id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19911 ChimeraX bug report submission zrizvi@… "{{{ The following bug report has been submitted: Platform: macOS-15.6.1-arm64-arm-64bit ChimeraX Version: 1.10.dev202503130118 (2025-03-13 01:18:56 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x000000020560a0c0 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 440 in quit File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 805 in closeEvent File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 302 in event File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 339 in event_loop File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init File 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""logWritingSignature"" : ""766e6a6e920b82d5d9e7313caf6f7c45a3f4394d"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""6410af69ed1e1e7ab93ed169"", ""factorPackIds"" : { }, ""deploymentId"" : 240000011 }, { ""rolloutId"" : ""6434420a89ec2e0a7a38bf5a"", ""factorPackIds"" : { }, ""deploymentId"" : 240000011 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.10.dev202503130118 (2025-03-13) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/Ward lab work/364 > fab and CSP.cxs"" Opened emdb 27789 as #2, grid size 220,220,220, pixel 1.15, shown at level 0.3, step 1, values float32 Opened J138_005_volume_map_emready2.mrc as #3, grid size 637,637,637, pixel 0.5, shown at level 3.78, step 1, values float32 Opened J138_005_volume_map_emready2.mrc z flip as #4, grid size 637,637,637, pixel 0.5, shown at level 4.4, step 1, values float32 Log from Thu Feb 12 17:06:40 2026UCSF ChimeraX version: 1.10.dev202503130118 (2025-03-13) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/zrizvi/Downloads/8DZ5.cif 8DZ5.cif title: Cryo-EM structure of 364 Fab in complex with recombinant shortened Plasmodium falciparum circumsporozoite protein (rsCSP) [more info...] Chain information for 8DZ5.cif #1 --- Chain | Description A C E H M | 364 Fab heavy chain B D F L N | 364 Fab light chain I | Circumsporozoite protein > open EMDB:27789 Opened emdb 27789 as #2, grid size 220,220,220, pixel 1.15, shown at level 0.3, step 1, values float32, fit PDB 8dz5 > hide atoms > show cartoons > open /Users/zrizvi/Desktop/J138_005_volume_map_emready2.mrc Opened J138_005_volume_map_emready2.mrc as #3, grid size 637,637,637, pixel 0.5, shown at level 0.082, step 4, values float32 > volume #3 step 1 > volume #3 level 1.727 > volume #3 level 3.448 > vop flip #3 Opened J138_005_volume_map_emready2.mrc z flip as #4, grid size 637,637,637, pixel 0.5, shown at step 1, values float32 > hide #1 models > set bgColor white > graphics silhouettes true > lighting shadows false > lighting soft > lighting full > hide #!4 models > show #!4 models > select add #4 2 models selected > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.99607,-0.080169,0.037668,327.4,0.067721,-0.96335,-0.25955,350.65,0.057095,-0.25598,0.965,38.156 > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.99607,-0.080169,0.037668,325.57,0.067721,-0.96335,-0.25955,327.43,0.057095,-0.25598,0.965,11.263 > ui mousemode right translate > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.99607,-0.080169,0.037668,297.17,0.067721,-0.96335,-0.25955,331.06,0.057095,-0.25598,0.965,15.212 > ui mousemode right translate > select up 8950 atoms, 9174 bonds, 1155 residues, 7 models selected > fitmap #4 inMap #2 Fit map J138_005_volume_map_emready2.mrc z flip in map emdb 27789 using 722271 points correlation = 0.7375, correlation about mean = 0.04011, overlap = 9.945e+05 steps = 136, shift = 5.32, angle = 14.3 degrees Position of J138_005_volume_map_emready2.mrc z flip (#4) relative to emdb 27789 (#2) coordinates: Matrix rotation and translation -0.99337646 0.10058286 0.05555444 264.91651700 -0.11457169 -0.90384363 -0.41223782 369.68694887 0.00874847 -0.41587231 0.90938094 55.13871083 Axis -0.01650415 0.21254486 -0.97701192 Axis point 142.31803628 183.34485876 0.00000000 Rotation angle (degrees) 173.67843250 Shift along axis 20.33165992 > select subtract #1 6 models selected > select subtract #2 4 models selected > hide #!2 models > show #1 models > select subtract #3 2 models selected > fitmap #1 inMap #4 Fit molecule 8DZ5.cif (#1) to map J138_005_volume_map_emready2.mrc z flip (#4) using 8950 atoms average map value = 2.582, steps = 2000 shifted from previous position = 3.12 rotated from previous position = 6.67 degrees atoms outside contour = 6103, contour level = 3.4477 Position of 8DZ5.cif (#1) relative to J138_005_volume_map_emready2.mrc z flip (#4) coordinates: Matrix rotation and translation -0.99477432 -0.09896582 0.02509620 304.20449803 0.08642159 -0.94707885 -0.30914875 323.81417332 0.05436324 -0.30536439 0.95068251 69.72705585 Axis 0.02015947 -0.15590668 0.98756605 Axis point 143.58853154 174.64329383 0.00000000 Rotation angle (degrees) 174.61424657 Shift along axis 24.50788175 > color #4 #ffffb2ab models > lighting full > select subtract #4 Nothing selected > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models Drag select of 2 residues > select up 280 atoms, 289 bonds, 40 residues, 1 model selected > color sel black > select clear > show #!4 models > show #!2 models > hide #!4 models > color #2 #b2b2b2b1 models > color #2 #b2b2b2b0 models > hide #!2 models > show #!4 models > volume #3 level 3.781 > hide #!3 models > volume #4 level 4.397 > show #!2 models > hide #!2 models > show #!2 models > hide #1 models > show #1 models > hide #!2 models > fitmap #1 inMap #4 Fit molecule 8DZ5.cif (#1) to map J138_005_volume_map_emready2.mrc z flip (#4) using 8950 atoms average map value = 2.581, steps = 2000 shifted from previous position = 0.242 rotated from previous position = 0.0941 degrees atoms outside contour = 6767, contour level = 4.3974 Position of 8DZ5.cif (#1) relative to J138_005_volume_map_emready2.mrc z flip (#4) coordinates: Matrix rotation and translation -0.99482591 -0.09809147 0.02644767 303.97868662 0.08519576 -0.94730131 -0.30880722 324.17704316 0.05534526 -0.30495620 0.95075687 69.63647307 Axis 0.02075004 -0.15570561 0.98758554 Axis point 143.53604341 174.72210576 0.00000000 Rotation angle (degrees) 174.67554238 Shift along axis 24.60336188 > fitmap #2 inMap #4 Fit map emdb 27789 in map J138_005_volume_map_emready2.mrc z flip using 67102 points correlation = 0.7187, correlation about mean = 0.1659, overlap = 8.451e+04 steps = 96, shift = 0.377, angle = 0.608 degrees Position of emdb 27789 (#2) relative to J138_005_volume_map_emready2.mrc z flip (#4) coordinates: Matrix rotation and translation -0.99393761 -0.10858956 0.01721448 303.06956338 0.09152362 -0.90395157 -0.41772596 331.71968624 0.06092174 -0.41361801 0.90840997 87.47175308 Axis 0.02005131 -0.21333946 0.97677235 Axis point 141.80065823 183.36819890 0.00000000 Rotation angle (degrees) 174.12053987 Shift along axis 20.74803338 > show #!2 models > hide #1 models > show #1 models > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/Ward lab work/364 > fab and CSP.cxs"" includeMaps true ——— End of log from Thu Feb 12 17:06:40 2026 ——— > view name session-start opened ChimeraX session > hide #!2 models > show #!2 models > hide #1 models > show #1 models > hide #!2 models > show #!2 models > hide #1 models > hide #!4 models > show #!3 models > hide #!3 models > show #!4 models > hide #!2 models > show #1 models > fitmap #1 inMap #4 Fit molecule 8DZ5.cif (#1) to map J138_005_volume_map_emready2.mrc z flip (#4) using 8950 atoms average map value = 2.582, steps = 2000 shifted from previous position = 0.108 rotated from previous position = 0.145 degrees atoms outside contour = 6785, contour level = 4.3974 Position of 8DZ5.cif (#1) relative to J138_005_volume_map_emready2.mrc z flip (#4) coordinates: Matrix rotation and translation -0.99459702 -0.10017085 0.02724993 304.11905575 0.08699560 -0.94749088 -0.30772195 323.74569560 0.05664383 -0.30368871 0.95108603 69.18569866 Axis 0.02128319 -0.15511012 0.98766790 Axis point 143.44028428 174.60330984 0.00000000 Rotation angle (degrees) 174.56297062 Shift along axis 24.58888421 > select add #4 2 models selected > select subtract #4 Nothing selected > select add #1 8950 atoms, 9174 bonds, 1155 residues, 1 model selected > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.6314,-0.73868,-0.23597,167.23,0.74572,0.49495,0.44601,-94.609,-0.21267,-0.45758,0.86336,102.65 > view matrix models > #1,-0.98558,-0.15069,0.077003,272.57,-0.010092,0.50657,0.86214,-47.02,-0.16892,0.84893,-0.50079,108.09 > view matrix models > #1,-0.94088,-0.28361,-0.18525,316.03,-0.28544,0.36925,0.88441,4.0657,-0.18242,0.885,-0.42837,96.327 > fitmap #1 inMap #4 Fit molecule 8DZ5.cif (#1) to map J138_005_volume_map_emready2.mrc z flip (#4) using 8950 atoms average map value = 4.14, steps = 540 shifted from previous position = 2.77 rotated from previous position = 11.8 degrees atoms outside contour = 4982, contour level = 4.3974 Position of 8DZ5.cif (#1) relative to J138_005_volume_map_emready2.mrc z flip (#4) coordinates: Matrix rotation and translation 0.99019989 0.13963739 -0.00236196 11.48961637 0.08976090 -0.64928916 -0.75522616 342.31421032 -0.10699140 0.74761285 -0.65546004 161.48976063 Axis 0.99703892 0.06941504 -0.03308991 Axis point 0.00000000 133.70365955 158.52805012 Rotation angle (degrees) 131.09235241 Shift along axis 29.87366836 > hide #1 models > show #1 models > volume #4 level 4.141 > hide #!4 models > show #!4 models > hide #1 models ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.10.dev202503130118 (2025-03-13) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/0. figure 2 making .cxs"" Opened 2. cryosparc_P341_J1614_localrefine. selected.mrc as #4, grid size 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 Opened 1. cryosparc_P341_J1735_NUrefine selected.mrc as #9, grid size 300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32 Opened 3a. composite_map on EMReady2 maps of 1735 and 1614.ccp4 as #10, grid size 300,300,300, pixel 0.833, shown at level 9.26, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 0 as #13.1, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 1 as #13.2, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 2 as #13.3, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 3 as #13.4, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 4 as #13.5, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 5 as #13.6, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 6 as #13.7, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 7 as #13.8, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 8 as #13.9, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 9 as #13.10, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 10 as #13.11, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 11 as #13.12, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened 4. open- vvd+imid NU J2526_map_emready2.mrc as #1, grid size 443,443,443, pixel 0.5, shown at level 1.01, step 1, values float32 Opened 5. open- vvd+imid local J2540_005_volume_map_emready2.mrc as #2, grid size 443,443,443, pixel 0.5, shown at level 1.2, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 as #3, grid size 443,443,443, pixel 0.5, shown at level 3.48, step 1, values float32 Opened 7. Clsoed- vvd+imid NU J2528_map_emready2.mrc as #5, grid size 443,443,443, pixel 0.5, shown at level 2.31, step 1, values float32 Opened 8. Closed- vvd+imid local J2544_007_volume_map_emready2.mrc as #7, grid size 443,443,443, pixel 0.5, shown at level 2.03, step 1, values float32 Opened 9a. combination of 2528 and 2544 emready2 as #8, grid size 443,443,443, pixel 0.5, shown at level 5.07, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy as #16, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 0 as #14.1, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 1 as #14.2, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 2 as #14.3, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 3 as #14.4, grid size 443,443,443, pixel 0.5, shown at level 4.95, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 4 as #14.5, grid size 443,443,443, pixel 0.5, shown at level 3.46, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 5 as #14.6, grid size 443,443,443, pixel 0.5, shown at level 4.45, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 6 as #14.7, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 7 as #14.8, grid size 443,443,443, pixel 0.5, shown at level 2.27, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 0 as #17.1, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 1 as #17.2, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 2 as #17.3, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 3 as #17.4, grid size 443,443,443, pixel 0.5, shown at level 2.89, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 4 as #17.5, grid size 443,443,443, pixel 0.5, shown at level 2.84, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 5 as #17.6, grid size 443,443,443, pixel 0.5, shown at level 2.85, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 6 as #17.7, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 7 as #17.8, grid size 443,443,443, pixel 0.5, shown at level 2.11, step 1, values float32 Opened 10. int1 vvd+imid NU J2527_map_emready2.mrc as #18, grid size 443,443,443, pixel 0.5, shown at level 0.9, step 1, values float32 Opened 11. int1 vvd+imid local J2541_004_volume_map_emready2.mrc as #19, grid size 443,443,443, pixel 0.5, shown at level 1.16, step 1, values float32 Opened 12. combination of 10 and 11 as #20, grid size 443,443,443, pixel 0.5, shown at level 6.81, step 1, values float32 Opened 14. int2 vvd+imid NU J2612_map_emready2.mrc as #21, grid size 438,438,438, pixel 0.5, shown at level 3.83, step 1, values float32 Opened 15. int2 vvd+imid local J2614_004_volume_map_emready2.mrc as #23, grid size 438,438,438, pixel 0.5, shown at level 1.74, step 1, values float32 Opened 16. combination of 2612 and 2614 as #24, grid size 438,438,438, pixel 0.5, shown at level 5.92, step 1, values float32 Opened 18. frustrated vvd+imid NU J2438_map_emready2.mrc as #26, grid size 443,443,443, pixel 0.5, shown at level 1.18, step 1, values float32 Opened 19. frustrated vvd+imid local J2456_004_volume_map_emready2.mrc as #27, grid size 443,443,443, pixel 0.5, shown at level 0.895, step 1, values float32 Opened 20 combination of 18 and 19 as #28, grid size 443,443,443, pixel 0.5, shown at level 6.9, step 1, values float32 Opened 12. combination of 10 and 11 0 as #29.1, grid size 443,443,443, pixel 0.5, shown at level 5.05, step 1, values float32 Opened 12. combination of 10 and 11 1 as #29.2, grid size 443,443,443, pixel 0.5, shown at level 5.67, step 1, values float32 Opened 12. combination of 10 and 11 2 as #29.3, grid size 443,443,443, pixel 0.5, shown at level 5.87, step 1, values float32 Opened 12. combination of 10 and 11 3 as #29.4, grid size 443,443,443, pixel 0.5, shown at level 5.62, step 1, values float32 Opened 12. combination of 10 and 11 4 as #29.5, grid size 443,443,443, pixel 0.5, shown at level 3.84, step 1, values float32 Opened 12. combination of 10 and 11 5 as #29.6, grid size 443,443,443, pixel 0.5, shown at level 4.7, step 1, values float32 Opened 12. combination of 10 and 11 6 as #29.7, grid size 443,443,443, pixel 0.5, shown at level 1.29, step 1, values float32 Opened 12. combination of 10 and 11 7 as #29.8, grid size 443,443,443, pixel 0.5, shown at level 0.584, step 1, values float32 Opened 22. intT NU J2618_map_emready2.mrc as #31, grid size 438,438,438, pixel 0.5, shown at level 1.39, step 1, values float32 Opened 23. intT local J2619_004_volume_map_emready2.mrc as #32, grid size 438,438,438, pixel 0.5, shown at level 1.71, step 1, values float32 Opened combination of 22 and 23 as #33, grid size 438,438,438, pixel 0.5, shown at level 3.68, step 1, values float32 Opened combination of 22 and 23 0 as #34.1, grid size 438,438,438, pixel 0.5, shown at level 6.34, step 1, values float32 Opened combination of 22 and 23 1 as #34.2, grid size 438,438,438, pixel 0.5, shown at level 6.71, step 1, values float32 Opened combination of 22 and 23 2 as #34.3, grid size 438,438,438, pixel 0.5, shown at level 5.88, step 1, values float32 Opened combination of 22 and 23 3 as #34.4, grid size 438,438,438, pixel 0.5, shown at level 4.06, step 1, values float32 Opened combination of 22 and 23 4 as #34.5, grid size 438,438,438, pixel 0.5, shown at level 5.07, step 1, values float32 Opened combination of 22 and 23 5 as #34.6, grid size 438,438,438, pixel 0.5, shown at level 3.33, step 1, values float32 Opened combination of 22 and 23 6 as #34.7, grid size 438,438,438, pixel 0.5, shown at level 3.11, step 1, values float32 Opened combination of 22 and 23 7 as #34.8, grid size 438,438,438, pixel 0.5, shown at level 7.44, step 1, values float32 Opened combination of 22 and 23 7 copy as #37, grid size 438,438,438, pixel 0.5, shown at level 1.65, step 1, values float32 Opened cryosparc_P341_J2527_map (3).mrc as #36, grid size 300,300,300, pixel 0.74, shown at level 0.00303, step 1, values float32 Opened cryosparc_P341_J2527_map (3).mrc 0 as #38.1, grid size 300,300,300, pixel 0.74, shown at level 0.00303, step 1, values float32 Opened cryosparc_P341_J2527_map (3).mrc 1 as #38.2, grid size 300,300,300, pixel 0.74, shown at level 0.00303, step 1, values float32 Opened cryosparc_P341_J2527_map (3).mrc 2 as #38.3, grid size 300,300,300, pixel 0.74, shown at level 0.00303, step 1, values float32 Opened cryosparc_P341_J2527_map (3).mrc 3 as #38.4, grid size 300,300,300, pixel 0.74, shown at level 0.00288, step 1, values float32 Opened cryosparc_P341_J2527_map (3).mrc 4 as #38.5, grid size 300,300,300, pixel 0.74, shown at level 0.00217, step 1, values float32 Opened cryosparc_P341_J2527_map (3).mrc 5 as #38.6, grid size 300,300,300, pixel 0.74, shown at level 0.00284, step 1, values float32 Opened cryosparc_P341_J2527_map (3).mrc 6 as #38.7, grid size 300,300,300, pixel 0.74, shown at level 0.00303, step 1, values float32 Opened cryosparc_P341_J2527_map (3).mrc 7 as #38.8, grid size 300,300,300, pixel 0.74, shown at level 0.00903, step 1, values float32 Opened cryosparc_P341_J2527_map (3).mrc 7 copy as #39, grid size 300,300,300, pixel 0.74, shown at level 0.00381, step 1, values float32 Opened cryosparc_P341_J2574_006_volume_map (4).mrc as #40, grid size 300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32 Opened cryosparc_P341_J2574_006_volume_map (4).mrc 0 as #41.1, grid size 300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32 Opened cryosparc_P341_J2574_006_volume_map (4).mrc 1 as #41.2, grid size 300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32 Opened cryosparc_P341_J2574_006_volume_map (4).mrc 2 as #41.3, grid size 300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32 Opened cryosparc_P341_J2574_006_volume_map (4).mrc 3 as #41.4, grid size 300,300,300, pixel 0.731, shown at level 0.0175, step 1, values float32 Opened cryosparc_P341_J2574_006_volume_map (4).mrc 4 as #41.5, grid size 300,300,300, pixel 0.731, shown at level 0.0363, step 1, values float32 Opened cryosparc_P341_J2574_006_volume_map (4).mrc 5 as #41.6, grid size 300,300,300, pixel 0.731, shown at level 0.0168, step 1, values float32 Opened cryosparc_P341_J2574_006_volume_map (4).mrc 6 as #41.7, grid size 300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32 Opened cryosparc_P341_J2574_006_volume_map (4).mrc 7 as #41.8, grid size 300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32 Opened cryosparc_P341_J2574_006_volume_map (4).mrc 8 as #41.9, grid size 300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32 Opened cryosparc_P341_J2526_map (3).mrc as #42, grid size 300,300,300, pixel 0.74, shown at level 0.00917, step 1, values float32 Opened INT1 cryosparc_P341_J2527_map (3).mrc as #43, grid size 300,300,300, pixel 0.74, shown at level 0.00274, step 1, values float32 Log from Fri Feb 27 10:44:17 2026UCSF ChimeraX version: 1.10.dev202503130118 (2025-03-13) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/0. figure 2 making .cxs"" Opened 2. cryosparc_P341_J1614_localrefine. selected.mrc as #4, grid size 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 Opened 1. cryosparc_P341_J1735_NUrefine selected.mrc as #9, grid size 300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32 Opened 3a. composite_map on EMReady2 maps of 1735 and 1614.ccp4 as #10, grid size 300,300,300, pixel 0.833, shown at level 9.26, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 0 as #13.1, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 1 as #13.2, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 2 as #13.3, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 3 as #13.4, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 4 as #13.5, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 5 as #13.6, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 6 as #13.7, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 7 as #13.8, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 8 as #13.9, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 9 as #13.10, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 10 as #13.11, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 11 as #13.12, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened 4. open- vvd+imid NU J2526_map_emready2.mrc as #1, grid size 443,443,443, pixel 0.5, shown at level 1.01, step 1, values float32 Opened 5. open- vvd+imid local J2540_005_volume_map_emready2.mrc as #2, grid size 443,443,443, pixel 0.5, shown at level 1.2, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 as #3, grid size 443,443,443, pixel 0.5, shown at level 3.48, step 1, values float32 Opened 7. Clsoed- vvd+imid NU J2528_map_emready2.mrc as #5, grid size 443,443,443, pixel 0.5, shown at level 2.31, step 1, values float32 Opened 8. Closed- vvd+imid local J2544_007_volume_map_emready2.mrc as #7, grid size 443,443,443, pixel 0.5, shown at level 2.03, step 1, values float32 Opened 9a. combination of 2528 and 2544 emready2 as #8, grid size 443,443,443, pixel 0.5, shown at level 5.07, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy as #16, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 0 as #14.1, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 1 as #14.2, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 2 as #14.3, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 3 as #14.4, grid size 443,443,443, pixel 0.5, shown at level 4.95, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 4 as #14.5, grid size 443,443,443, pixel 0.5, shown at level 3.46, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 5 as #14.6, grid size 443,443,443, pixel 0.5, shown at level 4.45, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 6 as #14.7, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 7 as #14.8, grid size 443,443,443, pixel 0.5, shown at level 2.27, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 0 as #17.1, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 1 as #17.2, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 2 as #17.3, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 3 as #17.4, grid size 443,443,443, pixel 0.5, shown at level 2.89, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 4 as #17.5, grid size 443,443,443, pixel 0.5, shown at level 2.84, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 5 as #17.6, grid size 443,443,443, pixel 0.5, shown at level 2.85, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 6 as #17.7, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 7 as #17.8, grid size 443,443,443, pixel 0.5, shown at level 2.11, step 1, values float32 Opened 10. int1 vvd+imid NU J2527_map_emready2.mrc as #18, grid size 443,443,443, pixel 0.5, shown at level 0.9, step 1, values float32 Opened 11. int1 vvd+imid local J2541_004_volume_map_emready2.mrc as #19, grid size 443,443,443, pixel 0.5, shown at level 1.16, step 1, values float32 Opened 12. combination of 10 and 11 as #20, grid size 443,443,443, pixel 0.5, shown at level 5.05, step 1, values float32 Opened 14. int2 vvd+imid NU J2612_map_emready2.mrc as #21, grid size 438,438,438, pixel 0.5, shown at level 3.83, step 1, values float32 Opened 15. int2 vvd+imid local J2614_004_volume_map_emready2.mrc as #23, grid size 438,438,438, pixel 0.5, shown at level 1.74, step 1, values float32 Opened 16. combination of 2612 and 2614 as #24, grid size 438,438,438, pixel 0.5, shown at level 5.92, step 1, values float32 Opened 18. frustrated vvd+imid NU J2438_map_emready2.mrc as #26, grid size 443,443,443, pixel 0.5, shown at level 1.18, step 1, values float32 Opened 19. frustrated vvd+imid local J2456_004_volume_map_emready2.mrc as #27, grid size 443,443,443, pixel 0.5, shown at level 0.895, step 1, values float32 Opened 20 combination of 18 and 19 as #28, grid size 443,443,443, pixel 0.5, shown at level 6.9, step 1, values float32 Opened 12. combination of 10 and 11 0 as #29.1, grid size 443,443,443, pixel 0.5, shown at level 5.05, step 1, values float32 Opened 12. combination of 10 and 11 1 as #29.2, grid size 443,443,443, pixel 0.5, shown at level 5.67, step 1, values float32 Opened 12. combination of 10 and 11 2 as #29.3, grid size 443,443,443, pixel 0.5, shown at level 5.87, step 1, values float32 Opened 12. combination of 10 and 11 3 as #29.4, grid size 443,443,443, pixel 0.5, shown at level 5.62, step 1, values float32 Opened 12. combination of 10 and 11 4 as #29.5, grid size 443,443,443, pixel 0.5, shown at level 3.84, step 1, values float32 Opened 12. combination of 10 and 11 5 as #29.6, grid size 443,443,443, pixel 0.5, shown at level 4.7, step 1, values float32 Opened 12. combination of 10 and 11 6 as #29.7, grid size 443,443,443, pixel 0.5, shown at level 1.29, step 1, values float32 Opened 12. combination of 10 and 11 7 as #29.8, grid size 443,443,443, pixel 0.5, shown at level 0.584, step 1, values float32 Opened 22. intT NU J2618_map_emready2.mrc as #31, grid size 438,438,438, pixel 0.5, shown at level 1.39, step 1, values float32 Opened 23. intT local J2619_004_volume_map_emready2.mrc as #32, grid size 438,438,438, pixel 0.5, shown at level 1.71, step 1, values float32 Opened combination of 22 and 23 as #33, grid size 438,438,438, pixel 0.5, shown at level 3.68, step 1, values float32 Opened combination of 22 and 23 0 as #34.1, grid size 438,438,438, pixel 0.5, shown at level 6.34, step 1, values float32 Opened combination of 22 and 23 1 as #34.2, grid size 438,438,438, pixel 0.5, shown at level 6.71, step 1, values float32 Opened combination of 22 and 23 2 as #34.3, grid size 438,438,438, pixel 0.5, shown at level 5.88, step 1, values float32 Opened combination of 22 and 23 3 as #34.4, grid size 438,438,438, pixel 0.5, shown at level 4.06, step 1, values float32 Opened combination of 22 and 23 4 as #34.5, grid size 438,438,438, pixel 0.5, shown at level 5.07, step 1, values float32 Opened combination of 22 and 23 5 as #34.6, grid size 438,438,438, pixel 0.5, shown at level 3.33, step 1, values float32 Opened combination of 22 and 23 6 as #34.7, grid size 438,438,438, pixel 0.5, shown at level 3.11, step 1, values float32 Opened combination of 22 and 23 7 as #34.8, grid size 438,438,438, pixel 0.5, shown at level 7.44, step 1, values float32 Opened combination of 22 and 23 7 copy as #37, grid size 438,438,438, pixel 0.5, shown at level 1.65, step 1, values float32 Log from Thu Feb 26 15:13:55 2026UCSF ChimeraX version: 1.10.dev202503130118 (2025-03-13) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/0. figure 2 making .cxs"" Opened 2. cryosparc_P341_J1614_localrefine. selected.mrc as #4, grid size 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 Opened 1. cryosparc_P341_J1735_NUrefine selected.mrc as #9, grid size 300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32 Opened 3a. composite_map on EMReady2 maps of 1735 and 1614.ccp4 as #10, grid size 300,300,300, pixel 0.833, shown at level 9.26, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 0 as #13.1, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 1 as #13.2, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 2 as #13.3, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 3 as #13.4, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 4 as #13.5, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 5 as #13.6, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 6 as #13.7, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 7 as #13.8, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 8 as #13.9, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 9 as #13.10, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 10 as #13.11, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 11 as #13.12, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened 4. open- vvd+imid NU J2526_map_emready2.mrc as #1, grid size 443,443,443, pixel 0.5, shown at level 1.01, step 1, values float32 Opened 5. open- vvd+imid local J2540_005_volume_map_emready2.mrc as #2, grid size 443,443,443, pixel 0.5, shown at level 1.2, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 as #3, grid size 443,443,443, pixel 0.5, shown at level 3.48, step 1, values float32 Opened 7. Clsoed- vvd+imid NU J2528_map_emready2.mrc as #5, grid size 443,443,443, pixel 0.5, shown at level 2.31, step 1, values float32 Opened 8. Closed- vvd+imid local J2544_007_volume_map_emready2.mrc as #7, grid size 443,443,443, pixel 0.5, shown at level 2.03, step 1, values float32 Opened 9a. combination of 2528 and 2544 emready2 as #8, grid size 443,443,443, pixel 0.5, shown at level 5.07, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy as #16, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 0 as #14.1, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 1 as #14.2, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 2 as #14.3, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 3 as #14.4, grid size 443,443,443, pixel 0.5, shown at level 4.95, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 4 as #14.5, grid size 443,443,443, pixel 0.5, shown at level 3.46, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 5 as #14.6, grid size 443,443,443, pixel 0.5, shown at level 4.45, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 6 as #14.7, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 7 as #14.8, grid size 443,443,443, pixel 0.5, shown at level 2.27, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 0 as #17.1, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 1 as #17.2, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 2 as #17.3, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 3 as #17.4, grid size 443,443,443, pixel 0.5, shown at level 2.89, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 4 as #17.5, grid size 443,443,443, pixel 0.5, shown at level 2.84, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 5 as #17.6, grid size 443,443,443, pixel 0.5, shown at level 2.85, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 6 as #17.7, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 7 as #17.8, grid size 443,443,443, pixel 0.5, shown at level 2.11, step 1, values float32 Opened 10. int1 vvd+imid NU J2527_map_emready2.mrc as #18, grid size 443,443,443, pixel 0.5, shown at level 0.9, step 1, values float32 Opened 11. int1 vvd+imid local J2541_004_volume_map_emready2.mrc as #19, grid size 443,443,443, pixel 0.5, shown at level 1.16, step 1, values float32 Opened 12. combination of 10 and 11 as #20, grid size 443,443,443, pixel 0.5, shown at level 5.05, step 1, values float32 Opened 14. int2 vvd+imid NU J2612_map_emready2.mrc as #21, grid size 438,438,438, pixel 0.5, shown at level 3.83, step 1, values float32 Opened 15. int2 vvd+imid local J2614_004_volume_map_emready2.mrc as #23, grid size 438,438,438, pixel 0.5, shown at level 1.74, step 1, values float32 Opened 16. combination of 2612 and 2614 as #24, grid size 438,438,438, pixel 0.5, shown at level 5.92, step 1, values float32 Opened 18. frustrated vvd+imid NU J2438_map_emready2.mrc as #26, grid size 443,443,443, pixel 0.5, shown at level 1.18, step 1, values float32 Opened 19. frustrated vvd+imid local J2456_004_volume_map_emready2.mrc as #27, grid size 443,443,443, pixel 0.5, shown at level 0.895, step 1, values float32 Opened 20 combination of 18 and 19 as #28, grid size 443,443,443, pixel 0.5, shown at level 6.9, step 1, values float32 Opened 12. combination of 10 and 11 0 as #29.1, grid size 443,443,443, pixel 0.5, shown at level 5.05, step 1, values float32 Opened 12. combination of 10 and 11 1 as #29.2, grid size 443,443,443, pixel 0.5, shown at level 5.67, step 1, values float32 Opened 12. combination of 10 and 11 2 as #29.3, grid size 443,443,443, pixel 0.5, shown at level 5.87, step 1, values float32 Opened 12. combination of 10 and 11 3 as #29.4, grid size 443,443,443, pixel 0.5, shown at level 5.62, step 1, values float32 Opened 12. combination of 10 and 11 4 as #29.5, grid size 443,443,443, pixel 0.5, shown at level 3.84, step 1, values float32 Opened 12. combination of 10 and 11 5 as #29.6, grid size 443,443,443, pixel 0.5, shown at level 4.7, step 1, values float32 Opened 12. combination of 10 and 11 6 as #29.7, grid size 443,443,443, pixel 0.5, shown at level 1.29, step 1, values float32 Opened 12. combination of 10 and 11 7 as #29.8, grid size 443,443,443, pixel 0.5, shown at level 0.584, step 1, values float32 Opened 22. intT NU J2618_map_emready2.mrc as #31, grid size 438,438,438, pixel 0.5, shown at level 1.39, step 1, values float32 Opened 23. intT local J2619_004_volume_map_emready2.mrc as #32, grid size 438,438,438, pixel 0.5, shown at level 1.71, step 1, values float32 Opened combination of 22 and 23 as #33, grid size 438,438,438, pixel 0.5, shown at level 4.67, step 1, values float32 Log from Thu Feb 26 14:52:15 2026UCSF ChimeraX version: 1.10.dev202503130118 (2025-03-13) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/0. figure 2 making .cxs"" Opened 2. cryosparc_P341_J1614_localrefine. selected.mrc as #4, grid size 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 Opened 1. cryosparc_P341_J1735_NUrefine selected.mrc as #9, grid size 300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32 Opened 3a. composite_map on EMReady2 maps of 1735 and 1614.ccp4 as #10, grid size 300,300,300, pixel 0.833, shown at level 14, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 0 as #13.1, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 1 as #13.2, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 2 as #13.3, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 3 as #13.4, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 4 as #13.5, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 5 as #13.6, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 6 as #13.7, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 7 as #13.8, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 8 as #13.9, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 9 as #13.10, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 10 as #13.11, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 11 as #13.12, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened 4. open- vvd+imid NU J2526_map_emready2.mrc as #1, grid size 443,443,443, pixel 0.5, shown at level 1.01, step 1, values float32 Opened 5. open- vvd+imid local J2540_005_volume_map_emready2.mrc as #2, grid size 443,443,443, pixel 0.5, shown at level 1.2, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 as #3, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 7. Clsoed- vvd+imid NU J2528_map_emready2.mrc as #5, grid size 443,443,443, pixel 0.5, shown at level 2.31, step 1, values float32 Opened 8. Closed- vvd+imid local J2544_007_volume_map_emready2.mrc as #7, grid size 443,443,443, pixel 0.5, shown at level 2.03, step 1, values float32 Opened 9a. combination of 2528 and 2544 emready2 as #8, grid size 443,443,443, pixel 0.5, shown at level 5.07, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy as #16, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 0 as #14.1, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 1 as #14.2, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 2 as #14.3, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 3 as #14.4, grid size 443,443,443, pixel 0.5, shown at level 4.95, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 4 as #14.5, grid size 443,443,443, pixel 0.5, shown at level 3.46, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 5 as #14.6, grid size 443,443,443, pixel 0.5, shown at level 4.45, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 6 as #14.7, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 7 as #14.8, grid size 443,443,443, pixel 0.5, shown at level 2.27, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 0 as #17.1, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 1 as #17.2, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 2 as #17.3, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 3 as #17.4, grid size 443,443,443, pixel 0.5, shown at level 2.89, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 4 as #17.5, grid size 443,443,443, pixel 0.5, shown at level 2.84, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 5 as #17.6, grid size 443,443,443, pixel 0.5, shown at level 2.85, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 6 as #17.7, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 7 as #17.8, grid size 443,443,443, pixel 0.5, shown at level 2.11, step 1, values float32 Opened 10. int1 vvd+imid NU J2527_map_emready2.mrc as #18, grid size 443,443,443, pixel 0.5, shown at level 0.9, step 1, values float32 Opened 11. int1 vvd+imid local J2541_004_volume_map_emready2.mrc as #19, grid size 443,443,443, pixel 0.5, shown at level 1.16, step 1, values float32 Opened 12. combination of 10 and 11 as #20, grid size 443,443,443, pixel 0.5, shown at level 5.05, step 1, values float32 Opened 14. int2 vvd+imid NU J2612_map_emready2.mrc as #21, grid size 438,438,438, pixel 0.5, shown at level 3.83, step 1, values float32 Opened 15. int2 vvd+imid local J2614_004_volume_map_emready2.mrc as #23, grid size 438,438,438, pixel 0.5, shown at level 1.74, step 1, values float32 Opened 16. combination of 2612 and 2614 as #24, grid size 438,438,438, pixel 0.5, shown at level 5.92, step 1, values float32 Opened 18. frustrated vvd+imid NU J2438_map_emready2.mrc as #26, grid size 443,443,443, pixel 0.5, shown at level 1.18, step 1, values float32 Opened 19. frustrated vvd+imid local J2456_004_volume_map_emready2.mrc as #27, grid size 443,443,443, pixel 0.5, shown at level 0.895, step 1, values float32 Opened 20 combination of 18 and 19 as #28, grid size 443,443,443, pixel 0.5, shown at level 6.9, step 1, values float32 Opened 12. combination of 10 and 11 0 as #29.1, grid size 443,443,443, pixel 0.5, shown at level 5.05, step 1, values float32 Opened 12. combination of 10 and 11 1 as #29.2, grid size 443,443,443, pixel 0.5, shown at level 5.67, step 1, values float32 Opened 12. combination of 10 and 11 2 as #29.3, grid size 443,443,443, pixel 0.5, shown at level 5.87, step 1, values float32 Opened 12. combination of 10 and 11 3 as #29.4, grid size 443,443,443, pixel 0.5, shown at level 5.62, step 1, values float32 Opened 12. combination of 10 and 11 4 as #29.5, grid size 443,443,443, pixel 0.5, shown at level 3.84, step 1, values float32 Opened 12. combination of 10 and 11 5 as #29.6, grid size 443,443,443, pixel 0.5, shown at level 4.7, step 1, values float32 Opened 12. combination of 10 and 11 6 as #29.7, grid size 443,443,443, pixel 0.5, shown at level 1.29, step 1, values float32 Opened 12. combination of 10 and 11 7 as #29.8, grid size 443,443,443, pixel 0.5, shown at level 0.584, step 1, values float32 Log from Wed Feb 25 16:39:20 2026UCSF ChimeraX version: 1.10.dev202503130118 (2025-03-13) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/0. figure 2 making .cxs"" Opened 2. cryosparc_P341_J1614_localrefine. selected.mrc as #4, grid size 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 Opened 1. cryosparc_P341_J1735_NUrefine selected.mrc as #9, grid size 300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32 Opened 3a. composite_map on EMReady2 maps of 1735 and 1614.ccp4 as #10, grid size 300,300,300, pixel 0.833, shown at level 14, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 0 as #13.1, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 1 as #13.2, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 2 as #13.3, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 3 as #13.4, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 4 as #13.5, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 5 as #13.6, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 6 as #13.7, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 7 as #13.8, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 8 as #13.9, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 9 as #13.10, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 10 as #13.11, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 11 as #13.12, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened 4. open- vvd+imid NU J2526_map_emready2.mrc as #1, grid size 443,443,443, pixel 0.5, shown at level 1.01, step 1, values float32 Opened 5. open- vvd+imid local J2540_005_volume_map_emready2.mrc as #2, grid size 443,443,443, pixel 0.5, shown at level 1.2, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 as #3, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 7. Clsoed- vvd+imid NU J2528_map_emready2.mrc as #5, grid size 443,443,443, pixel 0.5, shown at level 2.31, step 1, values float32 Opened 8. Closed- vvd+imid local J2544_007_volume_map_emready2.mrc as #7, grid size 443,443,443, pixel 0.5, shown at level 2.03, step 1, values float32 Opened 9a. combination of 2528 and 2544 emready2 as #8, grid size 443,443,443, pixel 0.5, shown at level 5.07, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy as #16, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 0 as #14.1, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 1 as #14.2, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 2 as #14.3, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 3 as #14.4, grid size 443,443,443, pixel 0.5, shown at level 4.95, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 4 as #14.5, grid size 443,443,443, pixel 0.5, shown at level 3.46, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 5 as #14.6, grid size 443,443,443, pixel 0.5, shown at level 4.45, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 6 as #14.7, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 7 as #14.8, grid size 443,443,443, pixel 0.5, shown at level 2.27, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 0 as #17.1, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 1 as #17.2, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 2 as #17.3, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 3 as #17.4, grid size 443,443,443, pixel 0.5, shown at level 2.89, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 4 as #17.5, grid size 443,443,443, pixel 0.5, shown at level 2.84, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 5 as #17.6, grid size 443,443,443, pixel 0.5, shown at level 2.85, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 6 as #17.7, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 7 as #17.8, grid size 443,443,443, pixel 0.5, shown at level 2.11, step 1, values float32 Opened 10. int1 vvd+imid NU J2527_map_emready2.mrc as #18, grid size 443,443,443, pixel 0.5, shown at level 0.9, step 1, values float32 Opened 11. int1 vvd+imid local J2541_004_volume_map_emready2.mrc as #19, grid size 443,443,443, pixel 0.5, shown at level 1.16, step 1, values float32 Opened 12. combination of 10 and 11 as #20, grid size 443,443,443, pixel 0.5, shown at level 4.96, step 1, values float32 Opened 14. int2 vvd+imid NU J2612_map_emready2.mrc as #21, grid size 438,438,438, pixel 0.5, shown at level 3.83, step 1, values float32 Opened 15. int2 vvd+imid local J2614_004_volume_map_emready2.mrc as #23, grid size 438,438,438, pixel 0.5, shown at level 1.74, step 1, values float32 Opened 16. combination of 2612 and 2614 as #24, grid size 438,438,438, pixel 0.5, shown at level 5.92, step 1, values float32 Opened 18. frustrated vvd+imid NU J2438_map_emready2.mrc as #26, grid size 443,443,443, pixel 0.5, shown at level 1.18, step 1, values float32 Opened 19. frustrated vvd+imid local J2456_004_volume_map_emready2.mrc as #27, grid size 443,443,443, pixel 0.5, shown at level 0.895, step 1, values float32 Opened 20 combination of 18 and 19 as #28, grid size 443,443,443, pixel 0.5, shown at level 6.9, step 1, values float32 Log from Wed Feb 25 16:20:52 2026UCSF ChimeraX version: 1.10.dev202503130118 (2025-03-13) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/0. figure 2 making .cxs"" Opened 2. cryosparc_P341_J1614_localrefine. selected.mrc as #4, grid size 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 Opened 1. cryosparc_P341_J1735_NUrefine selected.mrc as #9, grid size 300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32 Opened 3a. composite_map on EMReady2 maps of 1735 and 1614.ccp4 as #10, grid size 300,300,300, pixel 0.833, shown at level 14, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 0 as #13.1, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 1 as #13.2, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 2 as #13.3, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 3 as #13.4, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 4 as #13.5, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 5 as #13.6, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 6 as #13.7, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 7 as #13.8, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 8 as #13.9, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 9 as #13.10, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 10 as #13.11, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 11 as #13.12, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened 4. open- vvd+imid NU J2526_map_emready2.mrc as #1, grid size 443,443,443, pixel 0.5, shown at level 1.01, step 1, values float32 Opened 5. open- vvd+imid local J2540_005_volume_map_emready2.mrc as #2, grid size 443,443,443, pixel 0.5, shown at level 1.2, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 as #3, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 7. Clsoed- vvd+imid NU J2528_map_emready2.mrc as #5, grid size 443,443,443, pixel 0.5, shown at level 2.31, step 1, values float32 Opened 8. Closed- vvd+imid local J2544_007_volume_map_emready2.mrc as #7, grid size 443,443,443, pixel 0.5, shown at level 2.03, step 1, values float32 Opened 9a. combination of 2528 and 2544 emready2 as #8, grid size 443,443,443, pixel 0.5, shown at level 5.07, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy as #16, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 0 as #14.1, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 1 as #14.2, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 2 as #14.3, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 3 as #14.4, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 4 as #14.5, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 5 as #14.6, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 6 as #14.7, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 7 as #14.8, grid size 443,443,443, pixel 0.5, shown at level 6.22, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 0 as #17.1, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 1 as #17.2, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 2 as #17.3, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 3 as #17.4, grid size 443,443,443, pixel 0.5, shown at level 2.89, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 4 as #17.5, grid size 443,443,443, pixel 0.5, shown at level 2.84, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 5 as #17.6, grid size 443,443,443, pixel 0.5, shown at level 2.85, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 6 as #17.7, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 7 as #17.8, grid size 443,443,443, pixel 0.5, shown at level 2.11, step 1, values float32 Opened 10. int1 vvd+imid NU J2527_map_emready2.mrc as #18, grid size 443,443,443, pixel 0.5, shown at level 0.9, step 1, values float32 Opened 11. int1 vvd+imid local J2541_004_volume_map_emready2.mrc as #19, grid size 443,443,443, pixel 0.5, shown at level 1.16, step 1, values float32 Opened 12. combination of 10 and 11 as #20, grid size 443,443,443, pixel 0.5, shown at level 4.96, step 1, values float32 Opened 14. int2 vvd+imid NU J2612_map_emready2.mrc as #21, grid size 438,438,438, pixel 0.5, shown at level 3.83, step 1, values float32 Opened 15. int2 vvd+imid local J2614_004_volume_map_emready2.mrc as #23, grid size 438,438,438, pixel 0.5, shown at level 1.74, step 1, values float32 Opened 16. combination of 2612 and 2614 as #24, grid size 438,438,438, pixel 0.5, shown at level 5.92, step 1, values float32 Opened 18. frustrated vvd+imid NU J2438_map_emready2.mrc as #26, grid size 443,443,443, pixel 0.5, shown at level 1.18, step 1, values float32 Opened 19. frustrated vvd+imid local J2456_004_volume_map_emready2.mrc as #27, grid size 443,443,443, pixel 0.5, shown at level 0.895, step 1, values float32 Opened 20 combination of 18 and 19 as #28, grid size 443,443,443, pixel 0.5, shown at level 6.9, step 1, values float32 Log from Wed Feb 25 16:06:42 2026UCSF ChimeraX version: 1.10.dev202503130118 (2025-03-13) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/0. figure 2 making .cxs"" Opened 2. cryosparc_P341_J1614_localrefine. selected.mrc as #4, grid size 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 Opened 1. cryosparc_P341_J1735_NUrefine selected.mrc as #9, grid size 300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32 Opened 3a. composite_map on EMReady2 maps of 1735 and 1614.ccp4 as #10, grid size 300,300,300, pixel 0.833, shown at level 14, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 0 as #13.1, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 1 as #13.2, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 2 as #13.3, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 3 as #13.4, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 4 as #13.5, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 5 as #13.6, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 6 as #13.7, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 7 as #13.8, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 8 as #13.9, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 9 as #13.10, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 10 as #13.11, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 11 as #13.12, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened 4. open- vvd+imid NU J2526_map_emready2.mrc as #1, grid size 443,443,443, pixel 0.5, shown at level 1.01, step 1, values float32 Opened 5. open- vvd+imid local J2540_005_volume_map_emready2.mrc as #2, grid size 443,443,443, pixel 0.5, shown at level 1.2, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 as #3, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 7. Clsoed- vvd+imid NU J2528_map_emready2.mrc as #5, grid size 443,443,443, pixel 0.5, shown at level 2.31, step 1, values float32 Opened 8. Closed- vvd+imid local J2544_007_volume_map_emready2.mrc as #7, grid size 443,443,443, pixel 0.5, shown at level 2.03, step 1, values float32 Opened 9a. combination of 2528 and 2544 emready2 as #8, grid size 443,443,443, pixel 0.5, shown at level 5.07, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy as #16, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 0 as #14.1, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 1 as #14.2, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 2 as #14.3, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 3 as #14.4, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 4 as #14.5, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 5 as #14.6, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 6 as #14.7, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 7 as #14.8, grid size 443,443,443, pixel 0.5, shown at level 6.22, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 0 as #17.1, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 1 as #17.2, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 2 as #17.3, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 3 as #17.4, grid size 443,443,443, pixel 0.5, shown at level 2.89, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 4 as #17.5, grid size 443,443,443, pixel 0.5, shown at level 2.84, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 5 as #17.6, grid size 443,443,443, pixel 0.5, shown at level 2.85, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 6 as #17.7, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 7 as #17.8, grid size 443,443,443, pixel 0.5, shown at level 2.11, step 1, values float32 Opened 10. int1 vvd+imid NU J2527_map_emready2.mrc as #18, grid size 443,443,443, pixel 0.5, shown at level 0.9, step 1, values float32 Opened 11. int1 vvd+imid local J2541_004_volume_map_emready2.mrc as #19, grid size 443,443,443, pixel 0.5, shown at level 1.16, step 1, values float32 Opened 12. combination of 10 and 11 as #20, grid size 443,443,443, pixel 0.5, shown at level 0.862, step 1, values float32 Log from Tue Feb 24 16:13:45 2026UCSF ChimeraX version: 1.10.dev202503130118 (2025-03-13) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/ChimeraX/fig 2.cxs"" Opened cryosparc_P341_J1614_localrefine. selected.mrc as #4, grid size 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 Opened cryosparc_P341_J1735_NUrefine selected.mrc as #9, grid size 300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 as #10, grid size 300,300,300, pixel 0.833, shown at level 14, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 0 as #13.1, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 1 as #13.2, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 2 as #13.3, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 3 as #13.4, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 4 as #13.5, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 5 as #13.6, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 6 as #13.7, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 7 as #13.8, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 8 as #13.9, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 9 as #13.10, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 10 as #13.11, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 11 as #13.12, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Log from Thu Jul 24 11:26:36 2025UCSF ChimeraX version: 1.10.dev202503130118 (2025-03-13) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data, > presentation, and work/DDB1:CRBN with vvd compound processing/0.paper > writing/figure making/fig 2.cxs"" Opened cryosparc_P341_J1537_local refine on 1464.mrc as #1, grid size 300,300,300, pixel 0.833, shown at level 0.227, step 1, values float32 Opened cryosparc_P341_J1554_local refine on 1550.mrc as #2, grid size 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 Opened cryosparc_P341_J1575_map_sharp.mrc deepEM as #3, grid size 300,300,300, pixel 0.833, shown at level 0.253, step 1, values float32 Opened cryosparc_P341_J1614_localrefine. selected.mrc as #4, grid size 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 Opened cryosparc_P341_J1642_local refine.mrc as #5, grid size 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 Opened cryosparc_P341_J1464_NU refine.mrc as #6, grid size 300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32 Opened cryosparc_P341_J1473_localrefine.mrc as #7, grid size 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 Opened cryosparc_P341_J1550_Nurefine.mrc as #8, grid size 300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32 Opened cryosparc_P341_J1735_NUrefine selected.mrc as #9, grid size 300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 as #10, grid size 300,300,300, pixel 0.833, shown at level 14, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 0 as #13.1, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 1 as #13.2, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 2 as #13.3, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 3 as #13.4, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 4 as #13.5, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 5 as #13.6, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 6 as #13.7, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 7 as #13.8, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 8 as #13.9, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 9 as #13.10, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 10 as #13.11, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 11 as #13.12, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Log from Thu Jul 24 01:33:11 2025UCSF ChimeraX version: 1.10.dev202503130118 (2025-03-13) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data, > presentation, and work/DDB1:CRBN with vvd compound processing/0.paper > writing/figure making /fig 2.cxs"" Opened cryosparc_P341_J1537_local refine on 1464.mrc as #1, grid size 300,300,300, pixel 0.833, shown at level 0.227, step 1, values float32 Opened cryosparc_P341_J1554_local refine on 1550.mrc as #2, grid size 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 Opened cryosparc_P341_J1575_map_sharp.mrc deepEM as #3, grid size 300,300,300, pixel 0.833, shown at level 0.253, step 1, values float32 Opened cryosparc_P341_J1614_localrefine. selected.mrc as #4, grid size 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 Opened cryosparc_P341_J1642_local refine.mrc as #5, grid size 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 Opened cryosparc_P341_J1464_NU refine.mrc as #6, grid size 300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32 Opened cryosparc_P341_J1473_localrefine.mrc as #7, grid size 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 Opened cryosparc_P341_J1550_Nurefine.mrc as #8, grid size 300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32 Opened cryosparc_P341_J1735_NUrefine selected.mrc as #9, grid size 300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 as #10, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 0 as #13.1, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 1 as #13.2, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 2 as #13.3, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 3 as #13.4, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 4 as #13.5, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 5 as #13.6, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 6 as #13.7, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 7 as #13.8, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 8 as #13.9, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 9 as #13.10, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 10 as #13.11, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 11 as #13.12, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Log from Thu Jul 24 00:56:27 2025UCSF ChimeraX version: 1.10.dev202503130118 (2025-03-13) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data, > presentation, and work/DDB1:CRBN with vvd compound processing/figure for > Gabe modified/vvd figure making.cxs"" Opened cryosparc_P341_J1537_local refine on 1464.mrc as #1, grid size 300,300,300, pixel 0.833, shown at level 0.227, step 1, values float32 Opened cryosparc_P341_J1554_local refine on 1550.mrc as #2, grid size 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 Opened cryosparc_P341_J1575_map_sharp.mrc deepEM as #3, grid size 300,300,300, pixel 0.833, shown at level 0.253, step 1, values float32 Opened cryosparc_P341_J1614_localrefine. selected.mrc as #4, grid size 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 Opened cryosparc_P341_J1642_local refine.mrc as #5, grid size 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 Opened cryosparc_P341_J1464_NU refine.mrc as #6, grid size 300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32 Opened cryosparc_P341_J1473_localrefine.mrc as #7, grid size 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 Opened cryosparc_P341_J1550_Nurefine.mrc as #8, grid size 300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32 Opened cryosparc_P341_J1735_NUrefine selected.mrc as #9, grid size 300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 as #10, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Log from Tue Apr 29 15:52:59 2025UCSF ChimeraX version: 1.10.dev202503130118 (2025-03-13) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/zrizvi/Desktop/vvd figure making.cxs"" Opened cryosparc_P341_J1537_local refine on 1464.mrc as #1, grid size 300,300,300, pixel 0.833, shown at level 0.227, step 1, values float32 Opened cryosparc_P341_J1554_local refine on 1550.mrc as #2, grid size 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 Opened cryosparc_P341_J1575_map_sharp.mrc deepEM as #3, grid size 300,300,300, pixel 0.833, shown at level 0.253, step 1, values float32 Opened cryosparc_P341_J1614_localrefine. selected.mrc as #4, grid size 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 Opened cryosparc_P341_J1642_local refine.mrc as #5, grid size 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 Opened cryosparc_P341_J1464_NU refine.mrc as #6, grid size 300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32 Opened cryosparc_P341_J1473_localrefine.mrc as #7, grid size 300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32 Opened cryosparc_P341_J1550_Nurefine.mrc as #8, grid size 300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32 Opened cryosparc_P341_J1735_NUrefine selected.mrc as #9, grid size 300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32 Log from Tue Apr 29 13:11:33 2025UCSF ChimeraX version: 1.10.dev202503130118 (2025-03-13) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/zrizvi/Downloads/cryosparc_P341_J1537_004_volume_map.mrc Opened cryosparc_P341_J1537_004_volume_map.mrc as #1, grid size 300,300,300, pixel 0.833, shown at level 0.0281, step 2, values float32 > open /Users/zrizvi/Downloads/cryosparc_P341_J1554_005_volume_map.mrc Opened cryosparc_P341_J1554_005_volume_map.mrc as #2, grid size 300,300,300, pixel 0.833, shown at level 0.0434, step 2, values float32 > open /Users/zrizvi/Downloads/cryosparc_P341_J1575_map_sharp.mrc Opened cryosparc_P341_J1575_map_sharp.mrc as #3, grid size 300,300,300, pixel 0.833, shown at level 0.00032, step 2, values float32 > open /Users/zrizvi/Downloads/cryosparc_P341_J1614_005_volume_map.mrc Opened cryosparc_P341_J1614_005_volume_map.mrc as #4, grid size 300,300,300, pixel 0.833, shown at level 0.0429, step 2, values float32 > open /Users/zrizvi/Downloads/cryosparc_P341_J1642_005_volume_map.mrc Opened cryosparc_P341_J1642_005_volume_map.mrc as #5, grid size 300,300,300, pixel 0.833, shown at level 0.0424, step 2, values float32 > open ""/Users/zrizvi/Downloads/cryosparc_P341_J1464_008_volume_map (1).mrc"" Opened cryosparc_P341_J1464_008_volume_map (1).mrc as #6, grid size 300,300,300, pixel 0.833, shown at level 0.0314, step 2, values float32 > open ""/Users/zrizvi/Downloads/cryosparc_P341_J1473_004_volume_map (1).mrc"" Opened cryosparc_P341_J1473_004_volume_map (1).mrc as #7, grid size 300,300,300, pixel 0.833, shown at level 0.0324, step 2, values float32 > volume #1 step 1 > volume #2 step 1 > volume #3 step 1 > volume #4 step 1 > volume #5 step 1 > volume #6 step 1 > volume #7 step 1 > hide #!2 models > hide #!3 models > hide #!4 models > hide #!5 models > hide #!6 models > hide #!7 models > volume #1 level 0.201 > show #!2 models > volume #2 level 0.2044 > show #!6 models > volume #6 level 0.1538 > rename #2 ""cryosparc_P341_J1554_0local refine on 1464.mrc"" > rename #2 ""cryosparc_P341_J1554_local refine on 1464.mrc"" > rename #1 ""cryosparc_P341_J1537_local refine on 1464.mrc"" > rename #2 ""cryosparc_P341_J1554_local refine on 1550.mrc"" > open ""/Users/zrizvi/Downloads/cryosparc_P341_J1550_006_volume_map (2).mrc"" Opened cryosparc_P341_J1550_006_volume_map (2).mrc as #8, grid size 300,300,300, pixel 0.833, shown at level 0.0282, step 2, values float32 > volume #8 step 1 > volume #8 level 0.1757 > hide #!8 models > hide #!2 models > hide #!6 models > show #!6 models > hide #!1 models > show #!1 models > hide #!6 models > show #!6 models > hide #!1 models > show #!1 models > hide #!6 models > open /Users/zrizvi/Downloads/cryosparc_P341_J1735_007_volume_map.mrc Opened cryosparc_P341_J1735_007_volume_map.mrc as #9, grid size 300,300,300, pixel 0.833, shown at level 0.0299, step 2, values float32 > volume #9 step 1 > volume #9 level 0.1746 > tile 2 models tiled > show #!2 models > show #!3 models > show #!4 models > show #!5 models > show #!6 models > show #!7 models > show #!8 models > tile 9 models tiled > hide #!3 models > show #!3 models > volume #3 level 0.2531 > volume #4 level 0.2407 > volume #5 level 0.2597 > volume #6 level 0.2049 > volume #6 level 0.1582 > volume #7 level 0.1171 > volume #7 level 0.2217 > volume #8 level 0.2374 > volume #9 level 0.2058 > rename #3 ""cryosparc_P341_J1575_map_sharp.mrc deepEM"" > rename #4 cryosparc_P341_J1614_localrefine.mrc > rename #5 ""cryosparc_P341_J1642_local refine.mrc"" > rename #6 ""cryosparc_P341_J1464_NU refine.mrc"" > rename #7 cryosparc_P341_J1473_localrefine.mrc > rename #8 cryosparc_P341_J1550_Nurefine).mrc > rename #8 cryosparc_P341_J1550_Nurefine.mrc > rename #9 cryosparc_P341_J1735_NUrefine.mrc > hide #!1 models > hide #!2 models > hide #!3 models > hide #!4 models > hide #!5 models > hide #!7 models > ~tile > hide #!6 models > hide #!8 models > hide #!9 models > show #!6 models > hide #!6 models > show #!8 models > volume #8 level 0.158 > hide #!8 models > show #!9 models > volume #9 level 0.158 > show #!7 models > show #!6 models > hide #!7 models > show #!8 models > tile 3 models tiled > hide #!6 models > ~tile > tile 2 models tiled > ~tile > color #9 #99bfe56a models > color #9 #99bfe56d models > hide #!8 models > color #9 #99bfe5ff models > show #!1 models > show #!2 models > show #!4 models > show #!5 models > show #!7 models > ~tile > hide #!9 models > tile 5 models tiled > volume #1 level 0.2267 > hide #!1 models > volume #2 level 0.3042 > volume #4 level 0.304 > volume #5 level 0.304 > volume #7 level 0.304 > hide #!7 models > ~tile > tile 3 models tiled > hide #!5 models > hide #!2 models > show #!9 models > ~tile > rename #9 ""cryosparc_P341_J1735_NUrefine selected.mrc"" > rename #4 ""cryosparc_P341_J1614_localrefine. selected.mrc"" > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data, > presentation, and work/DDB1:CRBN with vvd compound processing/2. processing > in coot/vvd.pdb"" > hide #!9 models > hide #!4 models > close #10 > show #!4 models > show #!9 models > save ""/Users/zrizvi/Desktop/vvd figure making.cxs"" includeMaps true ——— End of log from Tue Apr 29 13:11:33 2025 ——— > view name session-start opened ChimeraX session > hide #!4 models > hide #!9 models > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/ACB manuscript > shared folder/4. Results extended/Figure 5/model building/2. With > ikaros/with deg47 only/CombineFocusedMaps_71/composite_map.ccp4"" Opened composite_map.ccp4 as #10, grid size 300,300,300, pixel 0.833, shown at level 0.744, step 2, values float32 > volume #10 step 1 > volume #10 level 10.76 > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data, > presentation, and work/DDB1:CRBN with vvd compound processing/2. processing > in coot/8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb"" Chain information for 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb #11 --- Chain | Description A | No description available B | No description available > hide #!10 models > select #11/A 6318 atoms, 6434 bonds, 824 residues, 1 model selected > color sel light gray > select clear > color #11/A:1-710 light blue > color #11/A:710-5000 steel blue > color #11/A:392-709 cornflower blue > color #11/B:1-190 navajowhite > color #11/B:191-320 light salmon > color #11/B:321-500 tomato > show #!10 models > volume #10 level 9.956 > select ::name=""101"" 28 atoms, 30 bonds, 1 residue, 1 model selected > color sel lime > select clear > color zone #10 near #11 distance 5 > color zone #11 near #10 distance 8 color zone: No surfaces specified. > color zone #10 near #11 distance 8 > hide #!11 models > graphics silhouettes true > lighting shadows true > lighting soft > set bgColor white > show #!11 models > hide #!11 models > rename #10 ""composite_map on EMReady2 maps of 1735 and 1614.ccp4"" > save ""/Users/zrizvi/Desktop/vvd figure making.cxs"" includeMaps true ——— End of log from Tue Apr 29 15:52:59 2025 ——— > view name session-start opened ChimeraX session > show #!11 models > hide #!10 models > show #!10 models > color #10 #b2b2b2da models > color #10 #b2b2b2ff models > color zone #10 near #11 distance 8 > color zone #10 near #11 distance 10 > hide #!11 models > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data, > presentation, and work/DDB1:CRBN with vvd compound processing/figure for > Gabe modified/vvd.pdb"" > hide #!10 models > show #!10 models > close #12 > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data, > presentation, and work/DDB1:CRBN with vvd compound processing/figure for > Gabe modified/final.pdb"" Chain information for final.pdb #12 --- Chain | Description B | No description available C | No description available > mmaker #12 to #11 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb, chain A (#11) with final.pdb, chain B (#12), sequence alignment score = 3652.5 RMSD between 786 pruned atom pairs is 0.524 angstroms; (across all 824 pairs: 0.911) > hide #!10 models > show #!11 models > hide #!11 models > hide #!12 models > show #!11 models > color #!11 byhetero > select clear > show #!12 models > hide #!12 models > show #!12 models > close #12 > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data, > presentation, and work/DDB1:CRBN with vvd compound processing/figure for > Gabe modified/7u8ffinallylinkedtoVVD.pdb"" Chain information for 7u8ffinallylinkedtoVVD.pdb #12 --- Chain | Description B | No description available C | No description available > close #12 > show #!10 models > hide #!11 models > camera ortho > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data, > presentation, and work/DDB1:CRBN with vvd compound processing/0.paper > writing/figure making /Figure 2a.png"" width 1800 height 1532 supersample 4 > transparentBackground true > show #!11 models > color #10 #b2b2b2c0 models > color #10 #b2b2b2bf models > ui tool show ""Show Sequence Viewer"" > sequence chain /B Alignment identifier is 11/B > select /B:264 14 atoms, 15 bonds, 1 residue, 1 model selected > select /B:264 14 atoms, 15 bonds, 1 residue, 1 model selected > select clear > ui tool show ""Side View"" > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data, > presentation, and work/DDB1:CRBN with vvd compound processing/0.paper > writing/figure making /Figure 2b.png"" width 1800 height 1532 supersample 4 > transparentBackground true > open 8cvp 8cvp title: Cereblon-DDB1 in the Apo form [more info...] Chain information for 8cvp #12 --- Chain | Description | UniProt A | DNA damage-binding protein 1 | DDB1_HUMAN 1-1140 B | Protein cereblon | CRBN_HUMAN 1-442 Non-standard residues in 8cvp #12 --- ZN — zinc ion > mmaker #12 to #11 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb, chain A (#11) with 8cvp, chain A (#12), sequence alignment score = 5335.5 RMSD between 824 pruned atom pairs is 0.011 angstroms; (across all 824 pairs: 0.011) > hide #!10 models > ui tool show ""Show Sequence Viewer"" > sequence chain #12/B Alignment identifier is 12/B > select #12/B:264 14 atoms, 15 bonds, 1 residue, 1 model selected > select #12/B:264 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > color #12 darkgrey > select clear > show #!10 models > hide #!11 models > show #!11 models > select add #12 10112 atoms, 10284 bonds, 6 pseudobonds, 1485 residues, 4 models selected > color (#!12 & sel) cornflower blue > select clear > color #12/A:1-710 light blue > color #12/A:710-5000 steel blue > color #12/A:392-709 cornflower blue > color #12/B:1-190 navajowhite > color #12/B:191-320 light salmon > color #12/B:321-500 tomato > hide #!11 models > show #!11 models > hide #!12 models > color #10 #b2b2b2ff models > ui tool show ""Surface Color"" > ui tool show ""Surface Zone"" > ui tool show ""Volume Viewer"" > ui tool show ""Color Zone"" > color zone #10 near #11 distance 3.83 > color single #10 > hide #!11 atoms > color zone #10 near #11 distance 3.83 > color single #10 > color #10 #b2b2b2d2 models > color #10 #b2b2b2d1 models > select ::name=""101"" 28 atoms, 30 bonds, 1 residue, 1 model selected > show sel atoms > select clear > select ::name=""101"" 28 atoms, 30 bonds, 1 residue, 1 model selected > color sel lime > select clear > hide #!10 models > select #11/B:264 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > select clear > show #!10 models > ui tool show ""Volume Viewer"" > ui tool show ""Surface Zone"" > ui tool show ""Surface Color"" > ui tool show ""Color Zone"" Need to color zone map before it can be split [Repeated 1 time(s)] > color zone #10 near #11 distance 5 > volume splitbyzone #10 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 0 as #13.1, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 1 as #13.2, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 2 as #13.3, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 3 as #13.4, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 4 as #13.5, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 5 as #13.6, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 6 as #13.7, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 7 as #13.8, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 8 as #13.9, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 9 as #13.10, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 10 as #13.11, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 11 as #13.12, grid size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32 > select add #13.12 2 models selected > hide #!13.11 models > hide #!13.10 models > hide #!13.9 models > hide #!13.8 models > hide #!13.7 models > hide #!13.6 models > hide #!13.5 models > hide #!13.4 models > hide #!13.3 models > hide #!13.2 models > hide #!13.1 models > show #!10 models > color single #10 > hide #!13 models > show #!13 models > hide #!13 models > select add #13 25 models selected > select subtract #13 Nothing selected > hide #!10 models > show #!13 models > show #!10 models > hide #!10 models > color #13.2 darkgrey models > color #13.3 darkgrey models > color #13.4 darkgrey models > color #13.5 darkgrey models > color #13.6 darkgrey models > color #13.7 darkgrey models > color #13.8 darkgrey models > color #13.9 darkgrey models > color #13.10 darkgrey models > color #13.11 darkgrey models > show #!13.1 models > show #!13.2 models > show #!13.3 models > show #!13.4 models > show #!13.5 models > show #!13.6 models > show #!13.7 models > show #!13.8 models > show #!13.9 models > show #!13.10 models > show #!13.11 models > select add #13 25 models selected > select subtract #13.12 23 models selected > combine sel No structures specified > show #!10 models > hide #!10 models > show #!10 models > hide #!13.1 models > select subtract #13.1 21 models selected > select subtract #13.3 19 models selected > select add #13 25 models selected > select subtract #13 Nothing selected > hide #!13.2 models > hide #!13.3 models > hide #!13.4 models > hide #!13.5 models > hide #!13.6 models > hide #!13.7 models > hide #!10 models > show #!13.1 models > show #!13.3 models > hide #!13.3 models > show #!13.2 models > show #!13.3 models > show #!13.4 models > show #!13.5 models > show #!13.6 models > show #!13.7 models > hide #!11 models > show #!12 models > hide #!13 models > color #!12 byhetero > hide #!12.2 models Cell requested for row 12 is out of bounds for table with 27 rows! Resizing table model. > show #!13 models > hide #!13.2 models > hide #!13.1 models > hide #!13.3 models > hide #!13.4 models > hide #!13.5 models > hide #!13.6 models > hide #!13.7 models > hide #!13.9 models > hide #!13.8 models > hide #!13.10 models > hide #!13.11 models > show #!10 models > color #10 #b2b2b277 models > color #10 #b2b2b278 models > hide #!13.12 models > show #!13.12 models > ui tool show ""Side View"" > color #13.12 #00ff00db models > color #13.12 #00ff00b1 models > color #13.12 #00ff00b0 models > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > graphics silhouettes false > graphics silhouettes true > lighting soft > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data, > presentation, and work/DDB1:CRBN with vvd compound processing/0.paper > writing/figure making /Figure 2c.png"" width 1800 height 1619 supersample 4 > transparentBackground true > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data, > presentation, and work/DDB1:CRBN with vvd compound processing/0.paper > writing/figure making /fig 2.cxs"" includeMaps true ——— End of log from Thu Jul 24 00:56:27 2025 ——— > view name session-start opened ChimeraX session > show #!11 models > hide #!12 models > hide #!13 models > color #!11 byhetero > select clear > color #10 #b2b2b2b3 models > ui tool show ""Side View"" > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data, > presentation, and work/DDB1:CRBN with vvd compound processing/0.paper > writing/figure making /Figure 2b.png"" width 1800 height 1532 supersample 4 > transparentBackground true > show #!13 models > hide #!11 models > show #!12 models > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data, > presentation, and work/DDB1:CRBN with vvd compound processing/0.paper > writing/figure making /Figure 2c.png"" width 1800 height 1532 supersample 4 > transparentBackground true > show #!11 models > hide #!12 models > hide #!13 models > hide #!10 models > select #11/B:287 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > select clear > show #!10 models > hide #!10 models > select #11/B:318 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > select clear > show #!10 models > color #10 #d6d6d6ff models > color #10 #d6d6d6b3 models > select clear > volume #10 level 12 > volume #10 level 14.05 > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data, > presentation, and work/DDB1:CRBN with vvd compound processing/0.paper > writing/figure making /Figure 2b.png"" width 1800 height 1532 supersample 4 > transparentBackground true > show #!13 models > hide #!11 models > show #!12 models > color #13 #d6d6d6ff models > color #13 #d6d6d6b3 models > hide #!10 models > select add #13 25 models selected > color #13.12.1 lime > select clear > show #!10 models > ui tool show ""Side View"" > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data, > presentation, and work/DDB1:CRBN with vvd compound processing/0.paper > writing/figure making /Figure 2c.png"" width 1800 height 1471 supersample 4 > transparentBackground true > hide #!13 models > hide #!10 models > hide #!12 models > show #!11 models Drag select of 43 atoms, 49 residues, 45 bonds > show sel atoms > select clear > ui mousemode right distance > distance #11/B:502@F27 #11/B:261@CD2 Distance between 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb #11/B 101 502 F27 and LEU 261 CD2: 3.388Å > distance #11/B:502@C25 #11/B:260@NE2 Distance between 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb #11/B 101 502 C25 and GLN 260 NE2: 1.665Å > distance #11/B:502@C20 #11/B:318@SG Distance between 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb #11/B 101 502 C20 and CYS 318 SG: 3.698Å Cell requested for row 0 is out of bounds for table with 15 rows! Resizing table model. > morph #12 to #11 Expected a keyword > volume morph #12 to #11 Expected a keyword > vop morph #12 to #11 > volume morph #12 to #11 Expected a keyword > vop morph #12 #11 volume morph requires 2 or more volumes, got 0 > morph #12 #11 Computed 51 frame morph #15 > coordset #15 1,51 > hide #!15 models > show #!12 models Drag select of 11 atoms, 70 residues, 12 bonds > show sel atoms > select clear > show #!11 models > hide #!12 models > show #!12 models > close #15 > morph #12 #11 Computed 51 frame morph #15 > coordset #15 1,51 > morph #12 #11 Computed 51 frame morph #16 > coordset #16 1,51 > morph #12 #11 Computed 51 frame morph #17 > coordset #17 1,51 > close #15 > close #16 > close #17 > show #!11 models > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data, > presentation, and work/DDB1:CRBN with vvd compound processing/0.paper > writing/figure making /fig 2.cxs"" includeMaps true ——— End of log from Thu Jul 24 01:33:11 2025 ——— > view name session-start opened ChimeraX session > close #1 > close #2 > close #3 > close #5 > close #6 > close #7 > close #8 > show #!10 models > show #!13 models > hide #!13 models > hide #!10 models > show #!12 models > hide #!14 models > color #12 #d6d6d6ff > color #12 silver > mmaker #12 to #11 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb, chain A (#11) with 8cvp, chain A (#12), sequence alignment score = 5335.5 RMSD between 824 pruned atom pairs is 0.011 angstroms; (across all 824 pairs: 0.011) > hide atoms > select ::name=""101"" 28 atoms, 30 bonds, 1 residue, 1 model selected > show sel atoms > select #11/B:264 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > select #12/B:264 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > select clear > color byhetero > select clear > ui tool show ""Side View"" > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/ChimeraX/fig 2.cxs"" includeMaps true > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/postdoc data, > presentation, and work/DDB1:CRBN with vvd compound processing/0.paper > writing/figure making/fig2a zoom2.png"" width 1800 height 1532 supersample 4 > transparentBackground true > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/ChimeraX/fig 2.cxs"" includeMaps true ——— End of log from Thu Jul 24 11:26:36 2025 ——— > view name session-start opened ChimeraX session > hide #!11 models > show #!11 models > show #!4 models > show #!9 models > view > show #!10 models > hide #!9 models > hide #!4 models > hide #!12 models > show #!13 models > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/open/J2526_map_emready2.mrc"" Opened J2526_map_emready2.mrc as #1, grid size 443,443,443, pixel 0.5, shown at level 1.01, step 2, values float32 > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig > maps/open/J2540_005_volume_map_emready2.mrc"" Opened J2540_005_volume_map_emready2.mrc as #2, grid size 443,443,443, pixel 0.5, shown at level 1.2, step 2, values float32 > vop max #1 #2 Opened volume maximum as #3, grid size 443,443,443, pixel 0.5, shown at step 1, values float32 > rename #3 ""combination of 2526 and 2540 emready2"" > rename #1 ""open- vvd+imid J2526_map_emready2.mrc"" > rename #1 ""open- vvd+imid NU J2526_map_emready2.mrc"" > rename #2 ""open- vvd+imid local J2540_005_volume_map_emready2.mrc"" > hide #!11 models > hide #!13 models > show #!13 models > hide #!13 models > select add #3 2 models selected > graphics silhouettes false > lighting shadows true intensity 0.5 > lighting soft > lighting full > volume #1 step 1 > volume #2 step 1 > volume #3 level 3.516 > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > view matrix models > #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 > ui mousemode right ""translate selected models"" > view matrix models > #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 > volume #3 level 5.573 > fitmap #3 inMap #10 Fit map combination of 2526 and 2540 emready2 in map composite_map on EMReady2 maps of 1735 and 1614.ccp4 using 340198 points correlation = 0.9503, correlation about mean = 0.6492, overlap = 5.013e+07 steps = 168, shift = 14.6, angle = 12.4 degrees Position of combination of 2526 and 2540 emready2 (#3) relative to composite_map on EMReady2 maps of 1735 and 1614.ccp4 (#10) coordinates: Matrix rotation and translation 0.96196967 -0.27233362 0.02118389 54.69880809 0.09346611 0.25529558 -0.96233479 187.78850372 0.25666796 0.92771686 0.27104057 -69.01712395 Axis 0.97451791 -0.12141649 0.18860775 Axis point 0.00000000 144.90433503 85.21030045 Rotation angle (degrees) 75.86822137 Shift along axis 17.48718173 > select clear > ui mousemode right translate > volume #3 level 2.711 > show #!11 models > hide #!10 models > color #3 #b2ffffa9 models > select clear > color zone #3 near #11 distance 8 > select clear > hide #!11 atoms > color zone #3 near #11 distance 8 > color #!11 bychain > undo > color zone #3 near #11 distance 8 > color #!11 byhetero [Repeated 1 time(s)] > ~heteroatom Unknown command: ~heteroatom > color zone #3 near #11 & protein distance 8 > color zone #3 near #11 distance 8 > color zone #3 near #11 & ~ligand & ~solvent distance 8 > color zone #3 near #11 & polymer distance 8 Expected a keyword > color #3 gray > color zone #3 near #11/A & protein distance 8 [Repeated 1 time(s)] > fitmap #11 inMap #3 Fit molecule 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb (#11) to map combination of 2526 and 2540 emready2 (#3) using 8554 atoms average map value = 9.415, steps = 44 shifted from previous position = 0.244 rotated from previous position = 0.266 degrees atoms outside contour = 1045, contour level = 2.7111 Position of 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb (#11) relative to combination of 2526 and 2540 emready2 (#3) coordinates: Matrix rotation and translation 0.96102761 0.09475034 0.25970812 -52.92644150 -0.27553875 0.25197696 0.92767775 31.87312977 0.02245732 -0.96308358 0.26826421 198.31177033 Axis -0.97400087 0.12221663 -0.19074956 Axis point 0.00000000 144.94453273 84.83756927 Rotation angle (degrees) 76.07601433 Shift along axis 17.61794287 > fitmap #11 inMap #3 Fit molecule 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb (#11) to map combination of 2526 and 2540 emready2 (#3) using 8554 atoms average map value = 9.414, steps = 28 shifted from previous position = 0.00835 rotated from previous position = 0.0108 degrees atoms outside contour = 1042, contour level = 2.7111 Position of 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb (#11) relative to combination of 2526 and 2540 emready2 (#3) coordinates: Matrix rotation and translation 0.96098510 0.09486625 0.25982307 -52.95701236 -0.27567867 0.25188266 0.92766179 31.90374037 0.02255887 -0.96309684 0.26820809 198.31213193 Axis -0.97397549 0.12222053 -0.19087665 Axis point 0.00000000 144.95021334 84.82634677 Rotation angle (degrees) 76.08170877 Shift along axis 17.62496843 > color #3 #b2ffffff models > color #3 #b2ffffc8 models > color #3 #b2ffffae models > color #3 #b2ffffaa models > color #3 #b2ffffab models > fitmap #11 inMap #3 Fit molecule 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb (#11) to map combination of 2526 and 2540 emready2 (#3) using 8554 atoms average map value = 9.415, steps = 40 shifted from previous position = 0.00992 rotated from previous position = 0.0117 degrees atoms outside contour = 1047, contour level = 2.7111 Position of 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb (#11) relative to combination of 2526 and 2540 emready2 (#3) coordinates: Matrix rotation and translation 0.96103238 0.09473372 0.25969653 -52.92173586 -0.27552298 0.25197233 0.92768369 31.87164356 0.02244658 -0.96308643 0.26825488 198.31472716 Axis -0.97400426 0.12221605 -0.19073265 Axis point 0.00000000 144.94452420 84.83909535 Rotation angle (degrees) 76.07628568 Shift along axis 17.61612817 > split #11 Split 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb (#11) into 2 models Chain information for 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb A #11.1 --- Chain | Description A | No description available Chain information for 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb B #11.2 --- Chain | Description B | No description available > select add #11.1 6318 atoms, 6434 bonds, 824 residues, 1 model selected > select subtract #11.1 Nothing selected > select add #11.2 2236 atoms, 2278 bonds, 4 pseudobonds, 351 residues, 2 models selected > fitmap sel inMap #3 Fit molecule 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb B (#11.2) to map combination of 2526 and 2540 emready2 (#3) using 2236 atoms average map value = 7.606, steps = 52 shifted from previous position = 0.506 rotated from previous position = 1.99 degrees atoms outside contour = 454, contour level = 2.7111 Position of 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb B (#11.2) relative to combination of 2526 and 2540 emready2 (#3) coordinates: Matrix rotation and translation 0.95997604 0.12501582 0.25063329 -55.21416768 -0.27579491 0.26595891 0.92368989 30.40664271 0.04881769 -0.95584355 0.28979291 191.85480848 Axis -0.97266091 0.10443982 -0.20742005 Axis point 0.00000000 143.00817251 82.65941765 Rotation angle (degrees) 75.05664688 Shift along axis 17.08579253 > select add #11.1 8554 atoms, 8712 bonds, 4 pseudobonds, 1175 residues, 3 models selected > select subtract #11.2 6318 atoms, 6434 bonds, 824 residues, 1 model selected > fitmap sel inMap #3 Fit molecule 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb A (#11.1) to map combination of 2526 and 2540 emready2 (#3) using 6318 atoms average map value = 10.3, steps = 60 shifted from previous position = 0.0792 rotated from previous position = 0.218 degrees atoms outside contour = 516, contour level = 2.7111 Position of 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb A (#11.1) relative to combination of 2526 and 2540 emready2 (#3) coordinates: Matrix rotation and translation 0.96153052 0.09164231 0.25896090 -52.47900982 -0.27402598 0.25408547 0.92755072 31.47801921 0.01920469 -0.96283034 0.26942331 198.46339739 Axis -0.97427609 0.12356701 -0.18846035 Axis point 0.00000000 145.04029338 85.04809926 Rotation angle (degrees) 75.96470021 Shift along axis 17.61620776 > select subtract #11.1 Nothing selected > select add #11.1 6318 atoms, 6434 bonds, 824 residues, 1 model selected > select add #11.2 8554 atoms, 8712 bonds, 4 pseudobonds, 1175 residues, 3 models selected > combine sel > hide #!11 models > select add #11 8554 atoms, 8712 bonds, 4 pseudobonds, 1175 residues, 4 models selected > select subtract #11 Nothing selected > select subtract #14 Nothing selected > select ::name=""101"" 56 atoms, 60 bonds, 2 residues, 2 models selected > show sel & #!5 atoms > select clear > color zone #3 near #5 distance 8 [Repeated 1 time(s)] > undo [Repeated 1 time(s)] > select clear > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/open/vvd+iberdo open.pdb"" > models #5 relModel #3 > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/open/vvd+iberdo open.pdb"" Chain information for vvd+iberdo open.pdb #6 --- Chain | Description A | No description available B | No description available > mmaker #6 to #5 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker combination, chain A (#5) with vvd+iberdo open.pdb, chain A (#6), sequence alignment score = 4201.9 RMSD between 824 pruned atom pairs is 0.000 angstroms; (across all 824 pairs: 0.000) > hide #!5 models > color zone #3 near #6 distance 8 > color #3,6 byhetero > color #3,6 byelement > ui tool show ""Color Actions"" > color bychain > color bychain target cs [Repeated 1 time(s)] > color zone #3 near #6 distance 8 > select subtract #14 Nothing selected > hide #!6 models > show #!6 models > hide #!3 models > color #6/A:1-710 light blue > color #6/A:710-5000 steel blue > color #6/B:1-190 navajowhite > color #6/B:191-320 light salmon > color #6/B:321-500 tomato > select ::name=""101"" 84 atoms, 90 bonds, 3 residues, 3 models selected > color (#!6 & sel) lime > select clear > show #!3 models > fitmap #6 inMap #3 Fit molecule vvd+iberdo open.pdb (#6) to map combination of 2526 and 2540 emready2 (#3) using 8554 atoms average map value = 9.593, steps = 40 shifted from previous position = 0.000478 rotated from previous position = 0.00651 degrees atoms outside contour = 971, contour level = 2.7111 Position of vvd+iberdo open.pdb (#6) relative to combination of 2526 and 2540 emready2 (#3) coordinates: Matrix rotation and translation 0.99999490 0.00318409 0.00025382 -0.40275030 -0.00318393 0.99999473 -0.00063666 0.25133637 -0.00025585 0.00063585 0.99999976 -0.38480119 Axis 0.19535237 0.07824435 -0.97760691 Axis point 70.90279314 146.06118062 0.00000000 Rotation angle (degrees) 0.18660948 Shift along axis 0.31717173 > close #14 > color zone #3 near #6 distance 8 > hide #!3 models > show #!3 models > hide #!3 models > ui tool show ""Show Sequence Viewer"" > sequence chain #6/B Alignment identifier is 6/B > select #6/B:380 14 atoms, 15 bonds, 1 residue, 1 model selected > select #6/B:380 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > select #6/B:386 14 atoms, 15 bonds, 1 residue, 1 model selected > select #6/B:386 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > select #6/B:400 14 atoms, 15 bonds, 1 residue, 1 model selected > select #6/B:400 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > select clear > show #!3 models > color #3 #b2ffff95 models > color #3 #b2ffff80 models > select add #6 8554 atoms, 8712 bonds, 4 pseudobonds, 1175 residues, 2 models selected > fitmap sel inMap #3 Fit molecule vvd+iberdo open.pdb (#6) to map combination of 2526 and 2540 emready2 (#3) using 8554 atoms average map value = 9.593, steps = 28 shifted from previous position = 0.00997 rotated from previous position = 0.00827 degrees atoms outside contour = 970, contour level = 2.7111 Position of vvd+iberdo open.pdb (#6) relative to combination of 2526 and 2540 emready2 (#3) coordinates: Matrix rotation and translation 0.99999451 0.00330818 0.00017995 -0.42084422 -0.00330806 0.99999432 -0.00063753 0.26238779 -0.00018206 0.00063693 0.99999978 -0.38918532 Axis 0.18887565 0.05365024 -0.98053436 Axis point 73.94006957 145.38881802 0.00000000 Rotation angle (degrees) 0.19330462 Shift along axis 0.31619952 > select clear > volume #3 level 1.638 > volume #3 level 1.191 > volume #3 level 1.861 > open 8W7 '8W7' has no suffix > open 8w7 '8w7' has no suffix > open PDB:8w7 PDB identifiers are either 4 or 8 characters long, got ""8w7"" > open ""/Users/zrizvi/Downloads/8W7 (1).cif"" Summary of feedback from opening /Users/zrizvi/Downloads/8W7 (1).cif --- warning | No mmCIF models found. > open ""/Users/zrizvi/Downloads/8W7 (1).cif"" Summary of feedback from opening /Users/zrizvi/Downloads/8W7 (1).cif --- warning | No mmCIF models found. > open ""/Users/zrizvi/Downloads/8W7 (1).cif"" Summary of feedback from opening /Users/zrizvi/Downloads/8W7 (1).cif --- warning | No mmCIF models found. > open ""/Users/zrizvi/Downloads/8W7 (1).cif"" Summary of feedback from opening /Users/zrizvi/Downloads/8W7 (1).cif --- warning | No mmCIF models found. > open ""/Users/zrizvi/Downloads/8W7 (1).cif"" Summary of feedback from opening /Users/zrizvi/Downloads/8W7 (1).cif --- warning | No mmCIF models found. > open 5v3o Summary of feedback from opening 5v3o fetched from pdb --- note | Fetching compressed mmCIF 5v3o from http://files.rcsb.org/download/5v3o.cif 5v3o title: Cereblon in complex with DDB1 and CC-220 [more info...] Chain information for 5v3o #7 --- Chain | Description | UniProt A | DNA damage-binding protein 1 | DDB1_HUMAN 1-1140 C | Protein cereblon | CRBN_HUMAN 40-442 Non-standard residues in 5v3o #7 --- 8W7 — (3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione ZN — zinc ion > mmaker #7 to #6 Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker vvd+iberdo open.pdb, chain A (#6) with 5v3o, chain A (#7), sequence alignment score = 3513.3 RMSD between 746 pruned atom pairs is 0.665 angstroms; (across all 775 pairs: 1.032) > hide #!3 models > select ::name=""8W7"" 33 atoms, 37 bonds, 1 residue, 1 model selected > color sel yellow > select clear > select #6/a 6318 atoms, 6434 bonds, 824 residues, 1 model selected > select #7/a/c 11175 atoms, 11396 bonds, 15 pseudobonds, 1452 residues, 3 models selected > select clear > split #7 Split 5v3o (#7) into 2 models Chain information for 5v3o A #7.1 --- Chain | Description A | No description available Chain information for 5v3o C #7.2 --- Chain | Description C | No description available > select add #7.1 8273 atoms, 8422 bonds, 9 pseudobonds, 1087 residues, 2 models selected > select subtract #7.1 Nothing selected > select add #7.2 2902 atoms, 2974 bonds, 6 pseudobonds, 365 residues, 3 models selected > select subtract #7.2 Nothing selected > hide #!6 models > split #7.2 Did not split 5v3o C, has only one piece Drag select of 1142 residues, 10 pseudobonds > delete sel Drag select of 162 residues, 5 pseudobonds > select up 1666 atoms, 1649 bonds, 5 pseudobonds, 212 residues, 4 models selected > select up 2415 atoms, 2431 bonds, 5 pseudobonds, 308 residues, 4 models selected > delete sel Drag select of 1 atoms > delete sel > show #!6 models > select add #7.2 33 atoms, 37 bonds, 1 residue, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models > #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 > ui mousemode right translate > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > view matrix models > #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 > ui mousemode right translate > ui mousemode right ""translate selected models"" > view matrix models > #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 > ui mousemode right ""rotate selected models"" > view matrix models > #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 > ui mousemode right ""translate selected models"" > view matrix models > #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 > ui mousemode right translate > ui mousemode right ""translate selected models"" > view matrix models > #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 > ui mousemode right ""rotate selected models"" > view matrix models > #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 > ui mousemode right ""translate selected models"" > view matrix models > #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 > ui mousemode right translate > show #!3 models > ui mousemode right ""translate selected models"" > view matrix models > #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 > ui mousemode right translate > select subtract #7.2 Nothing selected > select add #7.2 33 atoms, 37 bonds, 1 residue, 1 model selected > fitmap sel inMap #3 Fit molecule 5v3o C (#7.2) to map combination of 2526 and 2540 emready2 (#3) using 33 atoms average map value = 5.737, steps = 256 shifted from previous position = 7.36 rotated from previous position = 81 degrees atoms outside contour = 3, contour level = 1.8614 Position of 5v3o C (#7.2) relative to combination of 2526 and 2540 emready2 (#3) coordinates: Matrix rotation and translation 0.87027007 -0.19554474 -0.45209762 50.53821845 -0.20191453 -0.97878910 0.03467589 165.49997848 -0.44928891 0.06110769 -0.89129418 123.26330988 Axis 0.96702224 -0.10275818 -0.23304237 Axis point 0.00000000 84.99703244 68.30715524 Rotation angle (degrees) 179.21693737 Shift along axis 3.13952962 > select clear > select add #7.2 33 atoms, 37 bonds, 1 residue, 1 model selected > ui mousemode right ""rotate selected models"" > view matrix models > #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 > ui mousemode right ""translate selected models"" > view matrix models > #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 > select clear > select add #7.2 33 atoms, 37 bonds, 1 residue, 1 model selected > view matrix models > #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 > ui mousemode right translate > select clear > select add #7.2 33 atoms, 37 bonds, 1 residue, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models > #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 > select subtract #7.2 Nothing selected > ui mousemode right translate > select add #6 8554 atoms, 8712 bonds, 4 pseudobonds, 1175 residues, 2 models selected > select add #7.2 8587 atoms, 8749 bonds, 4 pseudobonds, 1176 residues, 3 models selected > combine sel > rename #8 ""vvd+iberdo open.pdb"" > close #6 > close #7 > select ::name=""8W7"" 33 atoms, 37 bonds, 1 residue, 1 model selected > color sel lime > ui tool show ""Show Sequence Viewer"" > sequence chain #8/B Alignment identifier is 8/B > select #8/B:380 14 atoms, 15 bonds, 1 residue, 1 model selected > select #8/B:380 14 atoms, 15 bonds, 1 residue, 1 model selected > hide sel atoms > select #8/B:386 14 atoms, 15 bonds, 1 residue, 1 model selected > select #8/B:386 14 atoms, 15 bonds, 1 residue, 1 model selected > hide sel atoms > select #8/B:400 14 atoms, 15 bonds, 1 residue, 1 model selected > select #8/B:400 14 atoms, 15 bonds, 1 residue, 1 model selected > hide sel atoms > select clear > color zone #3 near #8 distance 8 > hide #!8 models > show #!8 models > color #3 #b2ffff80 models > split #8 Split vvd+iberdo open.pdb (#8) into 3 models Chain information for vvd+iberdo open.pdb A #8.1 --- Chain | Description A | No description available Chain information for vvd+iberdo open.pdb B #8.2 --- Chain | Description B | No description available > select add #8.3 33 atoms, 37 bonds, 1 residue, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models > #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 > select clear > select add #8.3 33 atoms, 37 bonds, 1 residue, 1 model selected > view matrix models > #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 > ui mousemode right ""rotate selected models"" > view matrix models > #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 > ui mousemode right ""translate selected models"" > view matrix models > #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 > ui mousemode right translate > select add #8 8587 atoms, 8749 bonds, 4 pseudobonds, 1176 residues, 5 models selected > combine sel > select subtract #8 Nothing selected > hide #!8 models > hide #!6 models > show #!6 models > rename #6 ""vvd+iberdo open.pdb"" > close #8 > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > hide #!6 models > show #!5 models > close #5 > show #!6 models > color zone #3 near #6 distance 8 > hide #!6 models > ui mousemode right ""pick blobs"" > measure blob #!3.1 triangleNumber 951490 color #ff6b4dff Surface combination of 2526 and 2540 emready2 #3.1 blob: volume = 1.0432e+05 area = 80715 size = 105.54 83.9 82.228 > undo > select add #6 8587 atoms, 8749 bonds, 4 pseudobonds, 1176 residues, 2 models selected > copy sel Unknown command: copy sel > select clear Drag select of 5 atoms, 7 bonds > select up 8 atoms, 8 bonds, 1 residue, 1 model selected > select ::name=""8W7"" 33 atoms, 37 bonds, 1 residue, 1 model selected > color sel yellow > select clear Drag select of 7 atoms, 7 bonds > delete sel Drag select of 4 atoms, 6 bonds > delete sel Drag select of 1 atoms > delete sel Drag select of 1 atoms > delete sel Drag select of 2 atoms, 1 bonds > delete sel > select ::name=""8W7"" 18 atoms, 20 bonds, 1 residue, 1 model selected > color sel lime > color zone #3 near #6 distance 8 > select add #6 8572 atoms, 8732 bonds, 4 pseudobonds, 1176 residues, 2 models selected > select subtract #6 Nothing selected > hide #!6 models > graphics silhouettes true > lighting shadows false > lighting soft > volume #3 level 2.487 > volume #3 level 4.142 > volume #3 level 2.353 > volume #3 level 1.861 > volume #3 level 2.085 > volume #3 level 2.264 > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/fig2b.open.png"" width 1800 > height 1532 supersample 4 transparentBackground true > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/open/vvd+iberdo open.pdb"" Chain information for vvd+iberdo open.pdb #5 --- Chain | Description A | No description available B | No description available > hide #!3 models > close #5 > show #!6 models > show #!3 models > save vvd+iberdo open.pdb #6 Cannot determine format for 'vvd+iberdo' > save vvd+iberdo_open.pdb #6 > open /Users/zrizvi/Desktop/vvd+iberdo_open.pdb Chain information for vvd+iberdo_open.pdb #5 --- Chain | Description A | No description available B | No description available > hide #!6 models > hide #!3 models > close #5 > show #!3 models > rename #9 ""1. cryosparc_P341_J1735_NUrefine selected.mrc"" > rename #4 ""2. cryosparc_P341_J1614_localrefine. selected.mrc"" > rename #10 ""3. composite_map on EMReady2 maps of 1735 and 1614.ccp4"" > show #!10 models > hide #!3 models > show #!13 models > rename #10 ""3a. composite_map on EMReady2 maps of 1735 and 1614.ccp4"" > rename #13 ""3b. composite_map on EMReady2 maps of 1735 and 1614.ccp4 split"" > rename #1 ""4. open- vvd+imid NU J2526_map_emready2.mrc"" > rename #2 ""5. open- vvd+imid local J2540_005_volume_map_emready2.mrc"" > rename #3 ""6. combination of 2526 and 2540 emready2"" > rename #11 ""3c. 8cvp-1537sharpmap-based-coord-VVD-linked-cootNEW-0.pdb"" > rename #3 ""6a. combination of 2526 and 2540 emready2"" > rename #6 ""6b. vvd+iberdo open.pdb"" > hide #!10 models > hide #!13 models > show #!3 models > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig > maps/closed/J2528_map_emready2.mrc"" Opened J2528_map_emready2.mrc as #5, grid size 443,443,443, pixel 0.5, shown at level 1.11, step 2, values float32 > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig > maps/closed/J2544_007_volume_map_emready2.mrc"" Opened J2544_007_volume_map_emready2.mrc as #7, grid size 443,443,443, pixel 0.5, shown at level 0.445, step 2, values float32 > hide #!3 models > show #!3 models > hide #!3 models > hide #!5 models > show #!5 models > rename #5 ""7. J2528_map_emready2.mrc"" > rename #7 ""8. J2544_007_volume_map_emready2.mrc"" > vop max #5 #7 Opened volume maximum as #8, grid size 443,443,443, pixel 0.5, shown at step 1, values float32 > rename #8 ""9. combination of 2528 and 2544 emready2"" > rename #5 ""7. Clsoed- vvd+imid NU J2528_map_emready2.mrc"" > rename #7 ""8. Closed- vvd+imid local J2544_007_volume_map_emready2.mrc"" > volume #8 level 2.891 > volume #8 level 3.239 > show #!5 models > hide #!8 models > volume #5 level 1.869 > volume #5 step 1 > volume #7 step 1 > volume #5 level 2.307 > volume #7 level 2.027 > volume #8 level 4.502 > open 8w7 '8w7' has no suffix > open 5v3o 5v3o title: Cereblon in complex with DDB1 and CC-220 [more info...] Chain information for 5v3o #14 --- Chain | Description | UniProt A | DNA damage-binding protein 1 | DDB1_HUMAN 1-1140 C | Protein cereblon | CRBN_HUMAN 40-442 Non-standard residues in 5v3o #14 --- 8W7 — (3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione ZN — zinc ion > view > select add #14 11175 atoms, 11396 bonds, 15 pseudobonds, 1452 residues, 4 models selected > ui mousemode right ""translate selected models"" > view matrix models #14,1,0,0,48.358,0,1,0,11.289,0,0,1,14.423 > view matrix models > #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 > view matrix models > #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 > ui mousemode right translate > ui mousemode right ""translate selected models"" > view matrix models > #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 > ui mousemode right translate > ui mousemode right ""translate selected models"" > view matrix models > #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 > fitmap #14 inMap #8 Fit molecule 5v3o (#14) to map 9. combination of 2528 and 2544 emready2 (#8) using 11175 atoms average map value = 7.021, steps = 152 shifted from previous position = 3.28 rotated from previous position = 10.9 degrees atoms outside contour = 4670, contour level = 4.502 Position of 5v3o (#14) relative to 9. combination of 2528 and 2544 emready2 (#8) coordinates: Matrix rotation and translation 0.26528196 0.56680440 0.77997325 120.97229633 -0.46678619 -0.63233295 0.61827640 177.51482496 0.84364456 -0.52809831 0.09682995 121.14258530 Axis -0.74206572 -0.04121541 -0.66905885 Axis point 0.00000000 86.02124003 -48.12980321 Rotation angle (degrees) 129.42818226 Shift along axis -178.13725982 > select clear > hide #!8 models Drag select of 307 residues, 1 pseudobonds > delete sel Drag select of 5 residues, 2 pseudobonds > delete sel > show #!8 models > hide #!14.2 models > split #14 Split 5v3o (#14) into 2 models Chain information for 5v3o A #14.1 --- Chain | Description A | No description available Chain information for 5v3o C #14.2 --- Chain | Description C | No description available > select add #14.1 5977 atoms, 6081 bonds, 10 pseudobonds, 775 residues, 2 models selected > fitmap sel inMap #8 Fit molecule 5v3o A (#14.1) to map 9. combination of 2528 and 2544 emready2 (#8) using 5977 atoms average map value = 10.5, steps = 48 shifted from previous position = 0.0818 rotated from previous position = 0.0954 degrees atoms outside contour = 859, contour level = 4.502 Position of 5v3o A (#14.1) relative to 9. combination of 2528 and 2544 emready2 (#8) coordinates: Matrix rotation and translation 0.26556282 0.56807609 0.77895183 120.93900210 -0.46621575 -0.63154059 0.61951543 177.60964780 0.84387160 -0.52767987 0.09713232 121.11920711 Axis -0.74205410 -0.04199283 -0.66902340 Axis point 0.00000000 85.98100831 -48.17253109 Rotation angle (degrees) 129.37718193 Shift along axis -178.23319887 > select subtract #14.1 Nothing selected > select add #14.2 2902 atoms, 2974 bonds, 6 pseudobonds, 365 residues, 3 models selected > fitmap sel inMap #8 Fit molecule 5v3o C (#14.2) to map 9. combination of 2528 and 2544 emready2 (#8) using 2902 atoms average map value = 6.215, steps = 148 shifted from previous position = 0.846 rotated from previous position = 5.97 degrees atoms outside contour = 1226, contour level = 4.502 Position of 5v3o C (#14.2) relative to 9. combination of 2528 and 2544 emready2 (#8) coordinates: Matrix rotation and translation 0.32722427 0.49885846 0.80253631 122.38342857 -0.43918680 -0.67169932 0.59660287 176.79079036 0.83668347 -0.54768629 -0.00070427 118.63599032 Axis -0.77315201 -0.02307192 -0.63380096 Axis point 0.00000000 88.97949673 -40.28109264 Rotation angle (degrees) 132.26725177 Shift along axis -173.89150166 > select clear > select add #14 8879 atoms, 9055 bonds, 16 pseudobonds, 1140 residues, 6 models selected > combine sel > close #14 > rename #15 ""9b. "" > rename #15 ""9b. 5v3o- closed vvd+imid"" > color #15/A:1-710 light blue > hide #!8 models > color #15/A:710-5000 steel blue > color #15/B:1-190 navajowhite > color #15/C:1-190 navajowhite > color #15/C:191-320 light salmon > color #15/C:321-500 tomato > select clear > select ::name=""8W7"" 51 atoms, 57 bonds, 2 residues, 2 models selected > color (#!15 & sel) lime > select clear > show #!8 models > color #8 #ffb2b2a1 models > select #15/C:287 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > select clear > volume #8 level 5.503 > color zone #8 near #15 distance 8 > hide #!15 models > show #!15 models > hide #!8 models > show #!8 models > color #8 #ffb2b29c models > volume #8 level 2.935 > volume #8 level 5.547 > ui tool show ""Side View"" > hide #!8 models > select #15/C:377 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 68 atoms, 72 bonds, 8 residues, 1 model selected > show sel atoms > select clear > show #!8 models > color zone #8 near #15 distance 8 > hide #!15 models > volume #8 level 4.023 > volume #8 level 5.547 > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/closed/fig2b.closed.png"" > width 1800 height 1532 supersample 4 transparentBackground true > volume #8 level 4.807 > volume #8 level 1.672 > volume #8 level 2.107 > volume #8 level 3.109 > color zone #8 near #15 distance 10 > volume #8 level 5.068 > rename #8 ""9a. combination of 2528 and 2544 emready2"" > hide #!8 models > show #!6 models > show #!3 models > hide #!6 models > volume #3 level 6.557 > volume #3 level 3.829 > volume #3 level 2.04 > volume #3 level 3.069 > volume #3 level 4.053 > volume copy #3 modelId #16 Opened 6a. combination of 2526 and 2540 emready2 copy as #16, grid size 443,443,443, pixel 0.5, shown at step 1, values float32 > show #!3 models > hide #!16 models > show #!16 models > hide #!3 models > color #16 #b2ffffff models > show #!6 models > color zone #16 near #6 distance 10 > hide #!16 models > show #!16 models > hide #!6 models > rename #16 ""6b. combination of 2526 and 2540 emready2 copy"" > rename #6 ""6c. vvd+iberdo open.pdb"" > volume #16 level 2.622 > volume #16 level 2.174 > show #!3 models > hide #!16 models > volume #3 level 6.557 > show #!16 models > hide #!16 models > volume #3 level 5.26 > volume #3 level 4.41 > volume #3 level 4.321 > volume #3 level 6.02 > show #!6 models > ui tool show ""Map Eraser"" > ui tool show ""Segment Map"" > select add #6 8572 atoms, 8732 bonds, 4 pseudobonds, 1176 residues, 2 models selected > select subtract #6 Nothing selected > ui tool show ""Color Zone"" > volume splitbyzone #3 Opened 6a. combination of 2526 and 2540 emready2 0 as #14.1, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 1 as #14.2, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 2 as #14.3, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 3 as #14.4, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 4 as #14.5, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 5 as #14.6, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 6 as #14.7, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 Opened 6a. combination of 2526 and 2540 emready2 7 as #14.8, grid size 443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32 > hide #!14.8 models > show #!14.8 models > hide #!14.7 models > show #!14.7 models > hide #!14.7 models > show #!14.7 models > hide #!14.8 models > hide #!14.7 models > hide #!14.6 models > hide #!14.5 models > hide #!14.4 models > select add #14.1 2 models selected > select add #14.2 4 models selected > select add #14.3 6 models selected > select subtract #14.3 4 models selected > select subtract #14.2 2 models selected > select subtract #14.1 Nothing selected > show #!16 models > hide #!14 models > hide #!14.1 models > hide #!14.2 models > hide #!14.3 models > show #!14.3 models > show #!14.2 models > show #!14.1 models > hide #!14 models > volume splitbyzone #16 Opened 6b. combination of 2526 and 2540 emready2 copy 0 as #17.1, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 1 as #17.2, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 2 as #17.3, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 3 as #17.4, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 4 as #17.5, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 5 as #17.6, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 6 as #17.7, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 Opened 6b. combination of 2526 and 2540 emready2 copy 7 as #17.8, grid size 443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32 > hide #!17.1 models > hide #!17.2 models > hide #!17.3 models > hide #!17.4 models > show #!17.4 models > hide #!17.5 models > show #!17.5 models > show #!14 models > hide #!6 models > hide #!17.5 models > show #!17.5 models > hide #!17.5 models > show #!17.5 models > hide #!17.6 models > show #!17.6 models > hide #!17.6 models > show #!17.6 models > hide #!17.7 models > show #!17.7 models > volume #17.4 level 2.889 > volume #17.5 level 2.842 > volume #17.6 level 2.849 > volume #17.8 level 2.108 > volume #14.8 level 6.219 > select add #14 17 models selected > select subtract #14.4 15 models selected > select subtract #14.5 13 models selected > select subtract #14.6 11 models selected > select subtract #14.7 9 models selected > select subtract #14.8 7 models selected > hide #!14.8 models > select add #17.4 9 models selected > select add #17.5 11 models selected > select add #17.6 13 models selected > select add #17.7 15 models selected > select add #17.8 17 models selected > combine sel No structures specified > select clear > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/open/fig2b.open.png"" width > 1800 height 1802 supersample 4 transparentBackground true > hide #!14 models > hide #!17 models > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/figure 2 making .cxs"" > includeMaps true > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/int > 1/J2527_map_emready2.mrc"" Opened J2527_map_emready2.mrc as #18, grid size 443,443,443, pixel 0.5, shown at level 0.9, step 2, values float32 > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/int > 1/J2541_004_volume_map_emready2.mrc"" Opened J2541_004_volume_map_emready2.mrc as #19, grid size 443,443,443, pixel 0.5, shown at level 1.16, step 2, values float32 > volume #18 step 1 > volume #19 step 1 > vop max #18 #19 Opened volume maximum as #20, grid size 443,443,443, pixel 0.5, shown at step 1, values float32 > rename #18 ""10. int1 vvd+imid J2527_map_emready2.mrc"" > rename #19 ""11. int1 vvd+imid localJ2541_004_volume_map_emready2.mrc"" > rename #19 ""11. int1 vvd+imid local J2541_004_volume_map_emready2.mrc"" > rename #18 ""10. int1 vvd+imid NU J2527_map_emready2.mrc"" > rename #20 ""12. combination of 10 and 11"" > volume #20 level 2.786 > show #!6 models > hide #!6 models > volume copy #6 modelId #21 > combine #6 close false modelId #21 > rename #21 ""13. vvd+iberdo int1.pdb"" > volume #20 level 3.94 > select add #21 8572 atoms, 8732 bonds, 4 pseudobonds, 1176 residues, 2 models selected > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > view matrix models > #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 > ui mousemode right ""translate selected models"" > view matrix models > #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 > ui mousemode right translate > fitmap #21 inMap #20 Fit molecule 13. vvd+iberdo int1.pdb (#21) to map 12. combination of 10 and 11 (#20) using 8572 atoms average map value = 10.14, steps = 156 shifted from previous position = 3.61 rotated from previous position = 13.7 degrees atoms outside contour = 1471, contour level = 3.9404 Position of 13. vvd+iberdo int1.pdb (#21) relative to 12. combination of 10 and 11 (#20) coordinates: Matrix rotation and translation 0.99995221 -0.00495979 0.00842498 -0.14657304 0.00521895 0.99950504 -0.03102311 2.46328273 -0.00826694 0.03106560 0.99948316 -4.02043145 Axis 0.95383084 0.25642777 0.15636984 Axis point 0.00000000 130.03408034 78.45787904 Rotation angle (degrees) 1.86513633 Shift along axis -0.13682601 > split #21 Split 13. vvd+iberdo int1.pdb (#21) into 3 models Chain information for 13. vvd+iberdo int1.pdb A #21.1 --- Chain | Description A | No description available Chain information for 13. vvd+iberdo int1.pdb B #21.2 --- Chain | Description B | No description available > select add #21.1 6318 atoms, 6434 bonds, 824 residues, 1 model selected > fitmap sel inMap #20 Fit molecule 13. vvd+iberdo int1.pdb A (#21.1) to map 12. combination of 10 and 11 (#20) using 6318 atoms average map value = 11.2, steps = 64 shifted from previous position = 0.057 rotated from previous position = 0.261 degrees atoms outside contour = 716, contour level = 3.9404 Position of 13. vvd+iberdo int1.pdb A (#21.1) relative to 12. combination of 10 and 11 (#20) coordinates: Matrix rotation and translation 0.99997710 -0.00370364 0.00566496 -0.04489164 0.00385882 0.99961071 -0.02763236 2.26194806 -0.00556041 0.02765359 0.99960210 -3.76505421 Axis 0.97131472 0.19721768 0.13286424 Axis point 0.00000000 136.84114012 80.62843893 Rotation angle (degrees) 1.63082033 Shift along axis -0.09774884 > select subtract #21.1 Nothing selected > select add #21.2 2236 atoms, 2278 bonds, 4 pseudobonds, 351 residues, 2 models selected > fitmap sel inMap #20 Fit molecule 13. vvd+iberdo int1.pdb B (#21.2) to map 12. combination of 10 and 11 (#20) using 2236 atoms average map value = 7.656, steps = 72 shifted from previous position = 0.362 rotated from previous position = 1.2 degrees atoms outside contour = 705, contour level = 3.9404 Position of 13. vvd+iberdo int1.pdb B (#21.2) relative to 12. combination of 10 and 11 (#20) coordinates: Matrix rotation and translation 0.99957428 -0.00690597 0.02834733 -2.14892969 0.00760810 0.99966507 -0.02473610 1.22829977 -0.02816701 0.02494124 0.99929203 -1.15331989 Axis 0.64826372 0.73748312 0.18940116 Axis point -37.68629592 0.00000000 59.10362530 Rotation angle (degrees) 2.19586462 Shift along axis -0.70566292 > select subtract #21.2 Nothing selected > select add #21.3 18 atoms, 20 bonds, 1 residue, 1 model selected > fitmap sel inMap #20 Fit molecule 13. vvd+iberdo int1.pdb C (#21.3) to map 12. combination of 10 and 11 (#20) using 18 atoms average map value = 4.502, steps = 88 shifted from previous position = 2.28 rotated from previous position = 28.1 degrees atoms outside contour = 6, contour level = 3.9404 Position of 13. vvd+iberdo int1.pdb C (#21.3) relative to 12. combination of 10 and 11 (#20) coordinates: Matrix rotation and translation 0.88481403 0.46470450 -0.03396844 -31.04162349 -0.46574688 0.88420785 -0.03544474 62.18114561 0.01356383 0.04718270 0.99879418 -9.42993675 Axis 0.08834121 -0.05081918 -0.99479307 Axis point 110.31812113 94.80438715 0.00000000 Rotation angle (degrees) 27.88255888 Shift along axis 3.47858654 > select subtract #21.3 Nothing selected > select add #21 8572 atoms, 8732 bonds, 4 pseudobonds, 1176 residues, 5 models selected > combine sel > rename #22 ""13. vvd+iberdo int1.pdb"" > close #21 > volume #20 level 3.094 > volume #20 level 1.785 > volume #20 level 0.3997 > volume #20 level 0.6692 > volume #20 level 3.286 > color zone #20 near #22 distance 10 > hide #!20 models > ui tool show ""Show Sequence Viewer"" > sequence chain #22/B Alignment identifier is 22/B > select #22/B:304-380 364 atoms, 365 bonds, 61 residues, 1 model selected > select #22/B:304-380 364 atoms, 365 bonds, 61 residues, 1 model selected > select #22/B:380 14 atoms, 15 bonds, 1 residue, 1 model selected > select #22/B:380 14 atoms, 15 bonds, 1 residue, 1 model selected > select #22/B:386 14 atoms, 15 bonds, 1 residue, 1 model selected > select #22/B:386 14 atoms, 15 bonds, 1 residue, 1 model selected > select #22/B:400 14 atoms, 15 bonds, 1 residue, 1 model selected > select #22/B:400 14 atoms, 15 bonds, 1 residue, 1 model selected > select clear > select #22/B:380 14 atoms, 15 bonds, 1 residue, 1 model selected > select #22/B:380 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > select #22/B:385-386 19 atoms, 20 bonds, 2 residues, 1 model selected > select #22/B:385-386 19 atoms, 20 bonds, 2 residues, 1 model selected > select #22/B:386 14 atoms, 15 bonds, 1 residue, 1 model selected > select #22/B:386 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > select #22/B:400 14 atoms, 15 bonds, 1 residue, 1 model selected > select #22/B:400 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > select clear > select ::name=""8W7"" 69 atoms, 77 bonds, 3 residues, 3 models selected > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > view matrix models > #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 > undo > ui mousemode right translate > select add #22 8623 atoms, 8789 bonds, 4 pseudobonds, 1178 residues, 4 models selected > select subtract #22 51 atoms, 57 bonds, 2 residues, 2 models selected > hide #!22 models > show #!22 models > show #!20 models > split #22 Split 13. vvd+iberdo int1.pdb (#22) into 3 models Chain information for 13. vvd+iberdo int1.pdb A #22.1 --- Chain | Description A | No description available Chain information for 13. vvd+iberdo int1.pdb B #22.2 --- Chain | Description B | No description available > select add #22.3 69 atoms, 77 bonds, 3 residues, 3 models selected > hide #!20 models > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > view matrix models > #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 > ui mousemode right ""translate selected models"" > view matrix models > #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 > ui mousemode right translate > ui mousemode right ""translate selected models"" > view matrix models > #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 > ui mousemode right translate > show #!20 models > hide #!20 models > select add #22 8623 atoms, 8789 bonds, 4 pseudobonds, 1178 residues, 7 models selected > combine sel Remapping chain ID 'A' in 9b. 5v3o- closed vvd+imid #15 to 'D' Remapping chain ID 'C' in 9b. 5v3o- closed vvd+imid #15 to 'E' Remapping chain ID 'A' in 13. vvd+iberdo int1.pdb A #22.1 to 'F' Remapping chain ID 'B' in 13. vvd+iberdo int1.pdb B #22.2 to 'G' Remapping chain ID 'C' in 13. vvd+iberdo int1.pdb C #22.3 to 'H' > rename #21 ""13. vvd+iberdo int1.pdb"" > close #22 > select add #15 8897 atoms, 9075 bonds, 16 pseudobonds, 1141 residues, 4 models selected > select subtract #15 18 atoms, 20 bonds, 1 residue, 1 model selected > select add #6 8572 atoms, 8732 bonds, 4 pseudobonds, 1176 residues, 2 models selected > select subtract #6 Nothing selected > show #!20 models > split #13 > hide #21.2 models > show #21.2 models > hide #21.2 models > show #21.2 models > split #21 Split 13. vvd+iberdo int1.pdb (#21) into 8 models Chain information for 13. vvd+iberdo int1.pdb A #21.1 --- Chain | Description A | No description available Chain information for 13. vvd+iberdo int1.pdb B #21.2 --- Chain | Description B | No description available Chain information for 13. vvd+iberdo int1.pdb D #21.4 --- Chain | Description D | No description available Chain information for 13. vvd+iberdo int1.pdb E #21.5 --- Chain | Description E | No description available Chain information for 13. vvd+iberdo int1.pdb F #21.6 --- Chain | Description F | No description available Chain information for 13. vvd+iberdo int1.pdb G #21.7 --- Chain | Description G | No description available Cell requested for row 20 is out of bounds for table with 35 rows! Resizing table model. > ~split #13 Unknown command: ~split #13 > hide #!21 models > show #!21 models > hide #21.1 models > show #21.1 models > hide #21.1 models > hide #!21.2 models > hide #21.3 models > hide #!21.4 models > hide #!21.5 models > hide #21.6 models > show #21.6 models > hide #!21.7 models > show #!21.7 models > hide #21.8 models > show #21.8 models > close #21.1,3#21.2,4-5 > hide #!21 models > show #!21 models > hide #!20 models > select add #21.6 6318 atoms, 6434 bonds, 824 residues, 1 model selected > select add #21.7 8554 atoms, 8712 bonds, 4 pseudobonds, 1175 residues, 3 models selected > select add #21.8 8572 atoms, 8732 bonds, 4 pseudobonds, 1176 residues, 4 models selected > combine sel > rename #22 ""13. vvd+iberdo int1.pdb"" > close #21 > show #!20 models > color zone #20 near #22 distance 10 > color zone #20 near #22 distance 8 > hide #!22 models > volume #20 level 1.554 > volume #20 level 0.05338 > volume #20 level 0.5922 > volume #20 level 0.7461 > volume #20 level 0.8616 > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/0. figure 2 making .cxs"" > includeMaps true ——— End of log from Tue Feb 24 16:13:45 2026 ——— > view name session-start opened ChimeraX session > hide #!20 models > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/int > 2/J2612_map_emready2.mrc"" Opened J2612_map_emready2.mrc as #21, grid size 438,438,438, pixel 0.5, shown at level 1.43, step 2, values float32 > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/int > 2/J2614_004_volume_map_emready2.mrc"" Opened J2614_004_volume_map_emready2.mrc as #23, grid size 438,438,438, pixel 0.5, shown at level 1.74, step 2, values float32 > rename #21 ""14. int2 vvd+imid NU J2612_map_emready2.mrc"" > rename #23 ""15. int2 vvd+imid local J2614_004_volume_map_emready2.mrc"" > volume #21 step 1 > volume #23 step 1 > vop max #21 #23 Opened volume maximum as #24, grid size 438,438,438, pixel 0.5, shown at step 1, values float32 > rename #24 ""16. combination of 2612 and 2614"" > volume #24 level 3.89 > volume #21 level 3.831 > volume #24 level 5.718 > show #!22 models > show #!15 models > hide #!15 models > fitmap #22 inMap #24 Fit molecule 13. vvd+iberdo int1.pdb (#22) to map 16. combination of 2612 and 2614 (#24) using 8572 atoms average map value = 8.35, steps = 80 shifted from previous position = 2.43 rotated from previous position = 0.353 degrees atoms outside contour = 2629, contour level = 5.7183 Position of 13. vvd+iberdo int1.pdb (#22) relative to 16. combination of 2612 and 2614 (#24) coordinates: Matrix rotation and translation 0.45163826 -0.61293634 0.64833010 65.88218884 0.65218078 -0.26907192 -0.70870342 184.09421817 0.60883751 0.74290601 0.27822212 -72.06569896 Axis 0.75371416 0.02050560 0.65688240 Axis point 0.00000000 129.42532737 27.82438434 Rotation angle (degrees) 105.64080909 Shift along axis 6.09261176 > show #!15 models > mmaker #15 to #22 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 13. vvd+iberdo int1.pdb, chain F (#22) with 9b. 5v3o- closed vvd+imid, chain A (#15), sequence alignment score = 3564 RMSD between 740 pruned atom pairs is 0.665 angstroms; (across all 774 pairs: 1.333) > hide #!22 models > show #!22 models > hide #!15 models > fitmap #22 inMap #24 Fit molecule 13. vvd+iberdo int1.pdb (#22) to map 16. combination of 2612 and 2614 (#24) using 8572 atoms average map value = 8.351, steps = 28 shifted from previous position = 0.00666 rotated from previous position = 0.00313 degrees atoms outside contour = 2632, contour level = 5.7183 Position of 13. vvd+iberdo int1.pdb (#22) relative to 16. combination of 2612 and 2614 (#24) coordinates: Matrix rotation and translation 0.45167734 -0.61294587 0.64829387 65.87675748 0.65215206 -0.26904443 -0.70874028 184.09774684 0.60883929 0.74290811 0.27821264 -72.06340139 Axis 0.75372813 0.02048570 0.65686699 Axis point 0.00000000 129.42594701 27.83211750 Rotation angle (degrees) 105.63911106 Shift along axis 6.08846697 > show #!15 models > hide #!22 models > hide #!15 models > show #!15 models > show #!22 models > color zone #24 near #22 distance 8 > hide #!15 models > hide #!22 models > show #!15 models > color zone #24 near #15 distance 8 > hide #!15 models > show #!15 models > show #!22 models > select add #22 8572 atoms, 8732 bonds, 4 pseudobonds, 1176 residues, 2 models selected > select add #15 17451 atoms, 17787 bonds, 20 pseudobonds, 2316 residues, 5 models selected > hide #!24 models > combine sel > select subtract #22 8879 atoms, 9055 bonds, 16 pseudobonds, 1140 residues, 3 models selected > select subtract #15 Nothing selected > rename #25 ""combination of 15 and 22 for int2"" > show #!24 models > hide #!22 models > color zone #24 near #25 distance 8 > hide #!24 models > split #25 Split combination of 15 and 22 for int2 (#25) into 5 models Chain information for combination of 15 and 22 for int2 A #25.1 --- Chain | Description A | No description available Chain information for combination of 15 and 22 for int2 C #25.2 --- Chain | Description C | No description available Chain information for combination of 15 and 22 for int2 F #25.3 --- Chain | Description F | No description available Chain information for combination of 15 and 22 for int2 G #25.4 --- Chain | Description G | No description available > hide #25.5 models > show #25.5 models > hide #!25.1 models > show #!25.1 models > hide #!25.1 models > show #!25.1 models > hide #!25.1 models > show #!25.1 models > hide #!25.2 models > show #!25.2 models > select add #25.1 5977 atoms, 6081 bonds, 10 pseudobonds, 775 residues, 2 models selected > select subtract #25.1 Nothing selected > select add #25.2 2902 atoms, 2974 bonds, 6 pseudobonds, 365 residues, 3 models selected > select subtract #25.2 Nothing selected > select add #25.3 6318 atoms, 6434 bonds, 824 residues, 1 model selected > select subtract #25.3 Nothing selected > select add #25.4 2236 atoms, 2278 bonds, 4 pseudobonds, 351 residues, 2 models selected > select subtract #25.4 Nothing selected > select add #25.5 18 atoms, 20 bonds, 1 residue, 1 model selected > select subtract #25.5 Nothing selected > select add #25.4 2236 atoms, 2278 bonds, 4 pseudobonds, 351 residues, 2 models selected > select subtract #25.4 Nothing selected > show #!24 models > hide #!25 models > hide #!15 models > show #!22 models > color #24 #b2ffff9a models > close #25 > color #24 darkgrey models > volume copy #22 modelId #25 > copy #22 modelId #25 Unknown command: modelcif copy #22 modelId #25 > combine #22 close false modelId #25 > hide #!22 models > hide #!25 models > show #!25 models > split #25 Split copy of 13. vvd+iberdo int1.pdb (#25) into 3 models Chain information for copy of 13. vvd+iberdo int1.pdb F #25.1 --- Chain | Description F | No description available Chain information for copy of 13. vvd+iberdo int1.pdb G #25.2 --- Chain | Description G | No description available > hide #25.1 models > show #25.1 models > hide #!25.2 models > show #!25.2 models > hide #!25.2 models > show #!25.2 models > hide #25.3 models > show #25.3 models > hide #!24 models Drag select of 4 atoms, 5 bonds > select up 6 atoms, 5 bonds, 1 residue, 1 model selected > select up 28 atoms, 30 bonds, 1 residue, 1 model selected > show #!24 models > fitmap sel inMap #24 Fit molecule copy of 13. vvd+iberdo int1.pdb G (#25.2) to map 16. combination of 2612 and 2614 (#24) using 28 atoms average map value = 5.606, steps = 72 shifted from previous position = 0.741 rotated from previous position = 16 degrees atoms outside contour = 15, contour level = 5.7183 Position of copy of 13. vvd+iberdo int1.pdb G (#25.2) relative to 16. combination of 2612 and 2614 (#24) coordinates: Matrix rotation and translation 0.42141688 -0.42628134 0.80043240 23.16077837 0.65007113 -0.47341581 -0.59437783 195.98753721 0.63230954 0.77081884 0.07760778 -49.90209341 Axis 0.78163734 0.09625801 0.61626087 Axis point -0.00000000 116.75111860 39.31212244 Rotation angle (degrees) 119.15642117 Shift along axis 6.21599173 > select clear > select add #25.2 2236 atoms, 2278 bonds, 4 pseudobonds, 351 residues, 2 models selected > fitmap sel inMap #24 Fit molecule copy of 13. vvd+iberdo int1.pdb G (#25.2) to map 16. combination of 2612 and 2614 (#24) using 2236 atoms average map value = 6.352, steps = 140 shifted from previous position = 1.85 rotated from previous position = 15.9 degrees atoms outside contour = 1087, contour level = 5.7183 Position of copy of 13. vvd+iberdo int1.pdb G (#25.2) relative to 16. combination of 2612 and 2614 (#24) coordinates: Matrix rotation and translation 0.46020337 -0.60991945 0.64514426 65.00734733 0.64393234 -0.27095217 -0.71549707 186.31859717 0.61119882 0.74470342 0.26805376 -71.47008660 Axis 0.75856034 0.01763434 0.65136414 Axis point 0.00000000 130.03256142 29.27592670 Rotation angle (degrees) 105.74446776 Shift along axis 6.04454892 > select subtract #25.2 Nothing selected > select add #25.3 18 atoms, 20 bonds, 1 residue, 1 model selected > fitmap sel inMap #24 Fit molecule copy of 13. vvd+iberdo int1.pdb H (#25.3) to map 16. combination of 2612 and 2614 (#24) using 18 atoms average map value = 4.771, steps = 180 shifted from previous position = 7.43 rotated from previous position = 82.1 degrees atoms outside contour = 14, contour level = 5.7183 Position of copy of 13. vvd+iberdo int1.pdb H (#25.3) relative to 16. combination of 2612 and 2614 (#24) coordinates: Matrix rotation and translation 0.00128243 -0.82016674 0.57212313 145.80499439 -0.55258168 -0.47742246 -0.68317003 317.28361071 0.83345776 -0.31526864 -0.45382138 172.95855387 Axis 0.70124303 -0.49812015 0.51003385 Axis point 0.00000000 195.53758721 65.19329041 Rotation angle (degrees) 164.79218005 Shift along axis 32.41409441 > select clear > hide #!25 models > show #!15 models > fitmap #15 inMap #24 Fit molecule 9b. 5v3o- closed vvd+imid (#15) to map 16. combination of 2612 and 2614 (#24) using 8879 atoms average map value = 8.047, steps = 64 shifted from previous position = 0.096 rotated from previous position = 0.225 degrees atoms outside contour = 3061, contour level = 5.7183 Position of 9b. 5v3o- closed vvd+imid (#15) relative to 16. combination of 2612 and 2614 (#24) coordinates: Matrix rotation and translation 0.25938960 0.57250458 0.77778888 119.40701811 -0.46597542 -0.63122094 0.62002180 176.15425577 0.84592195 -0.52325771 0.10304092 119.95342407 Axis -0.73949960 -0.04407004 -0.67171286 Axis point 0.00000000 84.93576646 -48.09633206 Rotation angle (degrees) 129.37514280 Shift along axis -176.63882591 > show #!25 models > hide #!15 models > show #!15 models > close #25 > show #!22 models > mmaker #22 to #15 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 9b. 5v3o- closed vvd+imid, chain A (#15) with 13. vvd+iberdo int1.pdb, chain F (#22), sequence alignment score = 3564 RMSD between 740 pruned atom pairs is 0.665 angstroms; (across all 774 pairs: 1.333) > hide #!24 models > select add #15 8879 atoms, 9055 bonds, 16 pseudobonds, 1140 residues, 3 models selected > select add #22 17451 atoms, 17787 bonds, 20 pseudobonds, 2316 residues, 5 models selected > combine sel > select subtract #15 8572 atoms, 8732 bonds, 4 pseudobonds, 1176 residues, 2 models selected > select subtract #22 Nothing selected > hide #!22 models > hide #!15 models > show #!24 models > hide #!24 models Drag select of 6 atoms, 8 bonds > select up 8 atoms, 8 bonds, 1 residue, 1 model selected > select up 18 atoms, 20 bonds, 1 residue, 1 model selected > delete sel > show #!24 models > show #!25 atoms > color zone #24 near #25 distance 8 > hide #!25 models > color zone #24 near #25 distance 10 > volume #24 level 7.006 > volume #24 level 6.049 > volume #24 level 5.058 > volume #24 level 5.355 > show #!7 models > hide #!7 models > show #!8 models > hide #!24 models > show #!24 models > hide #!24 models > show #!24 models > hide #!8 models > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/int 2/int2.png"" width 1800 > height 1592 supersample 4 transparentBackground true > volume #24 level 5.916 > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/int 2/int2.png"" width 1800 > height 1592 supersample 4 transparentBackground true > rename #25 ""combination of open closed for int2 "" > show #!25 models > hide #!24 models > show #!24 models > hide #!25 models > hide #!24 models > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig > maps/frustrated/J2438_map_emready2.mrc"" Opened J2438_map_emready2.mrc as #26, grid size 443,443,443, pixel 0.5, shown at level 1.18, step 2, values float32 > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig > maps/frustrated/J2456_004_volume_map_emready2.mrc"" Opened J2456_004_volume_map_emready2.mrc as #27, grid size 443,443,443, pixel 0.5, shown at level 0.895, step 2, values float32 > volume #26 step 1 > volume #27 step 1 > vop max #26 #27 Opened volume maximum as #28, grid size 443,443,443, pixel 0.5, shown at step 1, values float32 > volume #28 level 6.445 > volume #28 level 7.422 > show #!22 models > hide #!22 models > show #!15 models > fitmap #15 inMap #28 Fit molecule 9b. 5v3o- closed vvd+imid (#15) to map volume maximum (#28) using 8879 atoms average map value = 7.722, steps = 104 shifted from previous position = 2.98 rotated from previous position = 1.03 degrees atoms outside contour = 4404, contour level = 7.4224 Position of 9b. 5v3o- closed vvd+imid (#15) relative to volume maximum (#28) coordinates: Matrix rotation and translation 0.26196635 0.57102732 0.77801120 120.77963399 -0.45094391 -0.64031849 0.62180529 178.24630452 0.85324277 -0.51373148 0.08975940 121.08780703 Axis -0.74239837 -0.04918537 -0.66815078 Axis point 0.00000000 85.51770183 -46.87834271 Rotation angle (degrees) 130.11293989 Shift along axis -179.33862535 > rename #25 ""17. combination of open closed for int2 "" > rename #26 ""18. frustrated vvd+imid J2438_map_emready2.mrc"" > rename #26 ""18. frustrated vvd+imid NU J2438_map_emready2.mrc"" > rename #27 ""19. frustrated vvd+imid local J2456_004_volume_map_emready2.mrc"" > rename #28 ""20 combination of 18 and 19"" > combine #15 close false modelId #29 > hide #!15 models > split #29 Split copy of 9b. 5v3o- closed vvd+imid (#29) into 2 models Chain information for copy of 9b. 5v3o- closed vvd+imid A #29.1 --- Chain | Description A | No description available Chain information for copy of 9b. 5v3o- closed vvd+imid C #29.2 --- Chain | Description C | No description available > hide #!29.1 models > show #!29.1 models > hide #!29.2 models > show #!29.2 models > select add #29.1 5977 atoms, 6081 bonds, 10 pseudobonds, 775 residues, 2 models selected > fitmap sel inMap #28 Fit molecule copy of 9b. 5v3o- closed vvd+imid A (#29.1) to map 20 combination of 18 and 19 (#28) using 5977 atoms average map value = 9.752, steps = 44 shifted from previous position = 0.0322 rotated from previous position = 0.183 degrees atoms outside contour = 1871, contour level = 7.4224 Position of copy of 9b. 5v3o- closed vvd+imid A (#29.1) relative to 20 combination of 18 and 19 (#28) coordinates: Matrix rotation and translation 0.26033122 0.57129679 0.77836215 120.76428612 -0.44883715 -0.64215101 0.62143969 178.28612949 0.85485255 -0.51113800 0.08924727 121.05962409 Axis -0.74209476 -0.05011852 -0.66841865 Axis point 0.00000000 85.40762225 -46.72862078 Rotation angle (degrees) 130.26218361 Shift along axis -179.47249291 > select subtract #29.1 Nothing selected > select add #29.2 2902 atoms, 2974 bonds, 6 pseudobonds, 365 residues, 3 models selected > fitmap sel inMap #28 Fit molecule copy of 9b. 5v3o- closed vvd+imid C (#29.2) to map 20 combination of 18 and 19 (#28) using 2902 atoms average map value = 4.105, steps = 100 shifted from previous position = 1.88 rotated from previous position = 4.04 degrees atoms outside contour = 2438, contour level = 7.4224 Position of copy of 9b. 5v3o- closed vvd+imid C (#29.2) relative to 20 combination of 18 and 19 (#28) coordinates: Matrix rotation and translation 0.27233221 0.52177145 0.80844897 123.48841484 -0.49550931 -0.64417995 0.58266862 177.43691566 0.82480646 -0.55927342 0.08311166 122.12419648 Axis -0.74664500 -0.01069515 -0.66513672 Axis point 0.00000000 89.54887059 -48.61646436 Rotation angle (degrees) 130.11830986 Shift along axis -175.32900958 > select clear > select add #29 8879 atoms, 9055 bonds, 16 pseudobonds, 1140 residues, 6 models selected > combine sel > close #29 > rename #30 ""21. model for frustrated"" > color zone #28 near #30 distance 10 > hide #!30 models > color zone #28 near #30 distance 15 > select clear > volume #28 level 6.67 > volume #28 level 6.933 > volume #28 level 6.896 > ui mousemode right ""map eraser"" > volume erase #28 center 146.05,96.223,129.13 radius 3.8053 > view > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/frustrated/frustrated.png"" > width 1800 height 1592 supersample 4 transparentBackground true > hide #!28 models > show #!28 models > show #!24 models > show #!20 models > hide #!20 models > show #!3 models > hide #!3 models > show #!8 models > show #!20 models > volume #20 level 4.956 > show #!16 models > hide #!16 models > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/0. figure 2 making .cxs"" > includeMaps true ——— End of log from Wed Feb 25 16:06:42 2026 ——— > view name session-start opened ChimeraX session > show #!14 models > hide #!8 models > hide #!24 models > hide #!28 models > hide #!20 models > show #!3 models > hide #!3 models > show #!14.4 models > show #!14.5 models > show #!14.6 models > show #!14.7 models > show #!14.8 models > volume #14.4 level 4.654 > volume #14.8 level 2.274 > volume #14.6 level 4.453 > volume #14.5 level 3.458 > volume #14.4 level 4.954 > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/open/fig2b.open.png"" width > 1800 height 1532 supersample 4 transparentBackground true > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/0. figure 2 making .cxs"" > includeMaps true ——— End of log from Wed Feb 25 16:20:52 2026 ——— > view name session-start opened ChimeraX session > hide #!14 models > show #!20 models > hide #!20 models > show #!18 models > show #!19 models > show #!20 models > hide #!19 models > hide #!18 models > show #!22 models > hide #!22 models > volume #20 level 0.9846 > volume #20 level 5.052 > show #!22 models > fitmap #22 inMap #20 Fit molecule 13. vvd+iberdo int1.pdb (#22) to map 12. combination of 10 and 11 (#20) using 8572 atoms average map value = 10.26, steps = 80 shifted from previous position = 2.39 rotated from previous position = 0.5 degrees atoms outside contour = 1849, contour level = 5.0525 Position of 13. vvd+iberdo int1.pdb (#22) relative to 12. combination of 10 and 11 (#20) coordinates: Matrix rotation and translation 0.45290121 -0.60806549 0.65202519 66.30022263 0.65359924 -0.27095091 -0.70667789 185.29085499 0.60637325 0.74621844 0.27471715 -70.50773735 Axis 0.75483642 0.02371797 0.65548413 Axis point 0.00000000 129.65147482 28.74738650 Rotation angle (degrees) 105.76344401 Shift along axis 8.22384205 > ui tool show ""Color Zone"" > volume splitbyzone #20 Opened 12. combination of 10 and 11 0 as #29.1, grid size 443,443,443, pixel 0.5, shown at level 5.05, step 1, values float32 Opened 12. combination of 10 and 11 1 as #29.2, grid size 443,443,443, pixel 0.5, shown at level 5.05, step 1, values float32 Opened 12. combination of 10 and 11 2 as #29.3, grid size 443,443,443, pixel 0.5, shown at level 5.05, step 1, values float32 Opened 12. combination of 10 and 11 3 as #29.4, grid size 443,443,443, pixel 0.5, shown at level 5.05, step 1, values float32 Opened 12. combination of 10 and 11 4 as #29.5, grid size 443,443,443, pixel 0.5, shown at level 5.05, step 1, values float32 Opened 12. combination of 10 and 11 5 as #29.6, grid size 443,443,443, pixel 0.5, shown at level 5.05, step 1, values float32 Opened 12. combination of 10 and 11 6 as #29.7, grid size 443,443,443, pixel 0.5, shown at level 5.05, step 1, values float32 Opened 12. combination of 10 and 11 7 as #29.8, grid size 443,443,443, pixel 0.5, shown at level 5.05, step 1, values float32 > volume #29.2 level 5.983 > volume #29.2 level 5.673 > volume #29.3 level 5.872 > hide #!22 models > volume #29.4 level 5.623 > volume #29.5 level 3.84 > volume #29.6 level 4.849 > volume #29.7 level 1.294 > volume #29.8 level 0.5091 > volume #29.6 level 4.704 > volume #29.8 level 0.5836 [Repeated 1 time(s)] > surface dust #29.1 size 5 > surface dust #29.2 size 5 > surface dust #29.3 size 5 > surface dust #29.4 size 5 > surface dust #29.5 size 5 > surface dust #29.6 size 5 > surface dust #29.7 size 5 > surface dust #29.8 size 5 > view > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/int 1/int1.png"" width 1800 > height 1536 supersample 4 transparentBackground true > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/0. figure 2 making .cxs"" > includeMaps true ——— End of log from Wed Feb 25 16:39:20 2026 ——— > view name session-start opened ChimeraX session > open /Users/zrizvi/Desktop/J2618_map_emready2.mrc Opened J2618_map_emready2.mrc as #31, grid size 438,438,438, pixel 0.5, shown at level 1.39, step 2, values float32 > open /Users/zrizvi/Desktop/J2619_004_volume_map_emready2.mrc Opened J2619_004_volume_map_emready2.mrc as #32, grid size 438,438,438, pixel 0.5, shown at level 1.71, step 2, values float32 > volume #31 step 1 > volume #32 step 1 > hide #!29 models > vop max #31 #32 Opened volume maximum as #33, grid size 438,438,438, pixel 0.5, shown at step 1, values float32 > rename #31 ""22. intT NU J2618_map_emready2.mrc"" > rename #32 ""23. intT local J2619_004_volume_map_emready2.mrc"" > rename #33 ""combination of 22 and 23"" > volume #33 level 2.381 > show #!22 models > color #33 darkgrey models > color #33 #a9a9a9c7 models > volume #33 level 5.874 > volume #33 level 4.545 > show #!20 models > hide #!22 models > volume #33 level 2.913 > fitmap #33 inMap #20 Fit map combination of 22 and 23 in map 12. combination of 10 and 11 using 652899 points correlation = 0.9014, correlation about mean = 0.6876, overlap = 3.196e+07 steps = 68, shift = 1.94, angle = 2.29 degrees Position of combination of 22 and 23 (#33) relative to 12. combination of 10 and 11 (#20) coordinates: Matrix rotation and translation 0.99985638 0.01511052 -0.00767438 -0.38329162 -0.01537770 0.99923205 -0.03603929 7.26333600 0.00712391 0.03615212 0.99932091 -4.77174349 Axis 0.90521734 -0.18555763 -0.38229561 Axis point 0.00000000 134.36592659 199.34294276 Rotation angle (degrees) 2.28528549 Shift along axis 0.12948695 > show #!22 models > hide #!20 models > fitmap #13 inMap #33 Multiple maps for #13 > fitmap #22 inMap #33 Fit molecule 13. vvd+iberdo int1.pdb (#22) to map combination of 22 and 23 (#33) using 8572 atoms average map value = 7.743, steps = 48 shifted from previous position = 0.0492 rotated from previous position = 0.175 degrees atoms outside contour = 1479, contour level = 2.9126 Position of 13. vvd+iberdo int1.pdb (#22) relative to combination of 22 and 23 (#33) coordinates: Matrix rotation and translation 0.44794773 -0.59759499 0.66499854 63.25832983 0.68016505 -0.25496860 -0.68728925 177.00102643 0.58027436 0.76017843 0.29225062 -72.48259428 Axis 0.74896737 0.04383907 0.66115506 Axis point 0.00000000 126.28354268 26.48493941 Rotation angle (degrees) 104.91496081 Shift along axis 7.21575224 > volume #33 level 2.799 > combine #22 close false modelId #34 > hide #!22 models > split #34 Split copy of 13. vvd+iberdo int1.pdb (#34) into 3 models Chain information for copy of 13. vvd+iberdo int1.pdb F #34.1 --- Chain | Description F | No description available Chain information for copy of 13. vvd+iberdo int1.pdb G #34.2 --- Chain | Description G | No description available > select add #34 8572 atoms, 8732 bonds, 4 pseudobonds, 1176 residues, 5 models selected > select subtract #34 Nothing selected > select add #34.1 6318 atoms, 6434 bonds, 824 residues, 1 model selected > fitmap sel inMap #33 Fit molecule copy of 13. vvd+iberdo int1.pdb F (#34.1) to map combination of 22 and 23 (#33) using 6318 atoms average map value = 8.754, steps = 48 shifted from previous position = 0.0938 rotated from previous position = 0.438 degrees atoms outside contour = 663, contour level = 2.7987 Position of copy of 13. vvd+iberdo int1.pdb F (#34.1) relative to combination of 22 and 23 (#33) coordinates: Matrix rotation and translation 0.44720607 -0.59287065 0.66970973 62.36924831 0.68026524 -0.26069452 -0.68503838 177.34741034 0.58072880 0.76193357 0.28672512 -72.18123785 Axis 0.74996599 0.04611884 0.65986671 Axis point 0.00000000 125.96199032 26.58252675 Rotation angle (degrees) 105.27081321 Shift along axis 7.32387673 > select subtract #34.1 Nothing selected > select add #34.2 2236 atoms, 2278 bonds, 4 pseudobonds, 351 residues, 2 models selected > fitmap sel inMap #33 Fit molecule copy of 13. vvd+iberdo int1.pdb G (#34.2) to map combination of 22 and 23 (#33) using 2236 atoms average map value = 5.896, steps = 76 shifted from previous position = 1.14 rotated from previous position = 2.85 degrees atoms outside contour = 589, contour level = 2.7987 Position of copy of 13. vvd+iberdo int1.pdb G (#34.2) relative to combination of 22 and 23 (#33) coordinates: Matrix rotation and translation 0.44344600 -0.63389462 0.63366652 71.75468851 0.67511779 -0.22879669 -0.70133305 176.58897148 0.58955205 0.73880287 0.32649456 -74.75561140 Axis 0.73980171 0.02266172 0.67244321 Axis point 0.00000000 129.64772120 24.41606470 Rotation angle (degrees) 103.26340176 Shift along axis 6.81714860 > select subtract #34.2 Nothing selected > select add #34.3 18 atoms, 20 bonds, 1 residue, 1 model selected > select subtract #34.3 Nothing selected > volume #33 level 4.263 > select add #34 8572 atoms, 8732 bonds, 4 pseudobonds, 1176 residues, 5 models selected > combine sel > rename #35 ""vvd+iberdo intT.pdb"" > close #34 > color zone #33 near #35 distance 8 > hide #!35 models > volume #33 level 5.801 > show #!20 models > hide #!20 models > show #!20 models > hide #!20 models > show #!20 models > hide #!20 models > show #!20 models > hide #!20 models > show #!20 models > hide #!20 models > show #!20 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!13 models > hide #!20 models > hide #!33 models > show #!33 models > show #!20 models > hide #!13 models > show #!10 models > show #!11 models > show #!13 models > hide #!20 models > hide #!33 models > volume #10 level 9.255 > hide #!10 models > show #!10 models > hide #!13 models > show #!13 models > hide #!13 models > hide #!11 models > show #!11 models > hide #!10 models > hide #!11 models > show #!20 models > show #!35 models > hide #!35 models > show #!33 models > show #!3 models > hide #!20 models > hide #!33 models > show #!33 models > hide #!33 models > show #!20 models > hide #!20 models > volume #3 level 4.554 > show #!14 models > hide #!3 models > show #!35 models > hide #!35 models > show #!33 models > hide #!14 models > volume #33 level 4.52 > volume #33 level 4.007 > volume #33 level 4.373 > volume #33 level 4.666 > show #!15 models > hide #!15 models > volume copy #33 modelId #36 Opened combination of 22 and 23 copy as #36, grid size 438,438,438, pixel 0.5, shown at step 1, values float32 > show #!35 models > color zone #36 near #35 distance 8 > hide #!35 models > show #!16 models > hide #!36 models > show #!14 models > hide #!16 models > show #!36 models > select add #36 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #36,0.97911,-0.16791,0.11466,13.358,0.15621,0.26023,-0.95283,192.83,0.13015,0.95083,0.28103,-63.585 > select subtract #36 Nothing selected > color #36 darkgrey models > color #36 #a9a9a9b1 models > color #36 #a9a9a9b0 models > select add #36 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #36,0.97911,-0.16791,0.11466,31.329,0.15621,0.26023,-0.95283,187.23,0.13015,0.95083,0.28103,-64.985 Must specify one map, got 8 > hide #!14 models > show #!3 models > fitmap #36 inMap #3 Fit map combination of 22 and 23 copy in map 6a. combination of 2526 and 2540 emready2 using 414467 points correlation = 0.9261, correlation about mean = 0.6457, overlap = 2.816e+07 steps = 204, shift = 12.5, angle = 7.94 degrees Position of combination of 22 and 23 copy (#36) relative to 6a. combination of 2526 and 2540 emready2 (#3) coordinates: Matrix rotation and translation 0.99962918 0.02226516 -0.01567676 -0.49377100 -0.02233593 0.99974104 -0.00435423 4.75196594 0.01557575 0.00470277 0.99986763 -1.11245630 Axis 0.16405010 -0.56607901 -0.80786269 Axis point 165.16995213 11.13270144 0.00000000 Rotation angle (degrees) 1.58181509 Shift along axis -1.87227942 > select clear > volume #3 level 3.39 > volume #3 level 4.252 > hide #!36 models > volume #3 level 3.476 > show #!36 models > volume #36 level 3.48 > hide #!36 models > show #!36 models > hide #!36 models > show #!36 models > hide #!3 models > show #!35 models > hide #!35 models > show #!6 models > hide #!6 models > show #!3 models > hide #!3 models > close #36 > show #!33 models > show #!35 models > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/0. figure 2 making .cxs"" > includeMaps true ——— End of log from Thu Feb 26 14:52:15 2026 ——— > view name session-start opened ChimeraX session > hide #!35 models > show #!35 models > ui tool show ""Color Zone"" > volume #33 level 3.679 > volume splitbyzone #33 Opened combination of 22 and 23 0 as #34.1, grid size 438,438,438, pixel 0.5, shown at level 3.68, step 1, values float32 Opened combination of 22 and 23 1 as #34.2, grid size 438,438,438, pixel 0.5, shown at level 3.68, step 1, values float32 Opened combination of 22 and 23 2 as #34.3, grid size 438,438,438, pixel 0.5, shown at level 3.68, step 1, values float32 Opened combination of 22 and 23 3 as #34.4, grid size 438,438,438, pixel 0.5, shown at level 3.68, step 1, values float32 Opened combination of 22 and 23 4 as #34.5, grid size 438,438,438, pixel 0.5, shown at level 3.68, step 1, values float32 Opened combination of 22 and 23 5 as #34.6, grid size 438,438,438, pixel 0.5, shown at level 3.68, step 1, values float32 Opened combination of 22 and 23 6 as #34.7, grid size 438,438,438, pixel 0.5, shown at level 3.68, step 1, values float32 Opened combination of 22 and 23 7 as #34.8, grid size 438,438,438, pixel 0.5, shown at level 3.68, step 1, values float32 > hide #!35 models > volume #34.1 level 6.344 > volume #34.2 level 5.958 > volume #34.3 level 5.16 > volume #34.4 level 3.856 > volume #34.5 level 4.357 > volume #34.6 level 4.173 > volume #34.7 level 3.106 > volume #34.8 level 0.8963 > split #34.8 > hide #34.8.1 models > show #34.8.1 models > hide #!34.8 models > show #!34.8 models > volume #34.8 level 2.434 > volume #34.6 level 3.308 > ui mousemode right ""map eraser"" Can only have one displayed volume when erasing [Repeated 1 time(s)] > hide #!34.7 models > hide #!34.6 models > hide #!34.5 models > hide #!34.4 models > hide #!34.3 models > hide #!34.2 models > hide #!34.1 models > hide #!34 models > show #!34 models > volume erase #34.8 center 120.33,109.23,128.57 radius 1.8615 > show #!34.1 models > hide #!34.1 models > show #!34.2 models > show #!34.3 models > show #!34.4 models > show #!34.5 models > show #!34.6 models > show #!34.7 models Can only have one displayed volume when erasing > hide #!34.7 models > hide #!34.6 models > hide #!34.5 models > hide #!34.4 models > hide #!34.3 models > hide #!34.2 models > volume erase #34.8 center 119.25,108.39,128.28 radius 1.2045 > show #!34.7 models > show #!34.6 models > show #!34.5 models > show #!34.4 models > hide #!34.4 models > hide #!34.5 models > show #!34.5 models > hide #!34.7 models > hide #!34.5 models > hide #!34.6 models > volume erase #34.8 center 121.8,109.59,127.84 radius 1.2045 > show #!34.7 models > show #!34.6 models > show #!34.5 models > hide #!34.7 models > hide #!34.6 models > hide #!34.5 models > volume erase #34.8 center 121.22,109.7,127.61 radius 1.2045 > hide #36 models > show #!34.2 models > show #!34.3 models > show #!34.4 models > show #!34.5 models > show #!34.6 models > show #!34.7 models > show #36 models > hide #!34.7 models > hide #!34.6 models > hide #!34.5 models > hide #!34.4 models > hide #!34.3 models > hide #!34.2 models > volume erase #34.8 center 115.77,109.2,129.16 radius 1.2045 > show #!34.5 models > show #!34.4 models > hide #!34.4 models > show #!34.6 models > hide #!34.5 models Can only have one displayed volume when erasing > hide #!34.6 models > volume erase #34.8 center 114.83,108.58,128.85 radius 0.438 > hide #36 models > show #!34.7 models > show #!34.6 models > show #!34.5 models > show #!34.4 models > show #!34.3 models > show #!34.2 models > volume #34.8 level 5.949 > volume #34.8 level 7.438 > show #!35 models > hide #!35 models > volume #34.6 level 2.123 > volume #34.6 level 2.716 > volume copy #34.8 modelId #37 Opened combination of 22 and 23 7 copy as #37, grid size 438,438,438, pixel 0.5, shown at step 1, values float32 > volume #34.6 level 3.531 > hide #!37 models > show #!37 models > show #!34.8 models > hide #!34.8 models > hide #34.8.1 models > hide #!34.7 models > hide #!34.6 models > hide #!34.5 models > show #!34.5 models > show #!34.6 models > show #!34.7 models > volume #37 level 1.653 > hide #!34.6 models > hide #!34.7 models > hide #!34.5 models > hide #!34.4 models > hide #!34.3 models > hide #!34.2 models > show #36 models > volume erase #37 center 118.25,112.1,126.67 radius 10.731 > show #!34.8 models > show #34.8.1 models > show #!34.7 models > show #!34.6 models > show #!34.5 models > show #!34.4 models > show #!34.3 models > show #!34.2 models > volume #34.4 level 4.063 > volume #34.2 level 6.366 > volume #34.2 level 6.706 > volume #34.3 level 5.881 > volume #34.5 level 5.067 > volume #34.6 level 3.333 > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/int 1/intT.png"" width 1800 > height 1541 supersample 4 transparentBackground true Cell requested for row 35 is out of bounds for table with 47 rows! Resizing table model. > close #36 > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/0. figure 2 making .cxs"" > includeMaps true ——— End of log from Thu Feb 26 15:13:55 2026 ——— > view name session-start opened ChimeraX session > hide #!34 models > hide #!37 models > show #!20 models > open ""/Users/zrizvi/Downloads/cryosparc_P341_J2527_map (3).mrc"" Opened cryosparc_P341_J2527_map (3).mrc as #36, grid size 300,300,300, pixel 0.74, shown at level 0.00925, step 2, values float32 > volume #36 step 1 > show #!22 models > volume #36 level 0.003026 > color #36 #b2b2b2ab models > hide #!22 models > show #!21 models > hide #!20 models > show #!22 models > hide #!21 models > ui tool show ""Color Zone"" Need to color zone map before it can be split > color zone #36 near #22 distance 4.44 > color zone #36 near #22 distance 4.54 > color zone #36 near #22 distance 4.64 > color zone #36 near #22 distance 4.74 > color zone #36 near #22 distance 1 > color zone #36 near #22 distance 10 [Repeated 1 time(s)] > color zone #36 near #22 distance 11 > color zone #36 near #22 distance 12 > color zone #36 near #22 distance 13 > color zone #36 near #22 distance 14 > color zone #36 near #22 distance 15 > color zone #36 near #22 distance 16 > color zone #36 near #22 distance 17 > color zone #36 near #22 distance 18 > color zone #36 near #22 distance 19 [Repeated 1 time(s)] > volume splitbyzone #36 Opened cryosparc_P341_J2527_map (3).mrc 0 as #38.1, grid size 300,300,300, pixel 0.74, shown at level 0.00303, step 1, values float32 Opened cryosparc_P341_J2527_map (3).mrc 1 as #38.2, grid size 300,300,300, pixel 0.74, shown at level 0.00303, step 1, values float32 Opened cryosparc_P341_J2527_map (3).mrc 2 as #38.3, grid size 300,300,300, pixel 0.74, shown at level 0.00303, step 1, values float32 Opened cryosparc_P341_J2527_map (3).mrc 3 as #38.4, grid size 300,300,300, pixel 0.74, shown at level 0.00303, step 1, values float32 Opened cryosparc_P341_J2527_map (3).mrc 4 as #38.5, grid size 300,300,300, pixel 0.74, shown at level 0.00303, step 1, values float32 Opened cryosparc_P341_J2527_map (3).mrc 5 as #38.6, grid size 300,300,300, pixel 0.74, shown at level 0.00303, step 1, values float32 Opened cryosparc_P341_J2527_map (3).mrc 6 as #38.7, grid size 300,300,300, pixel 0.74, shown at level 0.00303, step 1, values float32 Opened cryosparc_P341_J2527_map (3).mrc 7 as #38.8, grid size 300,300,300, pixel 0.74, shown at level 0.00303, step 1, values float32 > hide #!22 models > hide #!38.2 models > hide #!38.3 models > color #38.4 darkgrey models > color #38.5 darkgrey models > color #38.6 darkgrey models > color #38.6 #a9a9a9ae models > hide #!38.7 models > color #38.6 #a9a9a9ad models > color #38.5 #a9a9a9ad models > color #38.4 #a9a9a9ad models > show #!20 models > volume #20 level 6.805 > show #!29 models > hide #!29 models > show #!29 models > hide #!29 models > show #!29 models > hide #!29 models > hide #!38.8 models > show #!38.8 models > hide #!38.8 models > show #!38.8 models > hide #!38.6 models > show #!38.6 models > hide #!38.5 models > show #!38.5 models > hide #!38.4 models > show #!38.4 models > volume #38.8 level 0.009034 > volume copy #38.8 modelId #39 Opened cryosparc_P341_J2527_map (3).mrc 7 copy as #39, grid size 300,300,300, pixel 0.74, shown at step 1, values float32 > volume #39 level 0.009534 > volume #39 level 0.004671 > show #!38.8 models > hide #!38 models > hide #!20 models > show #!20 models > volume #39 level 0.003813 > hide #!20 models > ui mousemode right ""map eraser"" > volume erase #39 center 101.4,96.436,134.1 radius 9.6285 > volume erase #39 center 98.503,100.69,141.99 radius 9.6285 > volume erase #39 center 103.91,97.962,145.36 radius 9.6285 > show #!38 models > show #!38.8 models > show #!20 models > volume #38.6 level 0.002838 > volume #38.5 level 0.001958 > volume #38.4 level 0.002883 > volume #38.5 level 0.002171 > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/int 1/int1withLOWRES.png"" > width 1800 height 1643 supersample 4 transparentBackground true > hide #!38 models > hide #!39 models > hide #!20 models > show #!24 models > open ""/Users/zrizvi/Downloads/cryosparc_P341_J2574_006_volume_map (4).mrc"" Opened cryosparc_P341_J2574_006_volume_map (4).mrc as #40, grid size 300,300,300, pixel 0.731, shown at level 0.0255, step 2, values float32 > select add #40 2 models selected > show #!39 models > show #!38 models > select subtract #40 Nothing selected > hide #!40 models > hide #!24 models > show #!20 models > color #38.4 #d6d6d6ff models > color #38.5 #d6d6d6ff models > color #38.6 #d6d6d6ff models > color #38.4 #d6d6d680 models > color #38.5 #d6d6d680 models > color #38.6 #d6d6d680 models > select clear > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/int 1/int1withLOWRES.png"" > width 1800 height 1643 supersample 4 transparentBackground true > hide #!38 models > hide #!39 models > hide #!20 models > show #!40 models > show #!24 models > volume #40 step 1 > volume #40 level 0.08603 > select add #40 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #40,1,0,0,0.29592,0,1,0,38.019,0,0,1,1.4105 > ui mousemode right translate > fitmap #40 inMap #24 Fit map cryosparc_P341_J2574_006_volume_map (4).mrc in map 16. combination of 2612 and 2614 using 76567 points correlation = 0.9704, correlation about mean = 0.6325, overlap = 1.003e+05 steps = 76, shift = 1.78, angle = 0.0636 degrees Position of cryosparc_P341_J2574_006_volume_map (4).mrc (#40) relative to 16. combination of 2612 and 2614 (#24) coordinates: Matrix rotation and translation 0.99999997 -0.00011331 -0.00020616 0.84203922 0.00011353 0.99999940 0.00108507 36.29613778 0.00020603 -0.00108510 0.99999939 0.89143909 Axis -0.97729698 -0.18562141 0.10215333 Axis point 0.00000000 1542.77868389 -32171.78243850 Rotation angle (degrees) 0.06361512 Shift along axis -7.46919917 > select clear > volume #40 level 0.03029 > show #!25 models > hide #!24 models > color zone #40 near #25 distance 20 > volume splitbyzone #40 Opened cryosparc_P341_J2574_006_volume_map (4).mrc 0 as #41.1, grid size 300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32 Opened cryosparc_P341_J2574_006_volume_map (4).mrc 1 as #41.2, grid size 300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32 Opened cryosparc_P341_J2574_006_volume_map (4).mrc 2 as #41.3, grid size 300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32 Opened cryosparc_P341_J2574_006_volume_map (4).mrc 3 as #41.4, grid size 300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32 Opened cryosparc_P341_J2574_006_volume_map (4).mrc 4 as #41.5, grid size 300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32 Opened cryosparc_P341_J2574_006_volume_map (4).mrc 5 as #41.6, grid size 300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32 Opened cryosparc_P341_J2574_006_volume_map (4).mrc 6 as #41.7, grid size 300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32 Opened cryosparc_P341_J2574_006_volume_map (4).mrc 7 as #41.8, grid size 300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32 Opened cryosparc_P341_J2574_006_volume_map (4).mrc 8 as #41.9, grid size 300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32 > hide #!41.2 models > hide #!41.3 models > hide #!25 models > show #!24 models > hide #!24 models > show #!24 models > hide #!41.7 models > hide #!41.8 models > hide #!41.9 models > color #41.4 #d6d6d6ff models > color #41.5 #d6d6d6ff models > color #41.6 #d6d6d6ff models > color #41.4 #d6d6d680 models > color #41.5 #d6d6d680 models > color #41.6 #d6d6d680 models > volume #41.4 level 0.02525 > volume #41.5 level 0.03192 > volume #41.6 level 0.02225 > volume #41.6 level 0.01654 > volume #41.5 level 0.02215 > volume #41.4 level 0.0175 > volume #41.6 level 0.01676 > volume #41.5 level 0.03626 > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/int 2/int2withLOWRES.png"" > width 1800 height 2071 supersample 4 transparentBackground true > hide #!41.4 models > show #!41.4 models > hide #!41.1 models > show #!41.1 models > hide #!41 models > hide #!24 models > open ""/Users/zrizvi/Downloads/cryosparc_P341_J2526_map (3).mrc"" Opened cryosparc_P341_J2526_map (3).mrc as #42, grid size 300,300,300, pixel 0.74, shown at level 0.0102, step 2, values float32 > open ""/Users/zrizvi/Downloads/cryosparc_P341_J2527_map (3).mrc"" Opened cryosparc_P341_J2527_map (3).mrc as #43, grid size 300,300,300, pixel 0.74, shown at level 0.00925, step 2, values float32 > rename #42 ""OPEN cryosparc_P341_J2526_map (3).mrc"" > rename #43 ""INT1 cryosparc_P341_J2527_map (3).mrc"" > volume #42 step 1 > volume #43 step 1 > volume #42 level 0.008174 > volume #43 level 0.003606 > volume #43 level 0.004475 > fitmap #42 inMap #43 Fit map OPEN cryosparc_P341_J2526_map (3).mrc in map INT1 cryosparc_P341_J2527_map (3).mrc using 302851 points correlation = 0.9587, correlation about mean = 0.8943, overlap = 311.4 steps = 84, shift = 0.372, angle = 1.93 degrees Position of OPEN cryosparc_P341_J2526_map (3).mrc (#42) relative to INT1 cryosparc_P341_J2527_map (3).mrc (#43) coordinates: Matrix rotation and translation 0.99994514 -0.00782905 0.00695917 0.32141175 0.00804782 0.99945593 -0.03198565 2.52472465 -0.00670496 0.03203990 0.99946410 -3.99736918 Axis 0.95042634 0.20283696 0.23568399 Axis point 0.00000000 125.14400802 77.59405627 Rotation angle (degrees) 1.93023280 Shift along axis -0.12453025 > volume #42 level 0.009173 > ui tool show ""Side View"" > volume #42 color #d6d6d6 > volume #43 color #797979 > color #43 khaki > graphics silhouettes false > graphics silhouettes true > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting soft > volume #43 color #f0e68c68 > volume #43 color #f0e68c69 > volume #42 color #d6d6d6 > volume #42 color silver > volume #42 color darkgrey > volume #42 color #a9a9a980 > volume #43 color khaki > volume #43 level 0.003606 > volume #43 color #f0e68c80 > volume #42 color #d6d6d6 > volume #42 level 0.007674 > show #!6 models > hide #!6 models > show #!3 models > show #!43 models > ui mousemode right ""rotate selected models"" > hide #!43 models > select add #42 4 models selected > view matrix models > #42,0.74119,-0.63871,-0.20662,142.23,0.12355,0.43232,-0.89322,164.37,0.65983,0.63651,0.39934,-98.741 > view matrix models > #42,0.74119,-0.63871,-0.20662,144.66,0.12355,0.43232,-0.89322,143.85,0.65983,0.63651,0.39934,-102.15 > view matrix models > #42,0.44408,-0.89568,0.023216,189.36,0.37521,0.16238,-0.91261,154.39,0.81364,0.41398,0.40818,-89.996 > ui mousemode right translate > ui mousemode right ""rotate selected models"" > view matrix models > #42,0.91023,-0.37692,-0.17151,84.578,-0.039193,0.33389,-0.9418,181.92,0.41225,0.86397,0.28915,-92.763 > view matrix models > #42,0.91023,-0.37692,-0.17151,95.55,-0.039193,0.33389,-0.9418,183.8,0.41225,0.86397,0.28915,-76.869 > ui mousemode right translate > ui mousemode right ""translate selected models"" > view matrix models > #42,0.91023,-0.37692,-0.17151,99.112,-0.039193,0.33389,-0.9418,188.29,0.41225,0.86397,0.28915,-84.482 > fitmap #42 inMap #3 Fit map OPEN cryosparc_P341_J2526_map (3).mrc in map 6a. combination of 2526 and 2540 emready2 using 311826 points correlation = 0.9154, correlation about mean = 0.7726, overlap = 5.891e+04 steps = 164, shift = 5.11, angle = 13 degrees Position of OPEN cryosparc_P341_J2526_map (3).mrc (#42) relative to 6a. combination of 2526 and 2540 emready2 (#3) coordinates: Matrix rotation and translation 0.99999988 -0.00020781 -0.00043686 0.14986729 0.00020809 0.99999978 0.00063070 -0.27744247 0.00043673 -0.00063079 0.99999970 0.09652282 Axis -0.79348717 -0.54949254 0.26160285 Axis point 0.00000000 128.45846825 388.72679196 Rotation angle (degrees) 0.04554435 Shift along axis 0.05878544 > select clear > hide #!3 models > show #!6 models > hide #!6 models > show #!6 models > close #42-43 > open ""/Users/zrizvi/Downloads/cryosparc_P341_J2526_map (3).mrc"" Opened cryosparc_P341_J2526_map (3).mrc as #42, grid size 300,300,300, pixel 0.74, shown at level 0.0102, step 2, values float32 > select add #42 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #42,0.4114,-0.69485,0.58986,99.53,0.61004,-0.27092,-0.74462,189.76,0.6772,0.66618,0.31242,-94.907 > ui mousemode right ""translate selected models"" > view matrix models > #42,0.4114,-0.69485,0.58986,88.89,0.61004,-0.27092,-0.74462,181.52,0.6772,0.66618,0.31242,-80.942 > ui mousemode right translate > ui mousemode right ""translate selected models"" > view matrix models > #42,0.4114,-0.69485,0.58986,94.879,0.61004,-0.27092,-0.74462,190.11,0.6772,0.66618,0.31242,-70.537 > ui mousemode right translate > fitmap #6 inMap #42 Fit molecule 6c. vvd+iberdo open.pdb (#6) to map cryosparc_P341_J2526_map (3).mrc (#42) using 8572 atoms average map value = 0.03997, steps = 100 shifted from previous position = 5.84 rotated from previous position = 6.69 degrees atoms outside contour = 769, contour level = 0.010172 Position of 6c. vvd+iberdo open.pdb (#6) relative to cryosparc_P341_J2526_map (3).mrc (#42) coordinates: Matrix rotation and translation 0.99998883 0.00472722 0.00003282 -0.62446445 -0.00472717 0.99998796 -0.00131983 0.56931961 -0.00003906 0.00131966 0.99999913 -0.56430308 Axis 0.26889250 0.00732175 -0.96314237 Axis point 119.45514153 153.98357738 0.00000000 Rotation angle (degrees) 0.28121410 Shift along axis 0.37975882 > select clear > open ""/Users/zrizvi/Downloads/cryosparc_P341_J2527_map (3).mrc"" Opened INT1 cryosparc_P341_J2527_map (3).mrc as #43, grid size 300,300,300, pixel 0.74, shown at level 0.00925, step 2, values float32 > hide #!6 models > select add #43 2 models selected > ui mousemode right ""rotate selected models"" > ui mousemode right translate > ui mousemode right ""rotate selected models"" > view matrix models > #43,0.20325,-0.63332,0.74673,97.599,0.52292,-0.57456,-0.62963,229.83,0.8278,0.51845,0.2144,-80.796 > ui mousemode right ""translate selected models"" > view matrix models > #43,0.20325,-0.63332,0.74673,90.103,0.52292,-0.57456,-0.62963,217.46,0.8278,0.51845,0.2144,-64.405 > ui mousemode right translate > fitmap #43 inMap #42 Fit map INT1 cryosparc_P341_J2527_map (3).mrc in map cryosparc_P341_J2526_map (3).mrc using 33711 points correlation = 0.9633, correlation about mean = 0.8938, overlap = 38.63 steps = 208, shift = 16.4, angle = 21.5 degrees Position of INT1 cryosparc_P341_J2527_map (3).mrc (#43) relative to cryosparc_P341_J2526_map (3).mrc (#42) coordinates: Matrix rotation and translation 0.99994614 0.00789387 -0.00673806 -0.33316626 -0.00767360 0.99945480 0.03211278 -2.42129604 0.00698788 -0.03205935 0.99946154 4.08392857 Axis -0.95147544 -0.20351341 -0.23081764 Axis point 0.00000000 125.11362206 78.36602072 Rotation angle (degrees) 1.93251941 Shift along axis -0.13287701 > select clear > volume #42 step 1 > volume #43 step 1 > show #!6 models > color zone #42 near #6 distance 8 > color zone #42 near #6 distance 15 > hide #!6 models > show #!43 models > color #43 #d6d6d6ff models > color #43 #d6d6d682 models [Repeated 1 time(s)] > color #43 #d6d6d6ff models > volume #43 level 0.004475 > color #43 #d6d6d680 models > ui tool show ""Side View"" > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/openTOintVVDshift.png"" width > 1800 height 2071 supersample 4 transparentBackground true > ui tool show ""Side View"" > volume #43 level 0.002738 > volume #42 level 0.01417 > volume #42 level 0.009173 > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig > maps/openTOintVVDshiftFULLimage.png"" width 1800 height 2071 supersample 4 > transparentBackground true > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN- > inhibitor/Figures/Fig 2b final EMready fig maps/0. figure 2 making .cxs"" > includeMaps true [Repeated 1 time(s)] ——— End of log from Fri Feb 27 10:44:17 2026 ——— > view name session-start opened ChimeraX session OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M4 OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.8.1, Qt 6.8.2 Qt runtime version: 6.8.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac16,1 Model Number: MW2V3LL/A Chip: Apple M4 Total Number of Cores: 10 (4 performance and 6 efficiency) Memory: 16 GB System Firmware Version: 11881.140.96 OS Loader Version: 11881.140.96 Software: System Software Overview: System Version: macOS 15.6.1 (24G90) Kernel Version: Darwin 24.6.0 Time since boot: 26 minutes, 8 seconds Graphics/Displays: Apple M4: Chipset Model: Apple M4 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL U3011: Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array) UI Looks like: 1920 x 1200 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.2.0 autocommand: 2.2.2 babel: 2.17.0 backports.tarfile: 1.2.0 beautifulsoup4: 4.13.3 blockdiag: 3.0.0 blosc2: 3.2.0 build: 1.2.2.post1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.1 ChimeraX-AddCharge: 1.5.18 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