345 > show #!29 models
    6346 
    6347 > show #27 models
    6348 
    6349 > fitmap #27 inMap #29
    6350 
    6351 Fit molecule 1oph (#27) to map J1122.mrc (#29) using 1798 atoms 
    6352 average map value = 0.0518, steps = 144 
    6353 shifted from previous position = 4.11 
    6354 rotated from previous position = 22.4 degrees 
    6355 atoms outside contour = 1430, contour level = 0.070992 
    6356  
    6357 Position of 1oph (#27) relative to J1122.mrc (#29) coordinates: 
    6358 Matrix rotation and translation 
    6359 0.02106068 0.97914469 -0.20206962 114.64292873 
    6360 0.03717102 0.20120785 0.97884305 90.21390293 
    6361 0.99908697 -0.02812623 -0.03215823 122.53280686 
    6362 Axis -0.55065296 -0.65684271 -0.51511064 
    6363 Axis point 6.14168786 0.00000000 32.08271580 
    6364 Rotation angle (degrees) 113.88767131 
    6365 Shift along axis -185.50276510 
    6366  
    6367 
    6368 > select add #27
    6369 
    6370 1798 atoms, 1661 bonds, 397 residues, 1 model selected 
    6371 
    6372 > mmaker #27 to #32
    6373 
    6374 Parameters 
    6375 --- 
    6376 Chain pairing | bb 
    6377 Alignment algorithm | Needleman-Wunsch 
    6378 Similarity matrix | BLOSUM-62 
    6379 SS fraction | 0.3 
    6380 Gap open (HH/SS/other) | 18/18/6 
    6381 Gap extend | 1 
    6382 SS matrix |  |  | H | S | O 
    6383 ---|---|---|--- 
    6384 H | 6 | -9 | -6 
    6385 S |  | 6 | -6 
    6386 O |  |  | 4 
    6387 Iteration cutoff | 2 
    6388  
    6389 Matchmaker copy of copy of copy of 1ezx, chain C (#32) with 1oph, chain B
    6390 (#27), sequence alignment score = 997.3 
    6391 RMSD between 122 pruned atom pairs is 0.798 angstroms; (across all 140 pairs:
    6392 2.232) 
    6393  
    6394 
    6395 > view matrix models
    6396 > #27,-0.76366,-0.59209,0.2574,152.81,-0.32869,0.6997,0.63433,106.59,-0.55569,0.39981,-0.72895,190.1
    6397 
    6398 > view matrix models
    6399 > #27,-0.76366,-0.59209,0.2574,153.88,-0.32869,0.6997,0.63433,107.32,-0.55569,0.39981,-0.72895,188.09
    6400 
    6401 > view matrix models
    6402 > #27,-0.83313,-0.43989,0.33525,145.38,-0.083744,0.6995,0.70971,96.368,-0.54671,0.56321,-0.61961,175.22
    6403 
    6404 > view matrix models
    6405 > #27,-0.74236,-0.59158,0.31452,149.59,-0.27194,0.69508,0.66552,104.03,-0.61232,0.40852,-0.67688,185.76
    6406 
    6407 > view matrix models
    6408 > #27,-0.74236,-0.59158,0.31452,149.31,-0.27194,0.69508,0.66552,103.43,-0.61232,0.40852,-0.67688,186.03
    6409 
    6410 > view matrix models
    6411 > #27,-0.74236,-0.59158,0.31452,149.1,-0.27194,0.69508,0.66552,103.48,-0.61232,0.40852,-0.67688,187.73
    6412 
    6413 > view matrix models
    6414 > #27,-0.4433,-0.67999,0.58404,127,-0.43264,0.73295,0.52499,115.4,-0.78505,-0.019955,-0.61911,202.46
    6415 
    6416 > view matrix models
    6417 > #27,-0.4433,-0.67999,0.58404,130.64,-0.43264,0.73295,0.52499,113.63,-0.78505,-0.019955,-0.61911,205.53
    6418 
    6419 > fitmap #27 inMap #29
    6420 
    6421 Fit molecule 1oph (#27) to map J1122.mrc (#29) using 1798 atoms 
    6422 average map value = 0.05116, steps = 68 
    6423 shifted from previous position = 2.69 
    6424 rotated from previous position = 9.17 degrees 
    6425 atoms outside contour = 1446, contour level = 0.070992 
    6426  
    6427 Position of 1oph (#27) relative to J1122.mrc (#29) coordinates: 
    6428 Matrix rotation and translation 
    6429 -0.36812181 -0.63861563 0.67576357 123.53211487 
    6430 -0.32941202 0.76923775 0.54750435 107.83162875 
    6431 -0.86946769 -0.02105634 -0.49354086 197.89559046 
    6432 Axis -0.33937979 0.92236459 0.18456685 
    6433 Axis point 134.62181234 0.00000000 42.50689250 
    6434 Rotation angle (degrees) 123.10755810 
    6435 Shift along axis 94.06073906 
    6436  
    6437 
    6438 > view matrix models
    6439 > #27,0.36598,-0.2092,0.9068,76.029,-0.77877,0.46461,0.42149,137.29,-0.50949,-0.86045,0.0071194,184.16
    6440 
    6441 > view matrix models
    6442 > #27,0.36598,-0.2092,0.9068,76.706,-0.77877,0.46461,0.42149,135.37,-0.50949,-0.86045,0.0071194,183.36
    6443 
    6444 > fitmap #27 inMap #29
    6445 
    6446 Fit molecule 1oph (#27) to map J1122.mrc (#29) using 1798 atoms 
    6447 average map value = 0.05313, steps = 140 
    6448 shifted from previous position = 4.46 
    6449 rotated from previous position = 26.6 degrees 
    6450 atoms outside contour = 1440, contour level = 0.070992 
    6451  
    6452 Position of 1oph (#27) relative to J1122.mrc (#29) coordinates: 
    6453 Matrix rotation and translation 
    6454 0.65758974 -0.02081924 0.75308850 73.16880294 
    6455 -0.73687782 0.19027838 0.64869501 131.74587255 
    6456 -0.15680180 -0.98150940 0.10978387 176.26543706 
    6457 Axis -0.81528498 0.45504717 -0.35810958 
    6458 Axis point 0.00000000 178.61895966 -24.20653672 
    6459 Rotation angle (degrees) 91.21327181 
    6460 Shift along axis -62.82518106 
    6461  
    6462 
    6463 > show #!34 models
    6464 
    6465 > hide #!29 models
    6466 
    6467 > volume #34 level 0.07075
    6468 
    6469 > close #30
    6470 
    6471 > save /Users/apple/Downloads/csparc.cxs includeMaps true
    6472 
    6473 ——— End of log from Tue Jan 6 13:31:49 2026 ———
    6474 
    6475 > view name session-start
    6476 
    6477 opened ChimeraX session 
    6478 
    6479 > hide #!23 models
    6480 
    6481 > select subtract #27
    6482 
    6483 Nothing selected 
    6484 
    6485 > hide #27 models
    6486 
    6487 > hide #!34 models
    6488 
    6489 > show #!8 models
    6490 
    6491 > view
    6492 
    6493 > open 1oph fromDatabase pdb format mmcif
    6494 
    6495 Summary of feedback from opening 1oph fetched from pdb 
    6496 --- 
    6497 note | Fetching compressed mmCIF 1oph from http://files.rcsb.org/download/1oph.cif 
    6498  
    6499 1oph title: 
    6500 Non-covalent complex between α-1-π-pittsburgh and S195A trypsin [more info...] 
    6501  
    6502 Chain information for 1oph #30 
    6503 --- 
    6504 Chain | Description | UniProt 
    6505 A | Alpha-1-antitrypsin precursor | A1AT_HUMAN 1-394 
    6506 B | Trypsinogen, cationic precursor | TRY1_BOVIN -4-245 
    6507  
    6508 1oph mmCIF Assemblies 
    6509 --- 
    6510 1| author_and_software_defined_assembly 
    6511 2| software_defined_assembly 
    6512  
    6513 
    6514 > mmaker #30 to #8
    6515 
    6516 Parameters 
    6517 --- 
    6518 Chain pairing | bb 
    6519 Alignment algorithm | Needleman-Wunsch 
    6520 Similarity matrix | BLOSUM-62 
    6521 SS fraction | 0.3 
    6522 Gap open (HH/SS/other) | 18/18/6 
    6523 Gap extend | 1 
    6524 SS matrix |  |  | H | S | O 
    6525 ---|---|---|--- 
    6526 H | 6 | -9 | -6 
    6527 S |  | 6 | -6 
    6528 O |  |  | 4 
    6529 Iteration cutoff | 2 
    6530  
    6531 Matchmaker 1ezx, chain A (#8) with 1oph, chain A (#30), sequence alignment
    6532 score = 1610.1 
    6533 RMSD between 212 pruned atom pairs is 0.928 angstroms; (across all 335 pairs:
    6534 9.705) 
    6535  
    6536 
    6537 > hide #!8 models
    6538 
    6539 > ui tool show "Show Sequence Viewer"
    6540 
    6541 > sequence chain #30/A
    6542 
    6543 Alignment identifier is 30/A 
    6544 
    6545 > select #30/A:21-22
    6546 
    6547 14 atoms, 14 bonds, 2 residues, 1 model selected 
    6548 
    6549 > select #30/A:21-83
    6550 
    6551 484 atoms, 495 bonds, 63 residues, 1 model selected 
    6552 
    6553 > select #30/A:88
    6554 
    6555 7 atoms, 7 bonds, 1 residue, 1 model selected 
    6556 
    6557 > select #30/A:88-121
    6558 
    6559 263 atoms, 267 bonds, 34 residues, 1 model selected 
    6560 
    6561 > select #30/A:121
    6562 
    6563 6 atoms, 5 bonds, 1 residue, 1 model selected 
    6564 
    6565 > select #30/A:105-121
    6566 
    6567 127 atoms, 128 bonds, 17 residues, 1 model selected 
    6568 
    6569 > select #30/A:88
    6570 
    6571 7 atoms, 7 bonds, 1 residue, 1 model selected 
    6572 
    6573 > select #30/A:88-104
    6574 
    6575 136 atoms, 138 bonds, 17 residues, 1 model selected 
    6576 
    6577 > select #30/A:21-45,88-104
    6578 
    6579 341 atoms, 349 bonds, 42 residues, 1 model selected 
    6580 
    6581 > select #30/A:53
    6582 
    6583 6 atoms, 5 bonds, 1 residue, 1 model selected 
    6584 
    6585 > select #30/A:53-80
    6586 
    6587 196 atoms, 198 bonds, 28 residues, 1 model selected 
    6588 
    6589 > select #30/A:21-45,53-80
    6590 
    6591 401 atoms, 409 bonds, 53 residues, 1 model selected 
    6592 
    6593 > select #30/A:21-45,53-80,88-104
    6594 
    6595 537 atoms, 547 bonds, 70 residues, 1 model selected 
    6596 
    6597 > select #30/A:21-45,53-80,88-104,127-137
    6598 
    6599 622 atoms, 632 bonds, 81 residues, 1 model selected 
    6600 
    6601 > select #30/A:21-45,53-80,88-104,127-137,149-165
    6602 
    6603 747 atoms, 757 bonds, 98 residues, 1 model selected 
    6604 
    6605 > select #30/A:21-45,53-80,88-104,127-137,149-165,199-203
    6606 
    6607 783 atoms, 792 bonds, 103 residues, 1 model selected 
    6608 
    6609 > select #30/A:21-45,53-80,88-104,127-137,149-165,199-203,259-278
    6610 
    6611 954 atoms, 965 bonds, 123 residues, 1 model selected 
    6612 
    6613 > select #30/A:21-45,53-80,88-104,127-137,149-165,199-203,259-278,299-306
    6614 
    6615 1013 atoms, 1023 bonds, 131 residues, 1 model selected 
    6616 
    6617 > select
    6618 > #30/A:21-45,53-80,88-104,127-137,149-165,199-203,259-278,299-306,309-313
    6619 
    6620 1053 atoms, 1063 bonds, 136 residues, 1 model selected 
    6621 
    6622 > select
    6623 > #30/A:21-45,53-80,88-104,127-137,149-165,199-203,259-278,299-306,309-313,349-353
    6624 
    6625 1089 atoms, 1099 bonds, 141 residues, 1 model selected 
    6626 
    6627 > color sel hot pink
    6628 
    6629 > color sel dim gray
    6630 
    6631 > select clear
    6632 
    6633 [Repeated 3 time(s)]
    6634 
    6635 > select #30/A:112
    6636 
    6637 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6638 
    6639 > select #30/A:112-121
    6640 
    6641 71 atoms, 71 bonds, 10 residues, 1 model selected 
    6642 
    6643 > select #30/A:112-121,141-145
    6644 
    6645 110 atoms, 110 bonds, 15 residues, 1 model selected 
    6646 
    6647 > select #30/A:112-121,141-145,182-191
    6648 
    6649 200 atoms, 203 bonds, 25 residues, 1 model selected 
    6650 
    6651 > select #30/A:112-121,141-145,182-191,193-194
    6652 
    6653 219 atoms, 223 bonds, 27 residues, 1 model selected 
    6654 
    6655 > select #30/A:112-121,141-145,182-191,193-194
    6656 
    6657 219 atoms, 223 bonds, 27 residues, 1 model selected 
    6658 
    6659 > select #30/A:112-121,141-145,182-194
    6660 
    6661 223 atoms, 228 bonds, 28 residues, 1 model selected 
    6662 
    6663 > select #30/A:112-121,141-145,182-194,204-211
    6664 
    6665 294 atoms, 300 bonds, 36 residues, 1 model selected 
    6666 
    6667 > select #30/A:112-121,141-145,182-194,204-211,214
    6668 
    6669 301 atoms, 306 bonds, 37 residues, 1 model selected 
    6670 
    6671 > select #30/A:112-121,141-145,182-194,204-211,214
    6672 
    6673 301 atoms, 306 bonds, 37 residues, 1 model selected 
    6674 
    6675 > select #30/A:211
    6676 
    6677 8 atoms, 7 bonds, 1 residue, 1 model selected 
    6678 
    6679 > select #30/A:204-211
    6680 
    6681 71 atoms, 72 bonds, 8 residues, 1 model selected 
    6682 
    6683 > select #30/A:214
    6684 
    6685 7 atoms, 6 bonds, 1 residue, 1 model selected 
    6686 
    6687 > select #30/A:214-232
    6688 
    6689 152 atoms, 154 bonds, 19 residues, 1 model selected 
    6690 
    6691 > select #30/A:282
    6692 
    6693 11 atoms, 10 bonds, 1 residue, 1 model selected 
    6694 
    6695 > select #30/A:282-298
    6696 
    6697 130 atoms, 132 bonds, 17 residues, 1 model selected 
    6698 
    6699 > ui tool show "Show Sequence Viewer"
    6700 
    6701 > sequence chain #8/C #19/C #26/C #32/C
    6702 
    6703 Alignment identifier is 1 
    6704 
    6705 > select add #30
    6706 
    6707 4919 atoms, 4641 bonds, 975 residues, 1 model selected 
    6708 
    6709 > select subtract #30
    6710 
    6711 Nothing selected 
    6712 
    6713 > select #30/A
    6714 
    6715 3121 atoms, 2980 bonds, 578 residues, 1 model selected 
    6716 
    6717 > delete #30/A
    6718 
    6719 > show #!8 models
    6720 
    6721 > close #30
    6722 
    6723 > open 1oph fromDatabase pdb format mmcif
    6724 
    6725 1oph title: 
    6726 Non-covalent complex between α-1-π-pittsburgh and S195A trypsin [more info...] 
    6727  
    6728 Chain information for 1oph #30 
    6729 --- 
    6730 Chain | Description | UniProt 
    6731 A | Alpha-1-antitrypsin precursor | A1AT_HUMAN 1-394 
    6732 B | Trypsinogen, cationic precursor | TRY1_BOVIN -4-245 
    6733  
    6734 1oph mmCIF Assemblies 
    6735 --- 
    6736 1| author_and_software_defined_assembly 
    6737 2| software_defined_assembly 
    6738  
    6739 
    6740 > open 8pi2 fromDatabase pdb format mmcif
    6741 
    6742 Summary of feedback from opening 8pi2 fetched from pdb 
    6743 --- 
    6744 notes | Fetching compressed mmCIF 8pi2 from http://files.rcsb.org/download/8pi2.cif 
    6745 Fetching CCD DMS from
    6746 https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/DMS/DMS.cif 
    6747 Fetching CCD EDO from
    6748 https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/EDO/EDO.cif 
    6749  
    6750 8pi2 title: 
    6751 Native alpha-1-antitrypsin at 1.5 Angstrom (Cys232Ser) [more info...] 
    6752  
    6753 Chain information for 8pi2 #35 
    6754 --- 
    6755 Chain | Description | UniProt 
    6756 A | Alpha-1-antitrypsin | A1AT_HUMAN 2-394 
    6757  
    6758 Non-standard residues in 8pi2 #35 
    6759 --- 
    6760 DMS — dimethyl sulfoxide 
    6761 EDO — 1,2-ethanediol (ethylene glycol) 
    6762 GLY — glycine 
    6763  
    6764 203 atoms have alternate locations. Control/examine alternate locations with
    6765 Altloc Explorer [start tool...] or the altlocs command. 
    6766 2826 atoms have anisotropic B-factors. Depict anisotropic information with
    6767 Thermal Ellipsoids [start tool...] or the aniso command. 
    6768 
    6769 > mmaker #30 to #8
    6770 
    6771 Parameters 
    6772 --- 
    6773 Chain pairing | bb 
    6774 Alignment algorithm | Needleman-Wunsch 
    6775 Similarity matrix | BLOSUM-62 
    6776 SS fraction | 0.3 
    6777 Gap open (HH/SS/other) | 18/18/6 
    6778 Gap extend | 1 
    6779 SS matrix |  |  | H | S | O 
    6780 ---|---|---|--- 
    6781 H | 6 | -9 | -6 
    6782 S |  | 6 | -6 
    6783 O |  |  | 4 
    6784 Iteration cutoff | 2 
    6785  
    6786 Matchmaker 1ezx, chain A (#8) with 1oph, chain A (#30), sequence alignment
    6787 score = 1610.1 
    6788 RMSD between 212 pruned atom pairs is 0.928 angstroms; (across all 335 pairs:
    6789 9.705) 
    6790  
    6791 
    6792 > mmaker #35 to #30
    6793 
    6794 Parameters 
    6795 --- 
    6796 Chain pairing | bb 
    6797 Alignment algorithm | Needleman-Wunsch 
    6798 Similarity matrix | BLOSUM-62 
    6799 SS fraction | 0.3 
    6800 Gap open (HH/SS/other) | 18/18/6 
    6801 Gap extend | 1 
    6802 SS matrix |  |  | H | S | O 
    6803 ---|---|---|--- 
    6804 H | 6 | -9 | -6 
    6805 S |  | 6 | -6 
    6806 O |  |  | 4 
    6807 Iteration cutoff | 2 
    6808  
    6809 Matchmaker 1oph, chain A (#30) with 8pi2, chain A (#35), sequence alignment
    6810 score = 1934.1 
    6811 RMSD between 350 pruned atom pairs is 0.764 angstroms; (across all 371 pairs:
    6812 1.541) 
    6813  
    6814 
    6815 > hide #!8 models
    6816 
    6817 > hide #30 models
    6818 
    6819 > show #30 models
    6820 
    6821 > delete #30/A
    6822 
    6823 > select add #35
    6824 
    6825 5953 atoms, 5684 bonds, 699 residues, 1 model selected 
    6826 
    6827 > hide sel atoms
    6828 
    6829 > select subtract #35
    6830 
    6831 Nothing selected 
    6832 
    6833 > select helix
    6834 
    6835 13863 atoms, 13950 bonds, 1635 residues, 21 models selected 
    6836 
    6837 > select add #30
    6838 
    6839 15472 atoms, 15419 bonds, 2007 residues, 21 models selected 
    6840 
    6841 > select subtract #30
    6842 
    6843 13674 atoms, 13758 bonds, 1610 residues, 20 models selected 
    6844 
    6845 > select add #31
    6846 
    6847 15630 atoms, 15698 bonds, 1919 residues, 20 models selected 
    6848 
    6849 > select subtract #31
    6850 
    6851 12655 atoms, 12730 bonds, 1482 residues, 19 models selected 
    6852 
    6853 > select add #32
    6854 
    6855 15484 atoms, 15547 bonds, 5 pseudobonds, 1928 residues, 21 models selected 
    6856 
    6857 > select subtract #32
    6858 
    6859 11500 atoms, 11565 bonds, 1336 residues, 18 models selected 
    6860 
    6861 > select add #33
    6862 
    6863 14424 atoms, 14571 bonds, 2 pseudobonds, 1724 residues, 20 models selected 
    6864 
    6865 > select subtract #33
    6866 
    6867 11234 atoms, 11301 bonds, 1302 residues, 17 models selected 
    6868 
    6869 > select add #35
    6870 
    6871 15239 atoms, 15031 bonds, 1873 residues, 17 models selected 
    6872 
    6873 > select subtract #35
    6874 
    6875 9286 atoms, 9347 bonds, 1174 residues, 16 models selected 
    6876 
    6877 > select add #27
    6878 
    6879 10895 atoms, 10816 bonds, 1546 residues, 16 models selected 
    6880 
    6881 > select subtract #27
    6882 
    6883 9097 atoms, 9155 bonds, 1149 residues, 15 models selected 
    6884 
    6885 > select add #26
    6886 
    6887 11926 atoms, 11972 bonds, 5 pseudobonds, 1595 residues, 17 models selected 
    6888 
    6889 > select subtract #26
    6890 
    6891 7942 atoms, 7990 bonds, 1003 residues, 14 models selected 
    6892 
    6893 > select add #25
    6894 
    6895 9668 atoms, 9577 bonds, 1377 residues, 14 models selected 
    6896 
    6897 > select subtract #25
    6898 
    6899 7785 atoms, 7832 bonds, 983 residues, 13 models selected 
    6900 
    6901 > select add #24
    6902 
    6903 10709 atoms, 10838 bonds, 2 pseudobonds, 1371 residues, 15 models selected 
    6904 
    6905 > select subtract #24
    6906 
    6907 7519 atoms, 7568 bonds, 949 residues, 12 models selected 
    6908 
    6909 > select add #23
    6910 
    6911 9475 atoms, 9508 bonds, 1258 residues, 12 models selected 
    6912 
    6913 > select subtract #23
    6914 
    6915 6500 atoms, 6540 bonds, 821 residues, 11 models selected 
    6916 
    6917 > select add #20
    6918 
    6919 8226 atoms, 8127 bonds, 1195 residues, 11 models selected 
    6920 
    6921 > select subtract #20
    6922 
    6923 6343 atoms, 6382 bonds, 801 residues, 10 models selected 
    6924 
    6925 > select add #19
    6926 
    6927 9172 atoms, 9199 bonds, 5 pseudobonds, 1247 residues, 12 models selected 
    6928 
    6929 > select subtract #19
    6930 
    6931 5188 atoms, 5217 bonds, 655 residues, 9 models selected 
    6932 
    6933 > select add #18
    6934 
    6935 6914 atoms, 6804 bonds, 1029 residues, 9 models selected 
    6936 
    6937 > select subtract #18
    6938 
    6939 5031 atoms, 5059 bonds, 635 residues, 8 models selected 
    6940 
    6941 > select add #17
    6942 
    6943 7955 atoms, 8065 bonds, 2 pseudobonds, 1023 residues, 10 models selected 
    6944 
    6945 > select subtract #17
    6946 
    6947 4765 atoms, 4795 bonds, 601 residues, 7 models selected 
    6948 
    6949 > select add #16
    6950 
    6951 6721 atoms, 6735 bonds, 910 residues, 7 models selected 
    6952 
    6953 > select subtract #16
    6954 
    6955 3746 atoms, 3767 bonds, 473 residues, 6 models selected 
    6956 
    6957 > select add #8
    6958 
    6959 6575 atoms, 6584 bonds, 5 pseudobonds, 919 residues, 8 models selected 
    6960 
    6961 > select subtract #8
    6962 
    6963 2591 atoms, 2602 bonds, 327 residues, 5 models selected 
    6964 
    6965 > select add #7
    6966 
    6967 4317 atoms, 4189 bonds, 701 residues, 5 models selected 
    6968 
    6969 > select subtract #7
    6970 
    6971 2434 atoms, 2444 bonds, 307 residues, 4 models selected 
    6972 
    6973 > select add #6
    6974 
    6975 5358 atoms, 5450 bonds, 2 pseudobonds, 695 residues, 6 models selected 
    6976 
    6977 > select subtract #6
    6978 
    6979 2168 atoms, 2180 bonds, 273 residues, 3 models selected 
    6980 
    6981 > select #35/A:340
    6982 
    6983 19 atoms, 18 bonds, 1 residue, 1 model selected 
    6984 Drag select of 11 residues 
    6985 
    6986 > select clear
    6987 
    6988 > select #35/A:340
    6989 
    6990 19 atoms, 18 bonds, 1 residue, 1 model selected 
    6991 
    6992 > select #35/A:339
    6993 
    6994 14 atoms, 13 bonds, 1 residue, 1 model selected 
    6995 
    6996 > select #35/A:340
    6997 
    6998 19 atoms, 18 bonds, 1 residue, 1 model selected 
    6999 
    7000 > select add #35/A:339
    7001 
    7002 33 atoms, 31 bonds, 2 residues, 1 model selected 
    7003 
    7004 > select add #35/A:338
    7005 
    7006 52 atoms, 49 bonds, 3 residues, 1 model selected 
    7007 
    7008 > select add #35/A:337
    7009 
    7010 68 atoms, 64 bonds, 4 residues, 1 model selected 
    7011 
    7012 > select add #35/A:336
    7013 
    7014 78 atoms, 73 bonds, 5 residues, 1 model selected 
    7015 
    7016 > select add #35/A:335
    7017 
    7018 99 atoms, 93 bonds, 6 residues, 1 model selected 
    7019 
    7020 > select add #35/A:334
    7021 
    7022 116 atoms, 110 bonds, 7 residues, 1 model selected 
    7023 
    7024 > select add #35/A:333
    7025 
    7026 132 atoms, 125 bonds, 8 residues, 1 model selected 
    7027 
    7028 > select add #35/A:332
    7029 
    7030 142 atoms, 134 bonds, 9 residues, 1 model selected 
    7031 
    7032 > select add #35/A:331
    7033 
    7034 164 atoms, 155 bonds, 10 residues, 1 model selected 
    7035 
    7036 > select add #35/A:191
    7037 
    7038 186 atoms, 176 bonds, 11 residues, 1 model selected 
    7039 
    7040 > select add #35/A:190
    7041 
    7042 206 atoms, 196 bonds, 12 residues, 1 model selected 
    7043 
    7044 > select add #35/A:189
    7045 
    7046 226 atoms, 216 bonds, 13 residues, 1 model selected 
    7047 
    7048 > select add #35/A:188
    7049 
    7050 245 atoms, 234 bonds, 14 residues, 1 model selected 
    7051 
    7052 > select add #35/A:187
    7053 
    7054 266 atoms, 255 bonds, 15 residues, 1 model selected 
    7055 
    7056 > select add #35/A:186
    7057 
    7058 280 atoms, 268 bonds, 16 residues, 1 model selected 
    7059 
    7060 > select add #35/A:185
    7061 
    7062 296 atoms, 283 bonds, 17 residues, 1 model selected 
    7063 
    7064 > select add #35/A:184
    7065 
    7066 315 atoms, 301 bonds, 18 residues, 1 model selected 
    7067 
    7068 > select add #35/A:183
    7069 
    7070 325 atoms, 310 bonds, 19 residues, 1 model selected 
    7071 
    7072 > select add #35/A:182
    7073 
    7074 345 atoms, 330 bonds, 20 residues, 1 model selected 
    7075 
    7076 > select add #35/A:291
    7077 
    7078 364 atoms, 348 bonds, 21 residues, 1 model selected 
    7079 
    7080 > select add #35/A:292
    7081 
    7082 375 atoms, 358 bonds, 22 residues, 1 model selected 
    7083 
    7084 > select add #35/A:293
    7085 
    7086 394 atoms, 376 bonds, 23 residues, 1 model selected 
    7087 
    7088 > select add #35/A:294
    7089 
    7090 408 atoms, 389 bonds, 24 residues, 1 model selected 
    7091 
    7092 > select subtract #35/A:294
    7093 
    7094 394 atoms, 376 bonds, 23 residues, 1 model selected 
    7095 
    7096 > select add #35/A:294
    7097 
    7098 408 atoms, 389 bonds, 24 residues, 1 model selected 
    7099 
    7100 > select add #35/A:295
    7101 
    7102 415 atoms, 395 bonds, 25 residues, 1 model selected 
    7103 
    7104 > select add #35/A:296
    7105 
    7106 429 atoms, 408 bonds, 26 residues, 1 model selected 
    7107 
    7108 > select add #35/A:297
    7109 
    7110 450 atoms, 429 bonds, 27 residues, 1 model selected 
    7111 
    7112 > select add #35/A:298
    7113 
    7114 462 atoms, 440 bonds, 28 residues, 1 model selected 
    7115 
    7116 > select add #35/A:112
    7117 
    7118 481 atoms, 458 bonds, 29 residues, 1 model selected 
    7119 
    7120 > select add #35/A:113
    7121 
    7122 495 atoms, 471 bonds, 30 residues, 1 model selected 
    7123 
    7124 > select add #35/A:114
    7125 
    7126 509 atoms, 484 bonds, 31 residues, 1 model selected 
    7127 
    7128 > select add #35/A:115
    7129 
    7130 516 atoms, 490 bonds, 32 residues, 1 model selected 
    7131 
    7132 > select add #35/A:116
    7133 
    7134 530 atoms, 503 bonds, 33 residues, 1 model selected 
    7135 
    7136 > select add #35/A:117
    7137 
    7138 537 atoms, 509 bonds, 34 residues, 1 model selected 
    7139 
    7140 > select add #35/A:118
    7141 
    7142 556 atoms, 527 bonds, 35 residues, 1 model selected 
    7143 
    7144 > select add #35/A:119
    7145 
    7146 576 atoms, 547 bonds, 36 residues, 1 model selected 
    7147 
    7148 > select add #35/A:120
    7149 
    7150 595 atoms, 565 bonds, 37 residues, 1 model selected 
    7151 
    7152 > select add #35/A:121
    7153 
    7154 606 atoms, 575 bonds, 38 residues, 1 model selected 
    7155 
    7156 > select add #35/A:141
    7157 
    7158 621 atoms, 589 bonds, 39 residues, 1 model selected 
    7159 
    7160 > select add #35/A:142
    7161 
    7162 631 atoms, 598 bonds, 40 residues, 1 model selected 
    7163 
    7164 > select add #35/A:143
    7165 
    7166 651 atoms, 618 bonds, 41 residues, 1 model selected 
    7167 
    7168 > select add #35/A:144
    7169 
    7170 665 atoms, 631 bonds, 42 residues, 1 model selected 
    7171 
    7172 > select add #35/A:145
    7173 
    7174 681 atoms, 646 bonds, 43 residues, 1 model selected 
    7175 
    7176 > color sel forest green
    7177 
    7178 > color sel lime
    7179 
    7180 > select clear
    7181 
    7182 > select add #35/A:341
    7183 
    7184 12 atoms, 11 bonds, 1 residue, 1 model selected 
    7185 
    7186 > select add #35/A:342
    7187 
    7188 27 atoms, 25 bonds, 2 residues, 1 model selected 
    7189 
    7190 > select add #35/A:343
    7191 
    7192 40 atoms, 37 bonds, 3 residues, 1 model selected 
    7193 
    7194 > select add #35/A:344
    7195 
    7196 47 atoms, 43 bonds, 4 residues, 1 model selected 
    7197 
    7198 > select add #35/A:345
    7199 
    7200 61 atoms, 56 bonds, 5 residues, 1 model selected 
    7201 
    7202 > select add #35/A:193
    7203 
    7204 83 atoms, 77 bonds, 6 residues, 1 model selected 
    7205 
    7206 > select subtract #35/A:193
    7207 
    7208 61 atoms, 56 bonds, 5 residues, 1 model selected 
    7209 
    7210 > select add #35/A:346
    7211 
    7212 68 atoms, 62 bonds, 6 residues, 1 model selected 
    7213 
    7214 > select add #35/A:347
    7215 
    7216 78 atoms, 71 bonds, 7 residues, 1 model selected 
    7217 
    7218 > select add #35/A:348
    7219 
    7220 88 atoms, 80 bonds, 8 residues, 1 model selected 
    7221 
    7222 > select add #35/A:349
    7223 
    7224 95 atoms, 86 bonds, 9 residues, 1 model selected 
    7225 
    7226 > select add #35/A:350
    7227 
    7228 105 atoms, 95 bonds, 10 residues, 1 model selected 
    7229 
    7230 > select add #35/A:351
    7231 
    7232 112 atoms, 101 bonds, 11 residues, 1 model selected 
    7233 
    7234 > select add #35/A:352
    7235 
    7236 132 atoms, 121 bonds, 12 residues, 1 model selected 
    7237 
    7238 > select add #35/A:353
    7239 
    7240 151 atoms, 139 bonds, 13 residues, 1 model selected 
    7241 
    7242 > select add #35/A:354
    7243 
    7244 166 atoms, 153 bonds, 14 residues, 1 model selected 
    7245 
    7246 > select add #35/A:355
    7247 
    7248 176 atoms, 162 bonds, 15 residues, 1 model selected 
    7249 
    7250 > select add #35/A:356
    7251 
    7252 195 atoms, 180 bonds, 16 residues, 1 model selected 
    7253 
    7254 > select add #35/A:357
    7255 
    7256 209 atoms, 194 bonds, 17 residues, 1 model selected 
    7257 
    7258 > select add #35/A:358
    7259 
    7260 226 atoms, 210 bonds, 18 residues, 1 model selected 
    7261 
    7262 > select add #35/A:359
    7263 
    7264 237 atoms, 220 bonds, 19 residues, 1 model selected 
    7265 
    7266 > select add #35/A:360
    7267 
    7268 256 atoms, 238 bonds, 20 residues, 1 model selected 
    7269 
    7270 > select add #35/A:361
    7271 
    7272 270 atoms, 252 bonds, 21 residues, 1 model selected 
    7273 
    7274 > select add #35/A:362
    7275 
    7276 284 atoms, 266 bonds, 22 residues, 1 model selected 
    7277 
    7278 > select add #35/A:363
    7279 
    7280 299 atoms, 280 bonds, 23 residues, 1 model selected 
    7281 
    7282 > select subtract #35/A:363
    7283 
    7284 284 atoms, 266 bonds, 22 residues, 1 model selected 
    7285 
    7286 > color sel red
    7287 
    7288 > select clear
    7289 
    7290 > select add #35/A:363
    7291 
    7292 15 atoms, 14 bonds, 1 residue, 1 model selected 
    7293 
    7294 > select add #35/A:364
    7295 
    7296 31 atoms, 29 bonds, 2 residues, 1 model selected 
    7297 
    7298 > select add #35/A:365
    7299 
    7300 53 atoms, 50 bonds, 3 residues, 1 model selected 
    7301 
    7302 > select add #35/A:282
    7303 
    7304 77 atoms, 73 bonds, 4 residues, 1 model selected 
    7305 
    7306 > select add #35/A:283
    7307 
    7308 88 atoms, 83 bonds, 5 residues, 1 model selected 
    7309 
    7310 > select add #35/A:284
    7311 
    7312 98 atoms, 92 bonds, 6 residues, 1 model selected 
    7313 
    7314 > select add #35/A:285
    7315 
    7316 109 atoms, 102 bonds, 7 residues, 1 model selected 
    7317 
    7318 > select add #35/A:286
    7319 
    7320 128 atoms, 120 bonds, 8 residues, 1 model selected 
    7321 
    7322 > select add #35/A:287
    7323 
    7324 146 atoms, 138 bonds, 9 residues, 1 model selected 
    7325 
    7326 > select add #35/A:288
    7327 
    7328 165 atoms, 156 bonds, 10 residues, 1 model selected 
    7329 
    7330 > select add #35/A:289
    7331 
    7332 179 atoms, 170 bonds, 11 residues, 1 model selected 
    7333 
    7334 > select add #35/A:224
    7335 
    7336 198 atoms, 188 bonds, 12 residues, 1 model selected 
    7337 
    7338 > select add #35/A:223
    7339 
    7340 222 atoms, 211 bonds, 13 residues, 1 model selected 
    7341 
    7342 > select add #35/A:222
    7343 
    7344 244 atoms, 232 bonds, 14 residues, 1 model selected 
    7345 
    7346 > select add #35/A:221
    7347 
    7348 261 atoms, 248 bonds, 15 residues, 1 model selected 
    7349 
    7350 > select add #35/A:220
    7351 
    7352 278 atoms, 264 bonds, 16 residues, 1 model selected 
    7353 
    7354 > select add #35/A:219
    7355 
    7356 292 atoms, 278 bonds, 17 residues, 1 model selected 
    7357 
    7358 > select add #35/A:218
    7359 
    7360 308 atoms, 293 bonds, 18 residues, 1 model selected 
    7361 
    7362 > select add #35/A:217
    7363 
    7364 330 atoms, 314 bonds, 19 residues, 1 model selected 
    7365 
    7366 > select add #35/A:216
    7367 
    7368 346 atoms, 329 bonds, 20 residues, 1 model selected 
    7369 
    7370 > select add #35/A:215
    7371 
    7372 360 atoms, 342 bonds, 21 residues, 1 model selected 
    7373 
    7374 > select add #35/A:214
    7375 
    7376 374 atoms, 355 bonds, 22 residues, 1 model selected 
    7377 
    7378 > select add #35/A:204
    7379 
    7380 389 atoms, 369 bonds, 23 residues, 1 model selected 
    7381 
    7382 > select add #35/A:205
    7383 
    7384 404 atoms, 383 bonds, 24 residues, 1 model selected 
    7385 
    7386 > select add #35/A:206
    7387 
    7388 419 atoms, 397 bonds, 25 residues, 1 model selected 
    7389 
    7390 > select subtract #35/A:206
    7391 
    7392 404 atoms, 383 bonds, 24 residues, 1 model selected 
    7393 
    7394 > select add #35/A:207
    7395 
    7396 416 atoms, 394 bonds, 25 residues, 1 model selected 
    7397 
    7398 > select add #35/A:206
    7399 
    7400 431 atoms, 408 bonds, 26 residues, 1 model selected 
    7401 
    7402 > select add #35/A:208
    7403 
    7404 451 atoms, 428 bonds, 27 residues, 1 model selected 
    7405 
    7406 > select add #35/A:209
    7407 
    7408 468 atoms, 445 bonds, 28 residues, 1 model selected 
    7409 
    7410 > select add #35/A:210
    7411 
    7412 484 atoms, 460 bonds, 29 residues, 1 model selected 
    7413 
    7414 > select add #35/A:211
    7415 
    7416 496 atoms, 471 bonds, 30 residues, 1 model selected 
    7417 
    7418 > color sel light sea green
    7419 
    7420 > color sel blue
    7421 
    7422 > color sel cornflower blue
    7423 
    7424 > select clear
    7425 
    7426 > select add #35/A:228
    7427 
    7428 14 atoms, 13 bonds, 1 residue, 1 model selected 
    7429 
    7430 > select add #35/A:229
    7431 
    7432 33 atoms, 31 bonds, 2 residues, 1 model selected 
    7433 
    7434 > select add #35/A:230
    7435 
    7436 50 atoms, 47 bonds, 3 residues, 1 model selected 
    7437 
    7438 > select add #35/A:231
    7439 
    7440 67 atoms, 64 bonds, 4 residues, 1 model selected 
    7441 
    7442 > select add #35/A:232
    7443 
    7444 78 atoms, 74 bonds, 5 residues, 1 model selected 
    7445 
    7446 > select add #35/A:237
    7447 
    7448 89 atoms, 84 bonds, 6 residues, 1 model selected 
    7449 
    7450 > select add #35/A:238
    7451 
    7452 113 atoms, 109 bonds, 7 residues, 1 model selected 
    7453 
    7454 > select add #35/A:239
    7455 
    7456 129 atoms, 124 bonds, 8 residues, 1 model selected 
    7457 
    7458 > select add #35/A:240
    7459 
    7460 148 atoms, 142 bonds, 9 residues, 1 model selected 
    7461 
    7462 > select add #35/A:241
    7463 
    7464 167 atoms, 160 bonds, 10 residues, 1 model selected 
    7465 
    7466 > select add #35/A:242
    7467 
    7468 184 atoms, 176 bonds, 11 residues, 1 model selected 
    7469 
    7470 > select add #35/A:243
    7471 
    7472 200 atoms, 191 bonds, 12 residues, 1 model selected 
    7473 
    7474 > select add #35/A:244
    7475 
    7476 221 atoms, 212 bonds, 13 residues, 1 model selected 
    7477 
    7478 > select add #35/A:248
    7479 
    7480 231 atoms, 221 bonds, 14 residues, 1 model selected 
    7481 
    7482 > select add #35/A:249
    7483 
    7484 245 atoms, 234 bonds, 15 residues, 1 model selected 
    7485 
    7486 > select add #35/A:250
    7487 
    7488 255 atoms, 243 bonds, 16 residues, 1 model selected 
    7489 
    7490 > select add #35/A:251
    7491 
    7492 274 atoms, 261 bonds, 17 residues, 1 model selected 
    7493 
    7494 > select add #35/A:252
    7495 
    7496 294 atoms, 281 bonds, 18 residues, 1 model selected 
    7497 
    7498 > select add #35/A:253
    7499 
    7500 314 atoms, 301 bonds, 19 residues, 1 model selected 
    7501 
    7502 > select add #35/A:254
    7503 
    7504 333 atoms, 319 bonds, 20 residues, 1 model selected 
    7505 
    7506 > select add #35/A:255
    7507 
    7508 347 atoms, 333 bonds, 21 residues, 1 model selected 
    7509 
    7510 > select add #35/A:247
    7511 
    7512 361 atoms, 346 bonds, 22 residues, 1 model selected 
    7513 
    7514 > select add #35/A:246
    7515 
    7516 368 atoms, 352 bonds, 23 residues, 1 model selected 
    7517 
    7518 > select add #35/A:245
    7519 
    7520 387 atoms, 370 bonds, 24 residues, 1 model selected 
    7521 
    7522 > select add #35/A:376
    7523 
    7524 402 atoms, 384 bonds, 25 residues, 1 model selected 
    7525 
    7526 > select add #35/A:375
    7527 
    7528 421 atoms, 402 bonds, 26 residues, 1 model selected 
    7529 
    7530 > select add #35/A:374
    7531 
    7532 438 atoms, 418 bonds, 27 residues, 1 model selected 
    7533 
    7534 > select add #35/A:373
    7535 
    7536 457 atoms, 436 bonds, 28 residues, 1 model selected 
    7537 
    7538 > select add #35/A:372
    7539 
    7540 477 atoms, 456 bonds, 29 residues, 1 model selected 
    7541 
    7542 > select add #35/A:371
    7543 
    7544 493 atoms, 471 bonds, 30 residues, 1 model selected 
    7545 
    7546 > select add #35/A:370
    7547 
    7548 513 atoms, 491 bonds, 31 residues, 1 model selected 
    7549 
    7550 > select add #35/A:388
    7551 
    7552 529 atoms, 506 bonds, 32 residues, 1 model selected 
    7553 
    7554 > select add #35/A:387
    7555 
    7556 551 atoms, 527 bonds, 33 residues, 1 model selected 
    7557 
    7558 > select add #35/A:386
    7559 
    7560 558 atoms, 533 bonds, 34 residues, 1 model selected 
    7561 
    7562 > select add #35/A:385
    7563 
    7564 575 atoms, 549 bonds, 35 residues, 1 model selected 
    7565 
    7566 > select add #35/A:384
    7567 
    7568 595 atoms, 569 bonds, 36 residues, 1 model selected 
    7569 
    7570 > select add #35/A:383
    7571 
    7572 614 atoms, 587 bonds, 37 residues, 1 model selected 
    7573 
    7574 > select add #35/A:382
    7575 
    7576 628 atoms, 601 bonds, 38 residues, 1 model selected 
    7577 
    7578 > select add #35/A:50
    7579 
    7580 647 atoms, 619 bonds, 39 residues, 1 model selected 
    7581 
    7582 > select add #35/A:51
    7583 
    7584 667 atoms, 639 bonds, 40 residues, 1 model selected 
    7585 
    7586 > select add #35/A:52
    7587 
    7588 687 atoms, 659 bonds, 41 residues, 1 model selected 
    7589 
    7590 > select add #35/A:227
    7591 
    7592 707 atoms, 679 bonds, 42 residues, 1 model selected 
    7593 
    7594 > color sel yellow
    7595 
    7596 > select clear
    7597 
    7598 > select add #35/A:225
    7599 
    7600 7 atoms, 6 bonds, 1 residue, 1 model selected 
    7601 
    7602 > color sel cornflower blue
    7603 
    7604 > select clear
    7605 
    7606 > select add #35/A:226
    7607 
    7608 17 atoms, 16 bonds, 1 residue, 1 model selected 
    7609 
    7610 > color sel cornflower blue
    7611 
    7612 > select clear
    7613 
    7614 [Repeated 1 time(s)]
    7615 
    7616 > select add #35/A:165
    7617 
    7618 14 atoms, 13 bonds, 1 residue, 1 model selected 
    7619 
    7620 > select add #35/A:163
    7621 
    7622 27 atoms, 25 bonds, 2 residues, 1 model selected 
    7623 
    7624 > select add #35/A:162
    7625 
    7626 42 atoms, 39 bonds, 3 residues, 1 model selected 
    7627 
    7628 > select add #35/A:164
    7629 
    7630 49 atoms, 45 bonds, 4 residues, 1 model selected 
    7631 
    7632 > select add #35/A:161
    7633 
    7634 65 atoms, 60 bonds, 5 residues, 1 model selected 
    7635 
    7636 > select add #35/A:160
    7637 
    7638 86 atoms, 81 bonds, 6 residues, 1 model selected 
    7639 
    7640 > select add #35/A:159
    7641 
    7642 98 atoms, 92 bonds, 7 residues, 1 model selected 
    7643 
    7644 > select add #35/A:158
    7645 
    7646 112 atoms, 105 bonds, 8 residues, 1 model selected 
    7647 
    7648 > select add #35/A:157
    7649 
    7650 131 atoms, 123 bonds, 9 residues, 1 model selected 
    7651 
    7652 > select add #35/A:155
    7653 
    7654 153 atoms, 144 bonds, 10 residues, 1 model selected 
    7655 
    7656 > select add #35/A:156
    7657 
    7658 170 atoms, 160 bonds, 11 residues, 1 model selected 
    7659 
    7660 > select add #35/A:154
    7661 
    7662 192 atoms, 181 bonds, 12 residues, 1 model selected 
    7663 
    7664 > select add #35/A:153
    7665 
    7666 202 atoms, 190 bonds, 13 residues, 1 model selected 
    7667 
    7668 > select add #35/A:152
    7669 
    7670 217 atoms, 204 bonds, 14 residues, 1 model selected 
    7671 
    7672 > select add #35/A:151
    7673 
    7674 232 atoms, 218 bonds, 15 residues, 1 model selected 
    7675 
    7676 > select add #35/A:150
    7677 
    7678 246 atoms, 231 bonds, 16 residues, 1 model selected 
    7679 
    7680 > select add #35/A:149
    7681 
    7682 258 atoms, 242 bonds, 17 residues, 1 model selected 
    7683 
    7684 > select add #35/A:336
    7685 
    7686 268 atoms, 251 bonds, 18 residues, 1 model selected 
    7687 
    7688 > select subtract #35/A:336
    7689 
    7690 258 atoms, 242 bonds, 17 residues, 1 model selected 
    7691 
    7692 > select add #35/A:166
    7693 
    7694 275 atoms, 258 bonds, 18 residues, 1 model selected 
    7695 
    7696 > select add #35/A:167
    7697 
    7698 282 atoms, 264 bonds, 19 residues, 1 model selected 
    7699 
    7700 > select add #35/A:168
    7701 
    7702 292 atoms, 273 bonds, 20 residues, 1 model selected 
    7703 
    7704 > select add #35/A:169
    7705 
    7706 311 atoms, 291 bonds, 21 residues, 1 model selected 
    7707 
    7708 > select add #35/A:170
    7709 
    7710 327 atoms, 306 bonds, 22 residues, 1 model selected 
    7711 
    7712 > select add #35/A:171
    7713 
    7714 339 atoms, 317 bonds, 23 residues, 1 model selected 
    7715 
    7716 > select add #35/A:172
    7717 
    7718 358 atoms, 335 bonds, 24 residues, 1 model selected 
    7719 
    7720 > select add #35/A:173
    7721 
    7722 374 atoms, 350 bonds, 25 residues, 1 model selected 
    7723 
    7724 > select add #35/A:174
    7725 
    7726 396 atoms, 371 bonds, 26 residues, 1 model selected 
    7727 
    7728 > select add #35/A:175
    7729 
    7730 406 atoms, 380 bonds, 27 residues, 1 model selected 
    7731 
    7732 > select add #35/A:176
    7733 
    7734 425 atoms, 398 bonds, 28 residues, 1 model selected 
    7735 
    7736 > select add #35/A:177
    7737 
    7738 432 atoms, 404 bonds, 29 residues, 1 model selected 
    7739 
    7740 > select add #35/A:178
    7741 
    7742 439 atoms, 410 bonds, 30 residues, 1 model selected 
    7743 
    7744 > select add #35/A:179
    7745 
    7746 446 atoms, 416 bonds, 31 residues, 1 model selected 
    7747 
    7748 > select add #35/A:180
    7749 
    7750 460 atoms, 429 bonds, 32 residues, 1 model selected 
    7751 
    7752 > select add #35/A:181
    7753 
    7754 476 atoms, 444 bonds, 33 residues, 1 model selected 
    7755 
    7756 > select add #35
    7757 
    7758 5953 atoms, 5684 bonds, 699 residues, 1 model selected 
    7759 
    7760 > select subtract #35
    7761 
    7762 Nothing selected 
    7763 
    7764 > color #35 #bbb0abff
    7765 
    7766 > color #35 #bbb8b6ff
    7767 
    7768 > select add #35/A:340
    7769 
    7770 19 atoms, 18 bonds, 1 residue, 1 model selected 
    7771 
    7772 > select add #35/A:339
    7773 
    7774 33 atoms, 31 bonds, 2 residues, 1 model selected 
    7775 
    7776 > select add #35/A:338
    7777 
    7778 52 atoms, 49 bonds, 3 residues, 1 model selected 
    7779 
    7780 > select add #35/A:337
    7781 
    7782 68 atoms, 64 bonds, 4 residues, 1 model selected 
    7783 
    7784 > select add #35/A:336
    7785 
    7786 78 atoms, 73 bonds, 5 residues, 1 model selected 
    7787 
    7788 > select add #35/A:335
    7789 
    7790 99 atoms, 93 bonds, 6 residues, 1 model selected 
    7791 
    7792 > select add #35/A:334
    7793 
    7794 116 atoms, 110 bonds, 7 residues, 1 model selected 
    7795 
    7796 > select add #35/A:333
    7797 
    7798 132 atoms, 125 bonds, 8 residues, 1 model selected 
    7799 
    7800 > select add #35/A:332
    7801 
    7802 142 atoms, 134 bonds, 9 residues, 1 model selected 
    7803 
    7804 > select add #35/A:331
    7805 
    7806 164 atoms, 155 bonds, 10 residues, 1 model selected 
    7807 
    7808 > select add #35/A:291
    7809 
    7810 183 atoms, 173 bonds, 11 residues, 1 model selected 
    7811 
    7812 > select add #35/A:292
    7813 
    7814 194 atoms, 183 bonds, 12 residues, 1 model selected 
    7815 
    7816 > select add #35/A:293
    7817 
    7818 213 atoms, 201 bonds, 13 residues, 1 model selected 
    7819 
    7820 > select add #35/A:294
    7821 
    7822 227 atoms, 214 bonds, 14 residues, 1 model selected 
    7823 
    7824 > select add #35/A:295
    7825 
    7826 234 atoms, 220 bonds, 15 residues, 1 model selected 
    7827 
    7828 > select add #35/A:296
    7829 
    7830 248 atoms, 233 bonds, 16 residues, 1 model selected 
    7831 
    7832 > select add #35/A:297
    7833 
    7834 269 atoms, 254 bonds, 17 residues, 1 model selected 
    7835 
    7836 > select add #35/A:298
    7837 
    7838 281 atoms, 265 bonds, 18 residues, 1 model selected 
    7839 
    7840 > select add #35/A:191
    7841 
    7842 303 atoms, 286 bonds, 19 residues, 1 model selected 
    7843 
    7844 > select add #35/A:190
    7845 
    7846 323 atoms, 306 bonds, 20 residues, 1 model selected 
    7847 
    7848 > select add #35/A:189
    7849 
    7850 343 atoms, 326 bonds, 21 residues, 1 model selected 
    7851 
    7852 > select add #35/A:188
    7853 
    7854 362 atoms, 344 bonds, 22 residues, 1 model selected 
    7855 
    7856 > select add #35/A:187
    7857 
    7858 383 atoms, 365 bonds, 23 residues, 1 model selected 
    7859 
    7860 > select add #35/A:186
    7861 
    7862 397 atoms, 378 bonds, 24 residues, 1 model selected 
    7863 
    7864 > select add #35/A:185
    7865 
    7866 413 atoms, 393 bonds, 25 residues, 1 model selected 
    7867 
    7868 > select add #35/A:184
    7869 
    7870 432 atoms, 411 bonds, 26 residues, 1 model selected 
    7871 
    7872 > select add #35/A:183
    7873 
    7874 442 atoms, 420 bonds, 27 residues, 1 model selected 
    7875 
    7876 > select add #35/A:182
    7877 
    7878 462 atoms, 440 bonds, 28 residues, 1 model selected 
    7879 
    7880 > select add #35/A:121
    7881 
    7882 473 atoms, 450 bonds, 29 residues, 1 model selected 
    7883 
    7884 > select add #35/A:120
    7885 
    7886 492 atoms, 468 bonds, 30 residues, 1 model selected 
    7887 
    7888 > select add #35/A:119
    7889 
    7890 512 atoms, 488 bonds, 31 residues, 1 model selected 
    7891 
    7892 > select add #35/A:118
    7893 
    7894 531 atoms, 506 bonds, 32 residues, 1 model selected 
    7895 
    7896 > select add #35/A:117
    7897 
    7898 538 atoms, 512 bonds, 33 residues, 1 model selected 
    7899 
    7900 > select add #35/A:116
    7901 
    7902 552 atoms, 525 bonds, 34 residues, 1 model selected 
    7903 
    7904 > select add #35/A:115
    7905 
    7906 559 atoms, 531 bonds, 35 residues, 1 model selected 
    7907 
    7908 > select add #35/A:114
    7909 
    7910 573 atoms, 544 bonds, 36 residues, 1 model selected 
    7911 
    7912 > select add #35/A:113
    7913 
    7914 587 atoms, 557 bonds, 37 residues, 1 model selected 
    7915 
    7916 > select add #35/A:112
    7917 
    7918 606 atoms, 575 bonds, 38 residues, 1 model selected 
    7919 
    7920 > select add #35/A:141
    7921 
    7922 621 atoms, 589 bonds, 39 residues, 1 model selected 
    7923 
    7924 > select add #35/A:142
    7925 
    7926 631 atoms, 598 bonds, 40 residues, 1 model selected 
    7927 
    7928 > select add #35/A:143
    7929 
    7930 651 atoms, 618 bonds, 41 residues, 1 model selected 
    7931 
    7932 > select add #35/A:144
    7933 
    7934 665 atoms, 631 bonds, 42 residues, 1 model selected 
    7935 
    7936 > select add #35/A:145
    7937 
    7938 681 atoms, 646 bonds, 43 residues, 1 model selected 
    7939 
    7940 > color sel light sea green
    7941 
    7942 > color sel lime
    7943 
    7944 > select clear
    7945 
    7946 > select add #35/A:341
    7947 
    7948 12 atoms, 11 bonds, 1 residue, 1 model selected 
    7949 
    7950 > select add #35/A:342
    7951 
    7952 27 atoms, 25 bonds, 2 residues, 1 model selected 
    7953 
    7954 > select add #35/A:343
    7955 
    7956 40 atoms, 37 bonds, 3 residues, 1 model selected 
    7957 
    7958 > select add #35/A:344
    7959 
    7960 47 atoms, 43 bonds, 4 residues, 1 model selected 
    7961 
    7962 > select add #35/A:345
    7963 
    7964 61 atoms, 56 bonds, 5 residues, 1 model selected 
    7965 
    7966 > select add #35/A:346
    7967 
    7968 68 atoms, 62 bonds, 6 residues, 1 model selected 
    7969 
    7970 > select add #35/A:347
    7971 
    7972 78 atoms, 71 bonds, 7 residues, 1 model selected 
    7973 
    7974 > select add #35/A:348
    7975 
    7976 88 atoms, 80 bonds, 8 residues, 1 model selected 
    7977 
    7978 > select add #35/A:349
    7979 
    7980 95 atoms, 86 bonds, 9 residues, 1 model selected 
    7981 
    7982 > select add #35/A:350
    7983 
    7984 105 atoms, 95 bonds, 10 residues, 1 model selected 
    7985 
    7986 > select add #35/A:351
    7987 
    7988 112 atoms, 101 bonds, 11 residues, 1 model selected 
    7989 
    7990 > select add #35/A:352
    7991 
    7992 132 atoms, 121 bonds, 12 residues, 1 model selected 
    7993 
    7994 > select add #35/A:353
    7995 
    7996 151 atoms, 139 bonds, 13 residues, 1 model selected 
    7997 
    7998 > select add #35/A:354
    7999 
    8000 166 atoms, 153 bonds, 14 residues, 1 model selected 
    8001 
    8002 > select add #35/A:355
    8003 
    8004 176 atoms, 162 bonds, 15 residues, 1 model selected 
    8005 
    8006 > select add #35/A:356
    8007 
    8008 195 atoms, 180 bonds, 16 residues, 1 model selected 
    8009 
    8010 > select add #35/A:357
    8011 
    8012 209 atoms, 194 bonds, 17 residues, 1 model selected 
    8013 
    8014 > select add #35/A:358
    8015 
    8016 226 atoms, 210 bonds, 18 residues, 1 model selected 
    8017 
    8018 > select add #35/A:359
    8019 
    8020 237 atoms, 220 bonds, 19 residues, 1 model selected 
    8021 
    8022 > select add #35/A:360
    8023 
    8024 256 atoms, 238 bonds, 20 residues, 1 model selected 
    8025 
    8026 > select add #35/A:361
    8027 
    8028 270 atoms, 252 bonds, 21 residues, 1 model selected 
    8029 
    8030 > select add #35/A:362
    8031 
    8032 284 atoms, 266 bonds, 22 residues, 1 model selected 
    8033 
    8034 > color sel red
    8035 
    8036 > select clear
    8037 
    8038 > select add #35/A:165
    8039 
    8040 14 atoms, 13 bonds, 1 residue, 1 model selected 
    8041 
    8042 > select add #35/A:164
    8043 
    8044 21 atoms, 19 bonds, 2 residues, 1 model selected 
    8045 
    8046 > select add #35/A:163
    8047 
    8048 34 atoms, 31 bonds, 3 residues, 1 model selected 
    8049 
    8050 > select add #35/A:162
    8051 
    8052 49 atoms, 45 bonds, 4 residues, 1 model selected 
    8053 
    8054 > select add #35/A:161
    8055 
    8056 65 atoms, 60 bonds, 5 residues, 1 model selected 
    8057 
    8058 > select add #35/A:160
    8059 
    8060 86 atoms, 81 bonds, 6 residues, 1 model selected 
    8061 
    8062 > select add #35/A:159
    8063 
    8064 98 atoms, 92 bonds, 7 residues, 1 model selected 
    8065 
    8066 > select add #35/A:158
    8067 
    8068 112 atoms, 105 bonds, 8 residues, 1 model selected 
    8069 
    8070 > select add #35/A:157
    8071 
    8072 131 atoms, 123 bonds, 9 residues, 1 model selected 
    8073 
    8074 > select add #35/A:156
    8075 
    8076 148 atoms, 139 bonds, 10 residues, 1 model selected 
    8077 
    8078 > select add #35/A:155
    8079 
    8080 170 atoms, 160 bonds, 11 residues, 1 model selected 
    8081 
    8082 > select add #35/A:154
    8083 
    8084 192 atoms, 181 bonds, 12 residues, 1 model selected 
    8085 
    8086 > select add #35/A:153
    8087 
    8088 202 atoms, 190 bonds, 13 residues, 1 model selected 
    8089 
    8090 > select add #35/A:152
    8091 
    8092 217 atoms, 204 bonds, 14 residues, 1 model selected 
    8093 
    8094 > select add #35/A:151
    8095 
    8096 232 atoms, 218 bonds, 15 residues, 1 model selected 
    8097 
    8098 > select add #35/A:150
    8099 
    8100 246 atoms, 231 bonds, 16 residues, 1 model selected 
    8101 
    8102 > select add #35/A:149
    8103 
    8104 258 atoms, 242 bonds, 17 residues, 1 model selected 
    8105 
    8106 > color sel magenta
    8107 
    8108 > select clear
    8109 
    8110 [Repeated 1 time(s)]
    8111 
    8112 > color #30 #bcc7ceff
    8113 
    8114 > color #30 #67c7ceff
    8115 
    8116 > color #30 #0cc5ceff
    8117 
    8118 > color #30 #07ce85ff
    8119 
    8120 > color #30 #10ccceff
    8121 
    8122 > color #30 #016fceff
    8123 
    8124 > select #30/B:195
    8125 
    8126 5 atoms, 4 bonds, 1 residue, 1 model selected 
    8127 
    8128 > show sel atoms
    8129 
    8130 > hide sel atoms
    8131 
    8132 > swapp S
    8133 
    8134 Unknown command: swapp S 
    8135 
    8136 > delete #30/A swapaa S
    8137 
    8138 Expected a keyword 
    8139 
    8140 > swapaa #30/B:195 ser
    8141 
    8142 Using Dunbrack library 
    8143 1oph #30/B ALA 195: phi -47.1, psi 140.5 trans 
    8144 Density criteria with multiple volume models open; 
    8145 Need to specify one to use via 'density' keyword. 
    8146 
    8147 > ui tool show Rotamers
    8148 
    8149 Populating font family aliases took 55 ms. Replace uses of missing font family
    8150 "Times" with one that exists to avoid this cost. 
    8151 
    8152 > select #30/B:195
    8153 
    8154 5 atoms, 4 bonds, 1 residue, 1 model selected 
    8155 
    8156 > ui tool show Rotamers
    8157 
    8158 > swapaa interactive sel SER rotLib Dunbrack
    8159 
    8160 1oph #30/B ALA 195: phi -47.1, psi 140.5 trans 
    8161 Changed 9 bond radii 
    8162 No rotamers selected. Click the 'Calculate' button (not 'OK') to add a column
    8163 to the table. 
    8164 
    8165 > undo
    8166 
    8167 [Repeated 2 time(s)]
    8168 
    8169 > ui tool show Rotamers
    8170 
    8171 > swapaa interactive sel SER rotLib Dunbrack
    8172 
    8173 1oph #!30/B ALA 195: phi -47.1, psi 140.5 trans 
    8174 Changed 9 bond radii 
    8175 
    8176 > swapaa #!30/B:195 SER criteria 3 rotLib Dunbrack
    8177 
    8178 Using Dunbrack library 
    8179 1oph #!30/B ALA 195: phi -47.1, psi 140.5 trans 
    8180 Applying SER rotamer (chi angles: 64.0) to 1oph #!30/B SER 195 
    8181 
    8182 > hide sel atoms
    8183 
    8184 [Repeated 2 time(s)]
    8185 
    8186 > select #30/B:195
    8187 
    8188 6 atoms, 5 bonds, 1 residue, 1 model selected 
    8189 
    8190 > select #30/B:195
    8191 
    8192 6 atoms, 5 bonds, 1 residue, 1 model selected 
    8193 
    8194 > hide sel cartoons
    8195 
    8196 > show sel cartoons
    8197 
    8198 > select clear
    8199 
    8200 > select #30.1.1/A:1@CB
    8201 
    8202 1 atom, 1 residue, 1 model selected 
    8203 
    8204 > swapaa #!30/B:195 SER criteria 2 rotLib Dunbrack
    8205 
    8206 Using Dunbrack library 
    8207 1oph #!30/B SER 195: phi -47.1, psi 140.5 trans 
    8208 Applying SER rotamer (chi angles: -63.9) to 1oph #!30/B SER 195 
    8209 
    8210 > select #30/B:195
    8211 
    8212 6 atoms, 5 bonds, 1 residue, 1 model selected 
    8213 
    8214 > show sel atoms
    8215 
    8216 > rainbow sel
    8217 
    8218 > select clear
    8219 
    8220 > select #35/A:358
    8221 
    8222 17 atoms, 16 bonds, 1 residue, 1 model selected 
    8223 
    8224 > show sel atoms
    8225 
    8226 > rainbow sel
    8227 
    8228 [Repeated 1 time(s)]
    8229 
    8230 > color sel byhetero
    8231 
    8232 > color sel red
    8233 
    8234 > color sel byhetero
    8235 
    8236 > select clear
    8237 
    8238 > open 1oph fromDatabase pdb format mmcif
    8239 
    8240 1oph title: 
    8241 Non-covalent complex between α-1-π-pittsburgh and S195A trypsin [more info...] 
    8242  
    8243 Chain information for 1oph #36 
    8244 --- 
    8245 Chain | Description | UniProt 
    8246 A | Alpha-1-antitrypsin precursor | A1AT_HUMAN 1-394 
    8247 B | Trypsinogen, cationic precursor | TRY1_BOVIN -4-245 
    8248  
    8249 1oph mmCIF Assemblies 
    8250 --- 
    8251 1| author_and_software_defined_assembly 
    8252 2| software_defined_assembly 
    8253  
    8254 
    8255 > mmaker #36 to #35
    8256 
    8257 Parameters 
    8258 --- 
    8259 Chain pairing | bb 
    8260 Alignment algorithm | Needleman-Wunsch 
    8261 Similarity matrix | BLOSUM-62 
    8262 SS fraction | 0.3 
    8263 Gap open (HH/SS/other) | 18/18/6 
    8264 Gap extend | 1 
    8265 SS matrix |  |  | H | S | O 
    8266 ---|---|---|--- 
    8267 H | 6 | -9 | -6 
    8268 S |  | 6 | -6 
    8269 O |  |  | 4 
    8270 Iteration cutoff | 2 
    8271  
    8272 Matchmaker 8pi2, chain A (#35) with 1oph, chain A (#36), sequence alignment
    8273 score = 1934.1 
    8274 RMSD between 350 pruned atom pairs is 0.764 angstroms; (across all 371 pairs:
    8275 1.541) 
    8276  
    8277 
    8278 > select #36/A
    8279 
    8280 3121 atoms, 2980 bonds, 578 residues, 1 model selected 
    8281 
    8282 > select #36/A: 358
    8283 
    8284 11 atoms, 10 bonds, 1 residue, 1 model selected 
    8285 
    8286 > show sel atoms
    8287 
    8288 > hide #30 models
    8289 
    8290 > show #30 models
    8291 
    8292 > style sel stick
    8293 
    8294 Changed 11 atom styles 
    8295 
    8296 > style sel ball
    8297 
    8298 Changed 11 atom styles 
    8299 
    8300 > style sel stick
    8301 
    8302 Changed 11 atom styles 
    8303 
    8304 > hide #35 models
    8305 
    8306 > show #35 models
    8307 
    8308 > select #36/A: 57
    8309 
    8310 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8311 
    8312 > select add #36
    8313 
    8314 4919 atoms, 4641 bonds, 975 residues, 1 model selected 
    8315 
    8316 > select subtract #36
    8317 
    8318 Nothing selected 
    8319 
    8320 > hide #36 models
    8321 
    8322 > select #30/A: 57
    8323 
    8324 Nothing selected 
    8325 
    8326 > select #30/B: 57
    8327 
    8328 10 atoms, 10 bonds, 1 residue, 1 model selected 
    8329 
    8330 > show sel atoms
    8331 
    8332 > color sel byhetero
    8333 
    8334 > select #30/B: 202
    8335 
    8336 6 atoms, 5 bonds, 1 residue, 1 model selected 
    8337 
    8338 > select #30/B: 102
    8339 
    8340 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8341 
    8342 > show sel atoms
    8343 
    8344 > color sel byhetero
    8345 
    8346 > select #30/B: 194
    8347 
    8348 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8349 
    8350 > show sel atoms
    8351 
    8352 > color sel byhetero
    8353 
    8354 > select clear
    8355 
    8356 > select add #30
    8357 
    8358 1799 atoms, 1662 bonds, 397 residues, 1 model selected 
    8359 
    8360 > hide sel atoms
    8361 
    8362 > select add #35
    8363 
    8364 7752 atoms, 7346 bonds, 1096 residues, 2 models selected 
    8365 
    8366 > hide sel atoms
    8367 
    8368 > select subtract #30
    8369 
    8370 5953 atoms, 5684 bonds, 699 residues, 1 model selected 
    8371 
    8372 > select subtract #35
    8373 
    8374 Nothing selected 
    8375 
    8376 > show #!8 models
    8377 
    8378 > open 1ezx fromDatabase pdb format mmcif
    8379 
    8380 Summary of feedback from opening 1ezx fetched from pdb 
    8381 --- 
    8382 note | Fetching compressed mmCIF 1ezx from http://files.rcsb.org/download/1ezx.cif 
    8383  
    8384 1ezx title: 
    8385 Crystal structure of A serpin:protease complex [more info...] 
    8386  
    8387 Chain information for 1ezx #37 
    8388 --- 
    8389 Chain | Description | UniProt 
    8390 A | ALPHA-1-ANTITRYPSIN | A1AT_HUMAN 24-358 
    8391 B | ALPHA-1-ANTITRYPSIN | A1AT_HUMAN 359-394 
    8392 C | TRYPSIN | TRY1_BOVIN 42-245 
    8393  
    8394 
    8395 > mmaker #37 to #35
    8396 
    8397 Parameters 
    8398 --- 
    8399 Chain pairing | bb 
    8400 Alignment algorithm | Needleman-Wunsch 
    8401 Similarity matrix | BLOSUM-62 
    8402 SS fraction | 0.3 
    8403 Gap open (HH/SS/other) | 18/18/6 
    8404 Gap extend | 1 
    8405 SS matrix |  |  | H | S | O 
    8406 ---|---|---|--- 
    8407 H | 6 | -9 | -6 
    8408 S |  | 6 | -6 
    8409 O |  |  | 4 
    8410 Iteration cutoff | 2 
    8411  
    8412 Matchmaker 8pi2, chain A (#35) with 1ezx, chain A (#37), sequence alignment
    8413 score = 1629.2 
    8414 RMSD between 219 pruned atom pairs is 0.866 angstroms; (across all 335 pairs:
    8415 9.271) 
    8416  
    8417 
    8418 > hide #!8 models
    8419 
    8420 > hide #30 models
    8421 
    8422 > hide #35 models
    8423 
    8424 > select #37/A
    8425 
    8426 2686 atoms, 2674 bonds, 398 residues, 1 model selected 
    8427 
    8428 > select #37/A,B
    8429 
    8430 2975 atoms, 2968 bonds, 437 residues, 1 model selected 
    8431 
    8432 > color sel dark gray
    8433 
    8434 > select clear
    8435 
    8436 > show #35 models
    8437 
    8438 > hide #!37 models
    8439 
    8440 > show #!37 models
    8441 
    8442 > hide #35 models
    8443 
    8444 > show #35 models
    8445 
    8446 > hide #35 models
    8447 
    8448 > select #37/C
    8449 
    8450 1009 atoms, 1014 bonds, 5 pseudobonds, 155 residues, 2 models selected 
    8451 
    8452 > show #30 models
    8453 
    8454 > color (#!37 & sel) cornflower blue
    8455 
    8456 > color (#!37 & sel) blue
    8457 
    8458 > select clear
    8459 
    8460 > select #37/C
    8461 
    8462 1009 atoms, 1014 bonds, 5 pseudobonds, 155 residues, 2 models selected 
    8463 
    8464 > color (#!37 & sel) cornflower blue
    8465 
    8466 > select clear
    8467 
    8468 > select #37/C
    8469 
    8470 1009 atoms, 1014 bonds, 5 pseudobonds, 155 residues, 2 models selected 
    8471 
    8472 > color (#!37 & sel) medium blue
    8473 
    8474 > color (#!37 & sel) cornflower blue
    8475 
    8476 > select 30
    8477 
    8478 Expected an objects specifier or a keyword 
    8479 
    8480 > select 30/B
    8481 
    8482 Expected an objects specifier or a keyword 
    8483 
    8484 > select 30/A
    8485 
    8486 Expected an objects specifier or a keyword 
    8487 
    8488 > select #30
    8489 
    8490 1799 atoms, 1662 bonds, 397 residues, 1 model selected 
    8491 
    8492 > color sel cornflower blue
    8493 
    8494 > select clear
    8495 
    8496 > select #37/A:291
    8497 
    8498 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8499 
    8500 > select #37/A:292
    8501 
    8502 6 atoms, 5 bonds, 1 residue, 1 model selected 
    8503 
    8504 > select add #37/A:291
    8505 
    8506 14 atoms, 12 bonds, 2 residues, 1 model selected 
    8507 
    8508 > select add #37/A:293
    8509 
    8510 22 atoms, 19 bonds, 3 residues, 1 model selected 
    8511 
    8512 > select add #37/A:294
    8513 
    8514 29 atoms, 25 bonds, 4 residues, 1 model selected 
    8515 
    8516 > select add #37/A:295
    8517 
    8518 33 atoms, 28 bonds, 5 residues, 1 model selected 
    8519 
    8520 > select add #37/A:296
    8521 
    8522 40 atoms, 34 bonds, 6 residues, 1 model selected 
    8523 
    8524 > select add #37/A:297
    8525 
    8526 52 atoms, 46 bonds, 7 residues, 1 model selected 
    8527 
    8528 > select add #37/A:298
    8529 
    8530 60 atoms, 53 bonds, 8 residues, 1 model selected 
    8531 
    8532 > select add #37/A:340
    8533 
    8534 68 atoms, 60 bonds, 9 residues, 1 model selected 
    8535 
    8536 > select add #37/A:339
    8537 
    8538 75 atoms, 66 bonds, 10 residues, 1 model selected 
    8539 
    8540 > select add #37/A:338
    8541 
    8542 83 atoms, 73 bonds, 11 residues, 1 model selected 
    8543 
    8544 > select add #37/A:337
    8545 
    8546 90 atoms, 79 bonds, 12 residues, 1 model selected 
    8547 
    8548 > select add #37/A:336
    8549 
    8550 95 atoms, 83 bonds, 13 residues, 1 model selected 
    8551 
    8552 > select add #37/A:335
    8553 
    8554 104 atoms, 91 bonds, 14 residues, 1 model selected 
    8555 
    8556 > select add #37/A:334
    8557 
    8558 114 atoms, 101 bonds, 15 residues, 1 model selected 
    8559 
    8560 > select add #37/A:333
    8561 
    8562 121 atoms, 107 bonds, 16 residues, 1 model selected 
    8563 
    8564 > select add #37/A:332
    8565 
    8566 126 atoms, 111 bonds, 17 residues, 1 model selected 
    8567 
    8568 > select add #37/A:331
    8569 
    8570 135 atoms, 119 bonds, 18 residues, 1 model selected 
    8571 
    8572 > select add #37/A:330
    8573 
    8574 141 atoms, 124 bonds, 19 residues, 1 model selected 
    8575 
    8576 > select add #37/A:329
    8577 
    8578 149 atoms, 131 bonds, 20 residues, 1 model selected 
    8579 
    8580 > select add #37/A:328
    8581 
    8582 158 atoms, 139 bonds, 21 residues, 1 model selected 
    8583 
    8584 > select add #37/A:327
    8585 
    8586 166 atoms, 146 bonds, 22 residues, 1 model selected 
    8587 
    8588 > select add #37/A:357
    8589 
    8590 173 atoms, 153 bonds, 23 residues, 1 model selected 
    8591 
    8592 > select add #37/A:356
    8593 
    8594 181 atoms, 160 bonds, 24 residues, 1 model selected 
    8595 
    8596 > select add #37/A:355
    8597 
    8598 186 atoms, 164 bonds, 25 residues, 1 model selected 
    8599 
    8600 > select add #37/A:354
    8601 
    8602 195 atoms, 172 bonds, 26 residues, 1 model selected 
    8603 
    8604 > select add #37/A:353
    8605 
    8606 203 atoms, 179 bonds, 27 residues, 1 model selected 
    8607 
    8608 > select add #37/A:352
    8609 
    8610 214 atoms, 190 bonds, 28 residues, 1 model selected 
    8611 
    8612 > select add #37/A:351
    8613 
    8614 222 atoms, 197 bonds, 29 residues, 1 model selected 
    8615 
    8616 > select add #37/A:350
    8617 
    8618 227 atoms, 201 bonds, 30 residues, 1 model selected 
    8619 
    8620 > select add #37/A:349
    8621 
    8622 231 atoms, 204 bonds, 31 residues, 1 model selected 
    8623 
    8624 > select add #37/A:348
    8625 
    8626 236 atoms, 208 bonds, 32 residues, 1 model selected 
    8627 
    8628 > select add #37/A:347
    8629 
    8630 241 atoms, 212 bonds, 33 residues, 1 model selected 
    8631 
    8632 > select add #37/A:346
    8633 
    8634 250 atoms, 220 bonds, 34 residues, 1 model selected 
    8635 
    8636 > select add #37/A:345
    8637 
    8638 257 atoms, 226 bonds, 35 residues, 1 model selected 
    8639 
    8640 > select add #37/A:344
    8641 
    8642 261 atoms, 229 bonds, 36 residues, 1 model selected 
    8643 
    8644 > select add #37/A:193
    8645 
    8646 270 atoms, 237 bonds, 37 residues, 1 model selected 
    8647 
    8648 > select add #37/A:192
    8649 
    8650 274 atoms, 240 bonds, 38 residues, 1 model selected 
    8651 
    8652 > select add #37/A:191
    8653 
    8654 283 atoms, 248 bonds, 39 residues, 1 model selected 
    8655 
    8656 > select add #37/A:190
    8657 
    8658 294 atoms, 259 bonds, 40 residues, 1 model selected 
    8659 
    8660 > select add #37/A:189
    8661 
    8662 305 atoms, 270 bonds, 41 residues, 1 model selected 
    8663 
    8664 > select add #37/A:188
    8665 
    8666 313 atoms, 277 bonds, 42 residues, 1 model selected 
    8667 
    8668 > select add #37/A:187
    8669 
    8670 325 atoms, 289 bonds, 43 residues, 1 model selected 
    8671 
    8672 > select add #37/A:186
    8673 
    8674 333 atoms, 296 bonds, 44 residues, 1 model selected 
    8675 
    8676 > select add #37/A:185
    8677 
    8678 340 atoms, 302 bonds, 45 residues, 1 model selected 
    8679 
    8680 > select add #37/A:184
    8681 
    8682 348 atoms, 309 bonds, 46 residues, 1 model selected 
    8683 
    8684 > select add #37/A:183
    8685 
    8686 353 atoms, 313 bonds, 47 residues, 1 model selected 
    8687 
    8688 > select add #37/A:182
    8689 
    8690 364 atoms, 324 bonds, 48 residues, 1 model selected 
    8691 
    8692 > select subtract #37/A:182
    8693 
    8694 353 atoms, 313 bonds, 47 residues, 1 model selected 
    8695 
    8696 > select subtract #37/A:183
    8697 
    8698 348 atoms, 309 bonds, 46 residues, 1 model selected 
    8699 
    8700 > select subtract #37/A:184
    8701 
    8702 340 atoms, 302 bonds, 45 residues, 1 model selected 
    8703 
    8704 > select subtract #37/A:185
    8705 
    8706 333 atoms, 296 bonds, 44 residues, 1 model selected 
    8707 
    8708 > select subtract #37/A:186
    8709 
    8710 325 atoms, 289 bonds, 43 residues, 1 model selected 
    8711 
    8712 > select subtract #37/A:187
    8713 
    8714 313 atoms, 277 bonds, 42 residues, 1 model selected 
    8715 
    8716 > select subtract #37/A:188
    8717 
    8718 305 atoms, 270 bonds, 41 residues, 1 model selected 
    8719 
    8720 > select subtract #37/A:189
    8721 
    8722 294 atoms, 259 bonds, 40 residues, 1 model selected 
    8723 
    8724 > select subtract #37/A:190
    8725 
    8726 283 atoms, 248 bonds, 39 residues, 1 model selected 
    8727 
    8728 > select subtract #37/A:191
    8729 
    8730 274 atoms, 240 bonds, 38 residues, 1 model selected 
    8731 
    8732 > select subtract #37/A:192
    8733 
    8734 270 atoms, 237 bonds, 37 residues, 1 model selected 
    8735 
    8736 > select subtract #37/A:193
    8737 
    8738 261 atoms, 229 bonds, 36 residues, 1 model selected 
    8739 
    8740 > select subtract #37/A:357
    8741 
    8742 254 atoms, 222 bonds, 35 residues, 1 model selected 
    8743 
    8744 > select subtract #37/A:356
    8745 
    8746 246 atoms, 215 bonds, 34 residues, 1 model selected 
    8747 
    8748 > select subtract #37/A:355
    8749 
    8750 241 atoms, 211 bonds, 33 residues, 1 model selected 
    8751 
    8752 > select subtract #37/A:354
    8753 
    8754 232 atoms, 203 bonds, 32 residues, 1 model selected 
    8755 
    8756 > select subtract #37/A:353
    8757 
    8758 224 atoms, 196 bonds, 31 residues, 1 model selected 
    8759 
    8760 > select subtract #37/A:352
    8761 
    8762 213 atoms, 185 bonds, 30 residues, 1 model selected 
    8763 
    8764 > select subtract #37/A:351
    8765 
    8766 205 atoms, 178 bonds, 29 residues, 1 model selected 
    8767 
    8768 > select subtract #37/A:350
    8769 
    8770 200 atoms, 174 bonds, 28 residues, 1 model selected 
    8771 
    8772 > select subtract #37/A:349
    8773 
    8774 196 atoms, 171 bonds, 27 residues, 1 model selected 
    8775 
    8776 > select subtract #37/A:348
    8777 
    8778 191 atoms, 167 bonds, 26 residues, 1 model selected 
    8779 
    8780 > select subtract #37/A:347
    8781 
    8782 186 atoms, 163 bonds, 25 residues, 1 model selected 
    8783 
    8784 > select subtract #37/A:346
    8785 
    8786 177 atoms, 155 bonds, 24 residues, 1 model selected 
    8787 
    8788 > select subtract #37/A:345
    8789 
    8790 170 atoms, 149 bonds, 23 residues, 1 model selected 
    8791 
    8792 > select subtract #37/A:344
    8793 
    8794 166 atoms, 146 bonds, 22 residues, 1 model selected 
    8795 
    8796 > select add #37/A:193
    8797 
    8798 175 atoms, 154 bonds, 23 residues, 1 model selected 
    8799 
    8800 > select add #37/A:192
    8801 
    8802 179 atoms, 157 bonds, 24 residues, 1 model selected 
    8803 
    8804 > select add #37/A:191
    8805 
    8806 188 atoms, 165 bonds, 25 residues, 1 model selected 
    8807 
    8808 > select add #37/A:190
    8809 
    8810 199 atoms, 176 bonds, 26 residues, 1 model selected 
    8811 
    8812 > select add #37/A:189
    8813 
    8814 210 atoms, 187 bonds, 27 residues, 1 model selected 
    8815 
    8816 > select add #37/A:188
    8817 
    8818 218 atoms, 194 bonds, 28 residues, 1 model selected 
    8819 
    8820 > select add #37/A:187
    8821 
    8822 230 atoms, 206 bonds, 29 residues, 1 model selected 
    8823 
    8824 > select add #37/A:186
    8825 
    8826 238 atoms, 213 bonds, 30 residues, 1 model selected 
    8827 
    8828 > select add #37/A:185
    8829 
    8830 245 atoms, 219 bonds, 31 residues, 1 model selected 
    8831 
    8832 > select add #37/A:184
    8833 
    8834 253 atoms, 226 bonds, 32 residues, 1 model selected 
    8835 
    8836 > select add #37/A:183
    8837 
    8838 258 atoms, 230 bonds, 33 residues, 1 model selected 
    8839 
    8840 > select add #37/A:182
    8841 
    8842 269 atoms, 241 bonds, 34 residues, 1 model selected 
    8843 
    8844 > select add #37/A:111
    8845 
    8846 278 atoms, 249 bonds, 35 residues, 1 model selected 
    8847 
    8848 > select add #37/A:112
    8849 
    8850 286 atoms, 256 bonds, 36 residues, 1 model selected 
    8851 
    8852 > select subtract #37/A:112
    8853 
    8854 278 atoms, 249 bonds, 35 residues, 1 model selected 
    8855 
    8856 > select add #37/A:112
    8857 
    8858 286 atoms, 256 bonds, 36 residues, 1 model selected 
    8859 
    8860 > select add #37/A:113
    8861 
    8862 293 atoms, 262 bonds, 37 residues, 1 model selected 
    8863 
    8864 > select add #37/A:114
    8865 
    8866 300 atoms, 268 bonds, 38 residues, 1 model selected 
    8867 
    8868 > select add #37/A:115
    8869 
    8870 304 atoms, 271 bonds, 39 residues, 1 model selected 
    8871 
    8872 > select add #37/A:116
    8873 
    8874 312 atoms, 278 bonds, 40 residues, 1 model selected 
    8875 
    8876 > select add #37/A:117
    8877 
    8878 316 atoms, 281 bonds, 41 residues, 1 model selected 
    8879 
    8880 > select add #37/A:118
    8881 
    8882 324 atoms, 288 bonds, 42 residues, 1 model selected 
    8883 
    8884 > select subtract #37/A:118
    8885 
    8886 316 atoms, 281 bonds, 41 residues, 1 model selected 
    8887 
    8888 > select add #37/A:119
    8889 
    8890 327 atoms, 292 bonds, 42 residues, 1 model selected 
    8891 
    8892 > select add #37/A:118
    8893 
    8894 335 atoms, 299 bonds, 43 residues, 1 model selected 
    8895 
    8896 > select add #37/A:120
    8897 
    8898 343 atoms, 306 bonds, 44 residues, 1 model selected 
    8899 
    8900 > select add #37/A:121
    8901 
    8902 349 atoms, 311 bonds, 45 residues, 1 model selected 
    8903 
    8904 > select add #37/A:145
    8905 
    8906 356 atoms, 317 bonds, 46 residues, 1 model selected 
    8907 
    8908 > select add #37/A:144
    8909 
    8910 363 atoms, 323 bonds, 47 residues, 1 model selected 
    8911 
    8912 > select add #37/A:143
    8913 
    8914 374 atoms, 334 bonds, 48 residues, 1 model selected 
    8915 
    8916 > select add #37/A:142
    8917 
    8918 379 atoms, 338 bonds, 49 residues, 1 model selected 
    8919 
    8920 > select add #37/A:141
    8921 
    8922 388 atoms, 346 bonds, 50 residues, 1 model selected 
    8923 
    8924 > color sel cyan
    8925 
    8926 > color sel forest green
    8927 
    8928 > color sel lime
    8929 
    8930 > select clear
    8931 
    8932 > select add #37/A:358
    8933 
    8934 8 atoms, 7 bonds, 1 residue, 1 model selected 
    8935 
    8936 > select add #37/A:357
    8937 
    8938 15 atoms, 14 bonds, 2 residues, 1 model selected 
    8939 
    8940 > select add #37/A:356
    8941 
    8942 23 atoms, 21 bonds, 3 residues, 1 model selected 
    8943 
    8944 > select add #37/A:355
    8945 
    8946 28 atoms, 25 bonds, 4 residues, 1 model selected 
    8947 
    8948 > select add #37/A:354
    8949 
    8950 37 atoms, 33 bonds, 5 residues, 1 model selected 
    8951 
    8952 > select add #37/A:353
    8953 
    8954 45 atoms, 40 bonds, 6 residues, 1 model selected 
    8955 
    8956 > select add #37/A:352
    8957 
    8958 56 atoms, 51 bonds, 7 residues, 1 model selected 
    8959 
    8960 > select add #37/A:351
    8961 
    8962 64 atoms, 58 bonds, 8 residues, 1 model selected 
    8963 
    8964 > select add #37/A:350
    8965 
    8966 69 atoms, 62 bonds, 9 residues, 1 model selected 
    8967 
    8968 > select add #37/A:349
    8969 
    8970 73 atoms, 65 bonds, 10 residues, 1 model selected 
    8971 
    8972 > select add #37/A:348
    8973 
    8974 78 atoms, 69 bonds, 11 residues, 1 model selected 
    8975 
    8976 > select add #37/A:347
    8977 
    8978 83 atoms, 73 bonds, 12 residues, 1 model selected 
    8979 
    8980 > select add #37/A:346
    8981 
    8982 92 atoms, 81 bonds, 13 residues, 1 model selected 
    8983 
    8984 > select add #37/A:345
    8985 
    8986 99 atoms, 87 bonds, 14 residues, 1 model selected 
    8987 
    8988 > select add #37/A:344
    8989 
    8990 103 atoms, 90 bonds, 15 residues, 1 model selected 
    8991 
    8992 > select add #37/A:341
    8993 
    8994 111 atoms, 97 bonds, 16 residues, 1 model selected 
    8995 
    8996 > select add #37/A:342
    8997 
    8998 120 atoms, 105 bonds, 17 residues, 1 model selected 
    8999 
    9000 > select add #37/A:343
    9001 
    9002 129 atoms, 113 bonds, 18 residues, 1 model selected 
    9003 
    9004 > color sel red
    9005 
    9006 > select clear
    9007 
    9008 > hide #30 models
    9009 
    9010 > show #30 models
    9011 
    9012 > hide #30 models
    9013 
    9014 > hide #!37 models
    9015 
    9016 > show #!37 models
    9017 
    9018 > select add #37
    9019 
    9020 3984 atoms, 3982 bonds, 5 pseudobonds, 592 residues, 3 models selected 
    9021 
    9022 > select clear
    9023 
    9024 [Repeated 2 time(s)]
    9025 
    9026 > hide #37.1.1 models
    9027 
    9028 > select #37/C: 195
    9029 
    9030 6 atoms, 5 bonds, 1 residue, 1 model selected 
    9031 
    9032 > show sel atoms
    9033 
    9034 > color sel byhetero
    9035 
    9036 > select clear
    9037 
    9038 [Repeated 1 time(s)]
    9039 
    9040 > show #35 models
    9041 
    9042 > hide #35 models
    9043 
    9044 > select add #37/A:165
    9045 
    9046 7 atoms, 6 bonds, 1 residue, 1 model selected 
    9047 
    9048 > select add #37/A:164
    9049 
    9050 11 atoms, 9 bonds, 2 residues, 1 model selected 
    9051 
    9052 > select add #37/A:163
    9053 
    9054 16 atoms, 13 bonds, 3 residues, 1 model selected 
    9055 
    9056 > select add #37/A:162
    9057 
    9058 25 atoms, 21 bonds, 4 residues, 1 model selected 
    9059 
    9060 > select add #37/A:161
    9061 
    9062 32 atoms, 27 bonds, 5 residues, 1 model selected 
    9063 
    9064 > select add #37/A:159
    9065 
    9066 40 atoms, 34 bonds, 6 residues, 1 model selected 
    9067 
    9068 > select add #37/A:158
    9069 
    9070 48 atoms, 41 bonds, 7 residues, 1 model selected 
    9071 
    9072 > select add #37/A:160
    9073 
    9074 60 atoms, 53 bonds, 8 residues, 1 model selected 
    9075 
    9076 > select add #37/A:157
    9077 
    9078 68 atoms, 60 bonds, 9 residues, 1 model selected 
    9079 
    9080 > select add #37/A:156
    9081 
    9082 77 atoms, 68 bonds, 10 residues, 1 model selected 
    9083 
    9084 > select add #37/A:155
    9085 
    9086 83 atoms, 73 bonds, 11 residues, 1 model selected 
    9087 
    9088 > select add #37/A:154
    9089 
    9090 92 atoms, 81 bonds, 12 residues, 1 model selected 
    9091 
    9092 > select add #37/A:153
    9093 
    9094 97 atoms, 85 bonds, 13 residues, 1 model selected 
    9095 
    9096 > select add #37/A:152
    9097 
    9098 102 atoms, 89 bonds, 14 residues, 1 model selected 
    9099 
    9100 > select add #37/A:151
    9101 
    9102 111 atoms, 97 bonds, 15 residues, 1 model selected 
    9103 
    9104 > select add #37/A:150
    9105 
    9106 118 atoms, 103 bonds, 16 residues, 1 model selected 
    9107 
    9108 > select add #37/A:149
    9109 
    9110 126 atoms, 110 bonds, 17 residues, 1 model selected 
    9111 
    9112 > color sel magenta
    9113 
    9114 > select clear
    9115 
    9116 > show #35 models
    9117 
    9118 > show #30 models
    9119 
    9120 > hide #!37 models
    9121 
    9122 > select #30/B: 195
    9123 
    9124 6 atoms, 5 bonds, 1 residue, 1 model selected 
    9125 
    9126 > show sel atoms
    9127 
    9128 > color sel byhetero
    9129 
    9130 > select clear
    9131 
    9132 > save "/Users/amy/Desktop/3C11_Fab_AAT_NE/make pictures/1oph_michaelis
    9133 > complex.jpg" width 935 height 668 supersample 3
    9134 
    9135 > ui tool show Toolbar
    9136 
    9137 > save /Users/amy/Desktop/image1.png supersample 3
    9138 
    9139 > save "/Users/amy/Desktop/3C11_Fab_AAT_NE/make pictures/1oph_michaelis
    9140 > complex.png" width 935 height 668 supersample 3 transparentBackground true
    9141 
    9142 > show #!37 models
    9143 
    9144 > hide #30 models
    9145 
    9146 > hide #35 models
    9147 
    9148 > undo
    9149 
    9150 > hide #35 models
    9151 
    9152 > view
    9153 
    9154 > hide #!37 models
    9155 
    9156 > show #35 models
    9157 
    9158 > show #!37 models
    9159 
    9160 > hide #!37 models
    9161 
    9162 > show #30 models
    9163 
    9164 > save "/Users/amy/Desktop/3C11_Fab_AAT_NE/make pictures/1oph_michaelis
    9165 > complex.png" width 935 height 668 supersample 3 transparentBackground true
    9166 
    9167 > hide #30 models
    9168 
    9169 > hide #35 models
    9170 
    9171 > show #!37 models
    9172 
    9173 > save "/Users/amy/Desktop/3C11_Fab_AAT_NE/make pictures/1ezx_final
    9174 > complex.png" width 935 height 668 supersample 3 transparentBackground true
    9175 
    9176 > save /Users/amy/Desktop/3C11_Fab_AAT_NE/csparc.cxs includeMaps true
    9177 
    9178 ——— End of log from Sun Feb 1 23:24:08 2026 ———
    9179 
    9180 > view name session-start
    9181 
    9182 opened ChimeraX session 
    9183 
    9184 > open 9hud fromDatabase pdb format mmcif
    9185 
    9186 9hud title: 
    9187 Alpha-1-antitrypsin in the cleaved conformation in complex with a
    9188 conformationally nonselective Fab fragment [more info...] 
    9189  
    9190 Chain information for 9hud #38 
    9191 --- 
    9192 Chain | Description | UniProt 
    9193 A C | Alpha-1-antitrypsin | A1AT_HUMAN 2-354 
    9194 B D | Short peptide from AAT | A1AT_HUMAN 355-394 
    9195 H I | FAB 9C5 heavy chain |   
    9196 L M | FAB 9C5 light chain |   
    9197  
    9198 Non-standard residues in 9hud #38 
    9199 --- 
    9200 CL — chloride ion 
    9201 EDO — 1,2-ethanediol (ethylene glycol) 
    9202 GLY — glycine 
    9203 GOL — glycerol (glycerin; propane-1,2,3-triol) 
    9204 LYS — lysine 
    9205 NA — sodium ion 
    9206  
    9207 9hud mmCIF Assemblies 
    9208 --- 
    9209 1| author_defined_assembly 
    9210 2| author_defined_assembly 
    9211  
    9212 61 atoms have alternate locations. Control/examine alternate locations with
    9213 Altloc Explorer [start tool...] or the altlocs command. 
    9214 12039 atoms have anisotropic B-factors. Depict anisotropic information with
    9215 Thermal Ellipsoids [start tool...] or the aniso command. 
    9216 
    9217 > hide #!37-38 cartoons
    9218 
    9219 > show #!37-38 cartoons
    9220 
    9221 > hide #!37-38 atoms
    9222 
    9223 > select #38/A
    9224 
    9225 2567 atoms, 2550 bonds, 398 residues, 1 model selected 
    9226 
    9227 > select #38/B
    9228 
    9229 252 atoms, 251 bonds, 40 residues, 1 model selected 
    9230 
    9231 > select #38/C
    9232 
    9233 2612 atoms, 2578 bonds, 415 residues, 1 model selected 
    9234 
    9235 > select #38/C,D
    9236 
    9237 2873 atoms, 2840 bonds, 454 residues, 1 model selected 
    9238 
    9239 > delete #38/C,D
    9240 
    9241 > select #38/H
    9242 
    9243 1713 atoms, 1651 bonds, 322 residues, 1 model selected 
    9244 
    9245 > select #38/I
    9246 
    9247 1736 atoms, 1654 bonds, 1 pseudobond, 338 residues, 2 models selected 
    9248 
    9249 > delete #38/I
    9250 
    9251 > select #38/M
    9252 
    9253 1766 atoms, 1691 bonds, 328 residues, 1 model selected 
    9254 
    9255 > delete #38/M
    9256 
    9257 > hide #!37 models
    9258 
    9259 > show #!37 models
    9260 
    9261 > mmaker #38 to #37
    9262 
    9263 Parameters 
    9264 --- 
    9265 Chain pairing | bb 
    9266 Alignment algorithm | Needleman-Wunsch 
    9267 Similarity matrix | BLOSUM-62 
    9268 SS fraction | 0.3 
    9269 Gap open (HH/SS/other) | 18/18/6 
    9270 Gap extend | 1 
    9271 SS matrix |  |  | H | S | O 
    9272 ---|---|---|--- 
    9273 H | 6 | -9 | -6 
    9274 S |  | 6 | -6 
    9275 O |  |  | 4 
    9276 Iteration cutoff | 2 
    9277  
    9278 Matchmaker 1ezx, chain A (#37) with 9hud, chain A (#38), sequence alignment
    9279 score = 1674.4 
    9280 RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
    9281 0.519) 
    9282  
    9283 
    9284 > save /Users/amy/Desktop/3C11_Fab_AAT_NE/csparc.cxs includeMaps true
    9285 
    9286 ——— End of log from Wed Feb 11 13:24:40 2026 ———
    9287 
    9288 > view name session-start
    9289 
    9290 opened ChimeraX session 
    9291 
    9292 > open /Users/amy/Downloads/cryosparc_P483_J66_004_volume_map.mrc
    9293 
    9294 Opened cryosparc_P483_J66_004_volume_map.mrc as #39, grid size 400,400,400,
    9295 pixel 0.723, shown at level 0.00725, step 2, values float32 
    9296 
    9297 > volume #39 level 0.0301
    9298 
    9299 > hide #!37 models
    9300 
    9301 > hide #!38 models
    9302 
    9303 > volume #39 level 0.08437
    9304 
    9305 > open /Users/amy/Downloads/cryosparc_P483_J69_005_volume_map.mrc
    9306 
    9307 Opened cryosparc_P483_J69_005_volume_map.mrc as #40, grid size 400,400,400,
    9308 pixel 0.723, shown at level 0.00425, step 2, values float32 
    9309 
    9310 > volume #40 level 0.02603
    9311 
    9312 > volume #40 level 0.05112
    9313 
    9314 > transparency #40 50
    9315 
    9316 > show #!39 models
    9317 
    9318 > hide #!39 models
    9319 
    9320 > show #!38 models
    9321 
    9322 > select add #38
    9323 
    9324 6282 atoms, 6138 bonds, 1077 residues, 1 model selected 
    9325 
    9326 > ui mousemode right "translate selected models"
    9327 
    9328 > view matrix models
    9329 > #38,-0.23813,0.96316,-0.12499,103.01,0.23278,-0.068345,-0.97012,107.01,-0.94292,-0.26011,-0.20793,320.16
    9330 
    9331 > view matrix models
    9332 > #38,-0.35239,0.53131,-0.77041,145.72,-0.23758,-0.84704,-0.47549,205.11,-0.90519,0.015476,0.42472,295.71
    9333 
    9334 > view matrix models
    9335 > #38,0.095516,0.64963,-0.75423,70.134,0.59254,-0.64594,-0.48131,66.164,-0.79986,-0.40094,-0.44663,305.92
    9336 
    9337 > view matrix models
    9338 > #38,0.23814,0.79731,-0.5546,39.413,0.91725,-0.37235,-0.14145,0.058888,-0.31929,-0.47502,-0.82,237.42
    9339 
    9340 > view matrix models
    9341 > #38,-0.29619,0.8953,-0.33273,117.39,0.7752,0.42884,0.46386,-15.784,0.55798,-0.12055,-0.82105,85.078
    9342 
    9343 > view matrix models
    9344 > #38,-0.30596,0.51089,-0.80335,139.57,0.54659,0.78515,0.29115,8.8601,0.7795,-0.35003,-0.51948,55.076
    9345 
    9346 > view matrix models
    9347 > #38,-0.30596,0.51089,-0.80335,160.4,0.54659,0.78515,0.29115,-4.0241,0.7795,-0.35003,-0.51948,56.001
    9348 
    9349 > view matrix models
    9350 > #38,0.2554,0.95891,-0.12357,45.918,0.33368,0.032535,0.94213,50.395,0.90743,-0.28185,-0.31165,30.553
    9351 
    9352 > view matrix models
    9353 > #38,0.28907,0.71313,0.63866,40.495,-0.045867,-0.65606,0.75332,139.21,0.95621,-0.24706,-0.15694,19.569
    9354 
    9355 > view matrix models
    9356 > #38,0.66315,0.74847,0.0052223,-12.11,0.30094,-0.27301,0.91373,67.652,0.68532,-0.60437,-0.40629,79.243
    9357 
    9358 > view matrix models
    9359 > #38,0.66315,0.74847,0.0052223,-14.717,0.30094,-0.27301,0.91373,95.231,0.68532,-0.60437,-0.40629,75.309
    9360 
    9361 > view matrix models
    9362 > #38,0.66315,0.74847,0.0052223,9.7058,0.30094,-0.27301,0.91373,102.14,0.68532,-0.60437,-0.40629,70.114
    9363 
    9364 > ui tool show "Fit in Map"
    9365 
    9366 > fitmap #38 inMap #40
    9367 
    9368 Fit molecule 9hud (#38) to map cryosparc_P483_J69_005_volume_map.mrc (#40)
    9369 using 6282 atoms 
    9370 average map value = 0.0417, steps = 128 
    9371 shifted from previous position = 4.51 
    9372 rotated from previous position = 8.35 degrees 
    9373 atoms outside contour = 4033, contour level = 0.051121 
    9374  
    9375 Position of 9hud (#38) relative to cryosparc_P483_J69_005_volume_map.mrc (#40)
    9376 coordinates: 
    9377 Matrix rotation and translation 
    9378 0.65684785 0.74878514 0.08872268 11.05139992 
    9379 0.33454956 -0.39485965 0.85566491 105.25041377 
    9380 0.67574218 -0.53235953 -0.50986845 72.64892317 
    9381 Axis -0.88808312 -0.37558568 -0.26503541 
    9382 Axis point 0.00000000 65.04529101 13.14028850 
    9383 Rotation angle (degrees) 128.60443789 
    9384 Shift along axis -68.59964747 
    9385  
    9386 
    9387 > select subtract #38
    9388 
    9389 Nothing selected 
    9390 
    9391 > volume #40 level 0.0597
    9392 
    9393 > hide #!40 models
    9394 
    9395 > show #!40 models
    9396 
    9397 > hide #!38 models
    9398 
    9399 > show #!38 models
    9400 
    9401 > hide #!40 models
    9402 
    9403 > show #!40 models
    9404 
    9405 > hide #!38 models
    9406 
    9407 > show #!38 models
    9408 
    9409 > hide #!40 models
    9410 
    9411 > show #!40 models
    9412 
    9413 > hide #!40 models
    9414 
    9415 > show #!40 models
    9416 
    9417 > hide #!38 models
    9418 
    9419 > volume flip #40 axis z
    9420 
    9421 Opened cryosparc_P483_J69_005_volume_map.mrc z flip as #41, grid size
    9422 400,400,400, pixel 0.723, shown at step 1, values float32 
    9423 
    9424 > show #!38 models
    9425 
    9426 > select add #38
    9427 
    9428 6282 atoms, 6138 bonds, 1077 residues, 1 model selected 
    9429 
    9430 > view matrix models
    9431 > #38,0.65685,0.74879,0.088723,12.679,0.33455,-0.39486,0.85566,109.56,0.67574,-0.53236,-0.50987,57.685
    9432 
    9433 > view matrix models
    9434 > #38,-0.58254,0.54788,0.6004,210.02,0.59834,-0.2109,0.77299,61.815,0.55013,0.80954,-0.20496,22.25
    9435 
    9436 > view matrix models
    9437 > #38,-0.40435,-0.85962,0.31233,239.45,0.49216,0.083334,0.86651,66.149,-0.7709,0.50409,0.38937,235.48
    9438 
    9439 > view matrix models
    9440 > #38,-0.56895,-0.81456,0.11308,266.25,0.44686,-0.19079,0.87402,83.739,-0.69037,0.54781,0.47254,220.03
    9441 
    9442 > view matrix models
    9443 > #38,-0.56895,-0.81456,0.11308,265.73,0.44686,-0.19079,0.87402,80.959,-0.69037,0.54781,0.47254,214.99
    9444 
    9445 > fitmap #38 inMap #41
    9446 
    9447 Fit molecule 9hud (#38) to map cryosparc_P483_J69_005_volume_map.mrc z flip
    9448 (#41) using 6282 atoms 
    9449 average map value = 0.05473, steps = 216 
    9450 shifted from previous position = 2.37 
    9451 rotated from previous position = 33 degrees 
    9452 atoms outside contour = 3800, contour level = 0.059703 
    9453  
    9454 Position of 9hud (#38) relative to cryosparc_P483_J69_005_volume_map.mrc z
    9455 flip (#41) coordinates: 
    9456 Matrix rotation and translation 
    9457 -0.75082147 -0.55505166 -0.35802903 289.09205452 
    9458 0.04746292 -0.58599102 0.80892632 158.98706928 
    9459 -0.65879769 0.59036614 0.46631901 208.65076835 
    9460 Axis -0.30870385 0.42481867 0.85101765 
    9461 Axis point 172.41915491 63.65569402 0.00000000 
    9462 Rotation angle (degrees) 159.26804372 
    9463 Shift along axis 155.86233044 
    9464  
    9465 
    9466 > select subtract #38
    9467 
    9468 Nothing selected 
    9469 
    9470 > volume #41 level 0.05159
    9471 
    9472 > select add #38
    9473 
    9474 6282 atoms, 6138 bonds, 1077 residues, 1 model selected 
    9475 
    9476 > view matrix models
    9477 > #38,-0.75082,-0.55505,-0.35803,289.14,0.047463,-0.58599,0.80893,158.79,-0.6588,0.59037,0.46632,207.97
    9478 
    9479 > view matrix models
    9480 > #38,-0.75082,-0.55505,-0.35803,289.16,0.047463,-0.58599,0.80893,157.96,-0.6588,0.59037,0.46632,207.03
    9481 
    9482 > view matrix models
    9483 > #38,-0.75082,-0.55505,-0.35803,288.72,0.047463,-0.58599,0.80893,155.88,-0.6588,0.59037,0.46632,205.57
    9484 
    9485 > fitmap #38 inMap #41
    9486 
    9487 Fit molecule 9hud (#38) to map cryosparc_P483_J69_005_volume_map.mrc z flip
    9488 (#41) using 6282 atoms 
    9489 average map value = 0.05473, steps = 72 
    9490 shifted from previous position = 4.4 
    9491 rotated from previous position = 0.101 degrees 
    9492 atoms outside contour = 3342, contour level = 0.051588 
    9493  
    9494 Position of 9hud (#38) relative to cryosparc_P483_J69_005_volume_map.mrc z
    9495 flip (#41) coordinates: 
    9496 Matrix rotation and translation 
    9497 -0.75090265 -0.55404999 -0.35940760 289.07011046 
    9498 0.04645479 -0.58718152 0.80812117 159.19876899 
    9499 -0.65877702 0.59012412 0.46665444 208.66676414 
    9500 Axis -0.30899016 0.42432779 0.85115863 
    9501 Axis point 172.44704823 63.68649423 0.00000000 
    9502 Rotation angle (degrees) 159.34394496 
    9503 Shift along axis 155.84115924 
    9504  
    9505 
    9506 > view matrix models
    9507 > #38,-0.7509,-0.55405,-0.35941,287.93,0.046455,-0.58718,0.80812,155.5,-0.65878,0.59012,0.46665,206.09
    9508 
    9509 > fitmap #38 inMap #41
    9510 
    9511 Fit molecule 9hud (#38) to map cryosparc_P483_J69_005_volume_map.mrc z flip
    9512 (#41) using 6282 atoms 
    9513 average map value = 0.05473, steps = 92 
    9514 shifted from previous position = 4.65 
    9515 rotated from previous position = 0.00364 degrees 
    9516 atoms outside contour = 3341, contour level = 0.051588 
    9517  
    9518 Position of 9hud (#38) relative to cryosparc_P483_J69_005_volume_map.mrc z
    9519 flip (#41) coordinates: 
    9520 Matrix rotation and translation 
    9521 -0.75086696 -0.55406598 -0.35945751 289.07124867 
    9522 0.04643032 -0.58719553 0.80811239 159.20847697 
    9523 -0.65881943 0.59009517 0.46663119 208.66191835 
    9524 Axis -0.30902059 0.42431965 0.85115164 
    9525 Axis point 172.44904391 63.69342969 0.00000000 
    9526 Rotation angle (degrees) 159.34407294 
    9527 Shift along axis 155.82925281 
    9528  
    9529 
    9530 > select subtract #38
    9531 
    9532 Nothing selected 
    9533 
    9534 > combine #38 close false
    9535 
    9536 > hide #!38 models
    9537 
    9538 > select #42/A
    9539 
    9540 2567 atoms, 2550 bonds, 398 residues, 1 model selected 
    9541 
    9542 > select #42/M
    9543 
    9544 Nothing selected 
    9545 
    9546 > select #42/M
    9547 
    9548 Nothing selected 
    9549 
    9550 > select #42/I
    9551 
    9552 Nothing selected 
    9553 
    9554 > select #42/H
    9555 
    9556 1713 atoms, 1651 bonds, 322 residues, 1 model selected 
    9557 
    9558 > delete #42/H
    9559 
    9560 > select #42/N
    9561 
    9562 Nothing selected 
    9563 
    9564 > select #42/I
    9565 
    9566 Nothing selected 
    9567 
    9568 > select #42/L
    9569 
    9570 1750 atoms, 1686 bonds, 317 residues, 1 model selected 
    9571 
    9572 > delete #42/L
    9573 
    9574 > fitmap #42 inMap #41
    9575 
    9576 Fit molecule copy of 9hud (#42) to map cryosparc_P483_J69_005_volume_map.mrc z
    9577 flip (#41) using 2819 atoms 
    9578 average map value = 0.06533, steps = 56 
    9579 shifted from previous position = 0.821 
    9580 rotated from previous position = 3.38 degrees 
    9581 atoms outside contour = 1262, contour level = 0.051588 
    9582  
    9583 Position of copy of 9hud (#42) relative to
    9584 cryosparc_P483_J69_005_volume_map.mrc z flip (#41) coordinates: 
    9585 Matrix rotation and translation 
    9586 -0.73693347 -0.57914780 -0.34859273 288.27078922 
    9587 0.03048667 -0.54364745 0.83875981 157.64342584 
    9588 -0.67527744 0.60748274 0.41828829 210.31462354 
    9589 Axis -0.31712566 0.44794803 0.83592696 
    9590 Axis point 174.06638485 60.58096428 0.00000000 
    9591 Rotation angle (degrees) 158.61421520 
    9592 Shift along axis 155.00566094 
    9593  
    9594 
    9595 > volume #41 level 0.06516
    9596 
    9597 > select add #42
    9598 
    9599 2819 atoms, 2801 bonds, 438 residues, 1 model selected 
    9600 
    9601 > view matrix models
    9602 > #42,-0.73693,-0.57915,-0.34859,287.85,0.030487,-0.54365,0.83876,156.54,-0.67528,0.60748,0.41829,208.51
    9603 
    9604 > fitmap #42 inMap #41
    9605 
    9606 Fit molecule copy of 9hud (#42) to map cryosparc_P483_J69_005_volume_map.mrc z
    9607 flip (#41) using 2819 atoms 
    9608 average map value = 0.06533, steps = 76 
    9609 shifted from previous position = 2.15 
    9610 rotated from previous position = 0.0105 degrees 
    9611 atoms outside contour = 1566, contour level = 0.065161 
    9612  
    9613 Position of copy of 9hud (#42) relative to
    9614 cryosparc_P483_J69_005_volume_map.mrc z flip (#41) coordinates: 
    9615 Matrix rotation and translation 
    9616 -0.73689140 -0.57919551 -0.34860239 288.27541199 
    9617 0.03038436 -0.54353165 0.83883856 157.64897324 
    9618 -0.67532796 0.60754087 0.41812229 210.31189981 
    9619 Axis -0.31716299 0.44801683 0.83587592 
    9620 Axis point 174.07498439 60.57428048 0.00000000 
    9621 Rotation angle (degrees) 158.61485484 
    9622 Shift along axis 154.99375355 
    9623  
    9624 
    9625 > view matrix models
    9626 > #42,-0.73689,-0.5792,-0.3486,286.89,0.030384,-0.54353,0.83884,156.41,-0.67533,0.60754,0.41812,208.9
    9627 
    9628 > view matrix models
    9629 > #42,-0.73689,-0.5792,-0.3486,287.57,0.030384,-0.54353,0.83884,158.73,-0.67533,0.60754,0.41812,212.26
    9630 
    9631 > view matrix models
    9632 > #42,-0.73689,-0.5792,-0.3486,287.63,0.030384,-0.54353,0.83884,158.66,-0.67533,0.60754,0.41812,212.24
    9633 
    9634 > fitmap #42 inMap #41
    9635 
    9636 Fit molecule copy of 9hud (#42) to map cryosparc_P483_J69_005_volume_map.mrc z
    9637 flip (#41) using 2819 atoms 
    9638 average map value = 0.06533, steps = 76 
    9639 shifted from previous position = 2.27 
    9640 rotated from previous position = 0.0141 degrees 
    9641 atoms outside contour = 1565, contour level = 0.065161 
    9642  
    9643 Position of copy of 9hud (#42) relative to
    9644 cryosparc_P483_J69_005_volume_map.mrc z flip (#41) coordinates: 
    9645 Matrix rotation and translation 
    9646 -0.73682803 -0.57935101 -0.34847792 288.27467210 
    9647 0.03043622 -0.54334125 0.83896003 157.62886136 
    9648 -0.67539477 0.60756292 0.41798231 210.32004980 
    9649 Axis -0.31717295 0.44810058 0.83582725 
    9650 Axis point 174.07853761 60.56677345 0.00000000 
    9651 Rotation angle (degrees) 158.60591524 
    9652 Shift along axis 154.99188631 
    9653  
    9654 
    9655 > select subtract #42
    9656 
    9657 Nothing selected 
    9658 
    9659 > show #!38 models
    9660 
    9661 > mmaker #38 to #42
    9662 
    9663 Parameters 
    9664 --- 
    9665 Chain pairing | bb 
    9666 Alignment algorithm | Needleman-Wunsch 
    9667 Similarity matrix | BLOSUM-62 
    9668 SS fraction | 0.3 
    9669 Gap open (HH/SS/other) | 18/18/6 
    9670 Gap extend | 1 
    9671 SS matrix |  |  | H | S | O 
    9672 ---|---|---|--- 
    9673 H | 6 | -9 | -6 
    9674 S |  | 6 | -6 
    9675 O |  |  | 4 
    9676 Iteration cutoff | 2 
    9677  
    9678 Matchmaker copy of 9hud, chain A (#42) with 9hud, chain A (#38), sequence
    9679 alignment score = 1849.2 
    9680 RMSD between 332 pruned atom pairs is 0.000 angstroms; (across all 332 pairs:
    9681 0.000) 
    9682  
    9683 
    9684 > hide #!42 models
    9685 
    9686 > hide #!38 models
    9687 
    9688 > show #!38 models
    9689 
    9690 > show #!37 models
    9691 
    9692 > mmaker #37 to #38
    9693 
    9694 Parameters 
    9695 --- 
    9696 Chain pairing | bb 
    9697 Alignment algorithm | Needleman-Wunsch 
    9698 Similarity matrix | BLOSUM-62 
    9699 SS fraction | 0.3 
    9700 Gap open (HH/SS/other) | 18/18/6 
    9701 Gap extend | 1 
    9702 SS matrix |  |  | H | S | O 
    9703 ---|---|---|--- 
    9704 H | 6 | -9 | -6 
    9705 S |  | 6 | -6 
    9706 O |  |  | 4 
    9707 Iteration cutoff | 2 
    9708  
    9709 Matchmaker 9hud, chain A (#38) with 1ezx, chain A (#37), sequence alignment
    9710 score = 1674.4 
    9711 RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
    9712 0.519) 
    9713  
    9714 
    9715 > open /Users/amy/Downloads/cryosparc_P483_J81_008_volume_map.mrc
    9716 
    9717 Opened cryosparc_P483_J81_008_volume_map.mrc as #43, grid size 400,400,400,
    9718 pixel 0.723, shown at level 0.00732, step 2, values float32 
    9719 
    9720 > hide #!37 models
    9721 
    9722 > hide #!38 models
    9723 
    9724 > hide #!41 models
    9725 
    9726 > surface dust #43 size 7.23
    9727 
    9728 > volume #43 level 0.06119
    9729 
    9730 > volume #43 level 0.0273
    9731 
    9732 > volume flip #43 axis z
    9733 
    9734 Opened cryosparc_P483_J81_008_volume_map.mrc z flip as #44, grid size
    9735 400,400,400, pixel 0.723, shown at step 1, values float32 
    9736 
    9737 > transparency #44 50
    9738 
    9739 > volume #44 level 0.03941
    9740 
    9741 > volume #44 level 0.04042
    9742 
    9743 > open /Users/amy/Downloads/cryosparc_P483_J66_004_volume_map.mrc
    9744 
    9745 Opened cryosparc_P483_J66_004_volume_map.mrc as #45, grid size 400,400,400,
    9746 pixel 0.723, shown at level 0.00725, step 2, values float32 
    9747 
    9748 > volume #45 level 0.06094
    9749 
    9750 > open /Users/amy/Downloads/cryosparc_P483_J72_006_volume_map.mrc
    9751 
    9752 Opened cryosparc_P483_J72_006_volume_map.mrc as #46, grid size 400,400,400,
    9753 pixel 0.723, shown at level 0.0048, step 2, values float32 
    9754 
    9755 > volume #46 level 0.04807
    9756 
    9757 > transparency #46 50
    9758 
    9759 > show #!42 models
    9760 
    9761 > hide #!42 models
    9762 
    9763 > show #!38 models
    9764 
    9765 > select add #38
    9766 
    9767 6282 atoms, 6138 bonds, 1077 residues, 1 model selected 
    9768 
    9769 > view matrix models
    9770 > #38,-0.73683,-0.57935,-0.34848,292.33,0.030436,-0.54334,0.83896,164.74,-0.67539,0.60756,0.41798,237.37
    9771 
    9772 > view matrix models
    9773 > #38,-0.38309,-0.69929,0.60352,229.08,0.62032,0.28936,0.72902,40.857,-0.68443,0.65365,0.32294,238.22
    9774 
    9775 > view matrix models
    9776 > #38,-0.38309,-0.69929,0.60352,226.04,0.62032,0.28936,0.72902,38.256,-0.68443,0.65365,0.32294,241.06
    9777 
    9778 > view matrix models
    9779 > #38,-0.34943,-0.72907,0.58852,222.05,0.61787,0.29288,0.72969,38.499,-0.70437,0.61861,0.34813,245.24
    9780 
    9781 > view matrix models
    9782 > #38,-0.34943,-0.72907,0.58852,222.59,0.61787,0.29288,0.72969,38.714,-0.70437,0.61861,0.34813,242.8
    9783 
    9784 > fitmap #38 inMap #46
    9785 
    9786 Fit molecule 9hud (#38) to map cryosparc_P483_J72_006_volume_map.mrc (#46)
    9787 using 6282 atoms 
    9788 average map value = 0.0399, steps = 112 
    9789 shifted from previous position = 6.23 
    9790 rotated from previous position = 3.87 degrees 
    9791 atoms outside contour = 3940, contour level = 0.048075 
    9792  
    9793 Position of 9hud (#38) relative to cryosparc_P483_J72_006_volume_map.mrc (#46)
    9794 coordinates: 
    9795 Matrix rotation and translation 
    9796 -0.34701016 -0.76389374 0.54410505 226.91723804 
    9797 0.57651318 0.28385608 0.76619729 40.13005322 
    9798 -0.73974084 0.57956197 0.34189387 251.72894877 
    9799 Axis -0.10005014 0.68823502 0.71855586 
    9800 Axis point 172.83638513 16.61736328 0.00000000 
    9801 Rotation angle (degrees) 111.13889774 
    9802 Shift along axis 185.79711858 
    9803  
    9804 
    9805 > select subtract #38
    9806 
    9807 Nothing selected 
    9808 
    9809 > volume flip #46 axis z
    9810 
    9811 Opened cryosparc_P483_J72_006_volume_map.mrc z flip as #47, grid size
    9812 400,400,400, pixel 0.723, shown at step 1, values float32 
    9813 
    9814 > select add #38
    9815 
    9816 6282 atoms, 6138 bonds, 1077 residues, 1 model selected 
    9817 
    9818 > view matrix models
    9819 > #38,-0.43781,-0.43705,0.78569,225.72,0.89875,-0.18935,0.39548,11.956,-0.024068,0.87928,0.47569,125.36
    9820 
    9821 > view matrix models
    9822 > #38,0.17782,0.26753,0.947,99.291,0.050808,-0.96355,0.26266,177.44,0.98275,0.001409,-0.18493,8.0567
    9823 
    9824 > view matrix models
    9825 > #38,0.17782,0.26753,0.947,103.63,0.050808,-0.96355,0.26266,172.68,0.98275,0.001409,-0.18493,-1.716
    9826 
    9827 > view matrix models
    9828 > #38,0.63642,0.20154,0.74455,36.153,-0.42467,-0.71425,0.55633,234.65,0.64391,-0.67025,-0.36898,79.951
    9829 
    9830 > view matrix models
    9831 > #38,0.63642,0.20154,0.74455,34.766,-0.42467,-0.71425,0.55633,241.95,0.64391,-0.67025,-0.36898,57.4
    9832 
    9833 > fitmap #38 inMap #47
    9834 
    9835 Fit molecule 9hud (#38) to map cryosparc_P483_J72_006_volume_map.mrc z flip
    9836 (#47) using 6282 atoms 
    9837 average map value = 0.06343, steps = 124 
    9838 shifted from previous position = 5.23 
    9839 rotated from previous position = 14 degrees 
    9840 atoms outside contour = 2477, contour level = 0.048075 
    9841  
    9842 Position of 9hud (#38) relative to cryosparc_P483_J72_006_volume_map.mrc z
    9843 flip (#47) coordinates: 
    9844 Matrix rotation and translation 
    9845 0.48056680 0.06585233 0.87448215 60.37965921 
    9846 -0.56537086 -0.73901641 0.36634758 262.76707770 
    9847 0.67038150 -0.67046120 -0.31791576 52.06857630 
    9848 Axis -0.84232947 0.16581649 -0.51282156 
    9849 Axis point 0.00000000 144.40291810 -47.17976586 
    9850 Rotation angle (degrees) 142.01600325 
    9851 Shift along axis -33.99034036 
    9852  
    9853 
    9854 > select subtract #38
    9855 
    9856 Nothing selected 
    9857 
    9858 > hide #!47 models
    9859 
    9860 > show #!47 models
    9861 
    9862 > hide #!38 models
    9863 
    9864 > show #!38 models
    9865 
    9866 > hide #!38 models
    9867 
    9868 > hide #!45 models
    9869 
    9870 > show #!44 models
    9871 
    9872 > show #!38 models
    9873 
    9874 > select add #38
    9875 
    9876 6282 atoms, 6138 bonds, 1077 residues, 1 model selected 
    9877 
    9878 > view matrix models
    9879 > #38,0.48057,0.065852,0.87448,65.866,-0.56537,-0.73902,0.36635,260.8,0.67038,-0.67046,-0.31792,67.074
    9880 
    9881 > view matrix models
    9882 > #38,0.24561,0.13628,0.95974,99.26,-0.61016,-0.7476,0.2623,269.51,0.75324,-0.65002,-0.10047,50.465
    9883 
    9884 > view matrix models
    9885 > #38,0.24561,0.13628,0.95974,97.908,-0.61016,-0.7476,0.2623,267.42,0.75324,-0.65002,-0.10047,51.929
    9886 
    9887 > fitmap #38 inMap #44
    9888 
    9889 Fit molecule 9hud (#38) to map cryosparc_P483_J81_008_volume_map.mrc z flip
    9890 (#44) using 6282 atoms 
    9891 average map value = 0.03783, steps = 168 
    9892 shifted from previous position = 5.42 
    9893 rotated from previous position = 16.7 degrees 
    9894 atoms outside contour = 3802, contour level = 0.040419 
    9895  
    9896 Position of 9hud (#38) relative to cryosparc_P483_J81_008_volume_map.mrc z
    9897 flip (#44) coordinates: 
    9898 Matrix rotation and translation 
    9899 0.06820670 -0.05795023 0.99598676 133.26750912 
    9900 -0.73706857 -0.67572583 0.01115934 290.51260544 
    9901 0.67236729 -0.73487167 -0.08880232 64.60372631 
    9902 Axis -0.70414963 0.30545181 -0.64099336 
    9903 Axis point 0.00000000 181.24183814 -90.37493056 
    9904 Rotation angle (degrees) 148.01217964 
    9905 Shift along axis -46.51322447 
    9906  
    9907 
    9908 > select subtract #38
    9909 
    9910 Nothing selected 
    9911 
    9912 > hide #!44 models
    9913 
    9914 > show #!43 models
    9915 
    9916 > transparency #38 50
    9917 
    9918 > transparency #43 50
    9919 
    9920 > select add #38
    9921 
    9922 6282 atoms, 6138 bonds, 1077 residues, 1 model selected 
    9923 
    9924 > view matrix models
    9925 > #38,-0.34778,-0.62711,0.69698,224.64,0.7034,0.317,0.6362,16.77,-0.61991,0.71151,0.33086,208.25
    9926 
    9927 > view matrix models
    9928 > #38,-0.34778,-0.62711,0.69698,225.83,0.7034,0.317,0.6362,17.542,-0.61991,0.71151,0.33086,207.48
    9929 
    9930 > view matrix models
    9931 > #38,-0.28771,-0.41373,0.86374,206.06,0.80892,0.37784,0.45043,0.83954,-0.51271,0.82829,0.22596,187.36
    9932 
    9933 > view matrix models
    9934 > #38,-0.28771,-0.41373,0.86374,206.43,0.80892,0.37784,0.45043,-2.4203,-0.51271,0.82829,0.22596,194.27
    9935 
    9936 > view matrix models
    9937 > #38,-0.43329,-0.6387,0.63587,240.94,0.33837,0.53864,0.77161,61.821,-0.83533,0.54948,-0.01727,259.04
    9938 
    9939 > view matrix models
    9940 > #38,-0.43329,-0.6387,0.63587,240.15,0.33837,0.53864,0.77161,62.236,-0.83533,0.54948,-0.01727,256.27
    9941 
    9942 > view matrix models
    9943 > #38,-0.10971,-0.34204,0.93326,173.87,0.39597,0.84616,0.35667,46.512,-0.91169,0.40867,0.042608,273
    9944 
    9945 > view matrix models
    9946 > #38,-0.10971,-0.34204,0.93326,174.05,0.39597,0.84616,0.35667,43.272,-0.91169,0.40867,0.042608,270.13
    9947 
    9948 > hide #!43 models
    9949 
    9950 > show #!44 models
    9951 
    9952 > view matrix models
    9953 > #38,0.33372,0.10106,0.93724,86.86,-0.90444,-0.24596,0.34856,290.96,0.26575,-0.964,0.009315,136.98
    9954 
    9955 > view matrix models
    9956 > #38,-0.0077799,0.047421,0.99884,142.16,-0.55565,-0.83068,0.035109,262.15,0.83138,-0.55473,0.032812,31.52
    9957 
    9958 > view matrix models
    9959 > #38,-0.0077799,0.047421,0.99884,141.96,-0.55565,-0.83068,0.035109,262.22,0.83138,-0.55473,0.032812,29.958
    9960 
    9961 > fitmap #38 inMap #44
    9962 
    9963 Fit molecule 9hud (#38) to map cryosparc_P483_J81_008_volume_map.mrc z flip
    9964 (#44) using 6282 atoms 
    9965 average map value = 0.03751, steps = 112 
    9966 shifted from previous position = 5.86 
    9967 rotated from previous position = 9.02 degrees 
    9968 atoms outside contour = 3835, contour level = 0.040419 
    9969  
    9970 Position of 9hud (#38) relative to cryosparc_P483_J81_008_volume_map.mrc z
    9971 flip (#44) coordinates: 
    9972 Matrix rotation and translation 
    9973 0.05690807 -0.02329864 0.99810753 137.02419950 
    9974 -0.65514588 -0.75524488 0.01972424 280.23565345 
    9975 0.75335606 -0.65502851 -0.05824354 46.13973405 
    9976 Axis -0.70561938 0.25594766 -0.66075116 
    9977 Axis point 0.00000000 166.68305562 -94.19367789 
    9978 Rotation angle (degrees) 151.43679087 
    9979 Shift along axis -55.44815397 
    9980  
    9981 
    9982 > select subtract #38
    9983 
    9984 Nothing selected 
    9985 
    9986 > select add #38
    9987 
    9988 6282 atoms, 6138 bonds, 1077 residues, 1 model selected 
    9989 
    9990 > view matrix models
    9991 > #38,-0.54924,-0.83446,0.044834,275.94,-0.071518,-0.0065171,-0.99742,171.91,0.8326,-0.55103,-0.0561,29.588
    9992 
    9993 > view matrix models
    9994 > #38,-0.095818,-0.5899,-0.80177,205.42,-0.19261,0.80124,-0.56649,154.68,0.97659,0.10015,-0.1904,-16.494
    9995 
    9996 > view matrix models
    9997 > #38,-0.39728,-0.77299,0.49462,243.92,-0.63802,-0.15476,-0.75431,264.16,0.65962,-0.61525,-0.4317,64.108
    9998 
    9999 > view matrix models
    10000 > #38,0.28514,0.071787,0.95579,97.806,-0.70813,-0.65625,0.26054,281.81,0.64594,-0.75112,-0.13629,67.792
    10001 
    10002 > view matrix models
    10003 > #38,0.28514,0.071787,0.95579,96.286,-0.70813,-0.65625,0.26054,282.4,0.64594,-0.75112,-0.13629,66.958
    10004 
    10005 > fitmap #38 inMap #44
    10006 
    10007 Fit molecule 9hud (#38) to map cryosparc_P483_J81_008_volume_map.mrc z flip
    10008 (#44) using 6282 atoms 
    10009 average map value = 0.03783, steps = 168 
    10010 shifted from previous position = 3.71 
    10011 rotated from previous position = 14.8 degrees 
    10012 atoms outside contour = 3801, contour level = 0.040419 
    10013  
    10014 Position of 9hud (#38) relative to cryosparc_P483_J81_008_volume_map.mrc z
    10015 flip (#44) coordinates: 
    10016 Matrix rotation and translation 
    10017 0.06820710 -0.05791598 0.99598872 133.26635838 
    10018 -0.73705893 -0.67573598 0.01118160 290.51125280 
    10019 0.67237782 -0.73486504 -0.08877748 64.60105058 
    10020 Axis -0.70414832 0.30543677 -0.64100197 
    10021 Axis point 0.00000000 181.23877487 -90.37820158 
    10022 Rotation angle (degrees) 148.01136342 
    10023 Shift along axis -46.51586553 
    10024  
    10025 
    10026 > select subtract #38
    10027 
    10028 Nothing selected 
    10029 
    10030 > show #35 models
    10031 
    10032 > select add #35
    10033 
    10034 5953 atoms, 5684 bonds, 699 residues, 1 model selected 
    10035 
    10036 > view matrix models
    10037 > #35,-0.44103,0.30301,0.84479,116.92,-0.07491,-0.95043,0.30179,113.9,0.89436,0.069815,0.44187,126.48
    10038 
    10039 > view matrix models
    10040 > #35,0.84908,-0.51887,-0.099238,120.01,0.43126,0.7893,-0.43705,123.08,0.3051,0.3283,0.89394,124.61
    10041 
    10042 > mmaker #35 to #38
    10043 
    10044 Parameters 
    10045 --- 
    10046 Chain pairing | bb 
    10047 Alignment algorithm | Needleman-Wunsch 
    10048 Similarity matrix | BLOSUM-62 
    10049 SS fraction | 0.3 
    10050 Gap open (HH/SS/other) | 18/18/6 
    10051 Gap extend | 1 
    10052 SS matrix |  |  | H | S | O 
    10053 ---|---|---|--- 
    10054 H | 6 | -9 | -6 
    10055 S |  | 6 | -6 
    10056 O |  |  | 4 
    10057 Iteration cutoff | 2 
    10058  
    10059 Matchmaker 9hud, chain A (#38) with 8pi2, chain A (#35), sequence alignment
    10060 score = 1753.4 
    10061 RMSD between 220 pruned atom pairs is 0.913 angstroms; (across all 331 pairs:
    10062 6.169) 
    10063  
    10064 
    10065 > hide #!38 models
    10066 
    10067 > fitmap #35 inMap #44
    10068 
    10069 Fit molecule 8pi2 (#35) to map cryosparc_P483_J81_008_volume_map.mrc z flip
    10070 (#44) using 5953 atoms 
    10071 average map value = 0.03426, steps = 124 
    10072 shifted from previous position = 5.39 
    10073 rotated from previous position = 16.8 degrees 
    10074 atoms outside contour = 3776, contour level = 0.040419 
    10075  
    10076 Position of 8pi2 (#35) relative to cryosparc_P483_J81_008_volume_map.mrc z
    10077 flip (#44) coordinates: 
    10078 Matrix rotation and translation 
    10079 -0.91986475 0.28876257 0.26545250 167.24012801 
    10080 0.39170890 0.64122785 0.65984164 130.22015692 
    10081 0.02032204 0.71094517 -0.70295376 131.41006954 
    10082 Axis 0.18875717 0.90541952 0.38024495 
    10083 Axis point 72.13306632 0.00000000 33.49476567 
    10084 Rotation angle (degrees) 172.22007439 
    10085 Shift along axis 199.43966055 
    10086  
    10087 
    10088 > mmaker #35 to #38
    10089 
    10090 Parameters 
    10091 --- 
    10092 Chain pairing | bb 
    10093 Alignment algorithm | Needleman-Wunsch 
    10094 Similarity matrix | BLOSUM-62 
    10095 SS fraction | 0.3 
    10096 Gap open (HH/SS/other) | 18/18/6 
    10097 Gap extend | 1 
    10098 SS matrix |  |  | H | S | O 
    10099 ---|---|---|--- 
    10100 H | 6 | -9 | -6 
    10101 S |  | 6 | -6 
    10102 O |  |  | 4 
    10103 Iteration cutoff | 2 
    10104  
    10105 Matchmaker 9hud, chain A (#38) with 8pi2, chain A (#35), sequence alignment
    10106 score = 1753.4 
    10107 RMSD between 220 pruned atom pairs is 0.913 angstroms; (across all 331 pairs:
    10108 6.169) 
    10109  
    10110 
    10111 > select subtract #35
    10112 
    10113 Nothing selected 
    10114 
    10115 > hide #!44 models
    10116 
    10117 > show #!44 models
    10118 
    10119 > hide #35 models
    10120 
    10121 > show #!38 models
    10122 
    10123 > show #!37 models
    10124 
    10125 > mmaker #37 to #38
    10126 
    10127 Parameters 
    10128 --- 
    10129 Chain pairing | bb 
    10130 Alignment algorithm | Needleman-Wunsch 
    10131 Similarity matrix | BLOSUM-62 
    10132 SS fraction | 0.3 
    10133 Gap open (HH/SS/other) | 18/18/6 
    10134 Gap extend | 1 
    10135 SS matrix |  |  | H | S | O 
    10136 ---|---|---|--- 
    10137 H | 6 | -9 | -6 
    10138 S |  | 6 | -6 
    10139 O |  |  | 4 
    10140 Iteration cutoff | 2 
    10141  
    10142 Matchmaker 9hud, chain A (#38) with 1ezx, chain A (#37), sequence alignment
    10143 score = 1674.4 
    10144 RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
    10145 0.519) 
    10146  
    10147 
    10148 > hide #!38 models
    10149 
    10150 > show #!38 models
    10151 
    10152 > hide #!37 models
    10153 
    10154 > hide #!38 models
    10155 
    10156 > hide #!44 models
    10157 
    10158 > show #!47 models
    10159 
    10160 > show #!38 models
    10161 
    10162 > select add #38
    10163 
    10164 6282 atoms, 6138 bonds, 1077 residues, 1 model selected 
    10165 
    10166 > view matrix models
    10167 > #38,0.12454,-0.84591,0.51858,160.56,-0.95063,-0.25145,-0.18186,310.42,0.28423,-0.47033,-0.83547,125.18
    10168 
    10169 > view matrix models
    10170 > #38,0.67023,0.035917,0.74129,37.629,-0.48282,-0.73746,0.47227,246.9,0.56363,-0.67443,-0.47692,84.334
    10171 
    10172 > view matrix models
    10173 > #38,0.67023,0.035917,0.74129,35.095,-0.48282,-0.73746,0.47227,252.87,0.56363,-0.67443,-0.47692,70.069
    10174 
    10175 > view matrix models
    10176 > #38,0.72811,0.043332,0.68409,26.371,-0.55319,-0.55218,0.62376,255,0.40477,-0.8326,-0.37807,100.03
    10177 
    10178 > view matrix models
    10179 > #38,0.72811,0.043332,0.68409,24.921,-0.55319,-0.55218,0.62376,251.59,0.40477,-0.8326,-0.37807,100.94
    10180 
    10181 > fitmap #38 inMap #47
    10182 
    10183 Fit molecule 9hud (#38) to map cryosparc_P483_J72_006_volume_map.mrc z flip
    10184 (#47) using 6282 atoms 
    10185 average map value = 0.06343, steps = 212 
    10186 shifted from previous position = 1.3 
    10187 rotated from previous position = 22.3 degrees 
    10188 atoms outside contour = 2481, contour level = 0.048075 
    10189  
    10190 Position of 9hud (#38) relative to cryosparc_P483_J72_006_volume_map.mrc z
    10191 flip (#47) coordinates: 
    10192 Matrix rotation and translation 
    10193 0.48048529 0.06576118 0.87453379 60.39061577 
    10194 -0.56539285 -0.73906673 0.36621209 262.77340318 
    10195 0.67042137 -0.67041468 -0.31792978 52.06026777 
    10196 Axis -0.84230945 0.16585123 -0.51284322 
    10197 Axis point 0.00000000 144.40605826 -47.18056764 
    10198 Rotation angle (degrees) 142.02279334 
    10199 Shift along axis -33.98504950 
    10200  
    10201 
    10202 > select subtract #38
    10203 
    10204 Nothing selected 
    10205 
    10206 > volume #47 level 0.05522
    10207 
    10208 > volume #47 level 0.04807
    10209 
    10210 > show #!37 models
    10211 
    10212 > mmaker #37 to #38
    10213 
    10214 Parameters 
    10215 --- 
    10216 Chain pairing | bb 
    10217 Alignment algorithm | Needleman-Wunsch 
    10218 Similarity matrix | BLOSUM-62 
    10219 SS fraction | 0.3 
    10220 Gap open (HH/SS/other) | 18/18/6 
    10221 Gap extend | 1 
    10222 SS matrix |  |  | H | S | O 
    10223 ---|---|---|--- 
    10224 H | 6 | -9 | -6 
    10225 S |  | 6 | -6 
    10226 O |  |  | 4 
    10227 Iteration cutoff | 2 
    10228  
    10229 Matchmaker 9hud, chain A (#38) with 1ezx, chain A (#37), sequence alignment
    10230 score = 1674.4 
    10231 RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
    10232 0.519) 
    10233  
    10234 
    10235 > volume #47 level 0.0495
    10236 
    10237 > volume #47 level 0.01949
    10238 
    10239 > volume #47 level 0.02878
    10240 
    10241 > volume gaussian #47 sDev 2
    10242 
    10243 Opened cryosparc_P483_J72_006_volume_map.mrc z flip gaussian as #48, grid size
    10244 400,400,400, pixel 0.723, shown at step 1, values float32 
    10245 
    10246 > volume #48 level 0.002656
    10247 
    10248 > volume #48 level 0.001381
    10249 
    10250 > surface dust #48 size 7.23
    10251 
    10252 > show #!44 models
    10253 
    10254 > hide #!38 models
    10255 
    10256 > hide #!37 models
    10257 
    10258 > volume gaussian #44 sDev 2
    10259 
    10260 Opened cryosparc_P483_J81_008_volume_map.mrc z flip gaussian as #49, grid size
    10261 400,400,400, pixel 0.723, shown at step 1, values float32 
    10262 
    10263 > surface dust #49 size 7.23
    10264 
    10265 > volume #49 level 0.01018
    10266 
    10267 Cell requested for row 3 is out of bounds for table with 3 rows! Resizing
    10268 table model. 
    10269 
    10270 > save "/Users/amy/Desktop/SPA AAT_HNE/9C5_Fab_AAT_HNE/For mask
    10271 > generation/hne_J81localrefine.mrc" models #49
    10272 
    10273 > volume #49 level 0.01049
    10274 
    10275 > open /Users/amy/Downloads/cryosparc_P483_J82_005_volume_map.mrc
    10276 
    10277 Opened cryosparc_P483_J82_005_volume_map.mrc as #50, grid size 400,400,400,
    10278 pixel 0.723, shown at level 0.00546, step 2, values float32 
    10279 
    10280 > volume #50 level 0.0526
    10281 
    10282 > open /Users/amy/Downloads/cryosparc_P483_J90_004_volume_map.mrc
    10283 
    10284 Opened cryosparc_P483_J90_004_volume_map.mrc as #51, grid size 400,400,400,
    10285 pixel 0.723, shown at level 0.00654, step 2, values float32 
    10286 
    10287 > surface dust #51 size 7.23
    10288 
    10289 > volume #51 level 0.03836
    10290 
    10291 > open /Users/amy/Downloads/cryosparc_P483_J89_003_volume_map.mrc
    10292 
    10293 Opened cryosparc_P483_J89_003_volume_map.mrc as #52, grid size 400,400,400,
    10294 pixel 0.723, shown at level 0.00398, step 2, values float32 
    10295 
    10296 > volume #52 level 0.01728
    10297 
    10298 > volume #52 level 0.004928
    10299 
    10300 > hide #!52 models
    10301 
    10302 > show #!44 models
    10303 
    10304 > open /Users/amy/Downloads/cryosparc_P483_J93_005_volume_map.mrc
    10305 
    10306 Opened cryosparc_P483_J93_005_volume_map.mrc as #53, grid size 400,400,400,
    10307 pixel 0.723, shown at level 0.00624, step 2, values float32 
    10308 
    10309 > volume #53 level 0.03597
    10310 
    10311 > open /Users/amy/Downloads/cryosparc_P483_J96_002_volume_map.mrc
    10312 
    10313 Opened cryosparc_P483_J96_002_volume_map.mrc as #54, grid size 400,400,400,
    10314 pixel 0.723, shown at level 0.00203, step 2, values float32 
    10315 
    10316 > volume #54 level 0.01882
    10317 
    10318 > volume #54 level 0.01406
    10319 
    10320 > open /Users/amy/Downloads/cryosparc_P483_J99_003_volume_map.mrc
    10321 
    10322 Opened cryosparc_P483_J99_003_volume_map.mrc as #55, grid size 400,400,400,
    10323 pixel 0.723, shown at level 0.00233, step 2, values float32 
    10324 
    10325 > surface dust #55 size 7.23
    10326 
    10327 > volume #55 level 0.011
    10328 
    10329 > ui mousemode right "tape measure"
    10330 
    10331 > marker segment #56 position 137.9,161.4,84.92 toPosition 127.8,150.1,133.2
    10332 > color yellow radius 0.1807 label 50.59 labelHeight 5.059 labelColor yellow
    10333 
    10334 > marker segment #56 position 137.6,155.7,84.27 toPosition 148.8,133.1,193.5
    10335 > color yellow radius 0.1807 label 112.1 labelHeight 11.21 labelColor yellow
    10336 
    10337 > marker segment #56 position 139,177,192 toPosition 130,91.37,164 color
    10338 > yellow radius 0.1807 label 90.59 labelHeight 9.059 labelColor yellow
    10339 
    10340 > close #56
    10341 
    10342 > transparency #55 50
    10343 
    10344 > show #!38 models
    10345 
    10346 > select add #38
    10347 
    10348 6282 atoms, 6138 bonds, 1077 residues, 1 model selected 
    10349 
    10350 > select subtract #38
    10351 
    10352 Nothing selected 
    10353 
    10354 > volume flip #55 axis z
    10355 
    10356 Opened cryosparc_P483_J99_003_volume_map.mrc z flip as #56, grid size
    10357 400,400,400, pixel 0.723, shown at step 1, values float32 
    10358 
    10359 > transparency #56 50
    10360 
    10361 > select add #38
    10362 
    10363 6282 atoms, 6138 bonds, 1077 residues, 1 model selected 
    10364 
    10365 > ui mousemode right "translate selected models"
    10366 
    10367 > view matrix models
    10368 > #38,0.48049,0.065761,0.87453,61.743,-0.56539,-0.73907,0.36621,262.06,0.67042,-0.67041,-0.31793,59.233
    10369 
    10370 > view matrix models
    10371 > #38,0.61181,-0.23623,0.75491,54.055,-0.64298,-0.70439,0.30068,273.82,0.46072,-0.66935,-0.58285,95.671
    10372 
    10373 > view matrix models
    10374 > #38,0.50154,0.032674,0.86452,59.807,-0.035285,-0.99768,0.058177,191.99,0.86441,-0.059683,-0.49923,7.3804
    10375 
    10376 > view matrix models
    10377 > #38,0.50154,0.032674,0.86452,52.131,-0.035285,-0.99768,0.058177,176.02,0.86441,-0.059683,-0.49923,12.857
    10378 
    10379 > view matrix models
    10380 > #38,0.35345,0.1643,0.92091,69.799,-0.028974,-0.98206,0.18633,172.82,0.93501,-0.09254,-0.34235,0.99177
    10381 
    10382 > view matrix models
    10383 > #38,0.66671,0.39133,0.63431,15.122,-0.22913,-0.70224,0.67407,187.64,0.70922,-0.59475,-0.37853,56.427
    10384 
    10385 > view matrix models
    10386 > #38,0.66671,0.39133,0.63431,20.436,-0.22913,-0.70224,0.67407,208.21,0.70922,-0.59475,-0.37853,56.608
    10387 
    10388 > view matrix models
    10389 > #38,0.81008,0.3223,0.48979,2.2149,-0.16331,-0.67827,0.71643,196.35,0.56311,-0.66036,-0.49682,83.714
    10390 
    10391 > fitmap #38 inMap #56
    10392 
    10393 Fit molecule 9hud (#38) to map cryosparc_P483_J99_003_volume_map.mrc z flip
    10394 (#56) using 6282 atoms 
    10395 average map value = 0.03831, steps = 132 
    10396 shifted from previous position = 1.92 
    10397 rotated from previous position = 15.8 degrees 
    10398 atoms outside contour = 568, contour level = 0.011004 
    10399  
    10400 Position of 9hud (#38) relative to cryosparc_P483_J99_003_volume_map.mrc z
    10401 flip (#56) coordinates: 
    10402 Matrix rotation and translation 
    10403 0.71987433 0.56582857 0.40201864 5.33395219 
    10404 -0.00113467 -0.57823035 0.81587277 166.00801694 
    10405 0.69410350 -0.58778202 -0.41561115 58.96322716 
    10406 Axis -0.91042678 -0.18944963 -0.36773893 
    10407 Axis point 0.00000000 92.18313505 -11.68775993 
    10408 Rotation angle (degrees) 129.56725904 
    10409 Shift along axis -57.98940372 
    10410  
    10411 
    10412 > select subtract #38
    10413 
    10414 Nothing selected 
    10415 
    10416 > show #!37 models
    10417 
    10418 > mmaker #38 to #37
    10419 
    10420 Parameters 
    10421 --- 
    10422 Chain pairing | bb 
    10423 Alignment algorithm | Needleman-Wunsch 
    10424 Similarity matrix | BLOSUM-62 
    10425 SS fraction | 0.3 
    10426 Gap open (HH/SS/other) | 18/18/6 
    10427 Gap extend | 1 
    10428 SS matrix |  |  | H | S | O 
    10429 ---|---|---|--- 
    10430 H | 6 | -9 | -6 
    10431 S |  | 6 | -6 
    10432 O |  |  | 4 
    10433 Iteration cutoff | 2 
    10434  
    10435 Matchmaker 1ezx, chain A (#37) with 9hud, chain A (#38), sequence alignment
    10436 score = 1674.4 
    10437 RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
    10438 0.519) 
    10439  
    10440 
    10441 > select add #38
    10442 
    10443 6282 atoms, 6138 bonds, 1077 residues, 1 model selected 
    10444 
    10445 > view matrix models
    10446 > #38,0.48049,0.065761,0.87453,62.141,-0.56539,-0.73907,0.36621,264.84,0.67042,-0.67041,-0.31793,61.109
    10447 
    10448 > view matrix models
    10449 > #38,0.48049,0.065761,0.87453,61.431,-0.56539,-0.73907,0.36621,264.59,0.67042,-0.67041,-0.31793,64.599
    10450 
    10451 > fitmap #38 inMap #56
    10452 
    10453 Fit molecule 9hud (#38) to map cryosparc_P483_J99_003_volume_map.mrc z flip
    10454 (#56) using 6282 atoms 
    10455 average map value = 0.03831, steps = 216 
    10456 shifted from previous position = 1.65 
    10457 rotated from previous position = 43.4 degrees 
    10458 atoms outside contour = 569, contour level = 0.011004 
    10459  
    10460 Position of 9hud (#38) relative to cryosparc_P483_J99_003_volume_map.mrc z
    10461 flip (#56) coordinates: 
    10462 Matrix rotation and translation 
    10463 0.71990687 0.56573446 0.40209280 5.32940054 
    10464 -0.00119592 -0.57831351 0.81581374 166.01905071 
    10465 0.69406964 -0.58779078 -0.41565530 58.96739860 
    10466 Axis -0.91044042 -0.18938918 -0.36773629 
    10467 Axis point 0.00000000 92.19051844 -11.68521420 
    10468 Rotation angle (degrees) 129.57078110 
    10469 Shift along axis -57.97876700 
    10470  
    10471 
    10472 > select subtract #38
    10473 
    10474 Nothing selected 
    10475 
    10476 > show #!39 models
    10477 
    10478 > hide #!39 models
    10479 
    10480 > show #!37 models
    10481 
    10482 > mmaker #37 to #38
    10483 
    10484 Parameters 
    10485 --- 
    10486 Chain pairing | bb 
    10487 Alignment algorithm | Needleman-Wunsch 
    10488 Similarity matrix | BLOSUM-62 
    10489 SS fraction | 0.3 
    10490 Gap open (HH/SS/other) | 18/18/6 
    10491 Gap extend | 1 
    10492 SS matrix |  |  | H | S | O 
    10493 ---|---|---|--- 
    10494 H | 6 | -9 | -6 
    10495 S |  | 6 | -6 
    10496 O |  |  | 4 
    10497 Iteration cutoff | 2 
    10498  
    10499 Matchmaker 9hud, chain A (#38) with 1ezx, chain A (#37), sequence alignment
    10500 score = 1674.4 
    10501 RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
    10502 0.519) 
    10503  
    10504 
    10505 > volume #56 level 0.007481
    10506 
    10507 > show #!42 models
    10508 
    10509 > hide #!42 models
    10510 
    10511 > combine #37 close false
    10512 
    10513 > hide #!57.1 models
    10514 
    10515 > hide #!37 models
    10516 
    10517 > show #!37 models
    10518 
    10519 > hide #!38 models
    10520 
    10521 > hide #!37 models
    10522 
    10523 > select #57/A
    10524 
    10525 2686 atoms, 2674 bonds, 398 residues, 1 model selected 
    10526 
    10527 > delete #57/A
    10528 
    10529 > select #57/B
    10530 
    10531 289 atoms, 294 bonds, 39 residues, 1 model selected 
    10532 
    10533 > delete #57/B
    10534 
    10535 > show #!37 models
    10536 
    10537 > show #!38 models
    10538 
    10539 > fitmap #57 inMap #56
    10540 
    10541 Fit molecule copy of 1ezx (#57) to map cryosparc_P483_J99_003_volume_map.mrc z
    10542 flip (#56) using 1009 atoms 
    10543 average map value = 0.01739, steps = 256 
    10544 shifted from previous position = 13.8 
    10545 rotated from previous position = 53.3 degrees 
    10546 atoms outside contour = 290, contour level = 0.0074814 
    10547  
    10548 Position of copy of 1ezx (#57) relative to
    10549 cryosparc_P483_J99_003_volume_map.mrc z flip (#56) coordinates: 
    10550 Matrix rotation and translation 
    10551 0.75779051 -0.13010105 0.63939601 57.96350024 
    10552 0.04649693 0.98819623 0.14596657 79.83854912 
    10553 -0.65083914 -0.08088213 0.75489502 138.89870189 
    10554 Axis -0.17161128 0.97606430 0.13359657 
    10555 Axis point 208.75729766 0.00000000 -34.80031847 
    10556 Rotation angle (degrees) 41.37141702 
    10557 Shift along axis 86.53675668 
    10558  
    10559 
    10560 > hide #!38 models
    10561 
    10562 > hide #!37 models
    10563 
    10564 > show #!37 models
    10565 
    10566 > hide #!37 models
    10567 
    10568 > show #!38 models
    10569 
    10570 > show #!47 models
    10571 
    10572 > hide #!56 models
    10573 
    10574 > hide #!57 models
    10575 
    10576 > hide #!47 models
    10577 
    10578 > open /Users/amy/Downloads/cryosparc_P483_J103_003_volume_map.mrc
    10579 
    10580 Opened cryosparc_P483_J103_003_volume_map.mrc as #58, grid size 400,400,400,
    10581 pixel 0.723, shown at level 0.00468, step 2, values float32 
    10582 
    10583 > surface dust #58 size 7.23
    10584 
    10585 > volume #58 level 0.01873
    10586 
    10587 > transparency #58 50
    10588 
    10589 > select add #38
    10590 
    10591 6282 atoms, 6138 bonds, 1077 residues, 1 model selected 
    10592 
    10593 > view matrix models
    10594 > #38,0.79207,-0.60151,-0.10399,45.033,0.096519,-0.044809,0.99432,127.86,-0.60276,-0.79761,0.022565,266.66
    10595 
    10596 > view matrix models
    10597 > #38,-0.14652,-0.85779,0.49268,195.86,0.54759,0.34445,0.76256,44.475,-0.82382,0.38152,0.41925,251.42
    10598 
    10599 > view matrix models
    10600 > #38,-0.14652,-0.85779,0.49268,198.48,0.54759,0.34445,0.76256,48.533,-0.82382,0.38152,0.41925,263.76
    10601 
    10602 > view matrix models
    10603 > #38,-0.14652,-0.85779,0.49268,194.13,0.54759,0.34445,0.76256,44.618,-0.82382,0.38152,0.41925,261.43
    10604 
    10605 > view matrix models
    10606 > #38,-0.10749,-0.76087,0.63994,182.4,0.68336,0.41097,0.60342,22.58,-0.72212,0.50217,0.47577,240.01
    10607 
    10608 > volume flip #58 axis z
    10609 
    10610 Opened cryosparc_P483_J103_003_volume_map.mrc z flip as #59, grid size
    10611 400,400,400, pixel 0.723, shown at step 1, values float32 
    10612 
    10613 > view matrix models
    10614 > #38,0.47388,0.52578,0.70639,40.242,-0.49413,-0.50521,0.70753,242.68,0.72888,-0.68433,0.020401,61.728
    10615 
    10616 > view matrix models
    10617 > #38,0.47388,0.52578,0.70639,38.39,-0.49413,-0.50521,0.70753,241.35,0.72888,-0.68433,0.020401,61.925
    10618 
    10619 > view matrix models
    10620 > #38,0.62595,0.63777,0.44881,13.26,-0.13423,-0.47881,0.8676,181.41,0.76822,-0.60332,-0.2141,55.525
    10621 
    10622 > view matrix models
    10623 > #38,0.62595,0.63777,0.44881,16.43,-0.13423,-0.47881,0.8676,181.76,0.76822,-0.60332,-0.2141,47.364
    10624 
    10625 > view matrix models
    10626 > #38,0.62595,0.63777,0.44881,20.934,-0.13423,-0.47881,0.8676,183.19,0.76822,-0.60332,-0.2141,39.547
    10627 
    10628 > fitmap #38 inMap #59
    10629 
    10630 Fit molecule 9hud (#38) to map cryosparc_P483_J103_003_volume_map.mrc z flip
    10631 (#59) using 6282 atoms 
    10632 average map value = 0.04126, steps = 168 
    10633 shifted from previous position = 5.69 
    10634 rotated from previous position = 19.5 degrees 
    10635 atoms outside contour = 1297, contour level = 0.018732 
    10636  
    10637 Position of 9hud (#38) relative to cryosparc_P483_J103_003_volume_map.mrc z
    10638 flip (#59) coordinates: 
    10639 Matrix rotation and translation 
    10640 0.70777878 0.35342642 0.61166899 13.30926304 
    10641 -0.29975381 -0.63379066 0.71306173 215.20863100 
    10642 0.63968496 -0.68804008 -0.34264266 66.23170214 
    10643 Axis -0.90619968 -0.01812007 -0.42246160 
    10644 Axis point 0.00000000 119.91219967 -25.94584346 
    10645 Rotation angle (degrees) 129.37010768 
    10646 Shift along axis -43.94079555 
    10647  
    10648 
    10649 > mmaker #37 to #38
    10650 
    10651 Parameters 
    10652 --- 
    10653 Chain pairing | bb 
    10654 Alignment algorithm | Needleman-Wunsch 
    10655 Similarity matrix | BLOSUM-62 
    10656 SS fraction | 0.3 
    10657 Gap open (HH/SS/other) | 18/18/6 
    10658 Gap extend | 1 
    10659 SS matrix |  |  | H | S | O 
    10660 ---|---|---|--- 
    10661 H | 6 | -9 | -6 
    10662 S |  | 6 | -6 
    10663 O |  |  | 4 
    10664 Iteration cutoff | 2 
    10665  
    10666 Matchmaker 9hud, chain A (#38) with 1ezx, chain A (#37), sequence alignment
    10667 score = 1674.4 
    10668 RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
    10669 0.519) 
    10670  
    10671 
    10672 > select subtract #38
    10673 
    10674 Nothing selected 
    10675 
    10676 > show #!37 models
    10677 
    10678 > show #!57 models
    10679 
    10680 > mmaker #57 to #37
    10681 
    10682 Parameters 
    10683 --- 
    10684 Chain pairing | bb 
    10685 Alignment algorithm | Needleman-Wunsch 
    10686 Similarity matrix | BLOSUM-62 
    10687 SS fraction | 0.3 
    10688 Gap open (HH/SS/other) | 18/18/6 
    10689 Gap extend | 1 
    10690 SS matrix |  |  | H | S | O 
    10691 ---|---|---|--- 
    10692 H | 6 | -9 | -6 
    10693 S |  | 6 | -6 
    10694 O |  |  | 4 
    10695 Iteration cutoff | 2 
    10696  
    10697 Matchmaker 1ezx, chain C (#37) with copy of 1ezx, chain C (#57), sequence
    10698 alignment score = 1096 
    10699 RMSD between 140 pruned atom pairs is 0.000 angstroms; (across all 140 pairs:
    10700 0.000) 
    10701  
    10702 
    10703 > hide #!37 models
    10704 
    10705 > select #57/A
    10706 
    10707 Nothing selected 
    10708 
    10709 > select #57/C
    10710 
    10711 1009 atoms, 1014 bonds, 5 pseudobonds, 155 residues, 2 models selected 
    10712 
    10713 > select #57/C: 202
    10714 
    10715 6 atoms, 5 bonds, 1 residue, 1 model selected 
    10716 
    10717 > show #!37 models
    10718 
    10719 > ui tool show "Show Sequence Viewer"
    10720 
    10721 > select #57/C: 197
    10722 
    10723 4 atoms, 3 bonds, 1 residue, 1 model selected 
    10724 
    10725 > select #57/C: 195
    10726 
    10727 6 atoms, 5 bonds, 1 residue, 1 model selected 
    10728 
    10729 > show sel atoms
    10730 
    10731 > select add #57
    10732 
    10733 1009 atoms, 1014 bonds, 5 pseudobonds, 155 residues, 3 models selected 
    10734 
    10735 > select subtract #57
    10736 
    10737 Nothing selected 
    10738 
    10739 > hide #!37 models
    10740 
    10741 > select add #57
    10742 
    10743 1009 atoms, 1014 bonds, 5 pseudobonds, 155 residues, 3 models selected 
    10744 
    10745 > fitmap #57 inMap #59
    10746 
    10747 Fit molecule copy of 1ezx (#57) to map cryosparc_P483_J103_003_volume_map.mrc
    10748 z flip (#59) using 1009 atoms 
    10749 average map value = 0.03856, steps = 332 
    10750 shifted from previous position = 30.6 
    10751 rotated from previous position = 62.2 degrees 
    10752 atoms outside contour = 286, contour level = 0.018732 
    10753  
    10754 Position of copy of 1ezx (#57) relative to
    10755 cryosparc_P483_J103_003_volume_map.mrc z flip (#59) coordinates: 
    10756 Matrix rotation and translation 
    10757 0.57046373 0.04988227 0.81980662 55.55575937 
    10758 -0.78184304 0.33872670 0.52343642 167.07972587 
    10759 -0.25158019 -0.93956159 0.23223140 158.05911115 
    10760 Axis -0.73333465 0.53703769 -0.41690623 
    10761 Axis point 0.00000000 214.40037540 -65.68721584 
    10762 Rotation angle (degrees) 85.94517935 
    10763 Shift along axis -16.90868204 
    10764  
    10765 
    10766 > view matrix models
    10767 > #57,0.57046,0.049882,0.81981,53.391,-0.78184,0.33873,0.52344,146.96,-0.25158,-0.93956,0.23223,152.39
    10768 
    10769 > view matrix models
    10770 > #57,0.57046,0.049882,0.81981,51.548,-0.78184,0.33873,0.52344,139.36,-0.25158,-0.93956,0.23223,150.37
    10771 
    10772 > view matrix models
    10773 > #57,0.60961,0.26554,0.74691,47.106,-0.77216,0.41204,0.48373,138.91,-0.17931,-0.87162,0.45622,131.48
    10774 
    10775 > view matrix models
    10776 > #57,0.60961,0.26554,0.74691,46.208,-0.77216,0.41204,0.48373,140.83,-0.17931,-0.87162,0.45622,128.81
    10777 
    10778 > view matrix models
    10779 > #57,0.49766,0.67771,0.54133,56.234,-0.85191,0.49924,0.15817,161.92,-0.16306,-0.53988,0.8258,100.9
    10780 
    10781 > view matrix models
    10782 > #57,0.49766,0.67771,0.54133,55.941,-0.85191,0.49924,0.15817,159.37,-0.16306,-0.53988,0.8258,99.317
    10783 
    10784 > view matrix models
    10785 > #57,0.83968,0.36634,0.40093,42.637,-0.49094,0.82767,0.27193,116.69,-0.23222,-0.42516,0.87482,99.752
    10786 
    10787 > hide #!57 models
    10788 
    10789 > select subtract #57
    10790 
    10791 Nothing selected 
    10792 
    10793 > hide #!59 models
    10794 
    10795 > show #!47 models
    10796 
    10797 > fitmap #38 inMap #47
    10798 
    10799 Fit molecule 9hud (#38) to map cryosparc_P483_J72_006_volume_map.mrc z flip
    10800 (#47) using 6282 atoms 
    10801 average map value = 0.06343, steps = 180 
    10802 shifted from previous position = 8.63 
    10803 rotated from previous position = 26.1 degrees 
    10804 atoms outside contour = 1606, contour level = 0.028781 
    10805  
    10806 Position of 9hud (#38) relative to cryosparc_P483_J72_006_volume_map.mrc z
    10807 flip (#47) coordinates: 
    10808 Matrix rotation and translation 
    10809 0.48062832 0.06570846 0.87445915 60.38102135 
    10810 -0.56537857 -0.73904318 0.36628165 262.76806751 
    10811 0.67033088 -0.67044580 -0.31805493 52.08064169 
    10812 Axis -0.84235493 0.16585696 -0.51276666 
    10813 Axis point 0.00000000 144.40697546 -47.16273001 
    10814 Rotation angle (degrees) 142.02086420 
    10815 Shift along axis -33.98555515 
    10816  
    10817 
    10818 > show #35 models
    10819 
    10820 > mmaker #35 to #38
    10821 
    10822 Parameters 
    10823 --- 
    10824 Chain pairing | bb 
    10825 Alignment algorithm | Needleman-Wunsch 
    10826 Similarity matrix | BLOSUM-62 
    10827 SS fraction | 0.3 
    10828 Gap open (HH/SS/other) | 18/18/6 
    10829 Gap extend | 1 
    10830 SS matrix |  |  | H | S | O 
    10831 ---|---|---|--- 
    10832 H | 6 | -9 | -6 
    10833 S |  | 6 | -6 
    10834 O |  |  | 4 
    10835 Iteration cutoff | 2 
    10836  
    10837 Matchmaker 9hud, chain A (#38) with 8pi2, chain A (#35), sequence alignment
    10838 score = 1753.4 
    10839 RMSD between 220 pruned atom pairs is 0.913 angstroms; (across all 331 pairs:
    10840 6.169) 
    10841  
    10842 
    10843 > hide #!38 models
    10844 
    10845 > show #!38 models
    10846 
    10847 > hide #35 models
    10848 
    10849 > show #35 models
    10850 
    10851 > hide #35 models
    10852 
    10853 > show #35 models
    10854 
    10855 > hide #35 models
    10856 
    10857 > hide #!38 models
    10858 
    10859 > hide #!47 models
    10860 
    10861 > show #!59 models
    10862 
    10863 > open cryosparc_P483_J70_00018_volume_series vseries true
    10864 
    10865 'cryosparc_P483_J70_00018_volume_series' has no suffix 
    10866 
    10867 > open
    10868 > /Users/amy/Desktop/cryosparc_P483_J70_00018_volume_series/J70_class_00_00018_volume.mrc
    10869 > /Users/amy/Desktop/cryosparc_P483_J70_00018_volume_series/J70_class_01_00018_volume.mrc
    10870 > /Users/amy/Desktop/cryosparc_P483_J70_00018_volume_series/J70_class_02_00018_volume.mrc
    10871 > /Users/amy/Desktop/cryosparc_P483_J70_00018_volume_series/J70_class_03_00018_volume.mrc
    10872 > /Users/amy/Desktop/cryosparc_P483_J70_00018_volume_series/J70_class_04_00018_volume.mrc
    10873 > /Users/amy/Desktop/cryosparc_P483_J70_00018_volume_series/J70_class_05_00018_volume.mrc
    10874 > /Users/amy/Desktop/cryosparc_P483_J70_00018_volume_series/J70_class_06_00018_volume.mrc
    10875 > /Users/amy/Desktop/cryosparc_P483_J70_00018_volume_series/J70_class_07_00018_volume.mrc
    10876 > /Users/amy/Desktop/cryosparc_P483_J70_00018_volume_series/J70_class_08_00018_volume.mrc
    10877 > /Users/amy/Desktop/cryosparc_P483_J70_00018_volume_series/J70_class_09_00018_volume.mrc
    10878 
    10879 Opened J70_class_00_00018_volume.mrc as #60.1, grid size 64,64,64, pixel 4.52,
    10880 shown at level 0.113, step 1, values float32 
    10881 Opened J70_class_01_00018_volume.mrc as #60.2, grid size 64,64,64, pixel 4.52,
    10882 shown at level 0.104, step 1, values float32 
    10883 Opened J70_class_02_00018_volume.mrc as #60.3, grid size 64,64,64, pixel 4.52,
    10884 shown at level 0.109, step 1, values float32 
    10885 Opened J70_class_03_00018_volume.mrc as #60.4, grid size 64,64,64, pixel 4.52,
    10886 shown at level 0.116, step 1, values float32 
    10887 Opened J70_class_04_00018_volume.mrc as #60.5, grid size 64,64,64, pixel 4.52,
    10888 shown at level 0.106, step 1, values float32 
    10889 Opened J70_class_05_00018_volume.mrc as #60.6, grid size 64,64,64, pixel 4.52,
    10890 shown at level 0.106, step 1, values float32 
    10891 Opened J70_class_06_00018_volume.mrc as #60.7, grid size 64,64,64, pixel 4.52,
    10892 shown at level 0.116, step 1, values float32 
    10893 Opened J70_class_07_00018_volume.mrc as #60.8, grid size 64,64,64, pixel 4.52,
    10894 shown at level 0.109, step 1, values float32 
    10895 Opened J70_class_08_00018_volume.mrc as #60.9, grid size 64,64,64, pixel 4.52,
    10896 shown at level 0.106, step 1, values float32 
    10897 Opened J70_class_09_00018_volume.mrc as #60.10, grid size 64,64,64, pixel
    10898 4.52, shown at level 0.113, step 1, values float32 
    10899 
    10900 > hide #!59 models
    10901 
    10902 > surface dust #60.1 size 45.2
    10903 
    10904 > surface dust #60.2 size 45.2
    10905 
    10906 > surface dust #60.3 size 45.2
    10907 
    10908 > surface dust #60.4 size 45.2
    10909 
    10910 > surface dust #60.5 size 45.2
    10911 
    10912 > surface dust #60.6 size 45.2
    10913 
    10914 > surface dust #60.7 size 45.2
    10915 
    10916 > surface dust #60.8 size 45.2
    10917 
    10918 > surface dust #60.9 size 45.2
    10919 
    10920 > surface dust #60.10 size 45.2
    10921 
    10922 > hide #!60.1 models
    10923 
    10924 > hide #!60.2 models
    10925 
    10926 > hide #!60.3 models
    10927 
    10928 > hide #!60.4 models
    10929 
    10930 > hide #!60.5 models
    10931 
    10932 > hide #!60.6 models
    10933 
    10934 > hide #!60.7 models
    10935 
    10936 > hide #!60.8 models
    10937 
    10938 > hide #!60.9 models
    10939 
    10940 > hide #!60.10 models
    10941 
    10942 > show #!60.1 models
    10943 
    10944 > show #!60.2 models
    10945 
    10946 > hide #!60.1 models
    10947 
    10948 > hide #!60.2 models
    10949 
    10950 > show #!60.3 models
    10951 
    10952 > show #!60.2 models
    10953 
    10954 > hide #!60.2 models
    10955 
    10956 > show #!60.4 models
    10957 
    10958 > hide #!60.3 models
    10959 
    10960 > show #!60.5 models
    10961 
    10962 > hide #!60.4 models
    10963 
    10964 > show #!60.6 models
    10965 
    10966 > hide #!60.5 models
    10967 
    10968 > show #!60.7 models
    10969 
    10970 > hide #!60.6 models
    10971 
    10972 > show #!60.8 models
    10973 
    10974 > hide #!60.7 models
    10975 
    10976 > show #!60.9 models
    10977 
    10978 > hide #!60.8 models
    10979 
    10980 > show #!60.10 models
    10981 
    10982 > hide #!60.9 models
    10983 
    10984 > hide #!60 target m
    10985 
    10986 [Repeated 1 time(s)]
    10987 
    10988 > close #60
    10989 
    10990 > open
    10991 > /Users/amy/Downloads/cryosparc_P483_J124_00020_volume_series/J124_class_00_00020_volume.mrc
    10992 > /Users/amy/Downloads/cryosparc_P483_J124_00020_volume_series/J124_class_01_00020_volume.mrc
    10993 > /Users/amy/Downloads/cryosparc_P483_J124_00020_volume_series/J124_class_02_00020_volume.mrc
    10994 > /Users/amy/Downloads/cryosparc_P483_J124_00020_volume_series/J124_class_03_00020_volume.mrc
    10995 > /Users/amy/Downloads/cryosparc_P483_J124_00020_volume_series/J124_class_04_00020_volume.mrc
    10996 > /Users/amy/Downloads/cryosparc_P483_J124_00020_volume_series/J124_class_05_00020_volume.mrc
    10997 > /Users/amy/Downloads/cryosparc_P483_J124_00020_volume_series/J124_class_06_00020_volume.mrc
    10998 > /Users/amy/Downloads/cryosparc_P483_J124_00020_volume_series/J124_class_07_00020_volume.mrc
    10999 > /Users/amy/Downloads/cryosparc_P483_J124_00020_volume_series/J124_class_08_00020_volume.mrc
    11000 > /Users/amy/Downloads/cryosparc_P483_J124_00020_volume_series/J124_class_09_00020_volume.mrc
    11001 
    11002 Opened J124_class_00_00020_volume.mrc as #60.1, grid size 64,64,64, pixel
    11003 4.52, shown at level 0.058, step 1, values float32 
    11004 Opened J124_class_01_00020_volume.mrc as #60.2, grid size 64,64,64, pixel
    11005 4.52, shown at level 0.0583, step 1, values float32 
    11006 Opened J124_class_02_00020_volume.mrc as #60.3, grid size 64,64,64, pixel
    11007 4.52, shown at level 0.0581, step 1, values float32 
    11008 Opened J124_class_03_00020_volume.mrc as #60.4, grid size 64,64,64, pixel
    11009 4.52, shown at level 0.0576, step 1, values float32 
    11010 Opened J124_class_04_00020_volume.mrc as #60.5, grid size 64,64,64, pixel
    11011 4.52, shown at level 0.0607, step 1, values float32 
    11012 Opened J124_class_05_00020_volume.mrc as #60.6, grid size 64,64,64, pixel
    11013 4.52, shown at level 0.0608, step 1, values float32 
    11014 Opened J124_class_06_00020_volume.mrc as #60.7, grid size 64,64,64, pixel
    11015 4.52, shown at level 0.0585, step 1, values float32 
    11016 Opened J124_class_07_00020_volume.mrc as #60.8, grid size 64,64,64, pixel
    11017 4.52, shown at level 0.0573, step 1, values float32 
    11018 Opened J124_class_08_00020_volume.mrc as #60.9, grid size 64,64,64, pixel
    11019 4.52, shown at level 0.0591, step 1, values float32 
    11020 Opened J124_class_09_00020_volume.mrc as #60.10, grid size 64,64,64, pixel
    11021 4.52, shown at level 0.0602, step 1, values float32 
    11022 
    11023 > surface dust #60.1 size 45.2
    11024 
    11025 > surface dust #60.2 size 45.2
    11026 
    11027 > surface dust #60.3 size 45.2
    11028 
    11029 > surface dust #60.4 size 45.2
    11030 
    11031 > surface dust #60.5 size 45.2
    11032 
    11033 > surface dust #60.6 size 45.2
    11034 
    11035 > surface dust #60.7 size 45.2
    11036 
    11037 > surface dust #60.8 size 45.2
    11038 
    11039 > surface dust #60.9 size 45.2
    11040 
    11041 > surface dust #60.10 size 45.2
    11042 
    11043 > hide #!60 models
    11044 
    11045 > show #!60 models
    11046 
    11047 > hide #!60.1 models
    11048 
    11049 > hide #!60.2 models
    11050 
    11051 > hide #!60.3 models
    11052 
    11053 > hide #!60.4 models
    11054 
    11055 > hide #!60.5 models
    11056 
    11057 > hide #!60.6 models
    11058 
    11059 > hide #!60.7 models
    11060 
    11061 > hide #!60.8 models
    11062 
    11063 > hide #!60.9 models
    11064 
    11065 > hide #!60.10 models
    11066 
    11067 > show #!60.1 models
    11068 
    11069 > show #!60.2 models
    11070 
    11071 > hide #!60.1 models
    11072 
    11073 > show #!60.3 models
    11074 
    11075 > hide #!60.2 models
    11076 
    11077 > show #!60.4 models
    11078 
    11079 > hide #!60.3 models
    11080 
    11081 > show #!60.5 models
    11082 
    11083 > hide #!60.4 models
    11084 
    11085 > show #!60.6 models
    11086 
    11087 > hide #!60.5 models
    11088 
    11089 > show #!60.7 models
    11090 
    11091 > hide #!60.6 models
    11092 
    11093 > show #!60.8 models
    11094 
    11095 > hide #!60.7 models
    11096 
    11097 > show #!60.9 models
    11098 
    11099 > hide #!60.8 models
    11100 
    11101 > show #!60.10 models
    11102 
    11103 > hide #!60.9 models
    11104 
    11105 > hide #!60.10 models
    11106 
    11107 > open /Users/amy/Downloads/cryosparc_P483_J131_007_volume_map.mrc
    11108 
    11109 Opened cryosparc_P483_J131_007_volume_map.mrc as #61, grid size 400,400,400,
    11110 pixel 0.723, shown at level 0.00743, step 2, values float32 
    11111 
    11112 > volume #61 level 0.0358
    11113 
    11114 > transparency #61 50
    11115 
    11116 Cell requested for row 59 is out of bounds for table with 71 rows! Resizing
    11117 table model. 
    11118 
    11119 > close #60
    11120 
    11121 > show #!57 models
    11122 
    11123 > hide #!57 models
    11124 
    11125 > show #!38 models
    11126 
    11127 > select add #38
    11128 
    11129 6282 atoms, 6138 bonds, 1077 residues, 1 model selected 
    11130 
    11131 > view matrix models
    11132 > #38,0.28938,-0.95095,0.1093,139.21,-0.034645,0.10371,0.994,138.64,-0.95659,-0.29143,-0.0029341,290.92
    11133 
    11134 > view matrix models
    11135 > #38,-0.45918,-0.73297,0.50191,244.33,0.66345,0.092766,0.74245,31.785,-0.59075,0.67391,0.44369,190.43
    11136 
    11137 > view matrix models
    11138 > #38,-0.45918,-0.73297,0.50191,252.99,0.66345,0.092766,0.74245,27.709,-0.59075,0.67391,0.44369,215.88
    11139 
    11140 > view matrix models
    11141 > #38,-0.45918,-0.73297,0.50191,245.4,0.66345,0.092766,0.74245,38.203,-0.59075,0.67391,0.44369,230.11
    11142 
    11143 > view matrix models
    11144 > #38,0.7804,-0.38868,0.4898,36.281,-0.57699,-0.14577,0.80364,242.79,-0.24096,-0.90977,-0.33802,245.32
    11145 
    11146 > view matrix models
    11147 > #38,0.24076,-0.088229,0.96657,104.14,-0.7449,-0.65522,0.12574,297.37,0.62222,-0.75027,-0.22348,101.24
    11148 
    11149 > view matrix models
    11150 > #38,0.24076,-0.088229,0.96657,102.45,-0.7449,-0.65522,0.12574,304,0.62222,-0.75027,-0.22348,88.677
    11151 
    11152 > volume flip #61 axis z
    11153 
    11154 Opened cryosparc_P483_J131_007_volume_map.mrc z flip as #60, grid size
    11155 400,400,400, pixel 0.723, shown at step 1, values float32 
    11156 
    11157 > view matrix models
    11158 > #38,0.24076,-0.088229,0.96657,101.92,-0.7449,-0.65522,0.12574,291.88,0.62222,-0.75027,-0.22348,62.156
    11159 
    11160 > view matrix models
    11161 > #38,0.44059,0.20906,0.87303,60.073,-0.32965,-0.86689,0.37395,231.22,0.83499,-0.45255,-0.31303,18.198
    11162 
    11163 > view matrix models
    11164 > #38,0.44059,0.20906,0.87303,63.215,-0.32965,-0.86689,0.37395,234.58,0.83499,-0.45255,-0.31303,17.855
    11165 
    11166 > fitmap #38 inMap #61
    11167 
    11168 Fit molecule 9hud (#38) to map cryosparc_P483_J131_007_volume_map.mrc (#61)
    11169 using 6282 atoms 
    11170 average map value = 0.03062, steps = 228 
    11171 shifted from previous position = 12.1 
    11172 rotated from previous position = 10.2 degrees 
    11173 atoms outside contour = 4063, contour level = 0.0358 
    11174  
    11175 Position of 9hud (#38) relative to cryosparc_P483_J131_007_volume_map.mrc
    11176 (#61) coordinates: 
    11177 Matrix rotation and translation 
    11178 0.47633594 0.18597339 0.85937068 60.19776260 
    11179 -0.46622754 -0.77523836 0.42618936 248.08769926 
    11180 0.74547700 -0.60367159 -0.28256798 49.22817896 
    11181 Axis -0.84117201 0.09302633 -0.53270606 
    11182 Axis point 0.00000000 131.55393794 -45.87457813 
    11183 Rotation angle (degrees) 142.25427000 
    11184 Shift along axis -53.78213480 
    11185  
    11186 
    11187 > fitmap #38 inMap #60
    11188 
    11189 Fit molecule 9hud (#38) to map cryosparc_P483_J131_007_volume_map.mrc z flip
    11190 (#60) using 6282 atoms 
    11191 average map value = 0.07254, steps = 164 
    11192 shifted from previous position = 12.4 
    11193 rotated from previous position = 8.44 degrees 
    11194 atoms outside contour = 1769, contour level = 0.0358 
    11195  
    11196 Position of 9hud (#38) relative to cryosparc_P483_J131_007_volume_map.mrc z
    11197 flip (#60) coordinates: 
    11198 Matrix rotation and translation 
    11199 0.48808324 0.07900810 0.86921371 58.92380628 
    11200 -0.57432345 -0.72083004 0.38801627 263.44883633 
    11201 0.65721178 -0.68859406 -0.30644886 54.98864316 
    11202 Axis -0.84303960 0.16600809 -0.51159120 
    11203 Axis point 0.00000000 145.56353638 -47.97475612 
    11204 Rotation angle (degrees) 140.31778784 
    11205 Shift along axis -34.07217072 
    11206  
    11207 
    11208 > show #!37 models
    11209 
    11210 > mmaker #37 to #38
    11211 
    11212 Parameters 
    11213 --- 
    11214 Chain pairing | bb 
    11215 Alignment algorithm | Needleman-Wunsch 
    11216 Similarity matrix | BLOSUM-62 
    11217 SS fraction | 0.3 
    11218 Gap open (HH/SS/other) | 18/18/6 
    11219 Gap extend | 1 
    11220 SS matrix |  |  | H | S | O 
    11221 ---|---|---|--- 
    11222 H | 6 | -9 | -6 
    11223 S |  | 6 | -6 
    11224 O |  |  | 4 
    11225 Iteration cutoff | 2 
    11226  
    11227 Matchmaker 9hud, chain A (#38) with 1ezx, chain A (#37), sequence alignment
    11228 score = 1674.4 
    11229 RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
    11230 0.519) 
    11231  
    11232 
    11233 > open /Users/amy/Downloads/cryosparc_P483_J128_006_volume_map.mrc
    11234 
    11235 Opened cryosparc_P483_J128_006_volume_map.mrc as #62, grid size 400,400,400,
    11236 pixel 0.723, shown at level 0.00501, step 2, values float32 
    11237 
    11238 > select subtract #38
    11239 
    11240 Nothing selected 
    11241 
    11242 > hide #!38 models
    11243 
    11244 > hide #!37 models
    11245 
    11246 > hide #!60 models
    11247 
    11248 > hide #!62 models
    11249 
    11250 > open /Users/amy/Downloads/cryosparc_P483_J137_003_volume_map.mrc
    11251 
    11252 Opened cryosparc_P483_J137_003_volume_map.mrc as #63, grid size 400,400,400,
    11253 pixel 0.723, shown at level 0.00802, step 2, values float32 
    11254 
    11255 > volume #63 level 0.03618
    11256 
    11257 > volume flip #63 axis z
    11258 
    11259 Opened cryosparc_P483_J137_003_volume_map.mrc z flip as #64, grid size
    11260 400,400,400, pixel 0.723, shown at step 1, values float32 
    11261 
    11262 > transparency #63 50
    11263 
    11264 > transparency #64 50
    11265 
    11266 > show #!38 models
    11267 
    11268 > select add #38
    11269 
    11270 6282 atoms, 6138 bonds, 1077 residues, 1 model selected 
    11271 
    11272 > show #!63 models
    11273 
    11274 > hide #!64 models
    11275 
    11276 > view matrix models
    11277 > #38,0.48808,0.079008,0.86921,57.589,-0.57432,-0.72083,0.38802,273.61,0.65721,-0.68859,-0.30645,79.373
    11278 
    11279 > view matrix models
    11280 > #38,0.2297,0.46473,0.85514,83.832,-0.58104,-0.6394,0.50355,270.11,0.78079,-0.61253,0.12316,51.538
    11281 
    11282 > view matrix models
    11283 > #38,0.2297,0.46473,0.85514,85.324,-0.58104,-0.6394,0.50355,273.24,0.78079,-0.61253,0.12316,53.863
    11284 
    11285 > view matrix models
    11286 > #38,0.39662,0.46965,0.78875,59.564,-0.57284,-0.54478,0.61243,266.95,0.71732,-0.69472,0.052964,67.932
    11287 
    11288 > show #!64 models
    11289 
    11290 > hide #!63 models
    11291 
    11292 > view matrix models
    11293 > #38,-0.91348,-0.3347,0.23136,304.61,0.38224,-0.51103,0.7699,112.62,-0.13945,0.79172,0.59475,139.64
    11294 
    11295 > view matrix models
    11296 > #38,-0.59049,-0.80568,-0.046958,275.08,-0.087884,0.0063535,0.99611,164.3,-0.80225,0.59232,-0.074558,260.49
    11297 
    11298 > view matrix models
    11299 > #38,-0.59049,-0.80568,-0.046958,273.4,-0.087884,0.0063535,0.99611,163.84,-0.80225,0.59232,-0.074558,241.17
    11300 
    11301 > view matrix models
    11302 > #38,-0.55648,-0.77337,0.3037,262.39,0.12542,0.28314,0.95084,120.04,-0.82134,0.56721,-0.060566,244.98
    11303 
    11304 > fitmap #38 inMap #64
    11305 
    11306 Fit molecule 9hud (#38) to map cryosparc_P483_J137_003_volume_map.mrc z flip
    11307 (#64) using 6282 atoms 
    11308 average map value = 0.03426, steps = 96 
    11309 shifted from previous position = 4.73 
    11310 rotated from previous position = 4.41 degrees 
    11311 atoms outside contour = 3712, contour level = 0.036179 
    11312  
    11313 Position of 9hud (#38) relative to cryosparc_P483_J137_003_volume_map.mrc z
    11314 flip (#64) coordinates: 
    11315 Matrix rotation and translation 
    11316 -0.57799196 -0.77115445 0.26691966 270.23868060 
    11317 0.05229306 0.29141704 0.95516572 129.97421192 
    11318 -0.81436523 0.56603615 -0.12811068 246.02921542 
    11319 Axis -0.27524806 0.76483926 0.58245980 
    11320 Axis point 198.55971177 0.00000000 -12.15810570 
    11321 Rotation angle (degrees) 135.01912752 
    11322 Shift along axis 168.32883368 
    11323  
    11324 
    11325 > hide #!64 models
    11326 
    11327 > show #!63 models
    11328 
    11329 > view matrix models
    11330 > #38,0.28227,0.88622,0.36734,69.32,0.13351,-0.41547,0.89976,144.95,0.95,-0.20493,-0.23559,-2.1095
    11331 
    11332 > view matrix models
    11333 > #38,0.28227,0.88622,0.36734,65.915,0.13351,-0.41547,0.89976,149,0.95,-0.20493,-0.23559,14.639
    11334 
    11335 > view matrix models
    11336 > #38,-0.00068529,0.90537,0.42463,109.22,-0.0059164,-0.42462,0.90535,171.33,0.99998,-0.0018918,0.0056475,-4.0739
    11337 
    11338 > fitmap #38 inMap #63
    11339 
    11340 Fit molecule 9hud (#38) to map cryosparc_P483_J137_003_volume_map.mrc (#63)
    11341 using 6282 atoms 
    11342 average map value = 0.03246, steps = 440 
    11343 shifted from previous position = 6.15 
    11344 rotated from previous position = 34.9 degrees 
    11345 atoms outside contour = 3887, contour level = 0.036179 
    11346  
    11347 Position of 9hud (#38) relative to cryosparc_P483_J137_003_volume_map.mrc
    11348 (#63) coordinates: 
    11349 Matrix rotation and translation 
    11350 0.42909681 0.75362179 0.49792584 49.09248009 
    11351 -0.38069938 -0.34900840 0.85630668 221.91213193 
    11352 0.81911167 -0.55699852 0.13714496 46.28691655 
    11353 Axis -0.76791055 -0.17451431 -0.61632632 
    11354 Axis point -0.00000000 97.45467483 -84.23279059 
    11355 Rotation angle (degrees) 113.04060047 
    11356 Shift along axis -104.95332191 
    11357  
    11358 
    11359 > hide #!63 models
    11360 
    11361 > show #!64 models
    11362 
    11363 > view matrix models
    11364 > #38,0.6404,-0.29362,0.70969,53.209,-0.098072,0.88521,0.45474,134.87,-0.76175,-0.36082,0.5381,283.79
    11365 
    11366 > view matrix models
    11367 > #38,-0.26615,-0.29672,0.91713,194.12,0.6919,0.60364,0.39609,21.458,-0.67114,0.73998,0.044637,233.39
    11368 
    11369 > view matrix models
    11370 > #38,0.42821,0.78395,0.44952,48.675,0.43344,0.2583,-0.86337,91.334,-0.79295,0.56454,-0.22919,262.81
    11371 
    11372 > view matrix models
    11373 > #38,0.40387,0.68567,-0.6056,69.485,-0.40554,-0.4592,-0.79036,250.65,-0.82002,0.5648,0.092606,263.06
    11374 
    11375 > view matrix models
    11376 > #38,-0.85722,-0.30291,-0.41645,304.52,-0.2744,-0.41565,0.86714,207.52,-0.43576,0.8576,0.27319,188.79
    11377 
    11378 > view matrix models
    11379 > #38,-0.57679,-0.55417,0.60017,257.1,0.51884,0.31896,0.79314,54.792,-0.63097,0.76887,0.10355,225.19
    11380 
    11381 > view matrix models
    11382 > #38,-0.57679,-0.55417,0.60017,254.28,0.51884,0.31896,0.79314,61.36,-0.63097,0.76887,0.10355,204.28
    11383 
    11384 > view matrix models
    11385 > #38,-0.60566,-0.70889,0.36146,267.77,0.21101,0.29491,0.93193,109.24,-0.76724,0.64071,-0.029033,232.41
    11386 
    11387 > view matrix models
    11388 > #38,-0.60566,-0.70889,0.36146,266.58,0.21101,0.29491,0.93193,105.92,-0.76724,0.64071,-0.029033,230.06
    11389 
    11390 > view matrix models
    11391 > #38,-0.72224,-0.67174,0.16473,286.05,0.065572,0.1706,0.98316,133.05,-0.68853,0.72087,-0.079168,215.16
    11392 
    11393 > view matrix models
    11394 > #38,-0.47003,-0.67432,0.56953,241.2,0.17784,0.55967,0.80941,102.54,-0.86455,0.48173,-0.14315,252.98
    11395 
    11396 > view matrix models
    11397 > #38,-0.47003,-0.67432,0.56953,249.14,0.17784,0.55967,0.80941,98.999,-0.86455,0.48173,-0.14315,251.53
    11398 
    11399 > view matrix models
    11400 > #38,-0.59825,-0.70633,0.37841,273.04,0.21367,0.31452,0.92489,101.29,-0.77229,0.63417,-0.037243,229.77
    11401 
    11402 > fitmap #38 inMap #64
    11403 
    11404 Fit molecule 9hud (#38) to map cryosparc_P483_J137_003_volume_map.mrc z flip
    11405 (#64) using 6282 atoms 
    11406 average map value = 0.03512, steps = 80 
    11407 shifted from previous position = 5.4 
    11408 rotated from previous position = 3.39 degrees 
    11409 atoms outside contour = 3664, contour level = 0.036179 
    11410  
    11411 Position of 9hud (#38) relative to cryosparc_P483_J137_003_volume_map.mrc z
    11412 flip (#64) coordinates: 
    11413 Matrix rotation and translation 
    11414 -0.63147092 -0.69242738 0.34898254 278.13803163 
    11415 0.16768307 0.31747267 0.93332391 107.28593241 
    11416 -0.75705144 0.64788536 -0.08436641 232.43243148 
    11417 Axis -0.19962317 0.77351156 0.60152345 
    11418 Axis point 188.76264795 0.00000000 -10.22905426 
    11419 Rotation angle (degrees) 134.36143880 
    11420 Shift along axis 167.27766991 
    11421  
    11422 
    11423 > fitmap #38 inMap #64
    11424 
    11425 Fit molecule 9hud (#38) to map cryosparc_P483_J137_003_volume_map.mrc z flip
    11426 (#64) using 6282 atoms 
    11427 average map value = 0.03512, steps = 40 
    11428 shifted from previous position = 0.0099 
    11429 rotated from previous position = 0.0115 degrees 
    11430 atoms outside contour = 3662, contour level = 0.036179 
    11431  
    11432 Position of 9hud (#38) relative to cryosparc_P483_J137_003_volume_map.mrc z
    11433 flip (#64) coordinates: 
    11434 Matrix rotation and translation 
    11435 -0.63136485 -0.69247722 0.34907556 278.12932035 
    11436 0.16783951 0.31744825 0.93330409 107.26947039 
    11437 -0.75710524 0.64784406 -0.08420063 232.43949274 
    11438 Axis -0.19960443 0.77348336 0.60156592 
    11439 Axis point 188.76447494 0.00000000 -10.24425096 
    11440 Rotation angle (degrees) 134.35152473 
    11441 Shift along axis 167.28298509 
    11442  
    11443 
    11444 > view matrix models
    11445 > #38,-0.63136,-0.69248,0.34908,274.79,0.16784,0.31745,0.9333,108.96,-0.75711,0.64784,-0.084201,230.09
    11446 
    11447 > fitmap #38 inMap #64
    11448 
    11449 Fit molecule 9hud (#38) to map cryosparc_P483_J137_003_volume_map.mrc z flip
    11450 (#64) using 6282 atoms 
    11451 average map value = 0.03512, steps = 88 
    11452 shifted from previous position = 4.42 
    11453 rotated from previous position = 0.00894 degrees 
    11454 atoms outside contour = 3663, contour level = 0.036179 
    11455  
    11456 Position of 9hud (#38) relative to cryosparc_P483_J137_003_volume_map.mrc z
    11457 flip (#64) coordinates: 
    11458 Matrix rotation and translation 
    11459 -0.63139892 -0.69244150 0.34908479 278.12602696 
    11460 0.16773664 0.31755383 0.93328667 107.27376736 
    11461 -0.75709963 0.64783049 -0.08435534 232.44361126 
    11462 Axis -0.19961308 0.77352989 0.60150323 
    11463 Axis point 188.76295474 0.00000000 -10.22421164 
    11464 Rotation angle (degrees) 134.35485805 
    11465 Shift along axis 167.27745334 
    11466  
    11467 
    11468 > view matrix models
    11469 > #38,-0.64713,-0.6735,0.35724,279.79,0.16615,0.33274,0.92827,107.01,-0.74406,0.66006,-0.10342,230.15
    11470 
    11471 > view matrix models
    11472 > #38,-0.64713,-0.6735,0.35724,276.58,0.16615,0.33274,0.92827,108.12,-0.74406,0.66006,-0.10342,229.13
    11473 
    11474 > fitmap #38 inMap #64
    11475 
    11476 Fit molecule 9hud (#38) to map cryosparc_P483_J137_003_volume_map.mrc z flip
    11477 (#64) using 6282 atoms 
    11478 average map value = 0.03512, steps = 80 
    11479 shifted from previous position = 3.52 
    11480 rotated from previous position = 1.63 degrees 
    11481 atoms outside contour = 3659, contour level = 0.036179 
    11482  
    11483 Position of 9hud (#38) relative to cryosparc_P483_J137_003_volume_map.mrc z
    11484 flip (#64) coordinates: 
    11485 Matrix rotation and translation 
    11486 -0.63138477 -0.69243824 0.34911684 278.12114525 
    11487 0.16772204 0.31760740 0.93327106 107.27149167 
    11488 -0.75711466 0.64780772 -0.08439532 232.44867407 
    11489 Axis -0.19961431 0.77354815 0.60147934 
    11490 Axis point 188.76284344 0.00000000 -10.21708948 
    11491 Rotation angle (degrees) 134.35374707 
    11492 Shift along axis 167.27577632 
    11493  
    11494 
    11495 > hide #!64 models
    11496 
    11497 > show #!60 models
    11498 
    11499 > view matrix models
    11500 > #38,0.4887,0.003934,0.87244,67.696,-0.61017,-0.71321,0.345,277.22,0.6236,-0.70094,-0.34614,69.091
    11501 
    11502 > view matrix models
    11503 > #38,0.4887,0.003934,0.87244,62.759,-0.61017,-0.71321,0.345,271.12,0.6236,-0.70094,-0.34614,59.706
    11504 
    11505 > view matrix models
    11506 > #38,0.4887,0.003934,0.87244,62.878,-0.61017,-0.71321,0.345,270.83,0.6236,-0.70094,-0.34614,60.391
    11507 
    11508 > select subtract #38
    11509 
    11510 Nothing selected 
    11511 
    11512 > hide #!38 models
    11513 
    11514 > show #!38 models
    11515 
    11516 > open /Users/amy/Downloads/cryosparc_P483_J136_004_volume_map.mrc
    11517 
    11518 Opened cryosparc_P483_J136_004_volume_map.mrc as #65, grid size 400,400,400,
    11519 pixel 0.723, shown at level 0.00461, step 2, values float32 
    11520 
    11521 > hide #!60 models
    11522 
    11523 > hide #!38 models
    11524 
    11525 > surface dust #65 size 7.23
    11526 
    11527 > volume #65 level 0.02522
    11528 
    11529 > transparency #65 50
    11530 
    11531 > volume flip #65 axis z
    11532 
    11533 Opened cryosparc_P483_J136_004_volume_map.mrc z flip as #66, grid size
    11534 400,400,400, pixel 0.723, shown at step 1, values float32 
    11535 
    11536 > show #!38 models
    11537 
    11538 > fitmap #38 inMap #66
    11539 
    11540 Fit molecule 9hud (#38) to map cryosparc_P483_J136_004_volume_map.mrc z flip
    11541 (#66) using 6282 atoms 
    11542 average map value = 0.05359, steps = 80 
    11543 shifted from previous position = 1.58 
    11544 rotated from previous position = 4.51 degrees 
    11545 atoms outside contour = 1373, contour level = 0.025222 
    11546  
    11547 Position of 9hud (#38) relative to cryosparc_P483_J136_004_volume_map.mrc z
    11548 flip (#66) coordinates: 
    11549 Matrix rotation and translation 
    11550 0.49152778 0.08078197 0.86710711 58.94196264 
    11551 -0.57115257 -0.72173556 0.39100196 263.45649346 
    11552 0.65740794 -0.68743877 -0.30861424 55.13461431 
    11553 Axis -0.84417530 0.16414704 -0.51031737 
    11554 Axis point 0.00000000 145.46690985 -47.79590518 
    11555 Rotation angle (degrees) 140.30102750 
    11556 Shift along axis -34.64789549 
    11557  
    11558 
    11559 > mmaker #37 to #38
    11560 
    11561 Parameters 
    11562 --- 
    11563 Chain pairing | bb 
    11564 Alignment algorithm | Needleman-Wunsch 
    11565 Similarity matrix | BLOSUM-62 
    11566 SS fraction | 0.3 
    11567 Gap open (HH/SS/other) | 18/18/6 
    11568 Gap extend | 1 
    11569 SS matrix |  |  | H | S | O 
    11570 ---|---|---|--- 
    11571 H | 6 | -9 | -6 
    11572 S |  | 6 | -6 
    11573 O |  |  | 4 
    11574 Iteration cutoff | 2 
    11575  
    11576 Matchmaker 9hud, chain A (#38) with 1ezx, chain A (#37), sequence alignment
    11577 score = 1674.4 
    11578 RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
    11579 0.519) 
    11580  
    11581 
    11582 > show #!37 models
    11583 
    11584 > show #7 models
    11585 
    11586 > mmaker #7 to #37
    11587 
    11588 Parameters 
    11589 --- 
    11590 Chain pairing | bb 
    11591 Alignment algorithm | Needleman-Wunsch 
    11592 Similarity matrix | BLOSUM-62 
    11593 SS fraction | 0.3 
    11594 Gap open (HH/SS/other) | 18/18/6 
    11595 Gap extend | 1 
    11596 SS matrix |  |  | H | S | O 
    11597 ---|---|---|--- 
    11598 H | 6 | -9 | -6 
    11599 S |  | 6 | -6 
    11600 O |  |  | 4 
    11601 Iteration cutoff | 2 
    11602  
    11603 Matchmaker 1ezx, chain C (#37) with 5a0c, chain A (#7), sequence alignment
    11604 score = 241.2 
    11605 RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
    11606 3.073) 
    11607  
    11608 
    11609 > hide #!37 models
    11610 
    11611 > show #!37 models
    11612 
    11613 > hide #!38 models
    11614 
    11615 > show #!38 models
    11616 
    11617 > hide #!37 models
    11618 
    11619 > show #!37 models
    11620 
    11621 > hide #!38 models
    11622 
    11623 > hide #7 models
    11624 
    11625 > volume #65 level 0.03378
    11626 
    11627 > volume #66 level 0.03927
    11628 
    11629 > volume #66 level 0.03004
    11630 
    11631 > hide #!37 models
    11632 
    11633 > volume gaussian #65 sDev 2
    11634 
    11635 Opened cryosparc_P483_J136_004_volume_map.mrc gaussian as #67, grid size
    11636 400,400,400, pixel 0.723, shown at step 1, values float32 
    11637 
    11638 > ui tool show "Segment Map"
    11639 
    11640 Segmenting cryosparc_P483_J136_004_volume_map.mrc gaussian, density threshold
    11641 0.002595 
    11642 Only showing 60 of 69 regions. 
    11643 Showing 60 of 69 region surfaces 
    11644 165 watershed regions, grouped to 69 regions 
    11645 Showing cryosparc_P483_J136_004_volume_map gaussian.seg - 69 regions, 60
    11646 surfaces 
    11647 
    11648 > select #68.13
    11649 
    11650 1 model selected 
    11651 
    11652 > select add #68.6
    11653 
    11654 2 models selected 
    11655 
    11656 > select add #68.23
    11657 
    11658 3 models selected 
    11659 
    11660 > select add #68.24
    11661 
    11662 4 models selected 
    11663 
    11664 > select add #68.29
    11665 
    11666 5 models selected 
    11667 
    11668 > select add #68.20
    11669 
    11670 6 models selected 
    11671 
    11672 > select add #68.5
    11673 
    11674 7 models selected 
    11675 
    11676 > select add #68.37
    11677 
    11678 8 models selected 
    11679 
    11680 > select add #68.33
    11681 
    11682 9 models selected 
    11683 
    11684 > select add #68.11
    11685 
    11686 10 models selected 
    11687 
    11688 > select add #68.26
    11689 
    11690 11 models selected 
    11691 
    11692 > select add #68.14
    11693 
    11694 12 models selected 
    11695 
    11696 > select add #68.7
    11697 
    11698 13 models selected 
    11699 
    11700 > select add #68.3
    11701 
    11702 14 models selected 
    11703 
    11704 > select add #68.19
    11705 
    11706 15 models selected 
    11707 
    11708 > select add #68.8
    11709 
    11710 16 models selected 
    11711 
    11712 > select add #68.35
    11713 
    11714 17 models selected 
    11715 
    11716 > select add #68.28
    11717 
    11718 18 models selected 
    11719 
    11720 > select add #68.12
    11721 
    11722 19 models selected 
    11723 
    11724 > select add #68.15
    11725 
    11726 20 models selected 
    11727 
    11728 > select add #68.4
    11729 
    11730 21 models selected 
    11731 
    11732 > select add #68.40
    11733 
    11734 22 models selected 
    11735 
    11736 > select add #68.36
    11737 
    11738 23 models selected 
    11739 
    11740 > select add #68.48
    11741 
    11742 24 models selected 
    11743 
    11744 > select add #68.51
    11745 
    11746 25 models selected 
    11747 
    11748 > select add #68.53
    11749 
    11750 26 models selected 
    11751 
    11752 > select add #68.59
    11753 
    11754 27 models selected 
    11755 
    11756 > select add #68.58
    11757 
    11758 28 models selected 
    11759 
    11760 > select add #68.57
    11761 
    11762 29 models selected 
    11763 
    11764 > select add #68.54
    11765 
    11766 30 models selected 
    11767 
    11768 > select add #68.16
    11769 
    11770 31 models selected 
    11771 
    11772 > select add #68.44
    11773 
    11774 32 models selected 
    11775 
    11776 > select add #68.25
    11777 
    11778 33 models selected 
    11779 
    11780 > select add #68.50
    11781 
    11782 34 models selected 
    11783 
    11784 > select add #68.31
    11785 
    11786 35 models selected 
    11787 
    11788 > hide #!67 models
    11789 
    11790 > select add #68.45
    11791 
    11792 36 models selected 
    11793 
    11794 > select add #68.38
    11795 
    11796 37 models selected 
    11797 
    11798 > select add #68.17
    11799 
    11800 38 models selected 
    11801 
    11802 > select add #68.34
    11803 
    11804 39 models selected 
    11805 
    11806 > select add #68.52
    11807 
    11808 40 models selected 
    11809 
    11810 > select add #68.30
    11811 
    11812 41 models selected 
    11813 
    11814 > select add #68.27
    11815 
    11816 42 models selected 
    11817 
    11818 > select add #68.49
    11819 
    11820 43 models selected 
    11821 
    11822 > select add #68.46
    11823 
    11824 44 models selected 
    11825 
    11826 > select add #68.43
    11827 
    11828 45 models selected 
    11829 
    11830 > select add #68.39
    11831 
    11832 46 models selected 
    11833 
    11834 > select add #68.41
    11835 
    11836 47 models selected 
    11837 
    11838 > select add #68.56
    11839 
    11840 48 models selected 
    11841 
    11842 > select add #68.55
    11843 
    11844 49 models selected 
    11845 
    11846 > show #!67 models
    11847 
    11848 > show #!66 models
    11849 
    11850 > hide #!66 models
    11851 
    11852 > hide #!68 models
    11853 
    11854 > show #!68 models
    11855 
    11856 > hide #!68 models
    11857 
    11858 > show #!66 models
    11859 
    11860 > show #!68 models
    11861 
    11862 > hide #!67 models
    11863 
    11864 > hide #!66 models
    11865 
    11866 > show #!65 models
    11867 
    11868 > select add #68.42
    11869 
    11870 50 models selected 
    11871 
    11872 > hide #!65 models
    11873 
    11874 > select add #68.21
    11875 
    11876 51 models selected 
    11877 
    11878 > show #!66 models
    11879 
    11880 > hide #!66 models
    11881 
    11882 > show #!65 models
    11883 
    11884 > hide #!68 models
    11885 
    11886 > show #!68 models
    11887 
    11888 > hide #!68 models
    11889 
    11890 > show #!68 models
    11891 
    11892 > select add #68.47
    11893 
    11894 52 models selected 
    11895 
    11896 > select add #68.10
    11897 
    11898 53 models selected 
    11899 
    11900 > select subtract #68.10
    11901 
    11902 52 models selected 
    11903 
    11904 > select add #68.60
    11905 
    11906 53 models selected 
    11907 
    11908 > select add #68.1
    11909 
    11910 54 models selected 
    11911 
    11912 > select subtract #68.1
    11913 
    11914 53 models selected 
    11915 
    11916 > select add #68.1
    11917 
    11918 54 models selected 
    11919 
    11920 > select subtract #68.1
    11921 
    11922 53 models selected 
    11923 
    11924 > select #68.1
    11925 
    11926 1 model selected 
    11927 Segmenting cryosparc_P483_J136_004_volume_map.mrc gaussian, density threshold
    11928 0.002595 
    11929 Only showing 60 of 69 regions. 
    11930 Showing 60 of 69 region surfaces 
    11931 165 watershed regions, grouped to 69 regions 
    11932 Showing cryosparc_P483_J136_004_volume_map gaussian.seg - 69 regions, 60
    11933 surfaces 
    11934 
    11935 > close #68
    11936 
    11937 > show #!67 models
    11938 
    11939 > hide #!67 models
    11940 
    11941 > volume #65 level 0.009704
    11942 
    11943 > ui mousemode right "map eraser"
    11944 
    11945 > volume erase #65 center 171.23,100.86,184.61 radius 29.508
    11946 
    11947 Opened cryosparc_P483_J136_004_volume_map.mrc copy as #69, grid size
    11948 400,400,400, pixel 0.723, shown at step 1, values float32 
    11949 
    11950 > volume erase #69 center 84.398,121.62,173.8 radius 29.498
    11951 
    11952 > surface dust #69 size 7.23
    11953 
    11954 > volume #69 level 0.01365
    11955 
    11956 > volume #69 level 0.01523
    11957 
    11958 > ui mousemode right "translate selected models"
    11959 
    11960 > volume gaussian #65 sDev 2
    11961 
    11962 Opened cryosparc_P483_J136_004_volume_map.mrc gaussian as #68, grid size
    11963 400,400,400, pixel 0.723, shown at step 1, values float32 
    11964 
    11965 > ui mousemode right "map eraser"
    11966 
    11967 Can only have one displayed volume when erasing 
    11968 
    11969 > hide #!69 models
    11970 
    11971 > show #!69 models
    11972 
    11973 > hide #!69 models
    11974 
    11975 > hide #!68 models
    11976 
    11977 > show #!68 models
    11978 
    11979 > volume erase #68 center 199.87,114.16,177.51 radius 29.932
    11980 
    11981 > volume erase #68 center 223.51,161,191.94 radius 29.932
    11982 
    11983 > volume erase #68 center 230.79,129.47,140.96 radius 29.932
    11984 
    11985 > volume erase #68 center 137.16,147.6,54.19 radius 29.932
    11986 
    11987 > volume erase #68 center 74.443,93.395,201.66 radius 29.932
    11988 
    11989 > volume erase #68 center 60.662,109.56,169.96 radius 29.932
    11990 
    11991 > volume erase #68 center 81.784,129.86,147.37 radius 29.932
    11992 
    11993 > volume erase #68 center 97.833,142.74,184.92 radius 14.894
    11994 
    11995 > volume erase #68 center 93.234,158.27,115.41 radius 14.894
    11996 
    11997 > volume erase #68 center 110.51,164.91,187.37 radius 14.894
    11998 
    11999 > volume erase #68 center 126.3,181.61,190.42 radius 14.894
    12000 
    12001 > volume erase #68 center 190.02,108.44,206.29 radius 14.894
    12002 
    12003 > volume erase #68 center 212,136.35,210.5 radius 14.894
    12004 
    12005 > volume erase #68 center 66.419,147.34,177.91 radius 14.894
    12006 
    12007 > volume erase #68 center 94.954,148.62,156.51 radius 14.894
    12008 
    12009 > volume erase #68 center 105.75,136.11,158.02 radius 14.894
    12010 
    12011 > volume erase #68 center 169.12,113.8,156.36 radius 12.58
    12012 
    12013 > volume erase #68 center 179.1,115.64,198.32 radius 12.58
    12014 
    12015 > show #!65 models
    12016 
    12017 > hide #!68 models
    12018 
    12019 > volume #65 level 0.01773
    12020 
    12021 > show #!68 models
    12022 
    12023 Can only have one displayed volume when erasing 
    12024 
    12025 > hide #!65 models
    12026 
    12027 > hide #!68 models
    12028 
    12029 > show #!65 models
    12030 
    12031 > hide #!65 models
    12032 
    12033 > show #!68 models
    12034 
    12035 > volume erase #68 center 173.45,108.86,188.42 radius 22.124
    12036 
    12037 > volume erase #68 center 161.71,101.56,178.92 radius 22.124
    12038 
    12039 > undo
    12040 
    12041 [Repeated 1 time(s)]
    12042 
    12043 > show #!68 models
    12044 
    12045 > hide #!65 models
    12046 
    12047 > volume erase #68 center 92.336,122.06,161.51 radius 22.124
    12048 
    12049 Segmenting cryosparc_P483_J136_004_volume_map.mrc gaussian, density threshold
    12050 0.002595 
    12051 Showing 50 region surfaces 
    12052 124 watershed regions, grouped to 50 regions 
    12053 Showing cryosparc_P483_J136_004_volume_map gaussian.seg - 50 regions, 50
    12054 surfaces 
    12055 
    12056 > select add #70.10
    12057 
    12058 1 model selected 
    12059 
    12060 > select add #70.31
    12061 
    12062 2 models selected 
    12063 
    12064 > select add #70.6
    12065 
    12066 3 models selected 
    12067 
    12068 > select add #70.12
    12069 
    12070 4 models selected 
    12071 
    12072 > select add #70.23
    12073 
    12074 5 models selected 
    12075 
    12076 > select add #70.22
    12077 
    12078 6 models selected 
    12079 Drag select of 173, 7505 of 52828 triangles, 177, 26288 of 45472 triangles,
    12080 172, 156, 176, 25800 of 38068 triangles, 157, 17988 of 30408 triangles, 167,
    12081 152, 142, 6687 of 22324 triangles, 163, 64, 17140 of 19708 triangles, 12, 178,
    12082 169, 568 of 17388 triangles, 5, 143, 6044 of 15344 triangles, 144, 148, 135,
    12083 30, 12770 of 12984 triangles, 8, 52, 4331 of 12948 triangles, 125, 11085 of
    12084 12828 triangles, 6, 68, 5141 of 9284 triangles, 33, 35, 6919 of 6948
    12085 triangles, 68 cryosparc_P483_J136_004_volume_map.mrc gaussian 
    12086 Drag select of 177, 8907 of 45472 triangles, 172, 35825 of 37284 triangles,
    12087 156, 176, 5888 of 38068 triangles, 157, 7846 of 30408 triangles, 167, 152,
    12088 7570 of 25900 triangles, 163, 12, 17106 of 17656 triangles, 178, 5, 144, 148,
    12089 13560 of 13800 triangles, 135, 12555 of 14540 triangles, 30, 6391 of 12984
    12090 triangles, 8, 125, 1329 of 12828 triangles, 6, 33, 3490 of 7340 triangles, 35,
    12091 1963 of 6948 triangles, 68 cryosparc_P483_J136_004_volume_map.mrc gaussian 
    12092 
    12093 > hide #!68 models
    12094 
    12095 Drag select of 177, 10859 of 45472 triangles, 172, 176, 10027 of 38068
    12096 triangles, 149, 177 of 29032 triangles, 152, 12625 of 25900 triangles, 163, 5,
    12097 144, 135, 14423 of 14540 triangles, 30, 11045 of 12984 triangles, 8, 125, 2434
    12098 of 12828 triangles, 6, 33, 6568 of 7340 triangles, 35, 5541 of 6948 triangles 
    12099 
    12100 > close #70
    12101 
    12102 > show #!66 models
    12103 
    12104 > hide #!66 models
    12105 
    12106 > show #!65 models
    12107 
    12108 > show #!68 models
    12109 
    12110 > close #68-69
    12111 
    12112 > close #67
    12113 
    12114 > volume gaussian #65 sDev 2
    12115 
    12116 Opened cryosparc_P483_J136_004_volume_map.mrc gaussian as #67, grid size
    12117 400,400,400, pixel 0.723, shown at step 1, values float32 
    12118 
    12119 > open /Users/amy/Downloads/cryosparc_P371_J1247_003_volume_map.mrc
    12120 
    12121 Opened cryosparc_P371_J1247_003_volume_map.mrc as #68, grid size 300,300,300,
    12122 pixel 0.867, shown at level 0.0217, step 2, values float32 
    12123 
    12124 > hide #!67 models
    12125 
    12126 > volume #68 level 0.07077
    12127 
    12128 > show #!8 models
    12129 
    12130 > transparenct #68 50
    12131 
    12132 Unknown command: transparenct #68 50 
    12133 
    12134 > transparency #68 50
    12135 
    12136 > fitmap #8 inMap #68
    12137 
    12138 Fit molecule 1ezx (#8) to map cryosparc_P371_J1247_003_volume_map.mrc (#68)
    12139 using 3984 atoms 
    12140 average map value = 0.0799, steps = 64 
    12141 shifted from previous position = 1.9 
    12142 rotated from previous position = 5.61 degrees 
    12143 atoms outside contour = 1925, contour level = 0.07077 
    12144  
    12145 Position of 1ezx (#8) relative to cryosparc_P371_J1247_003_volume_map.mrc
    12146 (#68) coordinates: 
    12147 Matrix rotation and translation 
    12148 -0.34797185 0.02707514 -0.93711394 206.68051797 
    12149 0.14066384 -0.98675962 -0.08074121 177.03298135 
    12150 -0.92689227 -0.15991372 0.33955607 198.02271581 
    12151 Axis -0.57026324 -0.07362457 0.81815601 
    12152 Axis point 168.54386706 102.19253410 0.00000000 
    12153 Rotation angle (degrees) 176.01946831 
    12154 Shift along axis 31.11719577 
    12155  
    12156 
    12157 > show #!57 models
    12158 
    12159 > select add #57
    12160 
    12161 1009 atoms, 1014 bonds, 5 pseudobonds, 155 residues, 3 models selected 
    12162 
    12163 > mmaker #57 to #8
    12164 
    12165 Parameters 
    12166 --- 
    12167 Chain pairing | bb 
    12168 Alignment algorithm | Needleman-Wunsch 
    12169 Similarity matrix | BLOSUM-62 
    12170 SS fraction | 0.3 
    12171 Gap open (HH/SS/other) | 18/18/6 
    12172 Gap extend | 1 
    12173 SS matrix |  |  | H | S | O 
    12174 ---|---|---|--- 
    12175 H | 6 | -9 | -6 
    12176 S |  | 6 | -6 
    12177 O |  |  | 4 
    12178 Iteration cutoff | 2 
    12179  
    12180 Matchmaker 1ezx, chain C (#8) with copy of 1ezx, chain C (#57), sequence
    12181 alignment score = 1096 
    12182 RMSD between 140 pruned atom pairs is 0.000 angstroms; (across all 140 pairs:
    12183 0.000) 
    12184  
    12185 
    12186 > select subtract #57
    12187 
    12188 Nothing selected 
    12189 
    12190 > select add #57
    12191 
    12192 1009 atoms, 1014 bonds, 5 pseudobonds, 155 residues, 3 models selected 
    12193 
    12194 > hide #!8 models
    12195 
    12196 > show #!8 models
    12197 
    12198 > ui mousemode right "translate selected models"
    12199 
    12200 > view matrix models
    12201 > #57,-0.55581,-0.066238,-0.82867,220.13,0.27617,-0.95492,-0.10891,166.76,-0.7841,-0.28938,0.54905,178.74
    12202 
    12203 > view matrix models
    12204 > #57,-0.44814,0.013112,-0.89387,212.91,0.19695,-0.97388,-0.11303,173.83,-0.872,-0.2267,0.43385,190.3
    12205 
    12206 > view matrix models
    12207 > #57,-0.44814,0.013112,-0.89387,212.84,0.19695,-0.97388,-0.11303,176.3,-0.872,-0.2267,0.43385,191.28
    12208 
    12209 > view matrix models
    12210 > #57,-0.70986,-0.70171,-0.060879,208.01,0.69037,-0.67603,-0.25765,136.82,0.13964,-0.22492,0.96432,82.152
    12211 
    12212 > view matrix models
    12213 > #57,-0.70986,-0.70171,-0.060879,209.15,0.69037,-0.67603,-0.25765,137.83,0.13964,-0.22492,0.96432,86.098
    12214 
    12215 > view matrix models
    12216 > #57,-0.52828,-0.77583,-0.34499,210.69,0.84041,-0.53567,-0.082284,113.45,-0.12096,-0.3334,0.93499,111.22
    12217 
    12218 > fitmap #57 inMap #68
    12219 
    12220 Fit molecule copy of 1ezx (#57) to map cryosparc_P371_J1247_003_volume_map.mrc
    12221 (#68) using 1009 atoms 
    12222 average map value = 0.05715, steps = 92 
    12223 shifted from previous position = 1.85 
    12224 rotated from previous position = 22.4 degrees 
    12225 atoms outside contour = 740, contour level = 0.07077 
    12226  
    12227 Position of copy of 1ezx (#57) relative to
    12228 cryosparc_P371_J1247_003_volume_map.mrc (#68) coordinates: 
    12229 Matrix rotation and translation 
    12230 -0.60074737 -0.69741151 -0.39079378 215.40326299 
    12231 0.67365936 -0.70482938 0.22225799 115.60603445 
    12232 -0.43044821 -0.12974098 0.89324219 133.98043752 
    12233 Axis -0.24857103 0.02800277 0.96820880 
    12234 Axis point 100.60140928 106.25888332 0.00000000 
    12235 Rotation angle (degrees) 134.92392438 
    12236 Shift along axis 79.41531641 
    12237  
    12238 
    12239 > hide #!8 models
    12240 
    12241 > view matrix models
    12242 > #57,-0.55549,-0.80836,-0.19489,204.29,0.77301,-0.58839,0.23717,104.09,-0.30639,-0.018907,0.95172,118.37
    12243 
    12244 > view matrix models
    12245 > #57,-0.55549,-0.80836,-0.19489,206,0.77301,-0.58839,0.23717,104.98,-0.30639,-0.018907,0.95172,120.21
    12246 
    12247 > view matrix models
    12248 > #57,-0.33676,-0.93674,0.09544,176.41,0.94008,-0.34023,-0.022246,98.96,0.05331,0.08223,0.99519,86.499
    12249 
    12250 > view matrix models
    12251 > #57,-0.33676,-0.93674,0.09544,176.42,0.94008,-0.34023,-0.022246,99.819,0.05331,0.08223,0.99519,85.597
    12252 
    12253 > view matrix models
    12254 > #57,-0.11119,-0.60614,-0.78754,195.64,0.65285,-0.64203,0.40198,108.39,-0.74928,-0.46945,0.46711,190.42
    12255 
    12256 > view matrix models
    12257 > #57,0.78168,0.24914,-0.57175,92.445,0.18825,-0.96824,-0.16454,182.56,-0.59459,0.020991,-0.80376,231.51
    12258 
    12259 > view matrix models
    12260 > #57,0.51703,0.78986,-0.32985,88.973,0.65853,-0.61323,-0.43621,150.13,-0.54682,0.0083211,-0.83721,229.65
    12261 
    12262 > view matrix models
    12263 > #57,0.51703,0.78986,-0.32985,91.831,0.65853,-0.61323,-0.43621,150.09,-0.54682,0.0083211,-0.83721,234.12
    12264 
    12265 > view matrix models
    12266 > #57,0.55299,0.36331,-0.7498,120.29,0.22263,-0.93163,-0.28721,185.16,-0.80289,-0.0081052,-0.59607,242.91
    12267 
    12268 > view matrix models
    12269 > #57,0.55299,0.36331,-0.7498,118.48,0.22263,-0.93163,-0.28721,185.69,-0.80289,-0.0081052,-0.59607,239.55
    12270 
    12271 > view matrix models
    12272 > #57,0.92569,-0.35496,0.13079,59.902,0.0091285,-0.32469,-0.94578,222.6,0.37818,0.87669,-0.29732,108.08
    12273 
    12274 > view matrix models
    12275 > #57,-0.3165,-0.83947,0.44172,155.86,0.42443,-0.54177,-0.7255,182.72,0.84834,-0.042141,0.52777,49.092
    12276 
    12277 > view matrix models
    12278 > #57,-0.3165,-0.83947,0.44172,156.19,0.42443,-0.54177,-0.7255,182.46,0.84834,-0.042141,0.52777,49.883
    12279 
    12280 > view matrix models
    12281 > #57,0.040165,-0.95688,0.2877,137.9,0.92992,-0.069542,-0.36112,111.92,0.36556,0.28204,0.88703,63.1
    12282 
    12283 > view matrix models
    12284 > #57,0.040165,-0.95688,0.2877,138.99,0.92992,-0.069542,-0.36112,111.84,0.36556,0.28204,0.88703,64.867
    12285 
    12286 > view matrix models
    12287 > #57,0.18721,-0.98102,0.050423,139.78,0.96897,0.17599,-0.17355,93.385,0.16139,0.081349,0.98353,81.124
    12288 
    12289 > mmaker #7 to #8
    12290 
    12291 Parameters 
    12292 --- 
    12293 Chain pairing | bb 
    12294 Alignment algorithm | Needleman-Wunsch 
    12295 Similarity matrix | BLOSUM-62 
    12296 SS fraction | 0.3 
    12297 Gap open (HH/SS/other) | 18/18/6 
    12298 Gap extend | 1 
    12299 SS matrix |  |  | H | S | O 
    12300 ---|---|---|--- 
    12301 H | 6 | -9 | -6 
    12302 S |  | 6 | -6 
    12303 O |  |  | 4 
    12304 Iteration cutoff | 2 
    12305  
    12306 Matchmaker 1ezx, chain C (#8) with 5a0c, chain A (#7), sequence alignment
    12307 score = 241.2 
    12308 RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
    12309 3.073) 
    12310  
    12311 
    12312 > select add #7
    12313 
    12314 2892 atoms, 2759 bonds, 5 pseudobonds, 549 residues, 4 models selected 
    12315 
    12316 > show #7 models
    12317 
    12318 > select subtract #57
    12319 
    12320 1883 atoms, 1745 bonds, 394 residues, 1 model selected 
    12321 
    12322 > hide #!57 models
    12323 
    12324 > select #7/A
    12325 
    12326 1883 atoms, 1745 bonds, 394 residues, 1 model selected 
    12327 
    12328 > select subtract #7
    12329 
    12330 Nothing selected 
    12331 
    12332 > select #7/A
    12333 
    12334 1883 atoms, 1745 bonds, 394 residues, 1 model selected 
    12335 
    12336 > select #7/A: 202
    12337 
    12338 6 atoms, 5 bonds, 1 residue, 1 model selected 
    12339 
    12340 > select #7/A: 202
    12341 
    12342 6 atoms, 5 bonds, 1 residue, 1 model selected 
    12343 
    12344 > show sel atoms
    12345 
    12346 > style sel stick
    12347 
    12348 Changed 6 atom styles 
    12349 
    12350 > rainbow sel
    12351 
    12352 > select add #7
    12353 
    12354 1883 atoms, 1745 bonds, 394 residues, 1 model selected 
    12355 
    12356 > select subtract #7
    12357 
    12358 Nothing selected 
    12359 
    12360 > show #!37 models
    12361 
    12362 > hide #!37 models
    12363 
    12364 > show #!8 models
    12365 
    12366 > hide #!8 models
    12367 
    12368 > open /Users/amy/Downloads/cryosparc_P371_J1248_004_volume_map.mrc
    12369 
    12370 Opened cryosparc_P371_J1248_004_volume_map.mrc as #69, grid size 300,300,300,
    12371 pixel 0.867, shown at level 0.0367, step 2, values float32 
    12372 
    12373 > volume #69 level 0.08383
    12374 
    12375 > hide #!68 models
    12376 
    12377 > volume #69 level 0.0762
    12378 
    12379 > transparency #69 50
    12380 
    12381 > hide #7 models
    12382 
    12383 > close #50-56
    12384 
    12385 > close #43-48
    12386 
    12387 > show #!65 models
    12388 
    12389 > volume gaussian #65 sDev 2
    12390 
    12391 Opened cryosparc_P483_J136_004_volume_map.mrc gaussian as #43, grid size
    12392 400,400,400, pixel 0.723, shown at step 1, values float32 
    12393 
    12394 > ui mousemode right "map eraser"
    12395 
    12396 > volume erase #43 center 75.013,107.83,176.28 radius 23.833
    12397 
    12398 > volume erase #43 center 194.75,109.99,182.34 radius 28.983
    12399 
    12400 > volume erase #43 center 224.93,121.74,145.38 radius 28.983
    12401 
    12402 > volume erase #43 center 210.7,158.2,175.15 radius 28.983
    12403 
    12404 > volume erase #43 center 208.21,147.09,205.7 radius 28.983
    12405 
    12406 > volume erase #43 center 188.54,118.48,207.86 radius 28.983
    12407 
    12408 > volume erase #43 center 76.857,145.76,159.87 radius 28.983
    12409 
    12410 > volume erase #43 center 87.79,161.6,111.25 radius 28.983
    12411 
    12412 > volume erase #43 center 126.19,148.22,60.086 radius 28.983
    12413 
    12414 > surface dust #43 size 7.23
    12415 
    12416 [Repeated 2 time(s)]
    12417 
    12418 > volume erase #43 center 98.252,123.11,133.43 radius 28.983
    12419 
    12420 > ui mousemode right "translate selected models"
    12421 
    12422 > hide #!43 models
    12423 
    12424 > show #!43 models
    12425 
    12426 Segmenting cryosparc_P483_J136_004_volume_map.mrc gaussian, density threshold
    12427 0.002595 
    12428 Showing 54 region surfaces 
    12429 134 watershed regions, grouped to 54 regions 
    12430 Showing cryosparc_P483_J136_004_volume_map gaussian.seg - 54 regions, 54
    12431 surfaces 
    12432 Drag select of 180, 4556 of 45584 triangles, 187, 31245 of 37284 triangles,
    12433 177, 33991 of 34540 triangles, 179, 626 of 37968 triangles, 170, 1849 of 30408
    12434 triangles, 183, 146, 4014 of 25900 triangles, 166, 12, 182, 5, 151, 157, 9644
    12435 of 13800 triangles, 160, 7260 of 14540 triangles, 30, 3371 of 12984 triangles,
    12436 8, 6, 33, 892 of 7340 triangles, 35, 143 of 6948 triangles, 43
    12437 cryosparc_P483_J136_004_volume_map.mrc gaussian 
    12438 Drag select of 189, 15171 of 45152 triangles, 144, 28176 of 29416 triangles,
    12439 186, 153, 26060 of 29032 triangles, 165, 16225 of 23204 triangles, 171, 20862
    12440 of 21324 triangles, 181, 612 of 19816 triangles, 188, 9417 of 18732 triangles,
    12441 184, 11190 of 17388 triangles, 69, 12493 of 16160 triangles, 83, 159, 3373 of
    12442 15344 triangles, 100, 109, 4788 of 13396 triangles, 54, 54 of 12948 triangles,
    12443 190, 3956 of 13608 triangles, 148, 93 of 11564 triangles, 167, 713 of 12312
    12444 triangles, 136, 1067 of 12828 triangles, 95, 7439 of 9752 triangles, 82, 43
    12445 cryosparc_P483_J136_004_volume_map.mrc gaussian 
    12446 
    12447 > hide #!43 models
    12448 
    12449 > show #!43 models
    12450 
    12451 > select add #44.51
    12452 
    12453 41 models selected 
    12454 
    12455 > select add #44.53
    12456 
    12457 42 models selected 
    12458 
    12459 > hide #!43 models
    12460 
    12461 > select add #44.10
    12462 
    12463 43 models selected 
    12464 Ungrouped to 64 regions, but did not show all surfaces, see Options 
    12465 
    12466 > select clear
    12467 
    12468 > select #44.62
    12469 
    12470 1 model selected 
    12471 
    12472 > select #44.21
    12473 
    12474 1 model selected 
    12475 Ungrouped to 2 regions, but did not show their surfaces, see Options 
    12476 Smoothing and grouping, standard deviation 5 voxels 
    12477 Showing 28 region surfaces 
    12478 Got 28 regions after smoothing 5 voxels. 
    12479 Ungrouped to 86 regions, but did not show all surfaces, see Options 
    12480 Drag select of 134 
    12481 [Repeated 1 time(s)]
    12482 
    12483 > select clear
    12484 
    12485 > select #44.72
    12486 
    12487 1 model selected 
    12488 
    12489 > select clear
    12490 
    12491 > select #44.73
    12492 
    12493 1 model selected 
    12494 
    12495 > select add #44.74
    12496 
    12497 2 models selected 
    12498 
    12499 > show #!43 models
    12500 
    12501 > hide #!44 models
    12502 
    12503 > volume #43 level 0.01177
    12504 
    12505 > ui mousemode right "map eraser"
    12506 
    12507 > volume erase #43 center 170.19,107.1,177.93 radius 16.889
    12508 
    12509 > ui mousemode right "translate selected models"
    12510 
    12511 > close #44
    12512 
    12513 > volume gaussian #65 sDev 2
    12514 
    12515 Opened cryosparc_P483_J136_004_volume_map.mrc gaussian as #44, grid size
    12516 400,400,400, pixel 0.723, shown at step 1, values float32 
    12517 
    12518 > close #44
    12519 
    12520 Segmenting cryosparc_P483_J136_004_volume_map.mrc gaussian, density threshold
    12521 0.011767 
    12522 Showing 49 region surfaces 
    12523 113 watershed regions, grouped to 49 regions 
    12524 Showing cryosparc_P483_J136_004_volume_map gaussian.seg - 49 regions, 49
    12525 surfaces 
    12526 
    12527 > hide #!43 models
    12528 
    12529 Drag select of 152, 22015 of 40248 triangles, 160, 137, 162, 19815 of 27632
    12530 triangles, 145, 22686 of 24068 triangles, 154, 132, 19102 of 20860 triangles,
    12531 149, 128, 343 of 19360 triangles, 12, 157, 151, 5666 of 14648 triangles, 155,
    12532 15 of 14140 triangles, 121, 8147 of 14452 triangles, 126, 124, 5, 50, 4342 of
    12533 11924 triangles, 6, 133, 26, 116, 11741 of 11768 triangles, 7, 32, 34 
    12534 Drag select of 159, 9755 of 37648 triangles, 125, 24182 of 24328 triangles,
    12535 158, 18998 of 22744 triangles, 139, 10853 of 19468 triangles, 142, 17469 of
    12536 19372 triangles, 128, 5249 of 19360 triangles, 63, 3508 of 13216 triangles,
    12537 82, 11209 of 11804 triangles, 90, 161, 1720 of 12188 triangles, 84, 4555 of
    12538 9228 triangles, 71, 6615 of 6864 triangles 
    12539 Drag select of 128, 163, 7108 of 17660 triangles, 94, 10211 of 10636
    12540 triangles, 123, 7213 of 10336 triangles, 146, 6495 of 11584 triangles, 88,
    12541 3550 of 8592 triangles 
    12542 Showing 49 region surfaces 
    12543 
    12544 > select #44.46
    12545 
    12546 1 model selected 
    12547 
    12548 > show #!43 models
    12549 
    12550 > hide #!43 models
    12551 
    12552 > select #44.13
    12553 
    12554 1 model selected 
    12555 
    12556 > select #44.13
    12557 
    12558 1 model selected 
    12559 
    12560 > select #44.3
    12561 
    12562 1 model selected 
    12563 
    12564 > select #44.3
    12565 
    12566 1 model selected 
    12567 Ungrouped to 2 regions 
    12568 
    12569 > select #44.13
    12570 
    12571 1 model selected 
    12572 Ungrouped to 2 regions 
    12573 
    12574 > select #44.3
    12575 
    12576 1 model selected 
    12577 Ungrouped to 2 regions 
    12578 
    12579 > select #44.51
    12580 
    12581 1 model selected 
    12582 Ungrouped to 2 regions 
    12583 
    12584 > select #44.54
    12585 
    12586 1 model selected 
    12587 Ungrouped to 2 regions 
    12588 
    12589 > show #!43 models
    12590 
    12591 > hide #!43 models
    12592 
    12593 > show #!43 models
    12594 
    12595 > hide #!43 models
    12596 
    12597 > show #!43 models
    12598 
    12599 > hide #!43 models
    12600 
    12601 > select #44.55
    12602 
    12603 1 model selected 
    12604 
    12605 > select #44.55
    12606 
    12607 1 model selected 
    12608 
    12609 > select clear
    12610 
    12611 Please select one ore more regions to save to .mrc file 
    12612 Drag select of 156, 138, 61, 127, 65, 93, 87, 92, 76, 68, 79, 69 
    12613 Saving 12 regions to mrc file... 
    12614 Opened base_cryosparc_P483_J136_004_volume_map_12_regions.mrc as #45, grid
    12615 size 75,64,70, pixel 0.723, shown at step 1, values float32 
    12616 Wrote base_cryosparc_P483_J136_004_volume_map_12_regions.mrc 
    12617 
    12618 > volume #45 level 0.01277
    12619 
    12620 > hide #!44 models
    12621 
    12622 > show #!44 models
    12623 
    12624 Deleted 12 regions 
    12625 Showing 42 region surfaces 
    12626 
    12627 > hide #!45 models
    12628 
    12629 > show #!45 models
    12630 
    12631 > hide #!45 models
    12632 
    12633 Drag select of 152, 159, 160, 137, 162, 125, 158, 145, 154, 139, 132, 142,
    12634 149, 128, 163, 12, 157, 151, 155, 121, 126, 63, 82, 124, 5, 50, 6, 133, 90,
    12635 26, 161, 94, 116, 123, 146, 7, 84, 88, 74, 71, 32, 34 
    12636 Saving 42 regions to mrc file... 
    12637 Opened substract_cryosparc_P483_J136_004_volume_map_42_regions.mrc as #46,
    12638 grid size 90,89,178, pixel 0.723, shown at step 1, values float32 
    12639 Wrote substract_cryosparc_P483_J136_004_volume_map_42_regions.mrc 
    12640 
    12641 > select add #44
    12642 
    12643 43 models selected 
    12644 
    12645 > select subtract #44
    12646 
    12647 Nothing selected 
    12648 
    12649 > hide #!44 models
    12650 
    12651 > volume #46 level 0.01896
    12652 
    12653 > show #!44 models
    12654 
    12655 > hide #!44 models
    12656 
    12657 > show #!45 models
    12658 
    12659 > volume resample #45 onGrid #65
    12660 
    12661 Opened base_cryosparc_P483_J136_004_volume_map_12_regions.mrc resampled as
    12662 #47, grid size 400,400,400, pixel 0.723, shown at step 1, values float32 
    12663 
    12664 > show #!45 models
    12665 
    12666 > hide #!45 models
    12667 
    12668 > volume resample #46 onGrid #65
    12669 
    12670 Opened substract_cryosparc_P483_J136_004_volume_map_42_regions.mrc resampled
    12671 as #48, grid size 400,400,400, pixel 0.723, shown at step 1, values float32 
    12672 
    12673 > hide #!48 models
    12674 
    12675 > show #!48 models
    12676 
    12677 > save "/Users/amy/Desktop/SPA AAT_HNE/9C5_Fab_AAT_HNE/For mask
    12678 > generation/Base_mask_J136.mrc" models #47
    12679 
    12680 > save "/Users/amy/Desktop/SPA AAT_HNE/9C5_Fab_AAT_HNE/For mask
    12681 > generation/Substract_mask_J136.mrc" models #48
    12682 
    12683 > hide #!48 models
    12684 
    12685 > hide #!47 models
    12686 
    12687 > show #!66 models
    12688 
    12689 > volume #66 level 0.01465
    12690 
    12691 > hide #!66 models
    12692 
    12693 > show #!66 models
    12694 
    12695 > show #!65 models
    12696 
    12697 > hide #!66 models
    12698 
    12699 > hide #!65 models
    12700 
    12701 > show #!66 models
    12702 
    12703 > volume #66 level 0.0762
    12704 
    12705 > volume #66 level 0.05963
    12706 
    12707 > open /Users/amy/Downloads/Position_4_4_stack_Vol.mrc
    12708 
    12709 Opened Position_4_4_stack_Vol.mrc as #50, grid size 1024,1024,200, pixel
    12710 6.2,6.2,6.2, shown at level 0.00197, step 4, values float32 
    12711 
    12712 > open /Users/amy/Downloads/cryosparc_P483_J163_009_volume_map.mrc
    12713 
    12714 Opened cryosparc_P483_J163_009_volume_map.mrc as #51, grid size 400,400,400,
    12715 pixel 0.723, shown at level 0.00345, step 2, values float32 
    12716 
    12717 > hide #!50 models
    12718 
    12719 > hide #!66 models
    12720 
    12721 > close #50
    12722 
    12723 > volume #51 level 0.01856
    12724 
    12725 > transparency #51 50
    12726 
    12727 > show #!38 models
    12728 
    12729 > select add #38
    12730 
    12731 6282 atoms, 6138 bonds, 1077 residues, 1 model selected 
    12732 
    12733 > volume flip #51 axis z
    12734 
    12735 Opened cryosparc_P483_J163_009_volume_map.mrc z flip as #50, grid size
    12736 400,400,400, pixel 0.723, shown at step 1, values float32 
    12737 
    12738 > fitmap #38 inMap #50
    12739 
    12740 Fit molecule 9hud (#38) to map cryosparc_P483_J163_009_volume_map.mrc z flip
    12741 (#50) using 6282 atoms 
    12742 average map value = 0.07848, steps = 68 
    12743 shifted from previous position = 0.869 
    12744 rotated from previous position = 1.21 degrees 
    12745 atoms outside contour = 1202, contour level = 0.018564 
    12746  
    12747 Position of 9hud (#38) relative to cryosparc_P483_J163_009_volume_map.mrc z
    12748 flip (#50) coordinates: 
    12749 Matrix rotation and translation 
    12750 0.47930263 0.06820977 0.87499511 60.65156876 
    12751 -0.57459125 -0.72922061 0.37159415 263.89520826 
    12752 0.66341081 -0.68087058 -0.31032461 53.93040141 
    12753 Axis -0.84112622 0.16909745 -0.51372438 
    12754 Axis point 0.00000000 145.65173307 -47.89349763 
    12755 Rotation angle (degrees) 141.27168221 
    12756 Shift along axis -34.09698023 
    12757  
    12758 
    12759 > select subtract #38
    12760 
    12761 Nothing selected 
    12762 
    12763 > show #!37 models
    12764 
    12765 > mmaker #37 to #38
    12766 
    12767 Parameters 
    12768 --- 
    12769 Chain pairing | bb 
    12770 Alignment algorithm | Needleman-Wunsch 
    12771 Similarity matrix | BLOSUM-62 
    12772 SS fraction | 0.3 
    12773 Gap open (HH/SS/other) | 18/18/6 
    12774 Gap extend | 1 
    12775 SS matrix |  |  | H | S | O 
    12776 ---|---|---|--- 
    12777 H | 6 | -9 | -6 
    12778 S |  | 6 | -6 
    12779 O |  |  | 4 
    12780 Iteration cutoff | 2 
    12781  
    12782 Matchmaker 9hud, chain A (#38) with 1ezx, chain A (#37), sequence alignment
    12783 score = 1674.4 
    12784 RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
    12785 0.519) 
    12786  
    12787 
    12788 > hide #!37 models
    12789 
    12790 > hide #!38 models
    12791 
    12792 > show #!37 models
    12793 
    12794 > ui mousemode right "tape measure"
    12795 
    12796 > marker segment #52 position 174.9,170.7,80.95 toPosition 149.1,120.4,104.7
    12797 > color yellow radius 0.1807 label 61.39 labelHeight 6.139 labelColor yellow
    12798 
    12799 > marker segment #52 position 173.6,172.2,80.09 toPosition 131.7,129.6,94.55
    12800 > color yellow radius 0.1807 label 61.46 labelHeight 6.146 labelColor yellow
    12801 
    12802 > marker segment #52 position 168.9,170.1,79.92 toPosition 119.6,140.5,107.7
    12803 > color yellow radius 0.1807 label 63.85 labelHeight 6.385 labelColor yellow
    12804 
    12805 > marker segment #52 position 162.3,169.9,78.45 toPosition 131.8,125.9,101.6
    12806 > color yellow radius 0.1807 label 58.29 labelHeight 5.829 labelColor yellow
    12807 
    12808 > close #52
    12809 
    12810 > open /Users/amy/Downloads/cryosparc_P483_J166_007_volume_map.mrc
    12811 
    12812 Opened cryosparc_P483_J166_007_volume_map.mrc as #52, grid size 400,400,400,
    12813 pixel 0.723, shown at level 0.00871, step 2, values float32 
    12814 
    12815 > volume #52 level 0.03218
    12816 
    12817 > volume flip #52 50
    12818 
    12819 Expected a keyword 
    12820 
    12821 > volume flip #52 axis z
    12822 
    12823 Opened cryosparc_P483_J166_007_volume_map.mrc z flip as #53, grid size
    12824 400,400,400, pixel 0.723, shown at step 1, values float32 
    12825 
    12826 > transparency #53 50
    12827 
    12828 > fitmap #38 inMap #53
    12829 
    12830 Fit molecule 9hud (#38) to map cryosparc_P483_J166_007_volume_map.mrc z flip
    12831 (#53) using 6282 atoms 
    12832 average map value = 0.0755, steps = 88 
    12833 shifted from previous position = 0.675 
    12834 rotated from previous position = 2.29 degrees 
    12835 atoms outside contour = 1730, contour level = 0.032179 
    12836  
    12837 Position of 9hud (#38) relative to cryosparc_P483_J166_007_volume_map.mrc z
    12838 flip (#53) coordinates: 
    12839 Matrix rotation and translation 
    12840 0.48708054 0.10074896 0.86752649 58.26714282 
    12841 -0.57324776 -0.71251935 0.40460253 263.40109171 
    12842 0.65889268 -0.69438163 -0.28930019 55.22725475 
    12843 Axis -0.84150595 0.15975352 -0.51608774 
    12844 Axis point 0.00000000 145.38448995 -49.65713741 
    12845 Rotation angle (degrees) 139.23284387 
    12846 Shift along axis -35.45500404 
    12847  
    12848 
    12849 > show #!38 models
    12850 
    12851 > mmaker #37 to #38
    12852 
    12853 Parameters 
    12854 --- 
    12855 Chain pairing | bb 
    12856 Alignment algorithm | Needleman-Wunsch 
    12857 Similarity matrix | BLOSUM-62 
    12858 SS fraction | 0.3 
    12859 Gap open (HH/SS/other) | 18/18/6 
    12860 Gap extend | 1 
    12861 SS matrix |  |  | H | S | O 
    12862 ---|---|---|--- 
    12863 H | 6 | -9 | -6 
    12864 S |  | 6 | -6 
    12865 O |  |  | 4 
    12866 Iteration cutoff | 2 
    12867  
    12868 Matchmaker 9hud, chain A (#38) with 1ezx, chain A (#37), sequence alignment
    12869 score = 1674.4 
    12870 RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
    12871 0.519) 
    12872  
    12873 
    12874 > hide #!38 models
    12875 
    12876 > show #7 models
    12877 
    12878 > mmaker #7 to #37
    12879 
    12880 Parameters 
    12881 --- 
    12882 Chain pairing | bb 
    12883 Alignment algorithm | Needleman-Wunsch 
    12884 Similarity matrix | BLOSUM-62 
    12885 SS fraction | 0.3 
    12886 Gap open (HH/SS/other) | 18/18/6 
    12887 Gap extend | 1 
    12888 SS matrix |  |  | H | S | O 
    12889 ---|---|---|--- 
    12890 H | 6 | -9 | -6 
    12891 S |  | 6 | -6 
    12892 O |  |  | 4 
    12893 Iteration cutoff | 2 
    12894  
    12895 Matchmaker 1ezx, chain C (#37) with 5a0c, chain A (#7), sequence alignment
    12896 score = 241.2 
    12897 RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
    12898 3.073) 
    12899  
    12900 
    12901 > hide #!37 models
    12902 
    12903 > volume #53 level 0.09551
    12904 
    12905 > volume #53 level 0.05065
    12906 
    12907 > volume #53 level 0.04273
    12908 
    12909 > hide #7 models
    12910 
    12911 > open /Users/amy/Downloads/cryosparc_P483_J178_007_volume_map.mrc
    12912 
    12913 Opened cryosparc_P483_J178_007_volume_map.mrc as #54, grid size 400,400,400,
    12914 pixel 0.723, shown at level 0.00984, step 2, values float32 
    12915 
    12916 > volume #54 level 0.02797
    12917 
    12918 > volume flip #54 axis z
    12919 
    12920 Opened cryosparc_P483_J178_007_volume_map.mrc z flip as #55, grid size
    12921 400,400,400, pixel 0.723, shown at step 1, values float32 
    12922 
    12923 > transparency #55 50
    12924 
    12925 > show #7 models
    12926 
    12927 > hide #7 models
    12928 
    12929 > show #7 models
    12930 
    12931 > select add #7
    12932 
    12933 1883 atoms, 1745 bonds, 394 residues, 1 model selected 
    12934 
    12935 > select subtract #7
    12936 
    12937 Nothing selected 
    12938 
    12939 > hide #7 models
    12940 
    12941 > show #!8 models
    12942 
    12943 > select add #8
    12944 
    12945 3984 atoms, 3982 bonds, 5 pseudobonds, 592 residues, 3 models selected 
    12946 
    12947 > ui mousemode right "translate selected models"
    12948 
    12949 > view matrix models
    12950 > #8,-0.74339,-0.4472,0.49738,176.11,0.56886,-0.81386,0.11846,127.4,0.35182,0.371,0.85941,53.336
    12951 
    12952 > view matrix models
    12953 > #8,0.38457,0.070001,0.92044,48.03,0.66601,-0.71147,-0.22416,135.06,0.63917,0.69922,-0.32023,84.211
    12954 
    12955 > view matrix models
    12956 > #8,0.38457,0.070001,0.92044,48.132,0.66601,-0.71147,-0.22416,145.94,0.63917,0.69922,-0.32023,107.63
    12957 
    12958 > view matrix models
    12959 > #8,-0.11357,-0.011929,0.99346,82.463,0.67784,-0.73199,0.068701,129.45,0.72638,0.68121,0.091219,79.052
    12960 
    12961 > hide #!55 models
    12962 
    12963 > show #!54 models
    12964 
    12965 > transparency #54 50
    12966 
    12967 > view matrix models
    12968 > #8,-0.11357,-0.011929,0.99346,88.184,0.67784,-0.73199,0.068701,128.28,0.72638,0.68121,0.091219,43.943
    12969 
    12970 > view matrix models
    12971 > #8,0.98922,0.13889,-0.046321,63.821,0.14063,-0.98938,0.036662,180.17,-0.040737,-0.042781,-0.99825,195.61
    12972 
    12973 > view matrix models
    12974 > #8,-0.22454,0.34562,-0.91111,186.4,0.4892,-0.76865,-0.41214,170.57,-0.84277,-0.53826,0.0035149,218.83
    12975 
    12976 > view matrix models
    12977 > #8,-0.22454,0.34562,-0.91111,190.27,0.4892,-0.76865,-0.41214,172.31,-0.84277,-0.53826,0.0035149,198.32
    12978 
    12979 > hide #!8 models
    12980 
    12981 > select subtract #8
    12982 
    12983 Nothing selected 
    12984 
    12985 > show #!38 models
    12986 
    12987 > select add #38
    12988 
    12989 6282 atoms, 6138 bonds, 1077 residues, 1 model selected 
    12990 
    12991 > view matrix models
    12992 > #38,0.58456,0.63428,-0.50594,39.545,0.32988,0.3839,0.86244,72.759,0.74126,-0.67105,0.015176,37.498
    12993 
    12994 > view matrix models
    12995 > #38,-0.62989,-0.2889,-0.72095,269.75,0.43669,0.63589,-0.63635,64.932,0.64229,-0.71567,-0.27439,58.484
    12996 
    12997 > view matrix models
    12998 > #38,-0.79758,-0.56471,-0.21208,300.49,0.093917,0.23104,-0.9684,138.83,0.59586,-0.79229,-0.13123,66.978
    12999 
    13000 > view matrix models
    13001 > #38,-0.79758,-0.56471,-0.21208,298.65,0.093917,0.23104,-0.9684,128.19,0.59586,-0.79229,-0.13123,84.027
    13002 
    13003 > view matrix models
    13004 > #38,-0.65099,-0.75245,0.1001,278.77,-0.2865,0.12144,-0.95035,192.34,0.70294,-0.64735,-0.29463,63.572
    13005 
    13006 > view matrix models
    13007 > #38,-0.65099,-0.75245,0.1001,273.74,-0.2865,0.12144,-0.95035,188.77,0.70294,-0.64735,-0.29463,64.627
    13008 
    13009 > hide #!54 models
    13010 
    13011 > show #!55 models
    13012 
    13013 > view matrix models
    13014 > #38,0.92945,0.36602,-0.046307,-17.327,-0.12262,0.18809,-0.97447,160.6,-0.34796,0.9114,0.2197,164.6
    13015 
    13016 > view matrix models
    13017 > #38,0.68418,0.72711,0.05661,6.3245,-0.24646,0.30357,-0.92038,175.08,-0.6864,0.61576,0.3869,227.39
    13018 
    13019 > view matrix models
    13020 > #38,0.68418,0.72711,0.05661,6.2981,-0.24646,0.30357,-0.92038,173.03,-0.6864,0.61576,0.3869,222.11
    13021 
    13022 > fitmap #38 inMap #55
    13023 
    13024 Fit molecule 9hud (#38) to map cryosparc_P483_J178_007_volume_map.mrc z flip
    13025 (#55) using 6282 atoms 
    13026 average map value = 0.07095, steps = 260 
    13027 shifted from previous position = 2.45 
    13028 rotated from previous position = 40.2 degrees 
    13029 atoms outside contour = 1485, contour level = 0.027968 
    13030  
    13031 Position of 9hud (#38) relative to cryosparc_P483_J178_007_volume_map.mrc z
    13032 flip (#55) coordinates: 
    13033 Matrix rotation and translation 
    13034 0.68744757 0.35641921 0.63275685 15.52206548 
    13035 0.28938953 0.66468217 -0.68880429 73.81019326 
    13036 -0.66608526 0.65663002 0.35379014 216.09676949 
    13037 Axis 0.71899263 0.69409402 -0.03582029 
    13038 Axis point 0.00000000 -189.86123076 144.51310834 
    13039 Rotation angle (degrees) 69.33153492 
    13040 Shift along axis 54.65081588 
    13041  
    13042 
    13043 > mmaker #8 to #38
    13044 
    13045 Parameters 
    13046 --- 
    13047 Chain pairing | bb 
    13048 Alignment algorithm | Needleman-Wunsch 
    13049 Similarity matrix | BLOSUM-62 
    13050 SS fraction | 0.3 
    13051 Gap open (HH/SS/other) | 18/18/6 
    13052 Gap extend | 1 
    13053 SS matrix |  |  | H | S | O 
    13054 ---|---|---|--- 
    13055 H | 6 | -9 | -6 
    13056 S |  | 6 | -6 
    13057 O |  |  | 4 
    13058 Iteration cutoff | 2 
    13059  
    13060 Matchmaker 9hud, chain A (#38) with 1ezx, chain A (#8), sequence alignment
    13061 score = 1674.4 
    13062 RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
    13063 0.519) 
    13064  
    13065 
    13066 > hide #!38 models
    13067 
    13068 > select subtract #38
    13069 
    13070 Nothing selected 
    13071 
    13072 > show #!8 models
    13073 
    13074 > mmaker #7 to #8
    13075 
    13076 Parameters 
    13077 --- 
    13078 Chain pairing | bb 
    13079 Alignment algorithm | Needleman-Wunsch 
    13080 Similarity matrix | BLOSUM-62 
    13081 SS fraction | 0.3 
    13082 Gap open (HH/SS/other) | 18/18/6 
    13083 Gap extend | 1 
    13084 SS matrix |  |  | H | S | O 
    13085 ---|---|---|--- 
    13086 H | 6 | -9 | -6 
    13087 S |  | 6 | -6 
    13088 O |  |  | 4 
    13089 Iteration cutoff | 2 
    13090  
    13091 Matchmaker 1ezx, chain C (#8) with 5a0c, chain A (#7), sequence alignment
    13092 score = 241.2 
    13093 RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
    13094 3.073) 
    13095  
    13096 
    13097 > hide #!8 models
    13098 
    13099 > show #7 models
    13100 
    13101 > volume #55 level 0.03303
    13102 
    13103 > open /Users/amy/Downloads/cryosparc_P483_J178_007_volume_map.mrc
    13104 
    13105 Opened cryosparc_P483_J178_007_volume_map.mrc as #56, grid size 400,400,400,
    13106 pixel 0.723, shown at level 0.00984, step 2, values float32 
    13107 
    13108 > volume #56 level 0.0196
    13109 
    13110 > close #56
    13111 
    13112 > open /Users/amy/Downloads/cryosparc_P483_J179_005_volume_map.mrc
    13113 
    13114 Opened cryosparc_P483_J179_005_volume_map.mrc as #56, grid size 400,400,400,
    13115 pixel 0.723, shown at level 0.00903, step 2, values float32 
    13116 
    13117 > open /Users/amy/Downloads/cryosparc_P483_J180_002_volume_map.mrc
    13118 
    13119 Opened cryosparc_P483_J180_002_volume_map.mrc as #70, grid size 400,400,400,
    13120 pixel 0.723, shown at level 0.00199, step 2, values float32 
    13121 
    13122 > hide #!70 models
    13123 
    13124 > show #!66 models
    13125 
    13126 > hide #!66 models
    13127 
    13128 > show #!67 models
    13129 
    13130 > open /Users/amy/Downloads/cryosparc_P483_J183_007_volume_map.mrc
    13131 
    13132 Opened cryosparc_P483_J183_007_volume_map.mrc as #71, grid size 400,400,400,
    13133 pixel 0.723, shown at level 0.0116, step 2, values float32 
    13134 
    13135 > hide #!67 models
    13136 
    13137 > volume #71 level 0.03377
    13138 
    13139 > volume #71 level 0.03909
    13140 
    13141 > transparency #71 50
    13142 
    13143 > hide #7 models
    13144 
    13145 > show #!38 models
    13146 
    13147 > select add #38
    13148 
    13149 6282 atoms, 6138 bonds, 1077 residues, 1 model selected 
    13150 
    13151 > view matrix models
    13152 > #38,-0.91266,0.065596,-0.40341,292.72,0.36322,0.5827,-0.727,65.755,0.18738,-0.81003,-0.55564,148.75
    13153 
    13154 > view matrix models
    13155 > #38,-0.72502,-0.2597,-0.63788,278.46,0.38017,0.62139,-0.68509,61.067,0.57429,-0.73921,-0.3518,82.291
    13156 
    13157 > view matrix models
    13158 > #38,-0.72502,-0.2597,-0.63788,277.14,0.38017,0.62139,-0.68509,52.977,0.57429,-0.73921,-0.3518,86.091
    13159 
    13160 > view matrix models
    13161 > #38,-0.65947,-0.28553,-0.69539,268.48,0.35515,0.69696,-0.62299,53.205,0.66254,-0.65781,-0.35822,69.098
    13162 
    13163 > view matrix models
    13164 > #38,-0.65947,-0.28553,-0.69539,267.26,0.35515,0.69696,-0.62299,52.554,0.66254,-0.65781,-0.35822,69.625
    13165 
    13166 > close #58-69
    13167 
    13168 > fitmap #38 inMap #71
    13169 
    13170 Fit molecule 9hud (#38) to map cryosparc_P483_J183_007_volume_map.mrc (#71)
    13171 using 6282 atoms 
    13172 average map value = 0.07544, steps = 148 
    13173 shifted from previous position = 7.45 
    13174 rotated from previous position = 12.1 degrees 
    13175 atoms outside contour = 1976, contour level = 0.039086 
    13176  
    13177 Position of 9hud (#38) relative to cryosparc_P483_J183_007_volume_map.mrc
    13178 (#71) coordinates: 
    13179 Matrix rotation and translation 
    13180 -0.67498701 -0.41761657 -0.60826719 272.94445864 
    13181 0.34716985 0.54767448 -0.76126592 67.90283128 
    13182 0.65104966 -0.72501662 -0.22468927 71.15250272 
    13183 Axis 0.02459578 -0.85446836 0.51892087 
    13184 Axis point 117.22275735 0.00000000 126.50966305 
    13185 Rotation angle (degrees) 132.53192375 
    13186 Shift along axis -14.38502000 
    13187  
    13188 
    13189 > mmaker #8 to #38
    13190 
    13191 Parameters 
    13192 --- 
    13193 Chain pairing | bb 
    13194 Alignment algorithm | Needleman-Wunsch 
    13195 Similarity matrix | BLOSUM-62 
    13196 SS fraction | 0.3 
    13197 Gap open (HH/SS/other) | 18/18/6 
    13198 Gap extend | 1 
    13199 SS matrix |  |  | H | S | O 
    13200 ---|---|---|--- 
    13201 H | 6 | -9 | -6 
    13202 S |  | 6 | -6 
    13203 O |  |  | 4 
    13204 Iteration cutoff | 2 
    13205  
    13206 Matchmaker 9hud, chain A (#38) with 1ezx, chain A (#8), sequence alignment
    13207 score = 1674.4 
    13208 RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
    13209 0.519) 
    13210  
    13211 
    13212 > show #!8 models
    13213 
    13214 > select subtract #38
    13215 
    13216 Nothing selected 
    13217 
    13218 > hide #!38 models
    13219 
    13220 > show #7 models
    13221 
    13222 > mmaker #7 to #8
    13223 
    13224 Parameters 
    13225 --- 
    13226 Chain pairing | bb 
    13227 Alignment algorithm | Needleman-Wunsch 
    13228 Similarity matrix | BLOSUM-62 
    13229 SS fraction | 0.3 
    13230 Gap open (HH/SS/other) | 18/18/6 
    13231 Gap extend | 1 
    13232 SS matrix |  |  | H | S | O 
    13233 ---|---|---|--- 
    13234 H | 6 | -9 | -6 
    13235 S |  | 6 | -6 
    13236 O |  |  | 4 
    13237 Iteration cutoff | 2 
    13238  
    13239 Matchmaker 1ezx, chain C (#8) with 5a0c, chain A (#7), sequence alignment
    13240 score = 241.2 
    13241 RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
    13242 3.073) 
    13243  
    13244 
    13245 > hide #!8 models
    13246 
    13247 > open "/Users/amy/Downloads/cryosparc_P371_J1247_003_volume_map (1).mrc"
    13248 
    13249 Opened cryosparc_P371_J1247_003_volume_map (1).mrc as #58, grid size
    13250 300,300,300, pixel 0.867, shown at level 0.0217, step 2, values float32 
    13251 
    13252 > hide #7 models
    13253 
    13254 > volume #58 level 0.07127
    13255 
    13256 > transparency 58 50
    13257 
    13258 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
    13259 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword 
    13260 
    13261 > transparency #58 50
    13262 
    13263 > select add #58
    13264 
    13265 2 models selected 
    13266 
    13267 > select subtract #58
    13268 
    13269 Nothing selected 
    13270 
    13271 > show #!57 models
    13272 
    13273 > hide #!57 models
    13274 
    13275 > show #!37 models
    13276 
    13277 > select add #37
    13278 
    13279 3984 atoms, 3982 bonds, 5 pseudobonds, 592 residues, 3 models selected 
    13280 
    13281 > view matrix models
    13282 > #37,-0.92665,0.37309,0.046068,189.97,-0.3746,-0.92671,-0.029877,215.08,0.031544,-0.044943,0.99849,41.461
    13283 
    13284 > view matrix models
    13285 > #37,-0.95684,-0.22555,-0.18327,235.41,0.22555,-0.974,0.021102,173.18,-0.18327,-0.021145,0.98284,55.964
    13286 
    13287 > view matrix models
    13288 > #37,-0.95684,-0.22555,-0.18327,230.3,0.22555,-0.974,0.021102,164.37,-0.18327,-0.021145,0.98284,103.6
    13289 
    13290 > view matrix models
    13291 > #37,-0.71551,-0.36432,-0.59609,244.23,0.27076,-0.93118,0.24412,146.37,-0.644,0.013275,0.76491,146.06
    13292 
    13293 > view matrix models
    13294 > #37,-0.38059,-0.21113,-0.90032,230.74,0.23197,-0.96426,0.12806,157.34,-0.89517,-0.16011,0.41597,192.06
    13295 
    13296 > view matrix models
    13297 > #37,-0.38059,-0.21113,-0.90032,226.85,0.23197,-0.96426,0.12806,158.76,-0.89517,-0.16011,0.41597,189.5
    13298 
    13299 > fitmap #37 inMap #58
    13300 
    13301 Fit molecule 1ezx (#37) to map cryosparc_P371_J1247_003_volume_map (1).mrc
    13302 (#58) using 3984 atoms 
    13303 average map value = 0.0799, steps = 112 
    13304 shifted from previous position = 8.44 
    13305 rotated from previous position = 14 degrees 
    13306 atoms outside contour = 1944, contour level = 0.071265 
    13307  
    13308 Position of 1ezx (#37) relative to cryosparc_P371_J1247_003_volume_map (1).mrc
    13309 (#58) coordinates: 
    13310 Matrix rotation and translation 
    13311 -0.34799611 0.02716421 -0.93710235 206.67239671 
    13312 0.14052585 -0.98677538 -0.08078885 177.04596820 
    13313 -0.92690409 -0.15980131 0.33957672 198.01665488 
    13314 Axis -0.57025546 -0.07360376 0.81816330 
    13315 Axis point 168.54356692 102.18640974 0.00000000 
    13316 Rotation angle (degrees) 176.02747367 
    13317 Shift along axis 31.12264873 
    13318  
    13319 
    13320 > open "/Users/amy/Downloads/cryosparc_P371_J1247_003_volume_map (1).mrc"
    13321 
    13322 Opened cryosparc_P371_J1247_003_volume_map (1).mrc as #59, grid size
    13323 300,300,300, pixel 0.867, shown at level 0.0217, step 2, values float32 
    13324 
    13325 > volume #59 level 0.06978
    13326 
    13327 > hide #!58 models
    13328 
    13329 > mmaker #7 to #37
    13330 
    13331 Parameters 
    13332 --- 
    13333 Chain pairing | bb 
    13334 Alignment algorithm | Needleman-Wunsch 
    13335 Similarity matrix | BLOSUM-62 
    13336 SS fraction | 0.3 
    13337 Gap open (HH/SS/other) | 18/18/6 
    13338 Gap extend | 1 
    13339 SS matrix |  |  | H | S | O 
    13340 ---|---|---|--- 
    13341 H | 6 | -9 | -6 
    13342 S |  | 6 | -6 
    13343 O |  |  | 4 
    13344 Iteration cutoff | 2 
    13345  
    13346 Matchmaker 1ezx, chain C (#37) with 5a0c, chain A (#7), sequence alignment
    13347 score = 241.2 
    13348 RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
    13349 3.073) 
    13350  
    13351 
    13352 > show #7 models
    13353 
    13354 > hide #!59 models
    13355 
    13356 > show #!58 models
    13357 
    13358 > hide #!58 models
    13359 
    13360 > show #!59 models
    13361 
    13362 > transparency #59 50
    13363 
    13364 > ui mousemode right "map eraser"
    13365 
    13366 > hide #7 models
    13367 
    13368 > hide #!37 models
    13369 
    13370 > select subtract #37
    13371 
    13372 Nothing selected 
    13373 
    13374 > volume erase #59 center 116.15,104.56,160.67 radius 47.97
    13375 
    13376 Opened cryosparc_P371_J1247_003_volume_map (1).mrc copy as #61, grid size
    13377 300,300,300, pixel 0.867, shown at step 1, values float32 
    13378 
    13379 > volume erase #61 center 122.57,113.18,101.86 radius 47.97
    13380 
    13381 > ui mousemode right "translate selected models"
    13382 
    13383 > show #18 models
    13384 
    13385 > select #18/A:202
    13386 
    13387 6 atoms, 5 bonds, 1 residue, 1 model selected 
    13388 
    13389 > show sel atoms
    13390 
    13391 > rainbow sel
    13392 
    13393 > select add #18
    13394 
    13395 1883 atoms, 1745 bonds, 394 residues, 1 model selected 
    13396 
    13397 > select subtract #18
    13398 
    13399 Nothing selected 
    13400 
    13401 > show #!19 models
    13402 
    13403 > hide #!19 models
    13404 
    13405 > show #!19 models
    13406 
    13407 > hide #!19 models
    13408 
    13409 > hide #18 models
    13410 
    13411 > show #7 models
    13412 
    13413 > show #18 models
    13414 
    13415 > mmaker #18 to #7
    13416 
    13417 Parameters 
    13418 --- 
    13419 Chain pairing | bb 
    13420 Alignment algorithm | Needleman-Wunsch 
    13421 Similarity matrix | BLOSUM-62 
    13422 SS fraction | 0.3 
    13423 Gap open (HH/SS/other) | 18/18/6 
    13424 Gap extend | 1 
    13425 SS matrix |  |  | H | S | O 
    13426 ---|---|---|--- 
    13427 H | 6 | -9 | -6 
    13428 S |  | 6 | -6 
    13429 O |  |  | 4 
    13430 Iteration cutoff | 2 
    13431  
    13432 Matchmaker 5a0c, chain A (#7) with copy of 5a0c, chain A (#18), sequence
    13433 alignment score = 1112.7 
    13434 RMSD between 218 pruned atom pairs is 0.000 angstroms; (across all 218 pairs:
    13435 0.000) 
    13436  
    13437 
    13438 > color #18 #ed91dfff
    13439 
    13440 > color #18 #ebc5edff
    13441 
    13442 > fitmap #7 inMap #59
    13443 
    13444 Fit molecule 5a0c (#7) to map cryosparc_P371_J1247_003_volume_map (1).mrc
    13445 (#59) using 1883 atoms 
    13446 average map value = 0.0522, steps = 120 
    13447 shifted from previous position = 3.71 
    13448 rotated from previous position = 23.2 degrees 
    13449 atoms outside contour = 1476, contour level = 0.06978 
    13450  
    13451 Position of 5a0c (#7) relative to cryosparc_P371_J1247_003_volume_map (1).mrc
    13452 (#59) coordinates: 
    13453 Matrix rotation and translation 
    13454 -0.93248311 0.31677416 0.17357817 149.49808518 
    13455 -0.24611565 -0.20545531 -0.94721444 169.75896469 
    13456 -0.26439050 -0.92598178 0.26954669 154.83015425 
    13457 Axis 0.02975759 0.61381323 -0.78889024 
    13458 Axis point 98.48308815 127.59008236 0.00000000 
    13459 Rotation angle (degrees) 159.09861794 
    13460 Shift along axis -13.49499578 
    13461  
    13462 
    13463 > hide #18 models
    13464 
    13465 > ui mousemode right "map eraser"
    13466 
    13467 > volume erase #61 center 140.38,143.93,165.02 radius 9.1821
    13468 
    13469 > volume erase #61 center 135.35,144.22,156.8 radius 9.1821
    13470 
    13471 > volume erase #61 center 126.68,146.69,162.17 radius 9.1821
    13472 
    13473 > ui mousemode right "translate selected models"
    13474 
    13475 > fitmap #7 inMap #59
    13476 
    13477 Fit molecule 5a0c (#7) to map cryosparc_P371_J1247_003_volume_map (1).mrc
    13478 (#59) using 1883 atoms 
    13479 average map value = 0.0522, steps = 48 
    13480 shifted from previous position = 0.00729 
    13481 rotated from previous position = 0.02 degrees 
    13482 atoms outside contour = 1476, contour level = 0.06978 
    13483  
    13484 Position of 5a0c (#7) relative to cryosparc_P371_J1247_003_volume_map (1).mrc
    13485 (#59) coordinates: 
    13486 Matrix rotation and translation 
    13487 -0.93245587 0.31693119 0.17343780 149.49596389 
    13488 -0.24610156 -0.20574256 -0.94715575 169.75337215 
    13489 -0.26449966 -0.92586426 0.26984311 154.82942667 
    13490 Axis 0.02983605 0.61368746 -0.78898511 
    13491 Axis point 98.49093754 127.56704910 0.00000000 
    13492 Rotation angle (degrees) 159.09569307 
    13493 Shift along axis -13.52222698 
    13494  
    13495 
    13496 > mmaker #7 to #18
    13497 
    13498 Parameters 
    13499 --- 
    13500 Chain pairing | bb 
    13501 Alignment algorithm | Needleman-Wunsch 
    13502 Similarity matrix | BLOSUM-62 
    13503 SS fraction | 0.3 
    13504 Gap open (HH/SS/other) | 18/18/6 
    13505 Gap extend | 1 
    13506 SS matrix |  |  | H | S | O 
    13507 ---|---|---|--- 
    13508 H | 6 | -9 | -6 
    13509 S |  | 6 | -6 
    13510 O |  |  | 4 
    13511 Iteration cutoff | 2 
    13512  
    13513 Matchmaker copy of 5a0c, chain A (#18) with 5a0c, chain A (#7), sequence
    13514 alignment score = 1112.7 
    13515 RMSD between 218 pruned atom pairs is 0.000 angstroms; (across all 218 pairs:
    13516 0.000) 
    13517  
    13518 
    13519 > fitmap #7 inMap #59
    13520 
    13521 Fit molecule 5a0c (#7) to map cryosparc_P371_J1247_003_volume_map (1).mrc
    13522 (#59) using 1883 atoms 
    13523 average map value = 0.0522, steps = 120 
    13524 shifted from previous position = 3.71 
    13525 rotated from previous position = 23.2 degrees 
    13526 atoms outside contour = 1476, contour level = 0.06978 
    13527  
    13528 Position of 5a0c (#7) relative to cryosparc_P371_J1247_003_volume_map (1).mrc
    13529 (#59) coordinates: 
    13530 Matrix rotation and translation 
    13531 -0.93249206 0.31673033 0.17361005 149.49824725 
    13532 -0.24614085 -0.20547558 -0.94720350 169.75915732 
    13533 -0.26433545 -0.92599227 0.26956462 154.82905865 
    13534 Axis 0.02972878 0.61380618 -0.78889681 
    13535 Axis point 98.47960888 127.58948855 0.00000000 
    13536 Rotation angle (degrees) 159.09952411 
    13537 Shift along axis -13.50053159 
    13538  
    13539 
    13540 > volume #61 level 0.07557
    13541 
    13542 > open /Users/amy/Downloads/cryosparc_P483_J188_006_volume_map.mrc
    13543 
    13544 Opened cryosparc_P483_J188_006_volume_map.mrc as #60, grid size 400,400,400,
    13545 pixel 0.723, shown at level 0.0122, step 2, values float32 
    13546 
    13547 > volume #60 level 0.04049
    13548 
    13549 > hide #7 models
    13550 
    13551 > close #39-56
    13552 
    13553 > transparency #60 50
    13554 
    13555 > show #!57 models
    13556 
    13557 > select add #57
    13558 
    13559 1009 atoms, 1014 bonds, 5 pseudobonds, 155 residues, 3 models selected 
    13560 
    13561 > select subtract #57
    13562 
    13563 Nothing selected 
    13564 
    13565 > hide #!57 models
    13566 
    13567 > show #!38 models
    13568 
    13569 > select add #38
    13570 
    13571 6282 atoms, 6138 bonds, 1077 residues, 1 model selected 
    13572 
    13573 > view matrix models
    13574 > #38,0.70129,-0.71169,-0.041051,59.454,0.277,0.32511,-0.9042,89.328,0.65685,0.62274,0.42514,10.395
    13575 
    13576 > view matrix models
    13577 > #38,0.68049,0.72218,0.12406,5.6594,-0.15756,0.30955,-0.93774,159.08,-0.71562,0.61858,0.32443,228.89
    13578 
    13579 > view matrix models
    13580 > #38,0.7111,0.6991,0.074864,2.3195,-0.17274,0.27693,-0.94523,162.83,-0.68154,0.65922,0.31769,222.03
    13581 
    13582 > volume flip #60 axis z
    13583 
    13584 Opened cryosparc_P483_J188_006_volume_map.mrc z flip as #39, grid size
    13585 400,400,400, pixel 0.723, shown at step 1, values float32 
    13586 
    13587 > view matrix models
    13588 > #38,-0.79214,-0.23105,-0.56492,283.77,0.39756,0.50697,-0.76481,61.539,0.4631,-0.83042,-0.30973,105.99
    13589 
    13590 > view matrix models
    13591 > #38,-0.72246,-0.55636,-0.41051,283.31,0.053262,0.54717,-0.83532,115.33,0.68936,-0.62535,-0.36568,63.032
    13592 
    13593 > view matrix models
    13594 > #38,-0.72246,-0.55636,-0.41051,283.27,0.053262,0.54717,-0.83532,115.31,0.68936,-0.62535,-0.36568,63.21
    13595 
    13596 > view matrix models
    13597 > #38,-0.75346,-0.22412,-0.61812,278.02,0.32917,0.68524,-0.64969,64.051,0.56917,-0.69298,-0.44252,85.775
    13598 
    13599 > view matrix models
    13600 > #38,-0.75346,-0.22412,-0.61812,277.72,0.32917,0.68524,-0.64969,62.337,0.56917,-0.69298,-0.44252,89.988
    13601 
    13602 > view matrix models
    13603 > #38,-0.75346,-0.22412,-0.61812,274.8,0.32917,0.68524,-0.64969,60.25,0.56917,-0.69298,-0.44252,90.357
    13604 
    13605 > fitmap #38 inMap #39
    13606 
    13607 Fit molecule 9hud (#38) to map cryosparc_P483_J188_006_volume_map.mrc z flip
    13608 (#39) using 6282 atoms 
    13609 average map value = 0.07719, steps = 140 
    13610 shifted from previous position = 5.69 
    13611 rotated from previous position = 10.5 degrees 
    13612 atoms outside contour = 1975, contour level = 0.040487 
    13613  
    13614 Position of 9hud (#38) relative to cryosparc_P483_J188_006_volume_map.mrc z
    13615 flip (#39) coordinates: 
    13616 Matrix rotation and translation 
    13617 -0.69481285 -0.38668893 -0.60638839 274.92375859 
    13618 0.29518489 0.61552849 -0.73074671 73.34577149 
    13619 0.65582093 -0.68672881 -0.31353236 73.10268242 
    13620 Axis 0.03066826 -0.87940971 0.47507687 
    13621 Axis point 118.71936211 0.00000000 122.64604224 
    13622 Rotation angle (degrees) 134.13955008 
    13623 Shift along axis -21.34015667 
    13624  
    13625 
    13626 > mmaker #37 to #38
    13627 
    13628 Parameters 
    13629 --- 
    13630 Chain pairing | bb 
    13631 Alignment algorithm | Needleman-Wunsch 
    13632 Similarity matrix | BLOSUM-62 
    13633 SS fraction | 0.3 
    13634 Gap open (HH/SS/other) | 18/18/6 
    13635 Gap extend | 1 
    13636 SS matrix |  |  | H | S | O 
    13637 ---|---|---|--- 
    13638 H | 6 | -9 | -6 
    13639 S |  | 6 | -6 
    13640 O |  |  | 4 
    13641 Iteration cutoff | 2 
    13642  
    13643 Matchmaker 9hud, chain A (#38) with 1ezx, chain A (#37), sequence alignment
    13644 score = 1674.4 
    13645 RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
    13646 0.519) 
    13647  
    13648 
    13649 > select subtract #38
    13650 
    13651 Nothing selected 
    13652 
    13653 > show #!37 models
    13654 
    13655 > hide #!38 models
    13656 
    13657 > show #!57 models
    13658 
    13659 > mmaker #57 to #37
    13660 
    13661 Parameters 
    13662 --- 
    13663 Chain pairing | bb 
    13664 Alignment algorithm | Needleman-Wunsch 
    13665 Similarity matrix | BLOSUM-62 
    13666 SS fraction | 0.3 
    13667 Gap open (HH/SS/other) | 18/18/6 
    13668 Gap extend | 1 
    13669 SS matrix |  |  | H | S | O 
    13670 ---|---|---|--- 
    13671 H | 6 | -9 | -6 
    13672 S |  | 6 | -6 
    13673 O |  |  | 4 
    13674 Iteration cutoff | 2 
    13675  
    13676 Matchmaker 1ezx, chain C (#37) with copy of 1ezx, chain C (#57), sequence
    13677 alignment score = 1096 
    13678 RMSD between 140 pruned atom pairs is 0.000 angstroms; (across all 140 pairs:
    13679 0.000) 
    13680  
    13681 
    13682 > hide #!37 models
    13683 
    13684 > select add #57
    13685 
    13686 1009 atoms, 1014 bonds, 5 pseudobonds, 155 residues, 3 models selected 
    13687 
    13688 > view matrix models
    13689 > #57,-0.96139,-0.27328,-0.032326,225.27,0.26293,-0.87755,-0.40098,194.89,0.081212,-0.39399,0.91552,76.751
    13690 
    13691 > view matrix models
    13692 > #57,-0.98395,-0.080553,-0.1592,229.11,0.11527,-0.96807,-0.2226,199.83,-0.13619,-0.23738,0.96182,88.362
    13693 
    13694 > view matrix models
    13695 > #57,-0.98395,-0.080553,-0.1592,229.13,0.11527,-0.96807,-0.2226,200.95,-0.13619,-0.23738,0.96182,87.592
    13696 
    13697 > view matrix models
    13698 > #57,-0.94283,-0.24393,0.22707,209.83,0.18457,-0.94952,-0.25367,196.49,0.27748,-0.19726,0.94026,54.255
    13699 
    13700 > view matrix models
    13701 > #57,-0.94283,-0.24393,0.22707,211.13,0.18457,-0.94952,-0.25367,198.21,0.27748,-0.19726,0.94026,55.521
    13702 
    13703 > view matrix models
    13704 > #57,-0.93042,-0.31273,0.19109,213.56,0.19345,-0.86193,-0.46866,206.45,0.31127,-0.39909,0.86246,61.443
    13705 
    13706 > view matrix models
    13707 > #57,-0.93042,-0.31273,0.19109,212.58,0.19345,-0.86193,-0.46866,206.1,0.31127,-0.39909,0.86246,60.836
    13708 
    13709 > view matrix models
    13710 > #57,-0.84274,-0.44664,0.3005,202.99,0.29429,-0.84967,-0.43756,196.06,0.45076,-0.28032,0.84749,47.549
    13711 
    13712 > view matrix models
    13713 > #57,-0.84274,-0.44664,0.3005,204.01,0.29429,-0.84967,-0.43756,196.43,0.45076,-0.28032,0.84749,48.186
    13714 
    13715 > view matrix models
    13716 > #57,-0.84274,-0.44664,0.3005,205.89,0.29429,-0.84967,-0.43756,195.12,0.45076,-0.28032,0.84749,50.177
    13717 
    13718 > view matrix models
    13719 > #57,-0.40829,-0.80923,0.42242,172.87,0.75449,-0.55964,-0.34285,146.27,0.51385,0.17873,0.83905,34.853
    13720 
    13721 > view matrix models
    13722 > #57,-0.40829,-0.80923,0.42242,177.69,0.75449,-0.55964,-0.34285,148.99,0.51385,0.17873,0.83905,33.682
    13723 
    13724 > view matrix models
    13725 > #57,-0.26229,-0.78164,0.56591,157.89,0.82741,-0.48394,-0.28493,138.37,0.49658,0.39351,0.77367,33.446
    13726 
    13727 > view matrix models
    13728 > #57,-0.50448,-0.84508,0.17704,198.87,0.77252,-0.53335,-0.34461,147.01,0.38565,-0.037082,0.9219,44.834
    13729 
    13730 > view matrix models
    13731 > #57,-0.50448,-0.84508,0.17704,197.7,0.77252,-0.53335,-0.34461,146.01,0.38565,-0.037082,0.9219,43.5
    13732 
    13733 > view matrix models
    13734 > #57,-0.55352,-0.81516,0.17067,201.3,0.76006,-0.57821,-0.29661,145.6,0.34047,-0.03446,0.93962,46.193
    13735 
    13736 > view matrix models
    13737 > #57,-0.55352,-0.81516,0.17067,201,0.76006,-0.57821,-0.29661,144.01,0.34047,-0.03446,0.93962,46.083
    13738 
    13739 > view matrix models
    13740 > #57,0.19927,-0.70806,0.67745,111.26,0.40682,-0.56916,-0.71453,193.98,0.89151,0.41799,0.17463,30.057
    13741 
    13742 > fitmap #57 inMap #39
    13743 
    13744 Fit molecule copy of 1ezx (#57) to map cryosparc_P483_J188_006_volume_map.mrc
    13745 z flip (#39) using 1009 atoms 
    13746 average map value = 0.0293, steps = 168 
    13747 shifted from previous position = 3.46 
    13748 rotated from previous position = 14.9 degrees 
    13749 atoms outside contour = 704, contour level = 0.040487 
    13750  
    13751 Position of copy of 1ezx (#57) relative to
    13752 cryosparc_P483_J188_006_volume_map.mrc z flip (#39) coordinates: 
    13753 Matrix rotation and translation 
    13754 -0.00776067 -0.76663470 0.64203663 129.30975418 
    13755 0.53267917 -0.54654599 -0.64617367 178.30805215 
    13756 0.84628169 0.33698479 0.41261190 20.94708234 
    13757 Axis 0.59871569 -0.12437946 0.79124539 
    13758 Axis point -5.11418337 119.30863791 0.00000000 
    13759 Rotation angle (degrees) 124.80933717 
    13760 Shift along axis 71.81620095 
    13761  
    13762 
    13763 > view matrix models
    13764 > #57,-0.84354,-0.47018,0.25957,209.7,0.35522,-0.85092,-0.38698,186.48,0.40282,-0.23422,0.8848,45.964
    13765 
    13766 > view matrix models
    13767 > #57,-0.84354,-0.47018,0.25957,210.5,0.35522,-0.85092,-0.38698,187.68,0.40282,-0.23422,0.8848,46.627
    13768 
    13769 > view matrix models
    13770 > #57,-0.91572,-0.40165,-0.011594,228.63,0.39352,-0.89061,-0.22795,177.36,0.081229,-0.2133,0.9736,67.651
    13771 
    13772 > view matrix models
    13773 > #57,-0.91572,-0.40165,-0.011594,228.49,0.39352,-0.89061,-0.22795,177.31,0.081229,-0.2133,0.9736,67.495
    13774 
    13775 > fitmap #57 inMap #39
    13776 
    13777 Fit molecule copy of 1ezx (#57) to map cryosparc_P483_J188_006_volume_map.mrc
    13778 z flip (#39) using 1009 atoms 
    13779 average map value = 0.03023, steps = 128 
    13780 shifted from previous position = 2.17 
    13781 rotated from previous position = 27.6 degrees 
    13782 atoms outside contour = 692, contour level = 0.040487 
    13783  
    13784 Position of copy of 1ezx (#57) relative to
    13785 cryosparc_P483_J188_006_volume_map.mrc z flip (#39) coordinates: 
    13786 Matrix rotation and translation 
    13787 -0.97588300 -0.21795429 0.01217931 226.13416383 
    13788 0.16332980 -0.76604383 -0.62169145 212.61271533 
    13789 0.14483021 -0.60470887 0.78316756 80.91608083 
    13790 Axis 0.04203015 -0.32829732 0.94363888 
    13791 Axis point 99.48152797 132.57508735 0.00000000 
    13792 Rotation angle (degrees) 168.34438880 
    13793 Shift along axis 16.05982811 
    13794  
    13795 
    13796 > select subtract #57
    13797 
    13798 Nothing selected 
    13799 
    13800 > volume gaussian #39 sDev 2
    13801 
    13802 Opened cryosparc_P483_J188_006_volume_map.mrc z flip gaussian as #40, grid
    13803 size 400,400,400, pixel 0.723, shown at step 1, values float32 
    13804 
    13805 > open /Users/amy/Downloads/cryosparc_P483_molmap_of_combined_6A.mrc
    13806 
    13807 Opened cryosparc_P483_molmap_of_combined_6A.mrc as #41, grid size 200,200,200,
    13808 pixel 1, shown at level 0.293, step 1, values float32 
    13809 
    13810 > transparency #41 50
    13811 
    13812 > show #!37 models
    13813 
    13814 > select add #37
    13815 
    13816 3984 atoms, 3982 bonds, 5 pseudobonds, 592 residues, 3 models selected 
    13817 
    13818 > view matrix models
    13819 > #37,-0.96139,-0.27328,-0.032326,218.59,0.26293,-0.87755,-0.40098,146.69,0.081212,-0.39399,0.91552,81.851
    13820 
    13821 > view matrix models
    13822 > #37,-0.049922,0.49391,-0.86808,164.61,0.32699,-0.81318,-0.48148,143.6,-0.94371,-0.30789,-0.12091,207.3
    13823 
    13824 > view matrix models
    13825 > #37,0.78493,0.53816,-0.30703,72.795,0.33958,-0.78815,-0.51332,143.29,-0.51824,0.29866,-0.80139,186.1
    13826 
    13827 > view matrix models
    13828 > #37,0.48345,-0.22115,0.84698,66.159,0.004741,-0.96689,-0.25517,160.69,0.87536,0.12738,-0.46639,79.548
    13829 
    13830 > view matrix models
    13831 > #37,-0.49427,-0.19074,0.84812,131.98,0.13352,-0.98071,-0.14275,146.1,0.85899,0.04269,0.51021,29.25
    13832 
    13833 > view matrix models
    13834 > #37,-0.87073,-0.2065,0.44631,181.66,0.14198,-0.97448,-0.17389,146.97,0.47082,-0.088043,0.87782,41.66
    13835 
    13836 > view matrix models
    13837 > #37,-0.87073,-0.2065,0.44631,183.6,0.14198,-0.97448,-0.17389,140.36,0.47082,-0.088043,0.87782,41.006
    13838 
    13839 > view matrix models
    13840 > #37,-0.83015,0.067283,-0.55346,223.99,0.083286,-0.96659,-0.24243,147.91,-0.55128,-0.24735,0.79681,124.17
    13841 
    13842 > view matrix models
    13843 > #37,-0.83015,0.067283,-0.55346,229.16,0.083286,-0.96659,-0.24243,155.6,-0.55128,-0.24735,0.79681,121.21
    13844 
    13845 > view matrix models
    13846 > #37,-0.76415,-0.19095,-0.61612,241.25,0.333,-0.93483,-0.12329,129.98,-0.55243,-0.29938,0.77794,124.99
    13847 
    13848 > fitmap #37 inMap #41
    13849 
    13850 Fit molecule 1ezx (#37) to map cryosparc_P483_molmap_of_combined_6A.mrc (#41)
    13851 using 3984 atoms 
    13852 average map value = 0.4227, steps = 272 
    13853 shifted from previous position = 34.2 
    13854 rotated from previous position = 34.8 degrees 
    13855 atoms outside contour = 366, contour level = 0.29336 
    13856  
    13857 Position of 1ezx (#37) relative to cryosparc_P483_molmap_of_combined_6A.mrc
    13858 (#41) coordinates: 
    13859 Matrix rotation and translation 
    13860 -0.39076986 0.10890222 -0.91402362 198.79794072 
    13861 0.07022585 -0.98655567 -0.14756757 150.28581374 
    13862 -0.91780564 -0.12185304 0.37786848 136.15090391 
    13863 Axis 0.55183393 0.08116225 -0.82999519 
    13864 Axis point 145.70964793 80.43889324 0.00000000 
    13865 Rotation angle (degrees) 178.66493597 
    13866 Shift along axis 8.89638759 
    13867  
    13868 
    13869 > mmaker #7 to #37
    13870 
    13871 Parameters 
    13872 --- 
    13873 Chain pairing | bb 
    13874 Alignment algorithm | Needleman-Wunsch 
    13875 Similarity matrix | BLOSUM-62 
    13876 SS fraction | 0.3 
    13877 Gap open (HH/SS/other) | 18/18/6 
    13878 Gap extend | 1 
    13879 SS matrix |  |  | H | S | O 
    13880 ---|---|---|--- 
    13881 H | 6 | -9 | -6 
    13882 S |  | 6 | -6 
    13883 O |  |  | 4 
    13884 Iteration cutoff | 2 
    13885  
    13886 Matchmaker 1ezx, chain C (#37) with 5a0c, chain A (#7), sequence alignment
    13887 score = 241.2 
    13888 RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
    13889 3.073) 
    13890  
    13891 
    13892 > show #7 models
    13893 
    13894 > show #!8 models
    13895 
    13896 > mmaker #8 to #7
    13897 
    13898 Parameters 
    13899 --- 
    13900 Chain pairing | bb 
    13901 Alignment algorithm | Needleman-Wunsch 
    13902 Similarity matrix | BLOSUM-62 
    13903 SS fraction | 0.3 
    13904 Gap open (HH/SS/other) | 18/18/6 
    13905 Gap extend | 1 
    13906 SS matrix |  |  | H | S | O 
    13907 ---|---|---|--- 
    13908 H | 6 | -9 | -6 
    13909 S |  | 6 | -6 
    13910 O |  |  | 4 
    13911 Iteration cutoff | 2 
    13912  
    13913 Matchmaker 5a0c, chain A (#7) with 1ezx, chain C (#8), sequence alignment
    13914 score = 241.2 
    13915 RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
    13916 3.073) 
    13917  
    13918 
    13919 > select #8/A
    13920 
    13921 2686 atoms, 2674 bonds, 398 residues, 1 model selected 
    13922 
    13923 > delete #8/A
    13924 
    13925 > select #8/B
    13926 
    13927 289 atoms, 294 bonds, 39 residues, 1 model selected 
    13928 
    13929 > delete #8/B
    13930 
    13931 > close #8
    13932 
    13933 > show #!31 models
    13934 
    13935 > mmaker #31 t o#7
    13936 
    13937 > matchmaker #31 to o#7
    13938 
    13939 Invalid "to" argument: invalid atoms specifier 
    13940 
    13941 > mmaker #31 t to#7
    13942 
    13943 > matchmaker #31 to to#7
    13944 
    13945 Invalid "to" argument: invalid atoms specifier 
    13946 
    13947 > mmaker #31 to #7
    13948 
    13949 Parameters 
    13950 --- 
    13951 Chain pairing | bb 
    13952 Alignment algorithm | Needleman-Wunsch 
    13953 Similarity matrix | BLOSUM-62 
    13954 SS fraction | 0.3 
    13955 Gap open (HH/SS/other) | 18/18/6 
    13956 Gap extend | 1 
    13957 SS matrix |  |  | H | S | O 
    13958 ---|---|---|--- 
    13959 H | 6 | -9 | -6 
    13960 S |  | 6 | -6 
    13961 O |  |  | 4 
    13962 Iteration cutoff | 2 
    13963  
    13964 Matchmaker 5a0c, chain A (#7) with copy of copy of copy of 1ezx, chain A
    13965 (#31), sequence alignment score = 25.4 
    13966 RMSD between 4 pruned atom pairs is 1.006 angstroms; (across all 34 pairs:
    13967 19.211) 
    13968  
    13969 
    13970 > mmaker #31 to #37
    13971 
    13972 Parameters 
    13973 --- 
    13974 Chain pairing | bb 
    13975 Alignment algorithm | Needleman-Wunsch 
    13976 Similarity matrix | BLOSUM-62 
    13977 SS fraction | 0.3 
    13978 Gap open (HH/SS/other) | 18/18/6 
    13979 Gap extend | 1 
    13980 SS matrix |  |  | H | S | O 
    13981 ---|---|---|--- 
    13982 H | 6 | -9 | -6 
    13983 S |  | 6 | -6 
    13984 O |  |  | 4 
    13985 Iteration cutoff | 2 
    13986  
    13987 Matchmaker 1ezx, chain A (#37) with copy of copy of copy of 1ezx, chain A
    13988 (#31), sequence alignment score = 1734 
    13989 RMSD between 335 pruned atom pairs is 0.000 angstroms; (across all 335 pairs:
    13990 0.000) 
    13991  
    13992 
    13993 > hide #!37 models
    13994 
    13995 > hide #!41 models
    13996 
    13997 > hide #!57 models
    13998 
    13999 > combine #7,31 modelId #42 name AATHNEcombined
    14000 
    14001 Remapping chain ID 'A' in copy of copy of copy of 1ezx #31 to 'C' 
    14002 
    14003 > hide #!31 models
    14004 
    14005 > hide #7 models
    14006 
    14007 > molmap #42 6
    14008 
    14009 Opened AATHNEcombined map 6 as #8, grid size 43,51,63, pixel 2, shown at level
    14010 0.107, step 1, values float32 
    14011 
    14012 > volume #8 level 0.4678
    14013 
    14014 > hide #!42 models
    14015 
    14016 > volume #8 level 0.4143
    14017 
    14018 > transparency #8 50
    14019 
    14020 > show #!29 models
    14021 
    14022 > select add #8
    14023 
    14024 2 models selected 
    14025 
    14026 > view matrix models
    14027 > #8,-0.94731,0.3033,-0.10305,152.68,-0.052376,-0.46403,-0.88427,177.46,-0.31602,-0.83228,0.45547,210.1
    14028 
    14029 > view matrix models
    14030 > #8,-0.67966,0.68715,-0.25667,146.07,0.0014291,-0.34867,-0.93725,176.15,-0.73352,-0.63738,0.23599,220.93
    14031 
    14032 > select subtract #8
    14033 
    14034 Nothing selected 
    14035 
    14036 > select add #8
    14037 
    14038 2 models selected 
    14039 
    14040 > view matrix models
    14041 > #8,-0.80209,0.59535,-0.046957,144.36,-0.15685,-0.28587,-0.94534,180.87,-0.57624,-0.75089,0.32268,217.17
    14042 
    14043 > view matrix models
    14044 > #8,-0.98552,0.057058,-0.15966,159.48,0.11645,-0.45668,-0.88198,176.33,-0.12324,-0.8878,0.44342,206.47
    14045 
    14046 > select subtract #8
    14047 
    14048 Nothing selected 
    14049 
    14050 > fitmap #8 inMap #29
    14051 
    14052 Fit map AATHNEcombined map 6 in map J1122.mrc using 3370 points 
    14053 correlation = -0.06744, correlation about mean = 0.03351, overlap = -0.3948 
    14054 steps = 72, shift = 3.07, angle = 5.37 degrees 
    14055  
    14056 Position of AATHNEcombined map 6 (#8) relative to J1122.mrc (#29) coordinates: 
    14057 Matrix rotation and translation 
    14058 -0.99402372 -0.01790342 -0.10768616 160.40909895 
    14059 0.10457674 -0.43913839 -0.89231227 175.73306960 
    14060 -0.03131369 -0.89824103 0.43838626 207.83747749 
    14061 Axis -0.04104025 -0.52866794 0.84783601 
    14062 Axis point 80.62201678 156.15315639 0.00000000 
    14063 Rotation angle (degrees) 175.85785915 
    14064 Shift along axis 76.72442836 
    14065  
    14066 
    14067 > volume #8 level 0.3659
    14068 
    14069 > view
    14070 
    14071 > volume #29 level 0.06441
    14072 
    14073 > show #!42 models
    14074 
    14075 > select add #42
    14076 
    14077 4858 atoms, 4713 bonds, 831 residues, 1 model selected 
    14078 
    14079 > view matrix models
    14080 > #42,-0.94731,0.3033,-0.10305,202.51,-0.052376,-0.46403,-0.88427,151.25,-0.31602,-0.83228,0.45547,188.42
    14081 
    14082 > view matrix models
    14083 > #42,-0.065313,0.66691,-0.74227,198.13,-0.22175,-0.73496,-0.64083,151.68,-0.97291,0.12274,0.19589,194.19
    14084 
    14085 > view matrix models
    14086 > #42,0.76996,0.12763,-0.6252,186.82,-0.51684,-0.44988,-0.72835,155.58,-0.37422,0.88392,-0.28042,184.85
    14087 
    14088 > view matrix models
    14089 > #42,0.26956,0.68406,-0.67779,189.68,-0.23721,-0.63498,-0.73521,153.14,-0.93331,0.35896,-0.0088999,195.67
    14090 
    14091 > view matrix models
    14092 > #42,0.16808,0.4812,-0.86035,199.68,0.12383,-0.87616,-0.46585,142.27,-0.97797,-0.028238,-0.20685,207.72
    14093 
    14094 > view matrix models
    14095 > #42,0.16808,0.4812,-0.86035,176.9,0.12383,-0.87616,-0.46585,168.91,-0.97797,-0.028238,-0.20685,243.77
    14096 
    14097 > view matrix models
    14098 > #42,-0.098371,0.74921,-0.65499,172.34,0.16185,-0.63737,-0.75337,172.69,-0.9819,-0.18012,-0.058563,241.94
    14099 
    14100 > view matrix models
    14101 > #42,-0.098371,0.74921,-0.65499,168.3,0.16185,-0.63737,-0.75337,164.55,-0.9819,-0.18012,-0.058563,240.14
    14102 
    14103 > fitmap #42 inMap #8
    14104 
    14105 Fit molecule AATHNEcombined (#42) to map AATHNEcombined map 6 (#8) using 4858
    14106 atoms 
    14107 average map value = 0.4401, steps = 236 
    14108 shifted from previous position = 23.5 
    14109 rotated from previous position = 81.6 degrees 
    14110 atoms outside contour = 1171, contour level = 0.36586 
    14111  
    14112 Position of AATHNEcombined (#42) relative to AATHNEcombined map 6 (#8)
    14113 coordinates: 
    14114 Matrix rotation and translation 
    14115 0.99999997 0.00012320 0.00021381 -0.02142066 
    14116 -0.00012322 0.99999999 0.00009509 0.00213481 
    14117 -0.00021379 -0.00009512 0.99999997 0.00632785 
    14118 Axis -0.35962131 0.80845713 -0.46590727 
    14119 Axis point 43.71009619 0.00000000 89.29249519 
    14120 Rotation angle (degrees) 0.01515213 
    14121 Shift along axis 0.00648103 
    14122  
    14123 
    14124 > select subtract #42
    14125 
    14126 Nothing selected 
    14127 
    14128 > hide #!42 models
    14129 
    14130 > show #!42 models
    14131 
    14132 > combine #42 close false
    14133 
    14134 > select add #43
    14135 
    14136 4858 atoms, 4713 bonds, 831 residues, 1 model selected 
    14137 
    14138 > view matrix models
    14139 > #43,-0.994,-0.018016,-0.1079,166.09,0.10482,-0.43904,-0.89233,181.76,-0.031297,-0.89829,0.43829,253.22
    14140 
    14141 > view matrix models
    14142 > #43,-0.994,-0.018016,-0.1079,167.72,0.10482,-0.43904,-0.89233,183.32,-0.031297,-0.89829,0.43829,266.56
    14143 
    14144 > select subtract #43
    14145 
    14146 Nothing selected 
    14147 
    14148 > hide #!42 models
    14149 
    14150 > select add #43/A:94
    14151 
    14152 9 atoms, 8 bonds, 1 residue, 1 model selected 
    14153 
    14154 > select add #43/A:93
    14155 
    14156 20 atoms, 19 bonds, 2 residues, 1 model selected 
    14157 
    14158 > select add #43/A:92
    14159 
    14160 28 atoms, 26 bonds, 3 residues, 1 model selected 
    14161 
    14162 > select add #43/A:91
    14163 
    14164 39 atoms, 36 bonds, 4 residues, 1 model selected 
    14165 
    14166 > select add #43/A:90
    14167 
    14168 48 atoms, 44 bonds, 5 residues, 1 model selected 
    14169 
    14170 > select add #43/A:89
    14171 
    14172 55 atoms, 50 bonds, 6 residues, 1 model selected 
    14173 
    14174 > select add #43/A:88
    14175 
    14176 60 atoms, 54 bonds, 7 residues, 1 model selected 
    14177 
    14178 > select add #43/A:87
    14179 
    14180 71 atoms, 65 bonds, 8 residues, 1 model selected 
    14181 
    14182 > select add #43/A:86
    14183 
    14184 78 atoms, 71 bonds, 9 residues, 1 model selected 
    14185 
    14186 > select subtract #43/A:86
    14187 
    14188 71 atoms, 65 bonds, 8 residues, 1 model selected 
    14189 
    14190 > select add #43/A:86
    14191 
    14192 78 atoms, 71 bonds, 9 residues, 1 model selected 
    14193 
    14194 > select add #43/A:85
    14195 
    14196 87 atoms, 79 bonds, 10 residues, 1 model selected 
    14197 
    14198 > select add #43/A:84
    14199 
    14200 98 atoms, 89 bonds, 11 residues, 1 model selected 
    14201 
    14202 > select add #43/A:83
    14203 
    14204 105 atoms, 95 bonds, 12 residues, 1 model selected 
    14205 
    14206 > select add #43/A:82
    14207 
    14208 112 atoms, 102 bonds, 13 residues, 1 model selected 
    14209 
    14210 > select add #43/A:81
    14211 
    14212 121 atoms, 110 bonds, 14 residues, 1 model selected 
    14213 
    14214 > select add #43/A:80
    14215 
    14216 132 atoms, 120 bonds, 15 residues, 1 model selected 
    14217 
    14218 > select add #43/A:79
    14219 
    14220 143 atoms, 130 bonds, 16 residues, 1 model selected 
    14221 
    14222 > select add #43/A:77
    14223 
    14224 151 atoms, 137 bonds, 17 residues, 1 model selected 
    14225 
    14226 > select add #43/A:78
    14227 
    14228 157 atoms, 142 bonds, 18 residues, 1 model selected 
    14229 
    14230 > select add #43/A:76
    14231 
    14232 165 atoms, 149 bonds, 19 residues, 1 model selected 
    14233 
    14234 > select add #43/A:75
    14235 
    14236 175 atoms, 159 bonds, 20 residues, 1 model selected 
    14237 
    14238 > select add #43/A:74
    14239 
    14240 180 atoms, 163 bonds, 21 residues, 1 model selected 
    14241 
    14242 > select add #43/A:73
    14243 
    14244 184 atoms, 166 bonds, 22 residues, 1 model selected 
    14245 
    14246 > select add #43/A:72
    14247 
    14248 192 atoms, 173 bonds, 23 residues, 1 model selected 
    14249 
    14250 > select add #43/A:71
    14251 
    14252 199 atoms, 179 bonds, 24 residues, 1 model selected 
    14253 
    14254 > select add #43/A:70
    14255 
    14256 206 atoms, 185 bonds, 25 residues, 1 model selected 
    14257 
    14258 > select add #43/A:69
    14259 
    14260 217 atoms, 195 bonds, 26 residues, 1 model selected 
    14261 
    14262 > select add #43/A:54
    14263 
    14264 223 atoms, 200 bonds, 27 residues, 1 model selected 
    14265 
    14266 > select subtract #43/A:54
    14267 
    14268 217 atoms, 195 bonds, 26 residues, 1 model selected 
    14269 
    14270 > select add #43/A:68
    14271 
    14272 224 atoms, 201 bonds, 27 residues, 1 model selected 
    14273 
    14274 > select add #43/A:66
    14275 
    14276 229 atoms, 205 bonds, 28 residues, 1 model selected 
    14277 
    14278 > select add #43/A:65
    14279 
    14280 240 atoms, 215 bonds, 29 residues, 1 model selected 
    14281 
    14282 > select add #43/A:64
    14283 
    14284 247 atoms, 221 bonds, 30 residues, 1 model selected 
    14285 
    14286 > select add #43/A:63
    14287 
    14288 255 atoms, 228 bonds, 31 residues, 1 model selected 
    14289 
    14290 > select add #43/A:62
    14291 
    14292 262 atoms, 234 bonds, 32 residues, 1 model selected 
    14293 
    14294 > select add #43/A:61
    14295 
    14296 270 atoms, 241 bonds, 33 residues, 1 model selected 
    14297 
    14298 > select add #43/A:60
    14299 
    14300 275 atoms, 245 bonds, 34 residues, 1 model selected 
    14301 
    14302 > select add #43/A:59
    14303 
    14304 282 atoms, 251 bonds, 35 residues, 1 model selected 
    14305 
    14306 > select add #43/A:58
    14307 
    14308 288 atoms, 256 bonds, 36 residues, 1 model selected 
    14309 
    14310 > select add #43/A:57
    14311 
    14312 298 atoms, 266 bonds, 37 residues, 1 model selected 
    14313 
    14314 > select add #43/A:56
    14315 
    14316 303 atoms, 270 bonds, 38 residues, 1 model selected 
    14317 
    14318 > select add #43/A:55
    14319 
    14320 308 atoms, 274 bonds, 39 residues, 1 model selected 
    14321 
    14322 > select add #43/A:54
    14323 
    14324 314 atoms, 279 bonds, 40 residues, 1 model selected 
    14325 
    14326 > select add #43/A:53
    14327 
    14328 322 atoms, 286 bonds, 41 residues, 1 model selected 
    14329 
    14330 > select add #43/A:52
    14331 
    14332 329 atoms, 292 bonds, 42 residues, 1 model selected 
    14333 
    14334 > select add #43/A:51
    14335 
    14336 340 atoms, 303 bonds, 43 residues, 1 model selected 
    14337 
    14338 > select add #43/A:50
    14339 
    14340 348 atoms, 310 bonds, 44 residues, 1 model selected 
    14341 
    14342 > select add #43/A:48
    14343 
    14344 353 atoms, 314 bonds, 45 residues, 1 model selected 
    14345 
    14346 > select add #43/A:47
    14347 
    14348 361 atoms, 321 bonds, 46 residues, 1 model selected 
    14349 
    14350 > select add #43/A:46
    14351 
    14352 369 atoms, 328 bonds, 47 residues, 1 model selected 
    14353 
    14354 > select subtract #43/A:46
    14355 
    14356 361 atoms, 321 bonds, 46 residues, 1 model selected 
    14357 
    14358 > select add #43/A:45
    14359 
    14360 368 atoms, 327 bonds, 47 residues, 1 model selected 
    14361 
    14362 > select add #43/A:46
    14363 
    14364 376 atoms, 334 bonds, 48 residues, 1 model selected 
    14365 
    14366 > select add #43/A:44
    14367 
    14368 381 atoms, 338 bonds, 49 residues, 1 model selected 
    14369 
    14370 > select add #43/A:43
    14371 
    14372 385 atoms, 341 bonds, 50 residues, 1 model selected 
    14373 
    14374 > select add #43/A:42
    14375 
    14376 391 atoms, 346 bonds, 51 residues, 1 model selected 
    14377 
    14378 > select add #43/A:41
    14379 
    14380 402 atoms, 357 bonds, 52 residues, 1 model selected 
    14381 
    14382 > select add #43/A:40
    14383 
    14384 412 atoms, 367 bonds, 53 residues, 1 model selected 
    14385 
    14386 > select add #43/A:39
    14387 
    14388 416 atoms, 370 bonds, 54 residues, 1 model selected 
    14389 
    14390 > color sel forest green
    14391 
    14392 > select clear
    14393 
    14394 > select add #43/A:49
    14395 
    14396 7 atoms, 7 bonds, 1 residue, 1 model selected 
    14397 
    14398 > color sel forest green
    14399 
    14400 > select clear
    14401 
    14402 > select add #43/A:38
    14403 
    14404 4 atoms, 3 bonds, 1 residue, 1 model selected 
    14405 
    14406 > select add #43/A:36
    14407 
    14408 15 atoms, 13 bonds, 2 residues, 1 model selected 
    14409 
    14410 > select add #43/A:35
    14411 
    14412 23 atoms, 20 bonds, 3 residues, 1 model selected 
    14413 
    14414 > select add #43/A:34
    14415 
    14416 32 atoms, 28 bonds, 4 residues, 1 model selected 
    14417 
    14418 > select add #43/A:33
    14419 
    14420 40 atoms, 35 bonds, 5 residues, 1 model selected 
    14421 
    14422 > select add #43/A:32
    14423 
    14424 46 atoms, 40 bonds, 6 residues, 1 model selected 
    14425 
    14426 > select subtract #43/A:32
    14427 
    14428 40 atoms, 35 bonds, 5 residues, 1 model selected 
    14429 
    14430 > select add #43/A:32
    14431 
    14432 46 atoms, 40 bonds, 6 residues, 1 model selected 
    14433 
    14434 > select add #43/A:31
    14435 
    14436 53 atoms, 46 bonds, 7 residues, 1 model selected 
    14437 
    14438 > select add #43/A:30
    14439 
    14440 61 atoms, 53 bonds, 8 residues, 1 model selected 
    14441 
    14442 > color sel forest green
    14443 
    14444 > select clear
    14445 
    14446 > select add #43/A:108
    14447 
    14448 7 atoms, 6 bonds, 1 residue, 1 model selected 
    14449 
    14450 > select add #43/A:109
    14451 
    14452 15 atoms, 13 bonds, 2 residues, 1 model selected 
    14453 
    14454 > select add #43/A:110
    14455 
    14456 23 atoms, 20 bonds, 3 residues, 1 model selected 
    14457 
    14458 > select add #43/A:111
    14459 
    14460 32 atoms, 28 bonds, 4 residues, 1 model selected 
    14461 
    14462 > select add #43/A:112
    14463 
    14464 40 atoms, 35 bonds, 5 residues, 1 model selected 
    14465 
    14466 > color sel cyan
    14467 
    14468 > select add #43/A:90
    14469 
    14470 49 atoms, 43 bonds, 6 residues, 1 model selected 
    14471 
    14472 > select add #43/A:91
    14473 
    14474 60 atoms, 53 bonds, 7 residues, 1 model selected 
    14475 
    14476 > select add #43/A:92
    14477 
    14478 68 atoms, 60 bonds, 8 residues, 1 model selected 
    14479 
    14480 > select add #43/A:93
    14481 
    14482 79 atoms, 71 bonds, 9 residues, 1 model selected 
    14483 
    14484 > select add #43/A:94
    14485 
    14486 88 atoms, 79 bonds, 10 residues, 1 model selected 
    14487 
    14488 > color sel cyan
    14489 
    14490 > select add #43/A:54
    14491 
    14492 94 atoms, 84 bonds, 11 residues, 1 model selected 
    14493 
    14494 > select add #43/A:53
    14495 
    14496 102 atoms, 91 bonds, 12 residues, 1 model selected 
    14497 
    14498 > select add #43/A:52
    14499 
    14500 109 atoms, 97 bonds, 13 residues, 1 model selected 
    14501 
    14502 > select add #43/A:51
    14503 
    14504 120 atoms, 108 bonds, 14 residues, 1 model selected 
    14505 
    14506 > color sel cyan
    14507 
    14508 > select clear
    14509 
    14510 > show #!42 models
    14511 
    14512 > hide #!42 models
    14513 
    14514 > show #!42 models
    14515 
    14516 > hide #!42 models
    14517 
    14518 > hide #!43 models
    14519 
    14520 > show #!43 models
    14521 
    14522 > combine #43 close false
    14523 
    14524 > select add #44
    14525 
    14526 4858 atoms, 4713 bonds, 831 residues, 1 model selected 
    14527 
    14528 > view matrix models
    14529 > #44,-0.994,-0.018016,-0.1079,181.57,0.10482,-0.43904,-0.89233,189.57,-0.031297,-0.89829,0.43829,312.85
    14530 
    14531 > select subtract #44
    14532 
    14533 Nothing selected 
    14534 
    14535 > select add #44/A:127
    14536 
    14537 8 atoms, 7 bonds, 1 residue, 1 model selected 
    14538 
    14539 > select add #44/A:128
    14540 
    14541 15 atoms, 14 bonds, 2 residues, 1 model selected 
    14542 
    14543 > delete sel
    14544 
    14545 > select add #44/A:129
    14546 
    14547 5 atoms, 4 bonds, 1 residue, 1 model selected 
    14548 
    14549 > select add #44/A:130
    14550 
    14551 14 atoms, 12 bonds, 2 residues, 1 model selected 
    14552 
    14553 > select add #44/A:131
    14554 
    14555 18 atoms, 15 bonds, 3 residues, 1 model selected 
    14556 
    14557 > select add #44/A:132
    14558 
    14559 29 atoms, 25 bonds, 4 residues, 1 model selected 
    14560 
    14561 > select add #44/A:133
    14562 
    14563 40 atoms, 35 bonds, 5 residues, 1 model selected 
    14564 
    14565 > select add #44/A:134
    14566 
    14567 48 atoms, 42 bonds, 6 residues, 1 model selected 
    14568 
    14569 > select subtract #44/A:134
    14570 
    14571 40 atoms, 35 bonds, 5 residues, 1 model selected 
    14572 
    14573 > select add #44/A:134
    14574 
    14575 48 atoms, 42 bonds, 6 residues, 1 model selected 
    14576 
    14577 > select add #44/A:135
    14578 
    14579 52 atoms, 45 bonds, 7 residues, 1 model selected 
    14580 
    14581 > select add #44/A:136
    14582 
    14583 60 atoms, 52 bonds, 8 residues, 1 model selected 
    14584 
    14585 > select add #44/A:137
    14586 
    14587 64 atoms, 55 bonds, 9 residues, 1 model selected 
    14588 
    14589 > select add #44/A:138
    14590 
    14591 71 atoms, 61 bonds, 10 residues, 1 model selected 
    14592 
    14593 > delete sel
    14594 
    14595 > select add #44/A:96
    14596 
    14597 8 atoms, 7 bonds, 1 residue, 1 model selected 
    14598 
    14599 > select add #44/A:97
    14600 
    14601 12 atoms, 10 bonds, 2 residues, 1 model selected 
    14602 
    14603 > select add #44/A:98
    14604 
    14605 24 atoms, 22 bonds, 3 residues, 1 model selected 
    14606 
    14607 > select add #44/A:99
    14608 
    14609 32 atoms, 29 bonds, 4 residues, 1 model selected 
    14610 
    14611 > select add #44/A:100
    14612 
    14613 39 atoms, 36 bonds, 5 residues, 1 model selected 
    14614 
    14615 > select add #44/A:101
    14616 
    14617 46 atoms, 42 bonds, 6 residues, 1 model selected 
    14618 
    14619 > select add #44/A:102
    14620 
    14621 54 atoms, 49 bonds, 7 residues, 1 model selected 
    14622 
    14623 > select add #44/A:103
    14624 
    14625 62 atoms, 56 bonds, 8 residues, 1 model selected 
    14626 
    14627 > select add #44/A:104
    14628 
    14629 70 atoms, 63 bonds, 9 residues, 1 model selected 
    14630 
    14631 > select add #44/A:105
    14632 
    14633 78 atoms, 70 bonds, 10 residues, 1 model selected 
    14634 
    14635 > select add #44/A:106
    14636 
    14637 86 atoms, 77 bonds, 11 residues, 1 model selected 
    14638 
    14639 > select add #44/A:107
    14640 
    14641 94 atoms, 84 bonds, 12 residues, 1 model selected 
    14642 
    14643 > delete sel
    14644 
    14645 > select clear
    14646 
    14647 > select add #44/A:160
    14648 
    14649 9 atoms, 8 bonds, 1 residue, 1 model selected 
    14650 
    14651 > select subtract #44/A:160
    14652 
    14653 Nothing selected 
    14654 
    14655 > select #44/A:159
    14656 
    14657 8 atoms, 7 bonds, 1 residue, 1 model selected 
    14658 
    14659 > select subtract #44/A:159
    14660 
    14661 Nothing selected 
    14662 
    14663 > select add #44/A:159
    14664 
    14665 8 atoms, 7 bonds, 1 residue, 1 model selected 
    14666 
    14667 > select add #44/A:158
    14668 
    14669 15 atoms, 13 bonds, 2 residues, 1 model selected 
    14670 
    14671 > select add #44/A:157
    14672 
    14673 21 atoms, 18 bonds, 3 residues, 1 model selected 
    14674 
    14675 > select add #44/A:156
    14676 
    14677 26 atoms, 22 bonds, 4 residues, 1 model selected 
    14678 
    14679 > select add #44/A:155
    14680 
    14681 34 atoms, 29 bonds, 5 residues, 1 model selected 
    14682 
    14683 > select add #44/A:154
    14684 
    14685 38 atoms, 32 bonds, 6 residues, 1 model selected 
    14686 
    14687 > select add #44/A:152
    14688 
    14689 49 atoms, 42 bonds, 7 residues, 1 model selected 
    14690 
    14691 > select add #44/A:151
    14692 
    14693 57 atoms, 49 bonds, 8 residues, 1 model selected 
    14694 
    14695 > select add #44/A:150
    14696 
    14697 68 atoms, 59 bonds, 9 residues, 1 model selected 
    14698 
    14699 > select add #44/A:149
    14700 
    14701 72 atoms, 62 bonds, 10 residues, 1 model selected 
    14702 
    14703 > select add #44/A:148
    14704 
    14705 80 atoms, 69 bonds, 11 residues, 1 model selected 
    14706 
    14707 > select add #44/A:147
    14708 
    14709 88 atoms, 76 bonds, 12 residues, 1 model selected 
    14710 
    14711 > select add #44/A:146
    14712 
    14713 92 atoms, 79 bonds, 13 residues, 1 model selected 
    14714 
    14715 > select add #44/A:145
    14716 
    14717 106 atoms, 94 bonds, 14 residues, 1 model selected 
    14718 
    14719 > delete sel
    14720 
    14721 > select add #44/A:113
    14722 
    14723 8 atoms, 7 bonds, 1 residue, 1 model selected 
    14724 
    14725 > select add #44/A:114
    14726 
    14727 12 atoms, 10 bonds, 2 residues, 1 model selected 
    14728 
    14729 > select add #44/A:115
    14730 
    14731 18 atoms, 15 bonds, 3 residues, 1 model selected 
    14732 
    14733 > select add #44/A:116
    14734 
    14735 23 atoms, 19 bonds, 4 residues, 1 model selected 
    14736 
    14737 > select add #44/A:117
    14738 
    14739 30 atoms, 25 bonds, 5 residues, 1 model selected 
    14740 
    14741 > select add #44/A:118
    14742 
    14743 38 atoms, 32 bonds, 6 residues, 1 model selected 
    14744 
    14745 > select add #44/A:119
    14746 
    14747 46 atoms, 39 bonds, 7 residues, 1 model selected 
    14748 
    14749 > select add #44/A:120
    14750 
    14751 51 atoms, 43 bonds, 8 residues, 1 model selected 
    14752 
    14753 > select add #44/A:121
    14754 
    14755 59 atoms, 50 bonds, 9 residues, 1 model selected 
    14756 
    14757 > select add #44/A:122
    14758 
    14759 66 atoms, 56 bonds, 10 residues, 1 model selected 
    14760 
    14761 > select add #44/A:124
    14762 
    14763 73 atoms, 62 bonds, 11 residues, 1 model selected 
    14764 
    14765 > select add #44/A:125
    14766 
    14767 78 atoms, 66 bonds, 12 residues, 1 model selected 
    14768 
    14769 > select add #44/A:126
    14770 
    14771 87 atoms, 74 bonds, 13 residues, 1 model selected 
    14772 
    14773 > delete sel
    14774 
    14775 > open /Users/amy/Downloads/emd_8220.map
    14776 
    14777 Opened emd_8220.map as #45, grid size 100,86,100, pixel 0.554,0.564,0.577,
    14778 shown at level 0.0696, step 1, values float32 
    14779 
    14780 > volume #45 level 0.05639
    14781 
    14782 > close #45
    14783 
    14784 > select add #44/A:16
    14785 
    14786 8 atoms, 7 bonds, 1 residue, 1 model selected 
    14787 
    14788 > select add #44/A:17
    14789 
    14790 15 atoms, 13 bonds, 2 residues, 1 model selected 
    14791 
    14792 > select add #44/A:18
    14793 
    14794 19 atoms, 16 bonds, 3 residues, 1 model selected 
    14795 
    14796 > select add #44/A:19
    14797 
    14798 23 atoms, 19 bonds, 4 residues, 1 model selected 
    14799 
    14800 > select add #44/A:20
    14801 
    14802 34 atoms, 29 bonds, 5 residues, 1 model selected 
    14803 
    14804 > select add #44/A:21
    14805 
    14806 45 atoms, 39 bonds, 6 residues, 1 model selected 
    14807 
    14808 > select add #44/A:22
    14809 
    14810 50 atoms, 43 bonds, 7 residues, 1 model selected 
    14811 
    14812 > select add #44/A:23
    14813 
    14814 61 atoms, 53 bonds, 8 residues, 1 model selected 
    14815 
    14816 > select add #44/A:24
    14817 
    14818 68 atoms, 60 bonds, 9 residues, 1 model selected 
    14819 
    14820 > select add #44/A:25
    14821 
    14822 78 atoms, 70 bonds, 10 residues, 1 model selected 
    14823 
    14824 > select add #44/A:26
    14825 
    14826 83 atoms, 74 bonds, 11 residues, 1 model selected 
    14827 
    14828 > select add #44/A:27
    14829 
    14830 97 atoms, 89 bonds, 12 residues, 1 model selected 
    14831 
    14832 > select add #44/A:29
    14833 
    14834 108 atoms, 100 bonds, 13 residues, 1 model selected 
    14835 
    14836 > delete sel
    14837 
    14838 > select add #44
    14839 
    14840 4377 atoms, 4217 bonds, 5 pseudobonds, 767 residues, 2 models selected 
    14841 
    14842 > view matrix models
    14843 > #44,-0.994,-0.018016,-0.1079,167.02,0.10482,-0.43904,-0.89233,176.04,-0.031297,-0.89829,0.43829,207.55
    14844 
    14845 > fitmap #44 inMap #8
    14846 
    14847 Fit molecule copy of copy of AATHNEcombined (#44) to map AATHNEcombined map 6
    14848 (#8) using 4377 atoms 
    14849 average map value = 0.4393, steps = 56 
    14850 shifted from previous position = 6.58 
    14851 rotated from previous position = 0.0611 degrees 
    14852 atoms outside contour = 1072, contour level = 0.36586 
    14853  
    14854 Position of copy of copy of AATHNEcombined (#44) relative to AATHNEcombined
    14855 map 6 (#8) coordinates: 
    14856 Matrix rotation and translation 
    14857 0.99999971 0.00068256 0.00033276 -0.05114740 
    14858 -0.00068229 0.99999944 -0.00080618 0.06249724 
    14859 -0.00033331 0.00080595 0.99999962 -0.02902612 
    14860 Axis 0.72788203 0.30072989 -0.61623801 
    14861 Axis point 0.00000000 36.47000800 77.70180160 
    14862 Rotation angle (degrees) 0.06345003 
    14863 Shift along axis -0.00054749 
    14864  
    14865 
    14866 > view matrix models
    14867 > #44,-0.99398,-0.018669,-0.108,161.2,0.10517,-0.43979,-0.89192,171.06,-0.030847,-0.89791,0.4391,163.49
    14868 
    14869 > view matrix models
    14870 > #44,-0.99398,-0.018669,-0.108,160.92,0.10517,-0.43979,-0.89192,163.66,-0.030847,-0.89791,0.4391,148.99
    14871 
    14872 > fitmap #44 inMap #29
    14873 
    14874 Fit molecule copy of copy of AATHNEcombined (#44) to map J1122.mrc (#29) using
    14875 4377 atoms 
    14876 average map value = 0.08017, steps = 120 
    14877 shifted from previous position = 10.4 
    14878 rotated from previous position = 19 degrees 
    14879 atoms outside contour = 1934, contour level = 0.064406 
    14880  
    14881 Position of copy of copy of AATHNEcombined (#44) relative to J1122.mrc (#29)
    14882 coordinates: 
    14883 Matrix rotation and translation 
    14884 -0.93560766 0.29367131 -0.19594762 148.33622912 
    14885 0.04403975 -0.45360760 -0.89011271 165.90577632 
    14886 -0.35028390 -0.84142576 0.41146553 152.50362608 
    14887 Axis 0.16365385 0.51877807 -0.83909876 
    14888 Axis point 96.84111132 123.35674227 0.00000000 
    14889 Rotation angle (degrees) 171.44551676 
    14890 Shift along axis -17.62152966 
    14891  
    14892 
    14893 > view matrix models
    14894 > #44,-0.93561,0.29367,-0.19595,147.21,0.04404,-0.45361,-0.89011,177.11,-0.35028,-0.84143,0.41147,212.36
    14895 
    14896 > view matrix models
    14897 > #44,-0.93561,0.29367,-0.19595,156.61,0.04404,-0.45361,-0.89011,178.01,-0.35028,-0.84143,0.41147,216.59
    14898 
    14899 > fitmap #44 inMap #8
    14900 
    14901 Fit molecule copy of copy of AATHNEcombined (#44) to map AATHNEcombined map 6
    14902 (#8) using 4377 atoms 
    14903 average map value = 0.4394, steps = 64 
    14904 shifted from previous position = 3.67 
    14905 rotated from previous position = 19 degrees 
    14906 atoms outside contour = 1073, contour level = 0.36586 
    14907  
    14908 Position of copy of copy of AATHNEcombined (#44) relative to AATHNEcombined
    14909 map 6 (#8) coordinates: 
    14910 Matrix rotation and translation 
    14911 0.99999986 0.00044110 -0.00029615 0.00647815 
    14912 -0.00044140 0.99999940 -0.00099710 0.04994382 
    14913 0.00029571 0.00099723 0.99999946 -0.05779749 
    14914 Axis 0.88254618 -0.26191484 -0.39052893 
    14915 Axis point 0.00000000 52.03151904 54.05257298 
    14916 Rotation angle (degrees) 0.06473724 
    14917 Shift along axis 0.01520783 
    14918  
    14919 
    14920 > view matrix models
    14921 > #44,-0.99405,-0.018449,-0.10737,168.43,0.10451,-0.43998,-0.8919,162.5,-0.030788,-0.89782,0.43929,154.17
    14922 
    14923 > view matrix models
    14924 > #44,-0.99405,-0.018449,-0.10737,153.97,0.10451,-0.43998,-0.8919,165.28,-0.030788,-0.89782,0.43929,147.12
    14925 
    14926 > fitmap #44 inMap #29
    14927 
    14928 Fit molecule copy of copy of AATHNEcombined (#44) to map J1122.mrc (#29) using
    14929 4377 atoms 
    14930 average map value = 0.08017, steps = 112 
    14931 shifted from previous position = 3.23 
    14932 rotated from previous position = 19 degrees 
    14933 atoms outside contour = 1936, contour level = 0.064406 
    14934  
    14935 Position of copy of copy of AATHNEcombined (#44) relative to J1122.mrc (#29)
    14936 coordinates: 
    14937 Matrix rotation and translation 
    14938 -0.93553950 0.29370365 -0.19622436 148.34392039 
    14939 0.04417583 -0.45387692 -0.88996867 165.89259865 
    14940 -0.35044876 -0.84126922 0.41164519 152.49532201 
    14941 Axis 0.16377458 0.51865136 -0.83915354 
    14942 Axis point 96.84939042 123.33620103 0.00000000 
    14943 Rotation angle (degrees) 171.44966078 
    14944 Shift along axis -17.63160462 
    14945  
    14946 
    14947 > select add #8
    14948 
    14949 4377 atoms, 4217 bonds, 5 pseudobonds, 767 residues, 4 models selected 
    14950 
    14951 > select subtract #44
    14952 
    14953 2 models selected 
    14954 
    14955 > view matrix models
    14956 > #8,-0.94817,0.24716,-0.1997,158.38,0.060761,-0.47584,-0.87743,176.64,-0.31189,-0.84409,0.43616,212.3
    14957 
    14958 > select subtract #8
    14959 
    14960 Nothing selected 
    14961 
    14962 > select add #44
    14963 
    14964 4377 atoms, 4217 bonds, 5 pseudobonds, 767 residues, 2 models selected 
    14965 
    14966 > view matrix models
    14967 > #44,-0.93554,0.2937,-0.19622,141.41,0.044176,-0.45388,-0.88997,179.93,-0.35045,-0.84127,0.41165,213.18
    14968 
    14969 > view matrix models
    14970 > #44,-0.93554,0.2937,-0.19622,151.53,0.044176,-0.45388,-0.88997,179.57,-0.35045,-0.84127,0.41165,212.38
    14971 
    14972 > view matrix models
    14973 > #44,-0.93554,0.2937,-0.19622,155.41,0.044176,-0.45388,-0.88997,178.43,-0.35045,-0.84127,0.41165,216.37
    14974 
    14975 > view matrix models
    14976 > #44,-0.93554,0.2937,-0.19622,155.54,0.044176,-0.45388,-0.88997,176.75,-0.35045,-0.84127,0.41165,213.56
    14977 
    14978 > view matrix models
    14979 > #44,-0.93554,0.2937,-0.19622,156.39,0.044176,-0.45388,-0.88997,176.3,-0.35045,-0.84127,0.41165,214.67
    14980 
    14981 > fitmap #44 inMap #8
    14982 
    14983 Fit molecule copy of copy of AATHNEcombined (#44) to map AATHNEcombined map 6
    14984 (#8) using 4377 atoms 
    14985 average map value = 0.4394, steps = 52 
    14986 shifted from previous position = 1.68 
    14987 rotated from previous position = 3.02 degrees 
    14988 atoms outside contour = 1076, contour level = 0.36586 
    14989  
    14990 Position of copy of copy of AATHNEcombined (#44) relative to AATHNEcombined
    14991 map 6 (#8) coordinates: 
    14992 Matrix rotation and translation 
    14993 0.99999955 0.00082150 0.00046001 -0.00883030 
    14994 -0.00082119 0.99999944 -0.00066348 0.04456765 
    14995 -0.00046055 0.00066310 0.99999967 -0.03206776 
    14996 Axis 0.57592008 0.39965178 -0.71315813 
    14997 Axis point 36.92441346 35.72354775 0.00000000 
    14998 Rotation angle (degrees) 0.06598750 
    14999 Shift along axis 0.03559538 
    15000  
    15001 
    15002 > select subtract #44
    15003 
    15004 Nothing selected 
    15005 
    15006 > hide #!44 models
    15007 
    15008 > select add #43
    15009 
    15010 4858 atoms, 4713 bonds, 831 residues, 1 model selected 
    15011 
    15012 > select subtract #43
    15013 
    15014 Nothing selected 
    15015 
    15016 > show #!44 models
    15017 
    15018 > select add #44
    15019 
    15020 4377 atoms, 4217 bonds, 5 pseudobonds, 767 residues, 2 models selected 
    15021 
    15022 > view matrix models
    15023 > #44,-0.94828,0.24625,-0.2003,158.56,0.061556,-0.47637,-0.87709,164.14,-0.3114,-0.84406,0.43658,152.21
    15024 
    15025 > view matrix models
    15026 > #44,-0.94828,0.24625,-0.2003,153.59,0.061556,-0.47637,-0.87709,162.81,-0.3114,-0.84406,0.43658,148.12
    15027 
    15028 > fitmap #44 inMap #29
    15029 
    15030 Fit molecule copy of copy of AATHNEcombined (#44) to map J1122.mrc (#29) using
    15031 4377 atoms 
    15032 average map value = 0.08017, steps = 96 
    15033 shifted from previous position = 5.9 
    15034 rotated from previous position = 3.02 degrees 
    15035 atoms outside contour = 1937, contour level = 0.064406 
    15036  
    15037 Position of copy of copy of AATHNEcombined (#44) relative to J1122.mrc (#29)
    15038 coordinates: 
    15039 Matrix rotation and translation 
    15040 -0.93556337 0.29370123 -0.19611414 148.34082953 
    15041 0.04407128 -0.45387887 -0.88997286 165.89641444 
    15042 -0.35039819 -0.84126901 0.41168865 152.49037322 
    15043 Axis 0.16372475 0.51864729 -0.83916578 
    15044 Axis point 96.84588182 123.33307757 0.00000000 
    15045 Rotation angle (degrees) 171.44626082 
    15046 Shift along axis -17.63591277 
    15047  
    15048 
    15049 > view matrix models
    15050 > #44,-0.93556,0.2937,-0.19611,181.55,0.044071,-0.45388,-0.88997,200.58,-0.3504,-0.84127,0.41169,325.24
    15051 
    15052 > volume #29 level 0.05579
    15053 
    15054 > volume #29 level 0.0639
    15055 
    15056 > select subtract #44
    15057 
    15058 Nothing selected 
    15059 
    15060 > select add #44/A:83
    15061 
    15062 7 atoms, 6 bonds, 1 residue, 1 model selected 
    15063 
    15064 > select add #44/A:81
    15065 
    15066 16 atoms, 14 bonds, 2 residues, 1 model selected 
    15067 
    15068 > select add #44/A:82
    15069 
    15070 23 atoms, 21 bonds, 3 residues, 1 model selected 
    15071 
    15072 > select add #44/A:80
    15073 
    15074 34 atoms, 31 bonds, 4 residues, 1 model selected 
    15075 
    15076 > select add #44/A:79
    15077 
    15078 45 atoms, 41 bonds, 5 residues, 1 model selected 
    15079 
    15080 > select add #44/A:78
    15081 
    15082 51 atoms, 46 bonds, 6 residues, 1 model selected 
    15083 
    15084 > select add #44/A:77
    15085 
    15086 59 atoms, 53 bonds, 7 residues, 1 model selected 
    15087 
    15088 > select add #44/A:76
    15089 
    15090 67 atoms, 60 bonds, 8 residues, 1 model selected 
    15091 
    15092 > select add #44/A:75
    15093 
    15094 77 atoms, 70 bonds, 9 residues, 1 model selected 
    15095 
    15096 > delete sel
    15097 
    15098 > select add #44/A:231
    15099 
    15100 4 atoms, 3 bonds, 1 residue, 1 model selected 
    15101 
    15102 > select add #44/A:230
    15103 
    15104 10 atoms, 8 bonds, 2 residues, 1 model selected 
    15105 
    15106 > select add #44/A:228
    15107 
    15108 15 atoms, 12 bonds, 3 residues, 1 model selected 
    15109 
    15110 > select add #44/A:227
    15111 
    15112 21 atoms, 17 bonds, 4 residues, 1 model selected 
    15113 
    15114 > select add #44/A:226
    15115 
    15116 25 atoms, 20 bonds, 5 residues, 1 model selected 
    15117 
    15118 > select add #44/A:232
    15119 
    15120 33 atoms, 27 bonds, 6 residues, 1 model selected 
    15121 
    15122 > select add #44/A:143
    15123 
    15124 41 atoms, 34 bonds, 7 residues, 1 model selected 
    15125 
    15126 > select subtract #44/A:143
    15127 
    15128 33 atoms, 27 bonds, 6 residues, 1 model selected 
    15129 
    15130 > select add #44/A:233
    15131 
    15132 45 atoms, 39 bonds, 7 residues, 1 model selected 
    15133 
    15134 > delete sel
    15135 
    15136 > select add #44/A:190
    15137 
    15138 11 atoms, 10 bonds, 1 residue, 1 model selected 
    15139 
    15140 > select add #44/A:191
    15141 
    15142 15 atoms, 13 bonds, 2 residues, 1 model selected 
    15143 
    15144 > select add #44/A:192
    15145 
    15146 26 atoms, 23 bonds, 3 residues, 1 model selected 
    15147 
    15148 > select add #44/A:194
    15149 
    15150 35 atoms, 31 bonds, 4 residues, 1 model selected 
    15151 
    15152 > select add #44/A:195
    15153 
    15154 40 atoms, 35 bonds, 5 residues, 1 model selected 
    15155 
    15156 > select add #44/A:196
    15157 
    15158 44 atoms, 38 bonds, 6 residues, 1 model selected 
    15159 
    15160 > delete sel
    15161 
    15162 > select add #44/A:197
    15163 
    15164 7 atoms, 6 bonds, 1 residue, 1 model selected 
    15165 
    15166 > select add #44/A:198
    15167 
    15168 13 atoms, 11 bonds, 2 residues, 1 model selected 
    15169 
    15170 > delete sel
    15171 
    15172 > hide #!44 models
    15173 
    15174 > show #!44 models
    15175 
    15176 > molmap #44 6
    15177 
    15178 Opened copy of copy of AATHNEcombined map 6 as #45, grid size 43,51,63, pixel
    15179 2, shown at level 0.0888, step 1, values float32 
    15180 
    15181 > close #45
    15182 
    15183 > molmap #44 4
    15184 
    15185 Opened copy of copy of AATHNEcombined map 4 as #45, grid size 55,68,86, pixel
    15186 1.33, shown at level 0.0965, step 1, values float32 
    15187 
    15188 > hide #!45 models
    15189 
    15190 > close #45
    15191 
    15192 > molmap #44 6
    15193 
    15194 Opened copy of copy of AATHNEcombined map 6 as #45, grid size 43,51,63, pixel
    15195 2, shown at level 0.0888, step 1, values float32 
    15196 
    15197 > volume #29 level 0.07099
    15198 
    15199 > volume #45 level 0.3542
    15200 
    15201 > transparency #45 50
    15202 
    15203 > select add #45
    15204 
    15205 2 models selected 
    15206 
    15207 > select add #44
    15208 
    15209 4198 atoms, 4031 bonds, 8 pseudobonds, 743 residues, 4 models selected 
    15210 
    15211 > view matrix models
    15212 > #44,-0.93556,0.2937,-0.19611,146.23,0.044071,-0.45388,-0.88997,157.07,-0.3504,-0.84127,0.41169,60.574,#45,-0.93556,0.2937,-0.19611,146.23,0.044071,-0.45388,-0.88997,157.07,-0.3504,-0.84127,0.41169,60.574
    15213 
    15214 > view matrix models
    15215 > #44,-0.93556,0.2937,-0.19611,143.48,0.044071,-0.45388,-0.88997,147.76,-0.3504,-0.84127,0.41169,34.922,#45,-0.93556,0.2937,-0.19611,143.48,0.044071,-0.45388,-0.88997,147.76,-0.3504,-0.84127,0.41169,34.922
    15216 
    15217 > select subtract #45
    15218 
    15219 4198 atoms, 4031 bonds, 8 pseudobonds, 743 residues, 2 models selected 
    15220 
    15221 > select subtract #44
    15222 
    15223 Nothing selected 
    15224 
    15225 > hide #!44 models
    15226 
    15227 > select add #45
    15228 
    15229 2 models selected 
    15230 
    15231 > view matrix models
    15232 > #45,-0.93556,0.2937,-0.19611,145.49,0.044071,-0.45388,-0.88997,159.38,-0.3504,-0.84127,0.41169,39.151
    15233 
    15234 > view matrix models
    15235 > #45,-0.72949,0.54043,-0.41926,144.13,0.020765,-0.59518,-0.80333,159.59,-0.68367,-0.59473,0.42296,41.013
    15236 
    15237 > view matrix models
    15238 > #45,-0.71308,0.51521,-0.47548,145.84,0.057668,-0.6328,-0.77216,158.62,-0.69871,-0.57803,0.42153,41.063
    15239 
    15240 > view matrix models
    15241 > #45,-0.71308,0.51521,-0.47548,145.43,0.057668,-0.6328,-0.77216,156.8,-0.69871,-0.57803,0.42153,40.9
    15242 
    15243 > view matrix models
    15244 > #45,-0.71308,0.51521,-0.47548,145.15,0.057668,-0.6328,-0.77216,154.97,-0.69871,-0.57803,0.42153,40.73
    15245 
    15246 > view matrix models
    15247 > #45,-0.79988,0.54237,-0.25694,140.06,-0.020652,-0.45275,-0.8914,156.94,-0.5998,-0.70771,0.37335,42.366
    15248 
    15249 > select subtract #45
    15250 
    15251 Nothing selected 
    15252 
    15253 > show #!44 models
    15254 
    15255 > fitmap #44 inMap #45
    15256 
    15257 Fit molecule copy of copy of AATHNEcombined (#44) to map copy of copy of
    15258 AATHNEcombined map 6 (#45) using 4198 atoms 
    15259 average map value = 0.434, steps = 72 
    15260 shifted from previous position = 8.8 
    15261 rotated from previous position = 16.7 degrees 
    15262 atoms outside contour = 994, contour level = 0.3542 
    15263  
    15264 Position of copy of copy of AATHNEcombined (#44) relative to copy of copy of
    15265 AATHNEcombined map 6 (#45) coordinates: 
    15266 Matrix rotation and translation 
    15267 0.99999987 0.00004904 -0.00050917 0.03695210 
    15268 -0.00004923 0.99999993 -0.00038442 0.00896662 
    15269 0.00050915 0.00038445 0.99999980 -0.01640243 
    15270 Axis 0.60079207 -0.79570876 -0.07678841 
    15271 Axis point 29.77463683 0.00000000 53.30306429 
    15272 Rotation angle (degrees) 0.03666236 
    15273 Shift along axis 0.01632523 
    15274  
    15275 
    15276 > select add #44
    15277 
    15278 4198 atoms, 4031 bonds, 8 pseudobonds, 743 residues, 2 models selected 
    15279 
    15280 > view matrix models
    15281 > #44,-0.80004,0.54224,-0.25675,156.75,-0.021083,-0.45309,-0.89121,165.09,-0.59958,-0.70759,0.37392,145.97
    15282 
    15283 > view matrix models
    15284 > #44,-0.80004,0.54224,-0.25675,157.44,-0.021083,-0.45309,-0.89121,165.95,-0.59958,-0.70759,0.37392,150.1
    15285 
    15286 > fitmap #44 inMap #29
    15287 
    15288 Fit molecule copy of copy of AATHNEcombined (#44) to map J1122.mrc (#29) using
    15289 4198 atoms 
    15290 average map value = 0.08149, steps = 152 
    15291 shifted from previous position = 14.4 
    15292 rotated from previous position = 16.8 degrees 
    15293 atoms outside contour = 2047, contour level = 0.070992 
    15294  
    15295 Position of copy of copy of AATHNEcombined (#44) relative to J1122.mrc (#29)
    15296 coordinates: 
    15297 Matrix rotation and translation 
    15298 -0.93562730 0.29338154 -0.19628760 148.35386113 
    15299 0.04432994 -0.45401135 -0.88989243 165.88171301 
    15300 -0.35019481 -0.84130908 0.41177983 152.48885393 
    15301 Axis 0.16370521 0.51860171 -0.83919775 
    15302 Axis point 96.83079976 123.33491709 0.00000000 
    15303 Rotation angle (degrees) 171.46655392 
    15304 Shift along axis -17.65546343 
    15305  
    15306 
    15307 > select subtract #44
    15308 
    15309 Nothing selected 
    15310 
    15311 > select add #45
    15312 
    15313 2 models selected 
    15314 
    15315 > view matrix models
    15316 > #45,-0.93329,0.27115,-0.23547,146.24,0.06955,-0.50681,-0.85925,155.22,-0.35232,-0.81831,0.45414,37.269
    15317 
    15318 > select subtract #45
    15319 
    15320 Nothing selected 
    15321 
    15322 > hide #!44 models
    15323 
    15324 > open /Users/amy/Downloads/cryosparc_P483_J196_007_volume_map.mrc
    15325 
    15326 Opened cryosparc_P483_J196_007_volume_map.mrc as #46, grid size 400,400,400,
    15327 pixel 0.723, shown at level 0.00453, step 2, values float32 
    15328 
    15329 > hide #!45 models
    15330 
    15331 > hide #!43 models
    15332 
    15333 > hide #!29 models
    15334 
    15335 > hide #!8 models
    15336 
    15337 > volume #46 level 0.03417
    15338 
    15339 > open /Users/amy/Downloads/cryosparc_P483_J206_005_volume_map.mrc
    15340 
    15341 Opened cryosparc_P483_J206_005_volume_map.mrc as #47, grid size 400,400,400,
    15342 pixel 0.723, shown at level 0.0164, step 2, values float32 
    15343 
    15344 > volume #47 level 0.05223
    15345 
    15346 > volume #47 level 0.05304
    15347 
    15348 > volume #47 level 0.05549
    15349 
    15350 > close #58-61,70-71
    15351 
    15352 > show #!46 models
    15353 
    15354 > hide #!46 models
    15355 
    15356 > close #46-47
    15357 
    15358 > show #!39 models
    15359 
    15360 Error processing trigger "graphics update": 
    15361  
    15362 You deleted or moved a volume file that is still open in ChimeraX. 
    15363  
    15364 /Users/amy/Downloads/cryosparc_P483_J188_006_volume_map.mrc 
    15365  
    15366 To allow fast initial display of volume data ChimeraX does not read all data
    15367 from the file when it is first opened, and will later read more data when
    15368 needed. ChimeraX got an error trying to read the above file. 
    15369 
    15370 > close #39-40
    15371 
    15372 > save "/Users/amy/Desktop/SPA AAT_HNE/csparc.cxs"
    15373 
    15374 ——— End of log from Thu Mar 12 17:49:41 2026 ———
    15375 
    15376 > view name session-start
    15377 
    15378 opened ChimeraX session 
    15379 
    15380 > show #!29 models
    15381 
    15382 > show #!33 models
    15383 
    15384 > hide #!33 models
    15385 
    15386 > show #!42 models
    15387 
    15388 > hide #!42 models
    15389 
    15390 > open "/Users/amy/Desktop/SPA AAT_HNE/3C11_Fab_AAT_NE/model/combined.pdb"
    15391 
    15392 Chain information for combined.pdb #39 
    15393 --- 
    15394 Chain | Description 
    15395 A | No description available 
    15396 B | No description available 
    15397 C | No description available 
    15398 H | No description available 
    15399 L | No description available 
    15400  
    15401 128 atoms have alternate locations. Control/examine alternate locations with
    15402 Altloc Explorer [start tool...] or the altlocs command. 
    15403 
    15404 > show #!39 cartoons
    15405 
    15406 > hide #!39 atoms
    15407 
    15408 > volume #29 level 0.08659
    15409 
    15410 > volume #29 step 1
    15411 
    15412 > volume #29 level 0.1102
    15413 
    15414 > hide #!29 models
    15415 
    15416 > show #!29 models
    15417 
    15418 > hide #!39 models
    15419 
    15420 > show #!39 models
    15421 
    15422 > hide #!39 models
    15423 
    15424 > show #!39 models
    15425 
    15426 > volume #29 level 0.1043
    15427 
    15428 > select #39/A
    15429 
    15430 2686 atoms, 2674 bonds, 398 residues, 1 model selected 
    15431 
    15432 > select #39/A: 75
    15433 
    15434 9 atoms, 8 bonds, 1 residue, 1 model selected 
    15435 
    15436 > hide #!39 models
    15437 
    15438 > show #!39 models
    15439 
    15440 > hide #!39 models
    15441 
    15442 > show #!39 models
    15443 
    15444 > hide #!39 models
    15445 
    15446 > show #!39 models
    15447 
    15448 > ui tool show "Show Sequence Viewer"
    15449 
    15450 > sequence chain #4/H #6/H #17/H #24/H #33/H #39/H
    15451 
    15452 Alignment identifier is 1 
    15453 
    15454 > select #4/H:1-2 #6/H:1-2 #17/H:1-2 #24/H:1-2 #33/H:1-2 #39/H:1-2
    15455 
    15456 72 atoms, 66 bonds, 12 residues, 6 models selected 
    15457 
    15458 > select #4/H:1-116 #6/H:1-116 #17/H:1-116 #24/H:1-116 #33/H:1-116 #39/H:1-116
    15459 
    15460 5472 atoms, 5592 bonds, 708 residues, 6 models selected 
    15461 Fab 3C11 Heavy Chain [ID: 1] region 6 chains [1-118] RMSD: 27.271 
    15462  
    15463 
    15464 > select #4/H:117 #6/H:117 #17/H:117 #24/H:117 #33/H:117 #39/H:117
    15465 
    15466 42 atoms, 36 bonds, 6 residues, 6 models selected 
    15467 
    15468 > select #4/H:117-119 #6/H:117-119 #17/H:117-119 #24/H:117-119 #33/H:117-119
    15469 > #39/H:117-119
    15470 
    15471 114 atoms, 114 bonds, 18 residues, 6 models selected 
    15472 Fab 3C11 Heavy Chain [ID: 1] region 6 chains [119-121] RMSD: 60.098 
    15473  
    15474 
    15475 > select #4/H:120-121 #6/H:120-121 #17/H:120-121 #24/H:120-121 #33/H:120-121
    15476 > #39/H:120-121
    15477 
    15478 78 atoms, 72 bonds, 12 residues, 6 models selected 
    15479 
    15480 > select #4/H:120-124 #6/H:120-124 #17/H:120-124 #24/H:120-124 #33/H:120-124
    15481 > #39/H:120-124
    15482 
    15483 240 atoms, 246 bonds, 30 residues, 6 models selected 
    15484 Fab 3C11 Heavy Chain [ID: 1] region 6 chains [122-126] RMSD: 70.006 
    15485  
    15486 
    15487 > select #4/H:125 #6/H:125 #17/H:125 #24/H:125 #33/H:125 #39/H:125
    15488 
    15489 30 atoms, 24 bonds, 6 residues, 6 models selected 
    15490 
    15491 > select #4/H:125-132 #6/H:125-132 #17/H:125-132 #24/H:125-132 #33/H:125-132
    15492 > #39/H:125-132
    15493 
    15494 282 atoms, 282 bonds, 48 residues, 6 models selected 
    15495 Fab 3C11 Heavy Chain [ID: 1] region 6 chains [127-135] RMSD: 85.110 
    15496  
    15497 
    15498 > open /Applications/ccp4-9/examples/data/pdb_mmcif/input.fasta
    15499 
    15500 Summary of feedback from opening
    15501 /Applications/ccp4-9/examples/data/pdb_mmcif/input.fasta 
    15502 --- 
    15503 note | Alignment identifier is input.fasta 
    15504  
    15505 Opened 1 sequence from input.fasta 
    15506 
    15507 > select #4/H:1 #6/H:1 #17/H:1 #24/H:1 #33/H:1 #39/H:1
    15508 
    15509 30 atoms, 24 bonds, 6 residues, 6 models selected 
    15510 
    15511 > select #4/H:1-56 #6/H:1-56 #17/H:1-56 #24/H:1-56 #33/H:1-56 #39/H:1-56
    15512 
    15513 2556 atoms, 2610 bonds, 342 residues, 6 models selected 
    15514 Fab 3C11 Heavy Chain [ID: 1] region 6 chains [1-57] RMSD: 25.907 
    15515  
    15516 
    15517 > select #4/H:1 #6/H:1 #17/H:1 #24/H:1 #33/H:1 #39/H:1
    15518 
    15519 30 atoms, 24 bonds, 6 residues, 6 models selected 
    15520 
    15521 > select #4/H:1-104 #6/H:1-104 #17/H:1-104 #24/H:1-104 #33/H:1-104 #39/H:1-104
    15522 
    15523 4980 atoms, 5100 bonds, 636 residues, 6 models selected 
    15524 Fab 3C11 Heavy Chain [ID: 1] region 6 chains [1-106] RMSD: 25.181 
    15525  
    15526 
    15527 > select #4/H:1 #6/H:1 #17/H:1 #24/H:1 #33/H:1 #39/H:1
    15528 
    15529 30 atoms, 24 bonds, 6 residues, 6 models selected 
    15530 
    15531 > select #4/H #6/H #17/H #24/H #33/H #39/H
    15532 
    15533 9660 atoms, 9900 bonds, 6 pseudobonds, 1284 residues, 12 models selected 
    15534 Fab 3C11 Heavy Chain [ID: 1] region 6 chains [1-215] RMSD: 48.787 
    15535  
    15536 
    15537 > select clear
    15538 
    15539 > select #4/H:1 #6/H:1 #17/H:1 #24/H:1 #33/H:1 #39/H:1
    15540 
    15541 30 atoms, 24 bonds, 6 residues, 6 models selected 
    15542 
    15543 > select #4/H #6/H #17/H #24/H #33/H #39/H
    15544 
    15545 9660 atoms, 9900 bonds, 6 pseudobonds, 1284 residues, 12 models selected 
    15546 Fab 3C11 Heavy Chain [ID: 1] region 6 chains [1-215] RMSD: 48.787 
    15547  
    15548 
    15549 > save /Users/amy/Desktop/3c11-chainA format fasta alignment 1
    15550 
    15551 > ui tool show "Show Sequence Viewer"
    15552 
    15553 > sequence chain #4/L #6/L #17/L #24/L #33/L #39/L
    15554 
    15555 Alignment identifier is 1 
    15556 
    15557 > select clear
    15558 
    15559 > select #4/L #6/L #17/L #24/L #33/L #39/L
    15560 
    15561 9480 atoms, 9714 bonds, 6 pseudobonds, 1248 residues, 12 models selected 
    15562 Fab 3C11 Light Chain [ID: 1] region 6 chains [1-215] RMSD: 54.385 
    15563  
    15564 
    15565 > select clear
    15566 
    15567 > select #4/L #6/L #17/L #24/L #33/L #39/L
    15568 
    15569 9480 atoms, 9714 bonds, 6 pseudobonds, 1248 residues, 12 models selected 
    15570 
    15571 > select clear
    15572 
    15573 > select #4/L #6/L #17/L #24/L #33/L #39/L
    15574 
    15575 9480 atoms, 9714 bonds, 6 pseudobonds, 1248 residues, 12 models selected 
    15576 Fab 3C11 Light Chain [ID: 1] region 6 chains [1-215] RMSD: 54.385 
    15577  
    15578 
    15579 > save /Users/amy/Desktop/3c11-lightchain format fasta alignment 1
    15580 
    15581 > open "/Users/amy/Desktop/SPA AAT_HNE/9C5_Fab_AAT_HNE/9c5_aat_hne_seq.fasta"
    15582 
    15583 Failed opening file /Users/amy/Desktop/SPA
    15584 AAT_HNE/9C5_Fab_AAT_HNE/9c5_aat_hne_seq.fasta: 
    15585 Sequence 'ChainB' differs in length from preceding sequences, and it is
    15586 therefore impossible to open these sequences as an alignment. If you want to
    15587 open the sequences individually, specify 'false' as the value of the
    15588 'alignment' keyword in the 'open' command. 
    15589 
    15590 > open /Users/amy/Downloads/J1122-fit.cif
    15591 
    15592 Summary of feedback from opening /Users/amy/Downloads/J1122-fit.cif 
    15593 --- 
    15594 warnings | Missing entity information. Treating each chain as a separate entity. 
    15595 Missing or incorrect sequence information. Inferred polymer connectivity. 
    15596  
    15597  
    15598 Chain information for J1122-fit.cif #40 
    15599 --- 
    15600 Chain | Description 
    15601 Aa | No description available 
    15602 Ab | No description available 
    15603 Ba | No description available 
    15604 Bb | No description available 
    15605 Ca | No description available 
    15606 Cb | No description available 
    15607 Cc | No description available 
    15608 Cd | No description available 
    15609  
    15610 
    15611 > hide #!39 models
    15612 
    15613 > hide #!40 atoms
    15614 
    15615 > hide #!40 models
    15616 
    15617 > show #!40 models
    15618 
    15619 > show #!40 cartoons
    15620 
    15621 Computing secondary structure 
    15622 
    15623 > open /Users/amy/Downloads/J1122-fit_raw.cif
    15624 
    15625 Summary of feedback from opening /Users/amy/Downloads/J1122-fit_raw.cif 
    15626 --- 
    15627 warnings | Missing entity information. Treating each chain as a separate entity. 
    15628 Missing or incorrect sequence information. Inferred polymer connectivity. 
    15629  
    15630  
    15631 Chain information for J1122-fit_raw.cif #46 
    15632 --- 
    15633 Chain | Description 
    15634 0 | No description available 
    15635 1 | No description available 
    15636 2 | No description available 
    15637 3 V X | No description available 
    15638 4 | No description available 
    15639 5 | No description available 
    15640 6 | No description available 
    15641 7 | No description available 
    15642 8 | No description available 
    15643 9 | No description available 
    15644 A | No description available 
    15645 A0 | No description available 
    15646 A1 | No description available 
    15647 A2 | No description available 
    15648 A3 | No description available 
    15649 A4 | No description available 
    15650 A5 | No description available 
    15651 A6 | No description available 
    15652 A7 | No description available 
    15653 A8 | No description available 
    15654 A9 | No description available 
    15655 AA | No description available 
    15656 AB | No description available 
    15657 AC | No description available 
    15658 AD | No description available 
    15659 AE | No description available 
    15660 AF z | No description available 
    15661 AG | No description available 
    15662 AH An C0 C2 C9 Cl DE DS Dv Dw q | No description available 
    15663 AI CY | No description available 
    15664 AJ | No description available 
    15665 AK | No description available 
    15666 AL | No description available 
    15667 AM | No description available 
    15668 AN | No description available 
    15669 AO | No description available 
    15670 AP | No description available 
    15671 AQ | No description available 
    15672 AR | No description available 
    15673 AS | No description available 
    15674 AT | No description available 
    15675 AU | No description available 
    15676 AV | No description available 
    15677 AW | No description available 
    15678 AX | No description available 
    15679 AY | No description available 
    15680 AZ | No description available 
    15681 Aa | No description available 
    15682 Ab | No description available 
    15683 Ac | No description available 
    15684 Ad | No description available 
    15685 Ae | No description available 
    15686 Af | No description available 
    15687 Ag | No description available 
    15688 Ah | No description available 
    15689 Ai | No description available 
    15690 Aj | No description available 
    15691 Ak | No description available 
    15692 Al Cr Cx DP | No description available 
    15693 Am | No description available 
    15694 Ao | No description available 
    15695 Ap | No description available 
    15696 Aq | No description available 
    15697 Ar | No description available 
    15698 As | No description available 
    15699 At | No description available 
    15700 Au | No description available 
    15701 Av b l | No description available 
    15702 Aw | No description available 
    15703 Ax | No description available 
    15704 Ay BQ Bl Bm C8 CW Ce Cg Cp Cs Cu D3 D5 DC DH DL DN Dg Dh Dk Dq Dt h o | No description available 
    15705 Az g r | No description available 
    15706 B | No description available 
    15707 B0 Ck | No description available 
    15708 B1 | No description available 
    15709 B2 | No description available 
    15710 B3 Bw C1 DW Dj Dy S p | No description available 
    15711 B4 | No description available 
    15712 B5 | No description available 
    15713 B6 | No description available 
    15714 B7 | No description available 
    15715 B8 | No description available 
    15716 B9 | No description available 
    15717 BA | No description available 
    15718 BB | No description available 
    15719 BC | No description available 
    15720 BD | No description available 
    15721 BE | No description available 
    15722 BF | No description available 
    15723 BG | No description available 
    15724 BH | No description available 
    15725 BI | No description available 
    15726 BJ | No description available 
    15727 BK | No description available 
    15728 BL | No description available 
    15729 BM | No description available 
    15730 BN | No description available 
    15731 BO | No description available 
    15732 BP | No description available 
    15733 BR | No description available 
    15734 BS | No description available 
    15735 BT D4 Dp | No description available 
    15736 BU | No description available 
    15737 BV | No description available 
    15738 BW | No description available 
    15739 BX | No description available 
    15740 BY | No description available 
    15741 BZ | No description available 
    15742 Ba | No description available 
    15743 Bb | No description available 
    15744 Bc | No description available 
    15745 Bd | No description available 
    15746 Be | No description available 
    15747 Bf | No description available 
    15748 Bg | No description available 
    15749 Bh | No description available 
    15750 Bi | No description available 
    15751 Bj | No description available 
    15752 Bk | No description available 
    15753 Bn | No description available 
    15754 Bo | No description available 
    15755 Bp | No description available 
    15756 Bq e | No description available 
    15757 Br | No description available 
    15758 Bs | No description available 
    15759 Bt | No description available 
    15760 Bu | No description available 
    15761 Bv | No description available 
    15762 Bx | No description available 
    15763 By | No description available 
    15764 Bz | No description available 
    15765 C | No description available 
    15766 C3 | No description available 
    15767 C4 | No description available 
    15768 C5 | No description available 
    15769 C6 Cv D0 | No description available 
    15770 C7 | No description available 
    15771 CA | No description available 
    15772 CB | No description available 
    15773 CC | No description available 
    15774 CD | No description available 
    15775 CE | No description available 
    15776 CF | No description available 
    15777 CG | No description available 
    15778 CH | No description available 
    15779 CI | No description available 
    15780 CJ | No description available 
    15781 CK | No description available 
    15782 CL | No description available 
    15783 CM | No description available 
    15784 CN | No description available 
    15785 CO | No description available 
    15786 CP | No description available 
    15787 CQ | No description available 
    15788 CR | No description available 
    15789 CS | No description available 
    15790 CT | No description available 
    15791 CU | No description available 
    15792 CV | No description available 
    15793 CX | No description available 
    15794 CZ Cz D6 DF Da De Df j | No description available 
    15795 Ca k | No description available 
    15796 Cb DA Ds | No description available 
    15797 Cc | No description available 
    15798 Cd | No description available 
    15799 Cf Dm | No description available 
    15800 Ch | No description available 
    15801 Ci DQ | No description available 
    15802 Cj | No description available 
    15803 Cm | No description available 
    15804 Cn | No description available 
    15805 Co DB Dd | No description available 
    15806 Cq Dr | No description available 
    15807 Ct DM | No description available 
    15808 Cw | No description available 
    15809 Cy | No description available 
    15810 D | No description available 
    15811 D1 | No description available 
    15812 D2 Dz W | No description available 
    15813 D7 | No description available 
    15814 DD | No description available 
    15815 DG | No description available 
    15816 DI | No description available 
    15817 DJ | No description available 
    15818 DK | No description available 
    15819 DO | No description available 
    15820 DR | No description available 
    15821 DT | No description available 
    15822 DU | No description available 
    15823 DV | No description available 
    15824 DX Db | No description available 
    15825 DY | No description available 
    15826 DZ | No description available 
    15827 Dc | No description available 
    15828 Di Dl Do | No description available 
    15829 Dn | No description available 
    15830 Du | No description available 
    15831 Dx | No description available 
    15832 E | No description available 
    15833 F | No description available 
    15834 G | No description available 
    15835 H | No description available 
    15836 I | No description available 
    15837 J | No description available 
    15838 K | No description available 
    15839 L | No description available 
    15840 M | No description available 
    15841 N | No description available 
    15842 O | No description available 
    15843 P | No description available 
    15844 Q | No description available 
    15845 R | No description available 
    15846 T | No description available 
    15847 U | No description available 
    15848 Y | No description available 
    15849 Z | No description available 
    15850 a | No description available 
    15851 c | No description available 
    15852 d | No description available 
    15853 f | No description available 
    15854 i y | No description available 
    15855 m | No description available 
    15856 n | No description available 
    15857 s | No description available 
    15858 t | No description available 
    15859 u | No description available 
    15860 v | No description available 
    15861 w | No description available 
    15862 x | No description available 
    15863  
    15864 
    15865 > hide #46#!40 atoms
    15866 
    15867 > show #46#!40 cartoons
    15868 
    15869 Computing secondary structure 
    15870 
    15871 > hide #!40 models
    15872 
    15873 > hide #!29 models
    15874 
    15875 > show #!29 models
    15876 
    15877 > hide #!29 models
    15878 
    15879 > show #!29 models
    15880 
    15881 > hide #46 models
    15882 
    15883 > show #!39 models
    15884 
    15885 > select add #39
    15886 
    15887 15863 atoms, 15994 bonds, 7 pseudobonds, 2296 residues, 12 models selected 
    15888 
    15889 > select subtract #39
    15890 
    15891 7900 atoms, 8095 bonds, 5 pseudobonds, 1040 residues, 10 models selected 
    15892 
    15893 > hide #!39 cartoons
    15894 
    15895 > show #!39 atoms
    15896 
    15897 > hide #!39 atoms
    15898 
    15899 > show #!39 atoms
    15900 
    15901 > style #!39 stick
    15902 
    15903 Changed 7963 atom styles 
    15904 
    15905 > select #39/A: 39
    15906 
    15907 11 atoms, 10 bonds, 1 residue, 1 model selected 
    15908 
    15909 > select #39/A: 305
    15910 
    15911 9 atoms, 8 bonds, 1 residue, 1 model selected 
    15912 
    15913 > color sel byhetero
    15914 
    15915 > select #39/H: 96
    15916 
    15917 11 atoms, 10 bonds, 1 residue, 1 model selected 
    15918 
    15919 > color sel byhetero
    15920 
    15921 > select add #39
    15922 
    15923 7963 atoms, 7899 bonds, 2 pseudobonds, 1256 residues, 2 models selected 
    15924 
    15925 > select subtract #39
    15926 
    15927 Nothing selected 
    15928 
    15929 > select add #39
    15930 
    15931 7963 atoms, 7899 bonds, 2 pseudobonds, 1256 residues, 2 models selected 
    15932 
    15933 > hide sel atoms
    15934 
    15935 > show sel cartoons
    15936 
    15937 > select subtract #39
    15938 
    15939 Nothing selected 
    15940 
    15941 > select add #39
    15942 
    15943 7963 atoms, 7899 bonds, 2 pseudobonds, 1256 residues, 2 models selected 
    15944 
    15945 > ui tool show "Fit in Map"
    15946 
    15947 > fitmap #39 inMap #29
    15948 
    15949 Fit molecule combined.pdb (#39) to map J1122.mrc (#29) using 7963 atoms 
    15950 average map value = 0.08036, steps = 68 
    15951 shifted from previous position = 0.771 
    15952 rotated from previous position = 2.19 degrees 
    15953 atoms outside contour = 5609, contour level = 0.10431 
    15954  
    15955 Position of combined.pdb (#39) relative to J1122.mrc (#29) coordinates: 
    15956 Matrix rotation and translation 
    15957 0.99967761 0.02538913 0.00025294 -3.33021005 
    15958 -0.02538599 0.99926934 0.02857152 0.48178557 
    15959 0.00047265 -0.02856873 0.99959172 3.88702701 
    15960 Axis -0.74751146 -0.00287429 -0.66424269 
    15961 Axis point 0.00000000 134.06640595 -13.42452344 
    15962 Rotation angle (degrees) 2.19039607 
    15963 Shift along axis -0.09394389 
    15964  
    15965 
    15966 > select subtract #39
    15967 
    15968 Nothing selected 
    15969 
    15970 > volume #29 level 0.1191
    15971 
    15972 > style #!39 stick
    15973 
    15974 Changed 7963 atom styles 
    15975 
    15976 > hide #!39 cartoons
    15977 
    15978 > show #!39 atoms
    15979 
    15980 > nucleotides #!39 atoms
    15981 
    15982 > style nucleic & #!39 stick
    15983 
    15984 Changed 0 atom styles 
    15985 
    15986 > nucleotides #!39 atoms
    15987 
    15988 > style nucleic & #!39 stick
    15989 
    15990 Changed 0 atom styles 
    15991 
    15992 > nucleotides #!39 atoms
    15993 
    15994 > style nucleic & #!39 stick
    15995 
    15996 Changed 0 atom styles 
    15997 
    15998 > hide #!39 atoms
    15999 
    16000 > show #!39 atoms
    16001 
    16002 > nucleotides #!39 ladder
    16003 
    16004 > nucleotides #!39 fill
    16005 
    16006 > style nucleic & #!39 stick
    16007 
    16008 Changed 0 atom styles 
    16009 
    16010 > nucleotides #!39 tube/slab shape box
    16011 
    16012 > nucleotides #!39 ladder
     2829Deleted lines to meet Trac size limit.  Tom
    160132830
    160142831> hbonds #!39 reveal true
    … …  
    185475364
    185485365===== Log before crash end =====
    18549 
    18550 Log:
    18551 UCSF ChimeraX version: 1.11.1 (2026-01-23) 
    18552 © 2016-2025 Regents of the University of California. All rights reserved. 
    18553 
    18554 > open "/Users/amy/Desktop/SPA
    18555 > AAT_HNE/3C11_Fab_AAT_NE/3c11_aat_hen_csparc.cxs"
    18556 
    18557 Opened cryosparc_P371_J880_003_volume_map.mrc as #2, grid size 300,300,300,
    18558 pixel 0.867, shown at level 0.0665, step 2, values float32 
    18559 Opened flipped_J880.mrc as #3, grid size 300,300,300, pixel 0.867, shown at
    18560 level 0.0841, step 1, values float32 
    18561 Opened cryosparc_P371_J882_005_volume_map (1).mrc z flip as #9, grid size
    18562 300,300,300, pixel 0.867, shown at level 0.0602, step 1, values float32 
    18563 Opened cryosparc_P371_J881_class_08_00006_volume.mrc z flip as #10, grid size
    18564 180,180,180, pixel 1.44, shown at level 0.122, step 1, values float32 
    18565 Opened cryosparc_P371_J916_map.mrc as #11, grid size 300,300,300, pixel 0.867,
    18566 shown at level 0.0503, step 2, values float32 
    18567 Opened cryosparc_P371_J916_map.mrc z flip as #12, grid size 300,300,300, pixel
    18568 0.867, shown at level 0.0806, step 1, values float32 
    18569 Opened cryosparc_P371_J919_class_00_final_volume.mrc as #13, grid size
    18570 128,128,128, pixel 2.03, shown at level 0.08, step 1, values float32 
    18571 Opened cryosparc_P371_J937_003_volume_map.mrc as #14, grid size 300,300,300,
    18572 pixel 0.867, shown at level 0.0245, step 2, values float32 
    18573 Opened cryosparc_P371_J937_003_volume_map.mrc z flip as #15, grid size
    18574 300,300,300, pixel 0.867, shown at level 0.0683, step 1, values float32 
    18575 Opened cryosparc_P371_J948_003_volume_map.mrc as #21, grid size 300,300,300,
    18576 pixel 0.867, shown at level 0.0208, step 2, values float32 
    18577 Opened cryosparc_P371_J948_003_volume_map.mrc z flip as #22, grid size
    18578 300,300,300, pixel 0.867, shown at level 0.0938, step 1, values float32 
    18579 Opened J1122.mrc as #29, grid size 300,300,300, pixel 0.867, shown at level
    18580 0.071, step 2, values float32 
    18581 Opened J1134.mrc as #34, grid size 300,300,300, pixel 0.867, shown at level
    18582 0.0707, step 2, values float32 
    18583 Opened cryosparc_P483_molmap_of_combined_6A.mrc as #41, grid size 200,200,200,
    18584 pixel 1, shown at level 0.293, step 1, values float32 
    18585 Opened AATHNEcombined map 6 as #8, grid size 43,51,63, pixel 2, shown at level
    18586 0.366, step 1, values float32 
    18587 Opened copy of copy of AATHNEcombined map 6 as #45, grid size 43,51,63, pixel
    18588 2, shown at level 0.354, step 1, values float32 
    18589 Log from Thu Mar 12 17:49:41 2026UCSF ChimeraX version: 1.11.1 (2026-01-23) 
    18590 © 2016-2025 Regents of the University of California. All rights reserved. 
    18591 
    18592 > open "/Users/amy/Desktop/SPA AAT_HNE/csparc.cxs"
    18593 
    18594 Opened cryosparc_P371_J880_003_volume_map.mrc as #2, grid size 300,300,300,
    18595 pixel 0.867, shown at level 0.0665, step 2, values float32 
    18596 Opened flipped_J880.mrc as #3, grid size 300,300,300, pixel 0.867, shown at
    18597 level 0.0841, step 1, values float32 
    18598 Opened cryosparc_P371_J882_005_volume_map (1).mrc z flip as #9, grid size
    18599 300,300,300, pixel 0.867, shown at level 0.0602, step 1, values float32 
    18600 Opened cryosparc_P371_J881_class_08_00006_volume.mrc z flip as #10, grid size
    18601 180,180,180, pixel 1.44, shown at level 0.122, step 1, values float32 
    18602 Opened cryosparc_P371_J916_map.mrc as #11, grid size 300,300,300, pixel 0.867,
    18603 shown at level 0.0503, step 2, values float32 
    18604 Opened cryosparc_P371_J916_map.mrc z flip as #12, grid size 300,300,300, pixel
    18605 0.867, shown at level 0.0806, step 1, values float32 
    18606 Opened cryosparc_P371_J919_class_00_final_volume.mrc as #13, grid size
    18607 128,128,128, pixel 2.03, shown at level 0.08, step 1, values float32 
    18608 Opened cryosparc_P371_J937_003_volume_map.mrc as #14, grid size 300,300,300,
    18609 pixel 0.867, shown at level 0.0245, step 2, values float32 
    18610 Opened cryosparc_P371_J937_003_volume_map.mrc z flip as #15, grid size
    18611 300,300,300, pixel 0.867, shown at level 0.0683, step 1, values float32 
    18612 Opened cryosparc_P371_J948_003_volume_map.mrc as #21, grid size 300,300,300,
    18613 pixel 0.867, shown at level 0.0208, step 2, values float32 
    18614 Opened cryosparc_P371_J948_003_volume_map.mrc z flip as #22, grid size
    18615 300,300,300, pixel 0.867, shown at level 0.0938, step 1, values float32 
    18616 Opened J1122.mrc as #29, grid size 300,300,300, pixel 0.867, shown at level
    18617 0.071, step 2, values float32 
    18618 Opened J1134.mrc as #34, grid size 300,300,300, pixel 0.867, shown at level
    18619 0.0707, step 2, values float32 
    18620 Log from Wed Feb 11 13:24:40 2026UCSF ChimeraX version: 1.11.1 (2026-01-23) 
    18621 © 2016-2025 Regents of the University of California. All rights reserved. 
    18622 
    18623 > open /Users/amy/Desktop/3C11_Fab_AAT_NE/csparc.cxs
    18624 
    18625 Opened cryosparc_P371_J880_003_volume_map.mrc as #2, grid size 300,300,300,
    18626 pixel 0.867, shown at level 0.0665, step 2, values float32 
    18627 Opened flipped_J880.mrc as #3, grid size 300,300,300, pixel 0.867, shown at
    18628 level 0.0841, step 1, values float32 
    18629 Opened cryosparc_P371_J882_005_volume_map (1).mrc z flip as #9, grid size
    18630 300,300,300, pixel 0.867, shown at level 0.0602, step 1, values float32 
    18631 Opened cryosparc_P371_J881_class_08_00006_volume.mrc z flip as #10, grid size
    18632 180,180,180, pixel 1.44, shown at level 0.122, step 1, values float32 
    18633 Opened cryosparc_P371_J916_map.mrc as #11, grid size 300,300,300, pixel 0.867,
    18634 shown at level 0.0503, step 2, values float32 
    18635 Opened cryosparc_P371_J916_map.mrc z flip as #12, grid size 300,300,300, pixel
    18636 0.867, shown at level 0.0806, step 1, values float32 
    18637 Opened cryosparc_P371_J919_class_00_final_volume.mrc as #13, grid size
    18638 128,128,128, pixel 2.03, shown at level 0.08, step 1, values float32 
    18639 Opened cryosparc_P371_J937_003_volume_map.mrc as #14, grid size 300,300,300,
    18640 pixel 0.867, shown at level 0.0245, step 2, values float32 
    18641 Opened cryosparc_P371_J937_003_volume_map.mrc z flip as #15, grid size
    18642 300,300,300, pixel 0.867, shown at level 0.0683, step 1, values float32 
    18643 Opened cryosparc_P371_J948_003_volume_map.mrc as #21, grid size 300,300,300,
    18644 pixel 0.867, shown at level 0.0208, step 2, values float32 
    18645 Opened cryosparc_P371_J948_003_volume_map.mrc z flip as #22, grid size
    18646 300,300,300, pixel 0.867, shown at level 0.0938, step 1, values float32 
    18647 Opened J1122.mrc as #29, grid size 300,300,300, pixel 0.867, shown at level
    18648 0.071, step 2, values float32 
    18649 Opened J1134.mrc as #34, grid size 300,300,300, pixel 0.867, shown at level
    18650 0.0707, step 2, values float32 
    18651 Log from Sun Feb 1 23:24:08 2026UCSF ChimeraX version: 1.11.1 (2026-01-23) 
    18652 © 2016-2025 Regents of the University of California. All rights reserved. 
    18653 
    18654 > open /Users/amy/Desktop/3C11_Fab_AAT_NE/csparc.cxs format session
    18655 
    18656 Opened cryosparc_P371_J880_003_volume_map.mrc as #2, grid size 300,300,300,
    18657 pixel 0.867, shown at level 0.0665, step 2, values float32 
    18658 Opened flipped_J880.mrc as #3, grid size 300,300,300, pixel 0.867, shown at
    18659 level 0.0841, step 1, values float32 
    18660 Opened cryosparc_P371_J882_005_volume_map (1).mrc z flip as #9, grid size
    18661 300,300,300, pixel 0.867, shown at level 0.0602, step 1, values float32 
    18662 Opened cryosparc_P371_J881_class_08_00006_volume.mrc z flip as #10, grid size
    18663 180,180,180, pixel 1.44, shown at level 0.122, step 1, values float32 
    18664 Opened cryosparc_P371_J916_map.mrc as #11, grid size 300,300,300, pixel 0.867,
    18665 shown at level 0.0503, step 2, values float32 
    18666 Opened cryosparc_P371_J916_map.mrc z flip as #12, grid size 300,300,300, pixel
    18667 0.867, shown at level 0.0806, step 1, values float32 
    18668 Opened cryosparc_P371_J919_class_00_final_volume.mrc as #13, grid size
    18669 128,128,128, pixel 2.03, shown at level 0.08, step 1, values float32 
    18670 Opened cryosparc_P371_J937_003_volume_map.mrc as #14, grid size 300,300,300,
    18671 pixel 0.867, shown at level 0.0245, step 2, values float32 
    18672 Opened cryosparc_P371_J937_003_volume_map.mrc z flip as #15, grid size
    18673 300,300,300, pixel 0.867, shown at level 0.0683, step 1, values float32 
    18674 Opened cryosparc_P371_J948_003_volume_map.mrc as #21, grid size 300,300,300,
    18675 pixel 0.867, shown at level 0.0208, step 2, values float32 
    18676 Opened cryosparc_P371_J948_003_volume_map.mrc z flip as #22, grid size
    18677 300,300,300, pixel 0.867, shown at level 0.0938, step 1, values float32 
    18678 Opened J1122.mrc as #29, grid size 300,300,300, pixel 0.867, shown at level
    18679 0.071, step 2, values float32 
    18680 Opened J1134.mrc as #34, grid size 300,300,300, pixel 0.867, shown at level
    18681 0.0707, step 2, values float32 
    18682 Log from Tue Jan 6 13:31:49 2026UCSF ChimeraX version: 1.9rc202411230619
    18683 (2024-11-23) 
    18684 © 2016-2024 Regents of the University of California. All rights reserved. 
    18685 
    18686 > open /Users/apple/Downloads/csparc.cxs
    18687 
    18688 Opened cryosparc_P371_J880_003_volume_map.mrc as #2, grid size 300,300,300,
    18689 pixel 0.867, shown at level 0.0665, step 2, values float32 
    18690 Opened flipped_J880.mrc as #3, grid size 300,300,300, pixel 0.867, shown at
    18691 level 0.0841, step 1, values float32 
    18692 Opened cryosparc_P371_J882_005_volume_map (1).mrc z flip as #9, grid size
    18693 300,300,300, pixel 0.867, shown at level 0.0602, step 1, values float32 
    18694 Opened cryosparc_P371_J881_class_08_00006_volume.mrc z flip as #10, grid size
    18695 180,180,180, pixel 1.44, shown at level 0.122, step 1, values float32 
    18696 Opened cryosparc_P371_J916_map.mrc as #11, grid size 300,300,300, pixel 0.867,
    18697 shown at level 0.0503, step 2, values float32 
    18698 Opened cryosparc_P371_J916_map.mrc z flip as #12, grid size 300,300,300, pixel
    18699 0.867, shown at level 0.0806, step 1, values float32 
    18700 Opened cryosparc_P371_J919_class_00_final_volume.mrc as #13, grid size
    18701 128,128,128, pixel 2.03, shown at level 0.08, step 1, values float32 
    18702 Opened cryosparc_P371_J937_003_volume_map.mrc as #14, grid size 300,300,300,
    18703 pixel 0.867, shown at level 0.0245, step 2, values float32 
    18704 Opened cryosparc_P371_J937_003_volume_map.mrc z flip as #15, grid size
    18705 300,300,300, pixel 0.867, shown at level 0.0683, step 1, values float32 
    18706 Opened cryosparc_P371_J948_003_volume_map.mrc as #21, grid size 300,300,300,
    18707 pixel 0.867, shown at level 0.0208, step 2, values float32 
    18708 Opened cryosparc_P371_J948_003_volume_map.mrc z flip as #22, grid size
    18709 300,300,300, pixel 0.867, shown at level 0.0938, step 1, values float32 
    18710 Log from Wed Dec 31 02:28:23 2025UCSF ChimeraX version: 1.9rc202411230619
    18711 (2024-11-23) 
    18712 © 2016-2024 Regents of the University of California. All rights reserved. 
    18713 
    18714 > open /Users/apple/Downloads/csparc.cxs
    18715 
    18716 Opened cryosparc_P371_J880_003_volume_map.mrc as #2, grid size 300,300,300,
    18717 pixel 0.867, shown at level 0.0665, step 2, values float32 
    18718 Opened flipped_J880.mrc as #3, grid size 300,300,300, pixel 0.867, shown at
    18719 level 0.0841, step 1, values float32 
    18720 Opened cryosparc_P371_J882_005_volume_map (1).mrc z flip as #9, grid size
    18721 300,300,300, pixel 0.867, shown at level 0.0602, step 1, values float32 
    18722 Opened cryosparc_P371_J881_class_08_00006_volume.mrc z flip as #10, grid size
    18723 180,180,180, pixel 1.44, shown at level 0.122, step 1, values float32 
    18724 Opened cryosparc_P371_J916_map.mrc as #11, grid size 300,300,300, pixel 0.867,
    18725 shown at level 0.0503, step 2, values float32 
    18726 Opened cryosparc_P371_J916_map.mrc z flip as #12, grid size 300,300,300, pixel
    18727 0.867, shown at level 0.0806, step 1, values float32 
    18728 Opened cryosparc_P371_J919_class_00_final_volume.mrc as #13, grid size
    18729 128,128,128, pixel 2.03, shown at level 0.08, step 1, values float32 
    18730 Opened cryosparc_P371_J937_003_volume_map.mrc as #14, grid size 300,300,300,
    18731 pixel 0.867, shown at level 0.0245, step 2, values float32 
    18732 Opened cryosparc_P371_J937_003_volume_map.mrc z flip as #15, grid size
    18733 300,300,300, pixel 0.867, shown at level 0.0683, step 1, values float32 
    18734 Opened cryosparc_P371_J948_003_volume_map.mrc as #21, grid size 300,300,300,
    18735 pixel 0.867, shown at level 0.0208, step 2, values float32 
    18736 Opened cryosparc_P371_J948_003_volume_map.mrc z flip as #22, grid size
    18737 300,300,300, pixel 0.867, shown at level 0.0938, step 1, values float32 
    18738 Log from Wed Dec 10 00:50:43 2025UCSF ChimeraX version: 1.9rc202411230619
    18739 (2024-11-23) 
    18740 © 2016-2024 Regents of the University of California. All rights reserved. 
    18741 
    18742 > open /Users/apple/Downloads/csparc.cxs
    18743 
    18744 Opened cryosparc_P371_J880_003_volume_map.mrc as #2, grid size 300,300,300,
    18745 pixel 0.867, shown at level 0.0665, step 2, values float32 
    18746 Opened flipped_J880.mrc as #3, grid size 300,300,300, pixel 0.867, shown at
    18747 level 0.0841, step 1, values float32 
    18748 Opened cryosparc_P371_J882_005_volume_map (1).mrc z flip as #9, grid size
    18749 300,300,300, pixel 0.867, shown at level 0.0602, step 1, values float32 
    18750 Opened cryosparc_P371_J881_class_08_00006_volume.mrc z flip as #10, grid size
    18751 180,180,180, pixel 1.44, shown at level 0.122, step 1, values float32 
    18752 Opened cryosparc_P371_J916_map.mrc as #11, grid size 300,300,300, pixel 0.867,
    18753 shown at level 0.0503, step 2, values float32 
    18754 Opened cryosparc_P371_J916_map.mrc z flip as #12, grid size 300,300,300, pixel
    18755 0.867, shown at level 0.0806, step 1, values float32 
    18756 Opened cryosparc_P371_J919_class_00_final_volume.mrc as #13, grid size
    18757 128,128,128, pixel 2.03, shown at level 0.08, step 1, values float32 
    18758 Log from Fri Nov 28 18:17:17 2025UCSF ChimeraX version: 1.9rc202411230619
    18759 (2024-11-23) 
    18760 © 2016-2024 Regents of the University of California. All rights reserved. 
    18761 
    18762 > open /Users/apple/Downloads/csparc.cxs
    18763 
    18764 Opened cryosparc_P371_J880_003_volume_map.mrc as #2, grid size 300,300,300,
    18765 pixel 0.867, shown at level 0.0665, step 2, values float32 
    18766 Opened flipped_J880.mrc as #3, grid size 300,300,300, pixel 0.867, shown at
    18767 level 0.0841, step 1, values float32 
    18768 Opened cryosparc_P371_J882_005_volume_map (1).mrc z flip as #9, grid size
    18769 300,300,300, pixel 0.867, shown at level 0.0602, step 1, values float32 
    18770 Opened cryosparc_P371_J881_class_08_00006_volume.mrc z flip as #10, grid size
    18771 180,180,180, pixel 1.44, shown at level 0.122, step 1, values float32 
    18772 Log from Tue Nov 25 15:20:48 2025 Startup Messages 
    18773 --- 
    18774 note | available bundle cache has not been initialized yet 
    18775  
    18776 UCSF ChimeraX version: 1.9rc202411230619 (2024-11-23) 
    18777 © 2016-2024 Regents of the University of California. All rights reserved. 
    18778 How to cite UCSF ChimeraX 
    18779 
    18780 > open 1ezx format mmcif fromDatabase pdb
    18781 
    18782 1ezx title: 
    18783 Crystal structure of A serpin:protease complex [more info...] 
    18784  
    18785 Chain information for 1ezx #1 
    18786 --- 
    18787 Chain | Description | UniProt 
    18788 A | ALPHA-1-ANTITRYPSIN | A1AT_HUMAN 24-358 
    18789 B | ALPHA-1-ANTITRYPSIN | A1AT_HUMAN 359-394 
    18790 C | TRYPSIN | TRY1_BOVIN 42-245 
    18791  
    18792 
    18793 > open /Users/apple/Downloads/cryosparc_P371_J880_003_volume_map.mrc
    18794 
    18795 Opened cryosparc_P371_J880_003_volume_map.mrc as #2, grid size 300,300,300,
    18796 pixel 0.867, shown at level 0.0177, step 2, values float32 
    18797 
    18798 > volume #2 level 0.06652
    18799 
    18800 > ui mousemode right "translate selected models"
    18801 
    18802 > select add #1
    18803 
    18804 3984 atoms, 3982 bonds, 5 pseudobonds, 592 residues, 3 models selected 
    18805 
    18806 > view matrix models #1,1,0,0,22.115,0,1,0,63.09,0,0,1,71.823
    18807 
    18808 > view matrix models #1,1,0,0,69.177,0,1,0,79.741,0,0,1,64.119
    18809 
    18810 > view matrix models #1,1,0,0,67.012,0,1,0,77.327,0,0,1,54.335
    18811 
    18812 > view matrix models #1,1,0,0,68.613,0,1,0,71.318,0,0,1,51.449
    18813 
    18814 > ui tool show "Fit in Map"
    18815 
    18816 > fitmap #1 inMap #2
    18817 
    18818 Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
    18819 using 3984 atoms 
    18820 average map value = 0.0438, steps = 92 
    18821 shifted from previous position = 3.55 
    18822 rotated from previous position = 4.42 degrees 
    18823 atoms outside contour = 2880, contour level = 0.066523 
    18824  
    18825 Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
    18826 coordinates: 
    18827 Matrix rotation and translation 
    18828 0.99872483 -0.00989522 0.04950557 63.11308004 
    18829 0.00699761 0.99827076 0.05836545 67.58136236 
    18830 -0.04999751 -0.05794461 0.99706703 56.37622316 
    18831 Axis -0.75528783 0.64614759 0.10969770 
    18832 Axis point 0.00000000 1024.64866555 -1103.37084637 
    18833 Rotation angle (degrees) 4.41598404 
    18834 Shift along axis 2.18333524 
    18835  
    18836 
    18837 > view matrix models
    18838 > #1,0.99872,-0.0098952,0.049506,62.468,0.0069976,0.99827,0.058365,78.039,-0.049998,-0.057945,0.99707,58.786
    18839 
    18840 > ui mousemode right "rotate selected models"
    18841 
    18842 > view matrix models
    18843 > #1,-0.95028,-0.27274,-0.15028,221.56,0.30912,-0.88449,-0.34946,175.7,-0.037612,-0.37854,0.92482,78.268
    18844 
    18845 > fitmap #1 inMap #2
    18846 
    18847 Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
    18848 using 3984 atoms 
    18849 average map value = 0.04798, steps = 140 
    18850 shifted from previous position = 7.9 
    18851 rotated from previous position = 12.7 degrees 
    18852 atoms outside contour = 2817, contour level = 0.066523 
    18853  
    18854 Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
    18855 coordinates: 
    18856 Matrix rotation and translation 
    18857 -0.90965137 -0.21420693 -0.35587888 224.37202412 
    18858 0.34819532 -0.86039384 -0.37213231 169.35532345 
    18859 -0.22648268 -0.46242602 0.85724429 105.26930309 
    18860 Axis -0.15458157 -0.22152447 0.96282472 
    18861 Axis point 107.00674340 114.53127832 0.00000000 
    18862 Rotation angle (degrees) 163.01876555 
    18863 Shift along axis 29.15575838 
    18864  
    18865 
    18866 > view matrix models
    18867 > #1,-0.93537,-0.33888,0.10125,206.37,0.28885,-0.89713,-0.33425,173.15,0.2041,-0.2834,0.93703,61.97
    18868 
    18869 > remove /C
    18870 
    18871 Unknown command: remove /C 
    18872 
    18873 > delete /C
    18874 
    18875 > fitmap #1 inMap #2
    18876 
    18877 Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
    18878 using 2975 atoms 
    18879 average map value = 0.05683, steps = 168 
    18880 shifted from previous position = 10.2 
    18881 rotated from previous position = 20.9 degrees 
    18882 atoms outside contour = 1876, contour level = 0.066523 
    18883  
    18884 Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
    18885 coordinates: 
    18886 Matrix rotation and translation 
    18887 -0.98775248 -0.03216686 0.15267718 185.97005837 
    18888 0.01404291 -0.99287467 -0.11833294 193.09005228 
    18889 0.15539570 -0.11473962 0.98116614 52.60294093 
    18890 Axis 0.07739391 -0.05855237 0.99527976 
    18891 Axis point 89.79478279 99.15188295 0.00000000 
    18892 Rotation angle (degrees) 178.66978984 
    18893 Shift along axis 55.44171271 
    18894  
    18895 
    18896 > fitmap #1 inMap #2
    18897 
    18898 Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
    18899 using 2975 atoms 
    18900 average map value = 0.05683, steps = 44 
    18901 shifted from previous position = 0.00306 
    18902 rotated from previous position = 0.00868 degrees 
    18903 atoms outside contour = 1876, contour level = 0.066523 
    18904  
    18905 Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
    18906 coordinates: 
    18907 Matrix rotation and translation 
    18908 -0.98775300 -0.03230499 0.15264466 185.98147456 
    18909 0.01419042 -0.99287622 -0.11830233 193.08167122 
    18910 0.15537901 -0.11468739 0.98117489 52.59959002 
    18911 Axis 0.07738151 -0.05853153 0.99528195 
    18912 Axis point 89.79393478 99.15365724 0.00000000 
    18913 Rotation angle (degrees) 178.66156873 
    18914 Shift along axis 55.44158488 
    18915  
    18916 
    18917 > view matrix models
    18918 > #1,-0.34306,0.064653,-0.93709,202.25,-0.15112,-0.98843,-0.012871,197.23,-0.92708,0.1372,0.34886,143.06
    18919 
    18920 > view matrix models
    18921 > #1,0.89084,0.24868,-0.38022,79.922,0.1402,-0.94652,-0.29059,192.22,-0.43215,0.20556,-0.87806,178.59
    18922 
    18923 > view matrix models
    18924 > #1,0.98069,0.15076,0.12459,50.828,0.17789,-0.95233,-0.24786,187.69,0.081282,0.26523,-0.96075,146.99
    18925 
    18926 > transparency #2 50
    18927 
    18928 > view matrix models
    18929 > #1,0.29239,0.037619,0.95556,53.368,0.22932,-0.97283,-0.03187,173.11,0.9284,0.22844,-0.29308,56.382
    18930 
    18931 > view matrix models
    18932 > #1,-0.29179,0.14333,0.94568,84.773,0.13863,-0.97193,0.19008,165.94,0.94638,0.18656,0.26373,25.435
    18933 
    18934 > fitmap #1 inMap #2
    18935 
    18936 Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
    18937 using 2975 atoms 
    18938 average map value = 0.05731, steps = 92 
    18939 shifted from previous position = 3.83 
    18940 rotated from previous position = 8.94 degrees 
    18941 atoms outside contour = 1851, contour level = 0.066523 
    18942  
    18943 Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
    18944 coordinates: 
    18945 Matrix rotation and translation 
    18946 -0.32142151 0.28922900 0.90168442 78.62508488 
    18947 0.10483022 -0.93549119 0.33744164 157.26649378 
    18948 0.94111574 0.20298478 0.27036706 21.13366302 
    18949 Axis -0.58056816 -0.17025957 -0.79621121 
    18950 Axis point 36.79057462 75.39561878 -0.00000000 
    18951 Rotation angle (degrees) 173.35036530 
    18952 Shift along axis -89.25020548 
    18953  
    18954 
    18955 > fitmap #1 inMap #2
    18956 
    18957 Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
    18958 using 2975 atoms 
    18959 average map value = 0.05731, steps = 76 
    18960 shifted from previous position = 0.0143 
    18961 rotated from previous position = 0.0108 degrees 
    18962 atoms outside contour = 1850, contour level = 0.066523 
    18963  
    18964 Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
    18965 coordinates: 
    18966 Matrix rotation and translation 
    18967 -0.32139468 0.28930309 0.90167022 78.61286146 
    18968 0.10496741 -0.93543603 0.33755190 157.24594170 
    18969 0.94110961 0.20313337 0.27027676 21.11828838 
    18970 Axis -0.58058094 -0.17034675 -0.79618324 
    18971 Axis point 36.78722862 75.38632197 0.00000000 
    18972 Rotation angle (degrees) 173.35241654 
    18973 Shift along axis -89.24149146 
    18974  
    18975 
    18976 > view matrix models
    18977 > #1,0.48423,0.47971,0.73171,25.463,0.23276,-0.87679,0.42079,140.68,0.84341,-0.033442,-0.53622,88.647
    18978 
    18979 > fitmap #1 inMap #2
    18980 
    18981 Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
    18982 using 2975 atoms 
    18983 average map value = 0.05854, steps = 96 
    18984 shifted from previous position = 2.57 
    18985 rotated from previous position = 9.29 degrees 
    18986 atoms outside contour = 1796, contour level = 0.066523 
    18987  
    18988 Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
    18989 coordinates: 
    18990 Matrix rotation and translation 
    18991 0.39156198 0.46621567 0.79329828 28.63896931 
    18992 0.32834063 -0.87617582 0.35285743 137.96501568 
    18993 0.85957643 0.12230650 -0.49615469 78.33453532 
    18994 Axis -0.83325343 -0.23954143 -0.49830575 
    18995 Axis point 0.00000000 66.13906102 25.80824474 
    18996 Rotation angle (degrees) 172.04797842 
    18997 Shift along axis -95.94640636 
    18998  
    18999 
    19000 > fitmap #1 inMap #2
    19001 
    19002 Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
    19003 using 2975 atoms 
    19004 average map value = 0.05854, steps = 72 
    19005 shifted from previous position = 0.00208 
    19006 rotated from previous position = 0.0113 degrees 
    19007 atoms outside contour = 1796, contour level = 0.066523 
    19008  
    19009 Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
    19010 coordinates: 
    19011 Matrix rotation and translation 
    19012 0.39171342 0.46612484 0.79327690 28.63726861 
    19013 0.32836586 -0.87622221 0.35271873 137.97292978 
    19014 0.85949779 0.12232039 -0.49628748 78.34647546 
    19015 Axis -0.83330036 -0.23950649 -0.49824406 
    19016 Axis point 0.00000000 66.14388335 25.81952433 
    19017 Rotation angle (degrees) 172.05372561 
    19018 Shift along axis -95.94452502 
    19019  
    19020 
    19021 > view matrix models
    19022 > #1,0.76487,0.62103,0.17117,31.524,0.60943,-0.78369,0.12011,127.91,0.20873,0.012451,-0.97789,154.56
    19023 
    19024 > fitmap #1 inMap #2
    19025 
    19026 Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
    19027 using 2975 atoms 
    19028 average map value = 0.05756, steps = 152 
    19029 shifted from previous position = 4.36 
    19030 rotated from previous position = 22.9 degrees 
    19031 atoms outside contour = 1854, contour level = 0.066523 
    19032  
    19033 Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
    19034 coordinates: 
    19035 Matrix rotation and translation 
    19036 0.91851505 0.27415782 0.28489928 35.47934780 
    19037 0.28051968 -0.95965858 0.01908170 161.02943922 
    19038 0.27863743 0.06239303 -0.95836751 146.25557472 
    19039 Axis 0.97941439 0.14160128 0.14386290 
    19040 Axis point 0.00000000 77.18823065 71.36819300 
    19041 Rotation angle (degrees) 178.73303939 
    19042 Shift along axis 78.59170916 
    19043  
    19044 
    19045 > view matrix models
    19046 > #1,0.70928,0.23412,0.66491,29.192,0.22662,-0.9689,0.099416,160.36,0.6675,0.080168,-0.74028,107.68
    19047 
    19048 > view matrix models
    19049 > #1,0.38932,0.16756,0.90573,39.677,0.11688,-0.98435,0.13187,166.42,0.91366,0.054523,-0.40281,73.929
    19050 
    19051 > view matrix models
    19052 > #1,0.33533,0.23749,0.91168,38.512,0.22246,-0.9603,0.16833,156.1,0.91546,0.14637,-0.37485,66.587
    19053 
    19054 > view matrix models
    19055 > #1,0.33533,0.23749,0.91168,38.861,0.22246,-0.9603,0.16833,151.64,0.91546,0.14637,-0.37485,67.054
    19056 
    19057 > view matrix models
    19058 > #1,0.34573,0.097318,0.93327,45.492,0.021529,-0.99517,0.095797,170.8,0.93809,-0.013027,-0.34615,73.665
    19059 
    19060 > fitmap #1 inMap #2
    19061 
    19062 Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
    19063 using 2975 atoms 
    19064 average map value = 0.05854, steps = 136 
    19065 shifted from previous position = 9.44 
    19066 rotated from previous position = 25.1 degrees 
    19067 atoms outside contour = 1797, contour level = 0.066523 
    19068  
    19069 Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
    19070 coordinates: 
    19071 Matrix rotation and translation 
    19072 0.39128073 0.46623746 0.79342424 28.64047706 
    19073 0.32828593 -0.87615611 0.35295725 137.95838588 
    19074 0.85972538 0.12236464 -0.49588220 78.32133865 
    19075 Axis -0.83316813 -0.23955669 -0.49844103 
    19076 Axis point 0.00000000 66.13417831 25.79650241 
    19077 Rotation angle (degrees) 172.04571172 
    19078 Shift along axis -95.94975542 
    19079  
    19080 
    19081 > view matrix models
    19082 > #1,0.39128,0.46624,0.79342,25.073,0.32829,-0.87616,0.35296,137.6,0.85973,0.12236,-0.49588,78.077
    19083 
    19084 > view matrix models
    19085 > #1,-0.056102,0.1979,0.97862,59.23,0.073542,-0.97668,0.20173,168.77,0.99571,0.083287,0.04024,40.63
    19086 
    19087 > view matrix models
    19088 > #1,-0.064697,0.19676,0.97831,59.866,-0.033318,-0.98025,0.19495,176.2,0.99735,-0.019983,0.069975,45.097
    19089 
    19090 > view matrix models
    19091 > #1,-0.064697,0.19676,0.97831,60.856,-0.033318,-0.98025,0.19495,173.38,0.99735,-0.019983,0.069975,44.14
    19092 
    19093 > view matrix models
    19094 > #1,-0.064697,0.19676,0.97831,62.425,-0.033318,-0.98025,0.19495,171.85,0.99735,-0.019983,0.069975,46.927
    19095 
    19096 > view matrix models
    19097 > #1,0.048374,0.23427,0.97097,53.348,-0.027021,-0.97144,0.23574,168.54,0.99846,-0.037639,-0.040662,54.362
    19098 
    19099 > fitmap #1 inMap #2
    19100 
    19101 Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
    19102 using 2975 atoms 
    19103 average map value = 0.05548, steps = 116 
    19104 shifted from previous position = 2.18 
    19105 rotated from previous position = 10.2 degrees 
    19106 atoms outside contour = 1897, contour level = 0.066523 
    19107  
    19108 Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
    19109 coordinates: 
    19110 Matrix rotation and translation 
    19111 0.15476290 0.36480201 0.91813285 40.06056626 
    19112 0.00453943 -0.92958252 0.36858613 155.48377322 
    19113 0.98794121 -0.05287566 -0.14552088 61.55028255 
    19114 Axis -0.75418435 -0.12491849 -0.64467149 
    19115 Axis point 0.00000000 74.79947560 0.01397902 
    19116 Rotation angle (degrees) 163.77466905 
    19117 Shift along axis -89.31556288 
    19118  
    19119 
    19120 > view matrix models
    19121 > #1,0.15476,0.3648,0.91813,43.614,0.0045394,-0.92958,0.36859,155.22,0.98794,-0.052876,-0.14552,59.521
    19122 
    19123 > view matrix models
    19124 > #1,-0.2078,0.33394,0.9194,68.56,-0.052237,-0.94237,0.33048,161.84,0.97677,0.020648,0.21327,34.9
    19125 
    19126 > view matrix models
    19127 > #1,-0.21574,0.16972,0.96159,76.632,-0.13117,-0.98089,0.1437,180.08,0.9676,-0.095125,0.23388,41.35
    19128 
    19129 > fitmap #1 inMap #2
    19130 
    19131 Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
    19132 using 2975 atoms 
    19133 average map value = 0.05783, steps = 140 
    19134 shifted from previous position = 8.76 
    19135 rotated from previous position = 14.8 degrees 
    19136 atoms outside contour = 1859, contour level = 0.066523 
    19137  
    19138 Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
    19139 coordinates: 
    19140 Matrix rotation and translation 
    19141 -0.45352763 0.10818223 0.88465208 99.24914335 
    19142 -0.11633057 -0.99129935 0.06158562 193.39501529 
    19143 0.88361750 -0.07498130 0.46216655 30.32738546 
    19144 Axis -0.51968455 0.00393692 -0.85434915 
    19145 Axis point 47.88058461 94.47454852 0.00000000 
    19146 Rotation angle (degrees) 172.44984306 
    19147 Shift along axis -76.72704192 
    19148  
    19149 
    19150 > view matrix models
    19151 > #1,-0.44996,0.138,0.88232,97.338,-0.1451,-0.98616,0.080249,193.83,0.88118,-0.091912,0.46376,31.423
    19152 
    19153 > view matrix models
    19154 > #1,-0.44996,0.138,0.88232,96.943,-0.1451,-0.98616,0.080249,180.07,0.88118,-0.091912,0.46376,31.456
    19155 
    19156 > fitmap #1 inMap #2
    19157 
    19158 Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
    19159 using 2975 atoms 
    19160 average map value = 0.05816, steps = 144 
    19161 shifted from previous position = 5.29 
    19162 rotated from previous position = 25.5 degrees 
    19163 atoms outside contour = 1860, contour level = 0.066523 
    19164  
    19165 Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
    19166 coordinates: 
    19167 Matrix rotation and translation 
    19168 -0.76791109 0.07342342 0.63633447 137.05037337 
    19169 0.02287887 -0.98963117 0.14179815 171.02871657 
    19170 0.64014773 0.12344698 0.75826890 16.52925526 
    19171 Axis -0.34041716 -0.07073658 -0.93760999 
    19172 Axis point 66.71618726 84.08739228 0.00000000 
    19173 Rotation angle (degrees) 178.45546636 
    19174 Shift along axis -74.25028018 
    19175  
    19176 
    19177 > volume flip #2 axis z
    19178 
    19179 Opened cryosparc_P371_J880_003_volume_map.mrc z flip as #3, grid size
    19180 300,300,300, pixel 0.867, shown at step 1, values float32 
    19181 
    19182 > fitmap #1 inMap #2
    19183 
    19184 Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
    19185 using 2975 atoms 
    19186 average map value = 0.05816, steps = 44 
    19187 shifted from previous position = 0.00304 
    19188 rotated from previous position = 0.0131 degrees 
    19189 atoms outside contour = 1859, contour level = 0.066523 
    19190  
    19191 Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
    19192 coordinates: 
    19193 Matrix rotation and translation 
    19194 -0.76779231 0.07330789 0.63649111 137.03880955 
    19195 0.02299050 -0.98964048 0.14171507 171.02535003 
    19196 0.64028619 0.12344099 0.75815296 16.52599590 
    19197 Axis -0.34050650 -0.07071503 -0.93757917 
    19198 Axis point 66.70481841 84.08969330 0.00000000 
    19199 Rotation angle (degrees) 178.46235923 
    19200 Shift along axis -74.25109879 
    19201  
    19202 
    19203 > view matrix models
    19204 > #1,-0.52389,0.12388,0.84273,106.41,0.091727,-0.97541,0.20041,162.36,0.84683,0.18229,0.49964,14.777
    19205 
    19206 > select add #3
    19207 
    19208 2975 atoms, 2968 bonds, 437 residues, 3 models selected 
    19209 
    19210 > select subtract #3
    19211 
    19212 2975 atoms, 2968 bonds, 437 residues, 1 model selected 
    19213 
    19214 > view matrix models
    19215 > #1,-0.52389,0.12388,0.84273,105.24,0.091727,-0.97541,0.20041,169.49,0.84683,0.18229,0.49964,54.589
    19216 
    19217 > view matrix models
    19218 > #1,-0.52389,0.12388,0.84273,103,0.091727,-0.97541,0.20041,168.04,0.84683,0.18229,0.49964,53.744
    19219 
    19220 > fitmap #1 inMap #2
    19221 
    19222 Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
    19223 using 2975 atoms 
    19224 average map value = 0.05198, steps = 396 
    19225 shifted from previous position = 26.6 
    19226 rotated from previous position = 41.8 degrees 
    19227 atoms outside contour = 2024, contour level = 0.066523 
    19228  
    19229 Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
    19230 coordinates: 
    19231 Matrix rotation and translation 
    19232 -0.40282969 0.31103532 0.86080501 84.94134983 
    19233 0.59685966 -0.62373813 0.50468732 103.56065454 
    19234 0.69389249 0.71708282 0.06561581 32.32204409 
    19235 Axis 0.54006522 0.42441412 0.72677522 
    19236 Axis point 26.67261820 43.96459459 0.00000000 
    19237 Rotation angle (degrees) 168.65952926 
    19238 Shift along axis 113.31733317 
    19239  
    19240 
    19241 > view matrix models
    19242 > #1,-0.43926,0.065153,0.89599,100.22,0.59516,-0.72598,0.34457,119.21,0.67293,0.68462,0.28012,23.176
    19243 
    19244 > view matrix models
    19245 > #1,-0.43926,0.065153,0.89599,90.909,0.59516,-0.72598,0.34457,101.79,0.67293,0.68462,0.28012,39.972
    19246 
    19247 > view matrix models
    19248 > #1,-0.86466,-0.41381,0.28483,182.78,0.49939,-0.76955,0.39798,107.46,0.054503,0.48636,0.87206,57.135
    19249 
    19250 > view matrix models
    19251 > #1,-0.41714,-0.50359,-0.75657,220.21,0.34751,-0.85757,0.37922,123.61,-0.83978,-0.10473,0.53273,169.98
    19252 
    19253 > view matrix models
    19254 > #1,0.75417,0.076431,-0.65222,104.02,0.19721,-0.97372,0.11393,155.7,-0.62637,-0.21455,-0.74942,237.56
    19255 
    19256 > view matrix models
    19257 > #1,0.59893,0.091914,-0.79551,121.31,0.19286,-0.98071,0.031893,161.17,-0.77723,-0.17253,-0.6051,236.24
    19258 
    19259 > view matrix models
    19260 > #1,0.59893,0.091914,-0.79551,120.05,0.19286,-0.98071,0.031893,163.86,-0.77723,-0.17253,-0.6051,238.3
    19261 
    19262 > view matrix models
    19263 > #1,0.60587,0.10394,-0.78874,118.48,0.22025,-0.97459,0.040753,161.22,-0.76446,-0.19841,-0.61337,239.55
    19264 
    19265 > view matrix models
    19266 > #1,0.60587,0.10394,-0.78874,137.03,0.22025,-0.97459,0.040753,164.86,-0.76446,-0.19841,-0.61337,244.11
    19267 
    19268 > fitmap #1 inMap #2
    19269 
    19270 Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
    19271 using 2975 atoms 
    19272 average map value = 0.05241, steps = 240 
    19273 shifted from previous position = 27.2 
    19274 rotated from previous position = 10.6 degrees 
    19275 atoms outside contour = 2020, contour level = 0.066523 
    19276  
    19277 Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
    19278 coordinates: 
    19279 Matrix rotation and translation 
    19280 0.57403834 -0.00393553 -0.81881897 142.71357757 
    19281 0.04701479 -0.99818033 0.03775763 187.83819388 
    19282 -0.81747758 -0.06017093 -0.57280875 212.09998405 
    19283 Axis -0.88704943 -0.01215043 0.46151455 
    19284 Axis point 0.00000000 96.46648529 140.25698861 
    19285 Rotation angle (degrees) 176.83571969 
    19286 Shift along axis -30.98908429 
    19287  
    19288 
    19289 > view matrix models
    19290 > #1,0.50366,0.028512,-0.86343,147.82,0.16923,-0.98335,0.066244,177.48,-0.84716,-0.17948,-0.5001,217.05
    19291 
    19292 > view matrix models
    19293 > #1,0.50366,0.028512,-0.86343,159.38,0.16923,-0.98335,0.066244,163.53,-0.84716,-0.17948,-0.5001,218.36
    19294 
    19295 > view matrix models
    19296 > #1,0.77888,-0.021397,-0.6268,131.11,0.011385,-0.99877,0.048242,175.59,-0.62706,-0.044711,-0.77768,212.22
    19297 
    19298 > view matrix models
    19299 > #1,0.80541,-0.036391,-0.5916,128.29,-0.023432,-0.99929,0.029569,178.93,-0.59225,-0.0099531,-0.80569,209.51
    19300 
    19301 > view matrix models
    19302 > #1,0.80541,-0.036391,-0.5916,124.59,-0.023432,-0.99929,0.029569,182.08,-0.59225,-0.0099531,-0.80569,208.91
    19303 
    19304 > fitmap #1 inMap #2
    19305 
    19306 Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
    19307 using 2975 atoms 
    19308 average map value = 0.06114, steps = 180 
    19309 shifted from previous position = 15 
    19310 rotated from previous position = 14.2 degrees 
    19311 atoms outside contour = 1746, contour level = 0.066523 
    19312  
    19313 Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
    19314 coordinates: 
    19315 Matrix rotation and translation 
    19316 0.85347860 0.03851228 -0.51970287 104.90951223 
    19317 -0.07623353 -0.97731057 -0.19761705 201.13931543 
    19318 -0.51552180 0.20828070 -0.83117774 180.17182734 
    19319 Axis 0.96224006 -0.00991186 -0.27202175 
    19320 Axis point 0.00000000 90.37179533 116.08940430 
    19321 Rotation angle (degrees) 167.82414204 
    19322 Shift along axis 49.94381521 
    19323  
    19324 
    19325 > view matrix models
    19326 > #1,0.85348,0.038512,-0.5197,94.645,-0.076234,-0.97731,-0.19762,192.73,-0.51552,0.20828,-0.83118,215.52
    19327 
    19328 > fitmap #1 inMap #2
    19329 
    19330 Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
    19331 using 2975 atoms 
    19332 average map value = 0.04998, steps = 228 
    19333 shifted from previous position = 24.7 
    19334 rotated from previous position = 22.8 degrees 
    19335 atoms outside contour = 2007, contour level = 0.066523 
    19336  
    19337 Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
    19338 coordinates: 
    19339 Matrix rotation and translation 
    19340 0.83373907 0.05761081 -0.54914494 106.68752994 
    19341 -0.27258804 -0.82195371 -0.50008786 229.20333513 
    19342 -0.48018219 0.56663312 -0.66959090 165.21182517 
    19343 Axis 0.95346344 -0.06164073 -0.29514047 
    19344 Axis point 0.00000000 89.71271679 136.26536856 
    19345 Rotation angle (degrees) 145.98619039 
    19346 Shift along axis 38.83370161 
    19347  
    19348 
    19349 > view matrix models
    19350 > #1,0.85957,-0.051768,-0.50839,109.34,-0.30914,-0.84485,-0.43665,229.25,-0.40691,0.5325,-0.74221,166.84
    19351 
    19352 > view matrix models
    19353 > #1,0.85957,-0.051768,-0.50839,105.72,-0.30914,-0.84485,-0.43665,214.62,-0.40691,0.5325,-0.74221,185.48
    19354 
    19355 > view matrix models
    19356 > #1,0.90687,0.19702,-0.37252,79.626,0.12723,-0.97073,-0.20369,180.91,-0.40175,0.13732,-0.90539,218.74
    19357 
    19358 > view matrix models
    19359 > #1,0.67914,0.18357,0.71068,32.037,0.24568,-0.96923,0.015585,160.52,0.69167,0.16401,-0.70334,135.59
    19360 
    19361 > view matrix models
    19362 > #1,0.17493,0.05579,0.983,56.185,0.11322,-0.99291,0.036205,169.22,0.97805,0.10496,-0.18,90.508
    19363 
    19364 > view matrix models
    19365 > #1,0.77968,0.065182,0.62277,37.951,0.11391,-0.99274,-0.038712,173.52,0.61572,0.10113,-0.78145,148.81
    19366 
    19367 > view matrix models
    19368 > #1,0.92537,0.30742,-0.22176,62.951,0.27327,-0.94648,-0.17175,168.25,-0.26269,0.09833,-0.95986,215.41
    19369 
    19370 > view matrix models
    19371 > #1,0.70434,0.40439,-0.58342,92.157,0.29038,-0.9141,-0.28304,171.65,-0.64776,0.02994,-0.76126,232.61
    19372 
    19373 > view matrix models
    19374 > #1,0.63232,0.36591,-0.68285,104.88,0.25844,-0.93057,-0.25933,173.32,-0.73033,-0.012492,-0.68298,235.92
    19375 
    19376 > view matrix models
    19377 > #1,0.63232,0.36591,-0.68285,105.28,0.25844,-0.93057,-0.25933,173.87,-0.73033,-0.012492,-0.68298,234.43
    19378 
    19379 > view matrix models
    19380 > #1,0.62644,0.35038,-0.69628,107.38,0.25038,-0.93639,-0.24594,173.97,-0.73816,-0.020267,-0.67432,234.9
    19381 
    19382 > fitmap #1 inMap #2
    19383 
    19384 Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
    19385 using 2975 atoms 
    19386 average map value = 0.04135, steps = 172 
    19387 shifted from previous position = 17.5 
    19388 rotated from previous position = 15.7 degrees 
    19389 atoms outside contour = 2209, contour level = 0.066523 
    19390  
    19391 Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
    19392 coordinates: 
    19393 Matrix rotation and translation 
    19394 0.64106806 0.54805599 -0.53727682 84.29416786 
    19395 0.45670740 -0.83502441 -0.30684294 171.83349628 
    19396 -0.61680637 -0.04867109 -0.78560870 224.33733641 
    19397 Axis 0.90532451 0.27888420 -0.32032972 
    19398 Axis point 0.00000000 63.39099370 133.30398496 
    19399 Rotation angle (degrees) 171.80252826 
    19400 Shift along axis 52.37330856 
    19401  
    19402 
    19403 > volume #3 level 0.08411
    19404 
    19405 > view matrix models
    19406 > #1,0.89403,0.11377,0.43333,38.242,0.12475,-0.99218,0.0031177,184.59,0.43029,0.051272,-0.90123,158.14
    19407 
    19408 > view matrix models
    19409 > #1,-0.18632,0.03739,0.98178,79.976,-0.079477,-0.99657,0.02287,196.75,0.97927,-0.073767,0.18865,67.401
    19410 
    19411 > view matrix models
    19412 > #1,-0.90953,0.27518,-0.3115,186.77,-0.18965,-0.94164,-0.2781,217.91,-0.36985,-0.19387,0.90864,118.99
    19413 
    19414 > view matrix models
    19415 > #1,0.24398,0.16972,-0.95481,156.97,0.38319,-0.92132,-0.065848,167.79,-0.89086,-0.34981,-0.28982,231.39
    19416 
    19417 > view matrix models
    19418 > #1,0.42166,0.25626,-0.86979,135.42,0.41641,-0.90683,-0.065311,164.75,-0.80549,-0.33465,-0.48908,236.59
    19419 
    19420 > view matrix models
    19421 > #1,0.47933,0.24843,-0.84174,130.58,0.4184,-0.90778,-0.029658,162.61,-0.77148,-0.33797,-0.53907,237.53
    19422 
    19423 > ui mousemode right "translate selected models"
    19424 
    19425 > view matrix models
    19426 > #1,0.47933,0.24843,-0.84174,128.8,0.4184,-0.90778,-0.029658,153.85,-0.77148,-0.33797,-0.53907,247.51
    19427 
    19428 > fitmap #1 inMap #3
    19429 
    19430 Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc z flip
    19431 (#3) using 2975 atoms 
    19432 average map value = 0.05446, steps = 68 
    19433 shifted from previous position = 3.18 
    19434 rotated from previous position = 7.84 degrees 
    19435 atoms outside contour = 2178, contour level = 0.08411 
    19436  
    19437 Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc z
    19438 flip (#3) coordinates: 
    19439 Matrix rotation and translation 
    19440 0.52841759 0.14565472 -0.83639676 133.99651702 
    19441 0.41790523 -0.90217777 0.10691341 147.19357847 
    19442 -0.73900613 -0.40602951 -0.53759648 249.57659595 
    19443 Axis -0.87112860 -0.16539807 0.46236180 
    19444 Axis point 0.00000000 83.46704951 147.99690601 
    19445 Rotation angle (degrees) 162.87766715 
    19446 Shift along axis -25.67904816 
    19447  
    19448 
    19449 > view matrix models
    19450 > #1,0.228,0.04128,-0.97279,167.46,0.36006,-0.93185,0.04485,156.3,-0.90464,-0.36049,-0.22733,239.34
    19451 
    19452 > view matrix models
    19453 > #1,0.228,0.04128,-0.97279,168.72,0.36006,-0.93185,0.04485,153.1,-0.90464,-0.36049,-0.22733,238.66
    19454 
    19455 > fitmap #1 inMap #3
    19456 
    19457 Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc z flip
    19458 (#3) using 2975 atoms 
    19459 average map value = 0.08066, steps = 176 
    19460 shifted from previous position = 5.39 
    19461 rotated from previous position = 39.4 degrees 
    19462 atoms outside contour = 1661, contour level = 0.08411 
    19463  
    19464 Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc z
    19465 flip (#3) coordinates: 
    19466 Matrix rotation and translation 
    19467 -0.38244590 0.10991711 -0.91741668 203.00581119 
    19468 0.07750617 -0.98558322 -0.15039445 183.86146589 
    19469 -0.92072141 -0.12862319 0.36841301 193.39522834 
    19470 Axis 0.55561740 0.08433916 -0.82714945 
    19471 Axis point 167.56182272 100.48395710 0.00000000 
    19472 Rotation angle (degrees) 178.87739199 
    19473 Shift along axis -31.66647401 
    19474  
    19475 
    19476 > save /Users/apple/Downloads/csparc.cxs includeMaps true
    19477 
    19478 > select subtract #1
    19479 
    19480 Nothing selected 
    19481 
    19482 > select add #3
    19483 
    19484 2 models selected 
    19485 
    19486 > save /Users/apple/Downloads/flipped_J880.mrc models #3
    19487 
    19488 > open /Users/apple/Downloads/3C11_Fab_D_1292144377_model-annotate_P1_HL-
    19489 > coot-0.pdb /Users/apple/Downloads/1ezx_moved-coot-0.pdb
    19490 
    19491 Summary of feedback from opening
    19492 /Users/apple/Downloads/3C11_Fab_D_1292144377_model-annotate_P1_HL-coot-0.pdb 
    19493 --- 
    19494 warnings | Start residue of secondary structure not found: HELIX 8 AA8 THR I 28 TYR I 32 5 5 
    19495 Start residue of secondary structure not found: HELIX 9 AA9 ASN I 73 LYS I 75
    19496 5 3 
    19497 Start residue of secondary structure not found: HELIX 10 AB1 LYS I 83 THR I 87
    19498 5 5 
    19499 Start residue of secondary structure not found: HELIX 11 AB2 SER I 156 SER I
    19500 158 5 3 
    19501 Start residue of secondary structure not found: HELIX 12 AB3 PRO I 200 SER I
    19502 203 5 4 
    19503 49 messages similar to the above omitted 
    19504 Cannot find LINK/SSBOND residue CYS (22 ) 
    19505 Cannot find LINK/SSBOND residue CYS (128 ) 
    19506 Cannot find LINK/SSBOND residue CYS (140 ) 
    19507 Cannot find LINK/SSBOND residue CYS (24 ) 
    19508 Cannot find LINK/SSBOND residue CYS (135 ) 
    19509  
    19510 3C11_Fab_D_1292144377_model-annotate_P1_HL-coot-0.pdb title: 
    19511 Fab fragment of an antibody that recognises all conformations of
    19512 α-1-antitrypsin [more info...] 
    19513  
    19514 Chain information for 3C11_Fab_D_1292144377_model-annotate_P1_HL-coot-0.pdb #4 
    19515 --- 
    19516 Chain | Description 
    19517 H | fab 3C11 heavy chain 
    19518 L | fab 3C11 light chain 
    19519  
    19520 128 atoms have alternate locations. Control/examine alternate locations with
    19521 Altloc Explorer [start tool...] or the altlocs command. 
    19522 Chain information for 1ezx_moved-coot-0.pdb #5 
    19523 --- 
    19524 Chain | Description 
    19525 A | No description available 
    19526 B | No description available 
    19527  
    19528 Computing secondary structure 
    19529 
    19530 > hide #!1 models
    19531 
    19532 > show #!1 models
    19533 
    19534 > hide #!1 models
    19535 
    19536 > show #!1 models
    19537 
    19538 > hide #!1 models
    19539 
    19540 > show #!1 models
    19541 
    19542 > hide #!1 models
    19543 
    19544 > show #!1 models
    19545 
    19546 > hide #!1 models
    19547 
    19548 > save /Users/apple/Downloads/csparc.cxs includeMaps true
    19549 
    19550 > open /Users/apple/Downloads/3C11_Fab_D_1292144377_model-annotate_P1_HL.pdb
    19551 
    19552 Summary of feedback from opening
    19553 /Users/apple/Downloads/3C11_Fab_D_1292144377_model-annotate_P1_HL.pdb 
    19554 --- 
    19555 warnings | Start residue of secondary structure not found: HELIX 8 AA8 THR I 28 TYR I 32 5 5 
    19556 Start residue of secondary structure not found: HELIX 9 AA9 ASN I 73 LYS I 75
    19557 5 3 
    19558 Start residue of secondary structure not found: HELIX 10 AB1 LYS I 83 THR I 87
    19559 5 5 
    19560 Start residue of secondary structure not found: HELIX 11 AB2 SER I 156 SER I
    19561 158 5 3 
    19562 Start residue of secondary structure not found: HELIX 12 AB3 PRO I 200 SER I
    19563 203 5 4 
    19564 49 messages similar to the above omitted 
    19565 Cannot find LINK/SSBOND residue CYS (22 ) 
    19566 Cannot find LINK/SSBOND residue CYS (128 ) 
    19567 Cannot find LINK/SSBOND residue CYS (140 ) 
    19568 Cannot find LINK/SSBOND residue CYS (24 ) 
    19569 Cannot find LINK/SSBOND residue CYS (135 ) 
    19570  
    19571 3C11_Fab_D_1292144377_model-annotate_P1_HL.pdb title: 
    19572 Fab fragment of an antibody that recognises all conformations of
    19573 α-1-antitrypsin [more info...] 
    19574  
    19575 Chain information for 3C11_Fab_D_1292144377_model-annotate_P1_HL.pdb #6 
    19576 --- 
    19577 Chain | Description 
    19578 H | fab 3C11 heavy chain 
    19579 L | fab 3C11 light chain 
    19580  
    19581 128 atoms have alternate locations. Control/examine alternate locations with
    19582 Altloc Explorer [start tool...] or the altlocs command. 
    19583 
    19584 > mmaker #6 to #4
    19585 
    19586 Computing secondary structure 
    19587 [Repeated 1 time(s)]  Parameters 
    19588 --- 
    19589 Chain pairing | bb 
    19590 Alignment algorithm | Needleman-Wunsch 
    19591 Similarity matrix | BLOSUM-62 
    19592 SS fraction | 0.3 
    19593 Gap open (HH/SS/other) | 18/18/6 
    19594 Gap extend | 1 
    19595 SS matrix |  |  | H | S | O 
    19596 ---|---|---|--- 
    19597 H | 6 | -9 | -6 
    19598 S |  | 6 | -6 
    19599 O |  |  | 4 
    19600 Iteration cutoff | 2 
    19601  
    19602 Matchmaker 3C11_Fab_D_1292144377_model-annotate_P1_HL-coot-0.pdb, chain L (#4)
    19603 with 3C11_Fab_D_1292144377_model-annotate_P1_HL.pdb, chain L (#6), sequence
    19604 alignment score = 1108.5 
    19605 RMSD between 208 pruned atom pairs is 0.000 angstroms; (across all 208 pairs:
    19606 0.000) 
    19607  
    19608 
    19609 > hide #!4 models
    19610 
    19611 > save /Users/apple/Downloads/csparc.cxs includeMaps true
    19612 
    19613 > open /Users/apple/Downloads/cryosparc_P371_J891_003_volume_map.mrc
    19614 
    19615 Opened cryosparc_P371_J891_003_volume_map.mrc as #7, grid size 300,300,300,
    19616 pixel 0.867, shown at level 0.0162, step 2, values float32 
    19617 
    19618 > volume #7 level 0.0734
    19619 
    19620 > select subtract #3
    19621 
    19622 Nothing selected 
    19623 
    19624 > hide #5 models
    19625 
    19626 > hide #!6 models
    19627 
    19628 > volume #7 level 0.05238
    19629 
    19630 > hide #!7 models
    19631 
    19632 > show #!6 models
    19633 
    19634 > show #5 models
    19635 
    19636 > show #!3 models
    19637 
    19638 > show #!7 models
    19639 
    19640 > hide #!7 models
    19641 
    19642 > open "/Users/apple/Downloads/cryosparc_P371_J882_005_volume_map (1).mrc"
    19643 
    19644 Opened cryosparc_P371_J882_005_volume_map (1).mrc as #8, grid size
    19645 300,300,300, pixel 0.867, shown at level 0.0235, step 2, values float32 
    19646 
    19647 > hide #5 models
    19648 
    19649 > hide #!6 models
    19650 
    19651 > volume #8 level 0.0555
    19652 
    19653 > volume flip #8 axis z
    19654 
    19655 Opened cryosparc_P371_J882_005_volume_map (1).mrc z flip as #9, grid size
    19656 300,300,300, pixel 0.867, shown at step 1, values float32 
    19657 
    19658 > volume #9 level 0.06023
    19659 
    19660 > show #!1 models
    19661 
    19662 > hide #!1 models
    19663 
    19664 > show #5 models
    19665 
    19666 > hide #5 models
    19667 
    19668 > volume copy #5
    19669 
    19670 > show #5 models
    19671 
    19672 > hide #5 models
    19673 
    19674 > show #!1 models
    19675 
    19676 > transparency #8 50
    19677 
    19678 > transparency #9 50
    19679 
    19680 > show #!4 models
    19681 
    19682 > hide #!4 models
    19683 
    19684 > show #!6 models
    19685 
    19686 > close #8
    19687 
    19688 > show #!7 models
    19689 
    19690 > hide #!7 models
    19691 
    19692 > show #!4 models
    19693 
    19694 > hide #!4 models
    19695 
    19696 > show #!3 models
    19697 
    19698 > hide #!3 models
    19699 
    19700 > show #!3 models
    19701 
    19702 > hide #!9 models
    19703 
    19704 > show #!9 models
    19705 
    19706 > hide #!9 models
    19707 
    19708 > show #!9 models
    19709 
    19710 > hide #!9 models
    19711 
    19712 > show #!9 models
    19713 
    19714 > open /Users/apple/Downloads/cryosparc_P371_J881_class_08_00006_volume.mrc
    19715 
    19716 Opened cryosparc_P371_J881_class_08_00006_volume.mrc as #8, grid size
    19717 180,180,180, pixel 1.44, shown at level 0.0542, step 1, values float32 
    19718 
    19719 > volume #8 level 0.122
    19720 
    19721 > volume flip #8 axis z
    19722 
    19723 Opened cryosparc_P371_J881_class_08_00006_volume.mrc z flip as #10, grid size
    19724 180,180,180, pixel 1.44, shown at step 1, values float32 
    19725 
    19726 > select down
    19727 
    19728 Nothing selected 
    19729 
    19730 > select down
    19731 
    19732 Nothing selected 
    19733 
    19734 > transparency #8 50
    19735 
    19736 > transparency #10 50
    19737 
    19738 > hide #!10 models
    19739 
    19740 > show #!9 models
    19741 
    19742 > hide #!9 models
    19743 
    19744 > show #!8 models
    19745 
    19746 > hide #!8 models
    19747 
    19748 > close #8
    19749 
    19750 > show #!7 models
    19751 
    19752 > hide #!7 models
    19753 
    19754 > close #7
    19755 
    19756 > save /Users/apple/Downloads/csparc.cxs includeMaps true
    19757 
    19758 ——— End of log from Tue Nov 25 15:20:48 2025 ———
    19759 
    19760 opened ChimeraX session 
    19761 
    19762 > show #!3 models
    19763 
    19764 > open 5A0C fromDatabase pdb format mmcif
    19765 
    19766 5a0c title: 
    19767 Crystal Structure of human neutrophil elastase in complex with a
    19768 dihydropyrimidone inhibitor [more info...] 
    19769  
    19770 Chain information for 5a0c #7 
    19771 --- 
    19772 Chain | Description | UniProt 
    19773 A B | NEUTROPHIL ELASTASE | ELNE_HUMAN 16-252 
    19774  
    19775 Non-standard residues in 5a0c #7 
    19776 --- 
    19777 FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose;
    19778 L-fucose; fucose) 
    19779 JJV — (6S)-6-(4-cyano-2-methylsulfonyl-
    19780 phenyl)-4-methyl-2-oxidanylidene-3-[3-(trifluoromethyl)phenyl]-1,6-dihydropyrimidine-5-carbonitrile 
    19781 MES — 2-(N-morpholino)-ethanesulfonic acid 
    19782 NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
    19783 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
    19784 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) 
    19785 XPE — 3,6,9,12,15,18,21,24,27-nonaoxanonacosane-1,29-diol (decaethylene
    19786 glycol) 
    19787  
    19788 5a0c mmCIF Assemblies 
    19789 --- 
    19790 1| author_and_software_defined_assembly 
    19791 2| author_and_software_defined_assembly 
    19792  
    19793 
    19794 > hide #!1 models
    19795 
    19796 > show #!1 models
    19797 
    19798 > open 1ezx fromDatabase pdb format mmcif
    19799 
    19800 1ezx title: 
    19801 Crystal structure of A serpin:protease complex [more info...] 
    19802  
    19803 Chain information for 1ezx #8 
    19804 --- 
    19805 Chain | Description | UniProt 
    19806 A | ALPHA-1-ANTITRYPSIN | A1AT_HUMAN 24-358 
    19807 B | ALPHA-1-ANTITRYPSIN | A1AT_HUMAN 359-394 
    19808 C | TRYPSIN | TRY1_BOVIN 42-245 
    19809  
    19810 
    19811 > select #8/A
    19812 
    19813 2686 atoms, 2674 bonds, 398 residues, 1 model selected 
    19814 
    19815 > mmaker #8 to #1
    19816 
    19817 Computing secondary structure 
    19818 Parameters 
    19819 --- 
    19820 Chain pairing | bb 
    19821 Alignment algorithm | Needleman-Wunsch 
    19822 Similarity matrix | BLOSUM-62 
    19823 SS fraction | 0.3 
    19824 Gap open (HH/SS/other) | 18/18/6 
    19825 Gap extend | 1 
    19826 SS matrix |  |  | H | S | O 
    19827 ---|---|---|--- 
    19828 H | 6 | -9 | -6 
    19829 S |  | 6 | -6 
    19830 O |  |  | 4 
    19831 Iteration cutoff | 2 
    19832  
    19833 Matchmaker 1ezx, chain A (#1) with 1ezx, chain A (#8), sequence alignment
    19834 score = 1734 
    19835 RMSD between 335 pruned atom pairs is 0.000 angstroms; (across all 335 pairs:
    19836 0.000) 
    19837  
    19838 
    19839 > select #7/B, C, D, E, F
    19840 
    19841 1965 atoms, 1848 bonds, 391 residues, 1 model selected 
    19842 
    19843 > delete #7/B, C, D, E, F
    19844 
    19845 > mmaker #7 to #8
    19846 
    19847 Computing secondary structure 
    19848 [Repeated 1 time(s)]  Parameters 
    19849 --- 
    19850 Chain pairing | bb 
    19851 Alignment algorithm | Needleman-Wunsch 
    19852 Similarity matrix | BLOSUM-62 
    19853 SS fraction | 0.3 
    19854 Gap open (HH/SS/other) | 18/18/6 
    19855 Gap extend | 1 
    19856 SS matrix |  |  | H | S | O 
    19857 ---|---|---|--- 
    19858 H | 6 | -9 | -6 
    19859 S |  | 6 | -6 
    19860 O |  |  | 4 
    19861 Iteration cutoff | 2 
    19862  
    19863 Matchmaker 1ezx, chain C (#8) with 5a0c, chain A (#7), sequence alignment
    19864 score = 241.2 
    19865 RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
    19866 3.073) 
    19867  
    19868 
    19869 > hide #7#!1,6,8 atoms
    19870 
    19871 > save /Users/apple/Downloads/csparc.cxs includeMaps true
    19872 
    19873 > open /Users/apple/Downloads/cryosparc_P371_J916_map.mrc
    19874 
    19875 Opened cryosparc_P371_J916_map.mrc as #11, grid size 300,300,300, pixel 0.867,
    19876 shown at level 0.0238, step 2, values float32 
    19877 
    19878 > volume flip #11 axis z
    19879 
    19880 Opened cryosparc_P371_J916_map.mrc z flip as #12, grid size 300,300,300, pixel
    19881 0.867, shown at step 1, values float32 
    19882 
    19883 > volume #12 level 0.06229
    19884 
    19885 > transparency #12 50
    19886 
    19887 > hide #!1 models
    19888 
    19889 > show #!1 models
    19890 
    19891 > hide #!3 models
    19892 
    19893 > show #!3 models
    19894 
    19895 > hide #!6 models
    19896 
    19897 > show #!6 models
    19898 
    19899 > hide #!8 models
    19900 
    19901 > show #!8 models
    19902 
    19903 > hide #!1 models
    19904 
    19905 > show #!1 models
    19906 
    19907 > hide #!1 models
    19908 
    19909 > hide #7 models
    19910 
    19911 > show #7 models
    19912 
    19913 > hide #!8 models
    19914 
    19915 > ui tool show "Fit in Map"
    19916 
    19917 > fitmap #7 inMap #12
    19918 
    19919 Fit molecule 5a0c (#7) to map cryosparc_P371_J916_map.mrc z flip (#12) using
    19920 1883 atoms 
    19921 average map value = 0.05726, steps = 204 
    19922 shifted from previous position = 18.9 
    19923 rotated from previous position = 30.2 degrees 
    19924 atoms outside contour = 1095, contour level = 0.06229 
    19925  
    19926 Position of 5a0c (#7) relative to cryosparc_P371_J916_map.mrc z flip (#12)
    19927 coordinates: 
    19928 Matrix rotation and translation 
    19929 -0.89591156 -0.08748371 -0.43553310 147.09781032 
    19930 0.42229009 -0.47204043 -0.77385329 138.97672191 
    19931 -0.13788968 -0.87722542 0.45984998 149.26233444 
    19932 Axis -0.17249142 -0.49666131 0.85063168 
    19933 Axis point 74.69777418 126.82872456 0.00000000 
    19934 Rotation angle (degrees) 162.56376196 
    19935 Shift along axis 32.56979814 
    19936  
    19937 
    19938 > show #!1 models
    19939 
    19940 > hide #7 models
    19941 
    19942 > show #7 models
    19943 
    19944 > volume #11 level 0.05033
    19945 
    19946 > volume #12 level 0.08057
    19947 
    19948 > open /Users/apple/Downloads/cryosparc_P371_J919_class_00_final_volume.mrc
    19949 
    19950 Opened cryosparc_P371_J919_class_00_final_volume.mrc as #13, grid size
    19951 128,128,128, pixel 2.03, shown at level 0.08, step 1, values float32 
    19952 
    19953 > transparency #18 50
    19954 
    19955 > transparency #13 50
    19956 
    19957 > hide #!13 models
    19958 
    19959 > hide #7 models
    19960 
    19961 > hide #!6 models
    19962 
    19963 > hide #!3 models
    19964 
    19965 > show #!3 models
    19966 
    19967 > hide #!3 models
    19968 
    19969 > show #!3 models
    19970 
    19971 > hide #!12 models
    19972 
    19973 > show #!12 models
    19974 
    19975 > hide #!12 models
    19976 
    19977 > show #!12 models
    19978 
    19979 > hide #!12 models
    19980 
    19981 > hide #!1 models
    19982 
    19983 > show #7 models
    19984 
    19985 > show #!8 models
    19986 
    19987 > hide #!8 models
    19988 
    19989 > show #!1 models
    19990 
    19991 > show #!13 models
    19992 
    19993 > show #!4 models
    19994 
    19995 > hide #!4 models
    19996 
    19997 > show #5 models
    19998 
    19999 > hide #5 models
    20000 
    20001 > show #!6 models
    20002 
    20003 > hide #!6 models
    20004 
    20005 > save /Users/apple/Downloads/csparc.cxs includeMaps true
    20006 
    20007 ——— End of log from Fri Nov 28 18:17:17 2025 ———
    20008 
    20009 opened ChimeraX session 
    20010 
    20011 > hide #!13 models
    20012 
    20013 > open /Users/apple/Downloads/cryosparc_P371_J937_003_volume_map.mrc
    20014 
    20015 Opened cryosparc_P371_J937_003_volume_map.mrc as #14, grid size 300,300,300,
    20016 pixel 0.867, shown at level 0.0245, step 2, values float32 
    20017 
    20018 > volume flip #14 axis z
    20019 
    20020 Opened cryosparc_P371_J937_003_volume_map.mrc z flip as #15, grid size
    20021 300,300,300, pixel 0.867, shown at step 1, values float32 
    20022 
    20023 > hide #!15 models
    20024 
    20025 > hide #!1 models
    20026 
    20027 > show #!1 models
    20028 
    20029 > combine #1 close false
    20030 
    20031 > hide #!1 models
    20032 
    20033 > show #!6 models
    20034 
    20035 > combine #6 close false
    20036 
    20037 > combine #7 close false
    20038 
    20039 > hide #7 models
    20040 
    20041 > hide #!6 models
    20042 
    20043 > hide #!3 models
    20044 
    20045 > show #!15 models
    20046 
    20047 > transparency #15 50
    20048 
    20049 > volume #15 level 0.07742
    20050 
    20051 > hide #!17 models
    20052 
    20053 > hide #18 models
    20054 
    20055 > hide #!16 models
    20056 
    20057 > show #!16 models
    20058 
    20059 > show #!17 models
    20060 
    20061 > show #18 models
    20062 
    20063 > select add #16
    20064 
    20065 2975 atoms, 2968 bonds, 437 residues, 1 model selected 
    20066 
    20067 > ui mousemode right "translate selected models"
    20068 
    20069 > view matrix models
    20070 > #16,-0.38245,0.10992,-0.91742,194.95,0.077506,-0.98558,-0.15039,187,-0.92072,-0.12862,0.36841,167.53
    20071 
    20072 > view matrix models
    20073 > #16,-0.38245,0.10992,-0.91742,191.4,0.077506,-0.98558,-0.15039,187.17,-0.92072,-0.12862,0.36841,156.11
    20074 
    20075 > view matrix models
    20076 > #16,-0.014922,0.064965,-0.99778,175.36,0.069994,-0.99537,-0.065855,183.33,-0.99744,-0.070821,0.010305,178.28
    20077 
    20078 > hide #!17 models
    20079 
    20080 > view matrix models
    20081 > #16,-0.014922,0.064965,-0.99778,182.37,0.069994,-0.99537,-0.065855,183.4,-0.99744,-0.070821,0.010305,175.03
    20082 
    20083 > view matrix models
    20084 > #16,0.94124,0.016979,-0.33731,85.904,0.1062,-0.96295,0.24788,160.88,-0.32061,-0.26914,-0.90817,197.31
    20085 
    20086 > view matrix models
    20087 > #16,0.6158,0.19853,0.76248,31.693,-0.013436,-0.96495,0.26209,167.81,0.78779,-0.17164,-0.59155,102.23
    20088 
    20089 > view matrix models
    20090 > #16,-0.056736,0.045988,0.99733,70.269,-0.1345,-0.99018,0.038008,190.1,0.98929,-0.13198,0.062364,48.953
    20091 
    20092 > view matrix models
    20093 > #16,-0.056736,0.045988,0.99733,68.694,-0.1345,-0.99018,0.038008,189.37,0.98929,-0.13198,0.062364,47.206
    20094 
    20095 > ui tool show "Fit in Map"
    20096 
    20097 > fitmap #16 inMap #15
    20098 
    20099 Fit molecule copy of 1ezx (#16) to map cryosparc_P371_J937_003_volume_map.mrc
    20100 z flip (#15) using 2975 atoms 
    20101 average map value = 0.08682, steps = 136 
    20102 shifted from previous position = 1.54 
    20103 rotated from previous position = 27.4 degrees 
    20104 atoms outside contour = 1268, contour level = 0.077423 
    20105  
    20106 Position of copy of 1ezx (#16) relative to
    20107 cryosparc_P371_J937_003_volume_map.mrc z flip (#15) coordinates: 
    20108 Matrix rotation and translation 
    20109 0.36221471 -0.11330418 0.92518250 57.47272519 
    20110 -0.01922981 -0.99328137 -0.11411544 191.48317940 
    20111 0.93189630 0.02354321 -0.36195994 67.99746912 
    20112 Axis 0.82495481 -0.04023415 0.56376482 
    20113 Axis point 0.00000000 96.53522281 19.29015841 
    20114 Rotation angle (degrees) 175.21401689 
    20115 Shift along axis 78.04281848 
    20116  
    20117 
    20118 > show #!17 models
    20119 
    20120 > select subtract #16
    20121 
    20122 Nothing selected 
    20123 
    20124 > select add #17
    20125 
    20126 3190 atoms, 3270 bonds, 2 pseudobonds, 422 residues, 3 models selected 
    20127 
    20128 > view matrix models
    20129 > #17,-0.14524,0.98625,-0.078838,137.46,-0.95305,-0.11806,0.27883,132.77,0.26569,0.11563,0.9571,127.09
    20130 
    20131 > view matrix models
    20132 > #17,0.35108,0.87998,0.31997,116.61,0.41428,-0.45244,0.78973,93.952,0.83971,-0.14471,-0.5234,164.49
    20133 
    20134 > view matrix models
    20135 > #17,0.54911,0.70874,-0.44291,137.73,0.78853,-0.61496,-0.0064507,113,-0.27694,-0.3457,-0.89655,196.5
    20136 
    20137 > view matrix models
    20138 > #17,0.54911,0.70874,-0.44291,134.48,0.78853,-0.61496,-0.0064507,113.87,-0.27694,-0.3457,-0.89655,190.34
    20139 
    20140 > view matrix models
    20141 > #17,0.9378,-0.11961,-0.32592,126.95,-0.057609,-0.97937,0.19367,123.71,-0.34236,-0.16285,-0.92535,191.74
    20142 
    20143 > view matrix models
    20144 > #17,0.3628,-0.93186,-0.0012508,129.72,-0.91856,-0.35785,0.16792,137.38,-0.15693,-0.059774,-0.9858,190.03
    20145 
    20146 > view matrix models
    20147 > #17,-0.40726,-0.90893,0.089337,140.28,-0.91297,0.40784,-0.012447,140.22,-0.025122,-0.086631,-0.99592,188.13
    20148 
    20149 > view matrix models
    20150 > #17,-0.40726,-0.90893,0.089337,140.76,-0.91297,0.40784,-0.012447,134.78,-0.025122,-0.086631,-0.99592,187.94
    20151 
    20152 > view matrix models
    20153 > #17,-0.073903,-0.92576,-0.37083,149.44,-0.76049,-0.18823,0.62147,114.32,-0.64513,0.32794,-0.69012,187.71
    20154 
    20155 > view matrix models
    20156 > #17,-0.013726,-0.97437,-0.22454,143.96,-0.96969,-0.041822,0.24075,129.42,-0.24397,0.22104,-0.94426,189.05
    20157 
    20158 > view matrix models
    20159 > #17,-0.13546,-0.99065,0.016086,138.59,-0.95193,0.13463,0.27516,127.4,-0.27475,0.02196,-0.96126,190.84
    20160 
    20161 > view matrix models
    20162 > #17,-0.13546,-0.99065,0.016086,134.75,-0.95193,0.13463,0.27516,129.71,-0.27475,0.02196,-0.96126,190.41
    20163 
    20164 > view matrix models
    20165 > #17,-0.13546,-0.99065,0.016086,134.74,-0.95193,0.13463,0.27516,129.59,-0.27475,0.02196,-0.96126,189.59
    20166 
    20167 > fitmap #17 inMap #15
    20168 
    20169 Fit molecule copy of 3C11_Fab_D_1292144377_model-annotate_P1_HL.pdb (#17) to
    20170 map cryosparc_P371_J937_003_volume_map.mrc z flip (#15) using 3190 atoms 
    20171 average map value = 0.08611, steps = 92 
    20172 shifted from previous position = 1.81 
    20173 rotated from previous position = 13.7 degrees 
    20174 atoms outside contour = 1360, contour level = 0.077423 
    20175  
    20176 Position of copy of 3C11_Fab_D_1292144377_model-annotate_P1_HL.pdb (#17)
    20177 relative to cryosparc_P371_J937_003_volume_map.mrc z flip (#15) coordinates: 
    20178 Matrix rotation and translation 
    20179 0.06326154 -0.99140205 0.11454237 128.16146514 
    20180 -0.92943347 -0.01671960 0.36861077 128.17971107 
    20181 -0.36352637 -0.12977839 -0.92249995 190.93357303 
    20182 Axis -0.71877784 0.68947168 0.08937122 
    20183 Axis point 0.00000000 149.17005870 88.62629203 
    20184 Rotation angle (degrees) 159.71487953 
    20185 Shift along axis 13.32062667 
    20186  
    20187 
    20188 > select subtract #17
    20189 
    20190 Nothing selected 
    20191 
    20192 > select add #18
    20193 
    20194 1883 atoms, 1745 bonds, 394 residues, 1 model selected 
    20195 
    20196 > view matrix models
    20197 > #18,-0.26486,0.8524,-0.45085,130.11,0.42774,-0.31518,-0.84718,156.88,-0.86423,-0.41723,-0.28112,157.69
    20198 
    20199 > view matrix models
    20200 > #18,-0.26486,0.8524,-0.45085,127.04,0.42774,-0.31518,-0.84718,159.13,-0.86423,-0.41723,-0.28112,133.82
    20201 
    20202 > view matrix models
    20203 > #18,0.36105,0.83492,0.4154,114.71,0.60304,0.13074,-0.78692,152.96,-0.71132,0.53462,-0.45629,125.04
    20204 
    20205 > show #!8 models
    20206 
    20207 > select up
    20208 
    20209 26260 atoms, 26186 bonds, 3972 residues, 27 models selected 
    20210 
    20211 > select up
    20212 
    20213 26260 atoms, 26186 bonds, 3972 residues, 27 models selected 
    20214 
    20215 > select down
    20216 
    20217 1883 atoms, 1745 bonds, 394 residues, 1 model selected 
    20218 
    20219 > select down
    20220 
    20221 1883 atoms, 1745 bonds, 394 residues, 1 model selected 
    20222 
    20223 > combine #8 close false
    20224 
    20225 > hide #!8 models
    20226 
    20227 > select subtract #18
    20228 
    20229 Nothing selected 
    20230 
    20231 > mmaker #19 to #16
    20232 
    20233 Parameters 
    20234 --- 
    20235 Chain pairing | bb 
    20236 Alignment algorithm | Needleman-Wunsch 
    20237 Similarity matrix | BLOSUM-62 
    20238 SS fraction | 0.3 
    20239 Gap open (HH/SS/other) | 18/18/6 
    20240 Gap extend | 1 
    20241 SS matrix |  |  | H | S | O 
    20242 ---|---|---|--- 
    20243 H | 6 | -9 | -6 
    20244 S |  | 6 | -6 
    20245 O |  |  | 4 
    20246 Iteration cutoff | 2 
    20247  
    20248 Matchmaker copy of 1ezx, chain A (#16) with copy of 1ezx, chain A (#19),
    20249 sequence alignment score = 1734 
    20250 RMSD between 335 pruned atom pairs is 0.000 angstroms; (across all 335 pairs:
    20251 0.000) 
    20252  
    20253 
    20254 > hide #!16 models
    20255 
    20256 > show #!16 models
    20257 
    20258 > mmaker #18 to #19
    20259 
    20260 Parameters 
    20261 --- 
    20262 Chain pairing | bb 
    20263 Alignment algorithm | Needleman-Wunsch 
    20264 Similarity matrix | BLOSUM-62 
    20265 SS fraction | 0.3 
    20266 Gap open (HH/SS/other) | 18/18/6 
    20267 Gap extend | 1 
    20268 SS matrix |  |  | H | S | O 
    20269 ---|---|---|--- 
    20270 H | 6 | -9 | -6 
    20271 S |  | 6 | -6 
    20272 O |  |  | 4 
    20273 Iteration cutoff | 2 
    20274  
    20275 Matchmaker copy of 1ezx, chain C (#19) with copy of 5a0c, chain A (#18),
    20276 sequence alignment score = 241.2 
    20277 RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
    20278 3.073) 
    20279  
    20280 
    20281 > hide #!19 models
    20282 
    20283 > show #!19 models
    20284 
    20285 > hide #18 models
    20286 
    20287 > show #18 models
    20288 
    20289 > hide #!15 models
    20290 
    20291 > show #!15 models
    20292 
    20293 > volume #15 level 0.06266
    20294 
    20295 > combine #18 close false
    20296 
    20297 > hide #!19 models
    20298 
    20299 > hide #18 models
    20300 
    20301 > select add #20
    20302 
    20303 1883 atoms, 1745 bonds, 394 residues, 1 model selected 
    20304 
    20305 > view matrix models
    20306 > #20,0.93703,-0.32924,0.11649,110.54,-0.085791,-0.54033,-0.83707,168.71,0.33854,0.77436,-0.53456,110.95
    20307 
    20308 > fitmap #20 inMap #15
    20309 
    20310 Fit molecule copy of copy of 5a0c (#20) to map
    20311 cryosparc_P371_J937_003_volume_map.mrc z flip (#15) using 1883 atoms 
    20312 average map value = 0.05371, steps = 112 
    20313 shifted from previous position = 3.05 
    20314 rotated from previous position = 21.1 degrees 
    20315 atoms outside contour = 1163, contour level = 0.062657 
    20316  
    20317 Position of copy of copy of 5a0c (#20) relative to
    20318 cryosparc_P371_J937_003_volume_map.mrc z flip (#15) coordinates: 
    20319 Matrix rotation and translation 
    20320 0.82283210 -0.54792418 -0.15075286 115.81404414 
    20321 -0.42467040 -0.41658213 -0.80381240 174.25196583 
    20322 0.37762731 0.72542292 -0.57546433 108.00195017 
    20323 Axis 0.94244068 -0.32563135 0.07595913 
    20324 Axis point 0.00000000 79.04749924 102.02767242 
    20325 Rotation angle (degrees) 125.77524387 
    20326 Shift along axis 60.60969773 
    20327  
    20328 
    20329 > volume #15 level 0.07496
    20330 
    20331 > volume #15 level 0.102
    20332 
    20333 > fitmap #20 inMap #15
    20334 
    20335 Fit molecule copy of copy of 5a0c (#20) to map
    20336 cryosparc_P371_J937_003_volume_map.mrc z flip (#15) using 1883 atoms 
    20337 average map value = 0.05371, steps = 40 
    20338 shifted from previous position = 0.00581 
    20339 rotated from previous position = 0.0038 degrees 
    20340 atoms outside contour = 1822, contour level = 0.10203 
    20341  
    20342 Position of copy of copy of 5a0c (#20) relative to
    20343 cryosparc_P371_J937_003_volume_map.mrc z flip (#15) coordinates: 
    20344 Matrix rotation and translation 
    20345 0.82283660 -0.54793499 -0.15068899 115.81020155 
    20346 -0.42463523 -0.41661833 -0.80381222 174.25584664 
    20347 0.37765705 0.72539397 -0.57548131 108.00286277 
    20348 Axis 0.94244310 -0.32561736 0.07598910 
    20349 Axis point 0.00000000 79.04924478 102.02529443 
    20350 Rotation angle (degrees) 125.77696296 
    20351 Shift along axis 60.61083741 
    20352  
    20353 
    20354 > volume #15 level 0.08481
    20355 
    20356 > select #20/Ser195
    20357 
    20358 Nothing selected 
    20359 
    20360 > ui tool show "Show Sequence Viewer"
    20361 
    20362 > sequence chain #7/A #18/A #20/A
    20363 
    20364 Alignment identifier is 1 
    20365 
    20366 > select #7/A:157 #18/A:157 #20/A:157
    20367 
    20368 18 atoms, 15 bonds, 3 residues, 3 models selected 
    20369 
    20370 > select #7/A:157 #18/A:157 #20/A:157
    20371 
    20372 18 atoms, 15 bonds, 3 residues, 3 models selected 
    20373 NEUTROPHIL ELASTASE [ID: 1] region 3 chains [138] RMSD: 42.465 
    20374  
    20375 
    20376 > show #18 models
    20377 
    20378 > hide #20 models
    20379 
    20380 > select #7/A:157 #18/A:157 #20/A:157
    20381 
    20382 18 atoms, 15 bonds, 3 residues, 3 models selected 
    20383 
    20384 > select #7/A:157 #18/A:157 #20/A:157
    20385 
    20386 18 atoms, 15 bonds, 3 residues, 3 models selected 
    20387 NEUTROPHIL ELASTASE [ID: 1] region 3 chains [138] RMSD: 42.465 
    20388  
    20389 
    20390 > select #7/A:195 #18/A:195 #20/A:195
    20391 
    20392 15 atoms, 12 bonds, 3 residues, 3 models selected 
    20393 
    20394 > select #7/A:195 #18/A:195 #20/A:195
    20395 
    20396 15 atoms, 12 bonds, 3 residues, 3 models selected 
    20397 NEUTROPHIL ELASTASE [ID: 1] region 3 chains [166] RMSD: 29.400 
    20398  
    20399 
    20400 > show #!19 models
    20401 
    20402 > hide #!15 models
    20403 
    20404 > select #7/A:195 #18/A:195 #20/A:195
    20405 
    20406 15 atoms, 12 bonds, 3 residues, 3 models selected 
    20407 
    20408 > select #7/A:195 #18/A:195 #20/A:195
    20409 
    20410 15 atoms, 12 bonds, 3 residues, 3 models selected 
    20411 
    20412 > select #7/A:195-198 #18/A:195-198 #20/A:195-198
    20413 
    20414 66 atoms, 63 bonds, 12 residues, 3 models selected 
    20415 NEUTROPHIL ELASTASE [ID: 1] region 3 chains [166-169] RMSD: 25.331 
    20416  
    20417 
    20418 > select #7/A:196 #18/A:196 #20/A:196
    20419 
    20420 12 atoms, 9 bonds, 3 residues, 3 models selected 
    20421 
    20422 > select #7/A:195-196 #18/A:195-196 #20/A:195-196
    20423 
    20424 27 atoms, 24 bonds, 6 residues, 3 models selected 
    20425 NEUTROPHIL ELASTASE [ID: 1] region 3 chains [166-167] RMSD: 26.853 
    20426  
    20427 
    20428 > hide #18 models
    20429 
    20430 > ui tool show "Show Sequence Viewer"
    20431 
    20432 > sequence chain #8/C #19/C
    20433 
    20434 Alignment identifier is 2 
    20435 
    20436 > select #7/A:202 #18/A:202 #20/A:202
    20437 
    20438 18 atoms, 15 bonds, 3 residues, 3 models selected 
    20439 
    20440 > select #7/A:202 #18/A:202 #20/A:202
    20441 
    20442 18 atoms, 15 bonds, 3 residues, 3 models selected 
    20443 NEUTROPHIL ELASTASE [ID: 1] region 3 chains [173] RMSD: 20.338 
    20444  
    20445 
    20446 > show #18 models
    20447 
    20448 > hide #!19 models
    20449 
    20450 > show #20 models
    20451 
    20452 > hide #18 models
    20453 
    20454 > show #!15 models
    20455 
    20456 > fitmap #20 inMap #15
    20457 
    20458 Fit molecule copy of copy of 5a0c (#20) to map
    20459 cryosparc_P371_J937_003_volume_map.mrc z flip (#15) using 1883 atoms 
    20460 average map value = 0.05371, steps = 44 
    20461 shifted from previous position = 0.00953 
    20462 rotated from previous position = 0.0167 degrees 
    20463 atoms outside contour = 1647, contour level = 0.084806 
    20464  
    20465 Position of copy of copy of 5a0c (#20) relative to
    20466 cryosparc_P371_J937_003_volume_map.mrc z flip (#15) coordinates: 
    20467 Matrix rotation and translation 
    20468 0.82274117 -0.54810241 -0.15060115 115.80769501 
    20469 -0.42459237 -0.41645168 -0.80392121 174.26154718 
    20470 0.37791306 0.72536318 -0.57535204 108.00158372 
    20471 Axis 0.94240739 -0.32569200 0.07611192 
    20472 Axis point 0.00000000 79.05386504 102.02910751 
    20473 Rotation angle (degrees) 125.76988347 
    20474 Shift along axis 60.60264436 
    20475  
    20476 
    20477 > save /Users/apple/Downloads/csparc.cxs
    20478 
    20479 > show #!19 models
    20480 
    20481 > hide #20 models
    20482 
    20483 > show #20 models
    20484 
    20485 > hide #!19 models
    20486 
    20487 > save /Users/apple/Downloads/csparc.cxs includeMaps true
    20488 
    20489 > open /Users/apple/Downloads/cryosparc_P371_J936_volume_map.mrc
    20490 
    20491 Opened cryosparc_P371_J936_volume_map.mrc as #21, grid size 300,300,300, pixel
    20492 0.867, shown at level 0.0323, step 2, values float32 
    20493 
    20494 > volume #21 level 0.05076
    20495 
    20496 > volume flip #21 axis z
    20497 
    20498 Opened cryosparc_P371_J936_volume_map.mrc z flip as #22, grid size
    20499 300,300,300, pixel 0.867, shown at step 1, values float32 
    20500 
    20501 > transparency #22 50
    20502 
    20503 > volume #22 level 0.08397
    20504 
    20505 > hide #!15 models
    20506 
    20507 > hide #!22 models
    20508 
    20509 > show #!22 models
    20510 
    20511 > volume #22 level 0.09518
    20512 
    20513 > select add #21
    20514 
    20515 18 atoms, 15 bonds, 3 residues, 5 models selected 
    20516 
    20517 > select subtract #21
    20518 
    20519 18 atoms, 15 bonds, 3 residues, 3 models selected 
    20520 
    20521 > close #21-22
    20522 
    20523 > show #!15 models
    20524 
    20525 > volume #15 level 0.06828
    20526 
    20527 > show #!19 models
    20528 
    20529 > hide #!19 models
    20530 
    20531 > show #!19 models
    20532 
    20533 > select up
    20534 
    20535 309 atoms, 309 bonds, 45 residues, 3 models selected 
    20536 
    20537 > select up
    20538 
    20539 4908 atoms, 5010 bonds, 654 residues, 3 models selected 
    20540 
    20541 > select down
    20542 
    20543 309 atoms, 309 bonds, 45 residues, 3 models selected 
    20544 
    20545 > select down
    20546 
    20547 18 atoms, 15 bonds, 3 residues, 3 models selected 
    20548 
    20549 > mmaker #20 to #19
    20550 
    20551 Parameters 
    20552 --- 
    20553 Chain pairing | bb 
    20554 Alignment algorithm | Needleman-Wunsch 
    20555 Similarity matrix | BLOSUM-62 
    20556 SS fraction | 0.3 
    20557 Gap open (HH/SS/other) | 18/18/6 
    20558 Gap extend | 1 
    20559 SS matrix |  |  | H | S | O 
    20560 ---|---|---|--- 
    20561 H | 6 | -9 | -6 
    20562 S |  | 6 | -6 
    20563 O |  |  | 4 
    20564 Iteration cutoff | 2 
    20565  
    20566 Matchmaker copy of 1ezx, chain C (#19) with copy of copy of 5a0c, chain A
    20567 (#20), sequence alignment score = 241.2 
    20568 RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
    20569 3.073) 
    20570  
    20571 
    20572 > fitmap #20 inMap #15
    20573 
    20574 Fit molecule copy of copy of 5a0c (#20) to map
    20575 cryosparc_P371_J937_003_volume_map.mrc z flip (#15) using 1883 atoms 
    20576 average map value = 0.05371, steps = 112 
    20577 shifted from previous position = 3.64 
    20578 rotated from previous position = 21.1 degrees 
    20579 atoms outside contour = 1322, contour level = 0.068282 
    20580  
    20581 Position of copy of copy of 5a0c (#20) relative to
    20582 cryosparc_P371_J937_003_volume_map.mrc z flip (#15) coordinates: 
    20583 Matrix rotation and translation 
    20584 0.82286685 -0.54787123 -0.15075561 115.81112827 
    20585 -0.42466982 -0.41665469 -0.80377510 174.25405615 
    20586 0.37755223 0.72542124 -0.57551571 108.00346093 
    20587 Axis 0.94245398 -0.32559967 0.07592986 
    20588 Axis point 0.00000000 79.04723098 102.02619388 
    20589 Rotation angle (degrees) 125.77839312 
    20590 Shift along axis 60.61028363 
    20591  
    20592 
    20593 > hide #!19 models
    20594 
    20595 > show #18 models
    20596 
    20597 > hide #18 models
    20598 
    20599 > color #20 #ff9cd5ff
    20600 
    20601 > open /Users/apple/Downloads/cryosparc_P371_J948_003_volume_map.mrc
    20602 
    20603 Opened cryosparc_P371_J948_003_volume_map.mrc as #21, grid size 300,300,300,
    20604 pixel 0.867, shown at level 0.0208, step 2, values float32 
    20605 
    20606 > volume flip #21 axis z
    20607 
    20608 Opened cryosparc_P371_J948_003_volume_map.mrc z flip as #22, grid size
    20609 300,300,300, pixel 0.867, shown at step 1, values float32 
    20610 
    20611 > select add #22
    20612 
    20613 18 atoms, 15 bonds, 3 residues, 5 models selected 
    20614 
    20615 > select subtract #22
    20616 
    20617 18 atoms, 15 bonds, 3 residues, 3 models selected 
    20618 
    20619 > hide #20 models
    20620 
    20621 > show #20 models
    20622 
    20623 > hide #20 models
    20624 
    20625 > show #20 models
    20626 
    20627 > hide #20 models
    20628 
    20629 > hide #!17 models
    20630 
    20631 > hide #!16 models
    20632 
    20633 > select add #18
    20634 
    20635 1895 atoms, 1755 bonds, 396 residues, 3 models selected 
    20636 
    20637 > select subtract #18
    20638 
    20639 12 atoms, 10 bonds, 2 residues, 2 models selected 
    20640 
    20641 > select add #20
    20642 
    20643 1889 atoms, 1750 bonds, 395 residues, 2 models selected 
    20644 
    20645 > select subtract #20
    20646 
    20647 6 atoms, 5 bonds, 1 residue, 1 model selected 
    20648 
    20649 > select add #7
    20650 
    20651 1883 atoms, 1745 bonds, 394 residues, 1 model selected 
    20652 
    20653 > select subtract #7
    20654 
    20655 Nothing selected 
    20656 
    20657 > volume #22 level 0.07591
    20658 
    20659 > select down
    20660 
    20661 Nothing selected 
    20662 
    20663 > combine #16 close false
    20664 
    20665 > combine #17 close false
    20666 
    20667 > combine #118 close false
    20668 
    20669 No structures specified 
    20670 
    20671 > combine #18 close false
    20672 
    20673 > combine #19 close false
    20674 
    20675 > transparency #22 50
    20676 
    20677 > hide #!26 models
    20678 
    20679 > hide #25 models
    20680 
    20681 > hide #!24 models
    20682 
    20683 > select add #23
    20684 
    20685 2975 atoms, 2968 bonds, 437 residues, 1 model selected 
    20686 
    20687 > view matrix models
    20688 > #23,0.36221,-0.1133,0.92518,56.114,-0.01923,-0.99328,-0.11412,190.58,0.9319,0.023543,-0.36196,109.58
    20689 
    20690 > view matrix models
    20691 > #23,0.36479,-0.4655,-0.80637,178.05,-0.26782,-0.88191,0.38795,170.47,-0.89174,0.074435,-0.44638,227.76
    20692 
    20693 > view matrix models
    20694 > #23,0.44719,-0.25874,-0.8562,163.07,-0.021132,-0.96003,0.27908,165.82,-0.89419,-0.10671,-0.43478,238.29
    20695 
    20696 > fitmap #23 inMap #22
    20697 
    20698 Fit molecule copy of copy of 1ezx (#23) to map
    20699 cryosparc_P371_J948_003_volume_map.mrc z flip (#22) using 2975 atoms 
    20700 average map value = 0.09755, steps = 212 
    20701 shifted from previous position = 6.95 
    20702 rotated from previous position = 52.1 degrees 
    20703 atoms outside contour = 1049, contour level = 0.075909 
    20704  
    20705 Position of copy of copy of 1ezx (#23) relative to
    20706 cryosparc_P371_J948_003_volume_map.mrc z flip (#22) coordinates: 
    20707 Matrix rotation and translation 
    20708 -0.35370767 0.06701706 -0.93295209 204.77529060 
    20709 0.13164154 -0.98393545 -0.12058828 178.13445921 
    20710 -0.92604610 -0.16546825 0.33920329 197.74865607 
    20711 Axis -0.56822714 -0.08743693 0.81821311 
    20712 Axis point 168.87143840 102.30996261 0.00000000 
    20713 Rotation angle (degrees) 177.73673097 
    20714 Shift along axis 29.86613558 
    20715  
    20716 
    20717 > show #!24 models
    20718 
    20719 > select subtract #23
    20720 
    20721 Nothing selected 
    20722 
    20723 > select add #24
    20724 
    20725 3190 atoms, 3270 bonds, 2 pseudobonds, 422 residues, 3 models selected 
    20726 
    20727 > view matrix models
    20728 > #24,0.063262,-0.9914,0.11454,130.74,-0.92943,-0.01672,0.36861,129.85,-0.36353,-0.12978,-0.9225,142.93
    20729 
    20730 > view matrix models
    20731 > #24,-0.096416,0.97724,-0.18895,136.05,-0.93565,-0.024237,0.35209,130.5,0.33949,0.21074,0.9167,71.599
    20732 
    20733 > fitmap #24 inMap #22
    20734 
    20735 Fit molecule copy of copy of 3C11_Fab_D_1292144377_model-annotate_P1_HL.pdb
    20736 (#24) to map cryosparc_P371_J948_003_volume_map.mrc z flip (#22) using 3190
    20737 atoms 
    20738 average map value = 0.0891, steps = 132 
    20739 shifted from previous position = 5.66 
    20740 rotated from previous position = 8.17 degrees 
    20741 atoms outside contour = 1367, contour level = 0.075909 
    20742  
    20743 Position of copy of copy of 3C11_Fab_D_1292144377_model-annotate_P1_HL.pdb
    20744 (#24) relative to cryosparc_P371_J948_003_volume_map.mrc z flip (#22)
    20745 coordinates: 
    20746 Matrix rotation and translation 
    20747 -0.11543452 0.98844688 -0.09822239 132.09657369 
    20748 -0.96240593 -0.08681878 0.25736612 135.79332431 
    20749 0.24586519 0.12423874 0.96130902 66.63288452 
    20750 Axis -0.06705205 -0.17330603 -0.98258284 
    20751 Axis point 117.34974721 5.42399614 0.00000000 
    20752 Rotation angle (degrees) 96.91935179 
    20753 Shift along axis -97.86347693 
    20754  
    20755 
    20756 > select subtract #24
    20757 
    20758 Nothing selected 
    20759 
    20760 > show #25 models
    20761 
    20762 > hide #25 models
    20763 
    20764 > show #!26 models
    20765 
    20766 > mmaker #26 to #23
    20767 
    20768 Parameters 
    20769 --- 
    20770 Chain pairing | bb 
    20771 Alignment algorithm | Needleman-Wunsch 
    20772 Similarity matrix | BLOSUM-62 
    20773 SS fraction | 0.3 
    20774 Gap open (HH/SS/other) | 18/18/6 
    20775 Gap extend | 1 
    20776 SS matrix |  |  | H | S | O 
    20777 ---|---|---|--- 
    20778 H | 6 | -9 | -6 
    20779 S |  | 6 | -6 
    20780 O |  |  | 4 
    20781 Iteration cutoff | 2 
    20782  
    20783 Matchmaker copy of copy of 1ezx, chain A (#23) with copy of copy of 1ezx,
    20784 chain A (#26), sequence alignment score = 1734 
    20785 RMSD between 335 pruned atom pairs is 0.000 angstroms; (across all 335 pairs:
    20786 0.000) 
    20787  
    20788 
    20789 > hide #!24 models
    20790 
    20791 > show #!24 models
    20792 
    20793 > hide #!23 models
    20794 
    20795 > show #25 models
    20796 
    20797 > mmaker #25 to #26
    20798 
    20799 Parameters 
    20800 --- 
    20801 Chain pairing | bb 
    20802 Alignment algorithm | Needleman-Wunsch 
    20803 Similarity matrix | BLOSUM-62 
    20804 SS fraction | 0.3 
    20805 Gap open (HH/SS/other) | 18/18/6 
    20806 Gap extend | 1 
    20807 SS matrix |  |  | H | S | O 
    20808 ---|---|---|--- 
    20809 H | 6 | -9 | -6 
    20810 S |  | 6 | -6 
    20811 O |  |  | 4 
    20812 Iteration cutoff | 2 
    20813  
    20814 Matchmaker copy of copy of 1ezx, chain C (#26) with copy of copy of 5a0c,
    20815 chain A (#25), sequence alignment score = 241.2 
    20816 RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
    20817 3.073) 
    20818  
    20819 
    20820 > hide #!26 models
    20821 
    20822 > fitmap #25 inMap #22
    20823 
    20824 Fit molecule copy of copy of 5a0c (#25) to map
    20825 cryosparc_P371_J948_003_volume_map.mrc z flip (#22) using 1883 atoms 
    20826 average map value = 0.05123, steps = 108 
    20827 shifted from previous position = 4.84 
    20828 rotated from previous position = 10.8 degrees 
    20829 atoms outside contour = 1517, contour level = 0.075909 
    20830  
    20831 Position of copy of copy of 5a0c (#25) relative to
    20832 cryosparc_P371_J948_003_volume_map.mrc z flip (#22) coordinates: 
    20833 Matrix rotation and translation 
    20834 -0.96845122 0.24832236 -0.02093422 151.81572996 
    20835 -0.06074205 -0.31669183 -0.94658158 164.61638030 
    20836 -0.24168707 -0.91544650 0.32178420 153.13479473 
    20837 Axis 0.08170221 0.57928205 -0.81102223 
    20838 Axis point 93.94357397 127.91849703 0.00000000 
    20839 Rotation angle (degrees) 169.01569846 
    20840 Shift along axis -16.43272779 
    20841  
    20842 
    20843 > select add #25
    20844 
    20845 1883 atoms, 1745 bonds, 394 residues, 1 model selected 
    20846 
    20847 > view matrix models
    20848 > #25,-0.77469,0.63129,-0.036468,145.91,-0.26885,-0.38101,-0.88462,168.48,-0.57235,-0.6755,0.46489,156.84
    20849 
    20850 > select subtract #25
    20851 
    20852 Nothing selected 
    20853 
    20854 > show #!26 models
    20855 
    20856 > hide #!24 models
    20857 
    20858 > show #!24 models
    20859 
    20860 > hide #25 models
    20861 
    20862 > mmaker #25 to #26
    20863 
    20864 Parameters 
    20865 --- 
    20866 Chain pairing | bb 
    20867 Alignment algorithm | Needleman-Wunsch 
    20868 Similarity matrix | BLOSUM-62 
    20869 SS fraction | 0.3 
    20870 Gap open (HH/SS/other) | 18/18/6 
    20871 Gap extend | 1 
    20872 SS matrix |  |  | H | S | O 
    20873 ---|---|---|--- 
    20874 H | 6 | -9 | -6 
    20875 S |  | 6 | -6 
    20876 O |  |  | 4 
    20877 Iteration cutoff | 2 
    20878  
    20879 Matchmaker copy of copy of 1ezx, chain C (#26) with copy of copy of 5a0c,
    20880 chain A (#25), sequence alignment score = 241.2 
    20881 RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
    20882 3.073) 
    20883  
    20884 
    20885 > hide #!26 models
    20886 
    20887 > show #25 models
    20888 
    20889 > show #!26 models
    20890 
    20891 > mmaker #25 to #26
    20892 
    20893 Parameters 
    20894 --- 
    20895 Chain pairing | bb 
    20896 Alignment algorithm | Needleman-Wunsch 
    20897 Similarity matrix | BLOSUM-62 
    20898 SS fraction | 0.3 
    20899 Gap open (HH/SS/other) | 18/18/6 
    20900 Gap extend | 1 
    20901 SS matrix |  |  | H | S | O 
    20902 ---|---|---|--- 
    20903 H | 6 | -9 | -6 
    20904 S |  | 6 | -6 
    20905 O |  |  | 4 
    20906 Iteration cutoff | 2 
    20907  
    20908 Matchmaker copy of copy of 1ezx, chain C (#26) with copy of copy of 5a0c,
    20909 chain A (#25), sequence alignment score = 241.2 
    20910 RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
    20911 3.073) 
    20912  
    20913 
    20914 > show #!23 models
    20915 
    20916 > hide #!23 models
    20917 
    20918 > hide #!26 models
    20919 
    20920 > hide #25 models
    20921 
    20922 > show #!26 models
    20923 
    20924 > hide #!26 models
    20925 
    20926 > show #25 models
    20927 
    20928 > hide #25 models
    20929 
    20930 > show #25 models
    20931 
    20932 > show #!26 models
    20933 
    20934 > select add #25
    20935 
    20936 1883 atoms, 1745 bonds, 394 residues, 1 model selected 
    20937 
    20938 > view matrix models
    20939 > #25,-0.9367,0.31111,-0.16061,148.23,0.0082594,-0.43896,-0.89847,161.81,-0.35002,-0.84292,0.40861,148.72
    20940 
    20941 > mmaker #25 to #26
    20942 
    20943 Parameters 
    20944 --- 
    20945 Chain pairing | bb 
    20946 Alignment algorithm | Needleman-Wunsch 
    20947 Similarity matrix | BLOSUM-62 
    20948 SS fraction | 0.3 
    20949 Gap open (HH/SS/other) | 18/18/6 
    20950 Gap extend | 1 
    20951 SS matrix |  |  | H | S | O 
    20952 ---|---|---|--- 
    20953 H | 6 | -9 | -6 
    20954 S |  | 6 | -6 
    20955 O |  |  | 4 
    20956 Iteration cutoff | 2 
    20957  
    20958 Matchmaker copy of copy of 1ezx, chain C (#26) with copy of copy of 5a0c,
    20959 chain A (#25), sequence alignment score = 241.2 
    20960 RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
    20961 3.073) 
    20962  
    20963 
    20964 > hide #!22 models
    20965 
    20966 > hide #!26 models
    20967 
    20968 > select subtract #25
    20969 
    20970 Nothing selected 
    20971 
    20972 > show #!22 models
    20973 
    20974 > hide #!22 models
    20975 
    20976 > show #!26 models
    20977 
    20978 > hide #25 models
    20979 
    20980 > show #25 models
    20981 
    20982 > hide #25 models
    20983 
    20984 > show #25 models
    20985 
    20986 > select add #25
    20987 
    20988 1883 atoms, 1745 bonds, 394 residues, 1 model selected 
    20989 
    20990 > view matrix models
    20991 > #25,-0.9367,0.31111,-0.16061,148.98,0.0082594,-0.43896,-0.89847,185.49,-0.35002,-0.84292,0.40861,135.78
    20992 
    20993 > view matrix models
    20994 > #25,-0.94082,0.30916,-0.13882,149.02,0.0018899,-0.40484,-0.91439,185.4,-0.33889,-0.86054,0.3803,135.77
    20995 
    20996 > view matrix models
    20997 > #25,-0.94082,0.30916,-0.13882,149.87,0.0018899,-0.40484,-0.91439,185.44,-0.33889,-0.86054,0.3803,134.62
    20998 
    20999 > view matrix models
    21000 > #25,0.61831,0.086644,0.78114,122.91,0.644,0.51386,-0.56675,167.46,-0.45051,0.85348,0.26193,124.99
    21001 
    21002 > view matrix models
    21003 > #25,0.68702,0.1216,0.7164,121.63,0.51681,0.61128,-0.59937,169.03,-0.5108,0.78202,0.35712,126.32
    21004 
    21005 > view matrix models
    21006 > #25,-0.95703,-0.21929,0.18975,153.1,-0.15891,-0.15078,-0.97571,186.56,0.24258,-0.96394,0.10945,125.96
    21007 
    21008 > select #8/C:202 #19/C:202
    21009 
    21010 12 atoms, 10 bonds, 2 residues, 2 models selected 
    21011 
    21012 > select #8/C:202 #19/C:202
    21013 
    21014 12 atoms, 10 bonds, 2 residues, 2 models selected 
    21015 TRYPSIN [ID: 2] region 2 chains [204] RMSD: 14.654 
    21016  
    21017 
    21018 > select #8/C:195 #19/C:195
    21019 
    21020 12 atoms, 10 bonds, 2 residues, 2 models selected 
    21021 
    21022 > select #8/C:195 #19/C:195
    21023 
    21024 12 atoms, 10 bonds, 2 residues, 2 models selected 
    21025 TRYPSIN [ID: 2] region 2 chains [197] RMSD: 26.141 
    21026  
    21027 
    21028 > select #7/A:202 #18/A:202 #20/A:202
    21029 
    21030 18 atoms, 15 bonds, 3 residues, 3 models selected 
    21031 
    21032 > select #7/A:202 #18/A:202 #20/A:202
    21033 
    21034 18 atoms, 15 bonds, 3 residues, 3 models selected 
    21035 NEUTROPHIL ELASTASE [ID: 1] region 3 chains [173] RMSD: 20.338 
    21036  
    21037 
    21038 > show #20 models
    21039 
    21040 > hide #20 models
    21041 
    21042 > select #25/A Ser 202
    21043 
    21044 Expected a keyword 
    21045 
    21046 > select #25/A:Ser 202
    21047 
    21048 Expected a keyword 
    21049 
    21050 > select #25/A:Ser202
    21051 
    21052 Nothing selected 
    21053 
    21054 > select #25: 202.A
    21055 
    21056 Expected an objects specifier or a keyword 
    21057 
    21058 > select #25/A: 202
    21059 
    21060 6 atoms, 5 bonds, 1 residue, 1 model selected 
    21061 
    21062 > select add #25
    21063 
    21064 1883 atoms, 1745 bonds, 394 residues, 1 model selected 
    21065 
    21066 > select subtract #25
    21067 
    21068 Nothing selected 
    21069 
    21070 > select add #25
    21071 
    21072 1883 atoms, 1745 bonds, 394 residues, 1 model selected 
    21073 
    21074 > hide #!26 models
    21075 
    21076 > show #!22 models
    21077 
    21078 > show #!21 models
    21079 
    21080 > hide #!21 models
    21081 
    21082 > show #!23 models
    21083 
    21084 > view matrix models
    21085 > #25,-0.95703,-0.21929,0.18975,145.87,-0.15891,-0.15078,-0.97571,168.63,0.24258,-0.96394,0.10945,142.99
    21086 
    21087 > view matrix models
    21088 > #25,-0.92453,-0.26838,-0.2706,146.59,0.26503,0.057502,-0.96252,159.94,0.27389,-0.96159,0.017967,142.62
    21089 
    21090 > select #25/A: 202
    21091 
    21092 6 atoms, 5 bonds, 1 residue, 1 model selected 
    21093 
    21094 > fitmap #25 inMap #22
    21095 
    21096 Fit molecule copy of copy of 5a0c (#25) to map
    21097 cryosparc_P371_J948_003_volume_map.mrc z flip (#22) using 1883 atoms 
    21098 average map value = 0.05191, steps = 80 
    21099 shifted from previous position = 6.32 
    21100 rotated from previous position = 2.92 degrees 
    21101 atoms outside contour = 1497, contour level = 0.075909 
    21102  
    21103 Position of copy of copy of 5a0c (#25) relative to
    21104 cryosparc_P371_J948_003_volume_map.mrc z flip (#22) coordinates: 
    21105 Matrix rotation and translation 
    21106 -0.92706110 -0.29700612 -0.22879047 151.40778359 
    21107 0.22401549 0.05050483 -0.97327608 156.79876717 
    21108 0.30062397 -0.95353900 0.01971291 143.82999540 
    21109 Axis 0.02656202 -0.71248224 0.70118722 
    21110 Axis point 58.53175465 0.00000000 169.56684388 
    21111 Rotation angle (degrees) 158.19010570 
    21112 Shift along axis -6.84288466 
    21113  
    21114 
    21115 > hide #!22 models
    21116 
    21117 > show #!22 models
    21118 
    21119 > view
    21120 
    21121 > ui mousemode right "tape measure"
    21122 
    21123 > marker segment #27 position 135.4,127.7,167.7 toPosition 124.3,129.1,64.78
    21124 > color yellow radius 0.2167 label 103.5 labelHeight 10.35 labelColor yellow
    21125 
    21126 > marker segment #27 position 125.5,89.39,147.8 toPosition 125.6,178.4,143.9
    21127 > color yellow radius 0.2167 label 89.07 labelHeight 8.907 labelColor yellow
    21128 
    21129 > close #27
    21130 
    21131 > save /Users/apple/Downloads/csparc.cxs includeMaps true
    21132 
    21133 > open 1oph fromDatabase pdb format mmcif
    21134 
    21135 1oph title: 
    21136 Non-covalent complex between α-1-π-pittsburgh and S195A trypsin [more info...] 
    21137  
    21138 Chain information for 1oph #27 
    21139 --- 
    21140 Chain | Description | UniProt 
    21141 A | Alpha-1-antitrypsin precursor | A1AT_HUMAN 1-394 
    21142 B | Trypsinogen, cationic precursor | TRY1_BOVIN -4-245 
    21143  
    21144 1oph mmCIF Assemblies 
    21145 --- 
    21146 1| author_and_software_defined_assembly 
    21147 2| software_defined_assembly 
    21148  
    21149 
    21150 > select #27/A
    21151 
    21152 3121 atoms, 2980 bonds, 578 residues, 1 model selected 
    21153 
    21154 > delete #27/A
    21155 
    21156 > mmaker #27 to #26
    21157 
    21158 Computing secondary structure 
    21159 Parameters 
    21160 --- 
    21161 Chain pairing | bb 
    21162 Alignment algorithm | Needleman-Wunsch 
    21163 Similarity matrix | BLOSUM-62 
    21164 SS fraction | 0.3 
    21165 Gap open (HH/SS/other) | 18/18/6 
    21166 Gap extend | 1 
    21167 SS matrix |  |  | H | S | O 
    21168 ---|---|---|--- 
    21169 H | 6 | -9 | -6 
    21170 S |  | 6 | -6 
    21171 O |  |  | 4 
    21172 Iteration cutoff | 2 
    21173  
    21174 Matchmaker copy of copy of 1ezx, chain C (#26) with 1oph, chain B (#27),
    21175 sequence alignment score = 997.3 
    21176 RMSD between 122 pruned atom pairs is 0.798 angstroms; (across all 140 pairs:
    21177 2.232) 
    21178  
    21179 
    21180 > show #!26 models
    21181 
    21182 > hide #25 models
    21183 
    21184 > hide #!26 models
    21185 
    21186 > select add #27
    21187 
    21188 1798 atoms, 1661 bonds, 397 residues, 1 model selected 
    21189 
    21190 > ui mousemode right "translate selected models"
    21191 
    21192 > ui mousemode right "rotate selected models"
    21193 
    21194 > view matrix models
    21195 > #27,-0.045437,0.97583,0.21376,84.546,-0.056484,-0.21614,0.97473,106.46,0.99737,0.032215,0.06494,111.78
    21196 
    21197 > view matrix models
    21198 > #27,-0.045437,0.97583,0.21376,84.655,-0.056484,-0.21614,0.97473,107.21,0.99737,0.032215,0.06494,111.79
    21199 
    21200 > view matrix models
    21201 > #27,-0.028766,0.99015,0.13706,88.816,-0.25704,-0.13983,0.95623,110.79,0.96597,-0.0077222,0.25853,101.15
    21202 
    21203 > hide #27 models
    21204 
    21205 > show #25 models
    21206 
    21207 > show #27 models
    21208 
    21209 > hide #25 models
    21210 
    21211 > fitmap #27 inMap #22
    21212 
    21213 Fit molecule 1oph (#27) to map cryosparc_P371_J948_003_volume_map.mrc z flip
    21214 (#22) using 1798 atoms 
    21215 average map value = 0.05191, steps = 140 
    21216 shifted from previous position = 5.08 
    21217 rotated from previous position = 28.4 degrees 
    21218 atoms outside contour = 1427, contour level = 0.075909 
    21219  
    21220 Position of 1oph (#27) relative to cryosparc_P371_J948_003_volume_map.mrc z
    21221 flip (#22) coordinates: 
    21222 Matrix rotation and translation 
    21223 0.00693020 0.97101511 -0.23891762 117.08280460 
    21224 0.05673053 0.23815679 0.96956846 87.39953806 
    21225 0.99836547 -0.02027323 -0.05343572 123.84959279 
    21226 Axis -0.54108517 -0.67634607 -0.49978278 
    21227 Axis point 8.31144747 0.00000000 37.97716599 
    21228 Rotation angle (degrees) 113.83939914 
    21229 Shift along axis -184.36199747 
    21230  
    21231 
    21232 > ui tool show "Show Sequence Viewer"
    21233 
    21234 > sequence chain #27/B
    21235 
    21236 Alignment identifier is 27/B 
    21237 
    21238 > select #27/B:195
    21239 
    21240 5 atoms, 4 bonds, 1 residue, 1 model selected 
    21241 
    21242 > select #27/B:195
    21243 
    21244 5 atoms, 4 bonds, 1 residue, 1 model selected 
    21245 
    21246 > hide #27 models
    21247 
    21248 > select add #27
    21249 
    21250 1798 atoms, 1661 bonds, 397 residues, 1 model selected 
    21251 
    21252 > show #25 models
    21253 
    21254 > show #!26 models
    21255 
    21256 > hide #25 models
    21257 
    21258 > hide #!26 models
    21259 
    21260 > show #!26 models
    21261 
    21262 > select up
    21263 
    21264 45957 atoms, 45539 bonds, 7200 residues, 38 models selected 
    21265 
    21266 > select up
    21267 
    21268 45957 atoms, 45539 bonds, 7200 residues, 38 models selected 
    21269 
    21270 > select down
    21271 
    21272 1798 atoms, 1661 bonds, 397 residues, 1 model selected 
    21273 
    21274 > select down
    21275 
    21276 1798 atoms, 1661 bonds, 397 residues, 1 model selected 
    21277 
    21278 > select down
    21279 
    21280 1798 atoms, 1661 bonds, 397 residues, 1 model selected 
    21281 
    21282 > select #25/A: 202
    21283 
    21284 6 atoms, 5 bonds, 1 residue, 1 model selected 
    21285 
    21286 > show #25 models
    21287 
    21288 > hide #25 models
    21289 
    21290 > select add #25
    21291 
    21292 1883 atoms, 1745 bonds, 394 residues, 1 model selected 
    21293 
    21294 > select #26/B: 195
    21295 
    21296 Nothing selected 
    21297 
    21298 > select #26/A: 195
    21299 
    21300 9 atoms, 8 bonds, 1 residue, 1 model selected 
    21301 
    21302 > hide #!22 models
    21303 
    21304 > select #26/C: 195
    21305 
    21306 6 atoms, 5 bonds, 1 residue, 1 model selected 
    21307 
    21308 > style sel ball
    21309 
    21310 Changed 6 atom styles 
    21311 
    21312 > show sel atoms
    21313 
    21314 > show #25 models
    21315 
    21316 > hide #!26 models
    21317 
    21318 > select #25/A: 202
    21319 
    21320 6 atoms, 5 bonds, 1 residue, 1 model selected 
    21321 
    21322 > show sel atoms
    21323 
    21324 > style sel ball
    21325 
    21326 Changed 6 atom styles 
    21327 
    21328 > style sel sphere
    21329 
    21330 Changed 6 atom styles 
    21331 
    21332 > style sel ball
    21333 
    21334 Changed 6 atom styles 
    21335 
    21336 > select add #25
    21337 
    21338 1883 atoms, 1745 bonds, 394 residues, 1 model selected 
    21339 
    21340 > select subtract #25
    21341 
    21342 Nothing selected 
    21343 
    21344 > select #23/A: 358
    21345 
    21346 8 atoms, 7 bonds, 1 residue, 1 model selected 
    21347 
    21348 > show sel atoms
    21349 
    21350 > style sel sphere
    21351 
    21352 Changed 8 atom styles 
    21353 
    21354 > style sel stick
    21355 
    21356 Changed 8 atom styles 
    21357 
    21358 > style sel ball
    21359 
    21360 Changed 8 atom styles 
    21361 
    21362 > rainbow sel
    21363 
    21364 > style sel ball
    21365 
    21366 Changed 8 atom styles 
    21367 
    21368 > rainbow sel
    21369 
    21370 > select add #23
    21371 
    21372 2975 atoms, 2968 bonds, 437 residues, 1 model selected 
    21373 
    21374 > select subtract #23
    21375 
    21376 Nothing selected 
    21377 
    21378 > show #!22 models
    21379 
    21380 > hide #25 models
    21381 
    21382 > show #!26 models
    21383 
    21384 > hide #!26 models
    21385 
    21386 > show #25 models
    21387 
    21388 > hide #25 models
    21389 
    21390 > volume #22 level 0.09375
    21391 
    21392 > show #25 models
    21393 
    21394 > hide #25 models
    21395 
    21396 > show #!26 models
    21397 
    21398 > hide #!26 models
    21399 
    21400 > show #25 models
    21401 
    21402 > hide #25 models
    21403 
    21404 > open /Users/apple/Downloads/cryosparc_P371_J950_050_class_averages.mrc
    21405 
    21406 Opened cryosparc_P371_J950_050_class_averages.mrc as #28, grid size
    21407 256,256,200, pixel 1.02,1.02,1.02, shown at level 0.251, step 1, values
    21408 float32 
    21409 
    21410 > close #28
    21411 
    21412 > show #25 models
    21413 
    21414 > select #25/A: 358
    21415 
    21416 Nothing selected 
    21417 
    21418 > select #25/A: 202
    21419 
    21420 6 atoms, 5 bonds, 1 residue, 1 model selected 
    21421 
    21422 > show #!26 models
    21423 
    21424 > hide #!26 models
    21425 
    21426 > hide #25 models
    21427 
    21428 > hide #!24 models
    21429 
    21430 > hide #!23 models
    21431 
    21432 > show #!26 models
    21433 
    21434 > hide #!22 models
    21435 
    21436 > show #!22 models
    21437 
    21438 > show #25 models
    21439 
    21440 > hide #25 models
    21441 
    21442 > hide #!26 models
    21443 
    21444 > show #25 models
    21445 
    21446 > show #!23 models
    21447 
    21448 > ui mousemode right "mark center"
    21449 
    21450 > marker #28 position 123.2,156.9,145.8 color yellow radius 1
    21451 
    21452 > marker #28 position 123.8,156.1,145.9 color yellow radius 1
    21453 
    21454 > marker #28 position 124.3,155.3,145.5 color yellow radius 1
    21455 
    21456 > marker #28 position 125.1,154.7,145.3 color yellow radius 1
    21457 
    21458 > marker #28 position 133.4,155.3,146.7 color yellow radius 1
    21459 
    21460 > close #28
    21461 
    21462 > marker #28 position 138.7,150.2,141.7 color yellow radius 1
    21463 
    21464 > ui mousemode right "translate selected models"
    21465 
    21466 > view matrix models #28,1,0,0,-3.5551,0,1,0,1.3867,0,0,1,-2.5059
    21467 
    21468 > view matrix models #28,1,0,0,-9.6384,0,1,0,2.0334,0,0,1,1.97
    21469 
    21470 > view matrix models #28,1,0,0,-10.982,0,1,0,2.5507,0,0,1,3.0554
    21471 
    21472 > view matrix models #28,1,0,0,-10.831,0,1,0,1.6826,0,0,1,8.0306
    21473 
    21474 > view matrix models #28,1,0,0,-9.3846,0,1,0,2.9816,0,0,1,8.0266
    21475 
    21476 > view matrix models #28,1,0,0,-8.1692,0,1,0,2.6506,0,0,1,8.3086
    21477 
    21478 > save /Users/apple/Downloads/csparc.cxs includeMaps true
    21479 
    21480 ——— End of log from Wed Dec 10 00:50:43 2025 ———
    21481 
    21482 opened ChimeraX session 
    21483 
    21484 > open /Users/apple/Downloads/cryosparc_P371_J1081_flex_map.mrc
    21485 
    21486 Opened cryosparc_P371_J1081_flex_map.mrc as #29, grid size 300,300,300, pixel
    21487 0.867, shown at level 0.000695, step 2, values float32 
    21488 
    21489 > open /Users/apple/Downloads/cryosparc_P371_J1081_noflex_map.mrc
    21490 
    21491 Opened cryosparc_P371_J1081_noflex_map.mrc as #30, grid size 300,300,300,
    21492 pixel 0.867, shown at level 0.000724, step 2, values float32 
    21493 
    21494 > select subtract #28
    21495 
    21496 Nothing selected 
    21497 
    21498 > hide #28 models
    21499 
    21500 > hide #25 models
    21501 
    21502 > hide #!23 models
    21503 
    21504 > hide #!22 models
    21505 
    21506 > volume #29 level 0.002147
    21507 
    21508 > volume #30 level 0.002175
    21509 
    21510 > volume #29 level 0.003511
    21511 
    21512 > transparency #29 50
    21513 
    21514 > combine #23 close false
    21515 
    21516 > select #31
    21517 
    21518 2975 atoms, 2968 bonds, 437 residues, 1 model selected 
    21519 
    21520 > ui mousemode right "translate selected models"
    21521 
    21522 > view matrix models
    21523 > #31,0.50304,0.85251,0.14206,39.723,-0.75321,0.51304,-0.41165,160.2,-0.42382,0.10008,0.9002,116.9
    21524 
    21525 > view matrix models
    21526 > #31,-0.21174,-0.30564,-0.9283,218.18,-0.38185,0.90021,-0.2093,101.13,0.89964,0.31016,-0.30733,89.797
    21527 
    21528 > view matrix models
    21529 > #31,-0.21174,-0.30564,-0.9283,229.13,-0.38185,0.90021,-0.2093,126.74,0.89964,0.31016,-0.30733,63.57
    21530 
    21531 > view matrix models
    21532 > #31,-0.62266,-0.60519,-0.49602,248.5,-0.47185,0.79608,-0.37898,148.7,0.62422,-0.0019301,-0.78124,127.72
    21533 
    21534 > view matrix models
    21535 > #31,-0.0049269,-0.1605,-0.98702,210.49,-0.17098,0.97264,-0.15731,105.85,0.98526,0.16799,-0.032234,50.793
    21536 
    21537 > view matrix models
    21538 > #31,-0.0049269,-0.1605,-0.98702,193.82,-0.17098,0.97264,-0.15731,100.89,0.98526,0.16799,-0.032234,45.314
    21539 
    21540 > ui tool show "Fit to Segments"
    21541 
    21542 > ui tool show "Fit in Map"
    21543 
    21544 > fitmap #31 inMap #29
    21545 
    21546 Fit molecule copy of copy of copy of 1ezx (#31) to map
    21547 cryosparc_P371_J1081_flex_map.mrc (#29) using 2975 atoms 
    21548 average map value = 0.00359, steps = 168 
    21549 shifted from previous position = 8.5 
    21550 rotated from previous position = 22.8 degrees 
    21551 atoms outside contour = 1538, contour level = 0.003511 
    21552  
    21553 Position of copy of copy of copy of 1ezx (#31) relative to
    21554 cryosparc_P371_J1081_flex_map.mrc (#29) coordinates: 
    21555 Matrix rotation and translation 
    21556 -0.34543281 0.02159528 -0.93819498 206.18704506 
    21557 -0.19036417 0.97733785 0.09258621 89.05596314 
    21558 0.91893289 0.21058103 -0.33349359 58.61087565 
    21559 Axis 0.06300096 -0.99157607 -0.11317149 
    21560 Axis point 88.67581154 0.00000000 98.10599897 
    21561 Rotation angle (degrees) 110.53590433 
    21562 Shift along axis -81.94885947 
    21563  
    21564 
    21565 > combine #26 close false
    21566 
    21567 > mmaker #32 to #31
    21568 
    21569 Parameters 
    21570 --- 
    21571 Chain pairing | bb 
    21572 Alignment algorithm | Needleman-Wunsch 
    21573 Similarity matrix | BLOSUM-62 
    21574 SS fraction | 0.3 
    21575 Gap open (HH/SS/other) | 18/18/6 
    21576 Gap extend | 1 
    21577 SS matrix |  |  | H | S | O 
    21578 ---|---|---|--- 
    21579 H | 6 | -9 | -6 
    21580 S |  | 6 | -6 
    21581 O |  |  | 4 
    21582 Iteration cutoff | 2 
    21583  
    21584 Matchmaker copy of copy of copy of 1ezx, chain A (#31) with copy of copy of
    21585 copy of 1ezx, chain A (#32), sequence alignment score = 1734 
    21586 RMSD between 335 pruned atom pairs is 0.000 angstroms; (across all 335 pairs:
    21587 0.000) 
    21588  
    21589 
    21590 > volume #29 level 0.003107
    21591 
    21592 > hide #!32 models
    21593 
    21594 > show #!32 models
    21595 
    21596 > mmaker #27 to #32
    21597 
    21598 Parameters 
    21599 --- 
    21600 Chain pairing | bb 
    21601 Alignment algorithm | Needleman-Wunsch 
    21602 Similarity matrix | BLOSUM-62 
    21603 SS fraction | 0.3 
    21604 Gap open (HH/SS/other) | 18/18/6 
    21605 Gap extend | 1 
    21606 SS matrix |  |  | H | S | O 
    21607 ---|---|---|--- 
    21608 H | 6 | -9 | -6 
    21609 S |  | 6 | -6 
    21610 O |  |  | 4 
    21611 Iteration cutoff | 2 
    21612  
    21613 Matchmaker copy of copy of copy of 1ezx, chain C (#32) with 1oph, chain B
    21614 (#27), sequence alignment score = 997.3 
    21615 RMSD between 122 pruned atom pairs is 0.798 angstroms; (across all 140 pairs:
    21616 2.232) 
    21617  
    21618 
    21619 > show #27 models
    21620 
    21621 > select subtract #31
    21622 
    21623 Nothing selected 
    21624 
    21625 > hide #!32 models
    21626 
    21627 > fitmap #27 inMap #29
    21628 
    21629 Fit molecule 1oph (#27) to map cryosparc_P371_J1081_flex_map.mrc (#29) using
    21630 1798 atoms 
    21631 average map value = 0.001969, steps = 84 
    21632 shifted from previous position = 3.54 
    21633 rotated from previous position = 2.5 degrees 
    21634 atoms outside contour = 1466, contour level = 0.003107 
    21635  
    21636 Position of 1oph (#27) relative to cryosparc_P371_J1081_flex_map.mrc (#29)
    21637 coordinates: 
    21638 Matrix rotation and translation 
    21639 0.01488540 0.98783365 0.15480023 90.39787129 
    21640 0.09394517 0.15275083 -0.98378935 155.00101390 
    21641 -0.99546609 0.02918683 -0.09052845 143.69933185 
    21642 Axis 0.57090422 0.64827970 -0.50378746 
    21643 Axis point 63.02718238 0.00000000 111.05539948 
    21644 Rotation angle (degrees) 117.48046157 
    21645 Shift along axis 79.69861501 
    21646  
    21647 
    21648 > select #27/A: 195
    21649 
    21650 Nothing selected 
    21651 
    21652 > select #27/B: 195
    21653 
    21654 5 atoms, 4 bonds, 1 residue, 1 model selected 
    21655 
    21656 > show sel atoms
    21657 
    21658 > style sel ball
    21659 
    21660 Changed 5 atom styles 
    21661 
    21662 > rainbow sel
    21663 
    21664 > color sel red
    21665 
    21666 > select add #27
    21667 
    21668 1798 atoms, 1661 bonds, 397 residues, 1 model selected 
    21669 
    21670 > select subtract #27
    21671 
    21672 Nothing selected 
    21673 
    21674 > select add #27
    21675 
    21676 1798 atoms, 1661 bonds, 397 residues, 1 model selected 
    21677 
    21678 > view matrix models
    21679 > #27,0.014885,0.98783,0.1548,88.407,0.093945,0.15275,-0.98379,156.95,-0.99547,0.029187,-0.090528,145.09
    21680 
    21681 > view matrix models
    21682 > #27,0.50068,0.52374,0.68922,56.841,0.53814,0.43533,-0.72173,119.4,-0.67804,0.73225,-0.063887,112.1
    21683 
    21684 > view matrix models
    21685 > #27,0.50068,0.52374,0.68922,56.703,0.53814,0.43533,-0.72173,120.1,-0.67804,0.73225,-0.063887,108.86
    21686 
    21687 > fitmap #27 inMap #29
    21688 
    21689 Fit molecule 1oph (#27) to map cryosparc_P371_J1081_flex_map.mrc (#29) using
    21690 1798 atoms 
    21691 average map value = 0.002206, steps = 72 
    21692 shifted from previous position = 3.25 
    21693 rotated from previous position = 11.5 degrees 
    21694 atoms outside contour = 1384, contour level = 0.003107 
    21695  
    21696 Position of 1oph (#27) relative to cryosparc_P371_J1081_flex_map.mrc (#29)
    21697 coordinates: 
    21698 Matrix rotation and translation 
    21699 0.43383501 0.41278377 0.80087249 57.23345510 
    21700 0.54433424 0.58824117 -0.59805732 104.34070071 
    21701 -0.71797452 0.69540053 0.03050727 103.99925252 
    21702 Axis 0.64695257 0.75968612 0.06579798 
    21703 Axis point 48.98630646 0.00000000 62.63708921 
    21704 Rotation angle (degrees) 88.49342140 
    21705 Shift along axis 123.13645375 
    21706  
    21707 
    21708 > mmaker #27 to #32
    21709 
    21710 Parameters 
    21711 --- 
    21712 Chain pairing | bb 
    21713 Alignment algorithm | Needleman-Wunsch 
    21714 Similarity matrix | BLOSUM-62 
    21715 SS fraction | 0.3 
    21716 Gap open (HH/SS/other) | 18/18/6 
    21717 Gap extend | 1 
    21718 SS matrix |  |  | H | S | O 
    21719 ---|---|---|--- 
    21720 H | 6 | -9 | -6 
    21721 S |  | 6 | -6 
    21722 O |  |  | 4 
    21723 Iteration cutoff | 2 
    21724  
    21725 Matchmaker copy of copy of copy of 1ezx, chain C (#32) with 1oph, chain B
    21726 (#27), sequence alignment score = 997.3 
    21727 RMSD between 122 pruned atom pairs is 0.798 angstroms; (across all 140 pairs:
    21728 2.232) 
    21729  
    21730 
    21731 > hide #27 models
    21732 
    21733 > show #!32 models
    21734 
    21735 > hide #!31 models
    21736 
    21737 > volume #29 level 0.002349
    21738 
    21739 > show #27 models
    21740 
    21741 > color #27 #dbd548ff
    21742 
    21743 > select subtract #27
    21744 
    21745 Nothing selected 
    21746 
    21747 > select add #27
    21748 
    21749 1798 atoms, 1661 bonds, 397 residues, 1 model selected 
    21750 
    21751 > select subtract #27
    21752 
    21753 Nothing selected 
    21754 
    21755 > select add #32
    21756 
    21757 3984 atoms, 3982 bonds, 5 pseudobonds, 592 residues, 3 models selected 
    21758 
    21759 > hide #!32 models
    21760 
    21761 > hide #27 models
    21762 
    21763 > show #28 models
    21764 
    21765 > hide #28 models
    21766 
    21767 > show #27 models
    21768 
    21769 > select subtract #32
    21770 
    21771 Nothing selected 
    21772 
    21773 > select add #27
    21774 
    21775 1798 atoms, 1661 bonds, 397 residues, 1 model selected 
    21776 
    21777 > view matrix models
    21778 > #27,-0.014536,0.98302,0.18291,86.474,0.10897,0.18339,-0.97698,152.94,-0.99394,0.00573,-0.10979,145.21
    21779 
    21780 > view matrix models
    21781 > #27,-0.094668,0.98683,0.13115,91.714,0.12875,0.14277,-0.98135,154.1,-0.98715,-0.076017,-0.14057,149.8
    21782 
    21783 > view matrix models
    21784 > #27,-0.094668,0.98683,0.13115,93.34,0.12875,0.14277,-0.98135,151.17,-0.98715,-0.076017,-0.14057,149.26
    21785 
    21786 > view matrix models
    21787 > #27,-0.22979,0.97316,0.012679,104.9,0.38456,0.10276,-0.91736,142.04,-0.89404,-0.20593,-0.39785,168.25
    21788 
    21789 > view matrix models
    21790 > #27,-0.22979,0.97316,0.012679,104.93,0.38456,0.10276,-0.91736,141.75,-0.89404,-0.20593,-0.39785,167.14
    21791 
    21792 > view matrix models
    21793 > #27,-0.22979,0.97316,0.012679,104.2,0.38456,0.10276,-0.91736,144.37,-0.89404,-0.20593,-0.39785,166.13
    21794 
    21795 > hide #27 models
    21796 
    21797 > show #27 models
    21798 
    21799 > hide #27 models
    21800 
    21801 > show #27 models
    21802 
    21803 > view matrix models
    21804 > #27,-0.49784,0.70316,-0.50765,154.01,0.28651,-0.41914,-0.86153,160.52,-0.81858,-0.57435,0.0072046,149.92
    21805 
    21806 > view matrix models
    21807 > #27,-0.29847,0.7881,-0.53834,148.31,0.35815,-0.43034,-0.82857,156.97,-0.88467,-0.44011,-0.15381,157.66
    21808 
    21809 > view matrix models
    21810 > #27,-0.24543,0.58716,-0.77137,169.05,0.40215,-0.66234,-0.63212,150.71,-0.88207,-0.46535,-0.073571,153.15
    21811 
    21812 > view matrix models
    21813 > #27,-0.18594,0.44822,-0.87437,179.01,0.44471,-0.75513,-0.48167,142.87,-0.87616,-0.4784,-0.058915,152.48
    21814 
    21815 > view matrix models
    21816 > #27,0.22752,0.8665,-0.44432,126.63,0.092657,-0.47348,-0.87592,168.02,-0.96935,0.15812,-0.18801,142.01
    21817 
    21818 > view matrix models
    21819 > #27,0.50128,0.79078,-0.35126,116.34,0.31994,-0.54657,-0.77389,158.19,-0.80396,0.27556,-0.52699,156.35
    21820 
    21821 > view matrix models
    21822 > #27,0.70079,0.62982,-0.335,115.76,0.20665,-0.62869,-0.74969,162.11,-0.68278,0.45615,-0.57073,150.23
    21823 
    21824 > view matrix models
    21825 > #27,0.70079,0.62982,-0.335,118.94,0.20665,-0.62869,-0.74969,162.08,-0.68278,0.45615,-0.57073,148.91
    21826 
    21827 > view matrix models
    21828 > #27,-0.4262,0.53806,-0.72722,175.4,-0.24981,-0.84263,-0.47705,162.45,-0.86946,-0.021651,0.49354,99.401
    21829 
    21830 > view matrix models
    21831 > #27,-0.4262,0.53806,-0.72722,174.48,-0.24981,-0.84263,-0.47705,159.2,-0.86946,-0.021651,0.49354,98.413
    21832 
    21833 > hide #27 models
    21834 
    21835 > select subtract #27
    21836 
    21837 Nothing selected 
    21838 
    21839 > hide #!29 models
    21840 
    21841 > show #!30 models
    21842 
    21843 > show #!29 models
    21844 
    21845 > hide #!29 models
    21846 
    21847 > transparency #30 50
    21848 
    21849 > show #!29 models
    21850 
    21851 > hide #!29 models
    21852 
    21853 > volume #30 level 0.002739
    21854 
    21855 > show #!24 models
    21856 
    21857 > hide #!24 models
    21858 
    21859 > show #!6 models
    21860 
    21861 > hide #!6 models
    21862 
    21863 > combine #6 close false
    21864 
    21865 > select add #33
    21866 
    21867 3190 atoms, 3270 bonds, 2 pseudobonds, 422 residues, 3 models selected 
    21868 
    21869 > view matrix models
    21870 > #33,-0.12378,0.83325,-0.53886,145.44,-0.98558,-0.040107,0.16437,137.25,0.11535,0.55143,0.8262,70.943
    21871 
    21872 > view matrix models
    21873 > #33,-0.12378,0.83325,-0.53886,121.31,-0.98558,-0.040107,0.16437,137.63,0.11535,0.55143,0.8262,134.88
    21874 
    21875 > view matrix models
    21876 > #33,0.096483,0.85305,0.51282,84.33,-0.9177,-0.12324,0.37767,130.03,0.38537,-0.50706,0.77096,135.66
    21877 
    21878 > view matrix models
    21879 > #33,0.64301,0.74737,-0.16726,96.505,-0.76213,0.64595,-0.043654,137.8,0.075414,0.15554,0.98495,132
    21880 
    21881 > view matrix models
    21882 > #33,0.64301,0.74737,-0.16726,99.153,-0.76213,0.64595,-0.043654,141.43,0.075414,0.15554,0.98495,123.21
    21883 
    21884 > view matrix models
    21885 > #33,0.53757,0.81725,-0.20763,102.02,-0.84165,0.53507,-0.073018,144.14,0.051423,0.214,0.97548,123.72
    21886 
    21887 > view matrix models
    21888 > #33,0.56724,0.791,-0.22925,102.27,-0.77653,0.60643,0.17101,135.07,0.2743,0.081017,0.95823,120.83
    21889 
    21890 > view matrix models
    21891 > #33,0.56724,0.791,-0.22925,126.45,-0.77653,0.60643,0.17101,136.72,0.2743,0.081017,0.95823,121.23
    21892 
    21893 > view matrix models
    21894 > #33,0.56724,0.791,-0.22925,77.167,-0.77653,0.60643,0.17101,133.67,0.2743,0.081017,0.95823,119.95
    21895 
    21896 > view matrix models
    21897 > #33,0.74297,0.64514,-0.17831,73.008,0.66921,-0.71089,0.21633,111.62,0.012799,-0.28005,-0.9599,186.09
    21898 
    21899 > view matrix models
    21900 > #33,0.09813,0.99411,-0.046082,78.903,0.94172,-0.077789,0.32727,101.1,0.32175,-0.075511,-0.94381,179.45
    21901 
    21902 > view matrix models
    21903 > #33,0.09813,0.99411,-0.046082,125.57,0.94172,-0.077789,0.32727,97.242,0.32175,-0.075511,-0.94381,182.15
    21904 
    21905 > view matrix models
    21906 > #33,0.09813,0.99411,-0.046082,123.79,0.94172,-0.077789,0.32727,98.857,0.32175,-0.075511,-0.94381,179.28
    21907 
    21908 > view matrix models
    21909 > #33,0.09813,0.99411,-0.046082,130.36,0.94172,-0.077789,0.32727,110.04,0.32175,-0.075511,-0.94381,181.04
    21910 
    21911 > view matrix models
    21912 > #33,0.18807,0.98065,-0.054404,129.09,0.97234,-0.17809,0.15115,115.39,0.13853,-0.081324,-0.98701,185.63
    21913 
    21914 > view matrix models
    21915 > #33,0.12584,0.98709,-0.099091,131.56,0.99196,-0.12652,-0.00060121,119.63,-0.01313,-0.098219,-0.99508,188.6
    21916 
    21917 > view matrix models
    21918 > #33,0.12584,0.98709,-0.099091,132.15,0.99196,-0.12652,-0.00060121,116.48,-0.01313,-0.098219,-0.99508,193.2
    21919 
    21920 > fitmap #33 inMap #29
    21921 
    21922 Fit molecule copy of 3C11_Fab_D_1292144377_model-annotate_P1_HL.pdb (#33) to
    21923 map cryosparc_P371_J1081_flex_map.mrc (#29) using 3190 atoms 
    21924 average map value = 0.003475, steps = 104 
    21925 shifted from previous position = 6.47 
    21926 rotated from previous position = 18.9 degrees 
    21927 atoms outside contour = 969, contour level = 0.0023495 
    21928  
    21929 Position of copy of 3C11_Fab_D_1292144377_model-annotate_P1_HL.pdb (#33)
    21930 relative to cryosparc_P371_J1081_flex_map.mrc (#29) coordinates: 
    21931 Matrix rotation and translation 
    21932 -0.15475687 0.98403031 -0.08794666 131.65046804 
    21933 0.97076802 0.13493018 -0.19850246 120.81278809 
    21934 -0.18346579 -0.11609543 -0.97614657 191.47093637 
    21935 Axis 0.64964584 0.75301343 -0.10455170 
    21936 Axis point 18.09163929 0.00000000 103.49035885 
    21937 Rotation angle (degrees) 176.36359820 
    21938 Shift along axis 156.48121953 
    21939  
    21940 
    21941 > select subtract #33
    21942 
    21943 Nothing selected 
    21944 
    21945 > color #33 #dbda64ff
    21946 
    21947 > show #!30 models
    21948 
    21949 > hide #!29 models
    21950 
    21951 > hide #!30 models
    21952 
    21953 > hide #!33 models
    21954 
    21955 > open /Users/apple/Downloads/cryosparc_P371_J973_003_volume_map.mrc
    21956 
    21957 Opened cryosparc_P371_J973_003_volume_map.mrc as #34, grid size 300,300,300,
    21958 pixel 0.867, shown at level 0.0274, step 2, values float32 
    21959 
    21960 > volume #34 level 0.05742
    21961 
    21962 > transparency #34 50
    21963 
    21964 > show #27 models
    21965 
    21966 > volume flip #34 axis z
    21967 
    21968 Opened cryosparc_P371_J973_003_volume_map.mrc z flip as #35, grid size
    21969 300,300,300, pixel 0.867, shown at step 1, values float32 
    21970 
    21971 > select add #27
    21972 
    21973 1798 atoms, 1661 bonds, 397 residues, 1 model selected 
    21974 
    21975 > view matrix models
    21976 > #27,-0.4262,0.53806,-0.72722,176.2,-0.24981,-0.84263,-0.47705,165.62,-0.86946,-0.021651,0.49354,102.24
    21977 
    21978 > view matrix models
    21979 > #27,-0.4262,0.53806,-0.72722,178.78,-0.24981,-0.84263,-0.47705,174.86,-0.86946,-0.021651,0.49354,105.39
    21980 
    21981 > view matrix models
    21982 > #27,-0.4262,0.53806,-0.72722,181.47,-0.24981,-0.84263,-0.47705,184.66,-0.86946,-0.021651,0.49354,109.78
    21983 
    21984 > view matrix models
    21985 > #27,-0.4262,0.53806,-0.72722,190.87,-0.24981,-0.84263,-0.47705,217.94,-0.86946,-0.021651,0.49354,118.99
    21986 
    21987 > view matrix models
    21988 > #27,-0.3858,0.47048,-0.7936,196.51,0.046117,-0.84929,-0.52592,214.13,-0.92143,-0.2395,0.30596,139.88
    21989 
    21990 > view matrix models
    21991 > #27,-0.66587,0.4077,0.62482,112.13,-0.39323,0.51992,-0.75832,194.48,-0.63402,-0.75064,-0.18588,182.26
    21992 
    21993 > view matrix models
    21994 > #27,-0.68529,0.37699,0.6231,113.74,-0.37744,0.54787,-0.74658,192.39,-0.62283,-0.74681,-0.23315,184.97
    21995 
    21996 > view matrix models
    21997 > #27,-0.64501,-0.54498,0.53568,149.28,-0.48286,0.83399,0.26704,118.72,-0.59228,-0.086414,-0.80108,199.55
    21998 
    21999 > view matrix models
    22000 > #27,-0.64501,-0.54498,0.53568,147.06,-0.48286,0.83399,0.26704,118.55,-0.59228,-0.086414,-0.80108,205.77
    22001 
    22002 > view matrix models
    22003 > #27,-0.98854,-0.0066051,-0.15082,182.67,-0.13987,0.41609,0.8985,82.549,0.056821,0.9093,-0.41224,131.06
    22004 
    22005 > view matrix models
    22006 > #27,-0.98854,-0.0066051,-0.15082,167.04,-0.13987,0.41609,0.8985,91.832,0.056821,0.9093,-0.41224,120.45
    22007 
    22008 > view matrix models
    22009 > #27,-0.98854,-0.0066051,-0.15082,170.38,-0.13987,0.41609,0.8985,89.105,0.056821,0.9093,-0.41224,122.96
    22010 
    22011 > view matrix models
    22012 > #27,-0.98854,-0.0066051,-0.15082,170.42,-0.13987,0.41609,0.8985,90.399,0.056821,0.9093,-0.41224,133.48
    22013 
    22014 > volume #35 level 0.043
    22015 
    22016 > open /Users/apple/Downloads/cryosparc_P371_J937_003_volume_map.mrc
    22017 
    22018 Opened cryosparc_P371_J937_003_volume_map.mrc as #36, grid size 300,300,300,
    22019 pixel 0.867, shown at level 0.0245, step 2, values float32 
    22020 
    22021 > volume #36 level 0.06028
    22022 
    22023 > hide #27 models
    22024 
    22025 > select subtract #27
    22026 
    22027 Nothing selected 
    22028 
    22029 > volume flip #36 axis z
    22030 
    22031 Opened cryosparc_P371_J937_003_volume_map.mrc z flip as #37, grid size
    22032 300,300,300, pixel 0.867, shown at step 1, values float32 
    22033 
    22034 > transparency #37 50
    22035 
    22036 > show #!31 models
    22037 
    22038 > select add #31
    22039 
    22040 2975 atoms, 2968 bonds, 437 residues, 1 model selected 
    22041 
    22042 > view matrix models
    22043 > #31,0.39135,-0.20933,0.89611,66.667,-0.16444,-0.97402,-0.15572,220.86,0.90543,-0.086415,-0.41561,82.36
    22044 
    22045 > view matrix models
    22046 > #31,-0.095994,-0.17972,0.97902,91.144,-0.11035,-0.97558,-0.18991,219.49,0.98925,-0.12627,0.073818,51.003
    22047 
    22048 > view matrix models
    22049 > #31,-0.095994,-0.17972,0.97902,86.989,-0.11035,-0.97558,-0.18991,196.02,0.98925,-0.12627,0.073818,43.81
    22050 
    22051 > view matrix models
    22052 > #31,-0.14959,-0.29832,0.94267,99.755,-0.024842,-0.95196,-0.3052,195.83,0.98844,-0.069073,0.13499,36.818
    22053 
    22054 > view matrix models
    22055 > #31,-0.14959,-0.29832,0.94267,100.18,-0.024842,-0.95196,-0.3052,202.18,0.98844,-0.069073,0.13499,38.064
    22056 
    22057 > fitmap #31 inMap #37
    22058 
    22059 Fit molecule copy of copy of copy of 1ezx (#31) to map
    22060 cryosparc_P371_J937_003_volume_map.mrc z flip (#37) using 2975 atoms 
    22061 average map value = 0.08682, steps = 132 
    22062 shifted from previous position = 2.02 
    22063 rotated from previous position = 31.6 degrees 
    22064 atoms outside contour = 867, contour level = 0.06028 
    22065  
    22066 Position of copy of copy of copy of 1ezx (#31) relative to
    22067 cryosparc_P371_J937_003_volume_map.mrc z flip (#37) coordinates: 
    22068 Matrix rotation and translation 
    22069 0.36233036 -0.11333577 0.92513335 57.46362679 
    22070 -0.01935243 -0.99328021 -0.11410485 191.49517202 
    22071 0.93184880 0.02344008 -0.36208890 68.00033796 
    22072 Axis 0.82499051 -0.04027910 0.56370937 
    22073 Axis point 0.00000000 96.54263836 19.29334389 
    22074 Rotation angle (degrees) 175.21818737 
    22075 Shift along axis 78.02612084 
    22076  
    22077 
    22078 > mmaker #32 to #31
    22079 
    22080 Parameters 
    22081 --- 
    22082 Chain pairing | bb 
    22083 Alignment algorithm | Needleman-Wunsch 
    22084 Similarity matrix | BLOSUM-62 
    22085 SS fraction | 0.3 
    22086 Gap open (HH/SS/other) | 18/18/6 
    22087 Gap extend | 1 
    22088 SS matrix |  |  | H | S | O 
    22089 ---|---|---|--- 
    22090 H | 6 | -9 | -6 
    22091 S |  | 6 | -6 
    22092 O |  |  | 4 
    22093 Iteration cutoff | 2 
    22094  
    22095 Matchmaker copy of copy of copy of 1ezx, chain A (#31) with copy of copy of
    22096 copy of 1ezx, chain A (#32), sequence alignment score = 1734 
    22097 RMSD between 335 pruned atom pairs is 0.000 angstroms; (across all 335 pairs:
    22098 0.000) 
    22099  
    22100 
    22101 > show #!32 models
    22102 
    22103 > select subtract #31
    22104 
    22105 Nothing selected 
    22106 
    22107 > hide #!32 models
    22108 
    22109 > transparency #37 30
    22110 
    22111 > transparency #37 65
    22112 
    22113 > show #!32 models
    22114 
    22115 > show #27 models
    22116 
    22117 > mmaker #27 to #32
    22118 
    22119 Parameters 
    22120 --- 
    22121 Chain pairing | bb 
    22122 Alignment algorithm | Needleman-Wunsch 
    22123 Similarity matrix | BLOSUM-62 
    22124 SS fraction | 0.3 
    22125 Gap open (HH/SS/other) | 18/18/6 
    22126 Gap extend | 1 
    22127 SS matrix |  |  | H | S | O 
    22128 ---|---|---|--- 
    22129 H | 6 | -9 | -6 
    22130 S |  | 6 | -6 
    22131 O |  |  | 4 
    22132 Iteration cutoff | 2 
    22133  
    22134 Matchmaker copy of copy of copy of 1ezx, chain C (#32) with 1oph, chain B
    22135 (#27), sequence alignment score = 997.3 
    22136 RMSD between 122 pruned atom pairs is 0.798 angstroms; (across all 140 pairs:
    22137 2.232) 
    22138  
    22139 
    22140 > hide #!32 models
    22141 
    22142 > select #27/B: 195
    22143 
    22144 5 atoms, 4 bonds, 1 residue, 1 model selected 
    22145 
    22146 > color sel red
    22147 
    22148 > select add #27
    22149 
    22150 1798 atoms, 1661 bonds, 397 residues, 1 model selected 
    22151 
    22152 > select subtract #27
    22153 
    22154 Nothing selected 
    22155 
    22156 > select add #27
    22157 
    22158 1798 atoms, 1661 bonds, 397 residues, 1 model selected 
    22159 
    22160 > view matrix models
    22161 > #27,0.0036574,-0.99591,-0.090234,167.1,0.079873,-0.089656,0.99276,103.86,-0.9968,-0.010838,0.079218,136.78
    22162 
    22163 > view matrix models
    22164 > #27,0.0036574,-0.99591,-0.090234,167.32,0.079873,-0.089656,0.99276,103.5,-0.9968,-0.010838,0.079218,136.17
    22165 
    22166 > view matrix models
    22167 > #27,0.0036574,-0.99591,-0.090234,167.31,0.079873,-0.089656,0.99276,103.59,-0.9968,-0.010838,0.079218,135.71
    22168 
    22169 > view matrix models
    22170 > #27,-0.286,-0.74268,-0.6055,199.85,-0.56632,-0.37872,0.73202,146.21,-0.77297,0.55227,-0.31228,137.19
    22171 
    22172 > view matrix models
    22173 > #27,-0.286,-0.74268,-0.6055,200.26,-0.56632,-0.37872,0.73202,145.27,-0.77297,0.55227,-0.31228,137.56
    22174 
    22175 > view matrix models
    22176 > #27,-0.11735,-0.92157,-0.37006,186.61,-0.43047,-0.2886,0.85522,130.83,-0.89494,0.25966,-0.36284,153.64
    22177 
    22178 > view matrix models
    22179 > #27,-0.11735,-0.92157,-0.37006,187.37,-0.43047,-0.2886,0.85522,129.56,-0.89494,0.25966,-0.36284,153.71
    22180 
    22181 > fitmap #27 inMap #37
    22182 
    22183 Fit molecule 1oph (#27) to map cryosparc_P371_J937_003_volume_map.mrc z flip
    22184 (#37) using 1798 atoms 
    22185 average map value = 0.0548, steps = 128 
    22186 shifted from previous position = 3.42 
    22187 rotated from previous position = 38.8 degrees 
    22188 atoms outside contour = 1047, contour level = 0.06028 
    22189  
    22190 Position of 1oph (#27) relative to cryosparc_P371_J937_003_volume_map.mrc z
    22191 flip (#37) coordinates: 
    22192 Matrix rotation and translation 
    22193 -0.45346895 -0.89029021 0.04182410 166.01007315 
    22194 -0.59816316 0.33879139 0.72623772 117.01111106 
    22195 -0.66073198 0.30430862 -0.68617018 166.01554475 
    22196 Axis -0.48496079 0.80751043 0.33576770 
    22197 Axis point 138.35331070 0.00000000 30.35915407 
    22198 Rotation angle (degrees) 154.21383871 
    22199 Shift along axis 69.72197468 
    22200  
    22201 
    22202 > view matrix models
    22203 > #27,-0.92301,-0.085578,-0.37515,178.08,-0.38272,0.30509,0.87204,103.27,0.039826,0.94847,-0.31435,102.9
    22204 
    22205 > view matrix models
    22206 > #27,-0.92301,-0.085578,-0.37515,178.04,-0.38272,0.30509,0.87204,107.02,0.039826,0.94847,-0.31435,104.53
    22207 
    22208 > view matrix models
    22209 > #27,-0.8652,-0.36102,-0.348,184.03,-0.41726,0.13347,0.89893,111.83,-0.27809,0.92296,-0.26611,109.99
    22210 
    22211 > view matrix models
    22212 > #27,-0.8652,-0.36102,-0.348,184.08,-0.41726,0.13347,0.89893,110,-0.27809,0.92296,-0.26611,108.82
    22213 
    22214 > view matrix models
    22215 > #27,-0.74437,-0.58007,-0.33081,187.3,-0.42416,0.028093,0.90515,113.28,-0.51575,0.81408,-0.26695,118.33
    22216 
    22217 > fitmap #27 inMap #37
    22218 
    22219 Fit molecule 1oph (#27) to map cryosparc_P371_J937_003_volume_map.mrc z flip
    22220 (#37) using 1798 atoms 
    22221 average map value = 0.05355, steps = 84 
    22222 shifted from previous position = 0.767 
    22223 rotated from previous position = 14.4 degrees 
    22224 atoms outside contour = 1098, contour level = 0.06028 
    22225  
    22226 Position of 1oph (#27) relative to cryosparc_P371_J937_003_volume_map.mrc z
    22227 flip (#37) coordinates: 
    22228 Matrix rotation and translation 
    22229 -0.61577270 -0.75165872 -0.23629043 184.50519497 
    22230 -0.34375795 -0.01355748 0.93896042 110.78003691 
    22231 -0.70898128 0.65941290 -0.25004033 128.04401792 
    22232 Axis -0.40864695 0.69098691 0.59627574 
    22233 Axis point 135.45180710 0.00000000 -11.35956716 
    22234 Rotation angle (degrees) 159.99876589 
    22235 Shift along axis 77.49961288 
    22236  
    22237 
    22238 > hide #!31 models
    22239 
    22240 > close #34-37
    22241 
    22242 > hide #27 models
    22243 
    22244 > select subtract #27
    22245 
    22246 Nothing selected 
    22247 
    22248 > save /Users/apple/Downloads/csparc.cxs includeMaps true
    22249 
    22250  
    22251 You deleted or moved a volume file that is still open in ChimeraX. 
    22252  
    22253 /Users/apple/Downloads/cryosparc_P371_J1081_noflex_map.mrc 
    22254  
    22255 To allow fast initial display of volume data ChimeraX does not read all data
    22256 from the file when it is first opened, and will later read more data when
    22257 needed. ChimeraX got an error trying to read the above file. 
    22258 [Repeated 1 time(s)]
    22259 
    22260 > close #29-30
    22261 
    22262 > save /Users/apple/Downloads/csparc.cxs includeMaps true
    22263 
    22264 ——— End of log from Wed Dec 31 02:28:23 2025 ———
    22265 
    22266 opened ChimeraX session 
    22267 
    22268 > open /Users/apple/Downloads/J1122.mrc
    22269 
    22270 Opened J1122.mrc as #29, grid size 300,300,300, pixel 0.867, shown at level
    22271 0.0211, step 2, values float32 
    22272 
    22273 > volume #29 level 0.06448
    22274 
    22275 > transparency #29 50
    22276 
    22277 > show #!31 models
    22278 
    22279 > hide #!31 models
    22280 
    22281 > show #!32 models
    22282 
    22283 > select add #32
    22284 
    22285 3984 atoms, 3982 bonds, 5 pseudobonds, 592 residues, 3 models selected 
    22286 
    22287 > ui mousemode right "translate selected models"
    22288 
    22289 > view matrix models
    22290 > #32,-0.4387,-0.32363,-0.83834,223.29,0.093735,-0.94429,0.31548,159.1,-0.89373,0.059819,0.44459,173.61
    22291 
    22292 > view matrix models
    22293 > #32,-0.051177,-0.06552,-0.99654,192.53,-0.071281,-0.99506,0.069084,187.1,-0.99614,0.074569,0.046254,202.65
    22294 
    22295 > view matrix models
    22296 > #32,-0.051177,-0.06552,-0.99654,191.33,-0.071281,-0.99506,0.069084,184.14,-0.99614,0.074569,0.046254,203.41
    22297 
    22298 > view matrix models
    22299 > #32,0.026039,-0.29812,-0.95417,195.35,0.13022,-0.94535,0.29892,154.62,-0.99114,-0.13204,0.014206,215.34
    22300 
    22301 > view matrix models
    22302 > #32,0.026039,-0.29812,-0.95417,195.13,0.13022,-0.94535,0.29892,154.52,-0.99114,-0.13204,0.014206,218.61
    22303 
    22304 > view matrix models
    22305 > #32,0.32421,-0.1599,-0.93237,166.33,0.029424,-0.98343,0.17889,170.24,-0.94553,-0.085432,-0.31413,231.84
    22306 
    22307 > ui tool show "Fit in Map"
    22308 
    22309 > fitmap #32 inMap #29
    22310 
    22311 Fit molecule copy of copy of copy of 1ezx (#32) to map J1122.mrc (#29) using
    22312 3984 atoms 
    22313 average map value = 0.08314, steps = 224 
    22314 shifted from previous position = 4.3 
    22315 rotated from previous position = 41.5 degrees 
    22316 atoms outside contour = 1668, contour level = 0.06448 
    22317  
    22318 Position of copy of copy of copy of 1ezx (#32) relative to J1122.mrc (#29)
    22319 coordinates: 
    22320 Matrix rotation and translation 
    22321 -0.34900889 0.03003688 -0.93663792 206.58097603 
    22322 0.14034902 -0.98653802 -0.08393380 177.23372304 
    22323 -0.92655003 -0.16074986 0.34009489 197.98573410 
    22324 Axis -0.56984891 -0.07483556 0.81833481 
    22325 Axis point 168.52294892 102.29267921 0.00000000 
    22326 Rotation angle (degrees) 176.13531334 
    22327 Shift along axis 31.03528983 
    22328  
    22329 
    22330 > volume #29 level 0.07099
    22331 
    22332 > surface dust #29 size 8.67
    22333 
    22334 > select subtract #32
    22335 
    22336 Nothing selected 
    22337 
    22338 > open cryosparc_P371_J1130_component_001/J1130_component_001_frame_???.mrc
    22339 > vseries true
    22340 
    22341 Opened map series J1130_component_001_frame_000.mrc as #30, 20 images, grid
    22342 size 300,300,300, pixel 0.867, shown at level 0.033, step 2, values float32 
    22343 
    22344 > volume #30.1 level 0.04835
    22345 
    22346 > surface dust #29 size 8.67
    22347 
    22348 > surface dust #30.1 size 8.67
    22349 
    22350 > transparency #30 50
    22351 
    22352 > volume #30.7 level 0.06047
    22353 
    22354 > open /Users/apple/Downloads/J1134.mrc
    22355 
    22356 Opened J1134.mrc as #34, grid size 300,300,300, pixel 0.867, shown at level
    22357 0.0252, step 2, values float32 
    22358 
    22359 > transparency #31 50
    22360 
    22361 > volume #34 level 0.04544
    22362 
    22363 > transparency #31450
    22364 
    22365 Missing or invalid "percent" argument: Expected a number 
    22366 
    22367 > transparency #34 50
    22368 
    22369 > hide #!32 models
    22370 
    22371 > show #!34 models
    22372 
    22373 > volume #34 level 0.05837
    22374 
    22375 > hide #!30 models
    22376 
    22377 > show #!30 models
    22378 
    22379 > hide #!29 models
    22380 
    22381 > show #!32 models
    22382 
    22383 > show #!29 models
    22384 
    22385 > hide #!34 models
    22386 
    22387 > hide #!30 models
    22388 
    22389 > show #!34 models
    22390 
    22391 > hide #!29 models
    22392 
    22393 > volume #34 level 0.0685
    22394 
    22395 > mmaker #27 to #32
    22396 
    22397 Parameters 
    22398 --- 
    22399 Chain pairing | bb 
    22400 Alignment algorithm | Needleman-Wunsch 
    22401 Similarity matrix | BLOSUM-62 
    22402 SS fraction | 0.3 
    22403 Gap open (HH/SS/other) | 18/18/6 
    22404 Gap extend | 1 
    22405 SS matrix |  |  | H | S | O 
    22406 ---|---|---|--- 
    22407 H | 6 | -9 | -6 
    22408 S |  | 6 | -6 
    22409 O |  |  | 4 
    22410 Iteration cutoff | 2 
    22411  
    22412 Matchmaker copy of copy of copy of 1ezx, chain C (#32) with 1oph, chain B
    22413 (#27), sequence alignment score = 997.3 
    22414 RMSD between 122 pruned atom pairs is 0.798 angstroms; (across all 140 pairs:
    22415 2.232) 
    22416  
    22417 
    22418 > show #27 models
    22419 
    22420 > hide #!32 models
    22421 
    22422 > hide #27 models
    22423 
    22424 > show #!29 models
    22425 
    22426 > hide #!34 models
    22427 
    22428 > show #!23 models
    22429 
    22430 > hide #!29 models
    22431 
    22432 > show #!29 models
    22433 
    22434 > show #27 models
    22435 
    22436 > fitmap #27 inMap #29
    22437 
    22438 Fit molecule 1oph (#27) to map J1122.mrc (#29) using 1798 atoms 
    22439 average map value = 0.0518, steps = 144 
    22440 shifted from previous position = 4.11 
    22441 rotated from previous position = 22.4 degrees 
    22442 atoms outside contour = 1430, contour level = 0.070992 
    22443  
    22444 Position of 1oph (#27) relative to J1122.mrc (#29) coordinates: 
    22445 Matrix rotation and translation 
    22446 0.02106068 0.97914469 -0.20206962 114.64292873 
    22447 0.03717102 0.20120785 0.97884305 90.21390293 
    22448 0.99908697 -0.02812623 -0.03215823 122.53280686 
    22449 Axis -0.55065296 -0.65684271 -0.51511064 
    22450 Axis point 6.14168786 0.00000000 32.08271580 
    22451 Rotation angle (degrees) 113.88767131 
    22452 Shift along axis -185.50276510 
    22453  
    22454 
    22455 > select add #27
    22456 
    22457 1798 atoms, 1661 bonds, 397 residues, 1 model selected 
    22458 
    22459 > mmaker #27 to #32
    22460 
    22461 Parameters 
    22462 --- 
    22463 Chain pairing | bb 
    22464 Alignment algorithm | Needleman-Wunsch 
    22465 Similarity matrix | BLOSUM-62 
    22466 SS fraction | 0.3 
    22467 Gap open (HH/SS/other) | 18/18/6 
    22468 Gap extend | 1 
    22469 SS matrix |  |  | H | S | O 
    22470 ---|---|---|--- 
    22471 H | 6 | -9 | -6 
    22472 S |  | 6 | -6 
    22473 O |  |  | 4 
    22474 Iteration cutoff | 2 
    22475  
    22476 Matchmaker copy of copy of copy of 1ezx, chain C (#32) with 1oph, chain B
    22477 (#27), sequence alignment score = 997.3 
    22478 RMSD between 122 pruned atom pairs is 0.798 angstroms; (across all 140 pairs:
    22479 2.232) 
    22480  
    22481 
    22482 > view matrix models
    22483 > #27,-0.76366,-0.59209,0.2574,152.81,-0.32869,0.6997,0.63433,106.59,-0.55569,0.39981,-0.72895,190.1
    22484 
    22485 > view matrix models
    22486 > #27,-0.76366,-0.59209,0.2574,153.88,-0.32869,0.6997,0.63433,107.32,-0.55569,0.39981,-0.72895,188.09
    22487 
    22488 > view matrix models
    22489 > #27,-0.83313,-0.43989,0.33525,145.38,-0.083744,0.6995,0.70971,96.368,-0.54671,0.56321,-0.61961,175.22
    22490 
    22491 > view matrix models
    22492 > #27,-0.74236,-0.59158,0.31452,149.59,-0.27194,0.69508,0.66552,104.03,-0.61232,0.40852,-0.67688,185.76
    22493 
    22494 > view matrix models
    22495 > #27,-0.74236,-0.59158,0.31452,149.31,-0.27194,0.69508,0.66552,103.43,-0.61232,0.40852,-0.67688,186.03
    22496 
    22497 > view matrix models
    22498 > #27,-0.74236,-0.59158,0.31452,149.1,-0.27194,0.69508,0.66552,103.48,-0.61232,0.40852,-0.67688,187.73
    22499 
    22500 > view matrix models
    22501 > #27,-0.4433,-0.67999,0.58404,127,-0.43264,0.73295,0.52499,115.4,-0.78505,-0.019955,-0.61911,202.46
    22502 
    22503 > view matrix models
    22504 > #27,-0.4433,-0.67999,0.58404,130.64,-0.43264,0.73295,0.52499,113.63,-0.78505,-0.019955,-0.61911,205.53
    22505 
    22506 > fitmap #27 inMap #29
    22507 
    22508 Fit molecule 1oph (#27) to map J1122.mrc (#29) using 1798 atoms 
    22509 average map value = 0.05116, steps = 68 
    22510 shifted from previous position = 2.69 
    22511 rotated from previous position = 9.17 degrees 
    22512 atoms outside contour = 1446, contour level = 0.070992 
    22513  
    22514 Position of 1oph (#27) relative to J1122.mrc (#29) coordinates: 
    22515 Matrix rotation and translation 
    22516 -0.36812181 -0.63861563 0.67576357 123.53211487 
    22517 -0.32941202 0.76923775 0.54750435 107.83162875 
    22518 -0.86946769 -0.02105634 -0.49354086 197.89559046 
    22519 Axis -0.33937979 0.92236459 0.18456685 
    22520 Axis point 134.62181234 0.00000000 42.50689250 
    22521 Rotation angle (degrees) 123.10755810 
    22522 Shift along axis 94.06073906 
    22523  
    22524 
    22525 > view matrix models
    22526 > #27,0.36598,-0.2092,0.9068,76.029,-0.77877,0.46461,0.42149,137.29,-0.50949,-0.86045,0.0071194,184.16
    22527 
    22528 > view matrix models
    22529 > #27,0.36598,-0.2092,0.9068,76.706,-0.77877,0.46461,0.42149,135.37,-0.50949,-0.86045,0.0071194,183.36
    22530 
    22531 > fitmap #27 inMap #29
    22532 
    22533 Fit molecule 1oph (#27) to map J1122.mrc (#29) using 1798 atoms 
    22534 average map value = 0.05313, steps = 140 
    22535 shifted from previous position = 4.46 
    22536 rotated from previous position = 26.6 degrees 
    22537 atoms outside contour = 1440, contour level = 0.070992 
    22538  
    22539 Position of 1oph (#27) relative to J1122.mrc (#29) coordinates: 
    22540 Matrix rotation and translation 
    22541 0.65758974 -0.02081924 0.75308850 73.16880294 
    22542 -0.73687782 0.19027838 0.64869501 131.74587255 
    22543 -0.15680180 -0.98150940 0.10978387 176.26543706 
    22544 Axis -0.81528498 0.45504717 -0.35810958 
    22545 Axis point 0.00000000 178.61895966 -24.20653672 
    22546 Rotation angle (degrees) 91.21327181 
    22547 Shift along axis -62.82518106 
    22548  
    22549 
    22550 > show #!34 models
    22551 
    22552 > hide #!29 models
    22553 
    22554 > volume #34 level 0.07075
    22555 
    22556 > close #30
    22557 
    22558 > save /Users/apple/Downloads/csparc.cxs includeMaps true
    22559 
    22560 ——— End of log from Tue Jan 6 13:31:49 2026 ———
    22561 
    22562 > view name session-start
    22563 
    22564 opened ChimeraX session 
    22565 
    22566 > hide #!23 models
    22567 
    22568 > select subtract #27
    22569 
    22570 Nothing selected 
    22571 
    22572 > hide #27 models
    22573 
    22574 > hide #!34 models
    22575 
    22576 > show #!8 models
    22577 
    22578 > view
    22579 
    22580 > open 1oph fromDatabase pdb format mmcif
    22581 
    22582 Summary of feedback from opening 1oph fetched from pdb 
    22583 --- 
    22584 note | Fetching compressed mmCIF 1oph from http://files.rcsb.org/download/1oph.cif 
    22585  
    22586 1oph title: 
    22587 Non-covalent complex between α-1-π-pittsburgh and S195A trypsin [more info...] 
    22588  
    22589 Chain information for 1oph #30 
    22590 --- 
    22591 Chain | Description | UniProt 
    22592 A | Alpha-1-antitrypsin precursor | A1AT_HUMAN 1-394 
    22593 B | Trypsinogen, cationic precursor | TRY1_BOVIN -4-245 
    22594  
    22595 1oph mmCIF Assemblies 
    22596 --- 
    22597 1| author_and_software_defined_assembly 
    22598 2| software_defined_assembly 
    22599  
    22600 
    22601 > mmaker #30 to #8
    22602 
    22603 Parameters 
    22604 --- 
    22605 Chain pairing | bb 
    22606 Alignment algorithm | Needleman-Wunsch 
    22607 Similarity matrix | BLOSUM-62 
    22608 SS fraction | 0.3 
    22609 Gap open (HH/SS/other) | 18/18/6 
    22610 Gap extend | 1 
    22611 SS matrix |  |  | H | S | O 
    22612 ---|---|---|--- 
    22613 H | 6 | -9 | -6 
    22614 S |  | 6 | -6 
    22615 O |  |  | 4 
    22616 Iteration cutoff | 2 
    22617  
    22618 Matchmaker 1ezx, chain A (#8) with 1oph, chain A (#30), sequence alignment
    22619 score = 1610.1 
    22620 RMSD between 212 pruned atom pairs is 0.928 angstroms; (across all 335 pairs:
    22621 9.705) 
    22622  
    22623 
    22624 > hide #!8 models
    22625 
    22626 > ui tool show "Show Sequence Viewer"
    22627 
    22628 > sequence chain #30/A
    22629 
    22630 Alignment identifier is 30/A 
    22631 
    22632 > select #30/A:21-22
    22633 
    22634 14 atoms, 14 bonds, 2 residues, 1 model selected 
    22635 
    22636 > select #30/A:21-83
    22637 
    22638 484 atoms, 495 bonds, 63 residues, 1 model selected 
    22639 
    22640 > select #30/A:88
    22641 
    22642 7 atoms, 7 bonds, 1 residue, 1 model selected 
    22643 
    22644 > select #30/A:88-121
    22645 
    22646 263 atoms, 267 bonds, 34 residues, 1 model selected 
    22647 
    22648 > select #30/A:121
    22649 
    22650 6 atoms, 5 bonds, 1 residue, 1 model selected 
    22651 
    22652 > select #30/A:105-121
    22653 
    22654 127 atoms, 128 bonds, 17 residues, 1 model selected 
    22655 
    22656 > select #30/A:88
    22657 
    22658 7 atoms, 7 bonds, 1 residue, 1 model selected 
    22659 
    22660 > select #30/A:88-104
    22661 
    22662 136 atoms, 138 bonds, 17 residues, 1 model selected 
    22663 
    22664 > select #30/A:21-45,88-104
    22665 
    22666 341 atoms, 349 bonds, 42 residues, 1 model selected 
    22667 
    22668 > select #30/A:53
    22669 
    22670 6 atoms, 5 bonds, 1 residue, 1 model selected 
    22671 
    22672 > select #30/A:53-80
    22673 
    22674 196 atoms, 198 bonds, 28 residues, 1 model selected 
    22675 
    22676 > select #30/A:21-45,53-80
    22677 
    22678 401 atoms, 409 bonds, 53 residues, 1 model selected 
    22679 
    22680 > select #30/A:21-45,53-80,88-104
    22681 
    22682 537 atoms, 547 bonds, 70 residues, 1 model selected 
    22683 
    22684 > select #30/A:21-45,53-80,88-104,127-137
    22685 
    22686 622 atoms, 632 bonds, 81 residues, 1 model selected 
    22687 
    22688 > select #30/A:21-45,53-80,88-104,127-137,149-165
    22689 
    22690 747 atoms, 757 bonds, 98 residues, 1 model selected 
    22691 
    22692 > select #30/A:21-45,53-80,88-104,127-137,149-165,199-203
    22693 
    22694 783 atoms, 792 bonds, 103 residues, 1 model selected 
    22695 
    22696 > select #30/A:21-45,53-80,88-104,127-137,149-165,199-203,259-278
    22697 
    22698 954 atoms, 965 bonds, 123 residues, 1 model selected 
    22699 
    22700 > select #30/A:21-45,53-80,88-104,127-137,149-165,199-203,259-278,299-306
    22701 
    22702 1013 atoms, 1023 bonds, 131 residues, 1 model selected 
    22703 
    22704 > select
    22705 > #30/A:21-45,53-80,88-104,127-137,149-165,199-203,259-278,299-306,309-313
    22706 
    22707 1053 atoms, 1063 bonds, 136 residues, 1 model selected 
    22708 
    22709 > select
    22710 > #30/A:21-45,53-80,88-104,127-137,149-165,199-203,259-278,299-306,309-313,349-353
    22711 
    22712 1089 atoms, 1099 bonds, 141 residues, 1 model selected 
    22713 
    22714 > color sel hot pink
    22715 
    22716 > color sel dim gray
    22717 
    22718 > select clear
    22719 
    22720 [Repeated 3 time(s)]
    22721 
    22722 > select #30/A:112
    22723 
    22724 8 atoms, 7 bonds, 1 residue, 1 model selected 
    22725 
    22726 > select #30/A:112-121
    22727 
    22728 71 atoms, 71 bonds, 10 residues, 1 model selected 
    22729 
    22730 > select #30/A:112-121,141-145
    22731 
    22732 110 atoms, 110 bonds, 15 residues, 1 model selected 
    22733 
    22734 > select #30/A:112-121,141-145,182-191
    22735 
    22736 200 atoms, 203 bonds, 25 residues, 1 model selected 
    22737 
    22738 > select #30/A:112-121,141-145,182-191,193-194
    22739 
    22740 219 atoms, 223 bonds, 27 residues, 1 model selected 
    22741 
    22742 > select #30/A:112-121,141-145,182-191,193-194
    22743 
    22744 219 atoms, 223 bonds, 27 residues, 1 model selected 
    22745 
    22746 > select #30/A:112-121,141-145,182-194
    22747 
    22748 223 atoms, 228 bonds, 28 residues, 1 model selected 
    22749 
    22750 > select #30/A:112-121,141-145,182-194,204-211
    22751 
    22752 294 atoms, 300 bonds, 36 residues, 1 model selected 
    22753 
    22754 > select #30/A:112-121,141-145,182-194,204-211,214
    22755 
    22756 301 atoms, 306 bonds, 37 residues, 1 model selected 
    22757 
    22758 > select #30/A:112-121,141-145,182-194,204-211,214
    22759 
    22760 301 atoms, 306 bonds, 37 residues, 1 model selected 
    22761 
    22762 > select #30/A:211
    22763 
    22764 8 atoms, 7 bonds, 1 residue, 1 model selected 
    22765 
    22766 > select #30/A:204-211
    22767 
    22768 71 atoms, 72 bonds, 8 residues, 1 model selected 
    22769 
    22770 > select #30/A:214
    22771 
    22772 7 atoms, 6 bonds, 1 residue, 1 model selected 
    22773 
    22774 > select #30/A:214-232
    22775 
    22776 152 atoms, 154 bonds, 19 residues, 1 model selected 
    22777 
    22778 > select #30/A:282
    22779 
    22780 11 atoms, 10 bonds, 1 residue, 1 model selected 
    22781 
    22782 > select #30/A:282-298
    22783 
    22784 130 atoms, 132 bonds, 17 residues, 1 model selected 
    22785 
    22786 > ui tool show "Show Sequence Viewer"
    22787 
    22788 > sequence chain #8/C #19/C #26/C #32/C
    22789 
    22790 Alignment identifier is 1 
    22791 
    22792 > select add #30
    22793 
    22794 4919 atoms, 4641 bonds, 975 residues, 1 model selected 
    22795 
    22796 > select subtract #30
    22797 
    22798 Nothing selected 
    22799 
    22800 > select #30/A
    22801 
    22802 3121 atoms, 2980 bonds, 578 residues, 1 model selected 
    22803 
    22804 > delete #30/A
    22805 
    22806 > show #!8 models
    22807 
    22808 > close #30
    22809 
    22810 > open 1oph fromDatabase pdb format mmcif
    22811 
    22812 1oph title: 
    22813 Non-covalent complex between α-1-π-pittsburgh and S195A trypsin [more info...] 
    22814  
    22815 Chain information for 1oph #30 
    22816 --- 
    22817 Chain | Description | UniProt 
    22818 A | Alpha-1-antitrypsin precursor | A1AT_HUMAN 1-394 
    22819 B | Trypsinogen, cationic precursor | TRY1_BOVIN -4-245 
    22820  
    22821 1oph mmCIF Assemblies 
    22822 --- 
    22823 1| author_and_software_defined_assembly 
    22824 2| software_defined_assembly 
    22825  
    22826 
    22827 > open 8pi2 fromDatabase pdb format mmcif
    22828 
    22829 Summary of feedback from opening 8pi2 fetched from pdb 
    22830 --- 
    22831 notes | Fetching compressed mmCIF 8pi2 from http://files.rcsb.org/download/8pi2.cif 
    22832 Fetching CCD DMS from
    22833 https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/DMS/DMS.cif 
    22834 Fetching CCD EDO from
    22835 https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/EDO/EDO.cif 
    22836  
    22837 8pi2 title: 
    22838 Native alpha-1-antitrypsin at 1.5 Angstrom (Cys232Ser) [more info...] 
    22839  
    22840 Chain information for 8pi2 #35 
    22841 --- 
    22842 Chain | Description | UniProt 
    22843 A | Alpha-1-antitrypsin | A1AT_HUMAN 2-394 
    22844  
    22845 Non-standard residues in 8pi2 #35 
    22846 --- 
    22847 DMS — dimethyl sulfoxide 
    22848 EDO — 1,2-ethanediol (ethylene glycol) 
    22849 GLY — glycine 
    22850  
    22851 203 atoms have alternate locations. Control/examine alternate locations with
    22852 Altloc Explorer [start tool...] or the altlocs command. 
    22853 2826 atoms have anisotropic B-factors. Depict anisotropic information with
    22854 Thermal Ellipsoids [start tool...] or the aniso command. 
    22855 
    22856 > mmaker #30 to #8
    22857 
    22858 Parameters 
    22859 --- 
    22860 Chain pairing | bb 
    22861 Alignment algorithm | Needleman-Wunsch 
    22862 Similarity matrix | BLOSUM-62 
    22863 SS fraction | 0.3 
    22864 Gap open (HH/SS/other) | 18/18/6 
    22865 Gap extend | 1 
    22866 SS matrix |  |  | H | S | O 
    22867 ---|---|---|--- 
    22868 H | 6 | -9 | -6 
    22869 S |  | 6 | -6 
    22870 O |  |  | 4 
    22871 Iteration cutoff | 2 
    22872  
    22873 Matchmaker 1ezx, chain A (#8) with 1oph, chain A (#30), sequence alignment
    22874 score = 1610.1 
    22875 RMSD between 212 pruned atom pairs is 0.928 angstroms; (across all 335 pairs:
    22876 9.705) 
    22877  
    22878 
    22879 > mmaker #35 to #30
    22880 
    22881 Parameters 
    22882 --- 
    22883 Chain pairing | bb 
    22884 Alignment algorithm | Needleman-Wunsch 
    22885 Similarity matrix | BLOSUM-62 
    22886 SS fraction | 0.3 
    22887 Gap open (HH/SS/other) | 18/18/6 
    22888 Gap extend | 1 
    22889 SS matrix |  |  | H | S | O 
    22890 ---|---|---|--- 
    22891 H | 6 | -9 | -6 
    22892 S |  | 6 | -6 
    22893 O |  |  | 4 
    22894 Iteration cutoff | 2 
    22895  
    22896 Matchmaker 1oph, chain A (#30) with 8pi2, chain A (#35), sequence alignment
    22897 score = 1934.1 
    22898 RMSD between 350 pruned atom pairs is 0.764 angstroms; (across all 371 pairs:
    22899 1.541) 
    22900  
    22901 
    22902 > hide #!8 models
    22903 
    22904 > hide #30 models
    22905 
    22906 > show #30 models
    22907 
    22908 > delete #30/A
    22909 
    22910 > select add #35
    22911 
    22912 5953 atoms, 5684 bonds, 699 residues, 1 model selected 
    22913 
    22914 > hide sel atoms
    22915 
    22916 > select subtract #35
    22917 
    22918 Nothing selected 
    22919 
    22920 > select helix
    22921 
    22922 13863 atoms, 13950 bonds, 1635 residues, 21 models selected 
    22923 
    22924 > select add #30
    22925 
    22926 15472 atoms, 15419 bonds, 2007 residues, 21 models selected 
    22927 
    22928 > select subtract #30
    22929 
    22930 13674 atoms, 13758 bonds, 1610 residues, 20 models selected 
    22931 
    22932 > select add #31
    22933 
    22934 15630 atoms, 15698 bonds, 1919 residues, 20 models selected 
    22935 
    22936 > select subtract #31
    22937 
    22938 12655 atoms, 12730 bonds, 1482 residues, 19 models selected 
    22939 
    22940 > select add #32
    22941 
    22942 15484 atoms, 15547 bonds, 5 pseudobonds, 1928 residues, 21 models selected 
    22943 
    22944 > select subtract #32
    22945 
    22946 11500 atoms, 11565 bonds, 1336 residues, 18 models selected 
    22947 
    22948 > select add #33
    22949 
    22950 14424 atoms, 14571 bonds, 2 pseudobonds, 1724 residues, 20 models selected 
    22951 
    22952 > select subtract #33
    22953 
    22954 11234 atoms, 11301 bonds, 1302 residues, 17 models selected 
    22955 
    22956 > select add #35
    22957 
    22958 15239 atoms, 15031 bonds, 1873 residues, 17 models selected 
    22959 
    22960 > select subtract #35
    22961 
    22962 9286 atoms, 9347 bonds, 1174 residues, 16 models selected 
    22963 
    22964 > select add #27
    22965 
    22966 10895 atoms, 10816 bonds, 1546 residues, 16 models selected 
    22967 
    22968 > select subtract #27
    22969 
    22970 9097 atoms, 9155 bonds, 1149 residues, 15 models selected 
    22971 
    22972 > select add #26
    22973 
    22974 11926 atoms, 11972 bonds, 5 pseudobonds, 1595 residues, 17 models selected 
    22975 
    22976 > select subtract #26
    22977 
    22978 7942 atoms, 7990 bonds, 1003 residues, 14 models selected 
    22979 
    22980 > select add #25
    22981 
    22982 9668 atoms, 9577 bonds, 1377 residues, 14 models selected 
    22983 
    22984 > select subtract #25
    22985 
    22986 7785 atoms, 7832 bonds, 983 residues, 13 models selected 
    22987 
    22988 > select add #24
    22989 
    22990 10709 atoms, 10838 bonds, 2 pseudobonds, 1371 residues, 15 models selected 
    22991 
    22992 > select subtract #24
    22993 
    22994 7519 atoms, 7568 bonds, 949 residues, 12 models selected 
    22995 
    22996 > select add #23
    22997 
    22998 9475 atoms, 9508 bonds, 1258 residues, 12 models selected 
    22999 
    23000 > select subtract #23
    23001 
    23002 6500 atoms, 6540 bonds, 821 residues, 11 models selected 
    23003 
    23004 > select add #20
    23005 
    23006 8226 atoms, 8127 bonds, 1195 residues, 11 models selected 
    23007 
    23008 > select subtract #20
    23009 
    23010 6343 atoms, 6382 bonds, 801 residues, 10 models selected 
    23011 
    23012 > select add #19
    23013 
    23014 9172 atoms, 9199 bonds, 5 pseudobonds, 1247 residues, 12 models selected 
    23015 
    23016 > select subtract #19
    23017 
    23018 5188 atoms, 5217 bonds, 655 residues, 9 models selected 
    23019 
    23020 > select add #18
    23021 
    23022 6914 atoms, 6804 bonds, 1029 residues, 9 models selected 
    23023 
    23024 > select subtract #18
    23025 
    23026 5031 atoms, 5059 bonds, 635 residues, 8 models selected 
    23027 
    23028 > select add #17
    23029 
    23030 7955 atoms, 8065 bonds, 2 pseudobonds, 1023 residues, 10 models selected 
    23031 
    23032 > select subtract #17
    23033 
    23034 4765 atoms, 4795 bonds, 601 residues, 7 models selected 
    23035 
    23036 > select add #16
    23037 
    23038 6721 atoms, 6735 bonds, 910 residues, 7 models selected 
    23039 
    23040 > select subtract #16
    23041 
    23042 3746 atoms, 3767 bonds, 473 residues, 6 models selected 
    23043 
    23044 > select add #8
    23045 
    23046 6575 atoms, 6584 bonds, 5 pseudobonds, 919 residues, 8 models selected 
    23047 
    23048 > select subtract #8
    23049 
    23050 2591 atoms, 2602 bonds, 327 residues, 5 models selected 
    23051 
    23052 > select add #7
    23053 
    23054 4317 atoms, 4189 bonds, 701 residues, 5 models selected 
    23055 
    23056 > select subtract #7
    23057 
    23058 2434 atoms, 2444 bonds, 307 residues, 4 models selected 
    23059 
    23060 > select add #6
    23061 
    23062 5358 atoms, 5450 bonds, 2 pseudobonds, 695 residues, 6 models selected 
    23063 
    23064 > select subtract #6
    23065 
    23066 2168 atoms, 2180 bonds, 273 residues, 3 models selected 
    23067 
    23068 > select #35/A:340
    23069 
    23070 19 atoms, 18 bonds, 1 residue, 1 model selected 
    23071 Drag select of 11 residues 
    23072 
    23073 > select clear
    23074 
    23075 > select #35/A:340
    23076 
    23077 19 atoms, 18 bonds, 1 residue, 1 model selected 
    23078 
    23079 > select #35/A:339
    23080 
    23081 14 atoms, 13 bonds, 1 residue, 1 model selected 
    23082 
    23083 > select #35/A:340
    23084 
    23085 19 atoms, 18 bonds, 1 residue, 1 model selected 
    23086 
    23087 > select add #35/A:339
    23088 
    23089 33 atoms, 31 bonds, 2 residues, 1 model selected 
    23090 
    23091 > select add #35/A:338
    23092 
    23093 52 atoms, 49 bonds, 3 residues, 1 model selected 
    23094 
    23095 > select add #35/A:337
    23096 
    23097 68 atoms, 64 bonds, 4 residues, 1 model selected 
    23098 
    23099 > select add #35/A:336
    23100 
    23101 78 atoms, 73 bonds, 5 residues, 1 model selected 
    23102 
    23103 > select add #35/A:335
    23104 
    23105 99 atoms, 93 bonds, 6 residues, 1 model selected 
    23106 
    23107 > select add #35/A:334
    23108 
    23109 116 atoms, 110 bonds, 7 residues, 1 model selected 
    23110 
    23111 > select add #35/A:333
    23112 
    23113 132 atoms, 125 bonds, 8 residues, 1 model selected 
    23114 
    23115 > select add #35/A:332
    23116 
    23117 142 atoms, 134 bonds, 9 residues, 1 model selected 
    23118 
    23119 > select add #35/A:331
    23120 
    23121 164 atoms, 155 bonds, 10 residues, 1 model selected 
    23122 
    23123 > select add #35/A:191
    23124 
    23125 186 atoms, 176 bonds, 11 residues, 1 model selected 
    23126 
    23127 > select add #35/A:190
    23128 
    23129 206 atoms, 196 bonds, 12 residues, 1 model selected 
    23130 
    23131 > select add #35/A:189
    23132 
    23133 226 atoms, 216 bonds, 13 residues, 1 model selected 
    23134 
    23135 > select add #35/A:188
    23136 
    23137 245 atoms, 234 bonds, 14 residues, 1 model selected 
    23138 
    23139 > select add #35/A:187
    23140 
    23141 266 atoms, 255 bonds, 15 residues, 1 model selected 
    23142 
    23143 > select add #35/A:186
    23144 
    23145 280 atoms, 268 bonds, 16 residues, 1 model selected 
    23146 
    23147 > select add #35/A:185
    23148 
    23149 296 atoms, 283 bonds, 17 residues, 1 model selected 
    23150 
    23151 > select add #35/A:184
    23152 
    23153 315 atoms, 301 bonds, 18 residues, 1 model selected 
    23154 
    23155 > select add #35/A:183
    23156 
    23157 325 atoms, 310 bonds, 19 residues, 1 model selected 
    23158 
    23159 > select add #35/A:182
    23160 
    23161 345 atoms, 330 bonds, 20 residues, 1 model selected 
    23162 
    23163 > select add #35/A:291
    23164 
    23165 364 atoms, 348 bonds, 21 residues, 1 model selected 
    23166 
    23167 > select add #35/A:292
    23168 
    23169 375 atoms, 358 bonds, 22 residues, 1 model selected 
    23170 
    23171 > select add #35/A:293
    23172 
    23173 394 atoms, 376 bonds, 23 residues, 1 model selected 
    23174 
    23175 > select add #35/A:294
    23176 
    23177 408 atoms, 389 bonds, 24 residues, 1 model selected 
    23178 
    23179 > select subtract #35/A:294
    23180 
    23181 394 atoms, 376 bonds, 23 residues, 1 model selected 
    23182 
    23183 > select add #35/A:294
    23184 
    23185 408 atoms, 389 bonds, 24 residues, 1 model selected 
    23186 
    23187 > select add #35/A:295
    23188 
    23189 415 atoms, 395 bonds, 25 residues, 1 model selected 
    23190 
    23191 > select add #35/A:296
    23192 
    23193 429 atoms, 408 bonds, 26 residues, 1 model selected 
    23194 
    23195 > select add #35/A:297
    23196 
    23197 450 atoms, 429 bonds, 27 residues, 1 model selected 
    23198 
    23199 > select add #35/A:298
    23200 
    23201 462 atoms, 440 bonds, 28 residues, 1 model selected 
    23202 
    23203 > select add #35/A:112
    23204 
    23205 481 atoms, 458 bonds, 29 residues, 1 model selected 
    23206 
    23207 > select add #35/A:113
    23208 
    23209 495 atoms, 471 bonds, 30 residues, 1 model selected 
    23210 
    23211 > select add #35/A:114
    23212 
    23213 509 atoms, 484 bonds, 31 residues, 1 model selected 
    23214 
    23215 > select add #35/A:115
    23216 
    23217 516 atoms, 490 bonds, 32 residues, 1 model selected 
    23218 
    23219 > select add #35/A:116
    23220 
    23221 530 atoms, 503 bonds, 33 residues, 1 model selected 
    23222 
    23223 > select add #35/A:117
    23224 
    23225 537 atoms, 509 bonds, 34 residues, 1 model selected 
    23226 
    23227 > select add #35/A:118
    23228 
    23229 556 atoms, 527 bonds, 35 residues, 1 model selected 
    23230 
    23231 > select add #35/A:119
    23232 
    23233 576 atoms, 547 bonds, 36 residues, 1 model selected 
    23234 
    23235 > select add #35/A:120
    23236 
    23237 595 atoms, 565 bonds, 37 residues, 1 model selected 
    23238 
    23239 > select add #35/A:121
    23240 
    23241 606 atoms, 575 bonds, 38 residues, 1 model selected 
    23242 
    23243 > select add #35/A:141
    23244 
    23245 621 atoms, 589 bonds, 39 residues, 1 model selected 
    23246 
    23247 > select add #35/A:142
    23248 
    23249 631 atoms, 598 bonds, 40 residues, 1 model selected 
    23250 
    23251 > select add #35/A:143
    23252 
    23253 651 atoms, 618 bonds, 41 residues, 1 model selected 
    23254 
    23255 > select add #35/A:144
    23256 
    23257 665 atoms, 631 bonds, 42 residues, 1 model selected 
    23258 
    23259 > select add #35/A:145
    23260 
    23261 681 atoms, 646 bonds, 43 residues, 1 model selected 
    23262 
    23263 > color sel forest green
    23264 
    23265 > color sel lime
    23266 
    23267 > select clear
    23268 
    23269 > select add #35/A:341
    23270 
    23271 12 atoms, 11 bonds, 1 residue, 1 model selected 
    23272 
    23273 > select add #35/A:342
    23274 
    23275 27 atoms, 25 bonds, 2 residues, 1 model selected 
    23276 
    23277 > select add #35/A:343
    23278 
    23279 40 atoms, 37 bonds, 3 residues, 1 model selected 
    23280 
    23281 > select add #35/A:344
    23282 
    23283 47 atoms, 43 bonds, 4 residues, 1 model selected 
    23284 
    23285 > select add #35/A:345
    23286 
    23287 61 atoms, 56 bonds, 5 residues, 1 model selected 
    23288 
    23289 > select add #35/A:193
    23290 
    23291 83 atoms, 77 bonds, 6 residues, 1 model selected 
    23292 
    23293 > select subtract #35/A:193
    23294 
    23295 61 atoms, 56 bonds, 5 residues, 1 model selected 
    23296 
    23297 > select add #35/A:346
    23298 
    23299 68 atoms, 62 bonds, 6 residues, 1 model selected 
    23300 
    23301 > select add #35/A:347
    23302 
    23303 78 atoms, 71 bonds, 7 residues, 1 model selected 
    23304 
    23305 > select add #35/A:348
    23306 
    23307 88 atoms, 80 bonds, 8 residues, 1 model selected 
    23308 
    23309 > select add #35/A:349
    23310 
    23311 95 atoms, 86 bonds, 9 residues, 1 model selected 
    23312 
    23313 > select add #35/A:350
    23314 
    23315 105 atoms, 95 bonds, 10 residues, 1 model selected 
    23316 
    23317 > select add #35/A:351
    23318 
    23319 112 atoms, 101 bonds, 11 residues, 1 model selected 
    23320 
    23321 > select add #35/A:352
    23322 
    23323 132 atoms, 121 bonds, 12 residues, 1 model selected 
    23324 
    23325 > select add #35/A:353
    23326 
    23327 151 atoms, 139 bonds, 13 residues, 1 model selected 
    23328 
    23329 > select add #35/A:354
    23330 
    23331 166 atoms, 153 bonds, 14 residues, 1 model selected 
    23332 
    23333 > select add #35/A:355
    23334 
    23335 176 atoms, 162 bonds, 15 residues, 1 model selected 
    23336 
    23337 > select add #35/A:356
    23338 
    23339 195 atoms, 180 bonds, 16 residues, 1 model selected 
    23340 
    23341 > select add #35/A:357
    23342 
    23343 209 atoms, 194 bonds, 17 residues, 1 model selected 
    23344 
    23345 > select add #35/A:358
    23346 
    23347 226 atoms, 210 bonds, 18 residues, 1 model selected 
    23348 
    23349 > select add #35/A:359
    23350 
    23351 237 atoms, 220 bonds, 19 residues, 1 model selected 
    23352 
    23353 > select add #35/A:360
    23354 
    23355 256 atoms, 238 bonds, 20 residues, 1 model selected 
    23356 
    23357 > select add #35/A:361
    23358 
    23359 270 atoms, 252 bonds, 21 residues, 1 model selected 
    23360 
    23361 > select add #35/A:362
    23362 
    23363 284 atoms, 266 bonds, 22 residues, 1 model selected 
    23364 
    23365 > select add #35/A:363
    23366 
    23367 299 atoms, 280 bonds, 23 residues, 1 model selected 
    23368 
    23369 > select subtract #35/A:363
    23370 
    23371 284 atoms, 266 bonds, 22 residues, 1 model selected 
    23372 
    23373 > color sel red
    23374 
    23375 > select clear
    23376 
    23377 > select add #35/A:363
    23378 
    23379 15 atoms, 14 bonds, 1 residue, 1 model selected 
    23380 
    23381 > select add #35/A:364
    23382 
    23383 31 atoms, 29 bonds, 2 residues, 1 model selected 
    23384 
    23385 > select add #35/A:365
    23386 
    23387 53 atoms, 50 bonds, 3 residues, 1 model selected 
    23388 
    23389 > select add #35/A:282
    23390 
    23391 77 atoms, 73 bonds, 4 residues, 1 model selected 
    23392 
    23393 > select add #35/A:283
    23394 
    23395 88 atoms, 83 bonds, 5 residues, 1 model selected 
    23396 
    23397 > select add #35/A:284
    23398 
    23399 98 atoms, 92 bonds, 6 residues, 1 model selected 
    23400 
    23401 > select add #35/A:285
    23402 
    23403 109 atoms, 102 bonds, 7 residues, 1 model selected 
    23404 
    23405 > select add #35/A:286
    23406 
    23407 128 atoms, 120 bonds, 8 residues, 1 model selected 
    23408 
    23409 > select add #35/A:287
    23410 
    23411 146 atoms, 138 bonds, 9 residues, 1 model selected 
    23412 
    23413 > select add #35/A:288
    23414 
    23415 165 atoms, 156 bonds, 10 residues, 1 model selected 
    23416 
    23417 > select add #35/A:289
    23418 
    23419 179 atoms, 170 bonds, 11 residues, 1 model selected 
    23420 
    23421 > select add #35/A:224
    23422 
    23423 198 atoms, 188 bonds, 12 residues, 1 model selected 
    23424 
    23425 > select add #35/A:223
    23426 
    23427 222 atoms, 211 bonds, 13 residues, 1 model selected 
    23428 
    23429 > select add #35/A:222
    23430 
    23431 244 atoms, 232 bonds, 14 residues, 1 model selected 
    23432 
    23433 > select add #35/A:221
    23434 
    23435 261 atoms, 248 bonds, 15 residues, 1 model selected 
    23436 
    23437 > select add #35/A:220
    23438 
    23439 278 atoms, 264 bonds, 16 residues, 1 model selected 
    23440 
    23441 > select add #35/A:219
    23442 
    23443 292 atoms, 278 bonds, 17 residues, 1 model selected 
    23444 
    23445 > select add #35/A:218
    23446 
    23447 308 atoms, 293 bonds, 18 residues, 1 model selected 
    23448 
    23449 > select add #35/A:217
    23450 
    23451 330 atoms, 314 bonds, 19 residues, 1 model selected 
    23452 
    23453 > select add #35/A:216
    23454 
    23455 346 atoms, 329 bonds, 20 residues, 1 model selected 
    23456 
    23457 > select add #35/A:215
    23458 
    23459 360 atoms, 342 bonds, 21 residues, 1 model selected 
    23460 
    23461 > select add #35/A:214
    23462 
    23463 374 atoms, 355 bonds, 22 residues, 1 model selected 
    23464 
    23465 > select add #35/A:204
    23466 
    23467 389 atoms, 369 bonds, 23 residues, 1 model selected 
    23468 
    23469 > select add #35/A:205
    23470 
    23471 404 atoms, 383 bonds, 24 residues, 1 model selected 
    23472 
    23473 > select add #35/A:206
    23474 
    23475 419 atoms, 397 bonds, 25 residues, 1 model selected 
    23476 
    23477 > select subtract #35/A:206
    23478 
    23479 404 atoms, 383 bonds, 24 residues, 1 model selected 
    23480 
    23481 > select add #35/A:207
    23482 
    23483 416 atoms, 394 bonds, 25 residues, 1 model selected 
    23484 
    23485 > select add #35/A:206
    23486 
    23487 431 atoms, 408 bonds, 26 residues, 1 model selected 
    23488 
    23489 > select add #35/A:208
    23490 
    23491 451 atoms, 428 bonds, 27 residues, 1 model selected 
    23492 
    23493 > select add #35/A:209
    23494 
    23495 468 atoms, 445 bonds, 28 residues, 1 model selected 
    23496 
    23497 > select add #35/A:210
    23498 
    23499 484 atoms, 460 bonds, 29 residues, 1 model selected 
    23500 
    23501 > select add #35/A:211
    23502 
    23503 496 atoms, 471 bonds, 30 residues, 1 model selected 
    23504 
    23505 > color sel light sea green
    23506 
    23507 > color sel blue
    23508 
    23509 > color sel cornflower blue
    23510 
    23511 > select clear
    23512 
    23513 > select add #35/A:228
    23514 
    23515 14 atoms, 13 bonds, 1 residue, 1 model selected 
    23516 
    23517 > select add #35/A:229
    23518 
    23519 33 atoms, 31 bonds, 2 residues, 1 model selected 
    23520 
    23521 > select add #35/A:230
    23522 
    23523 50 atoms, 47 bonds, 3 residues, 1 model selected 
    23524 
    23525 > select add #35/A:231
    23526 
    23527 67 atoms, 64 bonds, 4 residues, 1 model selected 
    23528 
    23529 > select add #35/A:232
    23530 
    23531 78 atoms, 74 bonds, 5 residues, 1 model selected 
    23532 
    23533 > select add #35/A:237
    23534 
    23535 89 atoms, 84 bonds, 6 residues, 1 model selected 
    23536 
    23537 > select add #35/A:238
    23538 
    23539 113 atoms, 109 bonds, 7 residues, 1 model selected 
    23540 
    23541 > select add #35/A:239
    23542 
    23543 129 atoms, 124 bonds, 8 residues, 1 model selected 
    23544 
    23545 > select add #35/A:240
    23546 
    23547 148 atoms, 142 bonds, 9 residues, 1 model selected 
    23548 
    23549 > select add #35/A:241
    23550 
    23551 167 atoms, 160 bonds, 10 residues, 1 model selected 
    23552 
    23553 > select add #35/A:242
    23554 
    23555 184 atoms, 176 bonds, 11 residues, 1 model selected 
    23556 
    23557 > select add #35/A:243
    23558 
    23559 200 atoms, 191 bonds, 12 residues, 1 model selected 
    23560 
    23561 > select add #35/A:244
    23562 
    23563 221 atoms, 212 bonds, 13 residues, 1 model selected 
    23564 
    23565 > select add #35/A:248
    23566 
    23567 231 atoms, 221 bonds, 14 residues, 1 model selected 
    23568 
    23569 > select add #35/A:249
    23570 
    23571 245 atoms, 234 bonds, 15 residues, 1 model selected 
    23572 
    23573 > select add #35/A:250
    23574 
    23575 255 atoms, 243 bonds, 16 residues, 1 model selected 
    23576 
    23577 > select add #35/A:251
    23578 
    23579 274 atoms, 261 bonds, 17 residues, 1 model selected 
    23580 
    23581 > select add #35/A:252
    23582 
    23583 294 atoms, 281 bonds, 18 residues, 1 model selected 
    23584 
    23585 > select add #35/A:253
    23586 
    23587 314 atoms, 301 bonds, 19 residues, 1 model selected 
    23588 
    23589 > select add #35/A:254
    23590 
    23591 333 atoms, 319 bonds, 20 residues, 1 model selected 
    23592 
    23593 > select add #35/A:255
    23594 
    23595 347 atoms, 333 bonds, 21 residues, 1 model selected 
    23596 
    23597 > select add #35/A:247
    23598 
    23599 361 atoms, 346 bonds, 22 residues, 1 model selected 
    23600 
    23601 > select add #35/A:246
    23602 
    23603 368 atoms, 352 bonds, 23 residues, 1 model selected 
    23604 
    23605 > select add #35/A:245
    23606 
    23607 387 atoms, 370 bonds, 24 residues, 1 model selected 
    23608 
    23609 > select add #35/A:376
    23610 
    23611 402 atoms, 384 bonds, 25 residues, 1 model selected 
    23612 
    23613 > select add #35/A:375
    23614 
    23615 421 atoms, 402 bonds, 26 residues, 1 model selected 
    23616 
    23617 > select add #35/A:374
    23618 
    23619 438 atoms, 418 bonds, 27 residues, 1 model selected 
    23620 
    23621 > select add #35/A:373
    23622 
    23623 457 atoms, 436 bonds, 28 residues, 1 model selected 
    23624 
    23625 > select add #35/A:372
    23626 
    23627 477 atoms, 456 bonds, 29 residues, 1 model selected 
    23628 
    23629 > select add #35/A:371
    23630 
    23631 493 atoms, 471 bonds, 30 residues, 1 model selected 
    23632 
    23633 > select add #35/A:370
    23634 
    23635 513 atoms, 491 bonds, 31 residues, 1 model selected 
    23636 
    23637 > select add #35/A:388
    23638 
    23639 529 atoms, 506 bonds, 32 residues, 1 model selected 
    23640 
    23641 > select add #35/A:387
    23642 
    23643 551 atoms, 527 bonds, 33 residues, 1 model selected 
    23644 
    23645 > select add #35/A:386
    23646 
    23647 558 atoms, 533 bonds, 34 residues, 1 model selected 
    23648 
    23649 > select add #35/A:385
    23650 
    23651 575 atoms, 549 bonds, 35 residues, 1 model selected 
    23652 
    23653 > select add #35/A:384
    23654 
    23655 595 atoms, 569 bonds, 36 residues, 1 model selected 
    23656 
    23657 > select add #35/A:383
    23658 
    23659 614 atoms, 587 bonds, 37 residues, 1 model selected 
    23660 
    23661 > select add #35/A:382
    23662 
    23663 628 atoms, 601 bonds, 38 residues, 1 model selected 
    23664 
    23665 > select add #35/A:50
    23666 
    23667 647 atoms, 619 bonds, 39 residues, 1 model selected 
    23668 
    23669 > select add #35/A:51
    23670 
    23671 667 atoms, 639 bonds, 40 residues, 1 model selected 
    23672 
    23673 > select add #35/A:52
    23674 
    23675 687 atoms, 659 bonds, 41 residues, 1 model selected 
    23676 
    23677 > select add #35/A:227
    23678 
    23679 707 atoms, 679 bonds, 42 residues, 1 model selected 
    23680 
    23681 > color sel yellow
    23682 
    23683 > select clear
    23684 
    23685 > select add #35/A:225
    23686 
    23687 7 atoms, 6 bonds, 1 residue, 1 model selected 
    23688 
    23689 > color sel cornflower blue
    23690 
    23691 > select clear
    23692 
    23693 > select add #35/A:226
    23694 
    23695 17 atoms, 16 bonds, 1 residue, 1 model selected 
    23696 
    23697 > color sel cornflower blue
    23698 
    23699 > select clear
    23700 
    23701 [Repeated 1 time(s)]
    23702 
    23703 > select add #35/A:165
    23704 
    23705 14 atoms, 13 bonds, 1 residue, 1 model selected 
    23706 
    23707 > select add #35/A:163
    23708 
    23709 27 atoms, 25 bonds, 2 residues, 1 model selected 
    23710 
    23711 > select add #35/A:162
    23712 
    23713 42 atoms, 39 bonds, 3 residues, 1 model selected 
    23714 
    23715 > select add #35/A:164
    23716 
    23717 49 atoms, 45 bonds, 4 residues, 1 model selected 
    23718 
    23719 > select add #35/A:161
    23720 
    23721 65 atoms, 60 bonds, 5 residues, 1 model selected 
    23722 
    23723 > select add #35/A:160
    23724 
    23725 86 atoms, 81 bonds, 6 residues, 1 model selected 
    23726 
    23727 > select add #35/A:159
    23728 
    23729 98 atoms, 92 bonds, 7 residues, 1 model selected 
    23730 
    23731 > select add #35/A:158
    23732 
    23733 112 atoms, 105 bonds, 8 residues, 1 model selected 
    23734 
    23735 > select add #35/A:157
    23736 
    23737 131 atoms, 123 bonds, 9 residues, 1 model selected 
    23738 
    23739 > select add #35/A:155
    23740 
    23741 153 atoms, 144 bonds, 10 residues, 1 model selected 
    23742 
    23743 > select add #35/A:156
    23744 
    23745 170 atoms, 160 bonds, 11 residues, 1 model selected 
    23746 
    23747 > select add #35/A:154
    23748 
    23749 192 atoms, 181 bonds, 12 residues, 1 model selected 
    23750 
    23751 > select add #35/A:153
    23752 
    23753 202 atoms, 190 bonds, 13 residues, 1 model selected 
    23754 
    23755 > select add #35/A:152
    23756 
    23757 217 atoms, 204 bonds, 14 residues, 1 model selected 
    23758 
    23759 > select add #35/A:151
    23760 
    23761 232 atoms, 218 bonds, 15 residues, 1 model selected 
    23762 
    23763 > select add #35/A:150
    23764 
    23765 246 atoms, 231 bonds, 16 residues, 1 model selected 
    23766 
    23767 > select add #35/A:149
    23768 
    23769 258 atoms, 242 bonds, 17 residues, 1 model selected 
    23770 
    23771 > select add #35/A:336
    23772 
    23773 268 atoms, 251 bonds, 18 residues, 1 model selected 
    23774 
    23775 > select subtract #35/A:336
    23776 
    23777 258 atoms, 242 bonds, 17 residues, 1 model selected 
    23778 
    23779 > select add #35/A:166
    23780 
    23781 275 atoms, 258 bonds, 18 residues, 1 model selected 
    23782 
    23783 > select add #35/A:167
    23784 
    23785 282 atoms, 264 bonds, 19 residues, 1 model selected 
    23786 
    23787 > select add #35/A:168
    23788 
    23789 292 atoms, 273 bonds, 20 residues, 1 model selected 
    23790 
    23791 > select add #35/A:169
    23792 
    23793 311 atoms, 291 bonds, 21 residues, 1 model selected 
    23794 
    23795 > select add #35/A:170
    23796 
    23797 327 atoms, 306 bonds, 22 residues, 1 model selected 
    23798 
    23799 > select add #35/A:171
    23800 
    23801 339 atoms, 317 bonds, 23 residues, 1 model selected 
    23802 
    23803 > select add #35/A:172
    23804 
    23805 358 atoms, 335 bonds, 24 residues, 1 model selected 
    23806 
    23807 > select add #35/A:173
    23808 
    23809 374 atoms, 350 bonds, 25 residues, 1 model selected 
    23810 
    23811 > select add #35/A:174
    23812 
    23813 396 atoms, 371 bonds, 26 residues, 1 model selected 
    23814 
    23815 > select add #35/A:175
    23816 
    23817 406 atoms, 380 bonds, 27 residues, 1 model selected 
    23818 
    23819 > select add #35/A:176
    23820 
    23821 425 atoms, 398 bonds, 28 residues, 1 model selected 
    23822 
    23823 > select add #35/A:177
    23824 
    23825 432 atoms, 404 bonds, 29 residues, 1 model selected 
    23826 
    23827 > select add #35/A:178
    23828 
    23829 439 atoms, 410 bonds, 30 residues, 1 model selected 
    23830 
    23831 > select add #35/A:179
    23832 
    23833 446 atoms, 416 bonds, 31 residues, 1 model selected 
    23834 
    23835 > select add #35/A:180
    23836 
    23837 460 atoms, 429 bonds, 32 residues, 1 model selected 
    23838 
    23839 > select add #35/A:181
    23840 
    23841 476 atoms, 444 bonds, 33 residues, 1 model selected 
    23842 
    23843 > select add #35
    23844 
    23845 5953 atoms, 5684 bonds, 699 residues, 1 model selected 
    23846 
    23847 > select subtract #35
    23848 
    23849 Nothing selected 
    23850 
    23851 > color #35 #bbb0abff
    23852 
    23853 > color #35 #bbb8b6ff
    23854 
    23855 > select add #35/A:340
    23856 
    23857 19 atoms, 18 bonds, 1 residue, 1 model selected 
    23858 
    23859 > select add #35/A:339
    23860 
    23861 33 atoms, 31 bonds, 2 residues, 1 model selected 
    23862 
    23863 > select add #35/A:338
    23864 
    23865 52 atoms, 49 bonds, 3 residues, 1 model selected 
    23866 
    23867 > select add #35/A:337
    23868 
    23869 68 atoms, 64 bonds, 4 residues, 1 model selected 
    23870 
    23871 > select add #35/A:336
    23872 
    23873 78 atoms, 73 bonds, 5 residues, 1 model selected 
    23874 
    23875 > select add #35/A:335
    23876 
    23877 99 atoms, 93 bonds, 6 residues, 1 model selected 
    23878 
    23879 > select add #35/A:334
    23880 
    23881 116 atoms, 110 bonds, 7 residues, 1 model selected 
    23882 
    23883 > select add #35/A:333
    23884 
    23885 132 atoms, 125 bonds, 8 residues, 1 model selected 
    23886 
    23887 > select add #35/A:332
    23888 
    23889 142 atoms, 134 bonds, 9 residues, 1 model selected 
    23890 
    23891 > select add #35/A:331
    23892 
    23893 164 atoms, 155 bonds, 10 residues, 1 model selected 
    23894 
    23895 > select add #35/A:291
    23896 
    23897 183 atoms, 173 bonds, 11 residues, 1 model selected 
    23898 
    23899 > select add #35/A:292
    23900 
    23901 194 atoms, 183 bonds, 12 residues, 1 model selected 
    23902 
    23903 > select add #35/A:293
    23904 
    23905 213 atoms, 201 bonds, 13 residues, 1 model selected 
    23906 
    23907 > select add #35/A:294
    23908 
    23909 227 atoms, 214 bonds, 14 residues, 1 model selected 
    23910 
    23911 > select add #35/A:295
    23912 
    23913 234 atoms, 220 bonds, 15 residues, 1 model selected 
    23914 
    23915 > select add #35/A:296
    23916 
    23917 248 atoms, 233 bonds, 16 residues, 1 model selected 
    23918 
    23919 > select add #35/A:297
    23920 
    23921 269 atoms, 254 bonds, 17 residues, 1 model selected 
    23922 
    23923 > select add #35/A:298
    23924 
    23925 281 atoms, 265 bonds, 18 residues, 1 model selected 
    23926 
    23927 > select add #35/A:191
    23928 
    23929 303 atoms, 286 bonds, 19 residues, 1 model selected 
    23930 
    23931 > select add #35/A:190
    23932 
    23933 323 atoms, 306 bonds, 20 residues, 1 model selected 
    23934 
    23935 > select add #35/A:189
    23936 
    23937 343 atoms, 326 bonds, 21 residues, 1 model selected 
    23938 
    23939 > select add #35/A:188
    23940 
    23941 362 atoms, 344 bonds, 22 residues, 1 model selected 
    23942 
    23943 > select add #35/A:187
    23944 
    23945 383 atoms, 365 bonds, 23 residues, 1 model selected 
    23946 
    23947 > select add #35/A:186
    23948 
    23949 397 atoms, 378 bonds, 24 residues, 1 model selected 
    23950 
    23951 > select add #35/A:185
    23952 
    23953 413 atoms, 393 bonds, 25 residues, 1 model selected 
    23954 
    23955 > select add #35/A:184
    23956 
    23957 432 atoms, 411 bonds, 26 residues, 1 model selected 
    23958 
    23959 > select add #35/A:183
    23960 
    23961 442 atoms, 420 bonds, 27 residues, 1 model selected 
    23962 
    23963 > select add #35/A:182
    23964 
    23965 462 atoms, 440 bonds, 28 residues, 1 model selected 
    23966 
    23967 > select add #35/A:121
    23968 
    23969 473 atoms, 450 bonds, 29 residues, 1 model selected 
    23970 
    23971 > select add #35/A:120
    23972 
    23973 492 atoms, 468 bonds, 30 residues, 1 model selected 
    23974 
    23975 > select add #35/A:119
    23976 
    23977 512 atoms, 488 bonds, 31 residues, 1 model selected 
    23978 
    23979 > select add #35/A:118
    23980 
    23981 531 atoms, 506 bonds, 32 residues, 1 model selected 
    23982 
    23983 > select add #35/A:117
    23984 
    23985 538 atoms, 512 bonds, 33 residues, 1 model selected 
    23986 
    23987 > select add #35/A:116
    23988 
    23989 552 atoms, 525 bonds, 34 residues, 1 model selected 
    23990 
    23991 > select add #35/A:115
    23992 
    23993 559 atoms, 531 bonds, 35 residues, 1 model selected 
    23994 
    23995 > select add #35/A:114
    23996 
    23997 573 atoms, 544 bonds, 36 residues, 1 model selected 
    23998 
    23999 > select add #35/A:113
    24000 
    24001 587 atoms, 557 bonds, 37 residues, 1 model selected 
    24002 
    24003 > select add #35/A:112
    24004 
    24005 606 atoms, 575 bonds, 38 residues, 1 model selected 
    24006 
    24007 > select add #35/A:141
    24008 
    24009 621 atoms, 589 bonds, 39 residues, 1 model selected 
    24010 
    24011 > select add #35/A:142
    24012 
    24013 631 atoms, 598 bonds, 40 residues, 1 model selected 
    24014 
    24015 > select add #35/A:143
    24016 
    24017 651 atoms, 618 bonds, 41 residues, 1 model selected 
    24018 
    24019 > select add #35/A:144
    24020 
    24021 665 atoms, 631 bonds, 42 residues, 1 model selected 
    24022 
    24023 > select add #35/A:145
    24024 
    24025 681 atoms, 646 bonds, 43 residues, 1 model selected 
    24026 
    24027 > color sel light sea green
    24028 
    24029 > color sel lime
    24030 
    24031 > select clear
    24032 
    24033 > select add #35/A:341
    24034 
    24035 12 atoms, 11 bonds, 1 residue, 1 model selected 
    24036 
    24037 > select add #35/A:342
    24038 
    24039 27 atoms, 25 bonds, 2 residues, 1 model selected 
    24040 
    24041 > select add #35/A:343
    24042 
    24043 40 atoms, 37 bonds, 3 residues, 1 model selected 
    24044 
    24045 > select add #35/A:344
    24046 
    24047 47 atoms, 43 bonds, 4 residues, 1 model selected 
    24048 
    24049 > select add #35/A:345
    24050 
    24051 61 atoms, 56 bonds, 5 residues, 1 model selected 
    24052 
    24053 > select add #35/A:346
    24054 
    24055 68 atoms, 62 bonds, 6 residues, 1 model selected 
    24056 
    24057 > select add #35/A:347
    24058 
    24059 78 atoms, 71 bonds, 7 residues, 1 model selected 
    24060 
    24061 > select add #35/A:348
    24062 
    24063 88 atoms, 80 bonds, 8 residues, 1 model selected 
    24064 
    24065 > select add #35/A:349
    24066 
    24067 95 atoms, 86 bonds, 9 residues, 1 model selected 
    24068 
    24069 > select add #35/A:350
    24070 
    24071 105 atoms, 95 bonds, 10 residues, 1 model selected 
    24072 
    24073 > select add #35/A:351
    24074 
    24075 112 atoms, 101 bonds, 11 residues, 1 model selected 
    24076 
    24077 > select add #35/A:352
    24078 
    24079 132 atoms, 121 bonds, 12 residues, 1 model selected 
    24080 
    24081 > select add #35/A:353
    24082 
    24083 151 atoms, 139 bonds, 13 residues, 1 model selected 
    24084 
    24085 > select add #35/A:354
    24086 
    24087 166 atoms, 153 bonds, 14 residues, 1 model selected 
    24088 
    24089 > select add #35/A:355
    24090 
    24091 176 atoms, 162 bonds, 15 residues, 1 model selected 
    24092 
    24093 > select add #35/A:356
    24094 
    24095 195 atoms, 180 bonds, 16 residues, 1 model selected 
    24096 
    24097 > select add #35/A:357
    24098 
    24099 209 atoms, 194 bonds, 17 residues, 1 model selected 
    24100 
    24101 > select add #35/A:358
    24102 
    24103 226 atoms, 210 bonds, 18 residues, 1 model selected 
    24104 
    24105 > select add #35/A:359
    24106 
    24107 237 atoms, 220 bonds, 19 residues, 1 model selected 
    24108 
    24109 > select add #35/A:360
    24110 
    24111 256 atoms, 238 bonds, 20 residues, 1 model selected 
    24112 
    24113 > select add #35/A:361
    24114 
    24115 270 atoms, 252 bonds, 21 residues, 1 model selected 
    24116 
    24117 > select add #35/A:362
    24118 
    24119 284 atoms, 266 bonds, 22 residues, 1 model selected 
    24120 
    24121 > color sel red
    24122 
    24123 > select clear
    24124 
    24125 > select add #35/A:165
    24126 
    24127 14 atoms, 13 bonds, 1 residue, 1 model selected 
    24128 
    24129 > select add #35/A:164
    24130 
    24131 21 atoms, 19 bonds, 2 residues, 1 model selected 
    24132 
    24133 > select add #35/A:163
    24134 
    24135 34 atoms, 31 bonds, 3 residues, 1 model selected 
    24136 
    24137 > select add #35/A:162
    24138 
    24139 49 atoms, 45 bonds, 4 residues, 1 model selected 
    24140 
    24141 > select add #35/A:161
    24142 
    24143 65 atoms, 60 bonds, 5 residues, 1 model selected 
    24144 
    24145 > select add #35/A:160
    24146 
    24147 86 atoms, 81 bonds, 6 residues, 1 model selected 
    24148 
    24149 > select add #35/A:159
    24150 
    24151 98 atoms, 92 bonds, 7 residues, 1 model selected 
    24152 
    24153 > select add #35/A:158
    24154 
    24155 112 atoms, 105 bonds, 8 residues, 1 model selected 
    24156 
    24157 > select add #35/A:157
    24158 
    24159 131 atoms, 123 bonds, 9 residues, 1 model selected 
    24160 
    24161 > select add #35/A:156
    24162 
    24163 148 atoms, 139 bonds, 10 residues, 1 model selected 
    24164 
    24165 > select add #35/A:155
    24166 
    24167 170 atoms, 160 bonds, 11 residues, 1 model selected 
    24168 
    24169 > select add #35/A:154
    24170 
    24171 192 atoms, 181 bonds, 12 residues, 1 model selected 
    24172 
    24173 > select add #35/A:153
    24174 
    24175 202 atoms, 190 bonds, 13 residues, 1 model selected 
    24176 
    24177 > select add #35/A:152
    24178 
    24179 217 atoms, 204 bonds, 14 residues, 1 model selected 
    24180 
    24181 > select add #35/A:151
    24182 
    24183 232 atoms, 218 bonds, 15 residues, 1 model selected 
    24184 
    24185 > select add #35/A:150
    24186 
    24187 246 atoms, 231 bonds, 16 residues, 1 model selected 
    24188 
    24189 > select add #35/A:149
    24190 
    24191 258 atoms, 242 bonds, 17 residues, 1 model selected 
    24192 
    24193 > color sel magenta
    24194 
    24195 > select clear
    24196 
    24197 [Repeated 1 time(s)]
    24198 
    24199 > color #30 #bcc7ceff
    24200 
    24201 > color #30 #67c7ceff
    24202 
    24203 > color #30 #0cc5ceff
    24204 
    24205 > color #30 #07ce85ff
    24206 
    24207 > color #30 #10ccceff
    24208 
    24209 > color #30 #016fceff
    24210 
    24211 > select #30/B:195
    24212 
    24213 5 atoms, 4 bonds, 1 residue, 1 model selected 
    24214 
    24215 > show sel atoms
    24216 
    24217 > hide sel atoms
    24218 
    24219 > swapp S
    24220 
    24221 Unknown command: swapp S 
    24222 
    24223 > delete #30/A swapaa S
    24224 
    24225 Expected a keyword 
    24226 
    24227 > swapaa #30/B:195 ser
    24228 
    24229 Using Dunbrack library 
    24230 1oph #30/B ALA 195: phi -47.1, psi 140.5 trans 
    24231 Density criteria with multiple volume models open; 
    24232 Need to specify one to use via 'density' keyword. 
    24233 
    24234 > ui tool show Rotamers
    24235 
    24236 Populating font family aliases took 55 ms. Replace uses of missing font family
    24237 "Times" with one that exists to avoid this cost. 
    24238 
    24239 > select #30/B:195
    24240 
    24241 5 atoms, 4 bonds, 1 residue, 1 model selected 
    24242 
    24243 > ui tool show Rotamers
    24244 
    24245 > swapaa interactive sel SER rotLib Dunbrack
    24246 
    24247 1oph #30/B ALA 195: phi -47.1, psi 140.5 trans 
    24248 Changed 9 bond radii 
    24249 No rotamers selected. Click the 'Calculate' button (not 'OK') to add a column
    24250 to the table. 
    24251 
    24252 > undo
    24253 
    24254 [Repeated 2 time(s)]
    24255 
    24256 > ui tool show Rotamers
    24257 
    24258 > swapaa interactive sel SER rotLib Dunbrack
    24259 
    24260 1oph #!30/B ALA 195: phi -47.1, psi 140.5 trans 
    24261 Changed 9 bond radii 
    24262 
    24263 > swapaa #!30/B:195 SER criteria 3 rotLib Dunbrack
    24264 
    24265 Using Dunbrack library 
    24266 1oph #!30/B ALA 195: phi -47.1, psi 140.5 trans 
    24267 Applying SER rotamer (chi angles: 64.0) to 1oph #!30/B SER 195 
    24268 
    24269 > hide sel atoms
    24270 
    24271 [Repeated 2 time(s)]
    24272 
    24273 > select #30/B:195
    24274 
    24275 6 atoms, 5 bonds, 1 residue, 1 model selected 
    24276 
    24277 > select #30/B:195
    24278 
    24279 6 atoms, 5 bonds, 1 residue, 1 model selected 
    24280 
    24281 > hide sel cartoons
    24282 
    24283 > show sel cartoons
    24284 
    24285 > select clear
    24286 
    24287 > select #30.1.1/A:1@CB
    24288 
    24289 1 atom, 1 residue, 1 model selected 
    24290 
    24291 > swapaa #!30/B:195 SER criteria 2 rotLib Dunbrack
    24292 
    24293 Using Dunbrack library 
    24294 1oph #!30/B SER 195: phi -47.1, psi 140.5 trans 
    24295 Applying SER rotamer (chi angles: -63.9) to 1oph #!30/B SER 195 
    24296 
    24297 > select #30/B:195
    24298 
    24299 6 atoms, 5 bonds, 1 residue, 1 model selected 
    24300 
    24301 > show sel atoms
    24302 
    24303 > rainbow sel
    24304 
    24305 > select clear
    24306 
    24307 > select #35/A:358
    24308 
    24309 17 atoms, 16 bonds, 1 residue, 1 model selected 
    24310 
    24311 > show sel atoms
    24312 
    24313 > rainbow sel
    24314 
    24315 [Repeated 1 time(s)]
    24316 
    24317 > color sel byhetero
    24318 
    24319 > color sel red
    24320 
    24321 > color sel byhetero
    24322 
    24323 > select clear
    24324 
    24325 > open 1oph fromDatabase pdb format mmcif
    24326 
    24327 1oph title: 
    24328 Non-covalent complex between α-1-π-pittsburgh and S195A trypsin [more info...] 
    24329  
    24330 Chain information for 1oph #36 
    24331 --- 
    24332 Chain | Description | UniProt 
    24333 A | Alpha-1-antitrypsin precursor | A1AT_HUMAN 1-394 
    24334 B | Trypsinogen, cationic precursor | TRY1_BOVIN -4-245 
    24335  
    24336 1oph mmCIF Assemblies 
    24337 --- 
    24338 1| author_and_software_defined_assembly 
    24339 2| software_defined_assembly 
    24340  
    24341 
    24342 > mmaker #36 to #35
    24343 
    24344 Parameters 
    24345 --- 
    24346 Chain pairing | bb 
    24347 Alignment algorithm | Needleman-Wunsch 
    24348 Similarity matrix | BLOSUM-62 
    24349 SS fraction | 0.3 
    24350 Gap open (HH/SS/other) | 18/18/6 
    24351 Gap extend | 1 
    24352 SS matrix |  |  | H | S | O 
    24353 ---|---|---|--- 
    24354 H | 6 | -9 | -6 
    24355 S |  | 6 | -6 
    24356 O |  |  | 4 
    24357 Iteration cutoff | 2 
    24358  
    24359 Matchmaker 8pi2, chain A (#35) with 1oph, chain A (#36), sequence alignment
    24360 score = 1934.1 
    24361 RMSD between 350 pruned atom pairs is 0.764 angstroms; (across all 371 pairs:
    24362 1.541) 
    24363  
    24364 
    24365 > select #36/A
    24366 
    24367 3121 atoms, 2980 bonds, 578 residues, 1 model selected 
    24368 
    24369 > select #36/A: 358
    24370 
    24371 11 atoms, 10 bonds, 1 residue, 1 model selected 
    24372 
    24373 > show sel atoms
    24374 
    24375 > hide #30 models
    24376 
    24377 > show #30 models
    24378 
    24379 > style sel stick
    24380 
    24381 Changed 11 atom styles 
    24382 
    24383 > style sel ball
    24384 
    24385 Changed 11 atom styles 
    24386 
    24387 > style sel stick
    24388 
    24389 Changed 11 atom styles 
    24390 
    24391 > hide #35 models
    24392 
    24393 > show #35 models
    24394 
    24395 > select #36/A: 57
    24396 
    24397 8 atoms, 7 bonds, 1 residue, 1 model selected 
    24398 
    24399 > select add #36
    24400 
    24401 4919 atoms, 4641 bonds, 975 residues, 1 model selected 
    24402 
    24403 > select subtract #36
    24404 
    24405 Nothing selected 
    24406 
    24407 > hide #36 models
    24408 
    24409 > select #30/A: 57
    24410 
    24411 Nothing selected 
    24412 
    24413 > select #30/B: 57
    24414 
    24415 10 atoms, 10 bonds, 1 residue, 1 model selected 
    24416 
    24417 > show sel atoms
    24418 
    24419 > color sel byhetero
    24420 
    24421 > select #30/B: 202
    24422 
    24423 6 atoms, 5 bonds, 1 residue, 1 model selected 
    24424 
    24425 > select #30/B: 102
    24426 
    24427 8 atoms, 7 bonds, 1 residue, 1 model selected 
    24428 
    24429 > show sel atoms
    24430 
    24431 > color sel byhetero
    24432 
    24433 > select #30/B: 194
    24434 
    24435 8 atoms, 7 bonds, 1 residue, 1 model selected 
    24436 
    24437 > show sel atoms
    24438 
    24439 > color sel byhetero
    24440 
    24441 > select clear
    24442 
    24443 > select add #30
    24444 
    24445 1799 atoms, 1662 bonds, 397 residues, 1 model selected 
    24446 
    24447 > hide sel atoms
    24448 
    24449 > select add #35
    24450 
    24451 7752 atoms, 7346 bonds, 1096 residues, 2 models selected 
    24452 
    24453 > hide sel atoms
    24454 
    24455 > select subtract #30
    24456 
    24457 5953 atoms, 5684 bonds, 699 residues, 1 model selected 
    24458 
    24459 > select subtract #35
    24460 
    24461 Nothing selected 
    24462 
    24463 > show #!8 models
    24464 
    24465 > open 1ezx fromDatabase pdb format mmcif
    24466 
    24467 Summary of feedback from opening 1ezx fetched from pdb 
    24468 --- 
    24469 note | Fetching compressed mmCIF 1ezx from http://files.rcsb.org/download/1ezx.cif 
    24470  
    24471 1ezx title: 
    24472 Crystal structure of A serpin:protease complex [more info...] 
    24473  
    24474 Chain information for 1ezx #37 
    24475 --- 
    24476 Chain | Description | UniProt 
    24477 A | ALPHA-1-ANTITRYPSIN | A1AT_HUMAN 24-358 
    24478 B | ALPHA-1-ANTITRYPSIN | A1AT_HUMAN 359-394 
    24479 C | TRYPSIN | TRY1_BOVIN 42-245 
    24480  
    24481 
    24482 > mmaker #37 to #35
    24483 
    24484 Parameters 
    24485 --- 
    24486 Chain pairing | bb 
    24487 Alignment algorithm | Needleman-Wunsch 
    24488 Similarity matrix | BLOSUM-62 
    24489 SS fraction | 0.3 
    24490 Gap open (HH/SS/other) | 18/18/6 
    24491 Gap extend | 1 
    24492 SS matrix |  |  | H | S | O 
    24493 ---|---|---|--- 
    24494 H | 6 | -9 | -6 
    24495 S |  | 6 | -6 
    24496 O |  |  | 4 
    24497 Iteration cutoff | 2 
    24498  
    24499 Matchmaker 8pi2, chain A (#35) with 1ezx, chain A (#37), sequence alignment
    24500 score = 1629.2 
    24501 RMSD between 219 pruned atom pairs is 0.866 angstroms; (across all 335 pairs:
    24502 9.271) 
    24503  
    24504 
    24505 > hide #!8 models
    24506 
    24507 > hide #30 models
    24508 
    24509 > hide #35 models
    24510 
    24511 > select #37/A
    24512 
    24513 2686 atoms, 2674 bonds, 398 residues, 1 model selected 
    24514 
    24515 > select #37/A,B
    24516 
    24517 2975 atoms, 2968 bonds, 437 residues, 1 model selected 
    24518 
    24519 > color sel dark gray
    24520 
    24521 > select clear
    24522 
    24523 > show #35 models
    24524 
    24525 > hide #!37 models
    24526 
    24527 > show #!37 models
    24528 
    24529 > hide #35 models
    24530 
    24531 > show #35 models
    24532 
    24533 > hide #35 models
    24534 
    24535 > select #37/C
    24536 
    24537 1009 atoms, 1014 bonds, 5 pseudobonds, 155 residues, 2 models selected 
    24538 
    24539 > show #30 models
    24540 
    24541 > color (#!37 & sel) cornflower blue
    24542 
    24543 > color (#!37 & sel) blue
    24544 
    24545 > select clear
    24546 
    24547 > select #37/C
    24548 
    24549 1009 atoms, 1014 bonds, 5 pseudobonds, 155 residues, 2 models selected 
    24550 
    24551 > color (#!37 & sel) cornflower blue
    24552 
    24553 > select clear
    24554 
    24555 > select #37/C
    24556 
    24557 1009 atoms, 1014 bonds, 5 pseudobonds, 155 residues, 2 models selected 
    24558 
    24559 > color (#!37 & sel) medium blue
    24560 
    24561 > color (#!37 & sel) cornflower blue
    24562 
    24563 > select 30
    24564 
    24565 Expected an objects specifier or a keyword 
    24566 
    24567 > select 30/B
    24568 
    24569 Expected an objects specifier or a keyword 
    24570 
    24571 > select 30/A
    24572 
    24573 Expected an objects specifier or a keyword 
    24574 
    24575 > select #30
    24576 
    24577 1799 atoms, 1662 bonds, 397 residues, 1 model selected 
    24578 
    24579 > color sel cornflower blue
    24580 
    24581 > select clear
    24582 
    24583 > select #37/A:291
    24584 
    24585 8 atoms, 7 bonds, 1 residue, 1 model selected 
    24586 
    24587 > select #37/A:292
    24588 
    24589 6 atoms, 5 bonds, 1 residue, 1 model selected 
    24590 
    24591 > select add #37/A:291
    24592 
    24593 14 atoms, 12 bonds, 2 residues, 1 model selected 
    24594 
    24595 > select add #37/A:293
    24596 
    24597 22 atoms, 19 bonds, 3 residues, 1 model selected 
    24598 
    24599 > select add #37/A:294
    24600 
    24601 29 atoms, 25 bonds, 4 residues, 1 model selected 
    24602 
    24603 > select add #37/A:295
    24604 
    24605 33 atoms, 28 bonds, 5 residues, 1 model selected 
    24606 
    24607 > select add #37/A:296
    24608 
    24609 40 atoms, 34 bonds, 6 residues, 1 model selected 
    24610 
    24611 > select add #37/A:297
    24612 
    24613 52 atoms, 46 bonds, 7 residues, 1 model selected 
    24614 
    24615 > select add #37/A:298
    24616 
    24617 60 atoms, 53 bonds, 8 residues, 1 model selected 
    24618 
    24619 > select add #37/A:340
    24620 
    24621 68 atoms, 60 bonds, 9 residues, 1 model selected 
    24622 
    24623 > select add #37/A:339
    24624 
    24625 75 atoms, 66 bonds, 10 residues, 1 model selected 
    24626 
    24627 > select add #37/A:338
    24628 
    24629 83 atoms, 73 bonds, 11 residues, 1 model selected 
    24630 
    24631 > select add #37/A:337
    24632 
    24633 90 atoms, 79 bonds, 12 residues, 1 model selected 
    24634 
    24635 > select add #37/A:336
    24636 
    24637 95 atoms, 83 bonds, 13 residues, 1 model selected 
    24638 
    24639 > select add #37/A:335
    24640 
    24641 104 atoms, 91 bonds, 14 residues, 1 model selected 
    24642 
    24643 > select add #37/A:334
    24644 
    24645 114 atoms, 101 bonds, 15 residues, 1 model selected 
    24646 
    24647 > select add #37/A:333
    24648 
    24649 121 atoms, 107 bonds, 16 residues, 1 model selected 
    24650 
    24651 > select add #37/A:332
    24652 
    24653 126 atoms, 111 bonds, 17 residues, 1 model selected 
    24654 
    24655 > select add #37/A:331
    24656 
    24657 135 atoms, 119 bonds, 18 residues, 1 model selected 
    24658 
    24659 > select add #37/A:330
    24660 
    24661 141 atoms, 124 bonds, 19 residues, 1 model selected 
    24662 
    24663 > select add #37/A:329
    24664 
    24665 149 atoms, 131 bonds, 20 residues, 1 model selected 
    24666 
    24667 > select add #37/A:328
    24668 
    24669 158 atoms, 139 bonds, 21 residues, 1 model selected 
    24670 
    24671 > select add #37/A:327
    24672 
    24673 166 atoms, 146 bonds, 22 residues, 1 model selected 
    24674 
    24675 > select add #37/A:357
    24676 
    24677 173 atoms, 153 bonds, 23 residues, 1 model selected 
    24678 
    24679 > select add #37/A:356
    24680 
    24681 181 atoms, 160 bonds, 24 residues, 1 model selected 
    24682 
    24683 > select add #37/A:355
    24684 
    24685 186 atoms, 164 bonds, 25 residues, 1 model selected 
    24686 
    24687 > select add #37/A:354
    24688 
    24689 195 atoms, 172 bonds, 26 residues, 1 model selected 
    24690 
    24691 > select add #37/A:353
    24692 
    24693 203 atoms, 179 bonds, 27 residues, 1 model selected 
    24694 
    24695 > select add #37/A:352
    24696 
    24697 214 atoms, 190 bonds, 28 residues, 1 model selected 
    24698 
    24699 > select add #37/A:351
    24700 
    24701 222 atoms, 197 bonds, 29 residues, 1 model selected 
    24702 
    24703 > select add #37/A:350
    24704 
    24705 227 atoms, 201 bonds, 30 residues, 1 model selected 
    24706 
    24707 > select add #37/A:349
    24708 
    24709 231 atoms, 204 bonds, 31 residues, 1 model selected 
    24710 
    24711 > select add #37/A:348
    24712 
    24713 236 atoms, 208 bonds, 32 residues, 1 model selected 
    24714 
    24715 > select add #37/A:347
    24716 
    24717 241 atoms, 212 bonds, 33 residues, 1 model selected 
    24718 
    24719 > select add #37/A:346
    24720 
    24721 250 atoms, 220 bonds, 34 residues, 1 model selected 
    24722 
    24723 > select add #37/A:345
    24724 
    24725 257 atoms, 226 bonds, 35 residues, 1 model selected 
    24726 
    24727 > select add #37/A:344
    24728 
    24729 261 atoms, 229 bonds, 36 residues, 1 model selected 
    24730 
    24731 > select add #37/A:193
    24732 
    24733 270 atoms, 237 bonds, 37 residues, 1 model selected 
    24734 
    24735 > select add #37/A:192
    24736 
    24737 274 atoms, 240 bonds, 38 residues, 1 model selected 
    24738 
    24739 > select add #37/A:191
    24740 
    24741 283 atoms, 248 bonds, 39 residues, 1 model selected 
    24742 
    24743 > select add #37/A:190
    24744 
    24745 294 atoms, 259 bonds, 40 residues, 1 model selected 
    24746 
    24747 > select add #37/A:189
    24748 
    24749 305 atoms, 270 bonds, 41 residues, 1 model selected 
    24750 
    24751 > select add #37/A:188
    24752 
    24753 313 atoms, 277 bonds, 42 residues, 1 model selected 
    24754 
    24755 > select add #37/A:187
    24756 
    24757 325 atoms, 289 bonds, 43 residues, 1 model selected 
    24758 
    24759 > select add #37/A:186
    24760 
    24761 333 atoms, 296 bonds, 44 residues, 1 model selected 
    24762 
    24763 > select add #37/A:185
    24764 
    24765 340 atoms, 302 bonds, 45 residues, 1 model selected 
    24766 
    24767 > select add #37/A:184
    24768 
    24769 348 atoms, 309 bonds, 46 residues, 1 model selected 
    24770 
    24771 > select add #37/A:183
    24772 
    24773 353 atoms, 313 bonds, 47 residues, 1 model selected 
    24774 
    24775 > select add #37/A:182
    24776 
    24777 364 atoms, 324 bonds, 48 residues, 1 model selected 
    24778 
    24779 > select subtract #37/A:182
    24780 
    24781 353 atoms, 313 bonds, 47 residues, 1 model selected 
    24782 
    24783 > select subtract #37/A:183
    24784 
    24785 348 atoms, 309 bonds, 46 residues, 1 model selected 
    24786 
    24787 > select subtract #37/A:184
    24788 
    24789 340 atoms, 302 bonds, 45 residues, 1 model selected 
    24790 
    24791 > select subtract #37/A:185
    24792 
    24793 333 atoms, 296 bonds, 44 residues, 1 model selected 
    24794 
    24795 > select subtract #37/A:186
    24796 
    24797 325 atoms, 289 bonds, 43 residues, 1 model selected 
    24798 
    24799 > select subtract #37/A:187
    24800 
    24801 313 atoms, 277 bonds, 42 residues, 1 model selected 
    24802 
    24803 > select subtract #37/A:188
    24804 
    24805 305 atoms, 270 bonds, 41 residues, 1 model selected 
    24806 
    24807 > select subtract #37/A:189
    24808 
    24809 294 atoms, 259 bonds, 40 residues, 1 model selected 
    24810 
    24811 > select subtract #37/A:190
    24812 
    24813 283 atoms, 248 bonds, 39 residues, 1 model selected 
    24814 
    24815 > select subtract #37/A:191
    24816 
    24817 274 atoms, 240 bonds, 38 residues, 1 model selected 
    24818 
    24819 > select subtract #37/A:192
    24820 
    24821 270 atoms, 237 bonds, 37 residues, 1 model selected 
    24822 
    24823 > select subtract #37/A:193
    24824 
    24825 261 atoms, 229 bonds, 36 residues, 1 model selected 
    24826 
    24827 > select subtract #37/A:357
    24828 
    24829 254 atoms, 222 bonds, 35 residues, 1 model selected 
    24830 
    24831 > select subtract #37/A:356
    24832 
    24833 246 atoms, 215 bonds, 34 residues, 1 model selected 
    24834 
    24835 > select subtract #37/A:355
    24836 
    24837 241 atoms, 211 bonds, 33 residues, 1 model selected 
    24838 
    24839 > select subtract #37/A:354
    24840 
    24841 232 atoms, 203 bonds, 32 residues, 1 model selected 
    24842 
    24843 > select subtract #37/A:353
    24844 
    24845 224 atoms, 196 bonds, 31 residues, 1 model selected 
    24846 
    24847 > select subtract #37/A:352
    24848 
    24849 213 atoms, 185 bonds, 30 residues, 1 model selected 
    24850 
    24851 > select subtract #37/A:351
    24852 
    24853 205 atoms, 178 bonds, 29 residues, 1 model selected 
    24854 
    24855 > select subtract #37/A:350
    24856 
    24857 200 atoms, 174 bonds, 28 residues, 1 model selected 
    24858 
    24859 > select subtract #37/A:349
    24860 
    24861 196 atoms, 171 bonds, 27 residues, 1 model selected 
    24862 
    24863 > select subtract #37/A:348
    24864 
    24865 191 atoms, 167 bonds, 26 residues, 1 model selected 
    24866 
    24867 > select subtract #37/A:347
    24868 
    24869 186 atoms, 163 bonds, 25 residues, 1 model selected 
    24870 
    24871 > select subtract #37/A:346
    24872 
    24873 177 atoms, 155 bonds, 24 residues, 1 model selected 
    24874 
    24875 > select subtract #37/A:345
    24876 
    24877 170 atoms, 149 bonds, 23 residues, 1 model selected 
    24878 
    24879 > select subtract #37/A:344
    24880 
    24881 166 atoms, 146 bonds, 22 residues, 1 model selected 
    24882 
    24883 > select add #37/A:193
    24884 
    24885 175 atoms, 154 bonds, 23 residues, 1 model selected 
    24886 
    24887 > select add #37/A:192
    24888 
    24889 179 atoms, 157 bonds, 24 residues, 1 model selected 
    24890 
    24891 > select add #37/A:191
    24892 
    24893 188 atoms, 165 bonds, 25 residues, 1 model selected 
    24894 
    24895 > select add #37/A:190
    24896 
    24897 199 atoms, 176 bonds, 26 residues, 1 model selected 
    24898 
    24899 > select add #37/A:189
    24900 
    24901 210 atoms, 187 bonds, 27 residues, 1 model selected 
    24902 
    24903 > select add #37/A:188
    24904 
    24905 218 atoms, 194 bonds, 28 residues, 1 model selected 
    24906 
    24907 > select add #37/A:187
    24908 
    24909 230 atoms, 206 bonds, 29 residues, 1 model selected 
    24910 
    24911 > select add #37/A:186
    24912 
    24913 238 atoms, 213 bonds, 30 residues, 1 model selected 
    24914 
    24915 > select add #37/A:185
    24916 
    24917 245 atoms, 219 bonds, 31 residues, 1 model selected 
    24918 
    24919 > select add #37/A:184
    24920 
    24921 253 atoms, 226 bonds, 32 residues, 1 model selected 
    24922 
    24923 > select add #37/A:183
    24924 
    24925 258 atoms, 230 bonds, 33 residues, 1 model selected 
    24926 
    24927 > select add #37/A:182
    24928 
    24929 269 atoms, 241 bonds, 34 residues, 1 model selected 
    24930 
    24931 > select add #37/A:111
    24932 
    24933 278 atoms, 249 bonds, 35 residues, 1 model selected 
    24934 
    24935 > select add #37/A:112
    24936 
    24937 286 atoms, 256 bonds, 36 residues, 1 model selected 
    24938 
    24939 > select subtract #37/A:112
    24940 
    24941 278 atoms, 249 bonds, 35 residues, 1 model selected 
    24942 
    24943 > select add #37/A:112
    24944 
    24945 286 atoms, 256 bonds, 36 residues, 1 model selected 
    24946 
    24947 > select add #37/A:113
    24948 
    24949 293 atoms, 262 bonds, 37 residues, 1 model selected 
    24950 
    24951 > select add #37/A:114
    24952 
    24953 300 atoms, 268 bonds, 38 residues, 1 model selected 
    24954 
    24955 > select add #37/A:115
    24956 
    24957 304 atoms, 271 bonds, 39 residues, 1 model selected 
    24958 
    24959 > select add #37/A:116
    24960 
    24961 312 atoms, 278 bonds, 40 residues, 1 model selected 
    24962 
    24963 > select add #37/A:117
    24964 
    24965 316 atoms, 281 bonds, 41 residues, 1 model selected 
    24966 
    24967 > select add #37/A:118
    24968 
    24969 324 atoms, 288 bonds, 42 residues, 1 model selected 
    24970 
    24971 > select subtract #37/A:118
    24972 
    24973 316 atoms, 281 bonds, 41 residues, 1 model selected 
    24974 
    24975 > select add #37/A:119
    24976 
    24977 327 atoms, 292 bonds, 42 residues, 1 model selected 
    24978 
    24979 > select add #37/A:118
    24980 
    24981 335 atoms, 299 bonds, 43 residues, 1 model selected 
    24982 
    24983 > select add #37/A:120
    24984 
    24985 343 atoms, 306 bonds, 44 residues, 1 model selected 
    24986 
    24987 > select add #37/A:121
    24988 
    24989 349 atoms, 311 bonds, 45 residues, 1 model selected 
    24990 
    24991 > select add #37/A:145
    24992 
    24993 356 atoms, 317 bonds, 46 residues, 1 model selected 
    24994 
    24995 > select add #37/A:144
    24996 
    24997 363 atoms, 323 bonds, 47 residues, 1 model selected 
    24998 
    24999 > select add #37/A:143
    25000 
    25001 374 atoms, 334 bonds, 48 residues, 1 model selected 
    25002 
    25003 > select add #37/A:142
    25004 
    25005 379 atoms, 338 bonds, 49 residues, 1 model selected 
    25006 
    25007 > select add #37/A:141
    25008 
    25009 388 atoms, 346 bonds, 50 residues, 1 model selected 
    25010 
    25011 > color sel cyan
    25012 
    25013 > color sel forest green
    25014 
    25015 > color sel lime
    25016 
    25017 > select clear
    25018 
    25019 > select add #37/A:358
    25020 
    25021 8 atoms, 7 bonds, 1 residue, 1 model selected 
    25022 
    25023 > select add #37/A:357
    25024 
    25025 15 atoms, 14 bonds, 2 residues, 1 model selected 
    25026 
    25027 > select add #37/A:356
    25028 
    25029 23 atoms, 21 bonds, 3 residues, 1 model selected 
    25030 
    25031 > select add #37/A:355
    25032 
    25033 28 atoms, 25 bonds, 4 residues, 1 model selected 
    25034 
    25035 > select add #37/A:354
    25036 
    25037 37 atoms, 33 bonds, 5 residues, 1 model selected 
    25038 
    25039 > select add #37/A:353
    25040 
    25041 45 atoms, 40 bonds, 6 residues, 1 model selected 
    25042 
    25043 > select add #37/A:352
    25044 
    25045 56 atoms, 51 bonds, 7 residues, 1 model selected 
    25046 
    25047 > select add #37/A:351
    25048 
    25049 64 atoms, 58 bonds, 8 residues, 1 model selected 
    25050 
    25051 > select add #37/A:350
    25052 
    25053 69 atoms, 62 bonds, 9 residues, 1 model selected 
    25054 
    25055 > select add #37/A:349
    25056 
    25057 73 atoms, 65 bonds, 10 residues, 1 model selected 
    25058 
    25059 > select add #37/A:348
    25060 
    25061 78 atoms, 69 bonds, 11 residues, 1 model selected 
    25062 
    25063 > select add #37/A:347
    25064 
    25065 83 atoms, 73 bonds, 12 residues, 1 model selected 
    25066 
    25067 > select add #37/A:346
    25068 
    25069 92 atoms, 81 bonds, 13 residues, 1 model selected 
    25070 
    25071 > select add #37/A:345
    25072 
    25073 99 atoms, 87 bonds, 14 residues, 1 model selected 
    25074 
    25075 > select add #37/A:344
    25076 
    25077 103 atoms, 90 bonds, 15 residues, 1 model selected 
    25078 
    25079 > select add #37/A:341
    25080 
    25081 111 atoms, 97 bonds, 16 residues, 1 model selected 
    25082 
    25083 > select add #37/A:342
    25084 
    25085 120 atoms, 105 bonds, 17 residues, 1 model selected 
    25086 
    25087 > select add #37/A:343
    25088 
    25089 129 atoms, 113 bonds, 18 residues, 1 model selected 
    25090 
    25091 > color sel red
    25092 
    25093 > select clear
    25094 
    25095 > hide #30 models
    25096 
    25097 > show #30 models
    25098 
    25099 > hide #30 models
    25100 
    25101 > hide #!37 models
    25102 
    25103 > show #!37 models
    25104 
    25105 > select add #37
    25106 
    25107 3984 atoms, 3982 bonds, 5 pseudobonds, 592 residues, 3 models selected 
    25108 
    25109 > select clear
    25110 
    25111 [Repeated 2 time(s)]
    25112 
    25113 > hide #37.1.1 models
    25114 
    25115 > select #37/C: 195
    25116 
    25117 6 atoms, 5 bonds, 1 residue, 1 model selected 
    25118 
    25119 > show sel atoms
    25120 
    25121 > color sel byhetero
    25122 
    25123 > select clear
    25124 
    25125 [Repeated 1 time(s)]
    25126 
    25127 > show #35 models
    25128 
    25129 > hide #35 models
    25130 
    25131 > select add #37/A:165
    25132 
    25133 7 atoms, 6 bonds, 1 residue, 1 model selected 
    25134 
    25135 > select add #37/A:164
    25136 
    25137 11 atoms, 9 bonds, 2 residues, 1 model selected 
    25138 
    25139 > select add #37/A:163
    25140 
    25141 16 atoms, 13 bonds, 3 residues, 1 model selected 
    25142 
    25143 > select add #37/A:162
    25144 
    25145 25 atoms, 21 bonds, 4 residues, 1 model selected 
    25146 
    25147 > select add #37/A:161
    25148 
    25149 32 atoms, 27 bonds, 5 residues, 1 model selected 
    25150 
    25151 > select add #37/A:159
    25152 
    25153 40 atoms, 34 bonds, 6 residues, 1 model selected 
    25154 
    25155 > select add #37/A:158
    25156 
    25157 48 atoms, 41 bonds, 7 residues, 1 model selected 
    25158 
    25159 > select add #37/A:160
    25160 
    25161 60 atoms, 53 bonds, 8 residues, 1 model selected 
    25162 
    25163 > select add #37/A:157
    25164 
    25165 68 atoms, 60 bonds, 9 residues, 1 model selected 
    25166 
    25167 > select add #37/A:156
    25168 
    25169 77 atoms, 68 bonds, 10 residues, 1 model selected 
    25170 
    25171 > select add #37/A:155
    25172 
    25173 83 atoms, 73 bonds, 11 residues, 1 model selected 
    25174 
    25175 > select add #37/A:154
    25176 
    25177 92 atoms, 81 bonds, 12 residues, 1 model selected 
    25178 
    25179 > select add #37/A:153
    25180 
    25181 97 atoms, 85 bonds, 13 residues, 1 model selected 
    25182 
    25183 > select add #37/A:152
    25184 
    25185 102 atoms, 89 bonds, 14 residues, 1 model selected 
    25186 
    25187 > select add #37/A:151
    25188 
    25189 111 atoms, 97 bonds, 15 residues, 1 model selected 
    25190 
    25191 > select add #37/A:150
    25192 
    25193 118 atoms, 103 bonds, 16 residues, 1 model selected 
    25194 
    25195 > select add #37/A:149
    25196 
    25197 126 atoms, 110 bonds, 17 residues, 1 model selected 
    25198 
    25199 > color sel magenta
    25200 
    25201 > select clear
    25202 
    25203 > show #35 models
    25204 
    25205 > show #30 models
    25206 
    25207 > hide #!37 models
    25208 
    25209 > select #30/B: 195
    25210 
    25211 6 atoms, 5 bonds, 1 residue, 1 model selected 
    25212 
    25213 > show sel atoms
    25214 
    25215 > color sel byhetero
    25216 
    25217 > select clear
    25218 
    25219 > save "/Users/amy/Desktop/3C11_Fab_AAT_NE/make pictures/1oph_michaelis
    25220 > complex.jpg" width 935 height 668 supersample 3
    25221 
    25222 > ui tool show Toolbar
    25223 
    25224 > save /Users/amy/Desktop/image1.png supersample 3
    25225 
    25226 > save "/Users/amy/Desktop/3C11_Fab_AAT_NE/make pictures/1oph_michaelis
    25227 > complex.png" width 935 height 668 supersample 3 transparentBackground true
    25228 
    25229 > show #!37 models
    25230 
    25231 > hide #30 models
    25232 
    25233 > hide #35 models
    25234 
    25235 > undo
    25236 
    25237 > hide #35 models
    25238 
    25239 > view
    25240 
    25241 > hide #!37 models
    25242 
    25243 > show #35 models
    25244 
    25245 > show #!37 models
    25246 
    25247 > hide #!37 models
    25248 
    25249 > show #30 models
    25250 
    25251 > save "/Users/amy/Desktop/3C11_Fab_AAT_NE/make pictures/1oph_michaelis
    25252 > complex.png" width 935 height 668 supersample 3 transparentBackground true
    25253 
    25254 > hide #30 models
    25255 
    25256 > hide #35 models
    25257 
    25258 > show #!37 models
    25259 
    25260 > save "/Users/amy/Desktop/3C11_Fab_AAT_NE/make pictures/1ezx_final
    25261 > complex.png" width 935 height 668 supersample 3 transparentBackground true
    25262 
    25263 > save /Users/amy/Desktop/3C11_Fab_AAT_NE/csparc.cxs includeMaps true
    25264 
    25265 ——— End of log from Sun Feb 1 23:24:08 2026 ———
    25266 
    25267 > view name session-start
    25268 
    25269 opened ChimeraX session 
    25270 
    25271 > open 9hud fromDatabase pdb format mmcif
    25272 
    25273 9hud title: 
    25274 Alpha-1-antitrypsin in the cleaved conformation in complex with a
    25275 conformationally nonselective Fab fragment [more info...] 
    25276  
    25277 Chain information for 9hud #38 
    25278 --- 
    25279 Chain | Description | UniProt 
    25280 A C | Alpha-1-antitrypsin | A1AT_HUMAN 2-354 
    25281 B D | Short peptide from AAT | A1AT_HUMAN 355-394 
    25282 H I | FAB 9C5 heavy chain |   
    25283 L M | FAB 9C5 light chain |   
    25284  
    25285 Non-standard residues in 9hud #38 
    25286 --- 
    25287 CL — chloride ion 
    25288 EDO — 1,2-ethanediol (ethylene glycol) 
    25289 GLY — glycine 
    25290 GOL — glycerol (glycerin; propane-1,2,3-triol) 
    25291 LYS — lysine 
    25292 NA — sodium ion 
    25293  
    25294 9hud mmCIF Assemblies 
    25295 --- 
    25296 1| author_defined_assembly 
    25297 2| author_defined_assembly 
    25298  
    25299 61 atoms have alternate locations. Control/examine alternate locations with
    25300 Altloc Explorer [start tool...] or the altlocs command. 
    25301 12039 atoms have anisotropic B-factors. Depict anisotropic information with
    25302 Thermal Ellipsoids [start tool...] or the aniso command. 
    25303 
    25304 > hide #!37-38 cartoons
    25305 
    25306 > show #!37-38 cartoons
    25307 
    25308 > hide #!37-38 atoms
    25309 
    25310 > select #38/A
    25311 
    25312 2567 atoms, 2550 bonds, 398 residues, 1 model selected 
    25313 
    25314 > select #38/B
    25315 
    25316 252 atoms, 251 bonds, 40 residues, 1 model selected 
    25317 
    25318 > select #38/C
    25319 
    25320 2612 atoms, 2578 bonds, 415 residues, 1 model selected 
    25321 
    25322 > select #38/C,D
    25323 
    25324 2873 atoms, 2840 bonds, 454 residues, 1 model selected 
    25325 
    25326 > delete #38/C,D
    25327 
    25328 > select #38/H
    25329 
    25330 1713 atoms, 1651 bonds, 322 residues, 1 model selected 
    25331 
    25332 > select #38/I
    25333 
    25334 1736 atoms, 1654 bonds, 1 pseudobond, 338 residues, 2 models selected 
    25335 
    25336 > delete #38/I
    25337 
    25338 > select #38/M
    25339 
    25340 1766 atoms, 1691 bonds, 328 residues, 1 model selected 
    25341 
    25342 > delete #38/M
    25343 
    25344 > hide #!37 models
    25345 
    25346 > show #!37 models
    25347 
    25348 > mmaker #38 to #37
    25349 
    25350 Parameters 
    25351 --- 
    25352 Chain pairing | bb 
    25353 Alignment algorithm | Needleman-Wunsch 
    25354 Similarity matrix | BLOSUM-62 
    25355 SS fraction | 0.3 
    25356 Gap open (HH/SS/other) | 18/18/6 
    25357 Gap extend | 1 
    25358 SS matrix |  |  | H | S | O 
    25359 ---|---|---|--- 
    25360 H | 6 | -9 | -6 
    25361 S |  | 6 | -6 
    25362 O |  |  | 4 
    25363 Iteration cutoff | 2 
    25364  
    25365 Matchmaker 1ezx, chain A (#37) with 9hud, chain A (#38), sequence alignment
    25366 score = 1674.4 
    25367 RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
    25368 0.519) 
    25369  
    25370 
    25371 > save /Users/amy/Desktop/3C11_Fab_AAT_NE/csparc.cxs includeMaps true
    25372 
    25373 ——— End of log from Wed Feb 11 13:24:40 2026 ———
    25374 
    25375 > view name session-start
    25376 
    25377 opened ChimeraX session 
    25378 
    25379 > open /Users/amy/Downloads/cryosparc_P483_J66_004_volume_map.mrc
    25380 
    25381 Opened cryosparc_P483_J66_004_volume_map.mrc as #39, grid size 400,400,400,
    25382 pixel 0.723, shown at level 0.00725, step 2, values float32 
    25383 
    25384 > volume #39 level 0.0301
    25385 
    25386 > hide #!37 models
    25387 
    25388 > hide #!38 models
    25389 
    25390 > volume #39 level 0.08437
    25391 
    25392 > open /Users/amy/Downloads/cryosparc_P483_J69_005_volume_map.mrc
    25393 
    25394 Opened cryosparc_P483_J69_005_volume_map.mrc as #40, grid size 400,400,400,
    25395 pixel 0.723, shown at level 0.00425, step 2, values float32 
    25396 
    25397 > volume #40 level 0.02603
    25398 
    25399 > volume #40 level 0.05112
    25400 
    25401 > transparency #40 50
    25402 
    25403 > show #!39 models
    25404 
    25405 > hide #!39 models
    25406 
    25407 > show #!38 models
    25408 
    25409 > select add #38
    25410 
    25411 6282 atoms, 6138 bonds, 1077 residues, 1 model selected 
    25412 
    25413 > ui mousemode right "translate selected models"
    25414 
    25415 > view matrix models
    25416 > #38,-0.23813,0.96316,-0.12499,103.01,0.23278,-0.068345,-0.97012,107.01,-0.94292,-0.26011,-0.20793,320.16
    25417 
    25418 > view matrix models
    25419 > #38,-0.35239,0.53131,-0.77041,145.72,-0.23758,-0.84704,-0.47549,205.11,-0.90519,0.015476,0.42472,295.71
    25420 
    25421 > view matrix models
    25422 > #38,0.095516,0.64963,-0.75423,70.134,0.59254,-0.64594,-0.48131,66.164,-0.79986,-0.40094,-0.44663,305.92
    25423 
    25424 > view matrix models
    25425 > #38,0.23814,0.79731,-0.5546,39.413,0.91725,-0.37235,-0.14145,0.058888,-0.31929,-0.47502,-0.82,237.42
    25426 
    25427 > view matrix models
    25428 > #38,-0.29619,0.8953,-0.33273,117.39,0.7752,0.42884,0.46386,-15.784,0.55798,-0.12055,-0.82105,85.078
    25429 
    25430 > view matrix models
    25431 > #38,-0.30596,0.51089,-0.80335,139.57,0.54659,0.78515,0.29115,8.8601,0.7795,-0.35003,-0.51948,55.076
    25432 
    25433 > view matrix models
    25434 > #38,-0.30596,0.51089,-0.80335,160.4,0.54659,0.78515,0.29115,-4.0241,0.7795,-0.35003,-0.51948,56.001
    25435 
    25436 > view matrix models
    25437 > #38,0.2554,0.95891,-0.12357,45.918,0.33368,0.032535,0.94213,50.395,0.90743,-0.28185,-0.31165,30.553
    25438 
    25439 > view matrix models
    25440 > #38,0.28907,0.71313,0.63866,40.495,-0.045867,-0.65606,0.75332,139.21,0.95621,-0.24706,-0.15694,19.569
    25441 
    25442 > view matrix models
    25443 > #38,0.66315,0.74847,0.0052223,-12.11,0.30094,-0.27301,0.91373,67.652,0.68532,-0.60437,-0.40629,79.243
    25444 
    25445 > view matrix models
    25446 > #38,0.66315,0.74847,0.0052223,-14.717,0.30094,-0.27301,0.91373,95.231,0.68532,-0.60437,-0.40629,75.309
    25447 
    25448 > view matrix models
    25449 > #38,0.66315,0.74847,0.0052223,9.7058,0.30094,-0.27301,0.91373,102.14,0.68532,-0.60437,-0.40629,70.114
    25450 
    25451 > ui tool show "Fit in Map"
    25452 
    25453 > fitmap #38 inMap #40
    25454 
    25455 Fit molecule 9hud (#38) to map cryosparc_P483_J69_005_volume_map.mrc (#40)
    25456 using 6282 atoms 
    25457 average map value = 0.0417, steps = 128 
    25458 shifted from previous position = 4.51 
    25459 rotated from previous position = 8.35 degrees 
    25460 atoms outside contour = 4033, contour level = 0.051121 
    25461  
    25462 Position of 9hud (#38) relative to cryosparc_P483_J69_005_volume_map.mrc (#40)
    25463 coordinates: 
    25464 Matrix rotation and translation 
    25465 0.65684785 0.74878514 0.08872268 11.05139992 
    25466 0.33454956 -0.39485965 0.85566491 105.25041377 
    25467 0.67574218 -0.53235953 -0.50986845 72.64892317 
    25468 Axis -0.88808312 -0.37558568 -0.26503541 
    25469 Axis point 0.00000000 65.04529101 13.14028850 
    25470 Rotation angle (degrees) 128.60443789 
    25471 Shift along axis -68.59964747 
    25472  
    25473 
    25474 > select subtract #38
    25475 
    25476 Nothing selected 
    25477 
    25478 > volume #40 level 0.0597
    25479 
    25480 > hide #!40 models
    25481 
    25482 > show #!40 models
    25483 
    25484 > hide #!38 models
    25485 
    25486 > show #!38 models
    25487 
    25488 > hide #!40 models
    25489 
    25490 > show #!40 models
    25491 
    25492 > hide #!38 models
    25493 
    25494 > show #!38 models
    25495 
    25496 > hide #!40 models
    25497 
    25498 > show #!40 models
    25499 
    25500 > hide #!40 models
    25501 
    25502 > show #!40 models
    25503 
    25504 > hide #!38 models
    25505 
    25506 > volume flip #40 axis z
    25507 
    25508 Opened cryosparc_P483_J69_005_volume_map.mrc z flip as #41, grid size
    25509 400,400,400, pixel 0.723, shown at step 1, values float32 
    25510 
    25511 > show #!38 models
    25512 
    25513 > select add #38
    25514 
    25515 6282 atoms, 6138 bonds, 1077 residues, 1 model selected 
    25516 
    25517 > view matrix models
    25518 > #38,0.65685,0.74879,0.088723,12.679,0.33455,-0.39486,0.85566,109.56,0.67574,-0.53236,-0.50987,57.685
    25519 
    25520 > view matrix models
    25521 > #38,-0.58254,0.54788,0.6004,210.02,0.59834,-0.2109,0.77299,61.815,0.55013,0.80954,-0.20496,22.25
    25522 
    25523 > view matrix models
    25524 > #38,-0.40435,-0.85962,0.31233,239.45,0.49216,0.083334,0.86651,66.149,-0.7709,0.50409,0.38937,235.48
    25525 
    25526 > view matrix models
    25527 > #38,-0.56895,-0.81456,0.11308,266.25,0.44686,-0.19079,0.87402,83.739,-0.69037,0.54781,0.47254,220.03
    25528 
    25529 > view matrix models
    25530 > #38,-0.56895,-0.81456,0.11308,265.73,0.44686,-0.19079,0.87402,80.959,-0.69037,0.54781,0.47254,214.99
    25531 
    25532 > fitmap #38 inMap #41
    25533 
    25534 Fit molecule 9hud (#38) to map cryosparc_P483_J69_005_volume_map.mrc z flip
    25535 (#41) using 6282 atoms 
    25536 average map value = 0.05473, steps = 216 
    25537 shifted from previous position = 2.37 
    25538 rotated from previous position = 33 degrees 
    25539 atoms outside contour = 3800, contour level = 0.059703 
    25540  
    25541 Position of 9hud (#38) relative to cryosparc_P483_J69_005_volume_map.mrc z
    25542 flip (#41) coordinates: 
    25543 Matrix rotation and translation 
    25544 -0.75082147 -0.55505166 -0.35802903 289.09205452 
    25545 0.04746292 -0.58599102 0.80892632 158.98706928 
    25546 -0.65879769 0.59036614 0.46631901 208.65076835 
    25547 Axis -0.30870385 0.42481867 0.85101765 
    25548 Axis point 172.41915491 63.65569402 0.00000000 
    25549 Rotation angle (degrees) 159.26804372 
    25550 Shift along axis 155.86233044 
    25551  
    25552 
    25553 > select subtract #38
    25554 
    25555 Nothing selected 
    25556 
    25557 > volume #41 level 0.05159
    25558 
    25559 > select add #38
    25560 
    25561 6282 atoms, 6138 bonds, 1077 residues, 1 model selected 
    25562 
    25563 > view matrix models
    25564 > #38,-0.75082,-0.55505,-0.35803,289.14,0.047463,-0.58599,0.80893,158.79,-0.6588,0.59037,0.46632,207.97
    25565 
    25566 > view matrix models
    25567 > #38,-0.75082,-0.55505,-0.35803,289.16,0.047463,-0.58599,0.80893,157.96,-0.6588,0.59037,0.46632,207.03
    25568 
    25569 > view matrix models
    25570 > #38,-0.75082,-0.55505,-0.35803,288.72,0.047463,-0.58599,0.80893,155.88,-0.6588,0.59037,0.46632,205.57
    25571 
    25572 > fitmap #38 inMap #41
    25573 
    25574 Fit molecule 9hud (#38) to map cryosparc_P483_J69_005_volume_map.mrc z flip
    25575 (#41) using 6282 atoms 
    25576 average map value = 0.05473, steps = 72 
    25577 shifted from previous position = 4.4 
    25578 rotated from previous position = 0.101 degrees 
    25579 atoms outside contour = 3342, contour level = 0.051588 
    25580  
    25581 Position of 9hud (#38) relative to cryosparc_P483_J69_005_volume_map.mrc z
    25582 flip (#41) coordinates: 
    25583 Matrix rotation and translation 
    25584 -0.75090265 -0.55404999 -0.35940760 289.07011046 
    25585 0.04645479 -0.58718152 0.80812117 159.19876899 
    25586 -0.65877702 0.59012412 0.46665444 208.66676414 
    25587 Axis -0.30899016 0.42432779 0.85115863 
    25588 Axis point 172.44704823 63.68649423 0.00000000 
    25589 Rotation angle (degrees) 159.34394496 
    25590 Shift along axis 155.84115924 
    25591  
    25592 
    25593 > view matrix models
    25594 > #38,-0.7509,-0.55405,-0.35941,287.93,0.046455,-0.58718,0.80812,155.5,-0.65878,0.59012,0.46665,206.09
    25595 
    25596 > fitmap #38 inMap #41
    25597 
    25598 Fit molecule 9hud (#38) to map cryosparc_P483_J69_005_volume_map.mrc z flip
    25599 (#41) using 6282 atoms 
    25600 average map value = 0.05473, steps = 92 
    25601 shifted from previous position = 4.65 
    25602 rotated from previous position = 0.00364 degrees 
    25603 atoms outside contour = 3341, contour level = 0.051588 
    25604  
    25605 Position of 9hud (#38) relative to cryosparc_P483_J69_005_volume_map.mrc z
    25606 flip (#41) coordinates: 
    25607 Matrix rotation and translation 
    25608 -0.75086696 -0.55406598 -0.35945751 289.07124867 
    25609 0.04643032 -0.58719553 0.80811239 159.20847697 
    25610 -0.65881943 0.59009517 0.46663119 208.66191835 
    25611 Axis -0.30902059 0.42431965 0.85115164 
    25612 Axis point 172.44904391 63.69342969 0.00000000 
    25613 Rotation angle (degrees) 159.34407294 
    25614 Shift along axis 155.82925281 
    25615  
    25616 
    25617 > select subtract #38
    25618 
    25619 Nothing selected 
    25620 
    25621 > combine #38 close false
    25622 
    25623 > hide #!38 models
    25624 
    25625 > select #42/A
    25626 
    25627 2567 atoms, 2550 bonds, 398 residues, 1 model selected 
    25628 
    25629 > select #42/M
    25630 
    25631 Nothing selected 
    25632 
    25633 > select #42/M
    25634 
    25635 Nothing selected 
    25636 
    25637 > select #42/I
    25638 
    25639 Nothing selected 
    25640 
    25641 > select #42/H
    25642 
    25643 1713 atoms, 1651 bonds, 322 residues, 1 model selected 
    25644 
    25645 > delete #42/H
    25646 
    25647 > select #42/N
    25648 
    25649 Nothing selected 
    25650 
    25651 > select #42/I
    25652 
    25653 Nothing selected 
    25654 
    25655 > select #42/L
    25656 
    25657 1750 atoms, 1686 bonds, 317 residues, 1 model selected 
    25658 
    25659 > delete #42/L
    25660 
    25661 > fitmap #42 inMap #41
    25662 
    25663 Fit molecule copy of 9hud (#42) to map cryosparc_P483_J69_005_volume_map.mrc z
    25664 flip (#41) using 2819 atoms 
    25665 average map value = 0.06533, steps = 56 
    25666 shifted from previous position = 0.821 
    25667 rotated from previous position = 3.38 degrees 
    25668 atoms outside contour = 1262, contour level = 0.051588 
    25669  
    25670 Position of copy of 9hud (#42) relative to
    25671 cryosparc_P483_J69_005_volume_map.mrc z flip (#41) coordinates: 
    25672 Matrix rotation and translation 
    25673 -0.73693347 -0.57914780 -0.34859273 288.27078922 
    25674 0.03048667 -0.54364745 0.83875981 157.64342584 
    25675 -0.67527744 0.60748274 0.41828829 210.31462354 
    25676 Axis -0.31712566 0.44794803 0.83592696 
    25677 Axis point 174.06638485 60.58096428 0.00000000 
    25678 Rotation angle (degrees) 158.61421520 
    25679 Shift along axis 155.00566094 
    25680  
    25681 
    25682 > volume #41 level 0.06516
    25683 
    25684 > select add #42
    25685 
    25686 2819 atoms, 2801 bonds, 438 residues, 1 model selected 
    25687 
    25688 > view matrix models
    25689 > #42,-0.73693,-0.57915,-0.34859,287.85,0.030487,-0.54365,0.83876,156.54,-0.67528,0.60748,0.41829,208.51
    25690 
    25691 > fitmap #42 inMap #41
    25692 
    25693 Fit molecule copy of 9hud (#42) to map cryosparc_P483_J69_005_volume_map.mrc z
    25694 flip (#41) using 2819 atoms 
    25695 average map value = 0.06533, steps = 76 
    25696 shifted from previous position = 2.15 
    25697 rotated from previous position = 0.0105 degrees 
    25698 atoms outside contour = 1566, contour level = 0.065161 
    25699  
    25700 Position of copy of 9hud (#42) relative to
    25701 cryosparc_P483_J69_005_volume_map.mrc z flip (#41) coordinates: 
    25702 Matrix rotation and translation 
    25703 -0.73689140 -0.57919551 -0.34860239 288.27541199 
    25704 0.03038436 -0.54353165 0.83883856 157.64897324 
    25705 -0.67532796 0.60754087 0.41812229 210.31189981 
    25706 Axis -0.31716299 0.44801683 0.83587592 
    25707 Axis point 174.07498439 60.57428048 0.00000000 
    25708 Rotation angle (degrees) 158.61485484 
    25709 Shift along axis 154.99375355 
    25710  
    25711 
    25712 > view matrix models
    25713 > #42,-0.73689,-0.5792,-0.3486,286.89,0.030384,-0.54353,0.83884,156.41,-0.67533,0.60754,0.41812,208.9
    25714 
    25715 > view matrix models
    25716 > #42,-0.73689,-0.5792,-0.3486,287.57,0.030384,-0.54353,0.83884,158.73,-0.67533,0.60754,0.41812,212.26
    25717 
    25718 > view matrix models
    25719 > #42,-0.73689,-0.5792,-0.3486,287.63,0.030384,-0.54353,0.83884,158.66,-0.67533,0.60754,0.41812,212.24
    25720 
    25721 > fitmap #42 inMap #41
    25722 
    25723 Fit molecule copy of 9hud (#42) to map cryosparc_P483_J69_005_volume_map.mrc z
    25724 flip (#41) using 2819 atoms 
    25725 average map value = 0.06533, steps = 76 
    25726 shifted from previous position = 2.27 
    25727 rotated from previous position = 0.0141 degrees 
    25728 atoms outside contour = 1565, contour level = 0.065161 
    25729  
    25730 Position of copy of 9hud (#42) relative to
    25731 cryosparc_P483_J69_005_volume_map.mrc z flip (#41) coordinates: 
    25732 Matrix rotation and translation 
    25733 -0.73682803 -0.57935101 -0.34847792 288.27467210 
    25734 0.03043622 -0.54334125 0.83896003 157.62886136 
    25735 -0.67539477 0.60756292 0.41798231 210.32004980 
    25736 Axis -0.31717295 0.44810058 0.83582725 
    25737 Axis point 174.07853761 60.56677345 0.00000000 
    25738 Rotation angle (degrees) 158.60591524 
    25739 Shift along axis 154.99188631 
    25740  
    25741 
    25742 > select subtract #42
    25743 
    25744 Nothing selected 
    25745 
    25746 > show #!38 models
    25747 
    25748 > mmaker #38 to #42
    25749 
    25750 Parameters 
    25751 --- 
    25752 Chain pairing | bb 
    25753 Alignment algorithm | Needleman-Wunsch 
    25754 Similarity matrix | BLOSUM-62 
    25755 SS fraction | 0.3 
    25756 Gap open (HH/SS/other) | 18/18/6 
    25757 Gap extend | 1 
    25758 SS matrix |  |  | H | S | O 
    25759 ---|---|---|--- 
    25760 H | 6 | -9 | -6 
    25761 S |  | 6 | -6 
    25762 O |  |  | 4 
    25763 Iteration cutoff | 2 
    25764  
    25765 Matchmaker copy of 9hud, chain A (#42) with 9hud, chain A (#38), sequence
    25766 alignment score = 1849.2 
    25767 RMSD between 332 pruned atom pairs is 0.000 angstroms; (across all 332 pairs:
    25768 0.000) 
    25769  
    25770 
    25771 > hide #!42 models
    25772 
    25773 > hide #!38 models
    25774 
    25775 > show #!38 models
    25776 
    25777 > show #!37 models
    25778 
    25779 > mmaker #37 to #38
    25780 
    25781 Parameters 
    25782 --- 
    25783 Chain pairing | bb 
    25784 Alignment algorithm | Needleman-Wunsch 
    25785 Similarity matrix | BLOSUM-62 
    25786 SS fraction | 0.3 
    25787 Gap open (HH/SS/other) | 18/18/6 
    25788 Gap extend | 1 
    25789 SS matrix |  |  | H | S | O 
    25790 ---|---|---|--- 
    25791 H | 6 | -9 | -6 
    25792 S |  | 6 | -6 
    25793 O |  |  | 4 
    25794 Iteration cutoff | 2 
    25795  
    25796 Matchmaker 9hud, chain A (#38) with 1ezx, chain A (#37), sequence alignment
    25797 score = 1674.4 
    25798 RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
    25799 0.519) 
    25800  
    25801 
    25802 > open /Users/amy/Downloads/cryosparc_P483_J81_008_volume_map.mrc
    25803 
    25804 Opened cryosparc_P483_J81_008_volume_map.mrc as #43, grid size 400,400,400,
    25805 pixel 0.723, shown at level 0.00732, step 2, values float32 
    25806 
    25807 > hide #!37 models
    25808 
    25809 > hide #!38 models
    25810 
    25811 > hide #!41 models
    25812 
    25813 > surface dust #43 size 7.23
    25814 
    25815 > volume #43 level 0.06119
    25816 
    25817 > volume #43 level 0.0273
    25818 
    25819 > volume flip #43 axis z
    25820 
    25821 Opened cryosparc_P483_J81_008_volume_map.mrc z flip as #44, grid size
    25822 400,400,400, pixel 0.723, shown at step 1, values float32 
    25823 
    25824 > transparency #44 50
    25825 
    25826 > volume #44 level 0.03941
    25827 
    25828 > volume #44 level 0.04042
    25829 
    25830 > open /Users/amy/Downloads/cryosparc_P483_J66_004_volume_map.mrc
    25831 
    25832 Opened cryosparc_P483_J66_004_volume_map.mrc as #45, grid size 400,400,400,
    25833 pixel 0.723, shown at level 0.00725, step 2, values float32 
    25834 
    25835 > volume #45 level 0.06094
    25836 
    25837 > open /Users/amy/Downloads/cryosparc_P483_J72_006_volume_map.mrc
    25838 
    25839 Opened cryosparc_P483_J72_006_volume_map.mrc as #46, grid size 400,400,400,
    25840 pixel 0.723, shown at level 0.0048, step 2, values float32 
    25841 
    25842 > volume #46 level 0.04807
    25843 
    25844 > transparency #46 50
    25845 
    25846 > show #!42 models
    25847 
    25848 > hide #!42 models
    25849 
    25850 > show #!38 models
    25851 
    25852 > select add #38
    25853 
    25854 6282 atoms, 6138 bonds, 1077 residues, 1 model selected 
    25855 
    25856 > view matrix models
    25857 > #38,-0.73683,-0.57935,-0.34848,292.33,0.030436,-0.54334,0.83896,164.74,-0.67539,0.60756,0.41798,237.37
    25858 
    25859 > view matrix models
    25860 > #38,-0.38309,-0.69929,0.60352,229.08,0.62032,0.28936,0.72902,40.857,-0.68443,0.65365,0.32294,238.22
    25861 
    25862 > view matrix models
    25863 > #38,-0.38309,-0.69929,0.60352,226.04,0.62032,0.28936,0.72902,38.256,-0.68443,0.65365,0.32294,241.06
    25864 
    25865 > view matrix models
    25866 > #38,-0.34943,-0.72907,0.58852,222.05,0.61787,0.29288,0.72969,38.499,-0.70437,0.61861,0.34813,245.24
    25867 
    25868 > view matrix models
    25869 > #38,-0.34943,-0.72907,0.58852,222.59,0.61787,0.29288,0.72969,38.714,-0.70437,0.61861,0.34813,242.8
    25870 
    25871 > fitmap #38 inMap #46
    25872 
    25873 Fit molecule 9hud (#38) to map cryosparc_P483_J72_006_volume_map.mrc (#46)
    25874 using 6282 atoms 
    25875 average map value = 0.0399, steps = 112 
    25876 shifted from previous position = 6.23 
    25877 rotated from previous position = 3.87 degrees 
    25878 atoms outside contour = 3940, contour level = 0.048075 
    25879  
    25880 Position of 9hud (#38) relative to cryosparc_P483_J72_006_volume_map.mrc (#46)
    25881 coordinates: 
    25882 Matrix rotation and translation 
    25883 -0.34701016 -0.76389374 0.54410505 226.91723804 
    25884 0.57651318 0.28385608 0.76619729 40.13005322 
    25885 -0.73974084 0.57956197 0.34189387 251.72894877 
    25886 Axis -0.10005014 0.68823502 0.71855586 
    25887 Axis point 172.83638513 16.61736328 0.00000000 
    25888 Rotation angle (degrees) 111.13889774 
    25889 Shift along axis 185.79711858 
    25890  
    25891 
    25892 > select subtract #38
    25893 
    25894 Nothing selected 
    25895 
    25896 > volume flip #46 axis z
    25897 
    25898 Opened cryosparc_P483_J72_006_volume_map.mrc z flip as #47, grid size
    25899 400,400,400, pixel 0.723, shown at step 1, values float32 
    25900 
    25901 > select add #38
    25902 
    25903 6282 atoms, 6138 bonds, 1077 residues, 1 model selected 
    25904 
    25905 > view matrix models
    25906 > #38,-0.43781,-0.43705,0.78569,225.72,0.89875,-0.18935,0.39548,11.956,-0.024068,0.87928,0.47569,125.36
    25907 
    25908 > view matrix models
    25909 > #38,0.17782,0.26753,0.947,99.291,0.050808,-0.96355,0.26266,177.44,0.98275,0.001409,-0.18493,8.0567
    25910 
    25911 > view matrix models
    25912 > #38,0.17782,0.26753,0.947,103.63,0.050808,-0.96355,0.26266,172.68,0.98275,0.001409,-0.18493,-1.716
    25913 
    25914 > view matrix models
    25915 > #38,0.63642,0.20154,0.74455,36.153,-0.42467,-0.71425,0.55633,234.65,0.64391,-0.67025,-0.36898,79.951
    25916 
    25917 > view matrix models
    25918 > #38,0.63642,0.20154,0.74455,34.766,-0.42467,-0.71425,0.55633,241.95,0.64391,-0.67025,-0.36898,57.4
    25919 
    25920 > fitmap #38 inMap #47
    25921 
    25922 Fit molecule 9hud (#38) to map cryosparc_P483_J72_006_volume_map.mrc z flip
    25923 (#47) using 6282 atoms 
    25924 average map value = 0.06343, steps = 124 
    25925 shifted from previous position = 5.23 
    25926 rotated from previous position = 14 degrees 
    25927 atoms outside contour = 2477, contour level = 0.048075 
    25928  
    25929 Position of 9hud (#38) relative to cryosparc_P483_J72_006_volume_map.mrc z
    25930 flip (#47) coordinates: 
    25931 Matrix rotation and translation 
    25932 0.48056680 0.06585233 0.87448215 60.37965921 
    25933 -0.56537086 -0.73901641 0.36634758 262.76707770 
    25934 0.67038150 -0.67046120 -0.31791576 52.06857630 
    25935 Axis -0.84232947 0.16581649 -0.51282156 
    25936 Axis point 0.00000000 144.40291810 -47.17976586 
    25937 Rotation angle (degrees) 142.01600325 
    25938 Shift along axis -33.99034036 
    25939  
    25940 
    25941 > select subtract #38
    25942 
    25943 Nothing selected 
    25944 
    25945 > hide #!47 models
    25946 
    25947 > show #!47 models
    25948 
    25949 > hide #!38 models
    25950 
    25951 > show #!38 models
    25952 
    25953 > hide #!38 models
    25954 
    25955 > hide #!45 models
    25956 
    25957 > show #!44 models
    25958 
    25959 > show #!38 models
    25960 
    25961 > select add #38
    25962 
    25963 6282 atoms, 6138 bonds, 1077 residues, 1 model selected 
    25964 
    25965 > view matrix models
    25966 > #38,0.48057,0.065852,0.87448,65.866,-0.56537,-0.73902,0.36635,260.8,0.67038,-0.67046,-0.31792,67.074
    25967 
    25968 > view matrix models
    25969 > #38,0.24561,0.13628,0.95974,99.26,-0.61016,-0.7476,0.2623,269.51,0.75324,-0.65002,-0.10047,50.465
    25970 
    25971 > view matrix models
    25972 > #38,0.24561,0.13628,0.95974,97.908,-0.61016,-0.7476,0.2623,267.42,0.75324,-0.65002,-0.10047,51.929
    25973 
    25974 > fitmap #38 inMap #44
    25975 
    25976 Fit molecule 9hud (#38) to map cryosparc_P483_J81_008_volume_map.mrc z flip
    25977 (#44) using 6282 atoms 
    25978 average map value = 0.03783, steps = 168 
    25979 shifted from previous position = 5.42 
    25980 rotated from previous position = 16.7 degrees 
    25981 atoms outside contour = 3802, contour level = 0.040419 
    25982  
    25983 Position of 9hud (#38) relative to cryosparc_P483_J81_008_volume_map.mrc z
    25984 flip (#44) coordinates: 
    25985 Matrix rotation and translation 
    25986 0.06820670 -0.05795023 0.99598676 133.26750912 
    25987 -0.73706857 -0.67572583 0.01115934 290.51260544 
    25988 0.67236729 -0.73487167 -0.08880232 64.60372631 
    25989 Axis -0.70414963 0.30545181 -0.64099336 
    25990 Axis point 0.00000000 181.24183814 -90.37493056 
    25991 Rotation angle (degrees) 148.01217964 
    25992 Shift along axis -46.51322447 
    25993  
    25994 
    25995 > select subtract #38
    25996 
    25997 Nothing selected 
    25998 
    25999 > hide #!44 models
    26000 
    26001 > show #!43 models
    26002 
    26003 > transparency #38 50
    26004 
    26005 > transparency #43 50
    26006 
    26007 > select add #38
    26008 
    26009 6282 atoms, 6138 bonds, 1077 residues, 1 model selected 
    26010 
    26011 > view matrix models
    26012 > #38,-0.34778,-0.62711,0.69698,224.64,0.7034,0.317,0.6362,16.77,-0.61991,0.71151,0.33086,208.25
    26013 
    26014 > view matrix models
    26015 > #38,-0.34778,-0.62711,0.69698,225.83,0.7034,0.317,0.6362,17.542,-0.61991,0.71151,0.33086,207.48
    26016 
    26017 > view matrix models
    26018 > #38,-0.28771,-0.41373,0.86374,206.06,0.80892,0.37784,0.45043,0.83954,-0.51271,0.82829,0.22596,187.36
    26019 
    26020 > view matrix models
    26021 > #38,-0.28771,-0.41373,0.86374,206.43,0.80892,0.37784,0.45043,-2.4203,-0.51271,0.82829,0.22596,194.27
    26022 
    26023 > view matrix models
    26024 > #38,-0.43329,-0.6387,0.63587,240.94,0.33837,0.53864,0.77161,61.821,-0.83533,0.54948,-0.01727,259.04
    26025 
    26026 > view matrix models
    26027 > #38,-0.43329,-0.6387,0.63587,240.15,0.33837,0.53864,0.77161,62.236,-0.83533,0.54948,-0.01727,256.27
    26028 
    26029 > view matrix models
    26030 > #38,-0.10971,-0.34204,0.93326,173.87,0.39597,0.84616,0.35667,46.512,-0.91169,0.40867,0.042608,273
    26031 
    26032 > view matrix models
    26033 > #38,-0.10971,-0.34204,0.93326,174.05,0.39597,0.84616,0.35667,43.272,-0.91169,0.40867,0.042608,270.13
    26034 
    26035 > hide #!43 models
    26036 
    26037 > show #!44 models
    26038 
    26039 > view matrix models
    26040 > #38,0.33372,0.10106,0.93724,86.86,-0.90444,-0.24596,0.34856,290.96,0.26575,-0.964,0.009315,136.98
    26041 
    26042 > view matrix models
    26043 > #38,-0.0077799,0.047421,0.99884,142.16,-0.55565,-0.83068,0.035109,262.15,0.83138,-0.55473,0.032812,31.52
    26044 
    26045 > view matrix models
    26046 > #38,-0.0077799,0.047421,0.99884,141.96,-0.55565,-0.83068,0.035109,262.22,0.83138,-0.55473,0.032812,29.958
    26047 
    26048 > fitmap #38 inMap #44
    26049 
    26050 Fit molecule 9hud (#38) to map cryosparc_P483_J81_008_volume_map.mrc z flip
    26051 (#44) using 6282 atoms 
    26052 average map value = 0.03751, steps = 112 
    26053 shifted from previous position = 5.86 
    26054 rotated from previous position = 9.02 degrees 
    26055 atoms outside contour = 3835, contour level = 0.040419 
    26056  
    26057 Position of 9hud (#38) relative to cryosparc_P483_J81_008_volume_map.mrc z
    26058 flip (#44) coordinates: 
    26059 Matrix rotation and translation 
    26060 0.05690807 -0.02329864 0.99810753 137.02419950 
    26061 -0.65514588 -0.75524488 0.01972424 280.23565345 
    26062 0.75335606 -0.65502851 -0.05824354 46.13973405 
    26063 Axis -0.70561938 0.25594766 -0.66075116 
    26064 Axis point 0.00000000 166.68305562 -94.19367789 
    26065 Rotation angle (degrees) 151.43679087 
    26066 Shift along axis -55.44815397 
    26067  
    26068 
    26069 > select subtract #38
    26070 
    26071 Nothing selected 
    26072 
    26073 > select add #38
    26074 
    26075 6282 atoms, 6138 bonds, 1077 residues, 1 model selected 
    26076 
    26077 > view matrix models
    26078 > #38,-0.54924,-0.83446,0.044834,275.94,-0.071518,-0.0065171,-0.99742,171.91,0.8326,-0.55103,-0.0561,29.588
    26079 
    26080 > view matrix models
    26081 > #38,-0.095818,-0.5899,-0.80177,205.42,-0.19261,0.80124,-0.56649,154.68,0.97659,0.10015,-0.1904,-16.494
    26082 
    26083 > view matrix models
    26084 > #38,-0.39728,-0.77299,0.49462,243.92,-0.63802,-0.15476,-0.75431,264.16,0.65962,-0.61525,-0.4317,64.108
    26085 
    26086 > view matrix models
    26087 > #38,0.28514,0.071787,0.95579,97.806,-0.70813,-0.65625,0.26054,281.81,0.64594,-0.75112,-0.13629,67.792
    26088 
    26089 > view matrix models
    26090 > #38,0.28514,0.071787,0.95579,96.286,-0.70813,-0.65625,0.26054,282.4,0.64594,-0.75112,-0.13629,66.958
    26091 
    26092 > fitmap #38 inMap #44
    26093 
    26094 Fit molecule 9hud (#38) to map cryosparc_P483_J81_008_volume_map.mrc z flip
    26095 (#44) using 6282 atoms 
    26096 average map value = 0.03783, steps = 168 
    26097 shifted from previous position = 3.71 
    26098 rotated from previous position = 14.8 degrees 
    26099 atoms outside contour = 3801, contour level = 0.040419 
    26100  
    26101 Position of 9hud (#38) relative to cryosparc_P483_J81_008_volume_map.mrc z
    26102 flip (#44) coordinates: 
    26103 Matrix rotation and translation 
    26104 0.06820710 -0.05791598 0.99598872 133.26635838 
    26105 -0.73705893 -0.67573598 0.01118160 290.51125280 
    26106 0.67237782 -0.73486504 -0.08877748 64.60105058 
    26107 Axis -0.70414832 0.30543677 -0.64100197 
    26108 Axis point 0.00000000 181.23877487 -90.37820158 
    26109 Rotation angle (degrees) 148.01136342 
    26110 Shift along axis -46.51586553 
    26111  
    26112 
    26113 > select subtract #38
    26114 
    26115 Nothing selected 
    26116 
    26117 > show #35 models
    26118 
    26119 > select add #35
    26120 
    26121 5953 atoms, 5684 bonds, 699 residues, 1 model selected 
    26122 
    26123 > view matrix models
    26124 > #35,-0.44103,0.30301,0.84479,116.92,-0.07491,-0.95043,0.30179,113.9,0.89436,0.069815,0.44187,126.48
    26125 
    26126 > view matrix models
    26127 > #35,0.84908,-0.51887,-0.099238,120.01,0.43126,0.7893,-0.43705,123.08,0.3051,0.3283,0.89394,124.61
    26128 
    26129 > mmaker #35 to #38
    26130 
    26131 Parameters 
    26132 --- 
    26133 Chain pairing | bb 
    26134 Alignment algorithm | Needleman-Wunsch 
    26135 Similarity matrix | BLOSUM-62 
    26136 SS fraction | 0.3 
    26137 Gap open (HH/SS/other) | 18/18/6 
    26138 Gap extend | 1 
    26139 SS matrix |  |  | H | S | O 
    26140 ---|---|---|--- 
    26141 H | 6 | -9 | -6 
    26142 S |  | 6 | -6 
    26143 O |  |  | 4 
    26144 Iteration cutoff | 2 
    26145  
    26146 Matchmaker 9hud, chain A (#38) with 8pi2, chain A (#35), sequence alignment
    26147 score = 1753.4 
    26148 RMSD between 220 pruned atom pairs is 0.913 angstroms; (across all 331 pairs:
    26149 6.169) 
    26150  
    26151 
    26152 > hide #!38 models
    26153 
    26154 > fitmap #35 inMap #44
    26155 
    26156 Fit molecule 8pi2 (#35) to map cryosparc_P483_J81_008_volume_map.mrc z flip
    26157 (#44) using 5953 atoms 
    26158 average map value = 0.03426, steps = 124 
    26159 shifted from previous position = 5.39 
    26160 rotated from previous position = 16.8 degrees 
    26161 atoms outside contour = 3776, contour level = 0.040419 
    26162  
    26163 Position of 8pi2 (#35) relative to cryosparc_P483_J81_008_volume_map.mrc z
    26164 flip (#44) coordinates: 
    26165 Matrix rotation and translation 
    26166 -0.91986475 0.28876257 0.26545250 167.24012801 
    26167 0.39170890 0.64122785 0.65984164 130.22015692 
    26168 0.02032204 0.71094517 -0.70295376 131.41006954 
    26169 Axis 0.18875717 0.90541952 0.38024495 
    26170 Axis point 72.13306632 0.00000000 33.49476567 
    26171 Rotation angle (degrees) 172.22007439 
    26172 Shift along axis 199.43966055 
    26173  
    26174 
    26175 > mmaker #35 to #38
    26176 
    26177 Parameters 
    26178 --- 
    26179 Chain pairing | bb 
    26180 Alignment algorithm | Needleman-Wunsch 
    26181 Similarity matrix | BLOSUM-62 
    26182 SS fraction | 0.3 
    26183 Gap open (HH/SS/other) | 18/18/6 
    26184 Gap extend | 1 
    26185 SS matrix |  |  | H | S | O 
    26186 ---|---|---|--- 
    26187 H | 6 | -9 | -6 
    26188 S |  | 6 | -6 
    26189 O |  |  | 4 
    26190 Iteration cutoff | 2 
    26191  
    26192 Matchmaker 9hud, chain A (#38) with 8pi2, chain A (#35), sequence alignment
    26193 score = 1753.4 
    26194 RMSD between 220 pruned atom pairs is 0.913 angstroms; (across all 331 pairs:
    26195 6.169) 
    26196  
    26197 
    26198 > select subtract #35
    26199 
    26200 Nothing selected 
    26201 
    26202 > hide #!44 models
    26203 
    26204 > show #!44 models
    26205 
    26206 > hide #35 models
    26207 
    26208 > show #!38 models
    26209 
    26210 > show #!37 models
    26211 
    26212 > mmaker #37 to #38
    26213 
    26214 Parameters 
    26215 --- 
    26216 Chain pairing | bb 
    26217 Alignment algorithm | Needleman-Wunsch 
    26218 Similarity matrix | BLOSUM-62 
    26219 SS fraction | 0.3 
    26220 Gap open (HH/SS/other) | 18/18/6 
    26221 Gap extend | 1 
    26222 SS matrix |  |  | H | S | O 
    26223 ---|---|---|--- 
    26224 H | 6 | -9 | -6 
    26225 S |  | 6 | -6 
    26226 O |  |  | 4 
    26227 Iteration cutoff | 2 
    26228  
    26229 Matchmaker 9hud, chain A (#38) with 1ezx, chain A (#37), sequence alignment
    26230 score = 1674.4 
    26231 RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
    26232 0.519) 
    26233  
    26234 
    26235 > hide #!38 models
    26236 
    26237 > show #!38 models
    26238 
    26239 > hide #!37 models
    26240 
    26241 > hide #!38 models
    26242 
    26243 > hide #!44 models
    26244 
    26245 > show #!47 models
    26246 
    26247 > show #!38 models
    26248 
    26249 > select add #38
    26250 
    26251 6282 atoms, 6138 bonds, 1077 residues, 1 model selected 
    26252 
    26253 > view matrix models
    26254 > #38,0.12454,-0.84591,0.51858,160.56,-0.95063,-0.25145,-0.18186,310.42,0.28423,-0.47033,-0.83547,125.18
    26255 
    26256 > view matrix models
    26257 > #38,0.67023,0.035917,0.74129,37.629,-0.48282,-0.73746,0.47227,246.9,0.56363,-0.67443,-0.47692,84.334
    26258 
    26259 > view matrix models
    26260 > #38,0.67023,0.035917,0.74129,35.095,-0.48282,-0.73746,0.47227,252.87,0.56363,-0.67443,-0.47692,70.069
    26261 
    26262 > view matrix models
    26263 > #38,0.72811,0.043332,0.68409,26.371,-0.55319,-0.55218,0.62376,255,0.40477,-0.8326,-0.37807,100.03
    26264 
    26265 > view matrix models
    26266 > #38,0.72811,0.043332,0.68409,24.921,-0.55319,-0.55218,0.62376,251.59,0.40477,-0.8326,-0.37807,100.94
    26267 
    26268 > fitmap #38 inMap #47
    26269 
    26270 Fit molecule 9hud (#38) to map cryosparc_P483_J72_006_volume_map.mrc z flip
    26271 (#47) using 6282 atoms 
    26272 average map value = 0.06343, steps = 212 
    26273 shifted from previous position = 1.3 
    26274 rotated from previous position = 22.3 degrees 
    26275 atoms outside contour = 2481, contour level = 0.048075 
    26276  
    26277 Position of 9hud (#38) relative to cryosparc_P483_J72_006_volume_map.mrc z
    26278 flip (#47) coordinates: 
    26279 Matrix rotation and translation 
    26280 0.48048529 0.06576118 0.87453379 60.39061577 
    26281 -0.56539285 -0.73906673 0.36621209 262.77340318 
    26282 0.67042137 -0.67041468 -0.31792978 52.06026777 
    26283 Axis -0.84230945 0.16585123 -0.51284322 
    26284 Axis point 0.00000000 144.40605826 -47.18056764 
    26285 Rotation angle (degrees) 142.02279334 
    26286 Shift along axis -33.98504950 
    26287  
    26288 
    26289 > select subtract #38
    26290 
    26291 Nothing selected 
    26292 
    26293 > volume #47 level 0.05522
    26294 
    26295 > volume #47 level 0.04807
    26296 
    26297 > show #!37 models
    26298 
    26299 > mmaker #37 to #38
    26300 
    26301 Parameters 
    26302 --- 
    26303 Chain pairing | bb 
    26304 Alignment algorithm | Needleman-Wunsch 
    26305 Similarity matrix | BLOSUM-62 
    26306 SS fraction | 0.3 
    26307 Gap open (HH/SS/other) | 18/18/6 
    26308 Gap extend | 1 
    26309 SS matrix |  |  | H | S | O 
    26310 ---|---|---|--- 
    26311 H | 6 | -9 | -6 
    26312 S |  | 6 | -6 
    26313 O |  |  | 4 
    26314 Iteration cutoff | 2 
    26315  
    26316 Matchmaker 9hud, chain A (#38) with 1ezx, chain A (#37), sequence alignment
    26317 score = 1674.4 
    26318 RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
    26319 0.519) 
    26320  
    26321 
    26322 > volume #47 level 0.0495
    26323 
    26324 > volume #47 level 0.01949
    26325 
    26326 > volume #47 level 0.02878
    26327 
    26328 > volume gaussian #47 sDev 2
    26329 
    26330 Opened cryosparc_P483_J72_006_volume_map.mrc z flip gaussian as #48, grid size
    26331 400,400,400, pixel 0.723, shown at step 1, values float32 
    26332 
    26333 > volume #48 level 0.002656
    26334 
    26335 > volume #48 level 0.001381
    26336 
    26337 > surface dust #48 size 7.23
    26338 
    26339 > show #!44 models
    26340 
    26341 > hide #!38 models
    26342 
    26343 > hide #!37 models
    26344 
    26345 > volume gaussian #44 sDev 2
    26346 
    26347 Opened cryosparc_P483_J81_008_volume_map.mrc z flip gaussian as #49, grid size
    26348 400,400,400, pixel 0.723, shown at step 1, values float32 
    26349 
    26350 > surface dust #49 size 7.23
    26351 
    26352 > volume #49 level 0.01018
    26353 
    26354 Cell requested for row 3 is out of bounds for table with 3 rows! Resizing
    26355 table model. 
    26356 
    26357 > save "/Users/amy/Desktop/SPA AAT_HNE/9C5_Fab_AAT_HNE/For mask
    26358 > generation/hne_J81localrefine.mrc" models #49
    26359 
    26360 > volume #49 level 0.01049
    26361 
    26362 > open /Users/amy/Downloads/cryosparc_P483_J82_005_volume_map.mrc
    26363 
    26364 Opened cryosparc_P483_J82_005_volume_map.mrc as #50, grid size 400,400,400,
    26365 pixel 0.723, shown at level 0.00546, step 2, values float32 
    26366 
    26367 > volume #50 level 0.0526
    26368 
    26369 > open /Users/amy/Downloads/cryosparc_P483_J90_004_volume_map.mrc
    26370 
    26371 Opened cryosparc_P483_J90_004_volume_map.mrc as #51, grid size 400,400,400,
    26372 pixel 0.723, shown at level 0.00654, step 2, values float32 
    26373 
    26374 > surface dust #51 size 7.23
    26375 
    26376 > volume #51 level 0.03836
    26377 
    26378 > open /Users/amy/Downloads/cryosparc_P483_J89_003_volume_map.mrc
    26379 
    26380 Opened cryosparc_P483_J89_003_volume_map.mrc as #52, grid size 400,400,400,
    26381 pixel 0.723, shown at level 0.00398, step 2, values float32 
    26382 
    26383 > volume #52 level 0.01728
    26384 
    26385 > volume #52 level 0.004928
    26386 
    26387 > hide #!52 models
    26388 
    26389 > show #!44 models
    26390 
    26391 > open /Users/amy/Downloads/cryosparc_P483_J93_005_volume_map.mrc
    26392 
    26393 Opened cryosparc_P483_J93_005_volume_map.mrc as #53, grid size 400,400,400,
    26394 pixel 0.723, shown at level 0.00624, step 2, values float32 
    26395 
    26396 > volume #53 level 0.03597
    26397 
    26398 > open /Users/amy/Downloads/cryosparc_P483_J96_002_volume_map.mrc
    26399 
    26400 Opened cryosparc_P483_J96_002_volume_map.mrc as #54, grid size 400,400,400,
    26401 pixel 0.723, shown at level 0.00203, step 2, values float32 
    26402 
    26403 > volume #54 level 0.01882
    26404 
    26405 > volume #54 level 0.01406
    26406 
    26407 > open /Users/amy/Downloads/cryosparc_P483_J99_003_volume_map.mrc
    26408 
    26409 Opened cryosparc_P483_J99_003_volume_map.mrc as #55, grid size 400,400,400,
    26410 pixel 0.723, shown at level 0.00233, step 2, values float32 
    26411 
    26412 > surface dust #55 size 7.23
    26413 
    26414 > volume #55 level 0.011
    26415 
    26416 > ui mousemode right "tape measure"
    26417 
    26418 > marker segment #56 position 137.9,161.4,84.92 toPosition 127.8,150.1,133.2
    26419 > color yellow radius 0.1807 label 50.59 labelHeight 5.059 labelColor yellow
    26420 
    26421 > marker segment #56 position 137.6,155.7,84.27 toPosition 148.8,133.1,193.5
    26422 > color yellow radius 0.1807 label 112.1 labelHeight 11.21 labelColor yellow
    26423 
    26424 > marker segment #56 position 139,177,192 toPosition 130,91.37,164 color
    26425 > yellow radius 0.1807 label 90.59 labelHeight 9.059 labelColor yellow
    26426 
    26427 > close #56
    26428 
    26429 > transparency #55 50
    26430 
    26431 > show #!38 models
    26432 
    26433 > select add #38
    26434 
    26435 6282 atoms, 6138 bonds, 1077 residues, 1 model selected 
    26436 
    26437 > select subtract #38
    26438 
    26439 Nothing selected 
    26440 
    26441 > volume flip #55 axis z
    26442 
    26443 Opened cryosparc_P483_J99_003_volume_map.mrc z flip as #56, grid size
    26444 400,400,400, pixel 0.723, shown at step 1, values float32 
    26445 
    26446 > transparency #56 50
    26447 
    26448 > select add #38
    26449 
    26450 6282 atoms, 6138 bonds, 1077 residues, 1 model selected 
    26451 
    26452 > ui mousemode right "translate selected models"
    26453 
    26454 > view matrix models
    26455 > #38,0.48049,0.065761,0.87453,61.743,-0.56539,-0.73907,0.36621,262.06,0.67042,-0.67041,-0.31793,59.233
    26456 
    26457 > view matrix models
    26458 > #38,0.61181,-0.23623,0.75491,54.055,-0.64298,-0.70439,0.30068,273.82,0.46072,-0.66935,-0.58285,95.671
    26459 
    26460 > view matrix models
    26461 > #38,0.50154,0.032674,0.86452,59.807,-0.035285,-0.99768,0.058177,191.99,0.86441,-0.059683,-0.49923,7.3804
    26462 
    26463 > view matrix models
    26464 > #38,0.50154,0.032674,0.86452,52.131,-0.035285,-0.99768,0.058177,176.02,0.86441,-0.059683,-0.49923,12.857
    26465 
    26466 > view matrix models
    26467 > #38,0.35345,0.1643,0.92091,69.799,-0.028974,-0.98206,0.18633,172.82,0.93501,-0.09254,-0.34235,0.99177
    26468 
    26469 > view matrix models
    26470 > #38,0.66671,0.39133,0.63431,15.122,-0.22913,-0.70224,0.67407,187.64,0.70922,-0.59475,-0.37853,56.427
    26471 
    26472 > view matrix models
    26473 > #38,0.66671,0.39133,0.63431,20.436,-0.22913,-0.70224,0.67407,208.21,0.70922,-0.59475,-0.37853,56.608
    26474 
    26475 > view matrix models
    26476 > #38,0.81008,0.3223,0.48979,2.2149,-0.16331,-0.67827,0.71643,196.35,0.56311,-0.66036,-0.49682,83.714
    26477 
    26478 > fitmap #38 inMap #56
    26479 
    26480 Fit molecule 9hud (#38) to map cryosparc_P483_J99_003_volume_map.mrc z flip
    26481 (#56) using 6282 atoms 
    26482 average map value = 0.03831, steps = 132 
    26483 shifted from previous position = 1.92 
    26484 rotated from previous position = 15.8 degrees 
    26485 atoms outside contour = 568, contour level = 0.011004 
    26486  
    26487 Position of 9hud (#38) relative to cryosparc_P483_J99_003_volume_map.mrc z
    26488 flip (#56) coordinates: 
    26489 Matrix rotation and translation 
    26490 0.71987433 0.56582857 0.40201864 5.33395219 
    26491 -0.00113467 -0.57823035 0.81587277 166.00801694 
    26492 0.69410350 -0.58778202 -0.41561115 58.96322716 
    26493 Axis -0.91042678 -0.18944963 -0.36773893 
    26494 Axis point 0.00000000 92.18313505 -11.68775993 
    26495 Rotation angle (degrees) 129.56725904 
    26496 Shift along axis -57.98940372 
    26497  
    26498 
    26499 > select subtract #38
    26500 
    26501 Nothing selected 
    26502 
    26503 > show #!37 models
    26504 
    26505 > mmaker #38 to #37
    26506 
    26507 Parameters 
    26508 --- 
    26509 Chain pairing | bb 
    26510 Alignment algorithm | Needleman-Wunsch 
    26511 Similarity matrix | BLOSUM-62 
    26512 SS fraction | 0.3 
    26513 Gap open (HH/SS/other) | 18/18/6 
    26514 Gap extend | 1 
    26515 SS matrix |  |  | H | S | O 
    26516 ---|---|---|--- 
    26517 H | 6 | -9 | -6 
    26518 S |  | 6 | -6 
    26519 O |  |  | 4 
    26520 Iteration cutoff | 2 
    26521  
    26522 Matchmaker 1ezx, chain A (#37) with 9hud, chain A (#38), sequence alignment
    26523 score = 1674.4 
    26524 RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
    26525 0.519) 
    26526  
    26527 
    26528 > select add #38
    26529 
    26530 6282 atoms, 6138 bonds, 1077 residues, 1 model selected 
    26531 
    26532 > view matrix models
    26533 > #38,0.48049,0.065761,0.87453,62.141,-0.56539,-0.73907,0.36621,264.84,0.67042,-0.67041,-0.31793,61.109
    26534 
    26535 > view matrix models
    26536 > #38,0.48049,0.065761,0.87453,61.431,-0.56539,-0.73907,0.36621,264.59,0.67042,-0.67041,-0.31793,64.599
    26537 
    26538 > fitmap #38 inMap #56
    26539 
    26540 Fit molecule 9hud (#38) to map cryosparc_P483_J99_003_volume_map.mrc z flip
    26541 (#56) using 6282 atoms 
    26542 average map value = 0.03831, steps = 216 
    26543 shifted from previous position = 1.65 
    26544 rotated from previous position = 43.4 degrees 
    26545 atoms outside contour = 569, contour level = 0.011004 
    26546  
    26547 Position of 9hud (#38) relative to cryosparc_P483_J99_003_volume_map.mrc z
    26548 flip (#56) coordinates: 
    26549 Matrix rotation and translation 
    26550 0.71990687 0.56573446 0.40209280 5.32940054 
    26551 -0.00119592 -0.57831351 0.81581374 166.01905071 
    26552 0.69406964 -0.58779078 -0.41565530 58.96739860 
    26553 Axis -0.91044042 -0.18938918 -0.36773629 
    26554 Axis point 0.00000000 92.19051844 -11.68521420 
    26555 Rotation angle (degrees) 129.57078110 
    26556 Shift along axis -57.97876700 
    26557  
    26558 
    26559 > select subtract #38
    26560 
    26561 Nothing selected 
    26562 
    26563 > show #!39 models
    26564 
    26565 > hide #!39 models
    26566 
    26567 > show #!37 models
    26568 
    26569 > mmaker #37 to #38
    26570 
    26571 Parameters 
    26572 --- 
    26573 Chain pairing | bb 
    26574 Alignment algorithm | Needleman-Wunsch 
    26575 Similarity matrix | BLOSUM-62 
    26576 SS fraction | 0.3 
    26577 Gap open (HH/SS/other) | 18/18/6 
    26578 Gap extend | 1 
    26579 SS matrix |  |  | H | S | O 
    26580 ---|---|---|--- 
    26581 H | 6 | -9 | -6 
    26582 S |  | 6 | -6 
    26583 O |  |  | 4 
    26584 Iteration cutoff | 2 
    26585  
    26586 Matchmaker 9hud, chain A (#38) with 1ezx, chain A (#37), sequence alignment
    26587 score = 1674.4 
    26588 RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
    26589 0.519) 
    26590  
    26591 
    26592 > volume #56 level 0.007481
    26593 
    26594 > show #!42 models
    26595 
    26596 > hide #!42 models
    26597 
    26598 > combine #37 close false
    26599 
    26600 > hide #!57.1 models
    26601 
    26602 > hide #!37 models
    26603 
    26604 > show #!37 models
    26605 
    26606 > hide #!38 models
    26607 
    26608 > hide #!37 models
    26609 
    26610 > select #57/A
    26611 
    26612 2686 atoms, 2674 bonds, 398 residues, 1 model selected 
    26613 
    26614 > delete #57/A
    26615 
    26616 > select #57/B
    26617 
    26618 289 atoms, 294 bonds, 39 residues, 1 model selected 
    26619 
    26620 > delete #57/B
    26621 
    26622 > show #!37 models
    26623 
    26624 > show #!38 models
    26625 
    26626 > fitmap #57 inMap #56
    26627 
    26628 Fit molecule copy of 1ezx (#57) to map cryosparc_P483_J99_003_volume_map.mrc z
    26629 flip (#56) using 1009 atoms 
    26630 average map value = 0.01739, steps = 256 
    26631 shifted from previous position = 13.8 
    26632 rotated from previous position = 53.3 degrees 
    26633 atoms outside contour = 290, contour level = 0.0074814 
    26634  
    26635 Position of copy of 1ezx (#57) relative to
    26636 cryosparc_P483_J99_003_volume_map.mrc z flip (#56) coordinates: 
    26637 Matrix rotation and translation 
    26638 0.75779051 -0.13010105 0.63939601 57.96350024 
    26639 0.04649693 0.98819623 0.14596657 79.83854912 
    26640 -0.65083914 -0.08088213 0.75489502 138.89870189 
    26641 Axis -0.17161128 0.97606430 0.13359657 
    26642 Axis point 208.75729766 0.00000000 -34.80031847 
    26643 Rotation angle (degrees) 41.37141702 
    26644 Shift along axis 86.53675668 
    26645  
    26646 
    26647 > hide #!38 models
    26648 
    26649 > hide #!37 models
    26650 
    26651 > show #!37 models
    26652 
    26653 > hide #!37 models
    26654 
    26655 > show #!38 models
    26656 
    26657 > show #!47 models
    26658 
    26659 > hide #!56 models
    26660 
    26661 > hide #!57 models
    26662 
    26663 > hide #!47 models
    26664 
    26665 > open /Users/amy/Downloads/cryosparc_P483_J103_003_volume_map.mrc
    26666 
    26667 Opened cryosparc_P483_J103_003_volume_map.mrc as #58, grid size 400,400,400,
    26668 pixel 0.723, shown at level 0.00468, step 2, values float32 
    26669 
    26670 > surface dust #58 size 7.23
    26671 
    26672 > volume #58 level 0.01873
    26673 
    26674 > transparency #58 50
    26675 
    26676 > select add #38
    26677 
    26678 6282 atoms, 6138 bonds, 1077 residues, 1 model selected 
    26679 
    26680 > view matrix models
    26681 > #38,0.79207,-0.60151,-0.10399,45.033,0.096519,-0.044809,0.99432,127.86,-0.60276,-0.79761,0.022565,266.66
    26682 
    26683 > view matrix models
    26684 > #38,-0.14652,-0.85779,0.49268,195.86,0.54759,0.34445,0.76256,44.475,-0.82382,0.38152,0.41925,251.42
    26685 
    26686 > view matrix models
    26687 > #38,-0.14652,-0.85779,0.49268,198.48,0.54759,0.34445,0.76256,48.533,-0.82382,0.38152,0.41925,263.76
    26688 
    26689 > view matrix models
    26690 > #38,-0.14652,-0.85779,0.49268,194.13,0.54759,0.34445,0.76256,44.618,-0.82382,0.38152,0.41925,261.43
    26691 
    26692 > view matrix models
    26693 > #38,-0.10749,-0.76087,0.63994,182.4,0.68336,0.41097,0.60342,22.58,-0.72212,0.50217,0.47577,240.01
    26694 
    26695 > volume flip #58 axis z
    26696 
    26697 Opened cryosparc_P483_J103_003_volume_map.mrc z flip as #59, grid size
    26698 400,400,400, pixel 0.723, shown at step 1, values float32 
    26699 
    26700 > view matrix models
    26701 > #38,0.47388,0.52578,0.70639,40.242,-0.49413,-0.50521,0.70753,242.68,0.72888,-0.68433,0.020401,61.728
    26702 
    26703 > view matrix models
    26704 > #38,0.47388,0.52578,0.70639,38.39,-0.49413,-0.50521,0.70753,241.35,0.72888,-0.68433,0.020401,61.925
    26705 
    26706 > view matrix models
    26707 > #38,0.62595,0.63777,0.44881,13.26,-0.13423,-0.47881,0.8676,181.41,0.76822,-0.60332,-0.2141,55.525
    26708 
    26709 > view matrix models
    26710 > #38,0.62595,0.63777,0.44881,16.43,-0.13423,-0.47881,0.8676,181.76,0.76822,-0.60332,-0.2141,47.364
    26711 
    26712 > view matrix models
    26713 > #38,0.62595,0.63777,0.44881,20.934,-0.13423,-0.47881,0.8676,183.19,0.76822,-0.60332,-0.2141,39.547
    26714 
    26715 > fitmap #38 inMap #59
    26716 
    26717 Fit molecule 9hud (#38) to map cryosparc_P483_J103_003_volume_map.mrc z flip
    26718 (#59) using 6282 atoms 
    26719 average map value = 0.04126, steps = 168 
    26720 shifted from previous position = 5.69 
    26721 rotated from previous position = 19.5 degrees 
    26722 atoms outside contour = 1297, contour level = 0.018732 
    26723  
    26724 Position of 9hud (#38) relative to cryosparc_P483_J103_003_volume_map.mrc z
    26725 flip (#59) coordinates: 
    26726 Matrix rotation and translation 
    26727 0.70777878 0.35342642 0.61166899 13.30926304 
    26728 -0.29975381 -0.63379066 0.71306173 215.20863100 
    26729 0.63968496 -0.68804008 -0.34264266 66.23170214 
    26730 Axis -0.90619968 -0.01812007 -0.42246160 
    26731 Axis point 0.00000000 119.91219967 -25.94584346 
    26732 Rotation angle (degrees) 129.37010768 
    26733 Shift along axis -43.94079555 
    26734  
    26735 
    26736 > mmaker #37 to #38
    26737 
    26738 Parameters 
    26739 --- 
    26740 Chain pairing | bb 
    26741 Alignment algorithm | Needleman-Wunsch 
    26742 Similarity matrix | BLOSUM-62 
    26743 SS fraction | 0.3 
    26744 Gap open (HH/SS/other) | 18/18/6 
    26745 Gap extend | 1 
    26746 SS matrix |  |  | H | S | O 
    26747 ---|---|---|--- 
    26748 H | 6 | -9 | -6 
    26749 S |  | 6 | -6 
    26750 O |  |  | 4 
    26751 Iteration cutoff | 2 
    26752  
    26753 Matchmaker 9hud, chain A (#38) with 1ezx, chain A (#37), sequence alignment
    26754 score = 1674.4 
    26755 RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
    26756 0.519) 
    26757  
    26758 
    26759 > select subtract #38
    26760 
    26761 Nothing selected 
    26762 
    26763 > show #!37 models
    26764 
    26765 > show #!57 models
    26766 
    26767 > mmaker #57 to #37
    26768 
    26769 Parameters 
    26770 --- 
    26771 Chain pairing | bb 
    26772 Alignment algorithm | Needleman-Wunsch 
    26773 Similarity matrix | BLOSUM-62 
    26774 SS fraction | 0.3 
    26775 Gap open (HH/SS/other) | 18/18/6 
    26776 Gap extend | 1 
    26777 SS matrix |  |  | H | S | O 
    26778 ---|---|---|--- 
    26779 H | 6 | -9 | -6 
    26780 S |  | 6 | -6 
    26781 O |  |  | 4 
    26782 Iteration cutoff | 2 
    26783  
    26784 Matchmaker 1ezx, chain C (#37) with copy of 1ezx, chain C (#57), sequence
    26785 alignment score = 1096 
    26786 RMSD between 140 pruned atom pairs is 0.000 angstroms; (across all 140 pairs:
    26787 0.000) 
    26788  
    26789 
    26790 > hide #!37 models
    26791 
    26792 > select #57/A
    26793 
    26794 Nothing selected 
    26795 
    26796 > select #57/C
    26797 
    26798 1009 atoms, 1014 bonds, 5 pseudobonds, 155 residues, 2 models selected 
    26799 
    26800 > select #57/C: 202
    26801 
    26802 6 atoms, 5 bonds, 1 residue, 1 model selected 
    26803 
    26804 > show #!37 models
    26805 
    26806 > ui tool show "Show Sequence Viewer"
    26807 
    26808 > select #57/C: 197
    26809 
    26810 4 atoms, 3 bonds, 1 residue, 1 model selected 
    26811 
    26812 > select #57/C: 195
    26813 
    26814 6 atoms, 5 bonds, 1 residue, 1 model selected 
    26815 
    26816 > show sel atoms
    26817 
    26818 > select add #57
    26819 
    26820 1009 atoms, 1014 bonds, 5 pseudobonds, 155 residues, 3 models selected 
    26821 
    26822 > select subtract #57
    26823 
    26824 Nothing selected 
    26825 
    26826 > hide #!37 models
    26827 
    26828 > select add #57
    26829 
    26830 1009 atoms, 1014 bonds, 5 pseudobonds, 155 residues, 3 models selected 
    26831 
    26832 > fitmap #57 inMap #59
    26833 
    26834 Fit molecule copy of 1ezx (#57) to map cryosparc_P483_J103_003_volume_map.mrc
    26835 z flip (#59) using 1009 atoms 
    26836 average map value = 0.03856, steps = 332 
    26837 shifted from previous position = 30.6 
    26838 rotated from previous position = 62.2 degrees 
    26839 atoms outside contour = 286, contour level = 0.018732 
    26840  
    26841 Position of copy of 1ezx (#57) relative to
    26842 cryosparc_P483_J103_003_volume_map.mrc z flip (#59) coordinates: 
    26843 Matrix rotation and translation 
    26844 0.57046373 0.04988227 0.81980662 55.55575937 
    26845 -0.78184304 0.33872670 0.52343642 167.07972587 
    26846 -0.25158019 -0.93956159 0.23223140 158.05911115 
    26847 Axis -0.73333465 0.53703769 -0.41690623 
    26848 Axis point 0.00000000 214.40037540 -65.68721584 
    26849 Rotation angle (degrees) 85.94517935 
    26850 Shift along axis -16.90868204 
    26851  
    26852 
    26853 > view matrix models
    26854 > #57,0.57046,0.049882,0.81981,53.391,-0.78184,0.33873,0.52344,146.96,-0.25158,-0.93956,0.23223,152.39
    26855 
    26856 > view matrix models
    26857 > #57,0.57046,0.049882,0.81981,51.548,-0.78184,0.33873,0.52344,139.36,-0.25158,-0.93956,0.23223,150.37
    26858 
    26859 > view matrix models
    26860 > #57,0.60961,0.26554,0.74691,47.106,-0.77216,0.41204,0.48373,138.91,-0.17931,-0.87162,0.45622,131.48
    26861 
    26862 > view matrix models
    26863 > #57,0.60961,0.26554,0.74691,46.208,-0.77216,0.41204,0.48373,140.83,-0.17931,-0.87162,0.45622,128.81
    26864 
    26865 > view matrix models
    26866 > #57,0.49766,0.67771,0.54133,56.234,-0.85191,0.49924,0.15817,161.92,-0.16306,-0.53988,0.8258,100.9
    26867 
    26868 > view matrix models
    26869 > #57,0.49766,0.67771,0.54133,55.941,-0.85191,0.49924,0.15817,159.37,-0.16306,-0.53988,0.8258,99.317
    26870 
    26871 > view matrix models
    26872 > #57,0.83968,0.36634,0.40093,42.637,-0.49094,0.82767,0.27193,116.69,-0.23222,-0.42516,0.87482,99.752
    26873 
    26874 > hide #!57 models
    26875 
    26876 > select subtract #57
    26877 
    26878 Nothing selected 
    26879 
    26880 > hide #!59 models
    26881 
    26882 > show #!47 models
    26883 
    26884 > fitmap #38 inMap #47
    26885 
    26886 Fit molecule 9hud (#38) to map cryosparc_P483_J72_006_volume_map.mrc z flip
    26887 (#47) using 6282 atoms 
    26888 average map value = 0.06343, steps = 180 
    26889 shifted from previous position = 8.63 
    26890 rotated from previous position = 26.1 degrees 
    26891 atoms outside contour = 1606, contour level = 0.028781 
    26892  
    26893 Position of 9hud (#38) relative to cryosparc_P483_J72_006_volume_map.mrc z
    26894 flip (#47) coordinates: 
    26895 Matrix rotation and translation 
    26896 0.48062832 0.06570846 0.87445915 60.38102135 
    26897 -0.56537857 -0.73904318 0.36628165 262.76806751 
    26898 0.67033088 -0.67044580 -0.31805493 52.08064169 
    26899 Axis -0.84235493 0.16585696 -0.51276666 
    26900 Axis point 0.00000000 144.40697546 -47.16273001 
    26901 Rotation angle (degrees) 142.02086420 
    26902 Shift along axis -33.98555515 
    26903  
    26904 
    26905 > show #35 models
    26906 
    26907 > mmaker #35 to #38
    26908 
    26909 Parameters 
    26910 --- 
    26911 Chain pairing | bb 
    26912 Alignment algorithm | Needleman-Wunsch 
    26913 Similarity matrix | BLOSUM-62 
    26914 SS fraction | 0.3 
    26915 Gap open (HH/SS/other) | 18/18/6 
    26916 Gap extend | 1 
    26917 SS matrix |  |  | H | S | O 
    26918 ---|---|---|--- 
    26919 H | 6 | -9 | -6 
    26920 S |  | 6 | -6 
    26921 O |  |  | 4 
    26922 Iteration cutoff | 2 
    26923  
    26924 Matchmaker 9hud, chain A (#38) with 8pi2, chain A (#35), sequence alignment
    26925 score = 1753.4 
    26926 RMSD between 220 pruned atom pairs is 0.913 angstroms; (across all 331 pairs:
    26927 6.169) 
    26928  
    26929 
    26930 > hide #!38 models
    26931 
    26932 > show #!38 models
    26933 
    26934 > hide #35 models
    26935 
    26936 > show #35 models
    26937 
    26938 > hide #35 models
    26939 
    26940 > show #35 models
    26941 
    26942 > hide #35 models
    26943 
    26944 > hide #!38 models
    26945 
    26946 > hide #!47 models
    26947 
    26948 > show #!59 models
    26949 
    26950 > open cryosparc_P483_J70_00018_volume_series vseries true
    26951 
    26952 'cryosparc_P483_J70_00018_volume_series' has no suffix 
    26953 
    26954 > open
    26955 > /Users/amy/Desktop/cryosparc_P483_J70_00018_volume_series/J70_class_00_00018_volume.mrc
    26956 > /Users/amy/Desktop/cryosparc_P483_J70_00018_volume_series/J70_class_01_00018_volume.mrc
    26957 > /Users/amy/Desktop/cryosparc_P483_J70_00018_volume_series/J70_class_02_00018_volume.mrc
    26958 > /Users/amy/Desktop/cryosparc_P483_J70_00018_volume_series/J70_class_03_00018_volume.mrc
    26959 > /Users/amy/Desktop/cryosparc_P483_J70_00018_volume_series/J70_class_04_00018_volume.mrc
    26960 > /Users/amy/Desktop/cryosparc_P483_J70_00018_volume_series/J70_class_05_00018_volume.mrc
    26961 > /Users/amy/Desktop/cryosparc_P483_J70_00018_volume_series/J70_class_06_00018_volume.mrc
    26962 > /Users/amy/Desktop/cryosparc_P483_J70_00018_volume_series/J70_class_07_00018_volume.mrc
    26963 > /Users/amy/Desktop/cryosparc_P483_J70_00018_volume_series/J70_class_08_00018_volume.mrc
    26964 > /Users/amy/Desktop/cryosparc_P483_J70_00018_volume_series/J70_class_09_00018_volume.mrc
    26965 
    26966 Opened J70_class_00_00018_volume.mrc as #60.1, grid size 64,64,64, pixel 4.52,
    26967 shown at level 0.113, step 1, values float32 
    26968 Opened J70_class_01_00018_volume.mrc as #60.2, grid size 64,64,64, pixel 4.52,
    26969 shown at level 0.104, step 1, values float32 
    26970 Opened J70_class_02_00018_volume.mrc as #60.3, grid size 64,64,64, pixel 4.52,
    26971 shown at level 0.109, step 1, values float32 
    26972 Opened J70_class_03_00018_volume.mrc as #60.4, grid size 64,64,64, pixel 4.52,
    26973 shown at level 0.116, step 1, values float32 
    26974 Opened J70_class_04_00018_volume.mrc as #60.5, grid size 64,64,64, pixel 4.52,
    26975 shown at level 0.106, step 1, values float32 
    26976 Opened J70_class_05_00018_volume.mrc as #60.6, grid size 64,64,64, pixel 4.52,
    26977 shown at level 0.106, step 1, values float32 
    26978 Opened J70_class_06_00018_volume.mrc as #60.7, grid size 64,64,64, pixel 4.52,
    26979 shown at level 0.116, step 1, values float32 
    26980 Opened J70_class_07_00018_volume.mrc as #60.8, grid size 64,64,64, pixel 4.52,
    26981 shown at level 0.109, step 1, values float32 
    26982 Opened J70_class_08_00018_volume.mrc as #60.9, grid size 64,64,64, pixel 4.52,
    26983 shown at level 0.106, step 1, values float32 
    26984 Opened J70_class_09_00018_volume.mrc as #60.10, grid size 64,64,64, pixel
    26985 4.52, shown at level 0.113, step 1, values float32 
    26986 
    26987 > hide #!59 models
    26988 
    26989 > surface dust #60.1 size 45.2
    26990 
    26991 > surface dust #60.2 size 45.2
    26992 
    26993 > surface dust #60.3 size 45.2
    26994 
    26995 > surface dust #60.4 size 45.2
    26996 
    26997 > surface dust #60.5 size 45.2
    26998 
    26999 > surface dust #60.6 size 45.2
    27000 
    27001 > surface dust #60.7 size 45.2
    27002 
    27003 > surface dust #60.8 size 45.2
    27004 
    27005 > surface dust #60.9 size 45.2
    27006 
    27007 > surface dust #60.10 size 45.2
    27008 
    27009 > hide #!60.1 models
    27010 
    27011 > hide #!60.2 models
    27012 
    27013 > hide #!60.3 models
    27014 
    27015 > hide #!60.4 models
    27016 
    27017 > hide #!60.5 models
    27018 
    27019 > hide #!60.6 models
    27020 
    27021 > hide #!60.7 models
    27022 
    27023 > hide #!60.8 models
    27024 
    27025 > hide #!60.9 models
    27026 
    27027 > hide #!60.10 models
    27028 
    27029 > show #!60.1 models
    27030 
    27031 > show #!60.2 models
    27032 
    27033 > hide #!60.1 models
    27034 
    27035 > hide #!60.2 models
    27036 
    27037 > show #!60.3 models
    27038 
    27039 > show #!60.2 models
    27040 
    27041 > hide #!60.2 models
    27042 
    27043 > show #!60.4 models
    27044 
    27045 > hide #!60.3 models
    27046 
    27047 > show #!60.5 models
    27048 
    27049 > hide #!60.4 models
    27050 
    27051 > show #!60.6 models
    27052 
    27053 > hide #!60.5 models
    27054 
    27055 > show #!60.7 models
    27056 
    27057 > hide #!60.6 models
    27058 
    27059 > show #!60.8 models
    27060 
    27061 > hide #!60.7 models
    27062 
    27063 > show #!60.9 models
    27064 
    27065 > hide #!60.8 models
    27066 
    27067 > show #!60.10 models
    27068 
    27069 > hide #!60.9 models
    27070 
    27071 > hide #!60 target m
    27072 
    27073 [Repeated 1 time(s)]
    27074 
    27075 > close #60
    27076 
    27077 > open
    27078 > /Users/amy/Downloads/cryosparc_P483_J124_00020_volume_series/J124_class_00_00020_volume.mrc
    27079 > /Users/amy/Downloads/cryosparc_P483_J124_00020_volume_series/J124_class_01_00020_volume.mrc
    27080 > /Users/amy/Downloads/cryosparc_P483_J124_00020_volume_series/J124_class_02_00020_volume.mrc
    27081 > /Users/amy/Downloads/cryosparc_P483_J124_00020_volume_series/J124_class_03_00020_volume.mrc
    27082 > /Users/amy/Downloads/cryosparc_P483_J124_00020_volume_series/J124_class_04_00020_volume.mrc
    27083 > /Users/amy/Downloads/cryosparc_P483_J124_00020_volume_series/J124_class_05_00020_volume.mrc
    27084 > /Users/amy/Downloads/cryosparc_P483_J124_00020_volume_series/J124_class_06_00020_volume.mrc
    27085 > /Users/amy/Downloads/cryosparc_P483_J124_00020_volume_series/J124_class_07_00020_volume.mrc
    27086 > /Users/amy/Downloads/cryosparc_P483_J124_00020_volume_series/J124_class_08_00020_volume.mrc
    27087 > /Users/amy/Downloads/cryosparc_P483_J124_00020_volume_series/J124_class_09_00020_volume.mrc
    27088 
    27089 Opened J124_class_00_00020_volume.mrc as #60.1, grid size 64,64,64, pixel
    27090 4.52, shown at level 0.058, step 1, values float32 
    27091 Opened J124_class_01_00020_volume.mrc as #60.2, grid size 64,64,64, pixel
    27092 4.52, shown at level 0.0583, step 1, values float32 
    27093 Opened J124_class_02_00020_volume.mrc as #60.3, grid size 64,64,64, pixel
    27094 4.52, shown at level 0.0581, step 1, values float32 
    27095 Opened J124_class_03_00020_volume.mrc as #60.4, grid size 64,64,64, pixel
    27096 4.52, shown at level 0.0576, step 1, values float32 
    27097 Opened J124_class_04_00020_volume.mrc as #60.5, grid size 64,64,64, pixel
    27098 4.52, shown at level 0.0607, step 1, values float32 
    27099 Opened J124_class_05_00020_volume.mrc as #60.6, grid size 64,64,64, pixel
    27100 4.52, shown at level 0.0608, step 1, values float32 
    27101 Opened J124_class_06_00020_volume.mrc as #60.7, grid size 64,64,64, pixel
    27102 4.52, shown at level 0.0585, step 1, values float32 
    27103 Opened J124_class_07_00020_volume.mrc as #60.8, grid size 64,64,64, pixel
    27104 4.52, shown at level 0.0573, step 1, values float32 
    27105 Opened J124_class_08_00020_volume.mrc as #60.9, grid size 64,64,64, pixel
    27106 4.52, shown at level 0.0591, step 1, values float32 
    27107 Opened J124_class_09_00020_volume.mrc as #60.10, grid size 64,64,64, pixel
    27108 4.52, shown at level 0.0602, step 1, values float32 
    27109 
    27110 > surface dust #60.1 size 45.2
    27111 
    27112 > surface dust #60.2 size 45.2
    27113 
    27114 > surface dust #60.3 size 45.2
    27115 
    27116 > surface dust #60.4 size 45.2
    27117 
    27118 > surface dust #60.5 size 45.2
    27119 
    27120 > surface dust #60.6 size 45.2
    27121 
    27122 > surface dust #60.7 size 45.2
    27123 
    27124 > surface dust #60.8 size 45.2
    27125 
    27126 > surface dust #60.9 size 45.2
    27127 
    27128 > surface dust #60.10 size 45.2
    27129 
    27130 > hide #!60 models
    27131 
    27132 > show #!60 models
    27133 
    27134 > hide #!60.1 models
    27135 
    27136 > hide #!60.2 models
    27137 
    27138 > hide #!60.3 models
    27139 
    27140 > hide #!60.4 models
    27141 
    27142 > hide #!60.5 models
    27143 
    27144 > hide #!60.6 models
    27145 
    27146 > hide #!60.7 models
    27147 
    27148 > hide #!60.8 models
    27149 
    27150 > hide #!60.9 models
    27151 
    27152 > hide #!60.10 models
    27153 
    27154 > show #!60.1 models
    27155 
    27156 > show #!60.2 models
    27157 
    27158 > hide #!60.1 models
    27159 
    27160 > show #!60.3 models
    27161 
    27162 > hide #!60.2 models
    27163 
    27164 > show #!60.4 models
    27165 
    27166 > hide #!60.3 models
    27167 
    27168 > show #!60.5 models
    27169 
    27170 > hide #!60.4 models
    27171 
    27172 > show #!60.6 models
    27173 
    27174 > hide #!60.5 models
    27175 
    27176 > show #!60.7 models
    27177 
    27178 > hide #!60.6 models
    27179 
    27180 > show #!60.8 models
    27181 
    27182 > hide #!60.7 models
    27183 
    27184 > show #!60.9 models
    27185 
    27186 > hide #!60.8 models
    27187 
    27188 > show #!60.10 models
    27189 
    27190 > hide #!60.9 models
    27191 
    27192 > hide #!60.10 models
    27193 
    27194 > open /Users/amy/Downloads/cryosparc_P483_J131_007_volume_map.mrc
    27195 
    27196 Opened cryosparc_P483_J131_007_volume_map.mrc as #61, grid size 400,400,400,
    27197 pixel 0.723, shown at level 0.00743, step 2, values float32 
    27198 
    27199 > volume #61 level 0.0358
    27200 
    27201 > transparency #61 50
    27202 
    27203 Cell requested for row 59 is out of bounds for table with 71 rows! Resizing
    27204 table model. 
    27205 
    27206 > close #60
    27207 
    27208 > show #!57 models
    27209 
    27210 > hide #!57 models
    27211 
    27212 > show #!38 models
    27213 
    27214 > select add #38
    27215 
    27216 6282 atoms, 6138 bonds, 1077 residues, 1 model selected 
    27217 
    27218 > view matrix models
    27219 > #38,0.28938,-0.95095,0.1093,139.21,-0.034645,0.10371,0.994,138.64,-0.95659,-0.29143,-0.0029341,290.92
    27220 
    27221 > view matrix models
    27222 > #38,-0.45918,-0.73297,0.50191,244.33,0.66345,0.092766,0.74245,31.785,-0.59075,0.67391,0.44369,190.43
    27223 
    27224 > view matrix models
    27225 > #38,-0.45918,-0.73297,0.50191,252.99,0.66345,0.092766,0.74245,27.709,-0.59075,0.67391,0.44369,215.88
    27226 
    27227 > view matrix models
    27228 > #38,-0.45918,-0.73297,0.50191,245.4,0.66345,0.092766,0.74245,38.203,-0.59075,0.67391,0.44369,230.11
    27229 
    27230 > view matrix models
    27231 > #38,0.7804,-0.38868,0.4898,36.281,-0.57699,-0.14577,0.80364,242.79,-0.24096,-0.90977,-0.33802,245.32
    27232 
    27233 > view matrix models
    27234 > #38,0.24076,-0.088229,0.96657,104.14,-0.7449,-0.65522,0.12574,297.37,0.62222,-0.75027,-0.22348,101.24
    27235 
    27236 > view matrix models
    27237 > #38,0.24076,-0.088229,0.96657,102.45,-0.7449,-0.65522,0.12574,304,0.62222,-0.75027,-0.22348,88.677
    27238 
    27239 > volume flip #61 axis z
    27240 
    27241 Opened cryosparc_P483_J131_007_volume_map.mrc z flip as #60, grid size
    27242 400,400,400, pixel 0.723, shown at step 1, values float32 
    27243 
    27244 > view matrix models
    27245 > #38,0.24076,-0.088229,0.96657,101.92,-0.7449,-0.65522,0.12574,291.88,0.62222,-0.75027,-0.22348,62.156
    27246 
    27247 > view matrix models
    27248 > #38,0.44059,0.20906,0.87303,60.073,-0.32965,-0.86689,0.37395,231.22,0.83499,-0.45255,-0.31303,18.198
    27249 
    27250 > view matrix models
    27251 > #38,0.44059,0.20906,0.87303,63.215,-0.32965,-0.86689,0.37395,234.58,0.83499,-0.45255,-0.31303,17.855
    27252 
    27253 > fitmap #38 inMap #61
    27254 
    27255 Fit molecule 9hud (#38) to map cryosparc_P483_J131_007_volume_map.mrc (#61)
    27256 using 6282 atoms 
    27257 average map value = 0.03062, steps = 228 
    27258 shifted from previous position = 12.1 
    27259 rotated from previous position = 10.2 degrees 
    27260 atoms outside contour = 4063, contour level = 0.0358 
    27261  
    27262 Position of 9hud (#38) relative to cryosparc_P483_J131_007_volume_map.mrc
    27263 (#61) coordinates: 
    27264 Matrix rotation and translation 
    27265 0.47633594 0.18597339 0.85937068 60.19776260 
    27266 -0.46622754 -0.77523836 0.42618936 248.08769926 
    27267 0.74547700 -0.60367159 -0.28256798 49.22817896 
    27268 Axis -0.84117201 0.09302633 -0.53270606 
    27269 Axis point 0.00000000 131.55393794 -45.87457813 
    27270 Rotation angle (degrees) 142.25427000 
    27271 Shift along axis -53.78213480 
    27272  
    27273 
    27274 > fitmap #38 inMap #60
    27275 
    27276 Fit molecule 9hud (#38) to map cryosparc_P483_J131_007_volume_map.mrc z flip
    27277 (#60) using 6282 atoms 
    27278 average map value = 0.07254, steps = 164 
    27279 shifted from previous position = 12.4 
    27280 rotated from previous position = 8.44 degrees 
    27281 atoms outside contour = 1769, contour level = 0.0358 
    27282  
    27283 Position of 9hud (#38) relative to cryosparc_P483_J131_007_volume_map.mrc z
    27284 flip (#60) coordinates: 
    27285 Matrix rotation and translation 
    27286 0.48808324 0.07900810 0.86921371 58.92380628 
    27287 -0.57432345 -0.72083004 0.38801627 263.44883633 
    27288 0.65721178 -0.68859406 -0.30644886 54.98864316 
    27289 Axis -0.84303960 0.16600809 -0.51159120 
    27290 Axis point 0.00000000 145.56353638 -47.97475612 
    27291 Rotation angle (degrees) 140.31778784 
    27292 Shift along axis -34.07217072 
    27293  
    27294 
    27295 > show #!37 models
    27296 
    27297 > mmaker #37 to #38
    27298 
    27299 Parameters 
    27300 --- 
    27301 Chain pairing | bb 
    27302 Alignment algorithm | Needleman-Wunsch 
    27303 Similarity matrix | BLOSUM-62 
    27304 SS fraction | 0.3 
    27305 Gap open (HH/SS/other) | 18/18/6 
    27306 Gap extend | 1 
    27307 SS matrix |  |  | H | S | O 
    27308 ---|---|---|--- 
    27309 H | 6 | -9 | -6 
    27310 S |  | 6 | -6 
    27311 O |  |  | 4 
    27312 Iteration cutoff | 2 
    27313  
    27314 Matchmaker 9hud, chain A (#38) with 1ezx, chain A (#37), sequence alignment
    27315 score = 1674.4 
    27316 RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
    27317 0.519) 
    27318  
    27319 
    27320 > open /Users/amy/Downloads/cryosparc_P483_J128_006_volume_map.mrc
    27321 
    27322 Opened cryosparc_P483_J128_006_volume_map.mrc as #62, grid size 400,400,400,
    27323 pixel 0.723, shown at level 0.00501, step 2, values float32 
    27324 
    27325 > select subtract #38
    27326 
    27327 Nothing selected 
    27328 
    27329 > hide #!38 models
    27330 
    27331 > hide #!37 models
    27332 
    27333 > hide #!60 models
    27334 
    27335 > hide #!62 models
    27336 
    27337 > open /Users/amy/Downloads/cryosparc_P483_J137_003_volume_map.mrc
    27338 
    27339 Opened cryosparc_P483_J137_003_volume_map.mrc as #63, grid size 400,400,400,
    27340 pixel 0.723, shown at level 0.00802, step 2, values float32 
    27341 
    27342 > volume #63 level 0.03618
    27343 
    27344 > volume flip #63 axis z
    27345 
    27346 Opened cryosparc_P483_J137_003_volume_map.mrc z flip as #64, grid size
    27347 400,400,400, pixel 0.723, shown at step 1, values float32 
    27348 
    27349 > transparency #63 50
    27350 
    27351 > transparency #64 50
    27352 
    27353 > show #!38 models
    27354 
    27355 > select add #38
    27356 
    27357 6282 atoms, 6138 bonds, 1077 residues, 1 model selected 
    27358 
    27359 > show #!63 models
    27360 
    27361 > hide #!64 models
    27362 
    27363 > view matrix models
    27364 > #38,0.48808,0.079008,0.86921,57.589,-0.57432,-0.72083,0.38802,273.61,0.65721,-0.68859,-0.30645,79.373
    27365 
    27366 > view matrix models
    27367 > #38,0.2297,0.46473,0.85514,83.832,-0.58104,-0.6394,0.50355,270.11,0.78079,-0.61253,0.12316,51.538
    27368 
    27369 > view matrix models
    27370 > #38,0.2297,0.46473,0.85514,85.324,-0.58104,-0.6394,0.50355,273.24,0.78079,-0.61253,0.12316,53.863
    27371 
    27372 > view matrix models
    27373 > #38,0.39662,0.46965,0.78875,59.564,-0.57284,-0.54478,0.61243,266.95,0.71732,-0.69472,0.052964,67.932
    27374 
    27375 > show #!64 models
    27376 
    27377 > hide #!63 models
    27378 
    27379 > view matrix models
    27380 > #38,-0.91348,-0.3347,0.23136,304.61,0.38224,-0.51103,0.7699,112.62,-0.13945,0.79172,0.59475,139.64
    27381 
    27382 > view matrix models
    27383 > #38,-0.59049,-0.80568,-0.046958,275.08,-0.087884,0.0063535,0.99611,164.3,-0.80225,0.59232,-0.074558,260.49
    27384 
    27385 > view matrix models
    27386 > #38,-0.59049,-0.80568,-0.046958,273.4,-0.087884,0.0063535,0.99611,163.84,-0.80225,0.59232,-0.074558,241.17
    27387 
    27388 > view matrix models
    27389 > #38,-0.55648,-0.77337,0.3037,262.39,0.12542,0.28314,0.95084,120.04,-0.82134,0.56721,-0.060566,244.98
    27390 
    27391 > fitmap #38 inMap #64
    27392 
    27393 Fit molecule 9hud (#38) to map cryosparc_P483_J137_003_volume_map.mrc z flip
    27394 (#64) using 6282 atoms 
    27395 average map value = 0.03426, steps = 96 
    27396 shifted from previous position = 4.73 
    27397 rotated from previous position = 4.41 degrees 
    27398 atoms outside contour = 3712, contour level = 0.036179 
    27399  
    27400 Position of 9hud (#38) relative to cryosparc_P483_J137_003_volume_map.mrc z
    27401 flip (#64) coordinates: 
    27402 Matrix rotation and translation 
    27403 -0.57799196 -0.77115445 0.26691966 270.23868060 
    27404 0.05229306 0.29141704 0.95516572 129.97421192 
    27405 -0.81436523 0.56603615 -0.12811068 246.02921542 
    27406 Axis -0.27524806 0.76483926 0.58245980 
    27407 Axis point 198.55971177 0.00000000 -12.15810570 
    27408 Rotation angle (degrees) 135.01912752 
    27409 Shift along axis 168.32883368 
    27410  
    27411 
    27412 > hide #!64 models
    27413 
    27414 > show #!63 models
    27415 
    27416 > view matrix models
    27417 > #38,0.28227,0.88622,0.36734,69.32,0.13351,-0.41547,0.89976,144.95,0.95,-0.20493,-0.23559,-2.1095
    27418 
    27419 > view matrix models
    27420 > #38,0.28227,0.88622,0.36734,65.915,0.13351,-0.41547,0.89976,149,0.95,-0.20493,-0.23559,14.639
    27421 
    27422 > view matrix models
    27423 > #38,-0.00068529,0.90537,0.42463,109.22,-0.0059164,-0.42462,0.90535,171.33,0.99998,-0.0018918,0.0056475,-4.0739
    27424 
    27425 > fitmap #38 inMap #63
    27426 
    27427 Fit molecule 9hud (#38) to map cryosparc_P483_J137_003_volume_map.mrc (#63)
    27428 using 6282 atoms 
    27429 average map value = 0.03246, steps = 440 
    27430 shifted from previous position = 6.15 
    27431 rotated from previous position = 34.9 degrees 
    27432 atoms outside contour = 3887, contour level = 0.036179 
    27433  
    27434 Position of 9hud (#38) relative to cryosparc_P483_J137_003_volume_map.mrc
    27435 (#63) coordinates: 
    27436 Matrix rotation and translation 
    27437 0.42909681 0.75362179 0.49792584 49.09248009 
    27438 -0.38069938 -0.34900840 0.85630668 221.91213193 
    27439 0.81911167 -0.55699852 0.13714496 46.28691655 
    27440 Axis -0.76791055 -0.17451431 -0.61632632 
    27441 Axis point -0.00000000 97.45467483 -84.23279059 
    27442 Rotation angle (degrees) 113.04060047 
    27443 Shift along axis -104.95332191 
    27444  
    27445 
    27446 > hide #!63 models
    27447 
    27448 > show #!64 models
    27449 
    27450 > view matrix models
    27451 > #38,0.6404,-0.29362,0.70969,53.209,-0.098072,0.88521,0.45474,134.87,-0.76175,-0.36082,0.5381,283.79
    27452 
    27453 > view matrix models
    27454 > #38,-0.26615,-0.29672,0.91713,194.12,0.6919,0.60364,0.39609,21.458,-0.67114,0.73998,0.044637,233.39
    27455 
    27456 > view matrix models
    27457 > #38,0.42821,0.78395,0.44952,48.675,0.43344,0.2583,-0.86337,91.334,-0.79295,0.56454,-0.22919,262.81
    27458 
    27459 > view matrix models
    27460 > #38,0.40387,0.68567,-0.6056,69.485,-0.40554,-0.4592,-0.79036,250.65,-0.82002,0.5648,0.092606,263.06
    27461 
    27462 > view matrix models
    27463 > #38,-0.85722,-0.30291,-0.41645,304.52,-0.2744,-0.41565,0.86714,207.52,-0.43576,0.8576,0.27319,188.79
    27464 
    27465 > view matrix models
    27466 > #38,-0.57679,-0.55417,0.60017,257.1,0.51884,0.31896,0.79314,54.792,-0.63097,0.76887,0.10355,225.19
    27467 
    27468 > view matrix models
    27469 > #38,-0.57679,-0.55417,0.60017,254.28,0.51884,0.31896,0.79314,61.36,-0.63097,0.76887,0.10355,204.28
    27470 
    27471 > view matrix models
    27472 > #38,-0.60566,-0.70889,0.36146,267.77,0.21101,0.29491,0.93193,109.24,-0.76724,0.64071,-0.029033,232.41
    27473 
    27474 > view matrix models
    27475 > #38,-0.60566,-0.70889,0.36146,266.58,0.21101,0.29491,0.93193,105.92,-0.76724,0.64071,-0.029033,230.06
    27476 
    27477 > view matrix models
    27478 > #38,-0.72224,-0.67174,0.16473,286.05,0.065572,0.1706,0.98316,133.05,-0.68853,0.72087,-0.079168,215.16
    27479 
    27480 > view matrix models
    27481 > #38,-0.47003,-0.67432,0.56953,241.2,0.17784,0.55967,0.80941,102.54,-0.86455,0.48173,-0.14315,252.98
    27482 
    27483 > view matrix models
    27484 > #38,-0.47003,-0.67432,0.56953,249.14,0.17784,0.55967,0.80941,98.999,-0.86455,0.48173,-0.14315,251.53
    27485 
    27486 > view matrix models
    27487 > #38,-0.59825,-0.70633,0.37841,273.04,0.21367,0.31452,0.92489,101.29,-0.77229,0.63417,-0.037243,229.77
    27488 
    27489 > fitmap #38 inMap #64
    27490 
    27491 Fit molecule 9hud (#38) to map cryosparc_P483_J137_003_volume_map.mrc z flip
    27492 (#64) using 6282 atoms 
    27493 average map value = 0.03512, steps = 80 
    27494 shifted from previous position = 5.4 
    27495 rotated from previous position = 3.39 degrees 
    27496 atoms outside contour = 3664, contour level = 0.036179 
    27497  
    27498 Position of 9hud (#38) relative to cryosparc_P483_J137_003_volume_map.mrc z
    27499 flip (#64) coordinates: 
    27500 Matrix rotation and translation 
    27501 -0.63147092 -0.69242738 0.34898254 278.13803163 
    27502 0.16768307 0.31747267 0.93332391 107.28593241 
    27503 -0.75705144 0.64788536 -0.08436641 232.43243148 
    27504 Axis -0.19962317 0.77351156 0.60152345 
    27505 Axis point 188.76264795 0.00000000 -10.22905426 
    27506 Rotation angle (degrees) 134.36143880 
    27507 Shift along axis 167.27766991 
    27508  
    27509 
    27510 > fitmap #38 inMap #64
    27511 
    27512 Fit molecule 9hud (#38) to map cryosparc_P483_J137_003_volume_map.mrc z flip
    27513 (#64) using 6282 atoms 
    27514 average map value = 0.03512, steps = 40 
    27515 shifted from previous position = 0.0099 
    27516 rotated from previous position = 0.0115 degrees 
    27517 atoms outside contour = 3662, contour level = 0.036179 
    27518  
    27519 Position of 9hud (#38) relative to cryosparc_P483_J137_003_volume_map.mrc z
    27520 flip (#64) coordinates: 
    27521 Matrix rotation and translation 
    27522 -0.63136485 -0.69247722 0.34907556 278.12932035 
    27523 0.16783951 0.31744825 0.93330409 107.26947039 
    27524 -0.75710524 0.64784406 -0.08420063 232.43949274 
    27525 Axis -0.19960443 0.77348336 0.60156592 
    27526 Axis point 188.76447494 0.00000000 -10.24425096 
    27527 Rotation angle (degrees) 134.35152473 
    27528 Shift along axis 167.28298509 
    27529  
    27530 
    27531 > view matrix models
    27532 > #38,-0.63136,-0.69248,0.34908,274.79,0.16784,0.31745,0.9333,108.96,-0.75711,0.64784,-0.084201,230.09
    27533 
    27534 > fitmap #38 inMap #64
    27535 
    27536 Fit molecule 9hud (#38) to map cryosparc_P483_J137_003_volume_map.mrc z flip
    27537 (#64) using 6282 atoms 
    27538 average map value = 0.03512, steps = 88 
    27539 shifted from previous position = 4.42 
    27540 rotated from previous position = 0.00894 degrees 
    27541 atoms outside contour = 3663, contour level = 0.036179 
    27542  
    27543 Position of 9hud (#38) relative to cryosparc_P483_J137_003_volume_map.mrc z
    27544 flip (#64) coordinates: 
    27545 Matrix rotation and translation 
    27546 -0.63139892 -0.69244150 0.34908479 278.12602696 
    27547 0.16773664 0.31755383 0.93328667 107.27376736 
    27548 -0.75709963 0.64783049 -0.08435534 232.44361126 
    27549 Axis -0.19961308 0.77352989 0.60150323 
    27550 Axis point 188.76295474 0.00000000 -10.22421164 
    27551 Rotation angle (degrees) 134.35485805 
    27552 Shift along axis 167.27745334 
    27553  
    27554 
    27555 > view matrix models
    27556 > #38,-0.64713,-0.6735,0.35724,279.79,0.16615,0.33274,0.92827,107.01,-0.74406,0.66006,-0.10342,230.15
    27557 
    27558 > view matrix models
    27559 > #38,-0.64713,-0.6735,0.35724,276.58,0.16615,0.33274,0.92827,108.12,-0.74406,0.66006,-0.10342,229.13
    27560 
    27561 > fitmap #38 inMap #64
    27562 
    27563 Fit molecule 9hud (#38) to map cryosparc_P483_J137_003_volume_map.mrc z flip
    27564 (#64) using 6282 atoms 
    27565 average map value = 0.03512, steps = 80 
    27566 shifted from previous position = 3.52 
    27567 rotated from previous position = 1.63 degrees 
    27568 atoms outside contour = 3659, contour level = 0.036179 
    27569  
    27570 Position of 9hud (#38) relative to cryosparc_P483_J137_003_volume_map.mrc z
    27571 flip (#64) coordinates: 
    27572 Matrix rotation and translation 
    27573 -0.63138477 -0.69243824 0.34911684 278.12114525 
    27574 0.16772204 0.31760740 0.93327106 107.27149167 
    27575 -0.75711466 0.64780772 -0.08439532 232.44867407 
    27576 Axis -0.19961431 0.77354815 0.60147934 
    27577 Axis point 188.76284344 0.00000000 -10.21708948 
    27578 Rotation angle (degrees) 134.35374707 
    27579 Shift along axis 167.27577632 
    27580  
    27581 
    27582 > hide #!64 models
    27583 
    27584 > show #!60 models
    27585 
    27586 > view matrix models
    27587 > #38,0.4887,0.003934,0.87244,67.696,-0.61017,-0.71321,0.345,277.22,0.6236,-0.70094,-0.34614,69.091
    27588 
    27589 > view matrix models
    27590 > #38,0.4887,0.003934,0.87244,62.759,-0.61017,-0.71321,0.345,271.12,0.6236,-0.70094,-0.34614,59.706
    27591 
    27592 > view matrix models
    27593 > #38,0.4887,0.003934,0.87244,62.878,-0.61017,-0.71321,0.345,270.83,0.6236,-0.70094,-0.34614,60.391
    27594 
    27595 > select subtract #38
    27596 
    27597 Nothing selected 
    27598 
    27599 > hide #!38 models
    27600 
    27601 > show #!38 models
    27602 
    27603 > open /Users/amy/Downloads/cryosparc_P483_J136_004_volume_map.mrc
    27604 
    27605 Opened cryosparc_P483_J136_004_volume_map.mrc as #65, grid size 400,400,400,
    27606 pixel 0.723, shown at level 0.00461, step 2, values float32 
    27607 
    27608 > hide #!60 models
    27609 
    27610 > hide #!38 models
    27611 
    27612 > surface dust #65 size 7.23
    27613 
    27614 > volume #65 level 0.02522
    27615 
    27616 > transparency #65 50
    27617 
    27618 > volume flip #65 axis z
    27619 
    27620 Opened cryosparc_P483_J136_004_volume_map.mrc z flip as #66, grid size
    27621 400,400,400, pixel 0.723, shown at step 1, values float32 
    27622 
    27623 > show #!38 models
    27624 
    27625 > fitmap #38 inMap #66
    27626 
    27627 Fit molecule 9hud (#38) to map cryosparc_P483_J136_004_volume_map.mrc z flip
    27628 (#66) using 6282 atoms 
    27629 average map value = 0.05359, steps = 80 
    27630 shifted from previous position = 1.58 
    27631 rotated from previous position = 4.51 degrees 
    27632 atoms outside contour = 1373, contour level = 0.025222 
    27633  
    27634 Position of 9hud (#38) relative to cryosparc_P483_J136_004_volume_map.mrc z
    27635 flip (#66) coordinates: 
    27636 Matrix rotation and translation 
    27637 0.49152778 0.08078197 0.86710711 58.94196264 
    27638 -0.57115257 -0.72173556 0.39100196 263.45649346 
    27639 0.65740794 -0.68743877 -0.30861424 55.13461431 
    27640 Axis -0.84417530 0.16414704 -0.51031737 
    27641 Axis point 0.00000000 145.46690985 -47.79590518 
    27642 Rotation angle (degrees) 140.30102750 
    27643 Shift along axis -34.64789549 
    27644  
    27645 
    27646 > mmaker #37 to #38
    27647 
    27648 Parameters 
    27649 --- 
    27650 Chain pairing | bb 
    27651 Alignment algorithm | Needleman-Wunsch 
    27652 Similarity matrix | BLOSUM-62 
    27653 SS fraction | 0.3 
    27654 Gap open (HH/SS/other) | 18/18/6 
    27655 Gap extend | 1 
    27656 SS matrix |  |  | H | S | O 
    27657 ---|---|---|--- 
    27658 H | 6 | -9 | -6 
    27659 S |  | 6 | -6 
    27660 O |  |  | 4 
    27661 Iteration cutoff | 2 
    27662  
    27663 Matchmaker 9hud, chain A (#38) with 1ezx, chain A (#37), sequence alignment
    27664 score = 1674.4 
    27665 RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
    27666 0.519) 
    27667  
    27668 
    27669 > show #!37 models
    27670 
    27671 > show #7 models
    27672 
    27673 > mmaker #7 to #37
    27674 
    27675 Parameters 
    27676 --- 
    27677 Chain pairing | bb 
    27678 Alignment algorithm | Needleman-Wunsch 
    27679 Similarity matrix | BLOSUM-62 
    27680 SS fraction | 0.3 
    27681 Gap open (HH/SS/other) | 18/18/6 
    27682 Gap extend | 1 
    27683 SS matrix |  |  | H | S | O 
    27684 ---|---|---|--- 
    27685 H | 6 | -9 | -6 
    27686 S |  | 6 | -6 
    27687 O |  |  | 4 
    27688 Iteration cutoff | 2 
    27689  
    27690 Matchmaker 1ezx, chain C (#37) with 5a0c, chain A (#7), sequence alignment
    27691 score = 241.2 
    27692 RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
    27693 3.073) 
    27694  
    27695 
    27696 > hide #!37 models
    27697 
    27698 > show #!37 models
    27699 
    27700 > hide #!38 models
    27701 
    27702 > show #!38 models
    27703 
    27704 > hide #!37 models
    27705 
    27706 > show #!37 models
    27707 
    27708 > hide #!38 models
    27709 
    27710 > hide #7 models
    27711 
    27712 > volume #65 level 0.03378
    27713 
    27714 > volume #66 level 0.03927
    27715 
    27716 > volume #66 level 0.03004
    27717 
    27718 > hide #!37 models
    27719 
    27720 > volume gaussian #65 sDev 2
    27721 
    27722 Opened cryosparc_P483_J136_004_volume_map.mrc gaussian as #67, grid size
    27723 400,400,400, pixel 0.723, shown at step 1, values float32 
    27724 
    27725 > ui tool show "Segment Map"
    27726 
    27727 Segmenting cryosparc_P483_J136_004_volume_map.mrc gaussian, density threshold
    27728 0.002595 
    27729 Only showing 60 of 69 regions. 
    27730 Showing 60 of 69 region surfaces 
    27731 165 watershed regions, grouped to 69 regions 
    27732 Showing cryosparc_P483_J136_004_volume_map gaussian.seg - 69 regions, 60
    27733 surfaces 
    27734 
    27735 > select #68.13
    27736 
    27737 1 model selected 
    27738 
    27739 > select add #68.6
    27740 
    27741 2 models selected 
    27742 
    27743 > select add #68.23
    27744 
    27745 3 models selected 
    27746 
    27747 > select add #68.24
    27748 
    27749 4 models selected 
    27750 
    27751 > select add #68.29
    27752 
    27753 5 models selected 
    27754 
    27755 > select add #68.20
    27756 
    27757 6 models selected 
    27758 
    27759 > select add #68.5
    27760 
    27761 7 models selected 
    27762 
    27763 > select add #68.37
    27764 
    27765 8 models selected 
    27766 
    27767 > select add #68.33
    27768 
    27769 9 models selected 
    27770 
    27771 > select add #68.11
    27772 
    27773 10 models selected 
    27774 
    27775 > select add #68.26
    27776 
    27777 11 models selected 
    27778 
    27779 > select add #68.14
    27780 
    27781 12 models selected 
    27782 
    27783 > select add #68.7
    27784 
    27785 13 models selected 
    27786 
    27787 > select add #68.3
    27788 
    27789 14 models selected 
    27790 
    27791 > select add #68.19
    27792 
    27793 15 models selected 
    27794 
    27795 > select add #68.8
    27796 
    27797 16 models selected 
    27798 
    27799 > select add #68.35
    27800 
    27801 17 models selected 
    27802 
    27803 > select add #68.28
    27804 
    27805 18 models selected 
    27806 
    27807 > select add #68.12
    27808 
    27809 19 models selected 
    27810 
    27811 > select add #68.15
    27812 
    27813 20 models selected 
    27814 
    27815 > select add #68.4
    27816 
    27817 21 models selected 
    27818 
    27819 > select add #68.40
    27820 
    27821 22 models selected 
    27822 
    27823 > select add #68.36
    27824 
    27825 23 models selected 
    27826 
    27827 > select add #68.48
    27828 
    27829 24 models selected 
    27830 
    27831 > select add #68.51
    27832 
    27833 25 models selected 
    27834 
    27835 > select add #68.53
    27836 
    27837 26 models selected 
    27838 
    27839 > select add #68.59
    27840 
    27841 27 models selected 
    27842 
    27843 > select add #68.58
    27844 
    27845 28 models selected 
    27846 
    27847 > select add #68.57
    27848 
    27849 29 models selected 
    27850 
    27851 > select add #68.54
    27852 
    27853 30 models selected 
    27854 
    27855 > select add #68.16
    27856 
    27857 31 models selected 
    27858 
    27859 > select add #68.44
    27860 
    27861 32 models selected 
    27862 
    27863 > select add #68.25
    27864 
    27865 33 models selected 
    27866 
    27867 > select add #68.50
    27868 
    27869 34 models selected 
    27870 
    27871 > select add #68.31
    27872 
    27873 35 models selected 
    27874 
    27875 > hide #!67 models
    27876 
    27877 > select add #68.45
    27878 
    27879 36 models selected 
    27880 
    27881 > select add #68.38
    27882 
    27883 37 models selected 
    27884 
    27885 > select add #68.17
    27886 
    27887 38 models selected 
    27888 
    27889 > select add #68.34
    27890 
    27891 39 models selected 
    27892 
    27893 > select add #68.52
    27894 
    27895 40 models selected 
    27896 
    27897 > select add #68.30
    27898 
    27899 41 models selected 
    27900 
    27901 > select add #68.27
    27902 
    27903 42 models selected 
    27904 
    27905 > select add #68.49
    27906 
    27907 43 models selected 
    27908 
    27909 > select add #68.46
    27910 
    27911 44 models selected 
    27912 
    27913 > select add #68.43
    27914 
    27915 45 models selected 
    27916 
    27917 > select add #68.39
    27918 
    27919 46 models selected 
    27920 
    27921 > select add #68.41
    27922 
    27923 47 models selected 
    27924 
    27925 > select add #68.56
    27926 
    27927 48 models selected 
    27928 
    27929 > select add #68.55
    27930 
    27931 49 models selected 
    27932 
    27933 > show #!67 models
    27934 
    27935 > show #!66 models
    27936 
    27937 > hide #!66 models
    27938 
    27939 > hide #!68 models
    27940 
    27941 > show #!68 models
    27942 
    27943 > hide #!68 models
    27944 
    27945 > show #!66 models
    27946 
    27947 > show #!68 models
    27948 
    27949 > hide #!67 models
    27950 
    27951 > hide #!66 models
    27952 
    27953 > show #!65 models
    27954 
    27955 > select add #68.42
    27956 
    27957 50 models selected 
    27958 
    27959 > hide #!65 models
    27960 
    27961 > select add #68.21
    27962 
    27963 51 models selected 
    27964 
    27965 > show #!66 models
    27966 
    27967 > hide #!66 models
    27968 
    27969 > show #!65 models
    27970 
    27971 > hide #!68 models
    27972 
    27973 > show #!68 models
    27974 
    27975 > hide #!68 models
    27976 
    27977 > show #!68 models
    27978 
    27979 > select add #68.47
    27980 
    27981 52 models selected 
    27982 
    27983 > select add #68.10
    27984 
    27985 53 models selected 
    27986 
    27987 > select subtract #68.10
    27988 
    27989 52 models selected 
    27990 
    27991 > select add #68.60
    27992 
    27993 53 models selected 
    27994 
    27995 > select add #68.1
    27996 
    27997 54 models selected 
    27998 
    27999 > select subtract #68.1
    28000 
    28001 53 models selected 
    28002 
    28003 > select add #68.1
    28004 
    28005 54 models selected 
    28006 
    28007 > select subtract #68.1
    28008 
    28009 53 models selected 
    28010 
    28011 > select #68.1
    28012 
    28013 1 model selected 
    28014 Segmenting cryosparc_P483_J136_004_volume_map.mrc gaussian, density threshold
    28015 0.002595 
    28016 Only showing 60 of 69 regions. 
    28017 Showing 60 of 69 region surfaces 
    28018 165 watershed regions, grouped to 69 regions 
    28019 Showing cryosparc_P483_J136_004_volume_map gaussian.seg - 69 regions, 60
    28020 surfaces 
    28021 
    28022 > close #68
    28023 
    28024 > show #!67 models
    28025 
    28026 > hide #!67 models
    28027 
    28028 > volume #65 level 0.009704
    28029 
    28030 > ui mousemode right "map eraser"
    28031 
    28032 > volume erase #65 center 171.23,100.86,184.61 radius 29.508
    28033 
    28034 Opened cryosparc_P483_J136_004_volume_map.mrc copy as #69, grid size
    28035 400,400,400, pixel 0.723, shown at step 1, values float32 
    28036 
    28037 > volume erase #69 center 84.398,121.62,173.8 radius 29.498
    28038 
    28039 > surface dust #69 size 7.23
    28040 
    28041 > volume #69 level 0.01365
    28042 
    28043 > volume #69 level 0.01523
    28044 
    28045 > ui mousemode right "translate selected models"
    28046 
    28047 > volume gaussian #65 sDev 2
    28048 
    28049 Opened cryosparc_P483_J136_004_volume_map.mrc gaussian as #68, grid size
    28050 400,400,400, pixel 0.723, shown at step 1, values float32 
    28051 
    28052 > ui mousemode right "map eraser"
    28053 
    28054 Can only have one displayed volume when erasing 
    28055 
    28056 > hide #!69 models
    28057 
    28058 > show #!69 models
    28059 
    28060 > hide #!69 models
    28061 
    28062 > hide #!68 models
    28063 
    28064 > show #!68 models
    28065 
    28066 > volume erase #68 center 199.87,114.16,177.51 radius 29.932
    28067 
    28068 > volume erase #68 center 223.51,161,191.94 radius 29.932
    28069 
    28070 > volume erase #68 center 230.79,129.47,140.96 radius 29.932
    28071 
    28072 > volume erase #68 center 137.16,147.6,54.19 radius 29.932
    28073 
    28074 > volume erase #68 center 74.443,93.395,201.66 radius 29.932
    28075 
    28076 > volume erase #68 center 60.662,109.56,169.96 radius 29.932
    28077 
    28078 > volume erase #68 center 81.784,129.86,147.37 radius 29.932
    28079 
    28080 > volume erase #68 center 97.833,142.74,184.92 radius 14.894
    28081 
    28082 > volume erase #68 center 93.234,158.27,115.41 radius 14.894
    28083 
    28084 > volume erase #68 center 110.51,164.91,187.37 radius 14.894
    28085 
    28086 > volume erase #68 center 126.3,181.61,190.42 radius 14.894
    28087 
    28088 > volume erase #68 center 190.02,108.44,206.29 radius 14.894
    28089 
    28090 > volume erase #68 center 212,136.35,210.5 radius 14.894
    28091 
    28092 > volume erase #68 center 66.419,147.34,177.91 radius 14.894
    28093 
    28094 > volume erase #68 center 94.954,148.62,156.51 radius 14.894
    28095 
    28096 > volume erase #68 center 105.75,136.11,158.02 radius 14.894
    28097 
    28098 > volume erase #68 center 169.12,113.8,156.36 radius 12.58
    28099 
    28100 > volume erase #68 center 179.1,115.64,198.32 radius 12.58
    28101 
    28102 > show #!65 models
    28103 
    28104 > hide #!68 models
    28105 
    28106 > volume #65 level 0.01773
    28107 
    28108 > show #!68 models
    28109 
    28110 Can only have one displayed volume when erasing 
    28111 
    28112 > hide #!65 models
    28113 
    28114 > hide #!68 models
    28115 
    28116 > show #!65 models
    28117 
    28118 > hide #!65 models
    28119 
    28120 > show #!68 models
    28121 
    28122 > volume erase #68 center 173.45,108.86,188.42 radius 22.124
    28123 
    28124 > volume erase #68 center 161.71,101.56,178.92 radius 22.124
    28125 
    28126 > undo
    28127 
    28128 [Repeated 1 time(s)]
    28129 
    28130 > show #!68 models
    28131 
    28132 > hide #!65 models
    28133 
    28134 > volume erase #68 center 92.336,122.06,161.51 radius 22.124
    28135 
    28136 Segmenting cryosparc_P483_J136_004_volume_map.mrc gaussian, density threshold
    28137 0.002595 
    28138 Showing 50 region surfaces 
    28139 124 watershed regions, grouped to 50 regions 
    28140 Showing cryosparc_P483_J136_004_volume_map gaussian.seg - 50 regions, 50
    28141 surfaces 
    28142 
    28143 > select add #70.10
    28144 
    28145 1 model selected 
    28146 
    28147 > select add #70.31
    28148 
    28149 2 models selected 
    28150 
    28151 > select add #70.6
    28152 
    28153 3 models selected 
    28154 
    28155 > select add #70.12
    28156 
    28157 4 models selected 
    28158 
    28159 > select add #70.23
    28160 
    28161 5 models selected 
    28162 
    28163 > select add #70.22
    28164 
    28165 6 models selected 
    28166 Drag select of 173, 7505 of 52828 triangles, 177, 26288 of 45472 triangles,
    28167 172, 156, 176, 25800 of 38068 triangles, 157, 17988 of 30408 triangles, 167,
    28168 152, 142, 6687 of 22324 triangles, 163, 64, 17140 of 19708 triangles, 12, 178,
    28169 169, 568 of 17388 triangles, 5, 143, 6044 of 15344 triangles, 144, 148, 135,
    28170 30, 12770 of 12984 triangles, 8, 52, 4331 of 12948 triangles, 125, 11085 of
    28171 12828 triangles, 6, 68, 5141 of 9284 triangles, 33, 35, 6919 of 6948
    28172 triangles, 68 cryosparc_P483_J136_004_volume_map.mrc gaussian 
    28173 Drag select of 177, 8907 of 45472 triangles, 172, 35825 of 37284 triangles,
    28174 156, 176, 5888 of 38068 triangles, 157, 7846 of 30408 triangles, 167, 152,
    28175 7570 of 25900 triangles, 163, 12, 17106 of 17656 triangles, 178, 5, 144, 148,
    28176 13560 of 13800 triangles, 135, 12555 of 14540 triangles, 30, 6391 of 12984
    28177 triangles, 8, 125, 1329 of 12828 triangles, 6, 33, 3490 of 7340 triangles, 35,
    28178 1963 of 6948 triangles, 68 cryosparc_P483_J136_004_volume_map.mrc gaussian 
    28179 
    28180 > hide #!68 models
    28181 
    28182 Drag select of 177, 10859 of 45472 triangles, 172, 176, 10027 of 38068
    28183 triangles, 149, 177 of 29032 triangles, 152, 12625 of 25900 triangles, 163, 5,
    28184 144, 135, 14423 of 14540 triangles, 30, 11045 of 12984 triangles, 8, 125, 2434
    28185 of 12828 triangles, 6, 33, 6568 of 7340 triangles, 35, 5541 of 6948 triangles 
    28186 
    28187 > close #70
    28188 
    28189 > show #!66 models
    28190 
    28191 > hide #!66 models
    28192 
    28193 > show #!65 models
    28194 
    28195 > show #!68 models
    28196 
    28197 > close #68-69
    28198 
    28199 > close #67
    28200 
    28201 > volume gaussian #65 sDev 2
    28202 
    28203 Opened cryosparc_P483_J136_004_volume_map.mrc gaussian as #67, grid size
    28204 400,400,400, pixel 0.723, shown at step 1, values float32 
    28205 
    28206 > open /Users/amy/Downloads/cryosparc_P371_J1247_003_volume_map.mrc
    28207 
    28208 Opened cryosparc_P371_J1247_003_volume_map.mrc as #68, grid size 300,300,300,
    28209 pixel 0.867, shown at level 0.0217, step 2, values float32 
    28210 
    28211 > hide #!67 models
    28212 
    28213 > volume #68 level 0.07077
    28214 
    28215 > show #!8 models
    28216 
    28217 > transparenct #68 50
    28218 
    28219 Unknown command: transparenct #68 50 
    28220 
    28221 > transparency #68 50
    28222 
    28223 > fitmap #8 inMap #68
    28224 
    28225 Fit molecule 1ezx (#8) to map cryosparc_P371_J1247_003_volume_map.mrc (#68)
    28226 using 3984 atoms 
    28227 average map value = 0.0799, steps = 64 
    28228 shifted from previous position = 1.9 
    28229 rotated from previous position = 5.61 degrees 
    28230 atoms outside contour = 1925, contour level = 0.07077 
    28231  
    28232 Position of 1ezx (#8) relative to cryosparc_P371_J1247_003_volume_map.mrc
    28233 (#68) coordinates: 
    28234 Matrix rotation and translation 
    28235 -0.34797185 0.02707514 -0.93711394 206.68051797 
    28236 0.14066384 -0.98675962 -0.08074121 177.03298135 
    28237 -0.92689227 -0.15991372 0.33955607 198.02271581 
    28238 Axis -0.57026324 -0.07362457 0.81815601 
    28239 Axis point 168.54386706 102.19253410 0.00000000 
    28240 Rotation angle (degrees) 176.01946831 
    28241 Shift along axis 31.11719577 
    28242  
    28243 
    28244 > show #!57 models
    28245 
    28246 > select add #57
    28247 
    28248 1009 atoms, 1014 bonds, 5 pseudobonds, 155 residues, 3 models selected 
    28249 
    28250 > mmaker #57 to #8
    28251 
    28252 Parameters 
    28253 --- 
    28254 Chain pairing | bb 
    28255 Alignment algorithm | Needleman-Wunsch 
    28256 Similarity matrix | BLOSUM-62 
    28257 SS fraction | 0.3 
    28258 Gap open (HH/SS/other) | 18/18/6 
    28259 Gap extend | 1 
    28260 SS matrix |  |  | H | S | O 
    28261 ---|---|---|--- 
    28262 H | 6 | -9 | -6 
    28263 S |  | 6 | -6 
    28264 O |  |  | 4 
    28265 Iteration cutoff | 2 
    28266  
    28267 Matchmaker 1ezx, chain C (#8) with copy of 1ezx, chain C (#57), sequence
    28268 alignment score = 1096 
    28269 RMSD between 140 pruned atom pairs is 0.000 angstroms; (across all 140 pairs:
    28270 0.000) 
    28271  
    28272 
    28273 > select subtract #57
    28274 
    28275 Nothing selected 
    28276 
    28277 > select add #57
    28278 
    28279 1009 atoms, 1014 bonds, 5 pseudobonds, 155 residues, 3 models selected 
    28280 
    28281 > hide #!8 models
    28282 
    28283 > show #!8 models
    28284 
    28285 > ui mousemode right "translate selected models"
    28286 
    28287 > view matrix models
    28288 > #57,-0.55581,-0.066238,-0.82867,220.13,0.27617,-0.95492,-0.10891,166.76,-0.7841,-0.28938,0.54905,178.74
    28289 
    28290 > view matrix models
    28291 > #57,-0.44814,0.013112,-0.89387,212.91,0.19695,-0.97388,-0.11303,173.83,-0.872,-0.2267,0.43385,190.3
    28292 
    28293 > view matrix models
    28294 > #57,-0.44814,0.013112,-0.89387,212.84,0.19695,-0.97388,-0.11303,176.3,-0.872,-0.2267,0.43385,191.28
    28295 
    28296 > view matrix models
    28297 > #57,-0.70986,-0.70171,-0.060879,208.01,0.69037,-0.67603,-0.25765,136.82,0.13964,-0.22492,0.96432,82.152
    28298 
    28299 > view matrix models
    28300 > #57,-0.70986,-0.70171,-0.060879,209.15,0.69037,-0.67603,-0.25765,137.83,0.13964,-0.22492,0.96432,86.098
    28301 
    28302 > view matrix models
    28303 > #57,-0.52828,-0.77583,-0.34499,210.69,0.84041,-0.53567,-0.082284,113.45,-0.12096,-0.3334,0.93499,111.22
    28304 
    28305 > fitmap #57 inMap #68
    28306 
    28307 Fit molecule copy of 1ezx (#57) to map cryosparc_P371_J1247_003_volume_map.mrc
    28308 (#68) using 1009 atoms 
    28309 average map value = 0.05715, steps = 92 
    28310 shifted from previous position = 1.85 
    28311 rotated from previous position = 22.4 degrees 
    28312 atoms outside contour = 740, contour level = 0.07077 
    28313  
    28314 Position of copy of 1ezx (#57) relative to
    28315 cryosparc_P371_J1247_003_volume_map.mrc (#68) coordinates: 
    28316 Matrix rotation and translation 
    28317 -0.60074737 -0.69741151 -0.39079378 215.40326299 
    28318 0.67365936 -0.70482938 0.22225799 115.60603445 
    28319 -0.43044821 -0.12974098 0.89324219 133.98043752 
    28320 Axis -0.24857103 0.02800277 0.96820880 
    28321 Axis point 100.60140928 106.25888332 0.00000000 
    28322 Rotation angle (degrees) 134.92392438 
    28323 Shift along axis 79.41531641 
    28324  
    28325 
    28326 > hide #!8 models
    28327 
    28328 > view matrix models
    28329 > #57,-0.55549,-0.80836,-0.19489,204.29,0.77301,-0.58839,0.23717,104.09,-0.30639,-0.018907,0.95172,118.37
    28330 
    28331 > view matrix models
    28332 > #57,-0.55549,-0.80836,-0.19489,206,0.77301,-0.58839,0.23717,104.98,-0.30639,-0.018907,0.95172,120.21
    28333 
    28334 > view matrix models
    28335 > #57,-0.33676,-0.93674,0.09544,176.41,0.94008,-0.34023,-0.022246,98.96,0.05331,0.08223,0.99519,86.499
    28336 
    28337 > view matrix models
    28338 > #57,-0.33676,-0.93674,0.09544,176.42,0.94008,-0.34023,-0.022246,99.819,0.05331,0.08223,0.99519,85.597
    28339 
    28340 > view matrix models
    28341 > #57,-0.11119,-0.60614,-0.78754,195.64,0.65285,-0.64203,0.40198,108.39,-0.74928,-0.46945,0.46711,190.42
    28342 
    28343 > view matrix models
    28344 > #57,0.78168,0.24914,-0.57175,92.445,0.18825,-0.96824,-0.16454,182.56,-0.59459,0.020991,-0.80376,231.51
    28345 
    28346 > view matrix models
    28347 > #57,0.51703,0.78986,-0.32985,88.973,0.65853,-0.61323,-0.43621,150.13,-0.54682,0.0083211,-0.83721,229.65
    28348 
    28349 > view matrix models
    28350 > #57,0.51703,0.78986,-0.32985,91.831,0.65853,-0.61323,-0.43621,150.09,-0.54682,0.0083211,-0.83721,234.12
    28351 
    28352 > view matrix models
    28353 > #57,0.55299,0.36331,-0.7498,120.29,0.22263,-0.93163,-0.28721,185.16,-0.80289,-0.0081052,-0.59607,242.91
    28354 
    28355 > view matrix models
    28356 > #57,0.55299,0.36331,-0.7498,118.48,0.22263,-0.93163,-0.28721,185.69,-0.80289,-0.0081052,-0.59607,239.55
    28357 
    28358 > view matrix models
    28359 > #57,0.92569,-0.35496,0.13079,59.902,0.0091285,-0.32469,-0.94578,222.6,0.37818,0.87669,-0.29732,108.08
    28360 
    28361 > view matrix models
    28362 > #57,-0.3165,-0.83947,0.44172,155.86,0.42443,-0.54177,-0.7255,182.72,0.84834,-0.042141,0.52777,49.092
    28363 
    28364 > view matrix models
    28365 > #57,-0.3165,-0.83947,0.44172,156.19,0.42443,-0.54177,-0.7255,182.46,0.84834,-0.042141,0.52777,49.883
    28366 
    28367 > view matrix models
    28368 > #57,0.040165,-0.95688,0.2877,137.9,0.92992,-0.069542,-0.36112,111.92,0.36556,0.28204,0.88703,63.1
    28369 
    28370 > view matrix models
    28371 > #57,0.040165,-0.95688,0.2877,138.99,0.92992,-0.069542,-0.36112,111.84,0.36556,0.28204,0.88703,64.867
    28372 
    28373 > view matrix models
    28374 > #57,0.18721,-0.98102,0.050423,139.78,0.96897,0.17599,-0.17355,93.385,0.16139,0.081349,0.98353,81.124
    28375 
    28376 > mmaker #7 to #8
    28377 
    28378 Parameters 
    28379 --- 
    28380 Chain pairing | bb 
    28381 Alignment algorithm | Needleman-Wunsch 
    28382 Similarity matrix | BLOSUM-62 
    28383 SS fraction | 0.3 
    28384 Gap open (HH/SS/other) | 18/18/6 
    28385 Gap extend | 1 
    28386 SS matrix |  |  | H | S | O 
    28387 ---|---|---|--- 
    28388 H | 6 | -9 | -6 
    28389 S |  | 6 | -6 
    28390 O |  |  | 4 
    28391 Iteration cutoff | 2 
    28392  
    28393 Matchmaker 1ezx, chain C (#8) with 5a0c, chain A (#7), sequence alignment
    28394 score = 241.2 
    28395 RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
    28396 3.073) 
    28397  
    28398 
    28399 > select add #7
    28400 
    28401 2892 atoms, 2759 bonds, 5 pseudobonds, 549 residues, 4 models selected 
    28402 
    28403 > show #7 models
    28404 
    28405 > select subtract #57
    28406 
    28407 1883 atoms, 1745 bonds, 394 residues, 1 model selected 
    28408 
    28409 > hide #!57 models
    28410 
    28411 > select #7/A
    28412 
    28413 1883 atoms, 1745 bonds, 394 residues, 1 model selected 
    28414 
    28415 > select subtract #7
    28416 
    28417 Nothing selected 
    28418 
    28419 > select #7/A
    28420 
    28421 1883 atoms, 1745 bonds, 394 residues, 1 model selected 
    28422 
    28423 > select #7/A: 202
    28424 
    28425 6 atoms, 5 bonds, 1 residue, 1 model selected 
    28426 
    28427 > select #7/A: 202
    28428 
    28429 6 atoms, 5 bonds, 1 residue, 1 model selected 
    28430 
    28431 > show sel atoms
    28432 
    28433 > style sel stick
    28434 
    28435 Changed 6 atom styles 
    28436 
    28437 > rainbow sel
    28438 
    28439 > select add #7
    28440 
    28441 1883 atoms, 1745 bonds, 394 residues, 1 model selected 
    28442 
    28443 > select subtract #7
    28444 
    28445 Nothing selected 
    28446 
    28447 > show #!37 models
    28448 
    28449 > hide #!37 models
    28450 
    28451 > show #!8 models
    28452 
    28453 > hide #!8 models
    28454 
    28455 > open /Users/amy/Downloads/cryosparc_P371_J1248_004_volume_map.mrc
    28456 
    28457 Opened cryosparc_P371_J1248_004_volume_map.mrc as #69, grid size 300,300,300,
    28458 pixel 0.867, shown at level 0.0367, step 2, values float32 
    28459 
    28460 > volume #69 level 0.08383
    28461 
    28462 > hide #!68 models
    28463 
    28464 > volume #69 level 0.0762
    28465 
    28466 > transparency #69 50
    28467 
    28468 > hide #7 models
    28469 
    28470 > close #50-56
    28471 
    28472 > close #43-48
    28473 
    28474 > show #!65 models
    28475 
    28476 > volume gaussian #65 sDev 2
    28477 
    28478 Opened cryosparc_P483_J136_004_volume_map.mrc gaussian as #43, grid size
    28479 400,400,400, pixel 0.723, shown at step 1, values float32 
    28480 
    28481 > ui mousemode right "map eraser"
    28482 
    28483 > volume erase #43 center 75.013,107.83,176.28 radius 23.833
    28484 
    28485 > volume erase #43 center 194.75,109.99,182.34 radius 28.983
    28486 
    28487 > volume erase #43 center 224.93,121.74,145.38 radius 28.983
    28488 
    28489 > volume erase #43 center 210.7,158.2,175.15 radius 28.983
    28490 
    28491 > volume erase #43 center 208.21,147.09,205.7 radius 28.983
    28492 
    28493 > volume erase #43 center 188.54,118.48,207.86 radius 28.983
    28494 
    28495 > volume erase #43 center 76.857,145.76,159.87 radius 28.983
    28496 
    28497 > volume erase #43 center 87.79,161.6,111.25 radius 28.983
    28498 
    28499 > volume erase #43 center 126.19,148.22,60.086 radius 28.983
    28500 
    28501 > surface dust #43 size 7.23
    28502 
    28503 [Repeated 2 time(s)]
    28504 
    28505 > volume erase #43 center 98.252,123.11,133.43 radius 28.983
    28506 
    28507 > ui mousemode right "translate selected models"
    28508 
    28509 > hide #!43 models
    28510 
    28511 > show #!43 models
    28512 
    28513 Segmenting cryosparc_P483_J136_004_volume_map.mrc gaussian, density threshold
    28514 0.002595 
    28515 Showing 54 region surfaces 
    28516 134 watershed regions, grouped to 54 regions 
    28517 Showing cryosparc_P483_J136_004_volume_map gaussian.seg - 54 regions, 54
    28518 surfaces 
    28519 Drag select of 180, 4556 of 45584 triangles, 187, 31245 of 37284 triangles,
    28520 177, 33991 of 34540 triangles, 179, 626 of 37968 triangles, 170, 1849 of 30408
    28521 triangles, 183, 146, 4014 of 25900 triangles, 166, 12, 182, 5, 151, 157, 9644
    28522 of 13800 triangles, 160, 7260 of 14540 triangles, 30, 3371 of 12984 triangles,
    28523 8, 6, 33, 892 of 7340 triangles, 35, 143 of 6948 triangles, 43
    28524 cryosparc_P483_J136_004_volume_map.mrc gaussian 
    28525 Drag select of 189, 15171 of 45152 triangles, 144, 28176 of 29416 triangles,
    28526 186, 153, 26060 of 29032 triangles, 165, 16225 of 23204 triangles, 171, 20862
    28527 of 21324 triangles, 181, 612 of 19816 triangles, 188, 9417 of 18732 triangles,
    28528 184, 11190 of 17388 triangles, 69, 12493 of 16160 triangles, 83, 159, 3373 of
    28529 15344 triangles, 100, 109, 4788 of 13396 triangles, 54, 54 of 12948 triangles,
    28530 190, 3956 of 13608 triangles, 148, 93 of 11564 triangles, 167, 713 of 12312
    28531 triangles, 136, 1067 of 12828 triangles, 95, 7439 of 9752 triangles, 82, 43
    28532 cryosparc_P483_J136_004_volume_map.mrc gaussian 
    28533 
    28534 > hide #!43 models
    28535 
    28536 > show #!43 models
    28537 
    28538 > select add #44.51
    28539 
    28540 41 models selected 
    28541 
    28542 > select add #44.53
    28543 
    28544 42 models selected 
    28545 
    28546 > hide #!43 models
    28547 
    28548 > select add #44.10
    28549 
    28550 43 models selected 
    28551 Ungrouped to 64 regions, but did not show all surfaces, see Options 
    28552 
    28553 > select clear
    28554 
    28555 > select #44.62
    28556 
    28557 1 model selected 
    28558 
    28559 > select #44.21
    28560 
    28561 1 model selected 
    28562 Ungrouped to 2 regions, but did not show their surfaces, see Options 
    28563 Smoothing and grouping, standard deviation 5 voxels 
    28564 Showing 28 region surfaces 
    28565 Got 28 regions after smoothing 5 voxels. 
    28566 Ungrouped to 86 regions, but did not show all surfaces, see Options 
    28567 Drag select of 134 
    28568 [Repeated 1 time(s)]
    28569 
    28570 > select clear
    28571 
    28572 > select #44.72
    28573 
    28574 1 model selected 
    28575 
    28576 > select clear
    28577 
    28578 > select #44.73
    28579 
    28580 1 model selected 
    28581 
    28582 > select add #44.74
    28583 
    28584 2 models selected 
    28585 
    28586 > show #!43 models
    28587 
    28588 > hide #!44 models
    28589 
    28590 > volume #43 level 0.01177
    28591 
    28592 > ui mousemode right "map eraser"
    28593 
    28594 > volume erase #43 center 170.19,107.1,177.93 radius 16.889
    28595 
    28596 > ui mousemode right "translate selected models"
    28597 
    28598 > close #44
    28599 
    28600 > volume gaussian #65 sDev 2
    28601 
    28602 Opened cryosparc_P483_J136_004_volume_map.mrc gaussian as #44, grid size
    28603 400,400,400, pixel 0.723, shown at step 1, values float32 
    28604 
    28605 > close #44
    28606 
    28607 Segmenting cryosparc_P483_J136_004_volume_map.mrc gaussian, density threshold
    28608 0.011767 
    28609 Showing 49 region surfaces 
    28610 113 watershed regions, grouped to 49 regions 
    28611 Showing cryosparc_P483_J136_004_volume_map gaussian.seg - 49 regions, 49
    28612 surfaces 
    28613 
    28614 > hide #!43 models
    28615 
    28616 Drag select of 152, 22015 of 40248 triangles, 160, 137, 162, 19815 of 27632
    28617 triangles, 145, 22686 of 24068 triangles, 154, 132, 19102 of 20860 triangles,
    28618 149, 128, 343 of 19360 triangles, 12, 157, 151, 5666 of 14648 triangles, 155,
    28619 15 of 14140 triangles, 121, 8147 of 14452 triangles, 126, 124, 5, 50, 4342 of
    28620 11924 triangles, 6, 133, 26, 116, 11741 of 11768 triangles, 7, 32, 34 
    28621 Drag select of 159, 9755 of 37648 triangles, 125, 24182 of 24328 triangles,
    28622 158, 18998 of 22744 triangles, 139, 10853 of 19468 triangles, 142, 17469 of
    28623 19372 triangles, 128, 5249 of 19360 triangles, 63, 3508 of 13216 triangles,
    28624 82, 11209 of 11804 triangles, 90, 161, 1720 of 12188 triangles, 84, 4555 of
    28625 9228 triangles, 71, 6615 of 6864 triangles 
    28626 Drag select of 128, 163, 7108 of 17660 triangles, 94, 10211 of 10636
    28627 triangles, 123, 7213 of 10336 triangles, 146, 6495 of 11584 triangles, 88,
    28628 3550 of 8592 triangles 
    28629 Showing 49 region surfaces 
    28630 
    28631 > select #44.46
    28632 
    28633 1 model selected 
    28634 
    28635 > show #!43 models
    28636 
    28637 > hide #!43 models
    28638 
    28639 > select #44.13
    28640 
    28641 1 model selected 
    28642 
    28643 > select #44.13
    28644 
    28645 1 model selected 
    28646 
    28647 > select #44.3
    28648 
    28649 1 model selected 
    28650 
    28651 > select #44.3
    28652 
    28653 1 model selected 
    28654 Ungrouped to 2 regions 
    28655 
    28656 > select #44.13
    28657 
    28658 1 model selected 
    28659 Ungrouped to 2 regions 
    28660 
    28661 > select #44.3
    28662 
    28663 1 model selected 
    28664 Ungrouped to 2 regions 
    28665 
    28666 > select #44.51
    28667 
    28668 1 model selected 
    28669 Ungrouped to 2 regions 
    28670 
    28671 > select #44.54
    28672 
    28673 1 model selected 
    28674 Ungrouped to 2 regions 
    28675 
    28676 > show #!43 models
    28677 
    28678 > hide #!43 models
    28679 
    28680 > show #!43 models
    28681 
    28682 > hide #!43 models
    28683 
    28684 > show #!43 models
    28685 
    28686 > hide #!43 models
    28687 
    28688 > select #44.55
    28689 
    28690 1 model selected 
    28691 
    28692 > select #44.55
    28693 
    28694 1 model selected 
    28695 
    28696 > select clear
    28697 
    28698 Please select one ore more regions to save to .mrc file 
    28699 Drag select of 156, 138, 61, 127, 65, 93, 87, 92, 76, 68, 79, 69 
    28700 Saving 12 regions to mrc file... 
    28701 Opened base_cryosparc_P483_J136_004_volume_map_12_regions.mrc as #45, grid
    28702 size 75,64,70, pixel 0.723, shown at step 1, values float32 
    28703 Wrote base_cryosparc_P483_J136_004_volume_map_12_regions.mrc 
    28704 
    28705 > volume #45 level 0.01277
    28706 
    28707 > hide #!44 models
    28708 
    28709 > show #!44 models
    28710 
    28711 Deleted 12 regions 
    28712 Showing 42 region surfaces 
    28713 
    28714 > hide #!45 models
    28715 
    28716 > show #!45 models
    28717 
    28718 > hide #!45 models
    28719 
    28720 Drag select of 152, 159, 160, 137, 162, 125, 158, 145, 154, 139, 132, 142,
    28721 149, 128, 163, 12, 157, 151, 155, 121, 126, 63, 82, 124, 5, 50, 6, 133, 90,
    28722 26, 161, 94, 116, 123, 146, 7, 84, 88, 74, 71, 32, 34 
    28723 Saving 42 regions to mrc file... 
    28724 Opened substract_cryosparc_P483_J136_004_volume_map_42_regions.mrc as #46,
    28725 grid size 90,89,178, pixel 0.723, shown at step 1, values float32 
    28726 Wrote substract_cryosparc_P483_J136_004_volume_map_42_regions.mrc 
    28727 
    28728 > select add #44
    28729 
    28730 43 models selected 
    28731 
    28732 > select subtract #44
    28733 
    28734 Nothing selected 
    28735 
    28736 > hide #!44 models
    28737 
    28738 > volume #46 level 0.01896
    28739 
    28740 > show #!44 models
    28741 
    28742 > hide #!44 models
    28743 
    28744 > show #!45 models
    28745 
    28746 > volume resample #45 onGrid #65
    28747 
    28748 Opened base_cryosparc_P483_J136_004_volume_map_12_regions.mrc resampled as
    28749 #47, grid size 400,400,400, pixel 0.723, shown at step 1, values float32 
    28750 
    28751 > show #!45 models
    28752 
    28753 > hide #!45 models
    28754 
    28755 > volume resample #46 onGrid #65
    28756 
    28757 Opened substract_cryosparc_P483_J136_004_volume_map_42_regions.mrc resampled
    28758 as #48, grid size 400,400,400, pixel 0.723, shown at step 1, values float32 
    28759 
    28760 > hide #!48 models
    28761 
    28762 > show #!48 models
    28763 
    28764 > save "/Users/amy/Desktop/SPA AAT_HNE/9C5_Fab_AAT_HNE/For mask
    28765 > generation/Base_mask_J136.mrc" models #47
    28766 
    28767 > save "/Users/amy/Desktop/SPA AAT_HNE/9C5_Fab_AAT_HNE/For mask
    28768 > generation/Substract_mask_J136.mrc" models #48
    28769 
    28770 > hide #!48 models
    28771 
    28772 > hide #!47 models
    28773 
    28774 > show #!66 models
    28775 
    28776 > volume #66 level 0.01465
    28777 
    28778 > hide #!66 models
    28779 
    28780 > show #!66 models
    28781 
    28782 > show #!65 models
    28783 
    28784 > hide #!66 models
    28785 
    28786 > hide #!65 models
    28787 
    28788 > show #!66 models
    28789 
    28790 > volume #66 level 0.0762
    28791 
    28792 > volume #66 level 0.05963
    28793 
    28794 > open /Users/amy/Downloads/Position_4_4_stack_Vol.mrc
    28795 
    28796 Opened Position_4_4_stack_Vol.mrc as #50, grid size 1024,1024,200, pixel
    28797 6.2,6.2,6.2, shown at level 0.00197, step 4, values float32 
    28798 
    28799 > open /Users/amy/Downloads/cryosparc_P483_J163_009_volume_map.mrc
    28800 
    28801 Opened cryosparc_P483_J163_009_volume_map.mrc as #51, grid size 400,400,400,
    28802 pixel 0.723, shown at level 0.00345, step 2, values float32 
    28803 
    28804 > hide #!50 models
    28805 
    28806 > hide #!66 models
    28807 
    28808 > close #50
    28809 
    28810 > volume #51 level 0.01856
    28811 
    28812 > transparency #51 50
    28813 
    28814 > show #!38 models
    28815 
    28816 > select add #38
    28817 
    28818 6282 atoms, 6138 bonds, 1077 residues, 1 model selected 
    28819 
    28820 > volume flip #51 axis z
    28821 
    28822 Opened cryosparc_P483_J163_009_volume_map.mrc z flip as #50, grid size
    28823 400,400,400, pixel 0.723, shown at step 1, values float32 
    28824 
    28825 > fitmap #38 inMap #50
    28826 
    28827 Fit molecule 9hud (#38) to map cryosparc_P483_J163_009_volume_map.mrc z flip
    28828 (#50) using 6282 atoms 
    28829 average map value = 0.07848, steps = 68 
    28830 shifted from previous position = 0.869 
    28831 rotated from previous position = 1.21 degrees 
    28832 atoms outside contour = 1202, contour level = 0.018564 
    28833  
    28834 Position of 9hud (#38) relative to cryosparc_P483_J163_009_volume_map.mrc z
    28835 flip (#50) coordinates: 
    28836 Matrix rotation and translation 
    28837 0.47930263 0.06820977 0.87499511 60.65156876 
    28838 -0.57459125 -0.72922061 0.37159415 263.89520826 
    28839 0.66341081 -0.68087058 -0.31032461 53.93040141 
    28840 Axis -0.84112622 0.16909745 -0.51372438 
    28841 Axis point 0.00000000 145.65173307 -47.89349763 
    28842 Rotation angle (degrees) 141.27168221 
    28843 Shift along axis -34.09698023 
    28844  
    28845 
    28846 > select subtract #38
    28847 
    28848 Nothing selected 
    28849 
    28850 > show #!37 models
    28851 
    28852 > mmaker #37 to #38
    28853 
    28854 Parameters 
    28855 --- 
    28856 Chain pairing | bb 
    28857 Alignment algorithm | Needleman-Wunsch 
    28858 Similarity matrix | BLOSUM-62 
    28859 SS fraction | 0.3 
    28860 Gap open (HH/SS/other) | 18/18/6 
    28861 Gap extend | 1 
    28862 SS matrix |  |  | H | S | O 
    28863 ---|---|---|--- 
    28864 H | 6 | -9 | -6 
    28865 S |  | 6 | -6 
    28866 O |  |  | 4 
    28867 Iteration cutoff | 2 
    28868  
    28869 Matchmaker 9hud, chain A (#38) with 1ezx, chain A (#37), sequence alignment
    28870 score = 1674.4 
    28871 RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
    28872 0.519) 
    28873  
    28874 
    28875 > hide #!37 models
    28876 
    28877 > hide #!38 models
    28878 
    28879 > show #!37 models
    28880 
    28881 > ui mousemode right "tape measure"
    28882 
    28883 > marker segment #52 position 174.9,170.7,80.95 toPosition 149.1,120.4,104.7
    28884 > color yellow radius 0.1807 label 61.39 labelHeight 6.139 labelColor yellow
    28885 
    28886 > marker segment #52 position 173.6,172.2,80.09 toPosition 131.7,129.6,94.55
    28887 > color yellow radius 0.1807 label 61.46 labelHeight 6.146 labelColor yellow
    28888 
    28889 > marker segment #52 position 168.9,170.1,79.92 toPosition 119.6,140.5,107.7
    28890 > color yellow radius 0.1807 label 63.85 labelHeight 6.385 labelColor yellow
    28891 
    28892 > marker segment #52 position 162.3,169.9,78.45 toPosition 131.8,125.9,101.6
    28893 > color yellow radius 0.1807 label 58.29 labelHeight 5.829 labelColor yellow
    28894 
    28895 > close #52
    28896 
    28897 > open /Users/amy/Downloads/cryosparc_P483_J166_007_volume_map.mrc
    28898 
    28899 Opened cryosparc_P483_J166_007_volume_map.mrc as #52, grid size 400,400,400,
    28900 pixel 0.723, shown at level 0.00871, step 2, values float32 
    28901 
    28902 > volume #52 level 0.03218
    28903 
    28904 > volume flip #52 50
    28905 
    28906 Expected a keyword 
    28907 
    28908 > volume flip #52 axis z
    28909 
    28910 Opened cryosparc_P483_J166_007_volume_map.mrc z flip as #53, grid size
    28911 400,400,400, pixel 0.723, shown at step 1, values float32 
    28912 
    28913 > transparency #53 50
    28914 
    28915 > fitmap #38 inMap #53
    28916 
    28917 Fit molecule 9hud (#38) to map cryosparc_P483_J166_007_volume_map.mrc z flip
    28918 (#53) using 6282 atoms 
    28919 average map value = 0.0755, steps = 88 
    28920 shifted from previous position = 0.675 
    28921 rotated from previous position = 2.29 degrees 
    28922 atoms outside contour = 1730, contour level = 0.032179 
    28923  
    28924 Position of 9hud (#38) relative to cryosparc_P483_J166_007_volume_map.mrc z
    28925 flip (#53) coordinates: 
    28926 Matrix rotation and translation 
    28927 0.48708054 0.10074896 0.86752649 58.26714282 
    28928 -0.57324776 -0.71251935 0.40460253 263.40109171 
    28929 0.65889268 -0.69438163 -0.28930019 55.22725475 
    28930 Axis -0.84150595 0.15975352 -0.51608774 
    28931 Axis point 0.00000000 145.38448995 -49.65713741 
    28932 Rotation angle (degrees) 139.23284387 
    28933 Shift along axis -35.45500404 
    28934  
    28935 
    28936 > show #!38 models
    28937 
    28938 > mmaker #37 to #38
    28939 
    28940 Parameters 
    28941 --- 
    28942 Chain pairing | bb 
    28943 Alignment algorithm | Needleman-Wunsch 
    28944 Similarity matrix | BLOSUM-62 
    28945 SS fraction | 0.3 
    28946 Gap open (HH/SS/other) | 18/18/6 
    28947 Gap extend | 1 
    28948 SS matrix |  |  | H | S | O 
    28949 ---|---|---|--- 
    28950 H | 6 | -9 | -6 
    28951 S |  | 6 | -6 
    28952 O |  |  | 4 
    28953 Iteration cutoff | 2 
    28954  
    28955 Matchmaker 9hud, chain A (#38) with 1ezx, chain A (#37), sequence alignment
    28956 score = 1674.4 
    28957 RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
    28958 0.519) 
    28959  
    28960 
    28961 > hide #!38 models
    28962 
    28963 > show #7 models
    28964 
    28965 > mmaker #7 to #37
    28966 
    28967 Parameters 
    28968 --- 
    28969 Chain pairing | bb 
    28970 Alignment algorithm | Needleman-Wunsch 
    28971 Similarity matrix | BLOSUM-62 
    28972 SS fraction | 0.3 
    28973 Gap open (HH/SS/other) | 18/18/6 
    28974 Gap extend | 1 
    28975 SS matrix |  |  | H | S | O 
    28976 ---|---|---|--- 
    28977 H | 6 | -9 | -6 
    28978 S |  | 6 | -6 
    28979 O |  |  | 4 
    28980 Iteration cutoff | 2 
    28981  
    28982 Matchmaker 1ezx, chain C (#37) with 5a0c, chain A (#7), sequence alignment
    28983 score = 241.2 
    28984 RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
    28985 3.073) 
    28986  
    28987 
    28988 > hide #!37 models
    28989 
    28990 > volume #53 level 0.09551
    28991 
    28992 > volume #53 level 0.05065
    28993 
    28994 > volume #53 level 0.04273
    28995 
    28996 > hide #7 models
    28997 
    28998 > open /Users/amy/Downloads/cryosparc_P483_J178_007_volume_map.mrc
    28999 
    29000 Opened cryosparc_P483_J178_007_volume_map.mrc as #54, grid size 400,400,400,
    29001 pixel 0.723, shown at level 0.00984, step 2, values float32 
    29002 
    29003 > volume #54 level 0.02797
    29004 
    29005 > volume flip #54 axis z
    29006 
    29007 Opened cryosparc_P483_J178_007_volume_map.mrc z flip as #55, grid size
    29008 400,400,400, pixel 0.723, shown at step 1, values float32 
    29009 
    29010 > transparency #55 50
    29011 
    29012 > show #7 models
    29013 
    29014 > hide #7 models
    29015 
    29016 > show #7 models
    29017 
    29018 > select add #7
    29019 
    29020 1883 atoms, 1745 bonds, 394 residues, 1 model selected 
    29021 
    29022 > select subtract #7
    29023 
    29024 Nothing selected 
    29025 
    29026 > hide #7 models
    29027 
    29028 > show #!8 models
    29029 
    29030 > select add #8
    29031 
    29032 3984 atoms, 3982 bonds, 5 pseudobonds, 592 residues, 3 models selected 
    29033 
    29034 > ui mousemode right "translate selected models"
    29035 
    29036 > view matrix models
    29037 > #8,-0.74339,-0.4472,0.49738,176.11,0.56886,-0.81386,0.11846,127.4,0.35182,0.371,0.85941,53.336
    29038 
    29039 > view matrix models
    29040 > #8,0.38457,0.070001,0.92044,48.03,0.66601,-0.71147,-0.22416,135.06,0.63917,0.69922,-0.32023,84.211
    29041 
    29042 > view matrix models
    29043 > #8,0.38457,0.070001,0.92044,48.132,0.66601,-0.71147,-0.22416,145.94,0.63917,0.69922,-0.32023,107.63
    29044 
    29045 > view matrix models
    29046 > #8,-0.11357,-0.011929,0.99346,82.463,0.67784,-0.73199,0.068701,129.45,0.72638,0.68121,0.091219,79.052
    29047 
    29048 > hide #!55 models
    29049 
    29050 > show #!54 models
    29051 
    29052 > transparency #54 50
    29053 
    29054 > view matrix models
    29055 > #8,-0.11357,-0.011929,0.99346,88.184,0.67784,-0.73199,0.068701,128.28,0.72638,0.68121,0.091219,43.943
    29056 
    29057 > view matrix models
    29058 > #8,0.98922,0.13889,-0.046321,63.821,0.14063,-0.98938,0.036662,180.17,-0.040737,-0.042781,-0.99825,195.61
    29059 
    29060 > view matrix models
    29061 > #8,-0.22454,0.34562,-0.91111,186.4,0.4892,-0.76865,-0.41214,170.57,-0.84277,-0.53826,0.0035149,218.83
    29062 
    29063 > view matrix models
    29064 > #8,-0.22454,0.34562,-0.91111,190.27,0.4892,-0.76865,-0.41214,172.31,-0.84277,-0.53826,0.0035149,198.32
    29065 
    29066 > hide #!8 models
    29067 
    29068 > select subtract #8
    29069 
    29070 Nothing selected 
    29071 
    29072 > show #!38 models
    29073 
    29074 > select add #38
    29075 
    29076 6282 atoms, 6138 bonds, 1077 residues, 1 model selected 
    29077 
    29078 > view matrix models
    29079 > #38,0.58456,0.63428,-0.50594,39.545,0.32988,0.3839,0.86244,72.759,0.74126,-0.67105,0.015176,37.498
    29080 
    29081 > view matrix models
    29082 > #38,-0.62989,-0.2889,-0.72095,269.75,0.43669,0.63589,-0.63635,64.932,0.64229,-0.71567,-0.27439,58.484
    29083 
    29084 > view matrix models
    29085 > #38,-0.79758,-0.56471,-0.21208,300.49,0.093917,0.23104,-0.9684,138.83,0.59586,-0.79229,-0.13123,66.978
    29086 
    29087 > view matrix models
    29088 > #38,-0.79758,-0.56471,-0.21208,298.65,0.093917,0.23104,-0.9684,128.19,0.59586,-0.79229,-0.13123,84.027
    29089 
    29090 > view matrix models
    29091 > #38,-0.65099,-0.75245,0.1001,278.77,-0.2865,0.12144,-0.95035,192.34,0.70294,-0.64735,-0.29463,63.572
    29092 
    29093 > view matrix models
    29094 > #38,-0.65099,-0.75245,0.1001,273.74,-0.2865,0.12144,-0.95035,188.77,0.70294,-0.64735,-0.29463,64.627
    29095 
    29096 > hide #!54 models
    29097 
    29098 > show #!55 models
    29099 
    29100 > view matrix models
    29101 > #38,0.92945,0.36602,-0.046307,-17.327,-0.12262,0.18809,-0.97447,160.6,-0.34796,0.9114,0.2197,164.6
    29102 
    29103 > view matrix models
    29104 > #38,0.68418,0.72711,0.05661,6.3245,-0.24646,0.30357,-0.92038,175.08,-0.6864,0.61576,0.3869,227.39
    29105 
    29106 > view matrix models
    29107 > #38,0.68418,0.72711,0.05661,6.2981,-0.24646,0.30357,-0.92038,173.03,-0.6864,0.61576,0.3869,222.11
    29108 
    29109 > fitmap #38 inMap #55
    29110 
    29111 Fit molecule 9hud (#38) to map cryosparc_P483_J178_007_volume_map.mrc z flip
    29112 (#55) using 6282 atoms 
    29113 average map value = 0.07095, steps = 260 
    29114 shifted from previous position = 2.45 
    29115 rotated from previous position = 40.2 degrees 
    29116 atoms outside contour = 1485, contour level = 0.027968 
    29117  
    29118 Position of 9hud (#38) relative to cryosparc_P483_J178_007_volume_map.mrc z
    29119 flip (#55) coordinates: 
    29120 Matrix rotation and translation 
    29121 0.68744757 0.35641921 0.63275685 15.52206548 
    29122 0.28938953 0.66468217 -0.68880429 73.81019326 
    29123 -0.66608526 0.65663002 0.35379014 216.09676949 
    29124 Axis 0.71899263 0.69409402 -0.03582029 
    29125 Axis point 0.00000000 -189.86123076 144.51310834 
    29126 Rotation angle (degrees) 69.33153492 
    29127 Shift along axis 54.65081588 
    29128  
    29129 
    29130 > mmaker #8 to #38
    29131 
    29132 Parameters 
    29133 --- 
    29134 Chain pairing | bb 
    29135 Alignment algorithm | Needleman-Wunsch 
    29136 Similarity matrix | BLOSUM-62 
    29137 SS fraction | 0.3 
    29138 Gap open (HH/SS/other) | 18/18/6 
    29139 Gap extend | 1 
    29140 SS matrix |  |  | H | S | O 
    29141 ---|---|---|--- 
    29142 H | 6 | -9 | -6 
    29143 S |  | 6 | -6 
    29144 O |  |  | 4 
    29145 Iteration cutoff | 2 
    29146  
    29147 Matchmaker 9hud, chain A (#38) with 1ezx, chain A (#8), sequence alignment
    29148 score = 1674.4 
    29149 RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
    29150 0.519) 
    29151  
    29152 
    29153 > hide #!38 models
    29154 
    29155 > select subtract #38
    29156 
    29157 Nothing selected 
    29158 
    29159 > show #!8 models
    29160 
    29161 > mmaker #7 to #8
    29162 
    29163 Parameters 
    29164 --- 
    29165 Chain pairing | bb 
    29166 Alignment algorithm | Needleman-Wunsch 
    29167 Similarity matrix | BLOSUM-62 
    29168 SS fraction | 0.3 
    29169 Gap open (HH/SS/other) | 18/18/6 
    29170 Gap extend | 1 
    29171 SS matrix |  |  | H | S | O 
    29172 ---|---|---|--- 
    29173 H | 6 | -9 | -6 
    29174 S |  | 6 | -6 
    29175 O |  |  | 4 
    29176 Iteration cutoff | 2 
    29177  
    29178 Matchmaker 1ezx, chain C (#8) with 5a0c, chain A (#7), sequence alignment
    29179 score = 241.2 
    29180 RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
    29181 3.073) 
    29182  
    29183 
    29184 > hide #!8 models
    29185 
    29186 > show #7 models
    29187 
    29188 > volume #55 level 0.03303
    29189 
    29190 > open /Users/amy/Downloads/cryosparc_P483_J178_007_volume_map.mrc
    29191 
    29192 Opened cryosparc_P483_J178_007_volume_map.mrc as #56, grid size 400,400,400,
    29193 pixel 0.723, shown at level 0.00984, step 2, values float32 
    29194 
    29195 > volume #56 level 0.0196
    29196 
    29197 > close #56
    29198 
    29199 > open /Users/amy/Downloads/cryosparc_P483_J179_005_volume_map.mrc
    29200 
    29201 Opened cryosparc_P483_J179_005_volume_map.mrc as #56, grid size 400,400,400,
    29202 pixel 0.723, shown at level 0.00903, step 2, values float32 
    29203 
    29204 > open /Users/amy/Downloads/cryosparc_P483_J180_002_volume_map.mrc
    29205 
    29206 Opened cryosparc_P483_J180_002_volume_map.mrc as #70, grid size 400,400,400,
    29207 pixel 0.723, shown at level 0.00199, step 2, values float32 
    29208 
    29209 > hide #!70 models
    29210 
    29211 > show #!66 models
    29212 
    29213 > hide #!66 models
    29214 
    29215 > show #!67 models
    29216 
    29217 > open /Users/amy/Downloads/cryosparc_P483_J183_007_volume_map.mrc
    29218 
    29219 Opened cryosparc_P483_J183_007_volume_map.mrc as #71, grid size 400,400,400,
    29220 pixel 0.723, shown at level 0.0116, step 2, values float32 
    29221 
    29222 > hide #!67 models
    29223 
    29224 > volume #71 level 0.03377
    29225 
    29226 > volume #71 level 0.03909
    29227 
    29228 > transparency #71 50
    29229 
    29230 > hide #7 models
    29231 
    29232 > show #!38 models
    29233 
    29234 > select add #38
    29235 
    29236 6282 atoms, 6138 bonds, 1077 residues, 1 model selected 
    29237 
    29238 > view matrix models
    29239 > #38,-0.91266,0.065596,-0.40341,292.72,0.36322,0.5827,-0.727,65.755,0.18738,-0.81003,-0.55564,148.75
    29240 
    29241 > view matrix models
    29242 > #38,-0.72502,-0.2597,-0.63788,278.46,0.38017,0.62139,-0.68509,61.067,0.57429,-0.73921,-0.3518,82.291
    29243 
    29244 > view matrix models
    29245 > #38,-0.72502,-0.2597,-0.63788,277.14,0.38017,0.62139,-0.68509,52.977,0.57429,-0.73921,-0.3518,86.091
    29246 
    29247 > view matrix models
    29248 > #38,-0.65947,-0.28553,-0.69539,268.48,0.35515,0.69696,-0.62299,53.205,0.66254,-0.65781,-0.35822,69.098
    29249 
    29250 > view matrix models
    29251 > #38,-0.65947,-0.28553,-0.69539,267.26,0.35515,0.69696,-0.62299,52.554,0.66254,-0.65781,-0.35822,69.625
    29252 
    29253 > close #58-69
    29254 
    29255 > fitmap #38 inMap #71
    29256 
    29257 Fit molecule 9hud (#38) to map cryosparc_P483_J183_007_volume_map.mrc (#71)
    29258 using 6282 atoms 
    29259 average map value = 0.07544, steps = 148 
    29260 shifted from previous position = 7.45 
    29261 rotated from previous position = 12.1 degrees 
    29262 atoms outside contour = 1976, contour level = 0.039086 
    29263  
    29264 Position of 9hud (#38) relative to cryosparc_P483_J183_007_volume_map.mrc
    29265 (#71) coordinates: 
    29266 Matrix rotation and translation 
    29267 -0.67498701 -0.41761657 -0.60826719 272.94445864 
    29268 0.34716985 0.54767448 -0.76126592 67.90283128 
    29269 0.65104966 -0.72501662 -0.22468927 71.15250272 
    29270 Axis 0.02459578 -0.85446836 0.51892087 
    29271 Axis point 117.22275735 0.00000000 126.50966305 
    29272 Rotation angle (degrees) 132.53192375 
    29273 Shift along axis -14.38502000 
    29274  
    29275 
    29276 > mmaker #8 to #38
    29277 
    29278 Parameters 
    29279 --- 
    29280 Chain pairing | bb 
    29281 Alignment algorithm | Needleman-Wunsch 
    29282 Similarity matrix | BLOSUM-62 
    29283 SS fraction | 0.3 
    29284 Gap open (HH/SS/other) | 18/18/6 
    29285 Gap extend | 1 
    29286 SS matrix |  |  | H | S | O 
    29287 ---|---|---|--- 
    29288 H | 6 | -9 | -6 
    29289 S |  | 6 | -6 
    29290 O |  |  | 4 
    29291 Iteration cutoff | 2 
    29292  
    29293 Matchmaker 9hud, chain A (#38) with 1ezx, chain A (#8), sequence alignment
    29294 score = 1674.4 
    29295 RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
    29296 0.519) 
    29297  
    29298 
    29299 > show #!8 models
    29300 
    29301 > select subtract #38
    29302 
    29303 Nothing selected 
    29304 
    29305 > hide #!38 models
    29306 
    29307 > show #7 models
    29308 
    29309 > mmaker #7 to #8
    29310 
    29311 Parameters 
    29312 --- 
    29313 Chain pairing | bb 
    29314 Alignment algorithm | Needleman-Wunsch 
    29315 Similarity matrix | BLOSUM-62 
    29316 SS fraction | 0.3 
    29317 Gap open (HH/SS/other) | 18/18/6 
    29318 Gap extend | 1 
    29319 SS matrix |  |  | H | S | O 
    29320 ---|---|---|--- 
    29321 H | 6 | -9 | -6 
    29322 S |  | 6 | -6 
    29323 O |  |  | 4 
    29324 Iteration cutoff | 2 
    29325  
    29326 Matchmaker 1ezx, chain C (#8) with 5a0c, chain A (#7), sequence alignment
    29327 score = 241.2 
    29328 RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
    29329 3.073) 
    29330  
    29331 
    29332 > hide #!8 models
    29333 
    29334 > open "/Users/amy/Downloads/cryosparc_P371_J1247_003_volume_map (1).mrc"
    29335 
    29336 Opened cryosparc_P371_J1247_003_volume_map (1).mrc as #58, grid size
    29337 300,300,300, pixel 0.867, shown at level 0.0217, step 2, values float32 
    29338 
    29339 > hide #7 models
    29340 
    29341 > volume #58 level 0.07127
    29342 
    29343 > transparency 58 50
    29344 
    29345 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
    29346 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword 
    29347 
    29348 > transparency #58 50
    29349 
    29350 > select add #58
    29351 
    29352 2 models selected 
    29353 
    29354 > select subtract #58
    29355 
    29356 Nothing selected 
    29357 
    29358 > show #!57 models
    29359 
    29360 > hide #!57 models
    29361 
    29362 > show #!37 models
    29363 
    29364 > select add #37
    29365 
    29366 3984 atoms, 3982 bonds, 5 pseudobonds, 592 residues, 3 models selected 
    29367 
    29368 > view matrix models
    29369 > #37,-0.92665,0.37309,0.046068,189.97,-0.3746,-0.92671,-0.029877,215.08,0.031544,-0.044943,0.99849,41.461
    29370 
    29371 > view matrix models
    29372 > #37,-0.95684,-0.22555,-0.18327,235.41,0.22555,-0.974,0.021102,173.18,-0.18327,-0.021145,0.98284,55.964
    29373 
    29374 > view matrix models
    29375 > #37,-0.95684,-0.22555,-0.18327,230.3,0.22555,-0.974,0.021102,164.37,-0.18327,-0.021145,0.98284,103.6
    29376 
    29377 > view matrix models
    29378 > #37,-0.71551,-0.36432,-0.59609,244.23,0.27076,-0.93118,0.24412,146.37,-0.644,0.013275,0.76491,146.06
    29379 
    29380 > view matrix models
    29381 > #37,-0.38059,-0.21113,-0.90032,230.74,0.23197,-0.96426,0.12806,157.34,-0.89517,-0.16011,0.41597,192.06
    29382 
    29383 > view matrix models
    29384 > #37,-0.38059,-0.21113,-0.90032,226.85,0.23197,-0.96426,0.12806,158.76,-0.89517,-0.16011,0.41597,189.5
    29385 
    29386 > fitmap #37 inMap #58
    29387 
    29388 Fit molecule 1ezx (#37) to map cryosparc_P371_J1247_003_volume_map (1).mrc
    29389 (#58) using 3984 atoms 
    29390 average map value = 0.0799, steps = 112 
    29391 shifted from previous position = 8.44 
    29392 rotated from previous position = 14 degrees 
    29393 atoms outside contour = 1944, contour level = 0.071265 
    29394  
    29395 Position of 1ezx (#37) relative to cryosparc_P371_J1247_003_volume_map (1).mrc
    29396 (#58) coordinates: 
    29397 Matrix rotation and translation 
    29398 -0.34799611 0.02716421 -0.93710235 206.67239671 
    29399 0.14052585 -0.98677538 -0.08078885 177.04596820 
    29400 -0.92690409 -0.15980131 0.33957672 198.01665488 
    29401 Axis -0.57025546 -0.07360376 0.81816330 
    29402 Axis point 168.54356692 102.18640974 0.00000000 
    29403 Rotation angle (degrees) 176.02747367 
    29404 Shift along axis 31.12264873 
    29405  
    29406 
    29407 > open "/Users/amy/Downloads/cryosparc_P371_J1247_003_volume_map (1).mrc"
    29408 
    29409 Opened cryosparc_P371_J1247_003_volume_map (1).mrc as #59, grid size
    29410 300,300,300, pixel 0.867, shown at level 0.0217, step 2, values float32 
    29411 
    29412 > volume #59 level 0.06978
    29413 
    29414 > hide #!58 models
    29415 
    29416 > mmaker #7 to #37
    29417 
    29418 Parameters 
    29419 --- 
    29420 Chain pairing | bb 
    29421 Alignment algorithm | Needleman-Wunsch 
    29422 Similarity matrix | BLOSUM-62 
    29423 SS fraction | 0.3 
    29424 Gap open (HH/SS/other) | 18/18/6 
    29425 Gap extend | 1 
    29426 SS matrix |  |  | H | S | O 
    29427 ---|---|---|--- 
    29428 H | 6 | -9 | -6 
    29429 S |  | 6 | -6 
    29430 O |  |  | 4 
    29431 Iteration cutoff | 2 
    29432  
    29433 Matchmaker 1ezx, chain C (#37) with 5a0c, chain A (#7), sequence alignment
    29434 score = 241.2 
    29435 RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
    29436 3.073) 
    29437  
    29438 
    29439 > show #7 models
    29440 
    29441 > hide #!59 models
    29442 
    29443 > show #!58 models
    29444 
    29445 > hide #!58 models
    29446 
    29447 > show #!59 models
    29448 
    29449 > transparency #59 50
    29450 
    29451 > ui mousemode right "map eraser"
    29452 
    29453 > hide #7 models
    29454 
    29455 > hide #!37 models
    29456 
    29457 > select subtract #37
    29458 
    29459 Nothing selected 
    29460 
    29461 > volume erase #59 center 116.15,104.56,160.67 radius 47.97
    29462 
    29463 Opened cryosparc_P371_J1247_003_volume_map (1).mrc copy as #61, grid size
    29464 300,300,300, pixel 0.867, shown at step 1, values float32 
    29465 
    29466 > volume erase #61 center 122.57,113.18,101.86 radius 47.97
    29467 
    29468 > ui mousemode right "translate selected models"
    29469 
    29470 > show #18 models
    29471 
    29472 > select #18/A:202
    29473 
    29474 6 atoms, 5 bonds, 1 residue, 1 model selected 
    29475 
    29476 > show sel atoms
    29477 
    29478 > rainbow sel
    29479 
    29480 > select add #18
    29481 
    29482 1883 atoms, 1745 bonds, 394 residues, 1 model selected 
    29483 
    29484 > select subtract #18
    29485 
    29486 Nothing selected 
    29487 
    29488 > show #!19 models
    29489 
    29490 > hide #!19 models
    29491 
    29492 > show #!19 models
    29493 
    29494 > hide #!19 models
    29495 
    29496 > hide #18 models
    29497 
    29498 > show #7 models
    29499 
    29500 > show #18 models
    29501 
    29502 > mmaker #18 to #7
    29503 
    29504 Parameters 
    29505 --- 
    29506 Chain pairing | bb 
    29507 Alignment algorithm | Needleman-Wunsch 
    29508 Similarity matrix | BLOSUM-62 
    29509 SS fraction | 0.3 
    29510 Gap open (HH/SS/other) | 18/18/6 
    29511 Gap extend | 1 
    29512 SS matrix |  |  | H | S | O 
    29513 ---|---|---|--- 
    29514 H | 6 | -9 | -6 
    29515 S |  | 6 | -6 
    29516 O |  |  | 4 
    29517 Iteration cutoff | 2 
    29518  
    29519 Matchmaker 5a0c, chain A (#7) with copy of 5a0c, chain A (#18), sequence
    29520 alignment score = 1112.7 
    29521 RMSD between 218 pruned atom pairs is 0.000 angstroms; (across all 218 pairs:
    29522 0.000) 
    29523  
    29524 
    29525 > color #18 #ed91dfff
    29526 
    29527 > color #18 #ebc5edff
    29528 
    29529 > fitmap #7 inMap #59
    29530 
    29531 Fit molecule 5a0c (#7) to map cryosparc_P371_J1247_003_volume_map (1).mrc
    29532 (#59) using 1883 atoms 
    29533 average map value = 0.0522, steps = 120 
    29534 shifted from previous position = 3.71 
    29535 rotated from previous position = 23.2 degrees 
    29536 atoms outside contour = 1476, contour level = 0.06978 
    29537  
    29538 Position of 5a0c (#7) relative to cryosparc_P371_J1247_003_volume_map (1).mrc
    29539 (#59) coordinates: 
    29540 Matrix rotation and translation 
    29541 -0.93248311 0.31677416 0.17357817 149.49808518 
    29542 -0.24611565 -0.20545531 -0.94721444 169.75896469 
    29543 -0.26439050 -0.92598178 0.26954669 154.83015425 
    29544 Axis 0.02975759 0.61381323 -0.78889024 
    29545 Axis point 98.48308815 127.59008236 0.00000000 
    29546 Rotation angle (degrees) 159.09861794 
    29547 Shift along axis -13.49499578 
    29548  
    29549 
    29550 > hide #18 models
    29551 
    29552 > ui mousemode right "map eraser"
    29553 
    29554 > volume erase #61 center 140.38,143.93,165.02 radius 9.1821
    29555 
    29556 > volume erase #61 center 135.35,144.22,156.8 radius 9.1821
    29557 
    29558 > volume erase #61 center 126.68,146.69,162.17 radius 9.1821
    29559 
    29560 > ui mousemode right "translate selected models"
    29561 
    29562 > fitmap #7 inMap #59
    29563 
    29564 Fit molecule 5a0c (#7) to map cryosparc_P371_J1247_003_volume_map (1).mrc
    29565 (#59) using 1883 atoms 
    29566 average map value = 0.0522, steps = 48 
    29567 shifted from previous position = 0.00729 
    29568 rotated from previous position = 0.02 degrees 
    29569 atoms outside contour = 1476, contour level = 0.06978 
    29570  
    29571 Position of 5a0c (#7) relative to cryosparc_P371_J1247_003_volume_map (1).mrc
    29572 (#59) coordinates: 
    29573 Matrix rotation and translation 
    29574 -0.93245587 0.31693119 0.17343780 149.49596389 
    29575 -0.24610156 -0.20574256 -0.94715575 169.75337215 
    29576 -0.26449966 -0.92586426 0.26984311 154.82942667 
    29577 Axis 0.02983605 0.61368746 -0.78898511 
    29578 Axis point 98.49093754 127.56704910 0.00000000 
    29579 Rotation angle (degrees) 159.09569307 
    29580 Shift along axis -13.52222698 
    29581  
    29582 
    29583 > mmaker #7 to #18
    29584 
    29585 Parameters 
    29586 --- 
    29587 Chain pairing | bb 
    29588 Alignment algorithm | Needleman-Wunsch 
    29589 Similarity matrix | BLOSUM-62 
    29590 SS fraction | 0.3 
    29591 Gap open (HH/SS/other) | 18/18/6 
    29592 Gap extend | 1 
    29593 SS matrix |  |  | H | S | O 
    29594 ---|---|---|--- 
    29595 H | 6 | -9 | -6 
    29596 S |  | 6 | -6 
    29597 O |  |  | 4 
    29598 Iteration cutoff | 2 
    29599  
    29600 Matchmaker copy of 5a0c, chain A (#18) with 5a0c, chain A (#7), sequence
    29601 alignment score = 1112.7 
    29602 RMSD between 218 pruned atom pairs is 0.000 angstroms; (across all 218 pairs:
    29603 0.000) 
    29604  
    29605 
    29606 > fitmap #7 inMap #59
    29607 
    29608 Fit molecule 5a0c (#7) to map cryosparc_P371_J1247_003_volume_map (1).mrc
    29609 (#59) using 1883 atoms 
    29610 average map value = 0.0522, steps = 120 
    29611 shifted from previous position = 3.71 
    29612 rotated from previous position = 23.2 degrees 
    29613 atoms outside contour = 1476, contour level = 0.06978 
    29614  
    29615 Position of 5a0c (#7) relative to cryosparc_P371_J1247_003_volume_map (1).mrc
    29616 (#59) coordinates: 
    29617 Matrix rotation and translation 
    29618 -0.93249206 0.31673033 0.17361005 149.49824725 
    29619 -0.24614085 -0.20547558 -0.94720350 169.75915732 
    29620 -0.26433545 -0.92599227 0.26956462 154.82905865 
    29621 Axis 0.02972878 0.61380618 -0.78889681 
    29622 Axis point 98.47960888 127.58948855 0.00000000 
    29623 Rotation angle (degrees) 159.09952411 
    29624 Shift along axis -13.50053159 
    29625  
    29626 
    29627 > volume #61 level 0.07557
    29628 
    29629 > open /Users/amy/Downloads/cryosparc_P483_J188_006_volume_map.mrc
    29630 
    29631 Opened cryosparc_P483_J188_006_volume_map.mrc as #60, grid size 400,400,400,
    29632 pixel 0.723, shown at level 0.0122, step 2, values float32 
    29633 
    29634 > volume #60 level 0.04049
    29635 
    29636 > hide #7 models
    29637 
    29638 > close #39-56
    29639 
    29640 > transparency #60 50
    29641 
    29642 > show #!57 models
    29643 
    29644 > select add #57
    29645 
    29646 1009 atoms, 1014 bonds, 5 pseudobonds, 155 residues, 3 models selected 
    29647 
    29648 > select subtract #57
    29649 
    29650 Nothing selected 
    29651 
    29652 > hide #!57 models
    29653 
    29654 > show #!38 models
    29655 
    29656 > select add #38
    29657 
    29658 6282 atoms, 6138 bonds, 1077 residues, 1 model selected 
    29659 
    29660 > view matrix models
    29661 > #38,0.70129,-0.71169,-0.041051,59.454,0.277,0.32511,-0.9042,89.328,0.65685,0.62274,0.42514,10.395
    29662 
    29663 > view matrix models
    29664 > #38,0.68049,0.72218,0.12406,5.6594,-0.15756,0.30955,-0.93774,159.08,-0.71562,0.61858,0.32443,228.89
    29665 
    29666 > view matrix models
    29667 > #38,0.7111,0.6991,0.074864,2.3195,-0.17274,0.27693,-0.94523,162.83,-0.68154,0.65922,0.31769,222.03
    29668 
    29669 > volume flip #60 axis z
    29670 
    29671 Opened cryosparc_P483_J188_006_volume_map.mrc z flip as #39, grid size
    29672 400,400,400, pixel 0.723, shown at step 1, values float32 
    29673 
    29674 > view matrix models
    29675 > #38,-0.79214,-0.23105,-0.56492,283.77,0.39756,0.50697,-0.76481,61.539,0.4631,-0.83042,-0.30973,105.99
    29676 
    29677 > view matrix models
    29678 > #38,-0.72246,-0.55636,-0.41051,283.31,0.053262,0.54717,-0.83532,115.33,0.68936,-0.62535,-0.36568,63.032
    29679 
    29680 > view matrix models
    29681 > #38,-0.72246,-0.55636,-0.41051,283.27,0.053262,0.54717,-0.83532,115.31,0.68936,-0.62535,-0.36568,63.21
    29682 
    29683 > view matrix models
    29684 > #38,-0.75346,-0.22412,-0.61812,278.02,0.32917,0.68524,-0.64969,64.051,0.56917,-0.69298,-0.44252,85.775
    29685 
    29686 > view matrix models
    29687 > #38,-0.75346,-0.22412,-0.61812,277.72,0.32917,0.68524,-0.64969,62.337,0.56917,-0.69298,-0.44252,89.988
    29688 
    29689 > view matrix models
    29690 > #38,-0.75346,-0.22412,-0.61812,274.8,0.32917,0.68524,-0.64969,60.25,0.56917,-0.69298,-0.44252,90.357
    29691 
    29692 > fitmap #38 inMap #39
    29693 
    29694 Fit molecule 9hud (#38) to map cryosparc_P483_J188_006_volume_map.mrc z flip
    29695 (#39) using 6282 atoms 
    29696 average map value = 0.07719, steps = 140 
    29697 shifted from previous position = 5.69 
    29698 rotated from previous position = 10.5 degrees 
    29699 atoms outside contour = 1975, contour level = 0.040487 
    29700  
    29701 Position of 9hud (#38) relative to cryosparc_P483_J188_006_volume_map.mrc z
    29702 flip (#39) coordinates: 
    29703 Matrix rotation and translation 
    29704 -0.69481285 -0.38668893 -0.60638839 274.92375859 
    29705 0.29518489 0.61552849 -0.73074671 73.34577149 
    29706 0.65582093 -0.68672881 -0.31353236 73.10268242 
    29707 Axis 0.03066826 -0.87940971 0.47507687 
    29708 Axis point 118.71936211 0.00000000 122.64604224 
    29709 Rotation angle (degrees) 134.13955008 
    29710 Shift along axis -21.34015667 
    29711  
    29712 
    29713 > mmaker #37 to #38
    29714 
    29715 Parameters 
    29716 --- 
    29717 Chain pairing | bb 
    29718 Alignment algorithm | Needleman-Wunsch 
    29719 Similarity matrix | BLOSUM-62 
    29720 SS fraction | 0.3 
    29721 Gap open (HH/SS/other) | 18/18/6 
    29722 Gap extend | 1 
    29723 SS matrix |  |  | H | S | O 
    29724 ---|---|---|--- 
    29725 H | 6 | -9 | -6 
    29726 S |  | 6 | -6 
    29727 O |  |  | 4 
    29728 Iteration cutoff | 2 
    29729  
    29730 Matchmaker 9hud, chain A (#38) with 1ezx, chain A (#37), sequence alignment
    29731 score = 1674.4 
    29732 RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
    29733 0.519) 
    29734  
    29735 
    29736 > select subtract #38
    29737 
    29738 Nothing selected 
    29739 
    29740 > show #!37 models
    29741 
    29742 > hide #!38 models
    29743 
    29744 > show #!57 models
    29745 
    29746 > mmaker #57 to #37
    29747 
    29748 Parameters 
    29749 --- 
    29750 Chain pairing | bb 
    29751 Alignment algorithm | Needleman-Wunsch 
    29752 Similarity matrix | BLOSUM-62 
    29753 SS fraction | 0.3 
    29754 Gap open (HH/SS/other) | 18/18/6 
    29755 Gap extend | 1 
    29756 SS matrix |  |  | H | S | O 
    29757 ---|---|---|--- 
    29758 H | 6 | -9 | -6 
    29759 S |  | 6 | -6 
    29760 O |  |  | 4 
    29761 Iteration cutoff | 2 
    29762  
    29763 Matchmaker 1ezx, chain C (#37) with copy of 1ezx, chain C (#57), sequence
    29764 alignment score = 1096 
    29765 RMSD between 140 pruned atom pairs is 0.000 angstroms; (across all 140 pairs:
    29766 0.000) 
    29767  
    29768 
    29769 > hide #!37 models
    29770 
    29771 > select add #57
    29772 
    29773 1009 atoms, 1014 bonds, 5 pseudobonds, 155 residues, 3 models selected 
    29774 
    29775 > view matrix models
    29776 > #57,-0.96139,-0.27328,-0.032326,225.27,0.26293,-0.87755,-0.40098,194.89,0.081212,-0.39399,0.91552,76.751
    29777 
    29778 > view matrix models
    29779 > #57,-0.98395,-0.080553,-0.1592,229.11,0.11527,-0.96807,-0.2226,199.83,-0.13619,-0.23738,0.96182,88.362
    29780 
    29781 > view matrix models
    29782 > #57,-0.98395,-0.080553,-0.1592,229.13,0.11527,-0.96807,-0.2226,200.95,-0.13619,-0.23738,0.96182,87.592
    29783 
    29784 > view matrix models
    29785 > #57,-0.94283,-0.24393,0.22707,209.83,0.18457,-0.94952,-0.25367,196.49,0.27748,-0.19726,0.94026,54.255
    29786 
    29787 > view matrix models
    29788 > #57,-0.94283,-0.24393,0.22707,211.13,0.18457,-0.94952,-0.25367,198.21,0.27748,-0.19726,0.94026,55.521
    29789 
    29790 > view matrix models
    29791 > #57,-0.93042,-0.31273,0.19109,213.56,0.19345,-0.86193,-0.46866,206.45,0.31127,-0.39909,0.86246,61.443
    29792 
    29793 > view matrix models
    29794 > #57,-0.93042,-0.31273,0.19109,212.58,0.19345,-0.86193,-0.46866,206.1,0.31127,-0.39909,0.86246,60.836
    29795 
    29796 > view matrix models
    29797 > #57,-0.84274,-0.44664,0.3005,202.99,0.29429,-0.84967,-0.43756,196.06,0.45076,-0.28032,0.84749,47.549
    29798 
    29799 > view matrix models
    29800 > #57,-0.84274,-0.44664,0.3005,204.01,0.29429,-0.84967,-0.43756,196.43,0.45076,-0.28032,0.84749,48.186
    29801 
    29802 > view matrix models
    29803 > #57,-0.84274,-0.44664,0.3005,205.89,0.29429,-0.84967,-0.43756,195.12,0.45076,-0.28032,0.84749,50.177
    29804 
    29805 > view matrix models
    29806 > #57,-0.40829,-0.80923,0.42242,172.87,0.75449,-0.55964,-0.34285,146.27,0.51385,0.17873,0.83905,34.853
    29807 
    29808 > view matrix models
    29809 > #57,-0.40829,-0.80923,0.42242,177.69,0.75449,-0.55964,-0.34285,148.99,0.51385,0.17873,0.83905,33.682
    29810 
    29811 > view matrix models
    29812 > #57,-0.26229,-0.78164,0.56591,157.89,0.82741,-0.48394,-0.28493,138.37,0.49658,0.39351,0.77367,33.446
    29813 
    29814 > view matrix models
    29815 > #57,-0.50448,-0.84508,0.17704,198.87,0.77252,-0.53335,-0.34461,147.01,0.38565,-0.037082,0.9219,44.834
    29816 
    29817 > view matrix models
    29818 > #57,-0.50448,-0.84508,0.17704,197.7,0.77252,-0.53335,-0.34461,146.01,0.38565,-0.037082,0.9219,43.5
    29819 
    29820 > view matrix models
    29821 > #57,-0.55352,-0.81516,0.17067,201.3,0.76006,-0.57821,-0.29661,145.6,0.34047,-0.03446,0.93962,46.193
    29822 
    29823 > view matrix models
    29824 > #57,-0.55352,-0.81516,0.17067,201,0.76006,-0.57821,-0.29661,144.01,0.34047,-0.03446,0.93962,46.083
    29825 
    29826 > view matrix models
    29827 > #57,0.19927,-0.70806,0.67745,111.26,0.40682,-0.56916,-0.71453,193.98,0.89151,0.41799,0.17463,30.057
    29828 
    29829 > fitmap #57 inMap #39
    29830 
    29831 Fit molecule copy of 1ezx (#57) to map cryosparc_P483_J188_006_volume_map.mrc
    29832 z flip (#39) using 1009 atoms 
    29833 average map value = 0.0293, steps = 168 
    29834 shifted from previous position = 3.46 
    29835 rotated from previous position = 14.9 degrees 
    29836 atoms outside contour = 704, contour level = 0.040487 
    29837  
    29838 Position of copy of 1ezx (#57) relative to
    29839 cryosparc_P483_J188_006_volume_map.mrc z flip (#39) coordinates: 
    29840 Matrix rotation and translation 
    29841 -0.00776067 -0.76663470 0.64203663 129.30975418 
    29842 0.53267917 -0.54654599 -0.64617367 178.30805215 
    29843 0.84628169 0.33698479 0.41261190 20.94708234 
    29844 Axis 0.59871569 -0.12437946 0.79124539 
    29845 Axis point -5.11418337 119.30863791 0.00000000 
    29846 Rotation angle (degrees) 124.80933717 
    29847 Shift along axis 71.81620095 
    29848  
    29849 
    29850 > view matrix models
    29851 > #57,-0.84354,-0.47018,0.25957,209.7,0.35522,-0.85092,-0.38698,186.48,0.40282,-0.23422,0.8848,45.964
    29852 
    29853 > view matrix models
    29854 > #57,-0.84354,-0.47018,0.25957,210.5,0.35522,-0.85092,-0.38698,187.68,0.40282,-0.23422,0.8848,46.627
    29855 
    29856 > view matrix models
    29857 > #57,-0.91572,-0.40165,-0.011594,228.63,0.39352,-0.89061,-0.22795,177.36,0.081229,-0.2133,0.9736,67.651
    29858 
    29859 > view matrix models
    29860 > #57,-0.91572,-0.40165,-0.011594,228.49,0.39352,-0.89061,-0.22795,177.31,0.081229,-0.2133,0.9736,67.495
    29861 
    29862 > fitmap #57 inMap #39
    29863 
    29864 Fit molecule copy of 1ezx (#57) to map cryosparc_P483_J188_006_volume_map.mrc
    29865 z flip (#39) using 1009 atoms 
    29866 average map value = 0.03023, steps = 128 
    29867 shifted from previous position = 2.17 
    29868 rotated from previous position = 27.6 degrees 
    29869 atoms outside contour = 692, contour level = 0.040487 
    29870  
    29871 Position of copy of 1ezx (#57) relative to
    29872 cryosparc_P483_J188_006_volume_map.mrc z flip (#39) coordinates: 
    29873 Matrix rotation and translation 
    29874 -0.97588300 -0.21795429 0.01217931 226.13416383 
    29875 0.16332980 -0.76604383 -0.62169145 212.61271533 
    29876 0.14483021 -0.60470887 0.78316756 80.91608083 
    29877 Axis 0.04203015 -0.32829732 0.94363888 
    29878 Axis point 99.48152797 132.57508735 0.00000000 
    29879 Rotation angle (degrees) 168.34438880 
    29880 Shift along axis 16.05982811 
    29881  
    29882 
    29883 > select subtract #57
    29884 
    29885 Nothing selected 
    29886 
    29887 > volume gaussian #39 sDev 2
    29888 
    29889 Opened cryosparc_P483_J188_006_volume_map.mrc z flip gaussian as #40, grid
    29890 size 400,400,400, pixel 0.723, shown at step 1, values float32 
    29891 
    29892 > open /Users/amy/Downloads/cryosparc_P483_molmap_of_combined_6A.mrc
    29893 
    29894 Opened cryosparc_P483_molmap_of_combined_6A.mrc as #41, grid size 200,200,200,
    29895 pixel 1, shown at level 0.293, step 1, values float32 
    29896 
    29897 > transparency #41 50
    29898 
    29899 > show #!37 models
    29900 
    29901 > select add #37
    29902 
    29903 3984 atoms, 3982 bonds, 5 pseudobonds, 592 residues, 3 models selected 
    29904 
    29905 > view matrix models
    29906 > #37,-0.96139,-0.27328,-0.032326,218.59,0.26293,-0.87755,-0.40098,146.69,0.081212,-0.39399,0.91552,81.851
    29907 
    29908 > view matrix models
    29909 > #37,-0.049922,0.49391,-0.86808,164.61,0.32699,-0.81318,-0.48148,143.6,-0.94371,-0.30789,-0.12091,207.3
    29910 
    29911 > view matrix models
    29912 > #37,0.78493,0.53816,-0.30703,72.795,0.33958,-0.78815,-0.51332,143.29,-0.51824,0.29866,-0.80139,186.1
    29913 
    29914 > view matrix models
    29915 > #37,0.48345,-0.22115,0.84698,66.159,0.004741,-0.96689,-0.25517,160.69,0.87536,0.12738,-0.46639,79.548
    29916 
    29917 > view matrix models
    29918 > #37,-0.49427,-0.19074,0.84812,131.98,0.13352,-0.98071,-0.14275,146.1,0.85899,0.04269,0.51021,29.25
    29919 
    29920 > view matrix models
    29921 > #37,-0.87073,-0.2065,0.44631,181.66,0.14198,-0.97448,-0.17389,146.97,0.47082,-0.088043,0.87782,41.66
    29922 
    29923 > view matrix models
    29924 > #37,-0.87073,-0.2065,0.44631,183.6,0.14198,-0.97448,-0.17389,140.36,0.47082,-0.088043,0.87782,41.006
    29925 
    29926 > view matrix models
    29927 > #37,-0.83015,0.067283,-0.55346,223.99,0.083286,-0.96659,-0.24243,147.91,-0.55128,-0.24735,0.79681,124.17
    29928 
    29929 > view matrix models
    29930 > #37,-0.83015,0.067283,-0.55346,229.16,0.083286,-0.96659,-0.24243,155.6,-0.55128,-0.24735,0.79681,121.21
    29931 
    29932 > view matrix models
    29933 > #37,-0.76415,-0.19095,-0.61612,241.25,0.333,-0.93483,-0.12329,129.98,-0.55243,-0.29938,0.77794,124.99
    29934 
    29935 > fitmap #37 inMap #41
    29936 
    29937 Fit molecule 1ezx (#37) to map cryosparc_P483_molmap_of_combined_6A.mrc (#41)
    29938 using 3984 atoms 
    29939 average map value = 0.4227, steps = 272 
    29940 shifted from previous position = 34.2 
    29941 rotated from previous position = 34.8 degrees 
    29942 atoms outside contour = 366, contour level = 0.29336 
    29943  
    29944 Position of 1ezx (#37) relative to cryosparc_P483_molmap_of_combined_6A.mrc
    29945 (#41) coordinates: 
    29946 Matrix rotation and translation 
    29947 -0.39076986 0.10890222 -0.91402362 198.79794072 
    29948 0.07022585 -0.98655567 -0.14756757 150.28581374 
    29949 -0.91780564 -0.12185304 0.37786848 136.15090391 
    29950 Axis 0.55183393 0.08116225 -0.82999519 
    29951 Axis point 145.70964793 80.43889324 0.00000000 
    29952 Rotation angle (degrees) 178.66493597 
    29953 Shift along axis 8.89638759 
    29954  
    29955 
    29956 > mmaker #7 to #37
    29957 
    29958 Parameters 
    29959 --- 
    29960 Chain pairing | bb 
    29961 Alignment algorithm | Needleman-Wunsch 
    29962 Similarity matrix | BLOSUM-62 
    29963 SS fraction | 0.3 
    29964 Gap open (HH/SS/other) | 18/18/6 
    29965 Gap extend | 1 
    29966 SS matrix |  |  | H | S | O 
    29967 ---|---|---|--- 
    29968 H | 6 | -9 | -6 
    29969 S |  | 6 | -6 
    29970 O |  |  | 4 
    29971 Iteration cutoff | 2 
    29972  
    29973 Matchmaker 1ezx, chain C (#37) with 5a0c, chain A (#7), sequence alignment
    29974 score = 241.2 
    29975 RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
    29976 3.073) 
    29977  
    29978 
    29979 > show #7 models
    29980 
    29981 > show #!8 models
    29982 
    29983 > mmaker #8 to #7
    29984 
    29985 Parameters 
    29986 --- 
    29987 Chain pairing | bb 
    29988 Alignment algorithm | Needleman-Wunsch 
    29989 Similarity matrix | BLOSUM-62 
    29990 SS fraction | 0.3 
    29991 Gap open (HH/SS/other) | 18/18/6 
    29992 Gap extend | 1 
    29993 SS matrix |  |  | H | S | O 
    29994 ---|---|---|--- 
    29995 H | 6 | -9 | -6 
    29996 S |  | 6 | -6 
    29997 O |  |  | 4 
    29998 Iteration cutoff | 2 
    29999  
    30000 Matchmaker 5a0c, chain A (#7) with 1ezx, chain C (#8), sequence alignment
    30001 score = 241.2 
    30002 RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
    30003 3.073) 
    30004  
    30005 
    30006 > select #8/A
    30007 
    30008 2686 atoms, 2674 bonds, 398 residues, 1 model selected 
    30009 
    30010 > delete #8/A
    30011 
    30012 > select #8/B
    30013 
    30014 289 atoms, 294 bonds, 39 residues, 1 model selected 
    30015 
    30016 > delete #8/B
    30017 
    30018 > close #8
    30019 
    30020 > show #!31 models
    30021 
    30022 > mmaker #31 t o#7
    30023 
    30024 > matchmaker #31 to o#7
    30025 
    30026 Invalid "to" argument: invalid atoms specifier 
    30027 
    30028 > mmaker #31 t to#7
    30029 
    30030 > matchmaker #31 to to#7
    30031 
    30032 Invalid "to" argument: invalid atoms specifier 
    30033 
    30034 > mmaker #31 to #7
    30035 
    30036 Parameters 
    30037 --- 
    30038 Chain pairing | bb 
    30039 Alignment algorithm | Needleman-Wunsch 
    30040 Similarity matrix | BLOSUM-62 
    30041 SS fraction | 0.3 
    30042 Gap open (HH/SS/other) | 18/18/6 
    30043 Gap extend | 1 
    30044 SS matrix |  |  | H | S | O 
    30045 ---|---|---|--- 
    30046 H | 6 | -9 | -6 
    30047 S |  | 6 | -6 
    30048 O |  |  | 4 
    30049 Iteration cutoff | 2 
    30050  
    30051 Matchmaker 5a0c, chain A (#7) with copy of copy of copy of 1ezx, chain A
    30052 (#31), sequence alignment score = 25.4 
    30053 RMSD between 4 pruned atom pairs is 1.006 angstroms; (across all 34 pairs:
    30054 19.211) 
    30055  
    30056 
    30057 > mmaker #31 to #37
    30058 
    30059 Parameters 
    30060 --- 
    30061 Chain pairing | bb 
    30062 Alignment algorithm | Needleman-Wunsch 
    30063 Similarity matrix | BLOSUM-62 
    30064 SS fraction | 0.3 
    30065 Gap open (HH/SS/other) | 18/18/6 
    30066 Gap extend | 1 
    30067 SS matrix |  |  | H | S | O 
    30068 ---|---|---|--- 
    30069 H | 6 | -9 | -6 
    30070 S |  | 6 | -6 
    30071 O |  |  | 4 
    30072 Iteration cutoff | 2 
    30073  
    30074 Matchmaker 1ezx, chain A (#37) with copy of copy of copy of 1ezx, chain A
    30075 (#31), sequence alignment score = 1734 
    30076 RMSD between 335 pruned atom pairs is 0.000 angstroms; (across all 335 pairs:
    30077 0.000) 
    30078  
    30079 
    30080 > hide #!37 models
    30081 
    30082 > hide #!41 models
    30083 
    30084 > hide #!57 models
    30085 
    30086 > combine #7,31 modelId #42 name AATHNEcombined
    30087 
    30088 Remapping chain ID 'A' in copy of copy of copy of 1ezx #31 to 'C' 
    30089 
    30090 > hide #!31 models
    30091 
    30092 > hide #7 models
    30093 
    30094 > molmap #42 6
    30095 
    30096 Opened AATHNEcombined map 6 as #8, grid size 43,51,63, pixel 2, shown at level
    30097 0.107, step 1, values float32 
    30098 
    30099 > volume #8 level 0.4678
    30100 
    30101 > hide #!42 models
    30102 
    30103 > volume #8 level 0.4143
    30104 
    30105 > transparency #8 50
    30106 
    30107 > show #!29 models
    30108 
    30109 > select add #8
    30110 
    30111 2 models selected 
    30112 
    30113 > view matrix models
    30114 > #8,-0.94731,0.3033,-0.10305,152.68,-0.052376,-0.46403,-0.88427,177.46,-0.31602,-0.83228,0.45547,210.1
    30115 
    30116 > view matrix models
    30117 > #8,-0.67966,0.68715,-0.25667,146.07,0.0014291,-0.34867,-0.93725,176.15,-0.73352,-0.63738,0.23599,220.93
    30118 
    30119 > select subtract #8
    30120 
    30121 Nothing selected 
    30122 
    30123 > select add #8
    30124 
    30125 2 models selected 
    30126 
    30127 > view matrix models
    30128 > #8,-0.80209,0.59535,-0.046957,144.36,-0.15685,-0.28587,-0.94534,180.87,-0.57624,-0.75089,0.32268,217.17
    30129 
    30130 > view matrix models
    30131 > #8,-0.98552,0.057058,-0.15966,159.48,0.11645,-0.45668,-0.88198,176.33,-0.12324,-0.8878,0.44342,206.47
    30132 
    30133 > select subtract #8
    30134 
    30135 Nothing selected 
    30136 
    30137 > fitmap #8 inMap #29
    30138 
    30139 Fit map AATHNEcombined map 6 in map J1122.mrc using 3370 points 
    30140 correlation = -0.06744, correlation about mean = 0.03351, overlap = -0.3948 
    30141 steps = 72, shift = 3.07, angle = 5.37 degrees 
    30142  
    30143 Position of AATHNEcombined map 6 (#8) relative to J1122.mrc (#29) coordinates: 
    30144 Matrix rotation and translation 
    30145 -0.99402372 -0.01790342 -0.10768616 160.40909895 
    30146 0.10457674 -0.43913839 -0.89231227 175.73306960 
    30147 -0.03131369 -0.89824103 0.43838626 207.83747749 
    30148 Axis -0.04104025 -0.52866794 0.84783601 
    30149 Axis point 80.62201678 156.15315639 0.00000000 
    30150 Rotation angle (degrees) 175.85785915 
    30151 Shift along axis 76.72442836 
    30152  
    30153 
    30154 > volume #8 level 0.3659
    30155 
    30156 > view
    30157 
    30158 > volume #29 level 0.06441
    30159 
    30160 > show #!42 models
    30161 
    30162 > select add #42
    30163 
    30164 4858 atoms, 4713 bonds, 831 residues, 1 model selected 
    30165 
    30166 > view matrix models
    30167 > #42,-0.94731,0.3033,-0.10305,202.51,-0.052376,-0.46403,-0.88427,151.25,-0.31602,-0.83228,0.45547,188.42
    30168 
    30169 > view matrix models
    30170 > #42,-0.065313,0.66691,-0.74227,198.13,-0.22175,-0.73496,-0.64083,151.68,-0.97291,0.12274,0.19589,194.19
    30171 
    30172 > view matrix models
    30173 > #42,0.76996,0.12763,-0.6252,186.82,-0.51684,-0.44988,-0.72835,155.58,-0.37422,0.88392,-0.28042,184.85
    30174 
    30175 > view matrix models
    30176 > #42,0.26956,0.68406,-0.67779,189.68,-0.23721,-0.63498,-0.73521,153.14,-0.93331,0.35896,-0.0088999,195.67
    30177 
    30178 > view matrix models
    30179 > #42,0.16808,0.4812,-0.86035,199.68,0.12383,-0.87616,-0.46585,142.27,-0.97797,-0.028238,-0.20685,207.72
    30180 
    30181 > view matrix models
    30182 > #42,0.16808,0.4812,-0.86035,176.9,0.12383,-0.87616,-0.46585,168.91,-0.97797,-0.028238,-0.20685,243.77
    30183 
    30184 > view matrix models
    30185 > #42,-0.098371,0.74921,-0.65499,172.34,0.16185,-0.63737,-0.75337,172.69,-0.9819,-0.18012,-0.058563,241.94
    30186 
    30187 > view matrix models
    30188 > #42,-0.098371,0.74921,-0.65499,168.3,0.16185,-0.63737,-0.75337,164.55,-0.9819,-0.18012,-0.058563,240.14
    30189 
    30190 > fitmap #42 inMap #8
    30191 
    30192 Fit molecule AATHNEcombined (#42) to map AATHNEcombined map 6 (#8) using 4858
    30193 atoms 
    30194 average map value = 0.4401, steps = 236 
    30195 shifted from previous position = 23.5 
    30196 rotated from previous position = 81.6 degrees 
    30197 atoms outside contour = 1171, contour level = 0.36586 
    30198  
    30199 Position of AATHNEcombined (#42) relative to AATHNEcombined map 6 (#8)
    30200 coordinates: 
    30201 Matrix rotation and translation 
    30202 0.99999997 0.00012320 0.00021381 -0.02142066 
    30203 -0.00012322 0.99999999 0.00009509 0.00213481 
    30204 -0.00021379 -0.00009512 0.99999997 0.00632785 
    30205 Axis -0.35962131 0.80845713 -0.46590727 
    30206 Axis point 43.71009619 0.00000000 89.29249519 
    30207 Rotation angle (degrees) 0.01515213 
    30208 Shift along axis 0.00648103 
    30209  
    30210 
    30211 > select subtract #42
    30212 
    30213 Nothing selected 
    30214 
    30215 > hide #!42 models
    30216 
    30217 > show #!42 models
    30218 
    30219 > combine #42 close false
    30220 
    30221 > select add #43
    30222 
    30223 4858 atoms, 4713 bonds, 831 residues, 1 model selected 
    30224 
    30225 > view matrix models
    30226 > #43,-0.994,-0.018016,-0.1079,166.09,0.10482,-0.43904,-0.89233,181.76,-0.031297,-0.89829,0.43829,253.22
    30227 
    30228 > view matrix models
    30229 > #43,-0.994,-0.018016,-0.1079,167.72,0.10482,-0.43904,-0.89233,183.32,-0.031297,-0.89829,0.43829,266.56
    30230 
    30231 > select subtract #43
    30232 
    30233 Nothing selected 
    30234 
    30235 > hide #!42 models
    30236 
    30237 > select add #43/A:94
    30238 
    30239 9 atoms, 8 bonds, 1 residue, 1 model selected 
    30240 
    30241 > select add #43/A:93
    30242 
    30243 20 atoms, 19 bonds, 2 residues, 1 model selected 
    30244 
    30245 > select add #43/A:92
    30246 
    30247 28 atoms, 26 bonds, 3 residues, 1 model selected 
    30248 
    30249 > select add #43/A:91
    30250 
    30251 39 atoms, 36 bonds, 4 residues, 1 model selected 
    30252 
    30253 > select add #43/A:90
    30254 
    30255 48 atoms, 44 bonds, 5 residues, 1 model selected 
    30256 
    30257 > select add #43/A:89
    30258 
    30259 55 atoms, 50 bonds, 6 residues, 1 model selected 
    30260 
    30261 > select add #43/A:88
    30262 
    30263 60 atoms, 54 bonds, 7 residues, 1 model selected 
    30264 
    30265 > select add #43/A:87
    30266 
    30267 71 atoms, 65 bonds, 8 residues, 1 model selected 
    30268 
    30269 > select add #43/A:86
    30270 
    30271 78 atoms, 71 bonds, 9 residues, 1 model selected 
    30272 
    30273 > select subtract #43/A:86
    30274 
    30275 71 atoms, 65 bonds, 8 residues, 1 model selected 
    30276 
    30277 > select add #43/A:86
    30278 
    30279 78 atoms, 71 bonds, 9 residues, 1 model selected 
    30280 
    30281 > select add #43/A:85
    30282 
    30283 87 atoms, 79 bonds, 10 residues, 1 model selected 
    30284 
    30285 > select add #43/A:84
    30286 
    30287 98 atoms, 89 bonds, 11 residues, 1 model selected 
    30288 
    30289 > select add #43/A:83
    30290 
    30291 105 atoms, 95 bonds, 12 residues, 1 model selected 
    30292 
    30293 > select add #43/A:82
    30294 
    30295 112 atoms, 102 bonds, 13 residues, 1 model selected 
    30296 
    30297 > select add #43/A:81
    30298 
    30299 121 atoms, 110 bonds, 14 residues, 1 model selected 
    30300 
    30301 > select add #43/A:80
    30302 
    30303 132 atoms, 120 bonds, 15 residues, 1 model selected 
    30304 
    30305 > select add #43/A:79
    30306 
    30307 143 atoms, 130 bonds, 16 residues, 1 model selected 
    30308 
    30309 > select add #43/A:77
    30310 
    30311 151 atoms, 137 bonds, 17 residues, 1 model selected 
    30312 
    30313 > select add #43/A:78
    30314 
    30315 157 atoms, 142 bonds, 18 residues, 1 model selected 
    30316 
    30317 > select add #43/A:76
    30318 
    30319 165 atoms, 149 bonds, 19 residues, 1 model selected 
    30320 
    30321 > select add #43/A:75
    30322 
    30323 175 atoms, 159 bonds, 20 residues, 1 model selected 
    30324 
    30325 > select add #43/A:74
    30326 
    30327 180 atoms, 163 bonds, 21 residues, 1 model selected 
    30328 
    30329 > select add #43/A:73
    30330 
    30331 184 atoms, 166 bonds, 22 residues, 1 model selected 
    30332 
    30333 > select add #43/A:72
    30334 
    30335 192 atoms, 173 bonds, 23 residues, 1 model selected 
    30336 
    30337 > select add #43/A:71
    30338 
    30339 199 atoms, 179 bonds, 24 residues, 1 model selected 
    30340 
    30341 > select add #43/A:70
    30342 
    30343 206 atoms, 185 bonds, 25 residues, 1 model selected 
    30344 
    30345 > select add #43/A:69
    30346 
    30347 217 atoms, 195 bonds, 26 residues, 1 model selected 
    30348 
    30349 > select add #43/A:54
    30350 
    30351 223 atoms, 200 bonds, 27 residues, 1 model selected 
    30352 
    30353 > select subtract #43/A:54
    30354 
    30355 217 atoms, 195 bonds, 26 residues, 1 model selected 
    30356 
    30357 > select add #43/A:68
    30358 
    30359 224 atoms, 201 bonds, 27 residues, 1 model selected 
    30360 
    30361 > select add #43/A:66
    30362 
    30363 229 atoms, 205 bonds, 28 residues, 1 model selected 
    30364 
    30365 > select add #43/A:65
    30366 
    30367 240 atoms, 215 bonds, 29 residues, 1 model selected 
    30368 
    30369 > select add #43/A:64
    30370 
    30371 247 atoms, 221 bonds, 30 residues, 1 model selected 
    30372 
    30373 > select add #43/A:63
    30374 
    30375 255 atoms, 228 bonds, 31 residues, 1 model selected 
    30376 
    30377 > select add #43/A:62
    30378 
    30379 262 atoms, 234 bonds, 32 residues, 1 model selected 
    30380 
    30381 > select add #43/A:61
    30382 
    30383 270 atoms, 241 bonds, 33 residues, 1 model selected 
    30384 
    30385 > select add #43/A:60
    30386 
    30387 275 atoms, 245 bonds, 34 residues, 1 model selected 
    30388 
    30389 > select add #43/A:59
    30390 
    30391 282 atoms, 251 bonds, 35 residues, 1 model selected 
    30392 
    30393 > select add #43/A:58
    30394 
    30395 288 atoms, 256 bonds, 36 residues, 1 model selected 
    30396 
    30397 > select add #43/A:57
    30398 
    30399 298 atoms, 266 bonds, 37 residues, 1 model selected 
    30400 
    30401 > select add #43/A:56
    30402 
    30403 303 atoms, 270 bonds, 38 residues, 1 model selected 
    30404 
    30405 > select add #43/A:55
    30406 
    30407 308 atoms, 274 bonds, 39 residues, 1 model selected 
    30408 
    30409 > select add #43/A:54
    30410 
    30411 314 atoms, 279 bonds, 40 residues, 1 model selected 
    30412 
    30413 > select add #43/A:53
    30414 
    30415 322 atoms, 286 bonds, 41 residues, 1 model selected 
    30416 
    30417 > select add #43/A:52
    30418 
    30419 329 atoms, 292 bonds, 42 residues, 1 model selected 
    30420 
    30421 > select add #43/A:51
    30422 
    30423 340 atoms, 303 bonds, 43 residues, 1 model selected 
    30424 
    30425 > select add #43/A:50
    30426 
    30427 348 atoms, 310 bonds, 44 residues, 1 model selected 
    30428 
    30429 > select add #43/A:48
    30430 
    30431 353 atoms, 314 bonds, 45 residues, 1 model selected 
    30432 
    30433 > select add #43/A:47
    30434 
    30435 361 atoms, 321 bonds, 46 residues, 1 model selected 
    30436 
    30437 > select add #43/A:46
    30438 
    30439 369 atoms, 328 bonds, 47 residues, 1 model selected 
    30440 
    30441 > select subtract #43/A:46
    30442 
    30443 361 atoms, 321 bonds, 46 residues, 1 model selected 
    30444 
    30445 > select add #43/A:45
    30446 
    30447 368 atoms, 327 bonds, 47 residues, 1 model selected 
    30448 
    30449 > select add #43/A:46
    30450 
    30451 376 atoms, 334 bonds, 48 residues, 1 model selected 
    30452 
    30453 > select add #43/A:44
    30454 
    30455 381 atoms, 338 bonds, 49 residues, 1 model selected 
    30456 
    30457 > select add #43/A:43
    30458 
    30459 385 atoms, 341 bonds, 50 residues, 1 model selected 
    30460 
    30461 > select add #43/A:42
    30462 
    30463 391 atoms, 346 bonds, 51 residues, 1 model selected 
    30464 
    30465 > select add #43/A:41
    30466 
    30467 402 atoms, 357 bonds, 52 residues, 1 model selected 
    30468 
    30469 > select add #43/A:40
    30470 
    30471 412 atoms, 367 bonds, 53 residues, 1 model selected 
    30472 
    30473 > select add #43/A:39
    30474 
    30475 416 atoms, 370 bonds, 54 residues, 1 model selected 
    30476 
    30477 > color sel forest green
    30478 
    30479 > select clear
    30480 
    30481 > select add #43/A:49
    30482 
    30483 7 atoms, 7 bonds, 1 residue, 1 model selected 
    30484 
    30485 > color sel forest green
    30486 
    30487 > select clear
    30488 
    30489 > select add #43/A:38
    30490 
    30491 4 atoms, 3 bonds, 1 residue, 1 model selected 
    30492 
    30493 > select add #43/A:36
    30494 
    30495 15 atoms, 13 bonds, 2 residues, 1 model selected 
    30496 
    30497 > select add #43/A:35
    30498 
    30499 23 atoms, 20 bonds, 3 residues, 1 model selected 
    30500 
    30501 > select add #43/A:34
    30502 
    30503 32 atoms, 28 bonds, 4 residues, 1 model selected 
    30504 
    30505 > select add #43/A:33
    30506 
    30507 40 atoms, 35 bonds, 5 residues, 1 model selected 
    30508 
    30509 > select add #43/A:32
    30510 
    30511 46 atoms, 40 bonds, 6 residues, 1 model selected 
    30512 
    30513 > select subtract #43/A:32
    30514 
    30515 40 atoms, 35 bonds, 5 residues, 1 model selected 
    30516 
    30517 > select add #43/A:32
    30518 
    30519 46 atoms, 40 bonds, 6 residues, 1 model selected 
    30520 
    30521 > select add #43/A:31
    30522 
    30523 53 atoms, 46 bonds, 7 residues, 1 model selected 
    30524 
    30525 > select add #43/A:30
    30526 
    30527 61 atoms, 53 bonds, 8 residues, 1 model selected 
    30528 
    30529 > color sel forest green
    30530 
    30531 > select clear
    30532 
    30533 > select add #43/A:108
    30534 
    30535 7 atoms, 6 bonds, 1 residue, 1 model selected 
    30536 
    30537 > select add #43/A:109
    30538 
    30539 15 atoms, 13 bonds, 2 residues, 1 model selected 
    30540 
    30541 > select add #43/A:110
    30542 
    30543 23 atoms, 20 bonds, 3 residues, 1 model selected 
    30544 
    30545 > select add #43/A:111
    30546 
    30547 32 atoms, 28 bonds, 4 residues, 1 model selected 
    30548 
    30549 > select add #43/A:112
    30550 
    30551 40 atoms, 35 bonds, 5 residues, 1 model selected 
    30552 
    30553 > color sel cyan
    30554 
    30555 > select add #43/A:90
    30556 
    30557 49 atoms, 43 bonds, 6 residues, 1 model selected 
    30558 
    30559 > select add #43/A:91
    30560 
    30561 60 atoms, 53 bonds, 7 residues, 1 model selected 
    30562 
    30563 > select add #43/A:92
    30564 
    30565 68 atoms, 60 bonds, 8 residues, 1 model selected 
    30566 
    30567 > select add #43/A:93
    30568 
    30569 79 atoms, 71 bonds, 9 residues, 1 model selected 
    30570 
    30571 > select add #43/A:94
    30572 
    30573 88 atoms, 79 bonds, 10 residues, 1 model selected 
    30574 
    30575 > color sel cyan
    30576 
    30577 > select add #43/A:54
    30578 
    30579 94 atoms, 84 bonds, 11 residues, 1 model selected 
    30580 
    30581 > select add #43/A:53
    30582 
    30583 102 atoms, 91 bonds, 12 residues, 1 model selected 
    30584 
    30585 > select add #43/A:52
    30586 
    30587 109 atoms, 97 bonds, 13 residues, 1 model selected 
    30588 
    30589 > select add #43/A:51
    30590 
    30591 120 atoms, 108 bonds, 14 residues, 1 model selected 
    30592 
    30593 > color sel cyan
    30594 
    30595 > select clear
    30596 
    30597 > show #!42 models
    30598 
    30599 > hide #!42 models
    30600 
    30601 > show #!42 models
    30602 
    30603 > hide #!42 models
    30604 
    30605 > hide #!43 models
    30606 
    30607 > show #!43 models
    30608 
    30609 > combine #43 close false
    30610 
    30611 > select add #44
    30612 
    30613 4858 atoms, 4713 bonds, 831 residues, 1 model selected 
    30614 
    30615 > view matrix models
    30616 > #44,-0.994,-0.018016,-0.1079,181.57,0.10482,-0.43904,-0.89233,189.57,-0.031297,-0.89829,0.43829,312.85
    30617 
    30618 > select subtract #44
    30619 
    30620 Nothing selected 
    30621 
    30622 > select add #44/A:127
    30623 
    30624 8 atoms, 7 bonds, 1 residue, 1 model selected 
    30625 
    30626 > select add #44/A:128
    30627 
    30628 15 atoms, 14 bonds, 2 residues, 1 model selected 
    30629 
    30630 > delete sel
    30631 
    30632 > select add #44/A:129
    30633 
    30634 5 atoms, 4 bonds, 1 residue, 1 model selected 
    30635 
    30636 > select add #44/A:130
    30637 
    30638 14 atoms, 12 bonds, 2 residues, 1 model selected 
    30639 
    30640 > select add #44/A:131
    30641 
    30642 18 atoms, 15 bonds, 3 residues, 1 model selected 
    30643 
    30644 > select add #44/A:132
    30645 
    30646 29 atoms, 25 bonds, 4 residues, 1 model selected 
    30647 
    30648 > select add #44/A:133
    30649 
    30650 40 atoms, 35 bonds, 5 residues, 1 model selected 
    30651 
    30652 > select add #44/A:134
    30653 
    30654 48 atoms, 42 bonds, 6 residues, 1 model selected 
    30655 
    30656 > select subtract #44/A:134
    30657 
    30658 40 atoms, 35 bonds, 5 residues, 1 model selected 
    30659 
    30660 > select add #44/A:134
    30661 
    30662 48 atoms, 42 bonds, 6 residues, 1 model selected 
    30663 
    30664 > select add #44/A:135
    30665 
    30666 52 atoms, 45 bonds, 7 residues, 1 model selected 
    30667 
    30668 > select add #44/A:136
    30669 
    30670 60 atoms, 52 bonds, 8 residues, 1 model selected 
    30671 
    30672 > select add #44/A:137
    30673 
    30674 64 atoms, 55 bonds, 9 residues, 1 model selected 
    30675 
    30676 > select add #44/A:138
    30677 
    30678 71 atoms, 61 bonds, 10 residues, 1 model selected 
    30679 
    30680 > delete sel
    30681 
    30682 > select add #44/A:96
    30683 
    30684 8 atoms, 7 bonds, 1 residue, 1 model selected 
    30685 
    30686 > select add #44/A:97
    30687 
    30688 12 atoms, 10 bonds, 2 residues, 1 model selected 
    30689 
    30690 > select add #44/A:98
    30691 
    30692 24 atoms, 22 bonds, 3 residues, 1 model selected 
    30693 
    30694 > select add #44/A:99
    30695 
    30696 32 atoms, 29 bonds, 4 residues, 1 model selected 
    30697 
    30698 > select add #44/A:100
    30699 
    30700 39 atoms, 36 bonds, 5 residues, 1 model selected 
    30701 
    30702 > select add #44/A:101
    30703 
    30704 46 atoms, 42 bonds, 6 residues, 1 model selected 
    30705 
    30706 > select add #44/A:102
    30707 
    30708 54 atoms, 49 bonds, 7 residues, 1 model selected 
    30709 
    30710 > select add #44/A:103
    30711 
    30712 62 atoms, 56 bonds, 8 residues, 1 model selected 
    30713 
    30714 > select add #44/A:104
    30715 
    30716 70 atoms, 63 bonds, 9 residues, 1 model selected 
    30717 
    30718 > select add #44/A:105
    30719 
    30720 78 atoms, 70 bonds, 10 residues, 1 model selected 
    30721 
    30722 > select add #44/A:106
    30723 
    30724 86 atoms, 77 bonds, 11 residues, 1 model selected 
    30725 
    30726 > select add #44/A:107
    30727 
    30728 94 atoms, 84 bonds, 12 residues, 1 model selected 
    30729 
    30730 > delete sel
    30731 
    30732 > select clear
    30733 
    30734 > select add #44/A:160
    30735 
    30736 9 atoms, 8 bonds, 1 residue, 1 model selected 
    30737 
    30738 > select subtract #44/A:160
    30739 
    30740 Nothing selected 
    30741 
    30742 > select #44/A:159
    30743 
    30744 8 atoms, 7 bonds, 1 residue, 1 model selected 
    30745 
    30746 > select subtract #44/A:159
    30747 
    30748 Nothing selected 
    30749 
    30750 > select add #44/A:159
    30751 
    30752 8 atoms, 7 bonds, 1 residue, 1 model selected 
    30753 
    30754 > select add #44/A:158
    30755 
    30756 15 atoms, 13 bonds, 2 residues, 1 model selected 
    30757 
    30758 > select add #44/A:157
    30759 
    30760 21 atoms, 18 bonds, 3 residues, 1 model selected 
    30761 
    30762 > select add #44/A:156
    30763 
    30764 26 atoms, 22 bonds, 4 residues, 1 model selected 
    30765 
    30766 > select add #44/A:155
    30767 
    30768 34 atoms, 29 bonds, 5 residues, 1 model selected 
    30769 
    30770 > select add #44/A:154
    30771 
    30772 38 atoms, 32 bonds, 6 residues, 1 model selected 
    30773 
    30774 > select add #44/A:152
    30775 
    30776 49 atoms, 42 bonds, 7 residues, 1 model selected 
    30777 
    30778 > select add #44/A:151
    30779 
    30780 57 atoms, 49 bonds, 8 residues, 1 model selected 
    30781 
    30782 > select add #44/A:150
    30783 
    30784 68 atoms, 59 bonds, 9 residues, 1 model selected 
    30785 
    30786 > select add #44/A:149
    30787 
    30788 72 atoms, 62 bonds, 10 residues, 1 model selected 
    30789 
    30790 > select add #44/A:148
    30791 
    30792 80 atoms, 69 bonds, 11 residues, 1 model selected 
    30793 
    30794 > select add #44/A:147
    30795 
    30796 88 atoms, 76 bonds, 12 residues, 1 model selected 
    30797 
    30798 > select add #44/A:146
    30799 
    30800 92 atoms, 79 bonds, 13 residues, 1 model selected 
    30801 
    30802 > select add #44/A:145
    30803 
    30804 106 atoms, 94 bonds, 14 residues, 1 model selected 
    30805 
    30806 > delete sel
    30807 
    30808 > select add #44/A:113
    30809 
    30810 8 atoms, 7 bonds, 1 residue, 1 model selected 
    30811 
    30812 > select add #44/A:114
    30813 
    30814 12 atoms, 10 bonds, 2 residues, 1 model selected 
    30815 
    30816 > select add #44/A:115
    30817 
    30818 18 atoms, 15 bonds, 3 residues, 1 model selected 
    30819 
    30820 > select add #44/A:116
    30821 
    30822 23 atoms, 19 bonds, 4 residues, 1 model selected 
    30823 
    30824 > select add #44/A:117
    30825 
    30826 30 atoms, 25 bonds, 5 residues, 1 model selected 
    30827 
    30828 > select add #44/A:118
    30829 
    30830 38 atoms, 32 bonds, 6 residues, 1 model selected 
    30831 
    30832 > select add #44/A:119
    30833 
    30834 46 atoms, 39 bonds, 7 residues, 1 model selected 
    30835 
    30836 > select add #44/A:120
    30837 
    30838 51 atoms, 43 bonds, 8 residues, 1 model selected 
    30839 
    30840 > select add #44/A:121
    30841 
    30842 59 atoms, 50 bonds, 9 residues, 1 model selected 
    30843 
    30844 > select add #44/A:122
    30845 
    30846 66 atoms, 56 bonds, 10 residues, 1 model selected 
    30847 
    30848 > select add #44/A:124
    30849 
    30850 73 atoms, 62 bonds, 11 residues, 1 model selected 
    30851 
    30852 > select add #44/A:125
    30853 
    30854 78 atoms, 66 bonds, 12 residues, 1 model selected 
    30855 
    30856 > select add #44/A:126
    30857 
    30858 87 atoms, 74 bonds, 13 residues, 1 model selected 
    30859 
    30860 > delete sel
    30861 
    30862 > open /Users/amy/Downloads/emd_8220.map
    30863 
    30864 Opened emd_8220.map as #45, grid size 100,86,100, pixel 0.554,0.564,0.577,
    30865 shown at level 0.0696, step 1, values float32 
    30866 
    30867 > volume #45 level 0.05639
    30868 
    30869 > close #45
    30870 
    30871 > select add #44/A:16
    30872 
    30873 8 atoms, 7 bonds, 1 residue, 1 model selected 
    30874 
    30875 > select add #44/A:17
    30876 
    30877 15 atoms, 13 bonds, 2 residues, 1 model selected 
    30878 
    30879 > select add #44/A:18
    30880 
    30881 19 atoms, 16 bonds, 3 residues, 1 model selected 
    30882 
    30883 > select add #44/A:19
    30884 
    30885 23 atoms, 19 bonds, 4 residues, 1 model selected 
    30886 
    30887 > select add #44/A:20
    30888 
    30889 34 atoms, 29 bonds, 5 residues, 1 model selected 
    30890 
    30891 > select add #44/A:21
    30892 
    30893 45 atoms, 39 bonds, 6 residues, 1 model selected 
    30894 
    30895 > select add #44/A:22
    30896 
    30897 50 atoms, 43 bonds, 7 residues, 1 model selected 
    30898 
    30899 > select add #44/A:23
    30900 
    30901 61 atoms, 53 bonds, 8 residues, 1 model selected 
    30902 
    30903 > select add #44/A:24
    30904 
    30905 68 atoms, 60 bonds, 9 residues, 1 model selected 
    30906 
    30907 > select add #44/A:25
    30908 
    30909 78 atoms, 70 bonds, 10 residues, 1 model selected 
    30910 
    30911 > select add #44/A:26
    30912 
    30913 83 atoms, 74 bonds, 11 residues, 1 model selected 
    30914 
    30915 > select add #44/A:27
    30916 
    30917 97 atoms, 89 bonds, 12 residues, 1 model selected 
    30918 
    30919 > select add #44/A:29
    30920 
    30921 108 atoms, 100 bonds, 13 residues, 1 model selected 
    30922 
    30923 > delete sel
    30924 
    30925 > select add #44
    30926 
    30927 4377 atoms, 4217 bonds, 5 pseudobonds, 767 residues, 2 models selected 
    30928 
    30929 > view matrix models
    30930 > #44,-0.994,-0.018016,-0.1079,167.02,0.10482,-0.43904,-0.89233,176.04,-0.031297,-0.89829,0.43829,207.55
    30931 
    30932 > fitmap #44 inMap #8
    30933 
    30934 Fit molecule copy of copy of AATHNEcombined (#44) to map AATHNEcombined map 6
    30935 (#8) using 4377 atoms 
    30936 average map value = 0.4393, steps = 56 
    30937 shifted from previous position = 6.58 
    30938 rotated from previous position = 0.0611 degrees 
    30939 atoms outside contour = 1072, contour level = 0.36586 
    30940  
    30941 Position of copy of copy of AATHNEcombined (#44) relative to AATHNEcombined
    30942 map 6 (#8) coordinates: 
    30943 Matrix rotation and translation 
    30944 0.99999971 0.00068256 0.00033276 -0.05114740 
    30945 -0.00068229 0.99999944 -0.00080618 0.06249724 
    30946 -0.00033331 0.00080595 0.99999962 -0.02902612 
    30947 Axis 0.72788203 0.30072989 -0.61623801 
    30948 Axis point 0.00000000 36.47000800 77.70180160 
    30949 Rotation angle (degrees) 0.06345003 
    30950 Shift along axis -0.00054749 
    30951  
    30952 
    30953 > view matrix models
    30954 > #44,-0.99398,-0.018669,-0.108,161.2,0.10517,-0.43979,-0.89192,171.06,-0.030847,-0.89791,0.4391,163.49
    30955 
    30956 > view matrix models
    30957 > #44,-0.99398,-0.018669,-0.108,160.92,0.10517,-0.43979,-0.89192,163.66,-0.030847,-0.89791,0.4391,148.99
    30958 
    30959 > fitmap #44 inMap #29
    30960 
    30961 Fit molecule copy of copy of AATHNEcombined (#44) to map J1122.mrc (#29) using
    30962 4377 atoms 
    30963 average map value = 0.08017, steps = 120 
    30964 shifted from previous position = 10.4 
    30965 rotated from previous position = 19 degrees 
    30966 atoms outside contour = 1934, contour level = 0.064406 
    30967  
    30968 Position of copy of copy of AATHNEcombined (#44) relative to J1122.mrc (#29)
    30969 coordinates: 
    30970 Matrix rotation and translation 
    30971 -0.93560766 0.29367131 -0.19594762 148.33622912 
    30972 0.04403975 -0.45360760 -0.89011271 165.90577632 
    30973 -0.35028390 -0.84142576 0.41146553 152.50362608 
    30974 Axis 0.16365385 0.51877807 -0.83909876 
    30975 Axis point 96.84111132 123.35674227 0.00000000 
    30976 Rotation angle (degrees) 171.44551676 
    30977 Shift along axis -17.62152966 
    30978  
    30979 
    30980 > view matrix models
    30981 > #44,-0.93561,0.29367,-0.19595,147.21,0.04404,-0.45361,-0.89011,177.11,-0.35028,-0.84143,0.41147,212.36
    30982 
    30983 > view matrix models
    30984 > #44,-0.93561,0.29367,-0.19595,156.61,0.04404,-0.45361,-0.89011,178.01,-0.35028,-0.84143,0.41147,216.59
    30985 
    30986 > fitmap #44 inMap #8
    30987 
    30988 Fit molecule copy of copy of AATHNEcombined (#44) to map AATHNEcombined map 6
    30989 (#8) using 4377 atoms 
    30990 average map value = 0.4394, steps = 64 
    30991 shifted from previous position = 3.67 
    30992 rotated from previous position = 19 degrees 
    30993 atoms outside contour = 1073, contour level = 0.36586 
    30994  
    30995 Position of copy of copy of AATHNEcombined (#44) relative to AATHNEcombined
    30996 map 6 (#8) coordinates: 
    30997 Matrix rotation and translation 
    30998 0.99999986 0.00044110 -0.00029615 0.00647815 
    30999 -0.00044140 0.99999940 -0.00099710 0.04994382 
    31000 0.00029571 0.00099723 0.99999946 -0.05779749 
    31001 Axis 0.88254618 -0.26191484 -0.39052893 
    31002 Axis point 0.00000000 52.03151904 54.05257298 
    31003 Rotation angle (degrees) 0.06473724 
    31004 Shift along axis 0.01520783 
    31005  
    31006 
    31007 > view matrix models
    31008 > #44,-0.99405,-0.018449,-0.10737,168.43,0.10451,-0.43998,-0.8919,162.5,-0.030788,-0.89782,0.43929,154.17
    31009 
    31010 > view matrix models
    31011 > #44,-0.99405,-0.018449,-0.10737,153.97,0.10451,-0.43998,-0.8919,165.28,-0.030788,-0.89782,0.43929,147.12
    31012 
    31013 > fitmap #44 inMap #29
    31014 
    31015 Fit molecule copy of copy of AATHNEcombined (#44) to map J1122.mrc (#29) using
    31016 4377 atoms 
    31017 average map value = 0.08017, steps = 112 
    31018 shifted from previous position = 3.23 
    31019 rotated from previous position = 19 degrees 
    31020 atoms outside contour = 1936, contour level = 0.064406 
    31021  
    31022 Position of copy of copy of AATHNEcombined (#44) relative to J1122.mrc (#29)
    31023 coordinates: 
    31024 Matrix rotation and translation 
    31025 -0.93553950 0.29370365 -0.19622436 148.34392039 
    31026 0.04417583 -0.45387692 -0.88996867 165.89259865 
    31027 -0.35044876 -0.84126922 0.41164519 152.49532201 
    31028 Axis 0.16377458 0.51865136 -0.83915354 
    31029 Axis point 96.84939042 123.33620103 0.00000000 
    31030 Rotation angle (degrees) 171.44966078 
    31031 Shift along axis -17.63160462 
    31032  
    31033 
    31034 > select add #8
    31035 
    31036 4377 atoms, 4217 bonds, 5 pseudobonds, 767 residues, 4 models selected 
    31037 
    31038 > select subtract #44
    31039 
    31040 2 models selected 
    31041 
    31042 > view matrix models
    31043 > #8,-0.94817,0.24716,-0.1997,158.38,0.060761,-0.47584,-0.87743,176.64,-0.31189,-0.84409,0.43616,212.3
    31044 
    31045 > select subtract #8
    31046 
    31047 Nothing selected 
    31048 
    31049 > select add #44
    31050 
    31051 4377 atoms, 4217 bonds, 5 pseudobonds, 767 residues, 2 models selected 
    31052 
    31053 > view matrix models
    31054 > #44,-0.93554,0.2937,-0.19622,141.41,0.044176,-0.45388,-0.88997,179.93,-0.35045,-0.84127,0.41165,213.18
    31055 
    31056 > view matrix models
    31057 > #44,-0.93554,0.2937,-0.19622,151.53,0.044176,-0.45388,-0.88997,179.57,-0.35045,-0.84127,0.41165,212.38
    31058 
    31059 > view matrix models
    31060 > #44,-0.93554,0.2937,-0.19622,155.41,0.044176,-0.45388,-0.88997,178.43,-0.35045,-0.84127,0.41165,216.37
    31061 
    31062 > view matrix models
    31063 > #44,-0.93554,0.2937,-0.19622,155.54,0.044176,-0.45388,-0.88997,176.75,-0.35045,-0.84127,0.41165,213.56
    31064 
    31065 > view matrix models
    31066 > #44,-0.93554,0.2937,-0.19622,156.39,0.044176,-0.45388,-0.88997,176.3,-0.35045,-0.84127,0.41165,214.67
    31067 
    31068 > fitmap #44 inMap #8
    31069 
    31070 Fit molecule copy of copy of AATHNEcombined (#44) to map AATHNEcombined map 6
    31071 (#8) using 4377 atoms 
    31072 average map value = 0.4394, steps = 52 
    31073 shifted from previous position = 1.68 
    31074 rotated from previous position = 3.02 degrees 
    31075 atoms outside contour = 1076, contour level = 0.36586 
    31076  
    31077 Position of copy of copy of AATHNEcombined (#44) relative to AATHNEcombined
    31078 map 6 (#8) coordinates: 
    31079 Matrix rotation and translation 
    31080 0.99999955 0.00082150 0.00046001 -0.00883030 
    31081 -0.00082119 0.99999944 -0.00066348 0.04456765 
    31082 -0.00046055 0.00066310 0.99999967 -0.03206776 
    31083 Axis 0.57592008 0.39965178 -0.71315813 
    31084 Axis point 36.92441346 35.72354775 0.00000000 
    31085 Rotation angle (degrees) 0.06598750 
    31086 Shift along axis 0.03559538 
    31087  
    31088 
    31089 > select subtract #44
    31090 
    31091 Nothing selected 
    31092 
    31093 > hide #!44 models
    31094 
    31095 > select add #43
    31096 
    31097 4858 atoms, 4713 bonds, 831 residues, 1 model selected 
    31098 
    31099 > select subtract #43
    31100 
    31101 Nothing selected 
    31102 
    31103 > show #!44 models
    31104 
    31105 > select add #44
    31106 
    31107 4377 atoms, 4217 bonds, 5 pseudobonds, 767 residues, 2 models selected 
    31108 
    31109 > view matrix models
    31110 > #44,-0.94828,0.24625,-0.2003,158.56,0.061556,-0.47637,-0.87709,164.14,-0.3114,-0.84406,0.43658,152.21
    31111 
    31112 > view matrix models
    31113 > #44,-0.94828,0.24625,-0.2003,153.59,0.061556,-0.47637,-0.87709,162.81,-0.3114,-0.84406,0.43658,148.12
    31114 
    31115 > fitmap #44 inMap #29
    31116 
    31117 Fit molecule copy of copy of AATHNEcombined (#44) to map J1122.mrc (#29) using
    31118 4377 atoms 
    31119 average map value = 0.08017, steps = 96 
    31120 shifted from previous position = 5.9 
    31121 rotated from previous position = 3.02 degrees 
    31122 atoms outside contour = 1937, contour level = 0.064406 
    31123  
    31124 Position of copy of copy of AATHNEcombined (#44) relative to J1122.mrc (#29)
    31125 coordinates: 
    31126 Matrix rotation and translation 
    31127 -0.93556337 0.29370123 -0.19611414 148.34082953 
    31128 0.04407128 -0.45387887 -0.88997286 165.89641444 
    31129 -0.35039819 -0.84126901 0.41168865 152.49037322 
    31130 Axis 0.16372475 0.51864729 -0.83916578 
    31131 Axis point 96.84588182 123.33307757 0.00000000 
    31132 Rotation angle (degrees) 171.44626082 
    31133 Shift along axis -17.63591277 
    31134  
    31135 
    31136 > view matrix models
    31137 > #44,-0.93556,0.2937,-0.19611,181.55,0.044071,-0.45388,-0.88997,200.58,-0.3504,-0.84127,0.41169,325.24
    31138 
    31139 > volume #29 level 0.05579
    31140 
    31141 > volume #29 level 0.0639
    31142 
    31143 > select subtract #44
    31144 
    31145 Nothing selected 
    31146 
    31147 > select add #44/A:83
    31148 
    31149 7 atoms, 6 bonds, 1 residue, 1 model selected 
    31150 
    31151 > select add #44/A:81
    31152 
    31153 16 atoms, 14 bonds, 2 residues, 1 model selected 
    31154 
    31155 > select add #44/A:82
    31156 
    31157 23 atoms, 21 bonds, 3 residues, 1 model selected 
    31158 
    31159 > select add #44/A:80
    31160 
    31161 34 atoms, 31 bonds, 4 residues, 1 model selected 
    31162 
    31163 > select add #44/A:79
    31164 
    31165 45 atoms, 41 bonds, 5 residues, 1 model selected 
    31166 
    31167 > select add #44/A:78
    31168 
    31169 51 atoms, 46 bonds, 6 residues, 1 model selected 
    31170 
    31171 > select add #44/A:77
    31172 
    31173 59 atoms, 53 bonds, 7 residues, 1 model selected 
    31174 
    31175 > select add #44/A:76
    31176 
    31177 67 atoms, 60 bonds, 8 residues, 1 model selected 
    31178 
    31179 > select add #44/A:75
    31180 
    31181 77 atoms, 70 bonds, 9 residues, 1 model selected 
    31182 
    31183 > delete sel
    31184 
    31185 > select add #44/A:231
    31186 
    31187 4 atoms, 3 bonds, 1 residue, 1 model selected 
    31188 
    31189 > select add #44/A:230
    31190 
    31191 10 atoms, 8 bonds, 2 residues, 1 model selected 
    31192 
    31193 > select add #44/A:228
    31194 
    31195 15 atoms, 12 bonds, 3 residues, 1 model selected 
    31196 
    31197 > select add #44/A:227
    31198 
    31199 21 atoms, 17 bonds, 4 residues, 1 model selected 
    31200 
    31201 > select add #44/A:226
    31202 
    31203 25 atoms, 20 bonds, 5 residues, 1 model selected 
    31204 
    31205 > select add #44/A:232
    31206 
    31207 33 atoms, 27 bonds, 6 residues, 1 model selected 
    31208 
    31209 > select add #44/A:143
    31210 
    31211 41 atoms, 34 bonds, 7 residues, 1 model selected 
    31212 
    31213 > select subtract #44/A:143
    31214 
    31215 33 atoms, 27 bonds, 6 residues, 1 model selected 
    31216 
    31217 > select add #44/A:233
    31218 
    31219 45 atoms, 39 bonds, 7 residues, 1 model selected 
    31220 
    31221 > delete sel
    31222 
    31223 > select add #44/A:190
    31224 
    31225 11 atoms, 10 bonds, 1 residue, 1 model selected 
    31226 
    31227 > select add #44/A:191
    31228 
    31229 15 atoms, 13 bonds, 2 residues, 1 model selected 
    31230 
    31231 > select add #44/A:192
    31232 
    31233 26 atoms, 23 bonds, 3 residues, 1 model selected 
    31234 
    31235 > select add #44/A:194
    31236 
    31237 35 atoms, 31 bonds, 4 residues, 1 model selected 
    31238 
    31239 > select add #44/A:195
    31240 
    31241 40 atoms, 35 bonds, 5 residues, 1 model selected 
    31242 
    31243 > select add #44/A:196
    31244 
    31245 44 atoms, 38 bonds, 6 residues, 1 model selected 
    31246 
    31247 > delete sel
    31248 
    31249 > select add #44/A:197
    31250 
    31251 7 atoms, 6 bonds, 1 residue, 1 model selected 
    31252 
    31253 > select add #44/A:198
    31254 
    31255 13 atoms, 11 bonds, 2 residues, 1 model selected 
    31256 
    31257 > delete sel
    31258 
    31259 > hide #!44 models
    31260 
    31261 > show #!44 models
    31262 
    31263 > molmap #44 6
    31264 
    31265 Opened copy of copy of AATHNEcombined map 6 as #45, grid size 43,51,63, pixel
    31266 2, shown at level 0.0888, step 1, values float32 
    31267 
    31268 > close #45
    31269 
    31270 > molmap #44 4
    31271 
    31272 Opened copy of copy of AATHNEcombined map 4 as #45, grid size 55,68,86, pixel
    31273 1.33, shown at level 0.0965, step 1, values float32 
    31274 
    31275 > hide #!45 models
    31276 
    31277 > close #45
    31278 
    31279 > molmap #44 6
    31280 
    31281 Opened copy of copy of AATHNEcombined map 6 as #45, grid size 43,51,63, pixel
    31282 2, shown at level 0.0888, step 1, values float32 
    31283 
    31284 > volume #29 level 0.07099
    31285 
    31286 > volume #45 level 0.3542
    31287 
    31288 > transparency #45 50
    31289 
    31290 > select add #45
    31291 
    31292 2 models selected 
    31293 
    31294 > select add #44
    31295 
    31296 4198 atoms, 4031 bonds, 8 pseudobonds, 743 residues, 4 models selected 
    31297 
    31298 > view matrix models
    31299 > #44,-0.93556,0.2937,-0.19611,146.23,0.044071,-0.45388,-0.88997,157.07,-0.3504,-0.84127,0.41169,60.574,#45,-0.93556,0.2937,-0.19611,146.23,0.044071,-0.45388,-0.88997,157.07,-0.3504,-0.84127,0.41169,60.574
    31300 
    31301 > view matrix models
    31302 > #44,-0.93556,0.2937,-0.19611,143.48,0.044071,-0.45388,-0.88997,147.76,-0.3504,-0.84127,0.41169,34.922,#45,-0.93556,0.2937,-0.19611,143.48,0.044071,-0.45388,-0.88997,147.76,-0.3504,-0.84127,0.41169,34.922
    31303 
    31304 > select subtract #45
    31305 
    31306 4198 atoms, 4031 bonds, 8 pseudobonds, 743 residues, 2 models selected 
    31307 
    31308 > select subtract #44
    31309 
    31310 Nothing selected 
    31311 
    31312 > hide #!44 models
    31313 
    31314 > select add #45
    31315 
    31316 2 models selected 
    31317 
    31318 > view matrix models
    31319 > #45,-0.93556,0.2937,-0.19611,145.49,0.044071,-0.45388,-0.88997,159.38,-0.3504,-0.84127,0.41169,39.151
    31320 
    31321 > view matrix models
    31322 > #45,-0.72949,0.54043,-0.41926,144.13,0.020765,-0.59518,-0.80333,159.59,-0.68367,-0.59473,0.42296,41.013
    31323 
    31324 > view matrix models
    31325 > #45,-0.71308,0.51521,-0.47548,145.84,0.057668,-0.6328,-0.77216,158.62,-0.69871,-0.57803,0.42153,41.063
    31326 
    31327 > view matrix models
    31328 > #45,-0.71308,0.51521,-0.47548,145.43,0.057668,-0.6328,-0.77216,156.8,-0.69871,-0.57803,0.42153,40.9
    31329 
    31330 > view matrix models
    31331 > #45,-0.71308,0.51521,-0.47548,145.15,0.057668,-0.6328,-0.77216,154.97,-0.69871,-0.57803,0.42153,40.73
    31332 
    31333 > view matrix models
    31334 > #45,-0.79988,0.54237,-0.25694,140.06,-0.020652,-0.45275,-0.8914,156.94,-0.5998,-0.70771,0.37335,42.366
    31335 
    31336 > select subtract #45
    31337 
    31338 Nothing selected 
    31339 
    31340 > show #!44 models
    31341 
    31342 > fitmap #44 inMap #45
    31343 
    31344 Fit molecule copy of copy of AATHNEcombined (#44) to map copy of copy of
    31345 AATHNEcombined map 6 (#45) using 4198 atoms 
    31346 average map value = 0.434, steps = 72 
    31347 shifted from previous position = 8.8 
    31348 rotated from previous position = 16.7 degrees 
    31349 atoms outside contour = 994, contour level = 0.3542 
    31350  
    31351 Position of copy of copy of AATHNEcombined (#44) relative to copy of copy of
    31352 AATHNEcombined map 6 (#45) coordinates: 
    31353 Matrix rotation and translation 
    31354 0.99999987 0.00004904 -0.00050917 0.03695210 
    31355 -0.00004923 0.99999993 -0.00038442 0.00896662 
    31356 0.00050915 0.00038445 0.99999980 -0.01640243 
    31357 Axis 0.60079207 -0.79570876 -0.07678841 
    31358 Axis point 29.77463683 0.00000000 53.30306429 
    31359 Rotation angle (degrees) 0.03666236 
    31360 Shift along axis 0.01632523 
    31361  
    31362 
    31363 > select add #44
    31364 
    31365 4198 atoms, 4031 bonds, 8 pseudobonds, 743 residues, 2 models selected 
    31366 
    31367 > view matrix models
    31368 > #44,-0.80004,0.54224,-0.25675,156.75,-0.021083,-0.45309,-0.89121,165.09,-0.59958,-0.70759,0.37392,145.97
    31369 
    31370 > view matrix models
    31371 > #44,-0.80004,0.54224,-0.25675,157.44,-0.021083,-0.45309,-0.89121,165.95,-0.59958,-0.70759,0.37392,150.1
    31372 
    31373 > fitmap #44 inMap #29
    31374 
    31375 Fit molecule copy of copy of AATHNEcombined (#44) to map J1122.mrc (#29) using
    31376 4198 atoms 
    31377 average map value = 0.08149, steps = 152 
    31378 shifted from previous position = 14.4 
    31379 rotated from previous position = 16.8 degrees 
    31380 atoms outside contour = 2047, contour level = 0.070992 
    31381  
    31382 Position of copy of copy of AATHNEcombined (#44) relative to J1122.mrc (#29)
    31383 coordinates: 
    31384 Matrix rotation and translation 
    31385 -0.93562730 0.29338154 -0.19628760 148.35386113 
    31386 0.04432994 -0.45401135 -0.88989243 165.88171301 
    31387 -0.35019481 -0.84130908 0.41177983 152.48885393 
    31388 Axis 0.16370521 0.51860171 -0.83919775 
    31389 Axis point 96.83079976 123.33491709 0.00000000 
    31390 Rotation angle (degrees) 171.46655392 
    31391 Shift along axis -17.65546343 
    31392  
    31393 
    31394 > select subtract #44
    31395 
    31396 Nothing selected 
    31397 
    31398 > select add #45
    31399 
    31400 2 models selected 
    31401 
    31402 > view matrix models
    31403 > #45,-0.93329,0.27115,-0.23547,146.24,0.06955,-0.50681,-0.85925,155.22,-0.35232,-0.81831,0.45414,37.269
    31404 
    31405 > select subtract #45
    31406 
    31407 Nothing selected 
    31408 
    31409 > hide #!44 models
    31410 
    31411 > open /Users/amy/Downloads/cryosparc_P483_J196_007_volume_map.mrc
    31412 
    31413 Opened cryosparc_P483_J196_007_volume_map.mrc as #46, grid size 400,400,400,
    31414 pixel 0.723, shown at level 0.00453, step 2, values float32 
    31415 
    31416 > hide #!45 models
    31417 
    31418 > hide #!43 models
    31419 
    31420 > hide #!29 models
    31421 
    31422 > hide #!8 models
    31423 
    31424 > volume #46 level 0.03417
    31425 
    31426 > open /Users/amy/Downloads/cryosparc_P483_J206_005_volume_map.mrc
    31427 
    31428 Opened cryosparc_P483_J206_005_volume_map.mrc as #47, grid size 400,400,400,
    31429 pixel 0.723, shown at level 0.0164, step 2, values float32 
    31430 
    31431 > volume #47 level 0.05223
    31432 
    31433 > volume #47 level 0.05304
    31434 
    31435 > volume #47 level 0.05549
    31436 
    31437 > close #58-61,70-71
    31438 
    31439 > show #!46 models
    31440 
    31441 > hide #!46 models
    31442 
    31443 > close #46-47
    31444 
    31445 > show #!39 models
    31446 
    31447 Error processing trigger "graphics update": 
    31448  
    31449 You deleted or moved a volume file that is still open in ChimeraX. 
    31450  
    31451 /Users/amy/Downloads/cryosparc_P483_J188_006_volume_map.mrc 
    31452  
    31453 To allow fast initial display of volume data ChimeraX does not read all data
    31454 from the file when it is first opened, and will later read more data when
    31455 needed. ChimeraX got an error trying to read the above file. 
    31456 
    31457 > close #39-40
    31458 
    31459 > save "/Users/amy/Desktop/SPA AAT_HNE/csparc.cxs"
    31460 
    31461 ——— End of log from Thu Mar 12 17:49:41 2026 ———
    31462 
    31463 > view name session-start
    31464 
    31465 opened ChimeraX session 
    31466 
    314675366
    314685367