Changes between Initial Version and Version 1 of Ticket #19911


Ignore:
Timestamp:
Mar 2, 2026, 10:26:38 AM (3 weeks ago)
Author:
Eric Pettersen
Comment:

Reported by Zeba Rizvi

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #19911

    • Property Component Unassigned → Graphics
    • Property Owner set to Tom Goddard
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → assigned
    • Property Summary ChimeraX bug report submission → Crash destroying OpenGL context on exit

  • Ticket #19911 – Description

    initial v1  
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    1951     "path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/mmcif.cpython-311-darwin.so",
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    1969     "path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/pdb\/_pdbio.cpython-311-darwin.so",
    1970     "name" : "_pdbio.cpython-311-darwin.so"
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    1978     "path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/etree.cpython-311-darwin.so",
    1979     "name" : "etree.cpython-311-darwin.so"
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    1986     "uuid" : "c9441298-6125-3b5c-8f21-032910e5184d",
    1987     "path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/_elementpath.cpython-311-darwin.so",
    1988     "name" : "_elementpath.cpython-311-darwin.so"
    1989   },
    1990   {
    1991     "source" : "P",
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    1994     "size" : 32768,
    1995     "uuid" : "8abbdcef-1901-3d4b-9e6b-a38214b79214",
    1996     "path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/_imagingmath.cpython-311-darwin.so",
    1997     "name" : "_imagingmath.cpython-311-darwin.so"
    1998   },
    1999   {
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    2004     "uuid" : "6e4a96ad-04b8-3e8a-b91d-087e62306246",
    2005     "path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
    2006     "name" : "libsystem_kernel.dylib"
    2007   },
    2008   {
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    2010     "arch" : "arm64e",
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    2013     "uuid" : "d6494ba9-171e-39fc-b1aa-28ecf87975d1",
    2014     "path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
    2015     "name" : "libsystem_pthread.dylib"
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    2017   {
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    2022     "uuid" : "dfea8794-80ce-37c3-8f6a-108aa1d0b1b0",
    2023     "path" : "\/usr\/lib\/system\/libsystem_c.dylib",
    2024     "name" : "libsystem_c.dylib"
    2025   },
    2026   {
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    2031     "uuid" : "fd19a599-8750-31f9-924f-c2810c938371",
    2032     "path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
    2033     "name" : "libsystem_platform.dylib"
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    2035   {
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    2052     "CFBundleIdentifier" : "com.apple.Foundation",
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    2054     "uuid" : "b9a92060-f21e-3ecf-9ded-94a65c68a6f4",
    2055     "path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
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    2067     "path" : "\/System\/Library\/Frameworks\/CoreServices.framework\/Versions\/A\/Frameworks\/AE.framework\/Versions\/A\/AE",
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     76[deleted to fit within ticket limits]
     77
    210978],
    211079  "sharedCache" : {
    … …  
    3028997Opened 9a. combination of 2528 and 2544 emready2 as #8, grid size 443,443,443,
    3029998pixel 0.5, shown at level 5.07, step 1, values float32 
    3030 Opened 6b. combination of 2526 and 2540 emready2 copy as #16, grid size
    3031 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 
    3032 Opened 6a. combination of 2526 and 2540 emready2 0 as #14.1, grid size
    3033 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 
    3034 Opened 6a. combination of 2526 and 2540 emready2 1 as #14.2, grid size
    3035 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 
    3036 Opened 6a. combination of 2526 and 2540 emready2 2 as #14.3, grid size
    3037 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 
    3038 Opened 6a. combination of 2526 and 2540 emready2 3 as #14.4, grid size
    3039 443,443,443, pixel 0.5, shown at level 4.95, step 1, values float32 
    3040 Opened 6a. combination of 2526 and 2540 emready2 4 as #14.5, grid size
    3041 443,443,443, pixel 0.5, shown at level 3.46, step 1, values float32 
    3042 Opened 6a. combination of 2526 and 2540 emready2 5 as #14.6, grid size
    3043 443,443,443, pixel 0.5, shown at level 4.45, step 1, values float32 
    3044 Opened 6a. combination of 2526 and 2540 emready2 6 as #14.7, grid size
    3045 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 
    3046 Opened 6a. combination of 2526 and 2540 emready2 7 as #14.8, grid size
    3047 443,443,443, pixel 0.5, shown at level 2.27, step 1, values float32 
    3048 Opened 6b. combination of 2526 and 2540 emready2 copy 0 as #17.1, grid size
    3049 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 
    3050 Opened 6b. combination of 2526 and 2540 emready2 copy 1 as #17.2, grid size
    3051 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 
    3052 Opened 6b. combination of 2526 and 2540 emready2 copy 2 as #17.3, grid size
    3053 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 
    3054 Opened 6b. combination of 2526 and 2540 emready2 copy 3 as #17.4, grid size
    3055 443,443,443, pixel 0.5, shown at level 2.89, step 1, values float32 
    3056 Opened 6b. combination of 2526 and 2540 emready2 copy 4 as #17.5, grid size
    3057 443,443,443, pixel 0.5, shown at level 2.84, step 1, values float32 
    3058 Opened 6b. combination of 2526 and 2540 emready2 copy 5 as #17.6, grid size
    3059 443,443,443, pixel 0.5, shown at level 2.85, step 1, values float32 
    3060 Opened 6b. combination of 2526 and 2540 emready2 copy 6 as #17.7, grid size
    3061 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 
    3062 Opened 6b. combination of 2526 and 2540 emready2 copy 7 as #17.8, grid size
    3063 443,443,443, pixel 0.5, shown at level 2.11, step 1, values float32 
    3064 Opened 10. int1 vvd+imid NU J2527_map_emready2.mrc as #18, grid size
    3065 443,443,443, pixel 0.5, shown at level 0.9, step 1, values float32 
    3066 Opened 11. int1 vvd+imid local J2541_004_volume_map_emready2.mrc as #19, grid
    3067 size 443,443,443, pixel 0.5, shown at level 1.16, step 1, values float32 
    3068 Opened 12. combination of 10 and 11 as #20, grid size 443,443,443, pixel 0.5,
    3069 shown at level 5.05, step 1, values float32 
    3070 Opened 14. int2 vvd+imid NU J2612_map_emready2.mrc as #21, grid size
    3071 438,438,438, pixel 0.5, shown at level 3.83, step 1, values float32 
    3072 Opened 15. int2 vvd+imid local J2614_004_volume_map_emready2.mrc as #23, grid
    3073 size 438,438,438, pixel 0.5, shown at level 1.74, step 1, values float32 
    3074 Opened 16. combination of 2612 and 2614 as #24, grid size 438,438,438, pixel
    3075 0.5, shown at level 5.92, step 1, values float32 
    3076 Opened 18. frustrated vvd+imid NU J2438_map_emready2.mrc as #26, grid size
    3077 443,443,443, pixel 0.5, shown at level 1.18, step 1, values float32 
    3078 Opened 19. frustrated vvd+imid local J2456_004_volume_map_emready2.mrc as #27,
    3079 grid size 443,443,443, pixel 0.5, shown at level 0.895, step 1, values float32 
    3080 Opened 20 combination of 18 and 19 as #28, grid size 443,443,443, pixel 0.5,
    3081 shown at level 6.9, step 1, values float32 
    3082 Opened 12. combination of 10 and 11 0 as #29.1, grid size 443,443,443, pixel
    3083 0.5, shown at level 5.05, step 1, values float32 
    3084 Opened 12. combination of 10 and 11 1 as #29.2, grid size 443,443,443, pixel
    3085 0.5, shown at level 5.67, step 1, values float32 
    3086 Opened 12. combination of 10 and 11 2 as #29.3, grid size 443,443,443, pixel
    3087 0.5, shown at level 5.87, step 1, values float32 
    3088 Opened 12. combination of 10 and 11 3 as #29.4, grid size 443,443,443, pixel
    3089 0.5, shown at level 5.62, step 1, values float32 
    3090 Opened 12. combination of 10 and 11 4 as #29.5, grid size 443,443,443, pixel
    3091 0.5, shown at level 3.84, step 1, values float32 
    3092 Opened 12. combination of 10 and 11 5 as #29.6, grid size 443,443,443, pixel
    3093 0.5, shown at level 4.7, step 1, values float32 
    3094 Opened 12. combination of 10 and 11 6 as #29.7, grid size 443,443,443, pixel
    3095 0.5, shown at level 1.29, step 1, values float32 
    3096 Opened 12. combination of 10 and 11 7 as #29.8, grid size 443,443,443, pixel
    3097 0.5, shown at level 0.584, step 1, values float32 
    3098 Log from Wed Feb 25 16:39:20 2026UCSF ChimeraX version: 1.10.dev202503130118
    3099 (2025-03-13) 
    3100 © 2016-2025 Regents of the University of California. All rights reserved. 
    3101 
    3102 > open "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
    3103 > inhibitor/Figures/Fig 2b final EMready fig maps/0. figure 2 making .cxs"
    3104 
    3105 Opened 2. cryosparc_P341_J1614_localrefine. selected.mrc as #4, grid size
    3106 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 
    3107 Opened 1. cryosparc_P341_J1735_NUrefine selected.mrc as #9, grid size
    3108 300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32 
    3109 Opened 3a. composite_map on EMReady2 maps of 1735 and 1614.ccp4 as #10, grid
    3110 size 300,300,300, pixel 0.833, shown at level 14, step 1, values float32 
    3111 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 0 as #13.1, grid
    3112 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3113 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 1 as #13.2, grid
    3114 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3115 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 2 as #13.3, grid
    3116 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3117 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 3 as #13.4, grid
    3118 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3119 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 4 as #13.5, grid
    3120 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3121 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 5 as #13.6, grid
    3122 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3123 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 6 as #13.7, grid
    3124 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3125 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 7 as #13.8, grid
    3126 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3127 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 8 as #13.9, grid
    3128 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3129 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 9 as #13.10, grid
    3130 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3131 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 10 as #13.11, grid
    3132 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3133 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 11 as #13.12, grid
    3134 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3135 Opened 4. open- vvd+imid NU J2526_map_emready2.mrc as #1, grid size
    3136 443,443,443, pixel 0.5, shown at level 1.01, step 1, values float32 
    3137 Opened 5. open- vvd+imid local J2540_005_volume_map_emready2.mrc as #2, grid
    3138 size 443,443,443, pixel 0.5, shown at level 1.2, step 1, values float32 
    3139 Opened 6a. combination of 2526 and 2540 emready2 as #3, grid size 443,443,443,
    3140 pixel 0.5, shown at level 6.02, step 1, values float32 
    3141 Opened 7. Clsoed- vvd+imid NU J2528_map_emready2.mrc as #5, grid size
    3142 443,443,443, pixel 0.5, shown at level 2.31, step 1, values float32 
    3143 Opened 8. Closed- vvd+imid local J2544_007_volume_map_emready2.mrc as #7, grid
    3144 size 443,443,443, pixel 0.5, shown at level 2.03, step 1, values float32 
    3145 Opened 9a. combination of 2528 and 2544 emready2 as #8, grid size 443,443,443,
    3146 pixel 0.5, shown at level 5.07, step 1, values float32 
    3147 Opened 6b. combination of 2526 and 2540 emready2 copy as #16, grid size
    3148 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 
    3149 Opened 6a. combination of 2526 and 2540 emready2 0 as #14.1, grid size
    3150 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 
    3151 Opened 6a. combination of 2526 and 2540 emready2 1 as #14.2, grid size
    3152 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 
    3153 Opened 6a. combination of 2526 and 2540 emready2 2 as #14.3, grid size
    3154 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 
    3155 Opened 6a. combination of 2526 and 2540 emready2 3 as #14.4, grid size
    3156 443,443,443, pixel 0.5, shown at level 4.95, step 1, values float32 
    3157 Opened 6a. combination of 2526 and 2540 emready2 4 as #14.5, grid size
    3158 443,443,443, pixel 0.5, shown at level 3.46, step 1, values float32 
    3159 Opened 6a. combination of 2526 and 2540 emready2 5 as #14.6, grid size
    3160 443,443,443, pixel 0.5, shown at level 4.45, step 1, values float32 
    3161 Opened 6a. combination of 2526 and 2540 emready2 6 as #14.7, grid size
    3162 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 
    3163 Opened 6a. combination of 2526 and 2540 emready2 7 as #14.8, grid size
    3164 443,443,443, pixel 0.5, shown at level 2.27, step 1, values float32 
    3165 Opened 6b. combination of 2526 and 2540 emready2 copy 0 as #17.1, grid size
    3166 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 
    3167 Opened 6b. combination of 2526 and 2540 emready2 copy 1 as #17.2, grid size
    3168 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 
    3169 Opened 6b. combination of 2526 and 2540 emready2 copy 2 as #17.3, grid size
    3170 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 
    3171 Opened 6b. combination of 2526 and 2540 emready2 copy 3 as #17.4, grid size
    3172 443,443,443, pixel 0.5, shown at level 2.89, step 1, values float32 
    3173 Opened 6b. combination of 2526 and 2540 emready2 copy 4 as #17.5, grid size
    3174 443,443,443, pixel 0.5, shown at level 2.84, step 1, values float32 
    3175 Opened 6b. combination of 2526 and 2540 emready2 copy 5 as #17.6, grid size
    3176 443,443,443, pixel 0.5, shown at level 2.85, step 1, values float32 
    3177 Opened 6b. combination of 2526 and 2540 emready2 copy 6 as #17.7, grid size
    3178 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 
    3179 Opened 6b. combination of 2526 and 2540 emready2 copy 7 as #17.8, grid size
    3180 443,443,443, pixel 0.5, shown at level 2.11, step 1, values float32 
    3181 Opened 10. int1 vvd+imid NU J2527_map_emready2.mrc as #18, grid size
    3182 443,443,443, pixel 0.5, shown at level 0.9, step 1, values float32 
    3183 Opened 11. int1 vvd+imid local J2541_004_volume_map_emready2.mrc as #19, grid
    3184 size 443,443,443, pixel 0.5, shown at level 1.16, step 1, values float32 
    3185 Opened 12. combination of 10 and 11 as #20, grid size 443,443,443, pixel 0.5,
    3186 shown at level 4.96, step 1, values float32 
    3187 Opened 14. int2 vvd+imid NU J2612_map_emready2.mrc as #21, grid size
    3188 438,438,438, pixel 0.5, shown at level 3.83, step 1, values float32 
    3189 Opened 15. int2 vvd+imid local J2614_004_volume_map_emready2.mrc as #23, grid
    3190 size 438,438,438, pixel 0.5, shown at level 1.74, step 1, values float32 
    3191 Opened 16. combination of 2612 and 2614 as #24, grid size 438,438,438, pixel
    3192 0.5, shown at level 5.92, step 1, values float32 
    3193 Opened 18. frustrated vvd+imid NU J2438_map_emready2.mrc as #26, grid size
    3194 443,443,443, pixel 0.5, shown at level 1.18, step 1, values float32 
    3195 Opened 19. frustrated vvd+imid local J2456_004_volume_map_emready2.mrc as #27,
    3196 grid size 443,443,443, pixel 0.5, shown at level 0.895, step 1, values float32 
    3197 Opened 20 combination of 18 and 19 as #28, grid size 443,443,443, pixel 0.5,
    3198 shown at level 6.9, step 1, values float32 
    3199 Log from Wed Feb 25 16:20:52 2026UCSF ChimeraX version: 1.10.dev202503130118
    3200 (2025-03-13) 
    3201 © 2016-2025 Regents of the University of California. All rights reserved. 
    3202 
    3203 > open "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
    3204 > inhibitor/Figures/Fig 2b final EMready fig maps/0. figure 2 making .cxs"
    3205 
    3206 Opened 2. cryosparc_P341_J1614_localrefine. selected.mrc as #4, grid size
    3207 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 
    3208 Opened 1. cryosparc_P341_J1735_NUrefine selected.mrc as #9, grid size
    3209 300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32 
    3210 Opened 3a. composite_map on EMReady2 maps of 1735 and 1614.ccp4 as #10, grid
    3211 size 300,300,300, pixel 0.833, shown at level 14, step 1, values float32 
    3212 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 0 as #13.1, grid
    3213 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3214 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 1 as #13.2, grid
    3215 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3216 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 2 as #13.3, grid
    3217 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3218 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 3 as #13.4, grid
    3219 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3220 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 4 as #13.5, grid
    3221 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3222 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 5 as #13.6, grid
    3223 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3224 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 6 as #13.7, grid
    3225 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3226 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 7 as #13.8, grid
    3227 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3228 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 8 as #13.9, grid
    3229 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3230 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 9 as #13.10, grid
    3231 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3232 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 10 as #13.11, grid
    3233 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3234 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 11 as #13.12, grid
    3235 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3236 Opened 4. open- vvd+imid NU J2526_map_emready2.mrc as #1, grid size
    3237 443,443,443, pixel 0.5, shown at level 1.01, step 1, values float32 
    3238 Opened 5. open- vvd+imid local J2540_005_volume_map_emready2.mrc as #2, grid
    3239 size 443,443,443, pixel 0.5, shown at level 1.2, step 1, values float32 
    3240 Opened 6a. combination of 2526 and 2540 emready2 as #3, grid size 443,443,443,
    3241 pixel 0.5, shown at level 6.02, step 1, values float32 
    3242 Opened 7. Clsoed- vvd+imid NU J2528_map_emready2.mrc as #5, grid size
    3243 443,443,443, pixel 0.5, shown at level 2.31, step 1, values float32 
    3244 Opened 8. Closed- vvd+imid local J2544_007_volume_map_emready2.mrc as #7, grid
    3245 size 443,443,443, pixel 0.5, shown at level 2.03, step 1, values float32 
    3246 Opened 9a. combination of 2528 and 2544 emready2 as #8, grid size 443,443,443,
    3247 pixel 0.5, shown at level 5.07, step 1, values float32 
    3248 Opened 6b. combination of 2526 and 2540 emready2 copy as #16, grid size
    3249 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 
    3250 Opened 6a. combination of 2526 and 2540 emready2 0 as #14.1, grid size
    3251 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 
    3252 Opened 6a. combination of 2526 and 2540 emready2 1 as #14.2, grid size
    3253 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 
    3254 Opened 6a. combination of 2526 and 2540 emready2 2 as #14.3, grid size
    3255 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 
    3256 Opened 6a. combination of 2526 and 2540 emready2 3 as #14.4, grid size
    3257 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 
    3258 Opened 6a. combination of 2526 and 2540 emready2 4 as #14.5, grid size
    3259 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 
    3260 Opened 6a. combination of 2526 and 2540 emready2 5 as #14.6, grid size
    3261 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 
    3262 Opened 6a. combination of 2526 and 2540 emready2 6 as #14.7, grid size
    3263 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 
    3264 Opened 6a. combination of 2526 and 2540 emready2 7 as #14.8, grid size
    3265 443,443,443, pixel 0.5, shown at level 6.22, step 1, values float32 
    3266 Opened 6b. combination of 2526 and 2540 emready2 copy 0 as #17.1, grid size
    3267 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 
    3268 Opened 6b. combination of 2526 and 2540 emready2 copy 1 as #17.2, grid size
    3269 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 
    3270 Opened 6b. combination of 2526 and 2540 emready2 copy 2 as #17.3, grid size
    3271 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 
    3272 Opened 6b. combination of 2526 and 2540 emready2 copy 3 as #17.4, grid size
    3273 443,443,443, pixel 0.5, shown at level 2.89, step 1, values float32 
    3274 Opened 6b. combination of 2526 and 2540 emready2 copy 4 as #17.5, grid size
    3275 443,443,443, pixel 0.5, shown at level 2.84, step 1, values float32 
    3276 Opened 6b. combination of 2526 and 2540 emready2 copy 5 as #17.6, grid size
    3277 443,443,443, pixel 0.5, shown at level 2.85, step 1, values float32 
    3278 Opened 6b. combination of 2526 and 2540 emready2 copy 6 as #17.7, grid size
    3279 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 
    3280 Opened 6b. combination of 2526 and 2540 emready2 copy 7 as #17.8, grid size
    3281 443,443,443, pixel 0.5, shown at level 2.11, step 1, values float32 
    3282 Opened 10. int1 vvd+imid NU J2527_map_emready2.mrc as #18, grid size
    3283 443,443,443, pixel 0.5, shown at level 0.9, step 1, values float32 
    3284 Opened 11. int1 vvd+imid local J2541_004_volume_map_emready2.mrc as #19, grid
    3285 size 443,443,443, pixel 0.5, shown at level 1.16, step 1, values float32 
    3286 Opened 12. combination of 10 and 11 as #20, grid size 443,443,443, pixel 0.5,
    3287 shown at level 4.96, step 1, values float32 
    3288 Opened 14. int2 vvd+imid NU J2612_map_emready2.mrc as #21, grid size
    3289 438,438,438, pixel 0.5, shown at level 3.83, step 1, values float32 
    3290 Opened 15. int2 vvd+imid local J2614_004_volume_map_emready2.mrc as #23, grid
    3291 size 438,438,438, pixel 0.5, shown at level 1.74, step 1, values float32 
    3292 Opened 16. combination of 2612 and 2614 as #24, grid size 438,438,438, pixel
    3293 0.5, shown at level 5.92, step 1, values float32 
    3294 Opened 18. frustrated vvd+imid NU J2438_map_emready2.mrc as #26, grid size
    3295 443,443,443, pixel 0.5, shown at level 1.18, step 1, values float32 
    3296 Opened 19. frustrated vvd+imid local J2456_004_volume_map_emready2.mrc as #27,
    3297 grid size 443,443,443, pixel 0.5, shown at level 0.895, step 1, values float32 
    3298 Opened 20 combination of 18 and 19 as #28, grid size 443,443,443, pixel 0.5,
    3299 shown at level 6.9, step 1, values float32 
    3300 Log from Wed Feb 25 16:06:42 2026UCSF ChimeraX version: 1.10.dev202503130118
    3301 (2025-03-13) 
    3302 © 2016-2025 Regents of the University of California. All rights reserved. 
    3303 
    3304 > open "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
    3305 > inhibitor/Figures/Fig 2b final EMready fig maps/0. figure 2 making .cxs"
    3306 
    3307 Opened 2. cryosparc_P341_J1614_localrefine. selected.mrc as #4, grid size
    3308 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 
    3309 Opened 1. cryosparc_P341_J1735_NUrefine selected.mrc as #9, grid size
    3310 300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32 
    3311 Opened 3a. composite_map on EMReady2 maps of 1735 and 1614.ccp4 as #10, grid
    3312 size 300,300,300, pixel 0.833, shown at level 14, step 1, values float32 
    3313 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 0 as #13.1, grid
    3314 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3315 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 1 as #13.2, grid
    3316 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3317 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 2 as #13.3, grid
    3318 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3319 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 3 as #13.4, grid
    3320 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3321 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 4 as #13.5, grid
    3322 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3323 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 5 as #13.6, grid
    3324 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3325 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 6 as #13.7, grid
    3326 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3327 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 7 as #13.8, grid
    3328 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3329 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 8 as #13.9, grid
    3330 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3331 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 9 as #13.10, grid
    3332 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3333 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 10 as #13.11, grid
    3334 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3335 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 11 as #13.12, grid
    3336 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3337 Opened 4. open- vvd+imid NU J2526_map_emready2.mrc as #1, grid size
    3338 443,443,443, pixel 0.5, shown at level 1.01, step 1, values float32 
    3339 Opened 5. open- vvd+imid local J2540_005_volume_map_emready2.mrc as #2, grid
    3340 size 443,443,443, pixel 0.5, shown at level 1.2, step 1, values float32 
    3341 Opened 6a. combination of 2526 and 2540 emready2 as #3, grid size 443,443,443,
    3342 pixel 0.5, shown at level 6.02, step 1, values float32 
    3343 Opened 7. Clsoed- vvd+imid NU J2528_map_emready2.mrc as #5, grid size
    3344 443,443,443, pixel 0.5, shown at level 2.31, step 1, values float32 
    3345 Opened 8. Closed- vvd+imid local J2544_007_volume_map_emready2.mrc as #7, grid
    3346 size 443,443,443, pixel 0.5, shown at level 2.03, step 1, values float32 
    3347 Opened 9a. combination of 2528 and 2544 emready2 as #8, grid size 443,443,443,
    3348 pixel 0.5, shown at level 5.07, step 1, values float32 
    3349 Opened 6b. combination of 2526 and 2540 emready2 copy as #16, grid size
    3350 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 
    3351 Opened 6a. combination of 2526 and 2540 emready2 0 as #14.1, grid size
    3352 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 
    3353 Opened 6a. combination of 2526 and 2540 emready2 1 as #14.2, grid size
    3354 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 
    3355 Opened 6a. combination of 2526 and 2540 emready2 2 as #14.3, grid size
    3356 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 
    3357 Opened 6a. combination of 2526 and 2540 emready2 3 as #14.4, grid size
    3358 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 
    3359 Opened 6a. combination of 2526 and 2540 emready2 4 as #14.5, grid size
    3360 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 
    3361 Opened 6a. combination of 2526 and 2540 emready2 5 as #14.6, grid size
    3362 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 
    3363 Opened 6a. combination of 2526 and 2540 emready2 6 as #14.7, grid size
    3364 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 
    3365 Opened 6a. combination of 2526 and 2540 emready2 7 as #14.8, grid size
    3366 443,443,443, pixel 0.5, shown at level 6.22, step 1, values float32 
    3367 Opened 6b. combination of 2526 and 2540 emready2 copy 0 as #17.1, grid size
    3368 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 
    3369 Opened 6b. combination of 2526 and 2540 emready2 copy 1 as #17.2, grid size
    3370 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 
    3371 Opened 6b. combination of 2526 and 2540 emready2 copy 2 as #17.3, grid size
    3372 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 
    3373 Opened 6b. combination of 2526 and 2540 emready2 copy 3 as #17.4, grid size
    3374 443,443,443, pixel 0.5, shown at level 2.89, step 1, values float32 
    3375 Opened 6b. combination of 2526 and 2540 emready2 copy 4 as #17.5, grid size
    3376 443,443,443, pixel 0.5, shown at level 2.84, step 1, values float32 
    3377 Opened 6b. combination of 2526 and 2540 emready2 copy 5 as #17.6, grid size
    3378 443,443,443, pixel 0.5, shown at level 2.85, step 1, values float32 
    3379 Opened 6b. combination of 2526 and 2540 emready2 copy 6 as #17.7, grid size
    3380 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 
    3381 Opened 6b. combination of 2526 and 2540 emready2 copy 7 as #17.8, grid size
    3382 443,443,443, pixel 0.5, shown at level 2.11, step 1, values float32 
    3383 Opened 10. int1 vvd+imid NU J2527_map_emready2.mrc as #18, grid size
    3384 443,443,443, pixel 0.5, shown at level 0.9, step 1, values float32 
    3385 Opened 11. int1 vvd+imid local J2541_004_volume_map_emready2.mrc as #19, grid
    3386 size 443,443,443, pixel 0.5, shown at level 1.16, step 1, values float32 
    3387 Opened 12. combination of 10 and 11 as #20, grid size 443,443,443, pixel 0.5,
    3388 shown at level 0.862, step 1, values float32 
    3389 Log from Tue Feb 24 16:13:45 2026UCSF ChimeraX version: 1.10.dev202503130118
    3390 (2025-03-13) 
    3391 © 2016-2025 Regents of the University of California. All rights reserved. 
    3392 
    3393 > open "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
    3394 > inhibitor/ChimeraX/fig 2.cxs"
    3395 
    3396 Opened cryosparc_P341_J1614_localrefine. selected.mrc as #4, grid size
    3397 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 
    3398 Opened cryosparc_P341_J1735_NUrefine selected.mrc as #9, grid size
    3399 300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32 
    3400 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 as #10, grid size
    3401 300,300,300, pixel 0.833, shown at level 14, step 1, values float32 
    3402 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 0 as #13.1, grid
    3403 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3404 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 1 as #13.2, grid
    3405 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3406 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 2 as #13.3, grid
    3407 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3408 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 3 as #13.4, grid
    3409 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3410 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 4 as #13.5, grid
    3411 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3412 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 5 as #13.6, grid
    3413 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3414 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 6 as #13.7, grid
    3415 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3416 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 7 as #13.8, grid
    3417 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3418 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 8 as #13.9, grid
    3419 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3420 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 9 as #13.10, grid
    3421 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3422 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 10 as #13.11, grid
    3423 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3424 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 11 as #13.12, grid
    3425 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3426 Log from Thu Jul 24 11:26:36 2025UCSF ChimeraX version: 1.10.dev202503130118
    3427 (2025-03-13) 
    3428 © 2016-2025 Regents of the University of California. All rights reserved. 
    3429 
    3430 > open "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data,
    3431 > presentation, and work/DDB1:CRBN with vvd compound processing/0.paper
    3432 > writing/figure making/fig 2.cxs"
    3433 
    3434 Opened cryosparc_P341_J1537_local refine on 1464.mrc as #1, grid size
    3435 300,300,300, pixel 0.833, shown at level 0.227, step 1, values float32 
    3436 Opened cryosparc_P341_J1554_local refine on 1550.mrc as #2, grid size
    3437 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 
    3438 Opened cryosparc_P341_J1575_map_sharp.mrc deepEM as #3, grid size 300,300,300,
    3439 pixel 0.833, shown at level 0.253, step 1, values float32 
    3440 Opened cryosparc_P341_J1614_localrefine. selected.mrc as #4, grid size
    3441 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 
    3442 Opened cryosparc_P341_J1642_local refine.mrc as #5, grid size 300,300,300,
    3443 pixel 0.833, shown at level 0.304, step 1, values float32 
    3444 Opened cryosparc_P341_J1464_NU refine.mrc as #6, grid size 300,300,300, pixel
    3445 0.833, shown at level 0.158, step 1, values float32 
    3446 Opened cryosparc_P341_J1473_localrefine.mrc as #7, grid size 300,300,300,
    3447 pixel 0.833, shown at level 0.304, step 1, values float32 
    3448 Opened cryosparc_P341_J1550_Nurefine.mrc as #8, grid size 300,300,300, pixel
    3449 0.833, shown at level 0.158, step 1, values float32 
    3450 Opened cryosparc_P341_J1735_NUrefine selected.mrc as #9, grid size
    3451 300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32 
    3452 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 as #10, grid size
    3453 300,300,300, pixel 0.833, shown at level 14, step 1, values float32 
    3454 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 0 as #13.1, grid
    3455 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3456 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 1 as #13.2, grid
    3457 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3458 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 2 as #13.3, grid
    3459 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3460 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 3 as #13.4, grid
    3461 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3462 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 4 as #13.5, grid
    3463 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3464 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 5 as #13.6, grid
    3465 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3466 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 6 as #13.7, grid
    3467 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3468 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 7 as #13.8, grid
    3469 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3470 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 8 as #13.9, grid
    3471 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3472 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 9 as #13.10, grid
    3473 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3474 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 10 as #13.11, grid
    3475 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3476 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 11 as #13.12, grid
    3477 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3478 Log from Thu Jul 24 01:33:11 2025UCSF ChimeraX version: 1.10.dev202503130118
    3479 (2025-03-13) 
    3480 © 2016-2025 Regents of the University of California. All rights reserved. 
    3481 
    3482 > open "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data,
    3483 > presentation, and work/DDB1:CRBN with vvd compound processing/0.paper
    3484 > writing/figure making /fig 2.cxs"
    3485 
    3486 Opened cryosparc_P341_J1537_local refine on 1464.mrc as #1, grid size
    3487 300,300,300, pixel 0.833, shown at level 0.227, step 1, values float32 
    3488 Opened cryosparc_P341_J1554_local refine on 1550.mrc as #2, grid size
    3489 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 
    3490 Opened cryosparc_P341_J1575_map_sharp.mrc deepEM as #3, grid size 300,300,300,
    3491 pixel 0.833, shown at level 0.253, step 1, values float32 
    3492 Opened cryosparc_P341_J1614_localrefine. selected.mrc as #4, grid size
    3493 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 
    3494 Opened cryosparc_P341_J1642_local refine.mrc as #5, grid size 300,300,300,
    3495 pixel 0.833, shown at level 0.304, step 1, values float32 
    3496 Opened cryosparc_P341_J1464_NU refine.mrc as #6, grid size 300,300,300, pixel
    3497 0.833, shown at level 0.158, step 1, values float32 
    3498 Opened cryosparc_P341_J1473_localrefine.mrc as #7, grid size 300,300,300,
    3499 pixel 0.833, shown at level 0.304, step 1, values float32 
    3500 Opened cryosparc_P341_J1550_Nurefine.mrc as #8, grid size 300,300,300, pixel
    3501 0.833, shown at level 0.158, step 1, values float32 
    3502 Opened cryosparc_P341_J1735_NUrefine selected.mrc as #9, grid size
    3503 300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32 
    3504 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 as #10, grid size
    3505 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3506 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 0 as #13.1, grid
    3507 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3508 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 1 as #13.2, grid
    3509 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3510 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 2 as #13.3, grid
    3511 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3512 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 3 as #13.4, grid
    3513 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3514 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 4 as #13.5, grid
    3515 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3516 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 5 as #13.6, grid
    3517 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3518 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 6 as #13.7, grid
    3519 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3520 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 7 as #13.8, grid
    3521 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3522 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 8 as #13.9, grid
    3523 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3524 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 9 as #13.10, grid
    3525 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3526 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 10 as #13.11, grid
    3527 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3528 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 11 as #13.12, grid
    3529 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3530 Log from Thu Jul 24 00:56:27 2025UCSF ChimeraX version: 1.10.dev202503130118
    3531 (2025-03-13) 
    3532 © 2016-2025 Regents of the University of California. All rights reserved. 
    3533 
    3534 > open "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data,
    3535 > presentation, and work/DDB1:CRBN with vvd compound processing/figure for
    3536 > Gabe modified/vvd figure making.cxs"
    3537 
    3538 Opened cryosparc_P341_J1537_local refine on 1464.mrc as #1, grid size
    3539 300,300,300, pixel 0.833, shown at level 0.227, step 1, values float32 
    3540 Opened cryosparc_P341_J1554_local refine on 1550.mrc as #2, grid size
    3541 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 
    3542 Opened cryosparc_P341_J1575_map_sharp.mrc deepEM as #3, grid size 300,300,300,
    3543 pixel 0.833, shown at level 0.253, step 1, values float32 
    3544 Opened cryosparc_P341_J1614_localrefine. selected.mrc as #4, grid size
    3545 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 
    3546 Opened cryosparc_P341_J1642_local refine.mrc as #5, grid size 300,300,300,
    3547 pixel 0.833, shown at level 0.304, step 1, values float32 
    3548 Opened cryosparc_P341_J1464_NU refine.mrc as #6, grid size 300,300,300, pixel
    3549 0.833, shown at level 0.158, step 1, values float32 
    3550 Opened cryosparc_P341_J1473_localrefine.mrc as #7, grid size 300,300,300,
    3551 pixel 0.833, shown at level 0.304, step 1, values float32 
    3552 Opened cryosparc_P341_J1550_Nurefine.mrc as #8, grid size 300,300,300, pixel
    3553 0.833, shown at level 0.158, step 1, values float32 
    3554 Opened cryosparc_P341_J1735_NUrefine selected.mrc as #9, grid size
    3555 300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32 
    3556 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 as #10, grid size
    3557 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    3558 Log from Tue Apr 29 15:52:59 2025UCSF ChimeraX version: 1.10.dev202503130118
    3559 (2025-03-13) 
    3560 © 2016-2025 Regents of the University of California. All rights reserved. 
    3561 
    3562 > open "/Users/zrizvi/Desktop/vvd figure making.cxs"
    3563 
    3564 Opened cryosparc_P341_J1537_local refine on 1464.mrc as #1, grid size
    3565 300,300,300, pixel 0.833, shown at level 0.227, step 1, values float32 
    3566 Opened cryosparc_P341_J1554_local refine on 1550.mrc as #2, grid size
    3567 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 
    3568 Opened cryosparc_P341_J1575_map_sharp.mrc deepEM as #3, grid size 300,300,300,
    3569 pixel 0.833, shown at level 0.253, step 1, values float32 
    3570 Opened cryosparc_P341_J1614_localrefine. selected.mrc as #4, grid size
    3571 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 
    3572 Opened cryosparc_P341_J1642_local refine.mrc as #5, grid size 300,300,300,
    3573 pixel 0.833, shown at level 0.304, step 1, values float32 
    3574 Opened cryosparc_P341_J1464_NU refine.mrc as #6, grid size 300,300,300, pixel
    3575 0.833, shown at level 0.158, step 1, values float32 
    3576 Opened cryosparc_P341_J1473_localrefine.mrc as #7, grid size 300,300,300,
    3577 pixel 0.833, shown at level 0.304, step 1, values float32 
    3578 Opened cryosparc_P341_J1550_Nurefine.mrc as #8, grid size 300,300,300, pixel
    3579 0.833, shown at level 0.158, step 1, values float32 
    3580 Opened cryosparc_P341_J1735_NUrefine selected.mrc as #9, grid size
    3581 300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32 
    3582 Log from Tue Apr 29 13:11:33 2025UCSF ChimeraX version: 1.10.dev202503130118
    3583 (2025-03-13) 
    3584 © 2016-2025 Regents of the University of California. All rights reserved. 
    3585 How to cite UCSF ChimeraX 
    3586 
    3587 > open /Users/zrizvi/Downloads/cryosparc_P341_J1537_004_volume_map.mrc
    3588 
    3589 Opened cryosparc_P341_J1537_004_volume_map.mrc as #1, grid size 300,300,300,
    3590 pixel 0.833, shown at level 0.0281, step 2, values float32 
    3591 
    3592 > open /Users/zrizvi/Downloads/cryosparc_P341_J1554_005_volume_map.mrc
    3593 
    3594 Opened cryosparc_P341_J1554_005_volume_map.mrc as #2, grid size 300,300,300,
    3595 pixel 0.833, shown at level 0.0434, step 2, values float32 
    3596 
    3597 > open /Users/zrizvi/Downloads/cryosparc_P341_J1575_map_sharp.mrc
    3598 
    3599 Opened cryosparc_P341_J1575_map_sharp.mrc as #3, grid size 300,300,300, pixel
    3600 0.833, shown at level 0.00032, step 2, values float32 
    3601 
    3602 > open /Users/zrizvi/Downloads/cryosparc_P341_J1614_005_volume_map.mrc
    3603 
    3604 Opened cryosparc_P341_J1614_005_volume_map.mrc as #4, grid size 300,300,300,
    3605 pixel 0.833, shown at level 0.0429, step 2, values float32 
    3606 
    3607 > open /Users/zrizvi/Downloads/cryosparc_P341_J1642_005_volume_map.mrc
    3608 
    3609 Opened cryosparc_P341_J1642_005_volume_map.mrc as #5, grid size 300,300,300,
    3610 pixel 0.833, shown at level 0.0424, step 2, values float32 
    3611 
    3612 > open "/Users/zrizvi/Downloads/cryosparc_P341_J1464_008_volume_map (1).mrc"
    3613 
    3614 Opened cryosparc_P341_J1464_008_volume_map (1).mrc as #6, grid size
    3615 300,300,300, pixel 0.833, shown at level 0.0314, step 2, values float32 
    3616 
    3617 > open "/Users/zrizvi/Downloads/cryosparc_P341_J1473_004_volume_map (1).mrc"
    3618 
    3619 Opened cryosparc_P341_J1473_004_volume_map (1).mrc as #7, grid size
    3620 300,300,300, pixel 0.833, shown at level 0.0324, step 2, values float32 
    3621 
    3622 > volume #1 step 1
    3623 
    3624 > volume #2 step 1
    3625 
    3626 > volume #3 step 1
    3627 
    3628 > volume #4 step 1
    3629 
    3630 > volume #5 step 1
    3631 
    3632 > volume #6 step 1
    3633 
    3634 > volume #7 step 1
    3635 
    3636 > hide #!2 models
    3637 
    3638 > hide #!3 models
    3639 
    3640 > hide #!4 models
    3641 
    3642 > hide #!5 models
    3643 
    3644 > hide #!6 models
    3645 
    3646 > hide #!7 models
    3647 
    3648 > volume #1 level 0.201
    3649 
    3650 > show #!2 models
    3651 
    3652 > volume #2 level 0.2044
    3653 
    3654 > show #!6 models
    3655 
    3656 > volume #6 level 0.1538
    3657 
    3658 > rename #2 "cryosparc_P341_J1554_0local refine on 1464.mrc"
    3659 
    3660 > rename #2 "cryosparc_P341_J1554_local refine on 1464.mrc"
    3661 
    3662 > rename #1 "cryosparc_P341_J1537_local refine on 1464.mrc"
    3663 
    3664 > rename #2 "cryosparc_P341_J1554_local refine on 1550.mrc"
    3665 
    3666 > open "/Users/zrizvi/Downloads/cryosparc_P341_J1550_006_volume_map (2).mrc"
    3667 
    3668 Opened cryosparc_P341_J1550_006_volume_map (2).mrc as #8, grid size
    3669 300,300,300, pixel 0.833, shown at level 0.0282, step 2, values float32 
    3670 
    3671 > volume #8 step 1
    3672 
    3673 > volume #8 level 0.1757
    3674 
    3675 > hide #!8 models
    3676 
    3677 > hide #!2 models
    3678 
    3679 > hide #!6 models
    3680 
    3681 > show #!6 models
    3682 
    3683 > hide #!1 models
    3684 
    3685 > show #!1 models
    3686 
    3687 > hide #!6 models
    3688 
    3689 > show #!6 models
    3690 
    3691 > hide #!1 models
    3692 
    3693 > show #!1 models
    3694 
    3695 > hide #!6 models
    3696 
    3697 > open /Users/zrizvi/Downloads/cryosparc_P341_J1735_007_volume_map.mrc
    3698 
    3699 Opened cryosparc_P341_J1735_007_volume_map.mrc as #9, grid size 300,300,300,
    3700 pixel 0.833, shown at level 0.0299, step 2, values float32 
    3701 
    3702 > volume #9 step 1
    3703 
    3704 > volume #9 level 0.1746
    3705 
    3706 > tile
    3707 
    3708 2 models tiled 
    3709 
    3710 > show #!2 models
    3711 
    3712 > show #!3 models
    3713 
    3714 > show #!4 models
    3715 
    3716 > show #!5 models
    3717 
    3718 > show #!6 models
    3719 
    3720 > show #!7 models
    3721 
    3722 > show #!8 models
    3723 
    3724 > tile
    3725 
    3726 9 models tiled 
    3727 
    3728 > hide #!3 models
    3729 
    3730 > show #!3 models
    3731 
    3732 > volume #3 level 0.2531
    3733 
    3734 > volume #4 level 0.2407
    3735 
    3736 > volume #5 level 0.2597
    3737 
    3738 > volume #6 level 0.2049
    3739 
    3740 > volume #6 level 0.1582
    3741 
    3742 > volume #7 level 0.1171
    3743 
    3744 > volume #7 level 0.2217
    3745 
    3746 > volume #8 level 0.2374
    3747 
    3748 > volume #9 level 0.2058
    3749 
    3750 > rename #3 "cryosparc_P341_J1575_map_sharp.mrc deepEM"
    3751 
    3752 > rename #4 cryosparc_P341_J1614_localrefine.mrc
    3753 
    3754 > rename #5 "cryosparc_P341_J1642_local refine.mrc"
    3755 
    3756 > rename #6 "cryosparc_P341_J1464_NU refine.mrc"
    3757 
    3758 > rename #7 cryosparc_P341_J1473_localrefine.mrc
    3759 
    3760 > rename #8 cryosparc_P341_J1550_Nurefine).mrc
    3761 
    3762 > rename #8 cryosparc_P341_J1550_Nurefine.mrc
    3763 
    3764 > rename #9 cryosparc_P341_J1735_NUrefine.mrc
    3765 
    3766 > hide #!1 models
    3767 
    3768 > hide #!2 models
    3769 
    3770 > hide #!3 models
    3771 
    3772 > hide #!4 models
    3773 
    3774 > hide #!5 models
    3775 
    3776 > hide #!7 models
    3777 
    3778 > ~tile
    3779 
    3780 > hide #!6 models
    3781 
    3782 > hide #!8 models
    3783 
    3784 > hide #!9 models
    3785 
    3786 > show #!6 models
    3787 
    3788 > hide #!6 models
    3789 
    3790 > show #!8 models
    3791 
    3792 > volume #8 level 0.158
    3793 
    3794 > hide #!8 models
    3795 
    3796 > show #!9 models
    3797 
    3798 > volume #9 level 0.158
    3799 
    3800 > show #!7 models
    3801 
    3802 > show #!6 models
    3803 
    3804 > hide #!7 models
    3805 
    3806 > show #!8 models
    3807 
    3808 > tile
    3809 
    3810 3 models tiled 
    3811 
    3812 > hide #!6 models
    3813 
    3814 > ~tile
    3815 
    3816 > tile
    3817 
    3818 2 models tiled 
    3819 
    3820 > ~tile
    3821 
    3822 > color #9 #99bfe56a models
    3823 
    3824 > color #9 #99bfe56d models
    3825 
    3826 > hide #!8 models
    3827 
    3828 > color #9 #99bfe5ff models
    3829 
    3830 > show #!1 models
    3831 
    3832 > show #!2 models
    3833 
    3834 > show #!4 models
    3835 
    3836 > show #!5 models
    3837 
    3838 > show #!7 models
    3839 
    3840 > ~tile
    3841 
    3842 > hide #!9 models
    3843 
    3844 > tile
    3845 
    3846 5 models tiled 
    3847 
    3848 > volume #1 level 0.2267
    3849 
    3850 > hide #!1 models
    3851 
    3852 > volume #2 level 0.3042
    3853 
    3854 > volume #4 level 0.304
    3855 
    3856 > volume #5 level 0.304
    3857 
    3858 > volume #7 level 0.304
    3859 
    3860 > hide #!7 models
    3861 
    3862 > ~tile
    3863 
    3864 > tile
    3865 
    3866 3 models tiled 
    3867 
    3868 > hide #!5 models
    3869 
    3870 > hide #!2 models
    3871 
    3872 > show #!9 models
    3873 
    3874 > ~tile
    3875 
    3876 > rename #9 "cryosparc_P341_J1735_NUrefine selected.mrc"
    3877 
    3878 > rename #4 "cryosparc_P341_J1614_localrefine. selected.mrc"
    3879 
    3880 > open "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data,
    3881 > presentation, and work/DDB1:CRBN with vvd compound processing/2. processing
    3882 > in coot/vvd.pdb"
    3883 
    3884 > hide #!9 models
    3885 
    3886 > hide #!4 models
    3887 
    3888 > close #10
    3889 
    3890 > show #!4 models
    3891 
    3892 > show #!9 models
    3893 
    3894 > save "/Users/zrizvi/Desktop/vvd figure making.cxs" includeMaps true
    3895 
    3896 ——— End of log from Tue Apr 29 13:11:33 2025 ———
    3897 
    3898 > view name session-start
    3899 
    3900 opened ChimeraX session 
    3901 
    3902 > hide #!4 models
    3903 
    3904 > hide #!9 models
    3905 
    3906 > open "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/ACB manuscript
    3907 > shared folder/4. Results extended/Figure 5/model building/2. With
    3908 > ikaros/with deg47 only/CombineFocusedMaps_71/composite_map.ccp4"
    3909 
    3910 Opened composite_map.ccp4 as #10, grid size 300,300,300, pixel 0.833, shown at
    3911 level 0.744, step 2, values float32 
    3912 
    3913 > volume #10 step 1
    3914 
    3915 > volume #10 level 10.76
    3916 
    3917 > open "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data,
    3918 > presentation, and work/DDB1:CRBN with vvd compound processing/2. processing
    3919 > in coot/8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb"
    3920 
    3921 Chain information for 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb
    3922 #11 
    3923 --- 
    3924 Chain | Description 
    3925 A | No description available 
    3926 B | No description available 
    3927  
    3928 
    3929 > hide #!10 models
    3930 
    3931 > select #11/A
    3932 
    3933 6318 atoms, 6434 bonds, 824 residues, 1 model selected 
    3934 
    3935 > color sel light gray
    3936 
    3937 > select clear
    3938 
    3939 > color #11/A:1-710 light blue
    3940 
    3941 > color #11/A:710-5000 steel blue
    3942 
    3943 > color #11/A:392-709 cornflower blue
    3944 
    3945 > color #11/B:1-190 navajowhite
    3946 
    3947 > color #11/B:191-320 light salmon
    3948 
    3949 > color #11/B:321-500 tomato
    3950 
    3951 > show #!10 models
    3952 
    3953 > volume #10 level 9.956
    3954 
    3955 > select ::name="101"
    3956 
    3957 28 atoms, 30 bonds, 1 residue, 1 model selected 
    3958 
    3959 > color sel lime
    3960 
    3961 > select clear
    3962 
    3963 > color zone #10 near #11 distance 5
    3964 
    3965 > color zone #11 near #10 distance 8
    3966 
    3967 color zone: No surfaces specified. 
    3968 
    3969 > color zone #10 near #11 distance 8
    3970 
    3971 > hide #!11 models
    3972 
    3973 > graphics silhouettes true
    3974 
    3975 > lighting shadows true
    3976 
    3977 > lighting soft
    3978 
    3979 > set bgColor white
    3980 
    3981 > show #!11 models
    3982 
    3983 > hide #!11 models
    3984 
    3985 > rename #10 "composite_map on EMReady2 maps of 1735 and 1614.ccp4"
    3986 
    3987 > save "/Users/zrizvi/Desktop/vvd figure making.cxs" includeMaps true
    3988 
    3989 ——— End of log from Tue Apr 29 15:52:59 2025 ———
    3990 
    3991 > view name session-start
    3992 
    3993 opened ChimeraX session 
    3994 
    3995 > show #!11 models
    3996 
    3997 > hide #!10 models
    3998 
    3999 > show #!10 models
    4000 
    4001 > color #10 #b2b2b2da models
    4002 
    4003 > color #10 #b2b2b2ff models
    4004 
    4005 > color zone #10 near #11 distance 8
    4006 
    4007 > color zone #10 near #11 distance 10
    4008 
    4009 > hide #!11 models
    4010 
    4011 > open "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data,
    4012 > presentation, and work/DDB1:CRBN with vvd compound processing/figure for
    4013 > Gabe modified/vvd.pdb"
    4014 
    4015 > hide #!10 models
    4016 
    4017 > show #!10 models
    4018 
    4019 > close #12
    4020 
    4021 > open "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data,
    4022 > presentation, and work/DDB1:CRBN with vvd compound processing/figure for
    4023 > Gabe modified/final.pdb"
    4024 
    4025 Chain information for final.pdb #12 
    4026 --- 
    4027 Chain | Description 
    4028 B | No description available 
    4029 C | No description available 
    4030  
    4031 
    4032 > mmaker #12 to #11
    4033 
    4034 Computing secondary structure 
    4035 Parameters 
    4036 --- 
    4037 Chain pairing | bb 
    4038 Alignment algorithm | Needleman-Wunsch 
    4039 Similarity matrix | BLOSUM-62 
    4040 SS fraction | 0.3 
    4041 Gap open (HH/SS/other) | 18/18/6 
    4042 Gap extend | 1 
    4043 SS matrix |  |  | H | S | O 
    4044 ---|---|---|--- 
    4045 H | 6 | -9 | -6 
    4046 S |  | 6 | -6 
    4047 O |  |  | 4 
    4048 Iteration cutoff | 2 
    4049  
    4050 Matchmaker 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb, chain A
    4051 (#11) with final.pdb, chain B (#12), sequence alignment score = 3652.5 
    4052 RMSD between 786 pruned atom pairs is 0.524 angstroms; (across all 824 pairs:
    4053 0.911) 
    4054  
    4055 
    4056 > hide #!10 models
    4057 
    4058 > show #!11 models
    4059 
    4060 > hide #!11 models
    4061 
    4062 > hide #!12 models
    4063 
    4064 > show #!11 models
    4065 
    4066 > color #!11 byhetero
    4067 
    4068 > select clear
    4069 
    4070 > show #!12 models
    4071 
    4072 > hide #!12 models
    4073 
    4074 > show #!12 models
    4075 
    4076 > close #12
    4077 
    4078 > open "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data,
    4079 > presentation, and work/DDB1:CRBN with vvd compound processing/figure for
    4080 > Gabe modified/7u8ffinallylinkedtoVVD.pdb"
    4081 
    4082 Chain information for 7u8ffinallylinkedtoVVD.pdb #12 
    4083 --- 
    4084 Chain | Description 
    4085 B | No description available 
    4086 C | No description available 
    4087  
    4088 
    4089 > close #12
    4090 
    4091 > show #!10 models
    4092 
    4093 > hide #!11 models
    4094 
    4095 > camera ortho
    4096 
    4097 > save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data,
    4098 > presentation, and work/DDB1:CRBN with vvd compound processing/0.paper
    4099 > writing/figure making /Figure 2a.png" width 1800 height 1532 supersample 4
    4100 > transparentBackground true
    4101 
    4102 > show #!11 models
    4103 
    4104 > color #10 #b2b2b2c0 models
    4105 
    4106 > color #10 #b2b2b2bf models
    4107 
    4108 > ui tool show "Show Sequence Viewer"
    4109 
    4110 > sequence chain /B
    4111 
    4112 Alignment identifier is 11/B 
    4113 
    4114 > select /B:264
    4115 
    4116 14 atoms, 15 bonds, 1 residue, 1 model selected 
    4117 
    4118 > select /B:264
    4119 
    4120 14 atoms, 15 bonds, 1 residue, 1 model selected 
    4121 
    4122 > select clear
    4123 
    4124 > ui tool show "Side View"
    4125 
    4126 > save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data,
    4127 > presentation, and work/DDB1:CRBN with vvd compound processing/0.paper
    4128 > writing/figure making /Figure 2b.png" width 1800 height 1532 supersample 4
    4129 > transparentBackground true
    4130 
    4131 > open 8cvp
    4132 
    4133 8cvp title: 
    4134 Cereblon-DDB1 in the Apo form [more info...] 
    4135  
    4136 Chain information for 8cvp #12 
    4137 --- 
    4138 Chain | Description | UniProt 
    4139 A | DNA damage-binding protein 1 | DDB1_HUMAN 1-1140 
    4140 B | Protein cereblon | CRBN_HUMAN 1-442 
    4141  
    4142 Non-standard residues in 8cvp #12 
    4143 --- 
    4144 ZN — zinc ion 
    4145  
    4146 
    4147 > mmaker #12 to #11
    4148 
    4149 Computing secondary structure 
    4150 Parameters 
    4151 --- 
    4152 Chain pairing | bb 
    4153 Alignment algorithm | Needleman-Wunsch 
    4154 Similarity matrix | BLOSUM-62 
    4155 SS fraction | 0.3 
    4156 Gap open (HH/SS/other) | 18/18/6 
    4157 Gap extend | 1 
    4158 SS matrix |  |  | H | S | O 
    4159 ---|---|---|--- 
    4160 H | 6 | -9 | -6 
    4161 S |  | 6 | -6 
    4162 O |  |  | 4 
    4163 Iteration cutoff | 2 
    4164  
    4165 Matchmaker 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb, chain A
    4166 (#11) with 8cvp, chain A (#12), sequence alignment score = 5335.5 
    4167 RMSD between 824 pruned atom pairs is 0.011 angstroms; (across all 824 pairs:
    4168 0.011) 
    4169  
    4170 
    4171 > hide #!10 models
    4172 
    4173 > ui tool show "Show Sequence Viewer"
    4174 
    4175 > sequence chain #12/B
    4176 
    4177 Alignment identifier is 12/B 
    4178 
    4179 > select #12/B:264
    4180 
    4181 14 atoms, 15 bonds, 1 residue, 1 model selected 
    4182 
    4183 > select #12/B:264
    4184 
    4185 14 atoms, 15 bonds, 1 residue, 1 model selected 
    4186 
    4187 > show sel atoms
    4188 
    4189 > color #12 darkgrey
    4190 
    4191 > select clear
    4192 
    4193 > show #!10 models
    4194 
    4195 > hide #!11 models
    4196 
    4197 > show #!11 models
    4198 
    4199 > select add #12
    4200 
    4201 10112 atoms, 10284 bonds, 6 pseudobonds, 1485 residues, 4 models selected 
    4202 
    4203 > color (#!12 & sel) cornflower blue
    4204 
    4205 > select clear
    4206 
    4207 > color #12/A:1-710 light blue
    4208 
    4209 > color #12/A:710-5000 steel blue
    4210 
    4211 > color #12/A:392-709 cornflower blue
    4212 
    4213 > color #12/B:1-190 navajowhite
    4214 
    4215 > color #12/B:191-320 light salmon
    4216 
    4217 > color #12/B:321-500 tomato
    4218 
    4219 > hide #!11 models
    4220 
    4221 > show #!11 models
    4222 
    4223 > hide #!12 models
    4224 
    4225 > color #10 #b2b2b2ff models
    4226 
    4227 > ui tool show "Surface Color"
    4228 
    4229 > ui tool show "Surface Zone"
    4230 
    4231 > ui tool show "Volume Viewer"
    4232 
    4233 > ui tool show "Color Zone"
    4234 
    4235 > color zone #10 near #11 distance 3.83
    4236 
    4237 > color single #10
    4238 
    4239 > hide #!11 atoms
    4240 
    4241 > color zone #10 near #11 distance 3.83
    4242 
    4243 > color single #10
    4244 
    4245 > color #10 #b2b2b2d2 models
    4246 
    4247 > color #10 #b2b2b2d1 models
    4248 
    4249 > select ::name="101"
    4250 
    4251 28 atoms, 30 bonds, 1 residue, 1 model selected 
    4252 
    4253 > show sel atoms
    4254 
    4255 > select clear
    4256 
    4257 > select ::name="101"
    4258 
    4259 28 atoms, 30 bonds, 1 residue, 1 model selected 
    4260 
    4261 > color sel lime
    4262 
    4263 > select clear
    4264 
    4265 > hide #!10 models
    4266 
    4267 > select #11/B:264
    4268 
    4269 14 atoms, 15 bonds, 1 residue, 1 model selected 
    4270 
    4271 > show sel atoms
    4272 
    4273 > select clear
    4274 
    4275 > show #!10 models
    4276 
    4277 > ui tool show "Volume Viewer"
    4278 
    4279 > ui tool show "Surface Zone"
    4280 
    4281 > ui tool show "Surface Color"
    4282 
    4283 > ui tool show "Color Zone"
    4284 
    4285 Need to color zone map before it can be split 
    4286 
    4287 [Repeated 1 time(s)]
    4288 
    4289 > color zone #10 near #11 distance 5
    4290 
    4291 > volume splitbyzone #10
    4292 
    4293 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 0 as #13.1, grid
    4294 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    4295 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 1 as #13.2, grid
    4296 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    4297 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 2 as #13.3, grid
    4298 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    4299 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 3 as #13.4, grid
    4300 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    4301 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 4 as #13.5, grid
    4302 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    4303 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 5 as #13.6, grid
    4304 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    4305 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 6 as #13.7, grid
    4306 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    4307 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 7 as #13.8, grid
    4308 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    4309 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 8 as #13.9, grid
    4310 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    4311 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 9 as #13.10, grid
    4312 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    4313 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 10 as #13.11, grid
    4314 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    4315 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 11 as #13.12, grid
    4316 size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 
    4317 
    4318 > select add #13.12
    4319 
    4320 2 models selected 
    4321 
    4322 > hide #!13.11 models
    4323 
    4324 > hide #!13.10 models
    4325 
    4326 > hide #!13.9 models
    4327 
    4328 > hide #!13.8 models
    4329 
    4330 > hide #!13.7 models
    4331 
    4332 > hide #!13.6 models
    4333 
    4334 > hide #!13.5 models
    4335 
    4336 > hide #!13.4 models
    4337 
    4338 > hide #!13.3 models
    4339 
    4340 > hide #!13.2 models
    4341 
    4342 > hide #!13.1 models
    4343 
    4344 > show #!10 models
    4345 
    4346 > color single #10
    4347 
    4348 > hide #!13 models
    4349 
    4350 > show #!13 models
    4351 
    4352 > hide #!13 models
    4353 
    4354 > select add #13
    4355 
    4356 25 models selected 
    4357 
    4358 > select subtract #13
    4359 
    4360 Nothing selected 
    4361 
    4362 > hide #!10 models
    4363 
    4364 > show #!13 models
    4365 
    4366 > show #!10 models
    4367 
    4368 > hide #!10 models
    4369 
    4370 > color #13.2 darkgrey models
    4371 
    4372 > color #13.3 darkgrey models
    4373 
    4374 > color #13.4 darkgrey models
    4375 
    4376 > color #13.5 darkgrey models
    4377 
    4378 > color #13.6 darkgrey models
    4379 
    4380 > color #13.7 darkgrey models
    4381 
    4382 > color #13.8 darkgrey models
    4383 
    4384 > color #13.9 darkgrey models
    4385 
    4386 > color #13.10 darkgrey models
    4387 
    4388 > color #13.11 darkgrey models
    4389 
    4390 > show #!13.1 models
    4391 
    4392 > show #!13.2 models
    4393 
    4394 > show #!13.3 models
    4395 
    4396 > show #!13.4 models
    4397 
    4398 > show #!13.5 models
    4399 
    4400 > show #!13.6 models
    4401 
    4402 > show #!13.7 models
    4403 
    4404 > show #!13.8 models
    4405 
    4406 > show #!13.9 models
    4407 
    4408 > show #!13.10 models
    4409 
    4410 > show #!13.11 models
    4411 
    4412 > select add #13
    4413 
    4414 25 models selected 
    4415 
    4416 > select subtract #13.12
    4417 
    4418 23 models selected 
    4419 
    4420 > combine sel
    4421 
    4422 No structures specified 
    4423 
    4424 > show #!10 models
    4425 
    4426 > hide #!10 models
    4427 
    4428 > show #!10 models
    4429 
    4430 > hide #!13.1 models
    4431 
    4432 > select subtract #13.1
    4433 
    4434 21 models selected 
    4435 
    4436 > select subtract #13.3
    4437 
    4438 19 models selected 
    4439 
    4440 > select add #13
    4441 
    4442 25 models selected 
    4443 
    4444 > select subtract #13
    4445 
    4446 Nothing selected 
    4447 
    4448 > hide #!13.2 models
    4449 
    4450 > hide #!13.3 models
    4451 
    4452 > hide #!13.4 models
    4453 
    4454 > hide #!13.5 models
    4455 
    4456 > hide #!13.6 models
    4457 
    4458 > hide #!13.7 models
    4459 
    4460 > hide #!10 models
    4461 
    4462 > show #!13.1 models
    4463 
    4464 > show #!13.3 models
    4465 
    4466 > hide #!13.3 models
    4467 
    4468 > show #!13.2 models
    4469 
    4470 > show #!13.3 models
    4471 
    4472 > show #!13.4 models
    4473 
    4474 > show #!13.5 models
    4475 
    4476 > show #!13.6 models
    4477 
    4478 > show #!13.7 models
    4479 
    4480 > hide #!11 models
    4481 
    4482 > show #!12 models
    4483 
    4484 > hide #!13 models
    4485 
    4486 > color #!12 byhetero
    4487 
    4488 > hide #!12.2 models
    4489 
    4490 Cell requested for row 12 is out of bounds for table with 27 rows! Resizing
    4491 table model. 
    4492 
    4493 > show #!13 models
    4494 
    4495 > hide #!13.2 models
    4496 
    4497 > hide #!13.1 models
    4498 
    4499 > hide #!13.3 models
    4500 
    4501 > hide #!13.4 models
    4502 
    4503 > hide #!13.5 models
    4504 
    4505 > hide #!13.6 models
    4506 
    4507 > hide #!13.7 models
    4508 
    4509 > hide #!13.9 models
    4510 
    4511 > hide #!13.8 models
    4512 
    4513 > hide #!13.10 models
    4514 
    4515 > hide #!13.11 models
    4516 
    4517 > show #!10 models
    4518 
    4519 > color #10 #b2b2b277 models
    4520 
    4521 > color #10 #b2b2b278 models
    4522 
    4523 > hide #!13.12 models
    4524 
    4525 > show #!13.12 models
    4526 
    4527 > ui tool show "Side View"
    4528 
    4529 > color #13.12 #00ff00db models
    4530 
    4531 > color #13.12 #00ff00b1 models
    4532 
    4533 > color #13.12 #00ff00b0 models
    4534 
    4535 > lighting shadows true intensity 0.5
    4536 
    4537 > lighting shadows false
    4538 
    4539 > lighting shadows true
    4540 
    4541 > graphics silhouettes false
    4542 
    4543 > graphics silhouettes true
    4544 
    4545 > lighting soft
    4546 
    4547 > save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data,
    4548 > presentation, and work/DDB1:CRBN with vvd compound processing/0.paper
    4549 > writing/figure making /Figure 2c.png" width 1800 height 1619 supersample 4
    4550 > transparentBackground true
    4551 
    4552 > save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data,
    4553 > presentation, and work/DDB1:CRBN with vvd compound processing/0.paper
    4554 > writing/figure making /fig 2.cxs" includeMaps true
    4555 
    4556 ——— End of log from Thu Jul 24 00:56:27 2025 ———
    4557 
    4558 > view name session-start
    4559 
    4560 opened ChimeraX session 
    4561 
    4562 > show #!11 models
    4563 
    4564 > hide #!12 models
    4565 
    4566 > hide #!13 models
    4567 
    4568 > color #!11 byhetero
    4569 
    4570 > select clear
    4571 
    4572 > color #10 #b2b2b2b3 models
    4573 
    4574 > ui tool show "Side View"
    4575 
    4576 > save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data,
    4577 > presentation, and work/DDB1:CRBN with vvd compound processing/0.paper
    4578 > writing/figure making /Figure 2b.png" width 1800 height 1532 supersample 4
    4579 > transparentBackground true
    4580 
    4581 > show #!13 models
    4582 
    4583 > hide #!11 models
    4584 
    4585 > show #!12 models
    4586 
    4587 > save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data,
    4588 > presentation, and work/DDB1:CRBN with vvd compound processing/0.paper
    4589 > writing/figure making /Figure 2c.png" width 1800 height 1532 supersample 4
    4590 > transparentBackground true
    4591 
    4592 > show #!11 models
    4593 
    4594 > hide #!12 models
    4595 
    4596 > hide #!13 models
    4597 
    4598 > hide #!10 models
    4599 
    4600 > select #11/B:287
    4601 
    4602 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4603 
    4604 > show sel atoms
    4605 
    4606 > select clear
    4607 
    4608 > show #!10 models
    4609 
    4610 > hide #!10 models
    4611 
    4612 > select #11/B:318
    4613 
    4614 6 atoms, 5 bonds, 1 residue, 1 model selected 
    4615 
    4616 > show sel atoms
    4617 
    4618 > select clear
    4619 
    4620 > show #!10 models
    4621 
    4622 > color #10 #d6d6d6ff models
    4623 
    4624 > color #10 #d6d6d6b3 models
    4625 
    4626 > select clear
    4627 
    4628 > volume #10 level 12
    4629 
    4630 > volume #10 level 14.05
    4631 
    4632 > save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data,
    4633 > presentation, and work/DDB1:CRBN with vvd compound processing/0.paper
    4634 > writing/figure making /Figure 2b.png" width 1800 height 1532 supersample 4
    4635 > transparentBackground true
    4636 
    4637 > show #!13 models
    4638 
    4639 > hide #!11 models
    4640 
    4641 > show #!12 models
    4642 
    4643 > color #13 #d6d6d6ff models
    4644 
    4645 > color #13 #d6d6d6b3 models
    4646 
    4647 > hide #!10 models
    4648 
    4649 > select add #13
    4650 
    4651 25 models selected 
    4652 
    4653 > color #13.12.1 lime
    4654 
    4655 > select clear
    4656 
    4657 > show #!10 models
    4658 
    4659 > ui tool show "Side View"
    4660 
    4661 > save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data,
    4662 > presentation, and work/DDB1:CRBN with vvd compound processing/0.paper
    4663 > writing/figure making /Figure 2c.png" width 1800 height 1471 supersample 4
    4664 > transparentBackground true
    4665 
    4666 > hide #!13 models
    4667 
    4668 > hide #!10 models
    4669 
    4670 > hide #!12 models
    4671 
    4672 > show #!11 models
    4673 
    4674 Drag select of 43 atoms, 49 residues, 45 bonds 
    4675 
    4676 > show sel atoms
    4677 
    4678 > select clear
    4679 
    4680 > ui mousemode right distance
    4681 
    4682 > distance #11/B:502@F27 #11/B:261@CD2
    4683 
    4684 Distance between 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb #11/B
    4685 101 502 F27 and LEU 261 CD2: 3.388Å 
    4686 
    4687 > distance #11/B:502@C25 #11/B:260@NE2
    4688 
    4689 Distance between 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb #11/B
    4690 101 502 C25 and GLN 260 NE2: 1.665Å 
    4691 
    4692 > distance #11/B:502@C20 #11/B:318@SG
    4693 
    4694 Distance between 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb #11/B
    4695 101 502 C20 and CYS 318 SG: 3.698Å 
    4696 
    4697 Cell requested for row 0 is out of bounds for table with 15 rows! Resizing
    4698 table model. 
    4699 
    4700 > morph #12 to #11
    4701 
    4702 Expected a keyword 
    4703 
    4704 > volume morph #12 to #11
    4705 
    4706 Expected a keyword 
    4707 
    4708 > vop morph #12 to #11
    4709 
    4710 > volume morph #12 to #11
    4711 
    4712 Expected a keyword 
    4713 
    4714 > vop morph #12 #11
    4715 
    4716 volume morph requires 2 or more volumes, got 0 
    4717 
    4718 > morph #12 #11
    4719 
    4720 Computed 51 frame morph #15 
    4721 
    4722 > coordset #15 1,51
    4723 
    4724 > hide #!15 models
    4725 
    4726 > show #!12 models
    4727 
    4728 Drag select of 11 atoms, 70 residues, 12 bonds 
    4729 
    4730 > show sel atoms
    4731 
    4732 > select clear
    4733 
    4734 > show #!11 models
    4735 
    4736 > hide #!12 models
    4737 
    4738 > show #!12 models
    4739 
    4740 > close #15
    4741 
    4742 > morph #12 #11
    4743 
    4744 Computed 51 frame morph #15 
    4745 
    4746 > coordset #15 1,51
    4747 
    4748 > morph #12 #11
    4749 
    4750 Computed 51 frame morph #16 
    4751 
    4752 > coordset #16 1,51
    4753 
    4754 > morph #12 #11
    4755 
    4756 Computed 51 frame morph #17 
    4757 
    4758 > coordset #17 1,51
    4759 
    4760 > close #15
    4761 
    4762 > close #16
    4763 
    4764 > close #17
    4765 
    4766 > show #!11 models
    4767 
    4768 > save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data,
    4769 > presentation, and work/DDB1:CRBN with vvd compound processing/0.paper
    4770 > writing/figure making /fig 2.cxs" includeMaps true
    4771 
    4772 ——— End of log from Thu Jul 24 01:33:11 2025 ———
    4773 
    4774 > view name session-start
    4775 
    4776 opened ChimeraX session 
    4777 
    4778 > close #1
    4779 
    4780 > close #2
    4781 
    4782 > close #3
    4783 
    4784 > close #5
    4785 
    4786 > close #6
    4787 
    4788 > close #7
    4789 
    4790 > close #8
    4791 
    4792 > show #!10 models
    4793 
    4794 > show #!13 models
    4795 
    4796 > hide #!13 models
    4797 
    4798 > hide #!10 models
    4799 
    4800 > show #!12 models
    4801 
    4802 > hide #!14 models
    4803 
    4804 > color #12 #d6d6d6ff
    4805 
    4806 > color #12 silver
    4807 
    4808 > mmaker #12 to #11
    4809 
    4810 Parameters 
    4811 --- 
    4812 Chain pairing | bb 
    4813 Alignment algorithm | Needleman-Wunsch 
    4814 Similarity matrix | BLOSUM-62 
    4815 SS fraction | 0.3 
    4816 Gap open (HH/SS/other) | 18/18/6 
    4817 Gap extend | 1 
    4818 SS matrix |  |  | H | S | O 
    4819 ---|---|---|--- 
    4820 H | 6 | -9 | -6 
    4821 S |  | 6 | -6 
    4822 O |  |  | 4 
    4823 Iteration cutoff | 2 
    4824  
    4825 Matchmaker 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb, chain A
    4826 (#11) with 8cvp, chain A (#12), sequence alignment score = 5335.5 
    4827 RMSD between 824 pruned atom pairs is 0.011 angstroms; (across all 824 pairs:
    4828 0.011) 
    4829  
    4830 
    4831 > hide atoms
    4832 
    4833 > select ::name="101"
    4834 
    4835 28 atoms, 30 bonds, 1 residue, 1 model selected 
    4836 
    4837 > show sel atoms
    4838 
    4839 > select #11/B:264
    4840 
    4841 14 atoms, 15 bonds, 1 residue, 1 model selected 
    4842 
    4843 > show sel atoms
    4844 
    4845 > select #12/B:264
    4846 
    4847 14 atoms, 15 bonds, 1 residue, 1 model selected 
    4848 
    4849 > show sel atoms
    4850 
    4851 > select clear
    4852 
    4853 > color byhetero
    4854 
    4855 > select clear
    4856 
    4857 > ui tool show "Side View"
    4858 
    4859 > save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
    4860 > inhibitor/ChimeraX/fig 2.cxs" includeMaps true
    4861 
    4862 > save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data,
    4863 > presentation, and work/DDB1:CRBN with vvd compound processing/0.paper
    4864 > writing/figure making/fig2a zoom2.png" width 1800 height 1532 supersample 4
    4865 > transparentBackground true
    4866 
    4867 > save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
    4868 > inhibitor/ChimeraX/fig 2.cxs" includeMaps true
    4869 
    4870 ——— End of log from Thu Jul 24 11:26:36 2025 ———
    4871 
    4872 > view name session-start
    4873 
    4874 opened ChimeraX session 
    4875 
    4876 > hide #!11 models
    4877 
    4878 > show #!11 models
    4879 
    4880 > show #!4 models
    4881 
    4882 > show #!9 models
    4883 
    4884 > view
    4885 
    4886 > show #!10 models
    4887 
    4888 > hide #!9 models
    4889 
    4890 > hide #!4 models
    4891 
    4892 > hide #!12 models
    4893 
    4894 > show #!13 models
    4895 
    4896 > open "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
    4897 > inhibitor/Figures/Fig 2b final EMready fig maps/open/J2526_map_emready2.mrc"
    4898 
    4899 Opened J2526_map_emready2.mrc as #1, grid size 443,443,443, pixel 0.5, shown
    4900 at level 1.01, step 2, values float32 
    4901 
    4902 > open "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
    4903 > inhibitor/Figures/Fig 2b final EMready fig
    4904 > maps/open/J2540_005_volume_map_emready2.mrc"
    4905 
    4906 Opened J2540_005_volume_map_emready2.mrc as #2, grid size 443,443,443, pixel
    4907 0.5, shown at level 1.2, step 2, values float32 
    4908 
    4909 > vop max #1 #2
    4910 
    4911 Opened volume maximum as #3, grid size 443,443,443, pixel 0.5, shown at step
    4912 1, values float32 
    4913 
    4914 > rename #3 "combination of 2526 and 2540 emready2"
    4915 
    4916 > rename #1 "open- vvd+imid J2526_map_emready2.mrc"
    4917 
    4918 > rename #1 "open- vvd+imid NU J2526_map_emready2.mrc"
    4919 
    4920 > rename #2 "open- vvd+imid local J2540_005_volume_map_emready2.mrc"
    4921 
    4922 > hide #!11 models
    4923 
    4924 > hide #!13 models
    4925 
    4926 > show #!13 models
    4927 
    4928 > hide #!13 models
    4929 
    4930 > select add #3
    4931 
    4932 2 models selected 
    4933 
    4934 > graphics silhouettes false
    4935 
    4936 > lighting shadows true intensity 0.5
    4937 
    4938 > lighting soft
    4939 
    4940 > lighting full
    4941 
    4942 > volume #1 step 1
    4943 
    4944 > volume #2 step 1
    4945 
    4946 > volume #3 level 3.516
    4947 
    4948 > ui mousemode right "translate selected models"
    4949 
    4950 > ui mousemode right "rotate selected models"
    4951 
    4952 > view matrix models
    4953 > #3,0.97508,-0.17567,0.13548,12.133,0.1943,0.38153,-0.9037,165.36,0.10706,0.90751,0.40616,-72.098
    4954 
    4955 > ui mousemode right "translate selected models"
    4956 
    4957 > view matrix models
    4958 > #3,0.97508,-0.17567,0.13548,26.737,0.1943,0.38153,-0.9037,162.12,0.10706,0.90751,0.40616,-74.124
    4959 
    4960 > volume #3 level 5.573
    4961 
    4962 > fitmap #3 inMap #10
    4963 
    4964 Fit map combination of 2526 and 2540 emready2 in map composite_map on EMReady2
    4965 maps of 1735 and 1614.ccp4 using 340198 points 
    4966 correlation = 0.9503, correlation about mean = 0.6492, overlap = 5.013e+07 
    4967 steps = 168, shift = 14.6, angle = 12.4 degrees 
    4968  
    4969 Position of combination of 2526 and 2540 emready2 (#3) relative to
    4970 composite_map on EMReady2 maps of 1735 and 1614.ccp4 (#10) coordinates: 
    4971 Matrix rotation and translation 
    4972 0.96196967 -0.27233362 0.02118389 54.69880809 
    4973 0.09346611 0.25529558 -0.96233479 187.78850372 
    4974 0.25666796 0.92771686 0.27104057 -69.01712395 
    4975 Axis 0.97451791 -0.12141649 0.18860775 
    4976 Axis point 0.00000000 144.90433503 85.21030045 
    4977 Rotation angle (degrees) 75.86822137 
    4978 Shift along axis 17.48718173 
    4979  
    4980 
    4981 > select clear
    4982 
    4983 > ui mousemode right translate
    4984 
    4985 > volume #3 level 2.711
    4986 
    4987 > show #!11 models
    4988 
    4989 > hide #!10 models
    4990 
    4991 > color #3 #b2ffffa9 models
    4992 
    4993 > select clear
    4994 
    4995 > color zone #3 near #11 distance 8
    4996 
    4997 > select clear
    4998 
    4999 > hide #!11 atoms
    5000 
    5001 > color zone #3 near #11 distance 8
    5002 
    5003 > color #!11 bychain
    5004 
    5005 > undo
    5006 
    5007 > color zone #3 near #11 distance 8
    5008 
    5009 > color #!11 byhetero
    5010 
    5011 [Repeated 1 time(s)]
    5012 
    5013 > ~heteroatom
    5014 
    5015 Unknown command: ~heteroatom 
    5016 
    5017 > color zone #3 near #11 & protein distance 8
    5018 
    5019 > color zone #3 near #11 distance 8
    5020 
    5021 > color zone #3 near #11 & ~ligand & ~solvent distance 8
    5022 
    5023 > color zone #3 near #11 & polymer distance 8
    5024 
    5025 Expected a keyword 
    5026 
    5027 > color #3 gray
    5028 
    5029 > color zone #3 near #11/A & protein distance 8
    5030 
    5031 [Repeated 1 time(s)]
    5032 
    5033 > fitmap #11 inMap #3
    5034 
    5035 Fit molecule 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb (#11) to
    5036 map combination of 2526 and 2540 emready2 (#3) using 8554 atoms 
    5037 average map value = 9.415, steps = 44 
    5038 shifted from previous position = 0.244 
    5039 rotated from previous position = 0.266 degrees 
    5040 atoms outside contour = 1045, contour level = 2.7111 
    5041  
    5042 Position of 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb (#11)
    5043 relative to combination of 2526 and 2540 emready2 (#3) coordinates: 
    5044 Matrix rotation and translation 
    5045 0.96102761 0.09475034 0.25970812 -52.92644150 
    5046 -0.27553875 0.25197696 0.92767775 31.87312977 
    5047 0.02245732 -0.96308358 0.26826421 198.31177033 
    5048 Axis -0.97400087 0.12221663 -0.19074956 
    5049 Axis point 0.00000000 144.94453273 84.83756927 
    5050 Rotation angle (degrees) 76.07601433 
    5051 Shift along axis 17.61794287 
    5052  
    5053 
    5054 > fitmap #11 inMap #3
    5055 
    5056 Fit molecule 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb (#11) to
    5057 map combination of 2526 and 2540 emready2 (#3) using 8554 atoms 
    5058 average map value = 9.414, steps = 28 
    5059 shifted from previous position = 0.00835 
    5060 rotated from previous position = 0.0108 degrees 
    5061 atoms outside contour = 1042, contour level = 2.7111 
    5062  
    5063 Position of 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb (#11)
    5064 relative to combination of 2526 and 2540 emready2 (#3) coordinates: 
    5065 Matrix rotation and translation 
    5066 0.96098510 0.09486625 0.25982307 -52.95701236 
    5067 -0.27567867 0.25188266 0.92766179 31.90374037 
    5068 0.02255887 -0.96309684 0.26820809 198.31213193 
    5069 Axis -0.97397549 0.12222053 -0.19087665 
    5070 Axis point 0.00000000 144.95021334 84.82634677 
    5071 Rotation angle (degrees) 76.08170877 
    5072 Shift along axis 17.62496843 
    5073  
    5074 
    5075 > color #3 #b2ffffff models
    5076 
    5077 > color #3 #b2ffffc8 models
    5078 
    5079 > color #3 #b2ffffae models
    5080 
    5081 > color #3 #b2ffffaa models
    5082 
    5083 > color #3 #b2ffffab models
    5084 
    5085 > fitmap #11 inMap #3
    5086 
    5087 Fit molecule 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb (#11) to
    5088 map combination of 2526 and 2540 emready2 (#3) using 8554 atoms 
    5089 average map value = 9.415, steps = 40 
    5090 shifted from previous position = 0.00992 
    5091 rotated from previous position = 0.0117 degrees 
    5092 atoms outside contour = 1047, contour level = 2.7111 
    5093  
    5094 Position of 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb (#11)
    5095 relative to combination of 2526 and 2540 emready2 (#3) coordinates: 
    5096 Matrix rotation and translation 
    5097 0.96103238 0.09473372 0.25969653 -52.92173586 
    5098 -0.27552298 0.25197233 0.92768369 31.87164356 
    5099 0.02244658 -0.96308643 0.26825488 198.31472716 
    5100 Axis -0.97400426 0.12221605 -0.19073265 
    5101 Axis point 0.00000000 144.94452420 84.83909535 
    5102 Rotation angle (degrees) 76.07628568 
    5103 Shift along axis 17.61612817 
    5104  
    5105 
    5106 > split #11
    5107 
    5108 Split 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb (#11) into 2
    5109 models 
    5110 Chain information for 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb A
    5111 #11.1 
    5112 --- 
    5113 Chain | Description 
    5114 A | No description available 
    5115  
    5116 Chain information for 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb B
    5117 #11.2 
    5118 --- 
    5119 Chain | Description 
    5120 B | No description available 
    5121  
    5122 
    5123 > select add #11.1
    5124 
    5125 6318 atoms, 6434 bonds, 824 residues, 1 model selected 
    5126 
    5127 > select subtract #11.1
    5128 
    5129 Nothing selected 
    5130 
    5131 > select add #11.2
    5132 
    5133 2236 atoms, 2278 bonds, 4 pseudobonds, 351 residues, 2 models selected 
    5134 
    5135 > fitmap sel inMap #3
    5136 
    5137 Fit molecule 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb B (#11.2)
    5138 to map combination of 2526 and 2540 emready2 (#3) using 2236 atoms 
    5139 average map value = 7.606, steps = 52 
    5140 shifted from previous position = 0.506 
    5141 rotated from previous position = 1.99 degrees 
    5142 atoms outside contour = 454, contour level = 2.7111 
    5143  
    5144 Position of 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb B (#11.2)
    5145 relative to combination of 2526 and 2540 emready2 (#3) coordinates: 
    5146 Matrix rotation and translation 
    5147 0.95997604 0.12501582 0.25063329 -55.21416768 
    5148 -0.27579491 0.26595891 0.92368989 30.40664271 
    5149 0.04881769 -0.95584355 0.28979291 191.85480848 
    5150 Axis -0.97266091 0.10443982 -0.20742005 
    5151 Axis point 0.00000000 143.00817251 82.65941765 
    5152 Rotation angle (degrees) 75.05664688 
    5153 Shift along axis 17.08579253 
    5154  
    5155 
    5156 > select add #11.1
    5157 
    5158 8554 atoms, 8712 bonds, 4 pseudobonds, 1175 residues, 3 models selected 
    5159 
    5160 > select subtract #11.2
    5161 
    5162 6318 atoms, 6434 bonds, 824 residues, 1 model selected 
    5163 
    5164 > fitmap sel inMap #3
    5165 
    5166 Fit molecule 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb A (#11.1)
    5167 to map combination of 2526 and 2540 emready2 (#3) using 6318 atoms 
    5168 average map value = 10.3, steps = 60 
    5169 shifted from previous position = 0.0792 
    5170 rotated from previous position = 0.218 degrees 
    5171 atoms outside contour = 516, contour level = 2.7111 
    5172  
    5173 Position of 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb A (#11.1)
    5174 relative to combination of 2526 and 2540 emready2 (#3) coordinates: 
    5175 Matrix rotation and translation 
    5176 0.96153052 0.09164231 0.25896090 -52.47900982 
    5177 -0.27402598 0.25408547 0.92755072 31.47801921 
    5178 0.01920469 -0.96283034 0.26942331 198.46339739 
    5179 Axis -0.97427609 0.12356701 -0.18846035 
    5180 Axis point 0.00000000 145.04029338 85.04809926 
    5181 Rotation angle (degrees) 75.96470021 
    5182 Shift along axis 17.61620776 
    5183  
    5184 
    5185 > select subtract #11.1
    5186 
    5187 Nothing selected 
    5188 
    5189 > select add #11.1
    5190 
    5191 6318 atoms, 6434 bonds, 824 residues, 1 model selected 
    5192 
    5193 > select add #11.2
    5194 
    5195 8554 atoms, 8712 bonds, 4 pseudobonds, 1175 residues, 3 models selected 
    5196 
    5197 > combine sel
    5198 
    5199 > hide #!11 models
    5200 
    5201 > select add #11
    5202 
    5203 8554 atoms, 8712 bonds, 4 pseudobonds, 1175 residues, 4 models selected 
    5204 
    5205 > select subtract #11
    5206 
    5207 Nothing selected 
    5208 
    5209 > select subtract #14
    5210 
    5211 Nothing selected 
    5212 
    5213 > select ::name="101"
    5214 
    5215 56 atoms, 60 bonds, 2 residues, 2 models selected 
    5216 
    5217 > show sel & #!5 atoms
    5218 
    5219 > select clear
    5220 
    5221 > color zone #3 near #5 distance 8
    5222 
    5223 [Repeated 1 time(s)]
    5224 
    5225 > undo
    5226 
    5227 [Repeated 1 time(s)]
    5228 
    5229 > select clear
    5230 
    5231 > save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
    5232 > inhibitor/Figures/Fig 2b final EMready fig maps/open/vvd+iberdo open.pdb"
    5233 > models #5 relModel #3
    5234 
    5235 > open "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
    5236 > inhibitor/Figures/Fig 2b final EMready fig maps/open/vvd+iberdo open.pdb"
    5237 
    5238 Chain information for vvd+iberdo open.pdb #6 
    5239 --- 
    5240 Chain | Description 
    5241 A | No description available 
    5242 B | No description available 
    5243  
    5244 
    5245 > mmaker #6 to #5
    5246 
    5247 Computing secondary structure 
    5248 Parameters 
    5249 --- 
    5250 Chain pairing | bb 
    5251 Alignment algorithm | Needleman-Wunsch 
    5252 Similarity matrix | BLOSUM-62 
    5253 SS fraction | 0.3 
    5254 Gap open (HH/SS/other) | 18/18/6 
    5255 Gap extend | 1 
    5256 SS matrix |  |  | H | S | O 
    5257 ---|---|---|--- 
    5258 H | 6 | -9 | -6 
    5259 S |  | 6 | -6 
    5260 O |  |  | 4 
    5261 Iteration cutoff | 2 
    5262  
    5263 Matchmaker combination, chain A (#5) with vvd+iberdo open.pdb, chain A (#6),
    5264 sequence alignment score = 4201.9 
    5265 RMSD between 824 pruned atom pairs is 0.000 angstroms; (across all 824 pairs:
    5266 0.000) 
    5267  
    5268 
    5269 > hide #!5 models
    5270 
    5271 > color zone #3 near #6 distance 8
    5272 
    5273 > color #3,6 byhetero
    5274 
    5275 > color #3,6 byelement
    5276 
    5277 > ui tool show "Color Actions"
    5278 
    5279 > color bychain
    5280 
    5281 > color bychain target cs
    5282 
    5283 [Repeated 1 time(s)]
    5284 
    5285 > color zone #3 near #6 distance 8
    5286 
    5287 > select subtract #14
    5288 
    5289 Nothing selected 
    5290 
    5291 > hide #!6 models
    5292 
    5293 > show #!6 models
    5294 
    5295 > hide #!3 models
    5296 
    5297 > color #6/A:1-710 light blue
    5298 
    5299 > color #6/A:710-5000 steel blue
    5300 
    5301 > color #6/B:1-190 navajowhite
    5302 
    5303 > color #6/B:191-320 light salmon
    5304 
    5305 > color #6/B:321-500 tomato
    5306 
    5307 > select ::name="101"
    5308 
    5309 84 atoms, 90 bonds, 3 residues, 3 models selected 
    5310 
    5311 > color (#!6 & sel) lime
    5312 
    5313 > select clear
    5314 
    5315 > show #!3 models
    5316 
    5317 > fitmap #6 inMap #3
    5318 
    5319 Fit molecule vvd+iberdo open.pdb (#6) to map combination of 2526 and 2540
    5320 emready2 (#3) using 8554 atoms 
    5321 average map value = 9.593, steps = 40 
    5322 shifted from previous position = 0.000478 
    5323 rotated from previous position = 0.00651 degrees 
    5324 atoms outside contour = 971, contour level = 2.7111 
    5325  
    5326 Position of vvd+iberdo open.pdb (#6) relative to combination of 2526 and 2540
    5327 emready2 (#3) coordinates: 
    5328 Matrix rotation and translation 
    5329 0.99999490 0.00318409 0.00025382 -0.40275030 
    5330 -0.00318393 0.99999473 -0.00063666 0.25133637 
    5331 -0.00025585 0.00063585 0.99999976 -0.38480119 
    5332 Axis 0.19535237 0.07824435 -0.97760691 
    5333 Axis point 70.90279314 146.06118062 0.00000000 
    5334 Rotation angle (degrees) 0.18660948 
    5335 Shift along axis 0.31717173 
    5336  
    5337 
    5338 > close #14
    5339 
    5340 > color zone #3 near #6 distance 8
    5341 
    5342 > hide #!3 models
    5343 
    5344 > show #!3 models
    5345 
    5346 > hide #!3 models
    5347 
    5348 > ui tool show "Show Sequence Viewer"
    5349 
    5350 > sequence chain #6/B
    5351 
    5352 Alignment identifier is 6/B 
    5353 
    5354 > select #6/B:380
    5355 
    5356 14 atoms, 15 bonds, 1 residue, 1 model selected 
    5357 
    5358 > select #6/B:380
    5359 
    5360 14 atoms, 15 bonds, 1 residue, 1 model selected 
    5361 
    5362 > show sel atoms
    5363 
    5364 > select #6/B:386
    5365 
    5366 14 atoms, 15 bonds, 1 residue, 1 model selected 
    5367 
    5368 > select #6/B:386
    5369 
    5370 14 atoms, 15 bonds, 1 residue, 1 model selected 
    5371 
    5372 > show sel atoms
    5373 
    5374 > select #6/B:400
    5375 
    5376 14 atoms, 15 bonds, 1 residue, 1 model selected 
    5377 
    5378 > select #6/B:400
    5379 
    5380 14 atoms, 15 bonds, 1 residue, 1 model selected 
    5381 
    5382 > show sel atoms
    5383 
    5384 > select clear
    5385 
    5386 > show #!3 models
    5387 
    5388 > color #3 #b2ffff95 models
    5389 
    5390 > color #3 #b2ffff80 models
    5391 
    5392 > select add #6
    5393 
    5394 8554 atoms, 8712 bonds, 4 pseudobonds, 1175 residues, 2 models selected 
    5395 
    5396 > fitmap sel inMap #3
    5397 
    5398 Fit molecule vvd+iberdo open.pdb (#6) to map combination of 2526 and 2540
    5399 emready2 (#3) using 8554 atoms 
    5400 average map value = 9.593, steps = 28 
    5401 shifted from previous position = 0.00997 
    5402 rotated from previous position = 0.00827 degrees 
    5403 atoms outside contour = 970, contour level = 2.7111 
    5404  
    5405 Position of vvd+iberdo open.pdb (#6) relative to combination of 2526 and 2540
    5406 emready2 (#3) coordinates: 
    5407 Matrix rotation and translation 
    5408 0.99999451 0.00330818 0.00017995 -0.42084422 
    5409 -0.00330806 0.99999432 -0.00063753 0.26238779 
    5410 -0.00018206 0.00063693 0.99999978 -0.38918532 
    5411 Axis 0.18887565 0.05365024 -0.98053436 
    5412 Axis point 73.94006957 145.38881802 0.00000000 
    5413 Rotation angle (degrees) 0.19330462 
    5414 Shift along axis 0.31619952 
    5415  
    5416 
    5417 > select clear
    5418 
    5419 > volume #3 level 1.638
    5420 
    5421 > volume #3 level 1.191
    5422 
    5423 > volume #3 level 1.861
    5424 
    5425 > open 8W7
    5426 
    5427 '8W7' has no suffix 
    5428 
    5429 > open 8w7
    5430 
    5431 '8w7' has no suffix 
    5432 
    5433 > open PDB:8w7
    5434 
    5435 PDB identifiers are either 4 or 8 characters long, got "8w7" 
    5436 
    5437 > open "/Users/zrizvi/Downloads/8W7 (1).cif"
    5438 
    5439 Summary of feedback from opening /Users/zrizvi/Downloads/8W7 (1).cif 
    5440 --- 
    5441 warning | No mmCIF models found. 
    5442  
    5443 
    5444 > open "/Users/zrizvi/Downloads/8W7 (1).cif"
    5445 
    5446 Summary of feedback from opening /Users/zrizvi/Downloads/8W7 (1).cif 
    5447 --- 
    5448 warning | No mmCIF models found. 
    5449  
    5450 
    5451 > open "/Users/zrizvi/Downloads/8W7 (1).cif"
    5452 
    5453 Summary of feedback from opening /Users/zrizvi/Downloads/8W7 (1).cif 
    5454 --- 
    5455 warning | No mmCIF models found. 
    5456  
    5457 
    5458 > open "/Users/zrizvi/Downloads/8W7 (1).cif"
    5459 
    5460 Summary of feedback from opening /Users/zrizvi/Downloads/8W7 (1).cif 
    5461 --- 
    5462 warning | No mmCIF models found. 
    5463  
    5464 
    5465 > open "/Users/zrizvi/Downloads/8W7 (1).cif"
    5466 
    5467 Summary of feedback from opening /Users/zrizvi/Downloads/8W7 (1).cif 
    5468 --- 
    5469 warning | No mmCIF models found. 
    5470  
    5471 
    5472 > open 5v3o
    5473 
    5474 Summary of feedback from opening 5v3o fetched from pdb 
    5475 --- 
    5476 note | Fetching compressed mmCIF 5v3o from http://files.rcsb.org/download/5v3o.cif 
    5477  
    5478 5v3o title: 
    5479 Cereblon in complex with DDB1 and CC-220 [more info...] 
    5480  
    5481 Chain information for 5v3o #7 
    5482 --- 
    5483 Chain | Description | UniProt 
    5484 A | DNA damage-binding protein 1 | DDB1_HUMAN 1-1140 
    5485 C | Protein cereblon | CRBN_HUMAN 40-442 
    5486  
    5487 Non-standard residues in 5v3o #7 
    5488 --- 
    5489 8W7 —
    5490 (3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione 
    5491 ZN — zinc ion 
    5492  
    5493 
    5494 > mmaker #7 to #6
    5495 
    5496 Computing secondary structure 
    5497 [Repeated 1 time(s)]  Parameters 
    5498 --- 
    5499 Chain pairing | bb 
    5500 Alignment algorithm | Needleman-Wunsch 
    5501 Similarity matrix | BLOSUM-62 
    5502 SS fraction | 0.3 
    5503 Gap open (HH/SS/other) | 18/18/6 
    5504 Gap extend | 1 
    5505 SS matrix |  |  | H | S | O 
    5506 ---|---|---|--- 
    5507 H | 6 | -9 | -6 
    5508 S |  | 6 | -6 
    5509 O |  |  | 4 
    5510 Iteration cutoff | 2 
    5511  
    5512 Matchmaker vvd+iberdo open.pdb, chain A (#6) with 5v3o, chain A (#7), sequence
    5513 alignment score = 3513.3 
    5514 RMSD between 746 pruned atom pairs is 0.665 angstroms; (across all 775 pairs:
    5515 1.032) 
    5516  
    5517 
    5518 > hide #!3 models
    5519 
    5520 > select ::name="8W7"
    5521 
    5522 33 atoms, 37 bonds, 1 residue, 1 model selected 
    5523 
    5524 > color sel yellow
    5525 
    5526 > select clear
    5527 
    5528 > select #6/a
    5529 
    5530 6318 atoms, 6434 bonds, 824 residues, 1 model selected 
    5531 
    5532 > select #7/a/c
    5533 
    5534 11175 atoms, 11396 bonds, 15 pseudobonds, 1452 residues, 3 models selected 
    5535 
    5536 > select clear
    5537 
    5538 > split #7
    5539 
    5540 Split 5v3o (#7) into 2 models 
    5541 Chain information for 5v3o A #7.1 
    5542 --- 
    5543 Chain | Description 
    5544 A | No description available 
    5545  
    5546 Chain information for 5v3o C #7.2 
    5547 --- 
    5548 Chain | Description 
    5549 C | No description available 
    5550  
    5551 
    5552 > select add #7.1
    5553 
    5554 8273 atoms, 8422 bonds, 9 pseudobonds, 1087 residues, 2 models selected 
    5555 
    5556 > select subtract #7.1
    5557 
    5558 Nothing selected 
    5559 
    5560 > select add #7.2
    5561 
    5562 2902 atoms, 2974 bonds, 6 pseudobonds, 365 residues, 3 models selected 
    5563 
    5564 > select subtract #7.2
    5565 
    5566 Nothing selected 
    5567 
    5568 > hide #!6 models
    5569 
    5570 > split #7.2
    5571 
    5572 Did not split 5v3o C, has only one piece 
    5573 Drag select of 1142 residues, 10 pseudobonds 
    5574 
    5575 > delete sel
    5576 
    5577 Drag select of 162 residues, 5 pseudobonds 
    5578 
    5579 > select up
    5580 
    5581 1666 atoms, 1649 bonds, 5 pseudobonds, 212 residues, 4 models selected 
    5582 
    5583 > select up
    5584 
    5585 2415 atoms, 2431 bonds, 5 pseudobonds, 308 residues, 4 models selected 
    5586 
    5587 > delete sel
    5588 
    5589 Drag select of 1 atoms 
    5590 
    5591 > delete sel
    5592 
    5593 > show #!6 models
    5594 
    5595 > select add #7.2
    5596 
    5597 33 atoms, 37 bonds, 1 residue, 1 model selected 
    5598 
    5599 > ui mousemode right "translate selected models"
    5600 
    5601 > view matrix models
    5602 > #7.2,0.38926,0.71182,0.58463,95.207,-0.9138,0.3783,0.14783,121.63,-0.11594,-0.59178,0.79772,151.44
    5603 
    5604 > ui mousemode right translate
    5605 
    5606 > ui mousemode right "rotate selected models"
    5607 
    5608 > ui mousemode right "translate selected models"
    5609 
    5610 > view matrix models
    5611 > #7.2,0.38926,0.71182,0.58463,96.147,-0.9138,0.3783,0.14783,122.74,-0.11594,-0.59178,0.79772,154.04
    5612 
    5613 > ui mousemode right translate
    5614 
    5615 > ui mousemode right "translate selected models"
    5616 
    5617 > view matrix models
    5618 > #7.2,0.38926,0.71182,0.58463,95.535,-0.9138,0.3783,0.14783,118.94,-0.11594,-0.59178,0.79772,152.93
    5619 
    5620 > ui mousemode right "rotate selected models"
    5621 
    5622 > view matrix models
    5623 > #7.2,0.58527,0.4424,0.67952,103.57,-0.3231,-0.64138,0.69587,163.23,0.74369,-0.62682,-0.23244,77.254
    5624 
    5625 > ui mousemode right "translate selected models"
    5626 
    5627 > view matrix models
    5628 > #7.2,0.58527,0.4424,0.67952,102.52,-0.3231,-0.64138,0.69587,162.38,0.74369,-0.62682,-0.23244,77.227
    5629 
    5630 > ui mousemode right translate
    5631 
    5632 > ui mousemode right "translate selected models"
    5633 
    5634 > view matrix models
    5635 > #7.2,0.58527,0.4424,0.67952,102.28,-0.3231,-0.64138,0.69587,162.87,0.74369,-0.62682,-0.23244,77.81
    5636 
    5637 > ui mousemode right "rotate selected models"
    5638 
    5639 > view matrix models
    5640 > #7.2,0.49337,0.54152,0.68069,101.54,-0.38847,-0.56301,0.72946,163.07,0.77825,-0.62432,-0.067408,81.726
    5641 
    5642 > ui mousemode right "translate selected models"
    5643 
    5644 > view matrix models
    5645 > #7.2,0.49337,0.54152,0.68069,100.97,-0.38847,-0.56301,0.72946,163.71,0.77825,-0.62432,-0.067408,82.414
    5646 
    5647 > ui mousemode right translate
    5648 
    5649 > show #!3 models
    5650 
    5651 > ui mousemode right "translate selected models"
    5652 
    5653 > view matrix models
    5654 > #7.2,0.49337,0.54152,0.68069,101.48,-0.38847,-0.56301,0.72946,162.04,0.77825,-0.62432,-0.067408,81.359
    5655 
    5656 > ui mousemode right translate
    5657 
    5658 > select subtract #7.2
    5659 
    5660 Nothing selected 
    5661 
    5662 > select add #7.2
    5663 
    5664 33 atoms, 37 bonds, 1 residue, 1 model selected 
    5665 
    5666 > fitmap sel inMap #3
    5667 
    5668 Fit molecule 5v3o C (#7.2) to map combination of 2526 and 2540 emready2 (#3)
    5669 using 33 atoms 
    5670 average map value = 5.737, steps = 256 
    5671 shifted from previous position = 7.36 
    5672 rotated from previous position = 81 degrees 
    5673 atoms outside contour = 3, contour level = 1.8614 
    5674  
    5675 Position of 5v3o C (#7.2) relative to combination of 2526 and 2540 emready2
    5676 (#3) coordinates: 
    5677 Matrix rotation and translation 
    5678 0.87027007 -0.19554474 -0.45209762 50.53821845 
    5679 -0.20191453 -0.97878910 0.03467589 165.49997848 
    5680 -0.44928891 0.06110769 -0.89129418 123.26330988 
    5681 Axis 0.96702224 -0.10275818 -0.23304237 
    5682 Axis point 0.00000000 84.99703244 68.30715524 
    5683 Rotation angle (degrees) 179.21693737 
    5684 Shift along axis 3.13952962 
    5685  
    5686 
    5687 > select clear
    5688 
    5689 > select add #7.2
    5690 
    5691 33 atoms, 37 bonds, 1 residue, 1 model selected 
    5692 
    5693 > ui mousemode right "rotate selected models"
    5694 
    5695 > view matrix models
    5696 > #7.2,-0.13555,0.48062,0.86639,135.27,-0.89289,-0.43824,0.10341,162.86,0.42939,-0.75958,0.48854,124.48
    5697 
    5698 > ui mousemode right "translate selected models"
    5699 
    5700 > view matrix models
    5701 > #7.2,-0.13555,0.48062,0.86639,141.75,-0.89289,-0.43824,0.10341,158.53,0.42939,-0.75958,0.48854,124.12
    5702 
    5703 > select clear
    5704 
    5705 > select add #7.2
    5706 
    5707 33 atoms, 37 bonds, 1 residue, 1 model selected 
    5708 
    5709 > view matrix models
    5710 > #7.2,-0.13555,0.48062,0.86639,141.75,-0.89289,-0.43824,0.10341,158.95,0.42939,-0.75958,0.48854,124.57
    5711 
    5712 > ui mousemode right translate
    5713 
    5714 > select clear
    5715 
    5716 > select add #7.2
    5717 
    5718 33 atoms, 37 bonds, 1 residue, 1 model selected 
    5719 
    5720 > ui mousemode right "translate selected models"
    5721 
    5722 > view matrix models
    5723 > #7.2,-0.13555,0.48062,0.86639,141.5,-0.89289,-0.43824,0.10341,158.01,0.42939,-0.75958,0.48854,123.53
    5724 
    5725 > select subtract #7.2
    5726 
    5727 Nothing selected 
    5728 
    5729 > ui mousemode right translate
    5730 
    5731 > select add #6
    5732 
    5733 8554 atoms, 8712 bonds, 4 pseudobonds, 1175 residues, 2 models selected 
    5734 
    5735 > select add #7.2
    5736 
    5737 8587 atoms, 8749 bonds, 4 pseudobonds, 1176 residues, 3 models selected 
    5738 
    5739 > combine sel
    5740 
    5741 > rename #8 "vvd+iberdo open.pdb"
    5742 
    5743 > close #6
    5744 
    5745 > close #7
    5746 
    5747 > select ::name="8W7"
    5748 
    5749 33 atoms, 37 bonds, 1 residue, 1 model selected 
    5750 
    5751 > color sel lime
    5752 
    5753 > ui tool show "Show Sequence Viewer"
    5754 
    5755 > sequence chain #8/B
    5756 
    5757 Alignment identifier is 8/B 
    5758 
    5759 > select #8/B:380
    5760 
    5761 14 atoms, 15 bonds, 1 residue, 1 model selected 
    5762 
    5763 > select #8/B:380
    5764 
    5765 14 atoms, 15 bonds, 1 residue, 1 model selected 
    5766 
    5767 > hide sel atoms
    5768 
    5769 > select #8/B:386
    5770 
    5771 14 atoms, 15 bonds, 1 residue, 1 model selected 
    5772 
    5773 > select #8/B:386
    5774 
    5775 14 atoms, 15 bonds, 1 residue, 1 model selected 
    5776 
    5777 > hide sel atoms
    5778 
    5779 > select #8/B:400
    5780 
    5781 14 atoms, 15 bonds, 1 residue, 1 model selected 
    5782 
    5783 > select #8/B:400
    5784 
    5785 14 atoms, 15 bonds, 1 residue, 1 model selected 
    5786 
    5787 > hide sel atoms
    5788 
    5789 > select clear
    5790 
    5791 > color zone #3 near #8 distance 8
    5792 
    5793 > hide #!8 models
    5794 
    5795 > show #!8 models
    5796 
    5797 > color #3 #b2ffff80 models
    5798 
    5799 > split #8
    5800 
    5801 Split vvd+iberdo open.pdb (#8) into 3 models 
    5802 Chain information for vvd+iberdo open.pdb A #8.1 
    5803 --- 
    5804 Chain | Description 
    5805 A | No description available 
    5806  
    5807 Chain information for vvd+iberdo open.pdb B #8.2 
    5808 --- 
    5809 Chain | Description 
    5810 B | No description available 
    5811  
    5812 
    5813 > select add #8.3
    5814 
    5815 33 atoms, 37 bonds, 1 residue, 1 model selected 
    5816 
    5817 > ui mousemode right "translate selected models"
    5818 
    5819 > view matrix models
    5820 > #8.3,0.96286,-0.26914,0.021531,52.392,0.092796,0.25499,-0.96248,184.87,0.25355,0.92873,0.2705,-69.001
    5821 
    5822 > select clear
    5823 
    5824 > select add #8.3
    5825 
    5826 33 atoms, 37 bonds, 1 residue, 1 model selected 
    5827 
    5828 > view matrix models
    5829 > #8.3,0.96286,-0.26914,0.021531,54.262,0.092796,0.25499,-0.96248,185.23,0.25355,0.92873,0.2705,-68.133
    5830 
    5831 > ui mousemode right "rotate selected models"
    5832 
    5833 > view matrix models
    5834 > #8.3,0.86549,-0.29977,0.40134,13.855,0.49866,0.59184,-0.6333,63.657,-0.047687,0.74824,0.66171,-74.281
    5835 
    5836 > ui mousemode right "translate selected models"
    5837 
    5838 > view matrix models
    5839 > #8.3,0.86549,-0.29977,0.40134,12.593,0.49866,0.59184,-0.6333,65.975,-0.047687,0.74824,0.66171,-72.26
    5840 
    5841 > ui mousemode right translate
    5842 
    5843 > select add #8
    5844 
    5845 8587 atoms, 8749 bonds, 4 pseudobonds, 1176 residues, 5 models selected 
    5846 
    5847 > combine sel
    5848 
    5849 > select subtract #8
    5850 
    5851 Nothing selected 
    5852 
    5853 > hide #!8 models
    5854 
    5855 > hide #!6 models
    5856 
    5857 > show #!6 models
    5858 
    5859 > rename #6 "vvd+iberdo open.pdb"
    5860 
    5861 > close #8
    5862 
    5863 > show #!5 models
    5864 
    5865 > hide #!5 models
    5866 
    5867 > show #!5 models
    5868 
    5869 > hide #!5 models
    5870 
    5871 > hide #!6 models
    5872 
    5873 > show #!5 models
    5874 
    5875 > close #5
    5876 
    5877 > show #!6 models
    5878 
    5879 > color zone #3 near #6 distance 8
    5880 
    5881 > hide #!6 models
    5882 
    5883 > ui mousemode right "pick blobs"
    5884 
    5885 > measure blob #!3.1 triangleNumber 951490 color #ff6b4dff
    5886 
    5887 Surface combination of 2526 and 2540 emready2 #3.1 blob: 
    5888 volume = 1.0432e+05 
    5889 area = 80715 
    5890 size = 105.54 83.9 82.228 
    5891  
    5892 
    5893 > undo
    5894 
    5895 > select add #6
    5896 
    5897 8587 atoms, 8749 bonds, 4 pseudobonds, 1176 residues, 2 models selected 
    5898 
    5899 > copy sel
    5900 
    5901 Unknown command: copy sel 
    5902 
    5903 > select clear
    5904 
    5905 Drag select of 5 atoms, 7 bonds 
    5906 
    5907 > select up
    5908 
    5909 8 atoms, 8 bonds, 1 residue, 1 model selected 
    5910 
    5911 > select ::name="8W7"
    5912 
    5913 33 atoms, 37 bonds, 1 residue, 1 model selected 
    5914 
    5915 > color sel yellow
    5916 
    5917 > select clear
    5918 
    5919 Drag select of 7 atoms, 7 bonds 
    5920 
    5921 > delete sel
    5922 
    5923 Drag select of 4 atoms, 6 bonds 
    5924 
    5925 > delete sel
    5926 
    5927 Drag select of 1 atoms 
    5928 
    5929 > delete sel
    5930 
    5931 Drag select of 1 atoms 
    5932 
    5933 > delete sel
    5934 
    5935 Drag select of 2 atoms, 1 bonds 
    5936 
    5937 > delete sel
    5938 
    5939 > select ::name="8W7"
    5940 
    5941 18 atoms, 20 bonds, 1 residue, 1 model selected 
    5942 
    5943 > color sel lime
    5944 
    5945 > color zone #3 near #6 distance 8
    5946 
    5947 > select add #6
    5948 
    5949 8572 atoms, 8732 bonds, 4 pseudobonds, 1176 residues, 2 models selected 
    5950 
    5951 > select subtract #6
    5952 
    5953 Nothing selected 
    5954 
    5955 > hide #!6 models
    5956 
    5957 > graphics silhouettes true
    5958 
    5959 > lighting shadows false
    5960 
    5961 > lighting soft
    5962 
    5963 > volume #3 level 2.487
    5964 
    5965 > volume #3 level 4.142
    5966 
    5967 > volume #3 level 2.353
    5968 
    5969 > volume #3 level 1.861
    5970 
    5971 > volume #3 level 2.085
    5972 
    5973 > volume #3 level 2.264
    5974 
    5975 > save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
    5976 > inhibitor/Figures/Fig 2b final EMready fig maps/fig2b.open.png" width 1800
    5977 > height 1532 supersample 4 transparentBackground true
    5978 
    5979 > open "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
    5980 > inhibitor/Figures/Fig 2b final EMready fig maps/open/vvd+iberdo open.pdb"
    5981 
    5982 Chain information for vvd+iberdo open.pdb #5 
    5983 --- 
    5984 Chain | Description 
    5985 A | No description available 
    5986 B | No description available 
    5987  
    5988 
    5989 > hide #!3 models
    5990 
    5991 > close #5
    5992 
    5993 > show #!6 models
    5994 
    5995 > show #!3 models
    5996 
    5997 > save vvd+iberdo open.pdb #6
    5998 
    5999 Cannot determine format for 'vvd+iberdo' 
    6000 
    6001 > save vvd+iberdo_open.pdb #6
    6002 
    6003 > open /Users/zrizvi/Desktop/vvd+iberdo_open.pdb
    6004 
    6005 Chain information for vvd+iberdo_open.pdb #5 
    6006 --- 
    6007 Chain | Description 
    6008 A | No description available 
    6009 B | No description available 
    6010  
    6011 
    6012 > hide #!6 models
    6013 
    6014 > hide #!3 models
    6015 
    6016 > close #5
    6017 
    6018 > show #!3 models
    6019 
    6020 > rename #9 "1. cryosparc_P341_J1735_NUrefine selected.mrc"
    6021 
    6022 > rename #4 "2. cryosparc_P341_J1614_localrefine. selected.mrc"
    6023 
    6024 > rename #10 "3. composite_map on EMReady2 maps of 1735 and 1614.ccp4"
    6025 
    6026 > show #!10 models
    6027 
    6028 > hide #!3 models
    6029 
    6030 > show #!13 models
    6031 
    6032 > rename #10 "3a. composite_map on EMReady2 maps of 1735 and 1614.ccp4"
    6033 
    6034 > rename #13 "3b. composite_map on EMReady2 maps of 1735 and 1614.ccp4 split"
    6035 
    6036 > rename #1 "4. open- vvd+imid NU J2526_map_emready2.mrc"
    6037 
    6038 > rename #2 "5. open- vvd+imid local J2540_005_volume_map_emready2.mrc"
    6039 
    6040 > rename #3 "6. combination of 2526 and 2540 emready2"
    6041 
    6042 > rename #11 "3c. 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb"
    6043 
    6044 > rename #3 "6a. combination of 2526 and 2540 emready2"
    6045 
    6046 > rename #6 "6b. vvd+iberdo open.pdb"
    6047 
    6048 > hide #!10 models
    6049 
    6050 > hide #!13 models
    6051 
    6052 > show #!3 models
    6053 
    6054 > open "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
    6055 > inhibitor/Figures/Fig 2b final EMready fig
    6056 > maps/closed/J2528_map_emready2.mrc"
    6057 
    6058 Opened J2528_map_emready2.mrc as #5, grid size 443,443,443, pixel 0.5, shown
    6059 at level 1.11, step 2, values float32 
    6060 
    6061 > open "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
    6062 > inhibitor/Figures/Fig 2b final EMready fig
    6063 > maps/closed/J2544_007_volume_map_emready2.mrc"
    6064 
    6065 Opened J2544_007_volume_map_emready2.mrc as #7, grid size 443,443,443, pixel
    6066 0.5, shown at level 0.445, step 2, values float32 
    6067 
    6068 > hide #!3 models
    6069 
    6070 > show #!3 models
    6071 
    6072 > hide #!3 models
    6073 
    6074 > hide #!5 models
    6075 
    6076 > show #!5 models
    6077 
    6078 > rename #5 "7. J2528_map_emready2.mrc"
    6079 
    6080 > rename #7 "8. J2544_007_volume_map_emready2.mrc"
    6081 
    6082 > vop max #5 #7
    6083 
    6084 Opened volume maximum as #8, grid size 443,443,443, pixel 0.5, shown at step
    6085 1, values float32 
    6086 
    6087 > rename #8 "9. combination of 2528 and 2544 emready2"
    6088 
    6089 > rename #5 "7. Clsoed- vvd+imid NU J2528_map_emready2.mrc"
    6090 
    6091 > rename #7 "8. Closed- vvd+imid local J2544_007_volume_map_emready2.mrc"
    6092 
    6093 > volume #8 level 2.891
    6094 
    6095 > volume #8 level 3.239
    6096 
    6097 > show #!5 models
    6098 
    6099 > hide #!8 models
    6100 
    6101 > volume #5 level 1.869
    6102 
    6103 > volume #5 step 1
    6104 
    6105 > volume #7 step 1
    6106 
    6107 > volume #5 level 2.307
    6108 
    6109 > volume #7 level 2.027
    6110 
    6111 > volume #8 level 4.502
    6112 
    6113 > open 8w7
    6114 
    6115 '8w7' has no suffix 
    6116 
    6117 > open 5v3o
    6118 
    6119 5v3o title: 
    6120 Cereblon in complex with DDB1 and CC-220 [more info...] 
    6121  
    6122 Chain information for 5v3o #14 
    6123 --- 
    6124 Chain | Description | UniProt 
    6125 A | DNA damage-binding protein 1 | DDB1_HUMAN 1-1140 
    6126 C | Protein cereblon | CRBN_HUMAN 40-442 
    6127  
    6128 Non-standard residues in 5v3o #14 
    6129 --- 
    6130 8W7 —
    6131 (3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione 
    6132 ZN — zinc ion 
    6133  
    6134 
    6135 > view
    6136 
    6137 > select add #14
    6138 
    6139 11175 atoms, 11396 bonds, 15 pseudobonds, 1452 residues, 4 models selected 
    6140 
    6141 > ui mousemode right "translate selected models"
    6142 
    6143 > view matrix models #14,1,0,0,48.358,0,1,0,11.289,0,0,1,14.423
    6144 
    6145 > view matrix models
    6146 > #14,0.31895,0.61517,0.72099,49.34,-0.57201,-0.48161,0.66397,53.169,0.75569,-0.62419,0.19828,12.134
    6147 
    6148 > view matrix models
    6149 > #14,0.31895,0.61517,0.72099,159.92,-0.57201,-0.48161,0.66397,132.09,0.75569,-0.62419,0.19828,22.744
    6150 
    6151 > ui mousemode right translate
    6152 
    6153 > ui mousemode right "translate selected models"
    6154 
    6155 > view matrix models
    6156 > #14,0.31895,0.61517,0.72099,155.88,-0.57201,-0.48161,0.66397,192.02,0.75569,-0.62419,0.19828,124.04
    6157 
    6158 > ui mousemode right translate
    6159 
    6160 > ui mousemode right "translate selected models"
    6161 
    6162 > view matrix models
    6163 > #14,0.31895,0.61517,0.72099,115.83,-0.57201,-0.48161,0.66397,174.7,0.75569,-0.62419,0.19828,127.25
    6164 
    6165 > fitmap #14 inMap #8
    6166 
    6167 Fit molecule 5v3o (#14) to map 9. combination of 2528 and 2544 emready2 (#8)
    6168 using 11175 atoms 
    6169 average map value = 7.021, steps = 152 
    6170 shifted from previous position = 3.28 
    6171 rotated from previous position = 10.9 degrees 
    6172 atoms outside contour = 4670, contour level = 4.502 
    6173  
    6174 Position of 5v3o (#14) relative to 9. combination of 2528 and 2544 emready2
    6175 (#8) coordinates: 
    6176 Matrix rotation and translation 
    6177 0.26528196 0.56680440 0.77997325 120.97229633 
    6178 -0.46678619 -0.63233295 0.61827640 177.51482496 
    6179 0.84364456 -0.52809831 0.09682995 121.14258530 
    6180 Axis -0.74206572 -0.04121541 -0.66905885 
    6181 Axis point 0.00000000 86.02124003 -48.12980321 
    6182 Rotation angle (degrees) 129.42818226 
    6183 Shift along axis -178.13725982 
    6184  
    6185 
    6186 > select clear
    6187 
    6188 > hide #!8 models
    6189 
    6190 Drag select of 307 residues, 1 pseudobonds 
    6191 
    6192 > delete sel
    6193 
    6194 Drag select of 5 residues, 2 pseudobonds 
    6195 
    6196 > delete sel
    6197 
    6198 > show #!8 models
    6199 
    6200 > hide #!14.2 models
    6201 
    6202 > split #14
    6203 
    6204 Split 5v3o (#14) into 2 models 
    6205 Chain information for 5v3o A #14.1 
    6206 --- 
    6207 Chain | Description 
    6208 A | No description available 
    6209  
    6210 Chain information for 5v3o C #14.2 
    6211 --- 
    6212 Chain | Description 
    6213 C | No description available 
    6214  
    6215 
    6216 > select add #14.1
    6217 
    6218 5977 atoms, 6081 bonds, 10 pseudobonds, 775 residues, 2 models selected 
    6219 
    6220 > fitmap sel inMap #8
    6221 
    6222 Fit molecule 5v3o A (#14.1) to map 9. combination of 2528 and 2544 emready2
    6223 (#8) using 5977 atoms 
    6224 average map value = 10.5, steps = 48 
    6225 shifted from previous position = 0.0818 
    6226 rotated from previous position = 0.0954 degrees 
    6227 atoms outside contour = 859, contour level = 4.502 
    6228  
    6229 Position of 5v3o A (#14.1) relative to 9. combination of 2528 and 2544
    6230 emready2 (#8) coordinates: 
    6231 Matrix rotation and translation 
    6232 0.26556282 0.56807609 0.77895183 120.93900210 
    6233 -0.46621575 -0.63154059 0.61951543 177.60964780 
    6234 0.84387160 -0.52767987 0.09713232 121.11920711 
    6235 Axis -0.74205410 -0.04199283 -0.66902340 
    6236 Axis point 0.00000000 85.98100831 -48.17253109 
    6237 Rotation angle (degrees) 129.37718193 
    6238 Shift along axis -178.23319887 
    6239  
    6240 
    6241 > select subtract #14.1
    6242 
    6243 Nothing selected 
    6244 
    6245 > select add #14.2
    6246 
    6247 2902 atoms, 2974 bonds, 6 pseudobonds, 365 residues, 3 models selected 
    6248 
    6249 > fitmap sel inMap #8
    6250 
    6251 Fit molecule 5v3o C (#14.2) to map 9. combination of 2528 and 2544 emready2
    6252 (#8) using 2902 atoms 
    6253 average map value = 6.215, steps = 148 
    6254 shifted from previous position = 0.846 
    6255 rotated from previous position = 5.97 degrees 
    6256 atoms outside contour = 1226, contour level = 4.502 
    6257  
    6258 Position of 5v3o C (#14.2) relative to 9. combination of 2528 and 2544
    6259 emready2 (#8) coordinates: 
    6260 Matrix rotation and translation 
    6261 0.32722427 0.49885846 0.80253631 122.38342857 
    6262 -0.43918680 -0.67169932 0.59660287 176.79079036 
    6263 0.83668347 -0.54768629 -0.00070427 118.63599032 
    6264 Axis -0.77315201 -0.02307192 -0.63380096 
    6265 Axis point 0.00000000 88.97949673 -40.28109264 
    6266 Rotation angle (degrees) 132.26725177 
    6267 Shift along axis -173.89150166 
    6268  
    6269 
    6270 > select clear
    6271 
    6272 > select add #14
    6273 
    6274 8879 atoms, 9055 bonds, 16 pseudobonds, 1140 residues, 6 models selected 
    6275 
    6276 > combine sel
    6277 
    6278 > close #14
    6279 
    6280 > rename #15 "9b. "
    6281 
    6282 > rename #15 "9b. 5v3o- closed vvd+imid"
    6283 
    6284 > color #15/A:1-710 light blue
    6285 
    6286 > hide #!8 models
    6287 
    6288 > color #15/A:710-5000 steel blue
    6289 
    6290 > color #15/B:1-190 navajowhite
    6291 
    6292 > color #15/C:1-190 navajowhite
    6293 
    6294 > color #15/C:191-320 light salmon
    6295 
    6296 > color #15/C:321-500 tomato
    6297 
    6298 > select clear
    6299 
    6300 > select ::name="8W7"
    6301 
    6302 51 atoms, 57 bonds, 2 residues, 2 models selected 
    6303 
    6304 > color (#!15 & sel) lime
    6305 
    6306 > select clear
    6307 
    6308 > show #!8 models
    6309 
    6310 > color #8 #ffb2b2a1 models
    6311 
    6312 > select #15/C:287
    6313 
    6314 6 atoms, 5 bonds, 1 residue, 1 model selected 
    6315 
    6316 > show sel atoms
    6317 
    6318 > select clear
    6319 
    6320 > volume #8 level 5.503
    6321 
    6322 > color zone #8 near #15 distance 8
    6323 
    6324 > hide #!15 models
    6325 
    6326 > show #!15 models
    6327 
    6328 > hide #!8 models
    6329 
    6330 > show #!8 models
    6331 
    6332 > color #8 #ffb2b29c models
    6333 
    6334 > volume #8 level 2.935
    6335 
    6336 > volume #8 level 5.547
    6337 
    6338 > ui tool show "Side View"
    6339 
    6340 > hide #!8 models
    6341 
    6342 > select #15/C:377
    6343 
    6344 9 atoms, 8 bonds, 1 residue, 1 model selected 
    6345 
    6346 > select up
    6347 
    6348 68 atoms, 72 bonds, 8 residues, 1 model selected 
    6349 
    6350 > show sel atoms
    6351 
    6352 > select clear
    6353 
    6354 > show #!8 models
    6355 
    6356 > color zone #8 near #15 distance 8
    6357 
    6358 > hide #!15 models
    6359 
    6360 > volume #8 level 4.023
    6361 
    6362 > volume #8 level 5.547
    6363 
    6364 > save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
    6365 > inhibitor/Figures/Fig 2b final EMready fig maps/closed/fig2b.closed.png"
    6366 > width 1800 height 1532 supersample 4 transparentBackground true
    6367 
    6368 > volume #8 level 4.807
    6369 
    6370 > volume #8 level 1.672
    6371 
    6372 > volume #8 level 2.107
    6373 
    6374 > volume #8 level 3.109
    6375 
    6376 > color zone #8 near #15 distance 10
    6377 
    6378 > volume #8 level 5.068
    6379 
    6380 > rename #8 "9a. combination of 2528 and 2544 emready2"
    6381 
    6382 > hide #!8 models
    6383 
    6384 > show #!6 models
    6385 
    6386 > show #!3 models
    6387 
    6388 > hide #!6 models
    6389 
    6390 > volume #3 level 6.557
    6391 
    6392 > volume #3 level 3.829
    6393 
    6394 > volume #3 level 2.04
    6395 
    6396 > volume #3 level 3.069
    6397 
    6398 > volume #3 level 4.053
    6399 
    6400 > volume copy #3 modelId #16
    6401 
    6402 Opened 6a. combination of 2526 and 2540 emready2 copy as #16, grid size
    6403 443,443,443, pixel 0.5, shown at step 1, values float32 
    6404 
    6405 > show #!3 models
    6406 
    6407 > hide #!16 models
    6408 
    6409 > show #!16 models
    6410 
    6411 > hide #!3 models
    6412 
    6413 > color #16 #b2ffffff models
    6414 
    6415 > show #!6 models
    6416 
    6417 > color zone #16 near #6 distance 10
    6418 
    6419 > hide #!16 models
    6420 
    6421 > show #!16 models
    6422 
    6423 > hide #!6 models
    6424 
    6425 > rename #16 "6b. combination of 2526 and 2540 emready2 copy"
    6426 
    6427 > rename #6 "6c. vvd+iberdo open.pdb"
    6428 
    6429 > volume #16 level 2.622
    6430 
    6431 > volume #16 level 2.174
    6432 
    6433 > show #!3 models
    6434 
    6435 > hide #!16 models
    6436 
    6437 > volume #3 level 6.557
    6438 
    6439 > show #!16 models
    6440 
    6441 > hide #!16 models
    6442 
    6443 > volume #3 level 5.26
    6444 
    6445 > volume #3 level 4.41
    6446 
    6447 > volume #3 level 4.321
    6448 
    6449 > volume #3 level 6.02
    6450 
    6451 > show #!6 models
    6452 
    6453 > ui tool show "Map Eraser"
    6454 
    6455 > ui tool show "Segment Map"
    6456 
    6457 > select add #6
    6458 
    6459 8572 atoms, 8732 bonds, 4 pseudobonds, 1176 residues, 2 models selected 
    6460 
    6461 > select subtract #6
    6462 
    6463 Nothing selected 
    6464 
    6465 > ui tool show "Color Zone"
    6466 
    6467 > volume splitbyzone #3
    6468 
    6469 Opened 6a. combination of 2526 and 2540 emready2 0 as #14.1, grid size
    6470 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 
    6471 Opened 6a. combination of 2526 and 2540 emready2 1 as #14.2, grid size
    6472 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 
    6473 Opened 6a. combination of 2526 and 2540 emready2 2 as #14.3, grid size
    6474 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 
    6475 Opened 6a. combination of 2526 and 2540 emready2 3 as #14.4, grid size
    6476 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 
    6477 Opened 6a. combination of 2526 and 2540 emready2 4 as #14.5, grid size
    6478 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 
    6479 Opened 6a. combination of 2526 and 2540 emready2 5 as #14.6, grid size
    6480 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 
    6481 Opened 6a. combination of 2526 and 2540 emready2 6 as #14.7, grid size
    6482 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 
    6483 Opened 6a. combination of 2526 and 2540 emready2 7 as #14.8, grid size
    6484 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 
    6485 
    6486 > hide #!14.8 models
    6487 
    6488 > show #!14.8 models
    6489 
    6490 > hide #!14.7 models
    6491 
    6492 > show #!14.7 models
    6493 
    6494 > hide #!14.7 models
    6495 
    6496 > show #!14.7 models
    6497 
    6498 > hide #!14.8 models
    6499 
    6500 > hide #!14.7 models
    6501 
    6502 > hide #!14.6 models
    6503 
    6504 > hide #!14.5 models
    6505 
    6506 > hide #!14.4 models
    6507 
    6508 > select add #14.1
    6509 
    6510 2 models selected 
    6511 
    6512 > select add #14.2
    6513 
    6514 4 models selected 
    6515 
    6516 > select add #14.3
    6517 
    6518 6 models selected 
    6519 
    6520 > select subtract #14.3
    6521 
    6522 4 models selected 
    6523 
    6524 > select subtract #14.2
    6525 
    6526 2 models selected 
    6527 
    6528 > select subtract #14.1
    6529 
    6530 Nothing selected 
    6531 
    6532 > show #!16 models
    6533 
    6534 > hide #!14 models
    6535 
    6536 > hide #!14.1 models
    6537 
    6538 > hide #!14.2 models
    6539 
    6540 > hide #!14.3 models
    6541 
    6542 > show #!14.3 models
    6543 
    6544 > show #!14.2 models
    6545 
    6546 > show #!14.1 models
    6547 
    6548 > hide #!14 models
    6549 
    6550 > volume splitbyzone #16
    6551 
    6552 Opened 6b. combination of 2526 and 2540 emready2 copy 0 as #17.1, grid size
    6553 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 
    6554 Opened 6b. combination of 2526 and 2540 emready2 copy 1 as #17.2, grid size
    6555 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 
    6556 Opened 6b. combination of 2526 and 2540 emready2 copy 2 as #17.3, grid size
    6557 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 
    6558 Opened 6b. combination of 2526 and 2540 emready2 copy 3 as #17.4, grid size
    6559 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 
    6560 Opened 6b. combination of 2526 and 2540 emready2 copy 4 as #17.5, grid size
    6561 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 
    6562 Opened 6b. combination of 2526 and 2540 emready2 copy 5 as #17.6, grid size
    6563 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 
    6564 Opened 6b. combination of 2526 and 2540 emready2 copy 6 as #17.7, grid size
    6565 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 
    6566 Opened 6b. combination of 2526 and 2540 emready2 copy 7 as #17.8, grid size
    6567 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 
    6568 
    6569 > hide #!17.1 models
    6570 
    6571 > hide #!17.2 models
    6572 
    6573 > hide #!17.3 models
    6574 
    6575 > hide #!17.4 models
    6576 
    6577 > show #!17.4 models
    6578 
    6579 > hide #!17.5 models
    6580 
    6581 > show #!17.5 models
    6582 
    6583 > show #!14 models
    6584 
    6585 > hide #!6 models
    6586 
    6587 > hide #!17.5 models
    6588 
    6589 > show #!17.5 models
    6590 
    6591 > hide #!17.5 models
    6592 
    6593 > show #!17.5 models
    6594 
    6595 > hide #!17.6 models
    6596 
    6597 > show #!17.6 models
    6598 
    6599 > hide #!17.6 models
    6600 
    6601 > show #!17.6 models
    6602 
    6603 > hide #!17.7 models
    6604 
    6605 > show #!17.7 models
    6606 
    6607 > volume #17.4 level 2.889
    6608 
    6609 > volume #17.5 level 2.842
    6610 
    6611 > volume #17.6 level 2.849
    6612 
    6613 > volume #17.8 level 2.108
    6614 
    6615 > volume #14.8 level 6.219
    6616 
    6617 > select add #14
    6618 
    6619 17 models selected 
    6620 
    6621 > select subtract #14.4
    6622 
    6623 15 models selected 
    6624 
    6625 > select subtract #14.5
    6626 
    6627 13 models selected 
    6628 
    6629 > select subtract #14.6
    6630 
    6631 11 models selected 
    6632 
    6633 > select subtract #14.7
    6634 
    6635 9 models selected 
    6636 
    6637 > select subtract #14.8
    6638 
    6639 7 models selected 
    6640 
    6641 > hide #!14.8 models
    6642 
    6643 > select add #17.4
    6644 
    6645 9 models selected 
    6646 
    6647 > select add #17.5
    6648 
    6649 11 models selected 
    6650 
    6651 > select add #17.6
    6652 
    6653 13 models selected 
    6654 
    6655 > select add #17.7
    6656 
    6657 15 models selected 
    6658 
    6659 > select add #17.8
    6660 
    6661 17 models selected 
    6662 
    6663 > combine sel
    6664 
    6665 No structures specified 
    6666 
    6667 > select clear
    6668 
    6669 > save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
    6670 > inhibitor/Figures/Fig 2b final EMready fig maps/open/fig2b.open.png" width
    6671 > 1800 height 1802 supersample 4 transparentBackground true
    6672 
    6673 > hide #!14 models
    6674 
    6675 > hide #!17 models
    6676 
    6677 > save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
    6678 > inhibitor/Figures/Fig 2b final EMready fig maps/figure 2 making .cxs"
    6679 > includeMaps true
    6680 
    6681 > open "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
    6682 > inhibitor/Figures/Fig 2b final EMready fig maps/int
    6683 > 1/J2527_map_emready2.mrc"
    6684 
    6685 Opened J2527_map_emready2.mrc as #18, grid size 443,443,443, pixel 0.5, shown
    6686 at level 0.9, step 2, values float32 
    6687 
    6688 > open "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
    6689 > inhibitor/Figures/Fig 2b final EMready fig maps/int
    6690 > 1/J2541_004_volume_map_emready2.mrc"
    6691 
    6692 Opened J2541_004_volume_map_emready2.mrc as #19, grid size 443,443,443, pixel
    6693 0.5, shown at level 1.16, step 2, values float32 
    6694 
    6695 > volume #18 step 1
    6696 
    6697 > volume #19 step 1
    6698 
    6699 > vop max #18 #19
    6700 
    6701 Opened volume maximum as #20, grid size 443,443,443, pixel 0.5, shown at step
    6702 1, values float32 
    6703 
    6704 > rename #18 "10. int1 vvd+imid J2527_map_emready2.mrc"
    6705 
    6706 > rename #19 "11. int1 vvd+imid localJ2541_004_volume_map_emready2.mrc"
    6707 
    6708 > rename #19 "11. int1 vvd+imid local J2541_004_volume_map_emready2.mrc"
    6709 
    6710 > rename #18 "10. int1 vvd+imid NU J2527_map_emready2.mrc"
    6711 
    6712 > rename #20 "12. combination of 10 and 11"
    6713 
    6714 > volume #20 level 2.786
    6715 
    6716 > show #!6 models
    6717 
    6718 > hide #!6 models
    6719 
    6720 > volume copy #6 modelId #21
    6721 
    6722 > combine #6 close false modelId #21
    6723 
    6724 > rename #21 "13. vvd+iberdo int1.pdb"
    6725 
    6726 > volume #20 level 3.94
    6727 
    6728 > select add #21
    6729 
    6730 8572 atoms, 8732 bonds, 4 pseudobonds, 1176 residues, 2 models selected 
    6731 
    6732 > ui mousemode right "translate selected models"
    6733 
    6734 > ui mousemode right "rotate selected models"
    6735 
    6736 > view matrix models
    6737 > #21,0.97808,0.10952,0.17709,-17.951,-0.12509,0.98898,0.079242,-5.2311,-0.16646,-0.099657,0.981,45.059
    6738 
    6739 > ui mousemode right "translate selected models"
    6740 
    6741 > view matrix models
    6742 > #21,0.97808,0.10952,0.17709,-30.302,-0.12509,0.98898,0.079242,8.1696,-0.16646,-0.099657,0.981,35.267
    6743 
    6744 > ui mousemode right translate
    6745 
    6746 > fitmap #21 inMap #20
    6747 
    6748 Fit molecule 13. vvd+iberdo int1.pdb (#21) to map 12. combination of 10 and 11
    6749 (#20) using 8572 atoms 
    6750 average map value = 10.14, steps = 156 
    6751 shifted from previous position = 3.61 
    6752 rotated from previous position = 13.7 degrees 
    6753 atoms outside contour = 1471, contour level = 3.9404 
    6754  
    6755 Position of 13. vvd+iberdo int1.pdb (#21) relative to 12. combination of 10
    6756 and 11 (#20) coordinates: 
    6757 Matrix rotation and translation 
    6758 0.99995221 -0.00495979 0.00842498 -0.14657304 
    6759 0.00521895 0.99950504 -0.03102311 2.46328273 
    6760 -0.00826694 0.03106560 0.99948316 -4.02043145 
    6761 Axis 0.95383084 0.25642777 0.15636984 
    6762 Axis point 0.00000000 130.03408034 78.45787904 
    6763 Rotation angle (degrees) 1.86513633 
    6764 Shift along axis -0.13682601 
    6765  
    6766 
    6767 > split #21
    6768 
    6769 Split 13. vvd+iberdo int1.pdb (#21) into 3 models 
    6770 Chain information for 13. vvd+iberdo int1.pdb A #21.1 
    6771 --- 
    6772 Chain | Description 
    6773 A | No description available 
    6774  
    6775 Chain information for 13. vvd+iberdo int1.pdb B #21.2 
    6776 --- 
    6777 Chain | Description 
    6778 B | No description available 
    6779  
    6780 
    6781 > select add #21.1
    6782 
    6783 6318 atoms, 6434 bonds, 824 residues, 1 model selected 
    6784 
    6785 > fitmap sel inMap #20
    6786 
    6787 Fit molecule 13. vvd+iberdo int1.pdb A (#21.1) to map 12. combination of 10
    6788 and 11 (#20) using 6318 atoms 
    6789 average map value = 11.2, steps = 64 
    6790 shifted from previous position = 0.057 
    6791 rotated from previous position = 0.261 degrees 
    6792 atoms outside contour = 716, contour level = 3.9404 
    6793  
    6794 Position of 13. vvd+iberdo int1.pdb A (#21.1) relative to 12. combination of
    6795 10 and 11 (#20) coordinates: 
    6796 Matrix rotation and translation 
    6797 0.99997710 -0.00370364 0.00566496 -0.04489164 
    6798 0.00385882 0.99961071 -0.02763236 2.26194806 
    6799 -0.00556041 0.02765359 0.99960210 -3.76505421 
    6800 Axis 0.97131472 0.19721768 0.13286424 
    6801 Axis point 0.00000000 136.84114012 80.62843893 
    6802 Rotation angle (degrees) 1.63082033 
    6803 Shift along axis -0.09774884 
    6804  
    6805 
    6806 > select subtract #21.1
    6807 
    6808 Nothing selected 
    6809 
    6810 > select add #21.2
    6811 
    6812 2236 atoms, 2278 bonds, 4 pseudobonds, 351 residues, 2 models selected 
    6813 
    6814 > fitmap sel inMap #20
    6815 
    6816 Fit molecule 13. vvd+iberdo int1.pdb B (#21.2) to map 12. combination of 10
    6817 and 11 (#20) using 2236 atoms 
    6818 average map value = 7.656, steps = 72 
    6819 shifted from previous position = 0.362 
    6820 rotated from previous position = 1.2 degrees 
    6821 atoms outside contour = 705, contour level = 3.9404 
    6822  
    6823 Position of 13. vvd+iberdo int1.pdb B (#21.2) relative to 12. combination of
    6824 10 and 11 (#20) coordinates: 
    6825 Matrix rotation and translation 
    6826 0.99957428 -0.00690597 0.02834733 -2.14892969 
    6827 0.00760810 0.99966507 -0.02473610 1.22829977 
    6828 -0.02816701 0.02494124 0.99929203 -1.15331989 
    6829 Axis 0.64826372 0.73748312 0.18940116 
    6830 Axis point -37.68629592 0.00000000 59.10362530 
    6831 Rotation angle (degrees) 2.19586462 
    6832 Shift along axis -0.70566292 
    6833  
    6834 
    6835 > select subtract #21.2
    6836 
    6837 Nothing selected 
    6838 
    6839 > select add #21.3
    6840 
    6841 18 atoms, 20 bonds, 1 residue, 1 model selected 
    6842 
    6843 > fitmap sel inMap #20
    6844 
    6845 Fit molecule 13. vvd+iberdo int1.pdb C (#21.3) to map 12. combination of 10
    6846 and 11 (#20) using 18 atoms 
    6847 average map value = 4.502, steps = 88 
    6848 shifted from previous position = 2.28 
    6849 rotated from previous position = 28.1 degrees 
    6850 atoms outside contour = 6, contour level = 3.9404 
    6851  
    6852 Position of 13. vvd+iberdo int1.pdb C (#21.3) relative to 12. combination of
    6853 10 and 11 (#20) coordinates: 
    6854 Matrix rotation and translation 
    6855 0.88481403 0.46470450 -0.03396844 -31.04162349 
    6856 -0.46574688 0.88420785 -0.03544474 62.18114561 
    6857 0.01356383 0.04718270 0.99879418 -9.42993675 
    6858 Axis 0.08834121 -0.05081918 -0.99479307 
    6859 Axis point 110.31812113 94.80438715 0.00000000 
    6860 Rotation angle (degrees) 27.88255888 
    6861 Shift along axis 3.47858654 
    6862  
    6863 
    6864 > select subtract #21.3
    6865 
    6866 Nothing selected 
    6867 
    6868 > select add #21
    6869 
    6870 8572 atoms, 8732 bonds, 4 pseudobonds, 1176 residues, 5 models selected 
    6871 
    6872 > combine sel
    6873 
    6874 > rename #22 "13. vvd+iberdo int1.pdb"
    6875 
    6876 > close #21
    6877 
    6878 > volume #20 level 3.094
    6879 
    6880 > volume #20 level 1.785
    6881 
    6882 > volume #20 level 0.3997
    6883 
    6884 > volume #20 level 0.6692
    6885 
    6886 > volume #20 level 3.286
    6887 
    6888 > color zone #20 near #22 distance 10
    6889 
    6890 > hide #!20 models
    6891 
    6892 > ui tool show "Show Sequence Viewer"
    6893 
    6894 > sequence chain #22/B
    6895 
    6896 Alignment identifier is 22/B 
    6897 
    6898 > select #22/B:304-380
    6899 
    6900 364 atoms, 365 bonds, 61 residues, 1 model selected 
    6901 
    6902 > select #22/B:304-380
    6903 
    6904 364 atoms, 365 bonds, 61 residues, 1 model selected 
    6905 
    6906 > select #22/B:380
    6907 
    6908 14 atoms, 15 bonds, 1 residue, 1 model selected 
    6909 
    6910 > select #22/B:380
    6911 
    6912 14 atoms, 15 bonds, 1 residue, 1 model selected 
    6913 
    6914 > select #22/B:386
    6915 
    6916 14 atoms, 15 bonds, 1 residue, 1 model selected 
    6917 
    6918 > select #22/B:386
    6919 
    6920 14 atoms, 15 bonds, 1 residue, 1 model selected 
    6921 
    6922 > select #22/B:400
    6923 
    6924 14 atoms, 15 bonds, 1 residue, 1 model selected 
    6925 
    6926 > select #22/B:400
    6927 
    6928 14 atoms, 15 bonds, 1 residue, 1 model selected 
    6929 
    6930 > select clear
    6931 
    6932 > select #22/B:380
    6933 
    6934 14 atoms, 15 bonds, 1 residue, 1 model selected 
    6935 
    6936 > select #22/B:380
    6937 
    6938 14 atoms, 15 bonds, 1 residue, 1 model selected 
    6939 
    6940 > show sel atoms
    6941 
    6942 > select #22/B:385-386
    6943 
    6944 19 atoms, 20 bonds, 2 residues, 1 model selected 
    6945 
    6946 > select #22/B:385-386
    6947 
    6948 19 atoms, 20 bonds, 2 residues, 1 model selected 
    6949 
    6950 > select #22/B:386
    6951 
    6952 14 atoms, 15 bonds, 1 residue, 1 model selected 
    6953 
    6954 > select #22/B:386
    6955 
    6956 14 atoms, 15 bonds, 1 residue, 1 model selected 
    6957 
    6958 > show sel atoms
    6959 
    6960 > select #22/B:400
    6961 
    6962 14 atoms, 15 bonds, 1 residue, 1 model selected 
    6963 
    6964 > select #22/B:400
    6965 
    6966 14 atoms, 15 bonds, 1 residue, 1 model selected 
    6967 
    6968 > show sel atoms
    6969 
    6970 > select clear
    6971 
    6972 > select ::name="8W7"
    6973 
    6974 69 atoms, 77 bonds, 3 residues, 3 models selected 
    6975 
    6976 > ui mousemode right "translate selected models"
    6977 
    6978 > ui mousemode right "rotate selected models"
    6979 
    6980 > view matrix models
    6981 > #6,0.98816,-0.15319,0.0089352,36.88,0.054684,0.29714,-0.95327,185.4,0.14337,0.94246,0.302,-62.636,#15,0.33655,0.47781,0.81144,123.71,-0.45116,-0.67455,0.58433,177.73,0.82655,-0.56275,-0.011449,119.32,#22,0.99241,0.043403,0.11506,-17.961,-0.044168,0.99902,0.0041065,4.463,-0.11476,-0.0091571,0.99335,14.959
    6982 
    6983 > undo
    6984 
    6985 > ui mousemode right translate
    6986 
    6987 > select add #22
    6988 
    6989 8623 atoms, 8789 bonds, 4 pseudobonds, 1178 residues, 4 models selected 
    6990 
    6991 > select subtract #22
    6992 
    6993 51 atoms, 57 bonds, 2 residues, 2 models selected 
    6994 
    6995 > hide #!22 models
    6996 
    6997 > show #!22 models
    6998 
    6999 > show #!20 models
    7000 
    7001 > split #22
    7002 
    7003 Split 13. vvd+iberdo int1.pdb (#22) into 3 models 
    7004 Chain information for 13. vvd+iberdo int1.pdb A #22.1 
    7005 --- 
    7006 Chain | Description 
    7007 A | No description available 
    7008  
    7009 Chain information for 13. vvd+iberdo int1.pdb B #22.2 
    7010 --- 
    7011 Chain | Description 
    7012 B | No description available 
    7013  
    7014 
    7015 > select add #22.3
    7016 
    7017 69 atoms, 77 bonds, 3 residues, 3 models selected 
    7018 
    7019 > hide #!20 models
    7020 
    7021 > ui mousemode right "translate selected models"
    7022 
    7023 > ui mousemode right "rotate selected models"
    7024 
    7025 > view matrix models
    7026 > #6,0.45288,-0.60813,0.65198,63.103,0.65358,-0.27093,-0.7067,186.66,0.60641,0.74617,0.27477,-71.309,#15,0.27736,0.96074,-0.0072709,59.877,-0.36454,0.11224,0.9244,172.73,0.88892,-0.25374,0.38136,129.94,#22.3,0.61242,-0.75011,-0.24956,149.65,0.69113,0.66128,-0.29162,6.4196,0.38378,0.0061171,0.9234,-29.009
    7027 
    7028 > ui mousemode right "translate selected models"
    7029 
    7030 > view matrix models
    7031 > #6,0.45288,-0.60813,0.65198,66.626,0.65358,-0.27093,-0.7067,185.57,0.60641,0.74617,0.27477,-70.936,#15,0.27736,0.96074,-0.0072709,63.4,-0.36454,0.11224,0.9244,171.63,0.88892,-0.25374,0.38136,130.31,#22.3,0.61242,-0.75011,-0.24956,153.17,0.69113,0.66128,-0.29162,5.324,0.38378,0.0061171,0.9234,-28.635
    7032 
    7033 > ui mousemode right translate
    7034 
    7035 > ui mousemode right "translate selected models"
    7036 
    7037 > view matrix models
    7038 > #6,0.45288,-0.60813,0.65198,66.315,0.65358,-0.27093,-0.7067,185.29,0.60641,0.74617,0.27477,-70.511,#15,0.27736,0.96074,-0.0072709,63.089,-0.36454,0.11224,0.9244,171.35,0.88892,-0.25374,0.38136,130.74,#22.3,0.61242,-0.75011,-0.24956,152.86,0.69113,0.66128,-0.29162,5.0465,0.38378,0.0061171,0.9234,-28.21
    7039 
    7040 > ui mousemode right translate
    7041 
    7042 > show #!20 models
    7043 
    7044 > hide #!20 models
    7045 
    7046 > select add #22
    7047 
    7048 8623 atoms, 8789 bonds, 4 pseudobonds, 1178 residues, 7 models selected 
    7049 
    7050 > combine sel
    7051 
    7052 Remapping chain ID 'A' in 9b. 5v3o- closed vvd+imid #15 to 'D' 
    7053 Remapping chain ID 'C' in 9b. 5v3o- closed vvd+imid #15 to 'E' 
    7054 Remapping chain ID 'A' in 13. vvd+iberdo int1.pdb A #22.1 to 'F' 
    7055 Remapping chain ID 'B' in 13. vvd+iberdo int1.pdb B #22.2 to 'G' 
    7056 Remapping chain ID 'C' in 13. vvd+iberdo int1.pdb C #22.3 to 'H' 
    7057 
    7058 > rename #21 "13. vvd+iberdo int1.pdb"
    7059 
    7060 > close #22
    7061 
    7062 > select add #15
    7063 
    7064 8897 atoms, 9075 bonds, 16 pseudobonds, 1141 residues, 4 models selected 
    7065 
    7066 > select subtract #15
    7067 
    7068 18 atoms, 20 bonds, 1 residue, 1 model selected 
    7069 
    7070 > select add #6
    7071 
    7072 8572 atoms, 8732 bonds, 4 pseudobonds, 1176 residues, 2 models selected 
    7073 
    7074 > select subtract #6
    7075 
    7076 Nothing selected 
    7077 
    7078 > show #!20 models
    7079 
    7080 > split #13
    7081 
    7082 > hide #21.2 models
    7083 
    7084 > show #21.2 models
    7085 
    7086 > hide #21.2 models
    7087 
    7088 > show #21.2 models
    7089 
    7090 > split #21
    7091 
    7092 Split 13. vvd+iberdo int1.pdb (#21) into 8 models 
    7093 Chain information for 13. vvd+iberdo int1.pdb A #21.1 
    7094 --- 
    7095 Chain | Description 
    7096 A | No description available 
    7097  
    7098 Chain information for 13. vvd+iberdo int1.pdb B #21.2 
    7099 --- 
    7100 Chain | Description 
    7101 B | No description available 
    7102  
    7103 Chain information for 13. vvd+iberdo int1.pdb D #21.4 
    7104 --- 
    7105 Chain | Description 
    7106 D | No description available 
    7107  
    7108 Chain information for 13. vvd+iberdo int1.pdb E #21.5 
    7109 --- 
    7110 Chain | Description 
    7111 E | No description available 
    7112  
    7113 Chain information for 13. vvd+iberdo int1.pdb F #21.6 
    7114 --- 
    7115 Chain | Description 
    7116 F | No description available 
    7117  
    7118 Chain information for 13. vvd+iberdo int1.pdb G #21.7 
    7119 --- 
    7120 Chain | Description 
    7121 G | No description available 
    7122  
    7123 
    7124 Cell requested for row 20 is out of bounds for table with 35 rows! Resizing
    7125 table model. 
    7126 
    7127 > ~split #13
    7128 
    7129 Unknown command: ~split #13 
    7130 
    7131 > hide #!21 models
    7132 
    7133 > show #!21 models
    7134 
    7135 > hide #21.1 models
    7136 
    7137 > show #21.1 models
    7138 
    7139 > hide #21.1 models
    7140 
    7141 > hide #!21.2 models
    7142 
    7143 > hide #21.3 models
    7144 
    7145 > hide #!21.4 models
    7146 
    7147 > hide #!21.5 models
    7148 
    7149 > hide #21.6 models
    7150 
    7151 > show #21.6 models
    7152 
    7153 > hide #!21.7 models
    7154 
    7155 > show #!21.7 models
    7156 
    7157 > hide #21.8 models
    7158 
    7159 > show #21.8 models
    7160 
    7161 > close #21.1,3#21.2,4-5
    7162 
    7163 > hide #!21 models
    7164 
    7165 > show #!21 models
    7166 
    7167 > hide #!20 models
    7168 
    7169 > select add #21.6
    7170 
    7171 6318 atoms, 6434 bonds, 824 residues, 1 model selected 
    7172 
    7173 > select add #21.7
    7174 
    7175 8554 atoms, 8712 bonds, 4 pseudobonds, 1175 residues, 3 models selected 
    7176 
    7177 > select add #21.8
    7178 
    7179 8572 atoms, 8732 bonds, 4 pseudobonds, 1176 residues, 4 models selected 
    7180 
    7181 > combine sel
    7182 
    7183 > rename #22 "13. vvd+iberdo int1.pdb"
    7184 
    7185 > close #21
    7186 
    7187 > show #!20 models
    7188 
    7189 > color zone #20 near #22 distance 10
    7190 
    7191 > color zone #20 near #22 distance 8
    7192 
    7193 > hide #!22 models
    7194 
    7195 > volume #20 level 1.554
    7196 
    7197 > volume #20 level 0.05338
    7198 
    7199 > volume #20 level 0.5922
    7200 
    7201 > volume #20 level 0.7461
    7202 
    7203 > volume #20 level 0.8616
    7204 
    7205 > save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
    7206 > inhibitor/Figures/Fig 2b final EMready fig maps/0. figure 2 making .cxs"
    7207 > includeMaps true
    7208 
    7209 ——— End of log from Tue Feb 24 16:13:45 2026 ———
    7210 
    7211 > view name session-start
    7212 
    7213 opened ChimeraX session 
    7214 
    7215 > hide #!20 models
    7216 
    7217 > open "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
    7218 > inhibitor/Figures/Fig 2b final EMready fig maps/int
    7219 > 2/J2612_map_emready2.mrc"
    7220 
    7221 Opened J2612_map_emready2.mrc as #21, grid size 438,438,438, pixel 0.5, shown
    7222 at level 1.43, step 2, values float32 
    7223 
    7224 > open "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
    7225 > inhibitor/Figures/Fig 2b final EMready fig maps/int
    7226 > 2/J2614_004_volume_map_emready2.mrc"
    7227 
    7228 Opened J2614_004_volume_map_emready2.mrc as #23, grid size 438,438,438, pixel
    7229 0.5, shown at level 1.74, step 2, values float32 
    7230 
    7231 > rename #21 "14. int2 vvd+imid NU J2612_map_emready2.mrc"
    7232 
    7233 > rename #23 "15. int2 vvd+imid local J2614_004_volume_map_emready2.mrc"
    7234 
    7235 > volume #21 step 1
    7236 
    7237 > volume #23 step 1
    7238 
    7239 > vop max #21 #23
    7240 
    7241 Opened volume maximum as #24, grid size 438,438,438, pixel 0.5, shown at step
    7242 1, values float32 
    7243 
    7244 > rename #24 "16. combination of 2612 and 2614"
    7245 
    7246 > volume #24 level 3.89
    7247 
    7248 > volume #21 level 3.831
    7249 
    7250 > volume #24 level 5.718
    7251 
    7252 > show #!22 models
    7253 
    7254 > show #!15 models
    7255 
    7256 > hide #!15 models
    7257 
    7258 > fitmap #22 inMap #24
    7259 
    7260 Fit molecule 13. vvd+iberdo int1.pdb (#22) to map 16. combination of 2612 and
    7261 2614 (#24) using 8572 atoms 
    7262 average map value = 8.35, steps = 80 
    7263 shifted from previous position = 2.43 
    7264 rotated from previous position = 0.353 degrees 
    7265 atoms outside contour = 2629, contour level = 5.7183 
    7266  
    7267 Position of 13. vvd+iberdo int1.pdb (#22) relative to 16. combination of 2612
    7268 and 2614 (#24) coordinates: 
    7269 Matrix rotation and translation 
    7270 0.45163826 -0.61293634 0.64833010 65.88218884 
    7271 0.65218078 -0.26907192 -0.70870342 184.09421817 
    7272 0.60883751 0.74290601 0.27822212 -72.06569896 
    7273 Axis 0.75371416 0.02050560 0.65688240 
    7274 Axis point 0.00000000 129.42532737 27.82438434 
    7275 Rotation angle (degrees) 105.64080909 
    7276 Shift along axis 6.09261176 
    7277  
    7278 
    7279 > show #!15 models
    7280 
    7281 > mmaker #15 to #22
    7282 
    7283 Parameters 
    7284 --- 
    7285 Chain pairing | bb 
    7286 Alignment algorithm | Needleman-Wunsch 
    7287 Similarity matrix | BLOSUM-62 
    7288 SS fraction | 0.3 
    7289 Gap open (HH/SS/other) | 18/18/6 
    7290 Gap extend | 1 
    7291 SS matrix |  |  | H | S | O 
    7292 ---|---|---|--- 
    7293 H | 6 | -9 | -6 
    7294 S |  | 6 | -6 
    7295 O |  |  | 4 
    7296 Iteration cutoff | 2 
    7297  
    7298 Matchmaker 13. vvd+iberdo int1.pdb, chain F (#22) with 9b. 5v3o- closed
    7299 vvd+imid, chain A (#15), sequence alignment score = 3564 
    7300 RMSD between 740 pruned atom pairs is 0.665 angstroms; (across all 774 pairs:
    7301 1.333) 
    7302  
    7303 
    7304 > hide #!22 models
    7305 
    7306 > show #!22 models
    7307 
    7308 > hide #!15 models
    7309 
    7310 > fitmap #22 inMap #24
    7311 
    7312 Fit molecule 13. vvd+iberdo int1.pdb (#22) to map 16. combination of 2612 and
    7313 2614 (#24) using 8572 atoms 
    7314 average map value = 8.351, steps = 28 
    7315 shifted from previous position = 0.00666 
    7316 rotated from previous position = 0.00313 degrees 
    7317 atoms outside contour = 2632, contour level = 5.7183 
    7318  
    7319 Position of 13. vvd+iberdo int1.pdb (#22) relative to 16. combination of 2612
    7320 and 2614 (#24) coordinates: 
    7321 Matrix rotation and translation 
    7322 0.45167734 -0.61294587 0.64829387 65.87675748 
    7323 0.65215206 -0.26904443 -0.70874028 184.09774684 
    7324 0.60883929 0.74290811 0.27821264 -72.06340139 
    7325 Axis 0.75372813 0.02048570 0.65686699 
    7326 Axis point 0.00000000 129.42594701 27.83211750 
    7327 Rotation angle (degrees) 105.63911106 
    7328 Shift along axis 6.08846697 
    7329  
    7330 
    7331 > show #!15 models
    7332 
    7333 > hide #!22 models
    7334 
    7335 > hide #!15 models
    7336 
    7337 > show #!15 models
    7338 
    7339 > show #!22 models
    7340 
    7341 > color zone #24 near #22 distance 8
    7342 
    7343 > hide #!15 models
    7344 
    7345 > hide #!22 models
    7346 
    7347 > show #!15 models
    7348 
    7349 > color zone #24 near #15 distance 8
    7350 
    7351 > hide #!15 models
    7352 
    7353 > show #!15 models
    7354 
    7355 > show #!22 models
    7356 
    7357 > select add #22
    7358 
    7359 8572 atoms, 8732 bonds, 4 pseudobonds, 1176 residues, 2 models selected 
    7360 
    7361 > select add #15
    7362 
    7363 17451 atoms, 17787 bonds, 20 pseudobonds, 2316 residues, 5 models selected 
    7364 
    7365 > hide #!24 models
    7366 
    7367 > combine sel
    7368 
    7369 > select subtract #22
    7370 
    7371 8879 atoms, 9055 bonds, 16 pseudobonds, 1140 residues, 3 models selected 
    7372 
    7373 > select subtract #15
    7374 
    7375 Nothing selected 
    7376 
    7377 > rename #25 "combination of 15 and 22 for int2"
    7378 
    7379 > show #!24 models
    7380 
    7381 > hide #!22 models
    7382 
    7383 > color zone #24 near #25 distance 8
    7384 
    7385 > hide #!24 models
    7386 
    7387 > split #25
    7388 
    7389 Split combination of 15 and 22 for int2 (#25) into 5 models 
    7390 Chain information for combination of 15 and 22 for int2 A #25.1 
    7391 --- 
    7392 Chain | Description 
    7393 A | No description available 
    7394  
    7395 Chain information for combination of 15 and 22 for int2 C #25.2 
    7396 --- 
    7397 Chain | Description 
    7398 C | No description available 
    7399  
    7400 Chain information for combination of 15 and 22 for int2 F #25.3 
    7401 --- 
    7402 Chain | Description 
    7403 F | No description available 
    7404  
    7405 Chain information for combination of 15 and 22 for int2 G #25.4 
    7406 --- 
    7407 Chain | Description 
    7408 G | No description available 
    7409  
    7410 
    7411 > hide #25.5 models
    7412 
    7413 > show #25.5 models
    7414 
    7415 > hide #!25.1 models
    7416 
    7417 > show #!25.1 models
    7418 
    7419 > hide #!25.1 models
    7420 
    7421 > show #!25.1 models
    7422 
    7423 > hide #!25.1 models
    7424 
    7425 > show #!25.1 models
    7426 
    7427 > hide #!25.2 models
    7428 
    7429 > show #!25.2 models
    7430 
    7431 > select add #25.1
    7432 
    7433 5977 atoms, 6081 bonds, 10 pseudobonds, 775 residues, 2 models selected 
    7434 
    7435 > select subtract #25.1
    7436 
    7437 Nothing selected 
    7438 
    7439 > select add #25.2
    7440 
    7441 2902 atoms, 2974 bonds, 6 pseudobonds, 365 residues, 3 models selected 
    7442 
    7443 > select subtract #25.2
    7444 
    7445 Nothing selected 
    7446 
    7447 > select add #25.3
    7448 
    7449 6318 atoms, 6434 bonds, 824 residues, 1 model selected 
    7450 
    7451 > select subtract #25.3
    7452 
    7453 Nothing selected 
    7454 
    7455 > select add #25.4
    7456 
    7457 2236 atoms, 2278 bonds, 4 pseudobonds, 351 residues, 2 models selected 
    7458 
    7459 > select subtract #25.4
    7460 
    7461 Nothing selected 
    7462 
    7463 > select add #25.5
    7464 
    7465 18 atoms, 20 bonds, 1 residue, 1 model selected 
    7466 
    7467 > select subtract #25.5
    7468 
    7469 Nothing selected 
    7470 
    7471 > select add #25.4
    7472 
    7473 2236 atoms, 2278 bonds, 4 pseudobonds, 351 residues, 2 models selected 
    7474 
    7475 > select subtract #25.4
    7476 
    7477 Nothing selected 
    7478 
    7479 > show #!24 models
    7480 
    7481 > hide #!25 models
    7482 
    7483 > hide #!15 models
    7484 
    7485 > show #!22 models
    7486 
    7487 > color #24 #b2ffff9a models
    7488 
    7489 > close #25
    7490 
    7491 > color #24 darkgrey models
    7492 
    7493 > volume copy #22 modelId #25
    7494 
    7495 > copy #22 modelId #25
    7496 
    7497 Unknown command: modelcif copy #22 modelId #25 
    7498 
    7499 > combine #22 close false modelId #25
    7500 
    7501 > hide #!22 models
    7502 
    7503 > hide #!25 models
    7504 
    7505 > show #!25 models
    7506 
    7507 > split #25
    7508 
    7509 Split copy of 13. vvd+iberdo int1.pdb (#25) into 3 models 
    7510 Chain information for copy of 13. vvd+iberdo int1.pdb F #25.1 
    7511 --- 
    7512 Chain | Description 
    7513 F | No description available 
    7514  
    7515 Chain information for copy of 13. vvd+iberdo int1.pdb G #25.2 
    7516 --- 
    7517 Chain | Description 
    7518 G | No description available 
    7519  
    7520 
    7521 > hide #25.1 models
    7522 
    7523 > show #25.1 models
    7524 
    7525 > hide #!25.2 models
    7526 
    7527 > show #!25.2 models
    7528 
    7529 > hide #!25.2 models
    7530 
    7531 > show #!25.2 models
    7532 
    7533 > hide #25.3 models
    7534 
    7535 > show #25.3 models
    7536 
    7537 > hide #!24 models
    7538 
    7539 Drag select of 4 atoms, 5 bonds 
    7540 
    7541 > select up
    7542 
    7543 6 atoms, 5 bonds, 1 residue, 1 model selected 
    7544 
    7545 > select up
    7546 
    7547 28 atoms, 30 bonds, 1 residue, 1 model selected 
    7548 
    7549 > show #!24 models
    7550 
    7551 > fitmap sel inMap #24
    7552 
    7553 Fit molecule copy of 13. vvd+iberdo int1.pdb G (#25.2) to map 16. combination
    7554 of 2612 and 2614 (#24) using 28 atoms 
    7555 average map value = 5.606, steps = 72 
    7556 shifted from previous position = 0.741 
    7557 rotated from previous position = 16 degrees 
    7558 atoms outside contour = 15, contour level = 5.7183 
    7559  
    7560 Position of copy of 13. vvd+iberdo int1.pdb G (#25.2) relative to 16.
    7561 combination of 2612 and 2614 (#24) coordinates: 
    7562 Matrix rotation and translation 
    7563 0.42141688 -0.42628134 0.80043240 23.16077837 
    7564 0.65007113 -0.47341581 -0.59437783 195.98753721 
    7565 0.63230954 0.77081884 0.07760778 -49.90209341 
    7566 Axis 0.78163734 0.09625801 0.61626087 
    7567 Axis point -0.00000000 116.75111860 39.31212244 
    7568 Rotation angle (degrees) 119.15642117 
    7569 Shift along axis 6.21599173 
    7570  
    7571 
    7572 > select clear
    7573 
    7574 > select add #25.2
    7575 
    7576 2236 atoms, 2278 bonds, 4 pseudobonds, 351 residues, 2 models selected 
    7577 
    7578 > fitmap sel inMap #24
    7579 
    7580 Fit molecule copy of 13. vvd+iberdo int1.pdb G (#25.2) to map 16. combination
    7581 of 2612 and 2614 (#24) using 2236 atoms 
    7582 average map value = 6.352, steps = 140 
    7583 shifted from previous position = 1.85 
    7584 rotated from previous position = 15.9 degrees 
    7585 atoms outside contour = 1087, contour level = 5.7183 
    7586  
    7587 Position of copy of 13. vvd+iberdo int1.pdb G (#25.2) relative to 16.
    7588 combination of 2612 and 2614 (#24) coordinates: 
    7589 Matrix rotation and translation 
    7590 0.46020337 -0.60991945 0.64514426 65.00734733 
    7591 0.64393234 -0.27095217 -0.71549707 186.31859717 
    7592 0.61119882 0.74470342 0.26805376 -71.47008660 
    7593 Axis 0.75856034 0.01763434 0.65136414 
    7594 Axis point 0.00000000 130.03256142 29.27592670 
    7595 Rotation angle (degrees) 105.74446776 
    7596 Shift along axis 6.04454892 
    7597  
    7598 
    7599 > select subtract #25.2
    7600 
    7601 Nothing selected 
    7602 
    7603 > select add #25.3
    7604 
    7605 18 atoms, 20 bonds, 1 residue, 1 model selected 
    7606 
    7607 > fitmap sel inMap #24
    7608 
    7609 Fit molecule copy of 13. vvd+iberdo int1.pdb H (#25.3) to map 16. combination
    7610 of 2612 and 2614 (#24) using 18 atoms 
    7611 average map value = 4.771, steps = 180 
    7612 shifted from previous position = 7.43 
    7613 rotated from previous position = 82.1 degrees 
    7614 atoms outside contour = 14, contour level = 5.7183 
    7615  
    7616 Position of copy of 13. vvd+iberdo int1.pdb H (#25.3) relative to 16.
    7617 combination of 2612 and 2614 (#24) coordinates: 
    7618 Matrix rotation and translation 
    7619 0.00128243 -0.82016674 0.57212313 145.80499439 
    7620 -0.55258168 -0.47742246 -0.68317003 317.28361071 
    7621 0.83345776 -0.31526864 -0.45382138 172.95855387 
    7622 Axis 0.70124303 -0.49812015 0.51003385 
    7623 Axis point 0.00000000 195.53758721 65.19329041 
    7624 Rotation angle (degrees) 164.79218005 
    7625 Shift along axis 32.41409441 
    7626  
    7627 
    7628 > select clear
    7629 
    7630 > hide #!25 models
    7631 
    7632 > show #!15 models
    7633 
    7634 > fitmap #15 inMap #24
    7635 
    7636 Fit molecule 9b. 5v3o- closed vvd+imid (#15) to map 16. combination of 2612
    7637 and 2614 (#24) using 8879 atoms 
    7638 average map value = 8.047, steps = 64 
    7639 shifted from previous position = 0.096 
    7640 rotated from previous position = 0.225 degrees 
    7641 atoms outside contour = 3061, contour level = 5.7183 
    7642  
    7643 Position of 9b. 5v3o- closed vvd+imid (#15) relative to 16. combination of
    7644 2612 and 2614 (#24) coordinates: 
    7645 Matrix rotation and translation 
    7646 0.25938960 0.57250458 0.77778888 119.40701811 
    7647 -0.46597542 -0.63122094 0.62002180 176.15425577 
    7648 0.84592195 -0.52325771 0.10304092 119.95342407 
    7649 Axis -0.73949960 -0.04407004 -0.67171286 
    7650 Axis point 0.00000000 84.93576646 -48.09633206 
    7651 Rotation angle (degrees) 129.37514280 
    7652 Shift along axis -176.63882591 
    7653  
    7654 
    7655 > show #!25 models
    7656 
    7657 > hide #!15 models
    7658 
    7659 > show #!15 models
    7660 
    7661 > close #25
    7662 
    7663 > show #!22 models
    7664 
    7665 > mmaker #22 to #15
    7666 
    7667 Parameters 
    7668 --- 
    7669 Chain pairing | bb 
    7670 Alignment algorithm | Needleman-Wunsch 
    7671 Similarity matrix | BLOSUM-62 
    7672 SS fraction | 0.3 
    7673 Gap open (HH/SS/other) | 18/18/6 
    7674 Gap extend | 1 
    7675 SS matrix |  |  | H | S | O 
    7676 ---|---|---|--- 
    7677 H | 6 | -9 | -6 
    7678 S |  | 6 | -6 
    7679 O |  |  | 4 
    7680 Iteration cutoff | 2 
    7681  
    7682 Matchmaker 9b. 5v3o- closed vvd+imid, chain A (#15) with 13. vvd+iberdo
    7683 int1.pdb, chain F (#22), sequence alignment score = 3564 
    7684 RMSD between 740 pruned atom pairs is 0.665 angstroms; (across all 774 pairs:
    7685 1.333) 
    7686  
    7687 
    7688 > hide #!24 models
    7689 
    7690 > select add #15
    7691 
    7692 8879 atoms, 9055 bonds, 16 pseudobonds, 1140 residues, 3 models selected 
    7693 
    7694 > select add #22
    7695 
    7696 17451 atoms, 17787 bonds, 20 pseudobonds, 2316 residues, 5 models selected 
    7697 
    7698 > combine sel
    7699 
    7700 > select subtract #15
    7701 
    7702 8572 atoms, 8732 bonds, 4 pseudobonds, 1176 residues, 2 models selected 
    7703 
    7704 > select subtract #22
    7705 
    7706 Nothing selected 
    7707 
    7708 > hide #!22 models
    7709 
    7710 > hide #!15 models
    7711 
    7712 > show #!24 models
    7713 
    7714 > hide #!24 models
    7715 
    7716 Drag select of 6 atoms, 8 bonds 
    7717 
    7718 > select up
    7719 
    7720 8 atoms, 8 bonds, 1 residue, 1 model selected 
    7721 
    7722 > select up
    7723 
    7724 18 atoms, 20 bonds, 1 residue, 1 model selected 
    7725 
    7726 > delete sel
    7727 
    7728 > show #!24 models
    7729 
    7730 > show #!25 atoms
    7731 
    7732 > color zone #24 near #25 distance 8
    7733 
    7734 > hide #!25 models
    7735 
    7736 > color zone #24 near #25 distance 10
    7737 
    7738 > volume #24 level 7.006
    7739 
    7740 > volume #24 level 6.049
    7741 
    7742 > volume #24 level 5.058
    7743 
    7744 > volume #24 level 5.355
    7745 
    7746 > show #!7 models
    7747 
    7748 > hide #!7 models
    7749 
    7750 > show #!8 models
    7751 
    7752 > hide #!24 models
    7753 
    7754 > show #!24 models
    7755 
    7756 > hide #!24 models
    7757 
    7758 > show #!24 models
    7759 
    7760 > hide #!8 models
    7761 
    7762 > save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
    7763 > inhibitor/Figures/Fig 2b final EMready fig maps/int 2/int2.png" width 1800
    7764 > height 1592 supersample 4 transparentBackground true
    7765 
    7766 > volume #24 level 5.916
    7767 
    7768 > save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
    7769 > inhibitor/Figures/Fig 2b final EMready fig maps/int 2/int2.png" width 1800
    7770 > height 1592 supersample 4 transparentBackground true
    7771 
    7772 > rename #25 "combination of open closed for int2 "
    7773 
    7774 > show #!25 models
    7775 
    7776 > hide #!24 models
    7777 
    7778 > show #!24 models
    7779 
    7780 > hide #!25 models
    7781 
    7782 > hide #!24 models
    7783 
    7784 > open "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
    7785 > inhibitor/Figures/Fig 2b final EMready fig
    7786 > maps/frustrated/J2438_map_emready2.mrc"
    7787 
    7788 Opened J2438_map_emready2.mrc as #26, grid size 443,443,443, pixel 0.5, shown
    7789 at level 1.18, step 2, values float32 
    7790 
    7791 > open "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
    7792 > inhibitor/Figures/Fig 2b final EMready fig
    7793 > maps/frustrated/J2456_004_volume_map_emready2.mrc"
    7794 
    7795 Opened J2456_004_volume_map_emready2.mrc as #27, grid size 443,443,443, pixel
    7796 0.5, shown at level 0.895, step 2, values float32 
    7797 
    7798 > volume #26 step 1
    7799 
    7800 > volume #27 step 1
    7801 
    7802 > vop max #26 #27
    7803 
    7804 Opened volume maximum as #28, grid size 443,443,443, pixel 0.5, shown at step
    7805 1, values float32 
    7806 
    7807 > volume #28 level 6.445
    7808 
    7809 > volume #28 level 7.422
    7810 
    7811 > show #!22 models
    7812 
    7813 > hide #!22 models
    7814 
    7815 > show #!15 models
    7816 
    7817 > fitmap #15 inMap #28
    7818 
    7819 Fit molecule 9b. 5v3o- closed vvd+imid (#15) to map volume maximum (#28) using
    7820 8879 atoms 
    7821 average map value = 7.722, steps = 104 
    7822 shifted from previous position = 2.98 
    7823 rotated from previous position = 1.03 degrees 
    7824 atoms outside contour = 4404, contour level = 7.4224 
    7825  
    7826 Position of 9b. 5v3o- closed vvd+imid (#15) relative to volume maximum (#28)
    7827 coordinates: 
    7828 Matrix rotation and translation 
    7829 0.26196635 0.57102732 0.77801120 120.77963399 
    7830 -0.45094391 -0.64031849 0.62180529 178.24630452 
    7831 0.85324277 -0.51373148 0.08975940 121.08780703 
    7832 Axis -0.74239837 -0.04918537 -0.66815078 
    7833 Axis point 0.00000000 85.51770183 -46.87834271 
    7834 Rotation angle (degrees) 130.11293989 
    7835 Shift along axis -179.33862535 
    7836  
    7837 
    7838 > rename #25 "17. combination of open closed for int2 "
    7839 
    7840 > rename #26 "18. frustrated vvd+imid J2438_map_emready2.mrc"
    7841 
    7842 > rename #26 "18. frustrated vvd+imid NU J2438_map_emready2.mrc"
    7843 
    7844 > rename #27 "19. frustrated vvd+imid local J2456_004_volume_map_emready2.mrc"
    7845 
    7846 > rename #28 "20 combination of 18 and 19"
    7847 
    7848 > combine #15 close false modelId #29
    7849 
    7850 > hide #!15 models
    7851 
    7852 > split #29
    7853 
    7854 Split copy of 9b. 5v3o- closed vvd+imid (#29) into 2 models 
    7855 Chain information for copy of 9b. 5v3o- closed vvd+imid A #29.1 
    7856 --- 
    7857 Chain | Description 
    7858 A | No description available 
    7859  
    7860 Chain information for copy of 9b. 5v3o- closed vvd+imid C #29.2 
    7861 --- 
    7862 Chain | Description 
    7863 C | No description available 
    7864  
    7865 
    7866 > hide #!29.1 models
    7867 
    7868 > show #!29.1 models
    7869 
    7870 > hide #!29.2 models
    7871 
    7872 > show #!29.2 models
    7873 
    7874 > select add #29.1
    7875 
    7876 5977 atoms, 6081 bonds, 10 pseudobonds, 775 residues, 2 models selected 
    7877 
    7878 > fitmap sel inMap #28
    7879 
    7880 Fit molecule copy of 9b. 5v3o- closed vvd+imid A (#29.1) to map 20 combination
    7881 of 18 and 19 (#28) using 5977 atoms 
    7882 average map value = 9.752, steps = 44 
    7883 shifted from previous position = 0.0322 
    7884 rotated from previous position = 0.183 degrees 
    7885 atoms outside contour = 1871, contour level = 7.4224 
    7886  
    7887 Position of copy of 9b. 5v3o- closed vvd+imid A (#29.1) relative to 20
    7888 combination of 18 and 19 (#28) coordinates: 
    7889 Matrix rotation and translation 
    7890 0.26033122 0.57129679 0.77836215 120.76428612 
    7891 -0.44883715 -0.64215101 0.62143969 178.28612949 
    7892 0.85485255 -0.51113800 0.08924727 121.05962409 
    7893 Axis -0.74209476 -0.05011852 -0.66841865 
    7894 Axis point 0.00000000 85.40762225 -46.72862078 
    7895 Rotation angle (degrees) 130.26218361 
    7896 Shift along axis -179.47249291 
    7897  
    7898 
    7899 > select subtract #29.1
    7900 
    7901 Nothing selected 
    7902 
    7903 > select add #29.2
    7904 
    7905 2902 atoms, 2974 bonds, 6 pseudobonds, 365 residues, 3 models selected 
     999[deleted to fit within ticket limits]
    79061000
    79071001> fitmap sel inMap #28