id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20870 ChimeraX bug report submission payal.pratap@… "{{{ The following bug report has been submitted: Platform: macOS-15.6.1-arm64-arm-64bit ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. Fatal Python error: Segmentation fault Thread 0x0000000332eeb000 (most recent call first): File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000331edf000 (most recent call first): File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000330ed3000 (most recent call first): File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000032fec7000 (most recent call first): File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000032eebb000 (most recent call first): File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000032deaf000 (most recent call first): File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000032cea3000 (most recent call first): File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000032be97000 (most recent call first): File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000032ae8b000 (most recent call first): File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000329e7f000 (most recent call first): File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000328e73000 (most recent call first): File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000327e67000 (most recent call first): File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000326e5b000 (most recent call first): File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x000000020cdfa0c0 (most recent call first): File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 368 in event_loop File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1057 in init File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1220 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: 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""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""6410af69ed1e1e7ab93ed169"", ""factorPackIds"" : { }, ""deploymentId"" : 240000011 }, { ""rolloutId"" : ""65a8173205d942272410674b"", ""factorPackIds"" : { ""SIRI_HOME_AUTOMATION_SERVER_FLOW_DEPRECATION"" : ""65d39fa4cb0e2417d11ce5f6"" }, ""deploymentId"" : 240000001 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.10 (2025-06-26) © 2016-2025 Regents of the University of California. All rights reserved. > open > /Users/payalpratap/Desktop/Structural_Biology/UCSF_Local_Directory/Fusion4_Tspan12_Bril/Chimera/Tspan12_Fzd4_FEVR_mutants.cxs Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 as #4, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 0 as #5.1, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 1 as #5.2, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 2 as #5.3, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 3 as #5.4, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 4 as #5.5, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 5 as #5.6, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 6 as #5.7, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 7 as #5.8, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened cryosparc_P9_J329_006_volume_map_sharp_deepEMhancer_resampled.mrc as #7, grid size 480,480,480, pixel 0.819, shown at level 1.09, step 1, values float32 Log from Wed Aug 12 15:30:28 2026UCSF ChimeraX version: 1.10 (2025-06-26) © 2016-2025 Regents of the University of California. All rights reserved. > open > /Users/payalpratap/Desktop/Structural_Biology/UCSF_Local_Directory/Fusion4_Tspan12_Bril/Chimera/Tspan12_Fzd4_FEVR_mutants.cxs > format session Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 as #4, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 0 as #5.1, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 1 as #5.2, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 2 as #5.3, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 3 as #5.4, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 4 as #5.5, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 5 as #5.6, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 6 as #5.7, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 7 as #5.8, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened cryosparc_P9_J329_006_volume_map_sharp_deepEMhancer_resampled.mrc as #7, grid size 480,480,480, pixel 0.819, shown at level 1.09, step 1, values float32 Log from Tue Aug 4 16:40:37 2026UCSF ChimeraX version: 1.10 (2025-06-26) © 2016-2025 Regents of the University of California. All rights reserved. > open > /Users/payalpratap/Desktop/Structural_Biology/UCSF_Local_Directory/Fusion4_Tspan12_Bril/Chimera/Tspan12_Fzd4_FEVR_mutants.cxs Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 as #4, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 0 as #5.1, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 1 as #5.2, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 2 as #5.3, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 3 as #5.4, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 4 as #5.5, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 5 as #5.6, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 6 as #5.7, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 7 as #5.8, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened cryosparc_P9_J329_006_volume_map_sharp_deepEMhancer_resampled.mrc as #7, grid size 480,480,480, pixel 0.819, shown at level 1.09, step 1, values float32 Log from Tue Aug 4 09:23:10 2026UCSF ChimeraX version: 1.10 (2025-06-26) © 2016-2025 Regents of the University of California. All rights reserved. > open > /Users/payalpratap/Desktop/Structural_Biology/UCSF_Local_Directory/Fusion4_Tspan12_Bril/Chimera/Tspan12_Fzd4_FEVR_mutants.cxs > format session Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 as #4, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 0 as #5.1, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 1 as #5.2, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 2 as #5.3, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 3 as #5.4, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 4 as #5.5, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 5 as #5.6, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 6 as #5.7, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 7 as #5.8, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened cryosparc_P9_J329_006_volume_map_sharp_deepEMhancer_resampled.mrc as #7, grid size 480,480,480, pixel 0.819, shown at level 1.09, step 1, values float32 Log from Mon Jul 27 21:06:11 2026UCSF ChimeraX version: 1.10 (2025-06-26) © 2016-2025 Regents of the University of California. All rights reserved. > open > /Users/payalpratap/Desktop/Structural_Biology/UCSF_Local_Directory/Fusion4_Tspan12_Bril/Chimera/Tspan12_Fzd4_Figure4.cxs > format session Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 as #4, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 0 as #5.1, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 1 as #5.2, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 2 as #5.3, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 3 as #5.4, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 4 as #5.5, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 5 as #5.6, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 6 as #5.7, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 7 as #5.8, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened cryosparc_P9_J329_006_volume_map_sharp_deepEMhancer_resampled.mrc as #7, grid size 480,480,480, pixel 0.819, shown at level 0.898, step 1, values float32 Log from Fri Jul 24 01:26:39 2026UCSF ChimeraX version: 1.10 (2025-06-26) © 2016-2025 Regents of the University of California. All rights reserved. > open > /Users/payalpratap/Desktop/Structural_Biology/UCSF_Local_Directory/Fusion4_Tspan12_Bril/Chimera/Tspan12_Fzd4_Figure4.cxs > format session Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 as #4, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 0 as #5.1, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 1 as #5.2, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 2 as #5.3, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 3 as #5.4, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 4 as #5.5, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 5 as #5.6, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 6 as #5.7, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 7 as #5.8, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Log from Mon Jul 20 00:02:01 2026UCSF ChimeraX version: 1.10 (2025-06-26) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/payalpratap/Desktop/Structural_Biology/UCSF_Local_Directory/Fusion4_Tspan12_Bril/Phenix/RealSpaceRefine_140/Fusion_BRIL4_real_space_refined_140.pdb Chain information for Fusion_BRIL4_real_space_refined_140.pdb #1 --- Chain | Description A | No description available B | No description available H | No description available K | No description available L | No description available > show cartoons > style stick Changed 17736 atom styles > hide atoms > select clear [Repeated 1 time(s)] > select /B:219 10 atoms, 9 bonds, 1 residue, 1 model selected > select up 220 atoms, 219 bonds, 22 residues, 1 model selected > select up 239 atoms, 238 bonds, 24 residues, 1 model selected > select clear > select /B:189 10 atoms, 9 bonds, 1 residue, 1 model selected > select up 87 atoms, 87 bonds, 6 residues, 1 model selected > select up 1337 atoms, 1364 bonds, 85 residues, 1 model selected > color sel red > select clear > select /B:226 10 atoms, 9 bonds, 1 residue, 1 model selected > select up 220 atoms, 219 bonds, 22 residues, 1 model selected > select up 239 atoms, 238 bonds, 24 residues, 1 model selected > select up 258 atoms, 256 bonds, 25 residues, 1 model selected > select down 239 atoms, 238 bonds, 24 residues, 1 model selected > color sel purple > color sel hot pink > color sel magenta Drag select of 655 residues, 1 pseudobonds > select up 11190 atoms, 11319 bonds, 1 pseudobond, 735 residues, 2 models selected > select up 14655 atoms, 14834 bonds, 1 pseudobond, 955 residues, 2 models selected > select up 17736 atoms, 17959 bonds, 5 pseudobonds, 1163 residues, 2 models selected > select down 14655 atoms, 14834 bonds, 1 pseudobond, 955 residues, 2 models selected > hide sel cartoons > dssp > undo > redo > undo [Repeated 3 time(s)] > redo [Repeated 3 time(s)] > undo > dssp > undo > open > /Users/payalpratap/Desktop/Structural_Biology/UCSF_Local_Directory/Fusion4_Tspan12_Bril/Phenix/RealSpaceRefine_140/Fusion_BRIL4_real_space_refined_140_edit.pdb Chain information for Fusion_BRIL4_real_space_refined_140_edit.pdb #2 --- Chain | Description A | No description available B | No description available H | No description available K | No description available L | No description available > show sel cartoons > style sel stick Changed 14655 atom styles > hide sel atoms > select add #2 32391 atoms, 32793 bonds, 6 pseudobonds, 2118 residues, 4 models selected > show sel cartoons > style sel stick Changed 32391 atom styles > hide sel atoms > hide #!1 models Drag select of 424 residues, 2 pseudobonds > select up 8823 atoms, 8926 bonds, 2 pseudobonds, 567 residues, 2 models selected > select up 14655 atoms, 14834 bonds, 2 pseudobonds, 955 residues, 2 models selected > select up 17736 atoms, 17959 bonds, 5 pseudobonds, 1163 residues, 2 models selected > select down 14655 atoms, 14834 bonds, 2 pseudobonds, 955 residues, 2 models selected > hide sel cartoons > show #!1 models Drag select of 181 residues, 2 pseudobonds > select up 4943 atoms, 5000 bonds, 2 pseudobonds, 315 residues, 2 models selected > select up 12872 atoms, 13031 bonds, 2 pseudobonds, 835 residues, 2 models selected > select up 17736 atoms, 17959 bonds, 5 pseudobonds, 1163 residues, 2 models selected > select down 12872 atoms, 13031 bonds, 2 pseudobonds, 835 residues, 2 models selected Drag select of 5 residues > select up 13313 atoms, 13474 bonds, 2 pseudobonds, 867 residues, 2 models selected > select up 14655 atoms, 14834 bonds, 2 pseudobonds, 955 residues, 2 models selected > hide sel cartoons > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > dssp > undo > close #2 > open > /Users/payalpratap/Desktop/Structural_Biology/UCSF_Local_Directory/Fusion4_Tspan12_Bril/Phenix/RealSpaceRefine_140/Fusion_BRIL4_real_space_refined_140_edit.pdb Chain information for Fusion_BRIL4_real_space_refined_140_edit.pdb #2 --- Chain | Description A | No description available B | No description available H | No description available K | No description available L | No description available > show sel cartoons > style sel stick Changed 14655 atom styles > hide sel cartoons > show sel cartoons > hide sel atoms > show sel atoms > select add #2 32391 atoms, 32793 bonds, 7 pseudobonds, 2118 residues, 4 models selected > hide sel atoms > show sel cartoons > dssp > hide #!2 models > undo [Repeated 1 time(s)] > hide #!2 models > hide #!1 models > show #!1 models Drag select of 493 residues, 2 pseudobonds Drag select of 409 residues, 1 pseudobonds > select up 8640 atoms, 8727 bonds, 1 pseudobond, 569 residues, 2 models selected > select up 14655 atoms, 14834 bonds, 1 pseudobond, 955 residues, 2 models selected > hide sel cartoons > dssp > undo > dssp > undo > redo > undo [Repeated 1 time(s)] > redo [Repeated 1 time(s)] > undo > hide #!1 models > show #!2 models > dssp > undo > redo > undo > redo [Repeated 1 time(s)]No redo action is available > undo > redo > undo Drag select of 464 residues, 1 pseudobonds > select up 9107 atoms, 9205 bonds, 1 pseudobond, 594 residues, 2 models selected > select up 14655 atoms, 14834 bonds, 1 pseudobond, 955 residues, 2 models selected > select up 17736 atoms, 17959 bonds, 5 pseudobonds, 1163 residues, 2 models selected > select down 14655 atoms, 14834 bonds, 1 pseudobond, 955 residues, 2 models selected > hide sel cartoons Drag select of 11 residues > select up 213 atoms, 219 bonds, 14 residues, 1 model selected > select up 1337 atoms, 1364 bonds, 85 residues, 1 model selected > color sel red > select #2/B:224 10 atoms, 9 bonds, 1 residue, 1 model selected > select up 220 atoms, 219 bonds, 22 residues, 1 model selected > select up 239 atoms, 238 bonds, 24 residues, 1 model selected > select up 258 atoms, 256 bonds, 25 residues, 1 model selected > select down 239 atoms, 238 bonds, 24 residues, 1 model selected > color sel magenta > select clear [Repeated 1 time(s)] > select #2/B:36 24 atoms, 23 bonds, 1 residue, 1 model selected > select add #2/B:59 45 atoms, 44 bonds, 2 residues, 1 model selected > select up 650 atoms, 659 bonds, 42 residues, 1 model selected > select down 45 atoms, 44 bonds, 2 residues, 1 model selected > select add #2/B:58 59 atoms, 57 bonds, 3 residues, 1 model selected > select add #2/B:56 78 atoms, 75 bonds, 4 residues, 1 model selected > select add #2/B:55 94 atoms, 90 bonds, 5 residues, 1 model selected > select add #2/B:57 113 atoms, 108 bonds, 6 residues, 1 model selected > select add #2/B:54 123 atoms, 117 bonds, 7 residues, 1 model selected > select add #2/B:53 130 atoms, 123 bonds, 8 residues, 1 model selected > select add #2/B:52 137 atoms, 129 bonds, 9 residues, 1 model selected > select add #2/B:51 153 atoms, 144 bonds, 10 residues, 1 model selected > select add #2/B:47 163 atoms, 153 bonds, 11 residues, 1 model selected > select add #2/B:48 170 atoms, 159 bonds, 12 residues, 1 model selected > select add #2/B:49 184 atoms, 172 bonds, 13 residues, 1 model selected > select add #2/B:50 191 atoms, 178 bonds, 14 residues, 1 model selected > select add #2/B:46 205 atoms, 191 bonds, 15 residues, 1 model selected > select add #2/B:45 224 atoms, 209 bonds, 16 residues, 1 model selected > select add #2/B:44 238 atoms, 222 bonds, 17 residues, 1 model selected > select add #2/B:42 254 atoms, 237 bonds, 18 residues, 1 model selected > select add #2/B:43 273 atoms, 255 bonds, 19 residues, 1 model selected > select add #2/B:41 287 atoms, 268 bonds, 20 residues, 1 model selected > select add #2/B:40 301 atoms, 281 bonds, 21 residues, 1 model selected > select add #2/B:39 320 atoms, 299 bonds, 22 residues, 1 model selected > select add #2/B:37 332 atoms, 310 bonds, 23 residues, 1 model selected > select add #2/B:38 353 atoms, 331 bonds, 24 residues, 1 model selected > color sel yellow > select clear > select add #2/B:72 11 atoms, 10 bonds, 1 residue, 1 model selected > select up 348 atoms, 350 bonds, 23 residues, 1 model selected > select add #2/B:64 365 atoms, 367 bonds, 24 residues, 1 model selected > select add #2/B:63 381 atoms, 382 bonds, 25 residues, 1 model selected > select add #2/B:61 395 atoms, 396 bonds, 26 residues, 1 model selected > select add #2/B:62 411 atoms, 411 bonds, 27 residues, 1 model selected > select add #2/B:60 431 atoms, 431 bonds, 28 residues, 1 model selected > color sel blue > color sel #00fdffff Drag select of 8 residues Drag select of 5 residues > select clear Drag select of 17 residues > select add #2/B:107 299 atoms, 9 bonds, 18 residues, 1 model selected > select subtract #2/B:90 280 atoms, 9 bonds, 17 residues, 1 model selected > select add #2/B:90 299 atoms, 27 bonds, 18 residues, 1 model selected > color sel lime > select clear > select #2/B:26 19 atoms, 18 bonds, 1 residue, 1 model selected > select up 546 atoms, 552 bonds, 36 residues, 1 model selected > select clear > select add #2/B:35 17 atoms, 16 bonds, 1 residue, 1 model selected > select add #2/B:34 41 atoms, 41 bonds, 2 residues, 1 model selected > select add #2/B:33 51 atoms, 50 bonds, 3 residues, 1 model selected > select add #2/B:31 67 atoms, 65 bonds, 4 residues, 1 model selected > select subtract #2/B:31 51 atoms, 50 bonds, 3 residues, 1 model selected > select add #2/B:31 67 atoms, 65 bonds, 4 residues, 1 model selected > select add #2/B:32 78 atoms, 75 bonds, 5 residues, 1 model selected > select add #2/B:30 88 atoms, 84 bonds, 6 residues, 1 model selected > select add #2/B:29 107 atoms, 102 bonds, 7 residues, 1 model selected > select add #2/B:28 123 atoms, 117 bonds, 8 residues, 1 model selected > select add #2/B:27 134 atoms, 127 bonds, 9 residues, 1 model selected > select add #2/B:26 153 atoms, 145 bonds, 10 residues, 1 model selected > select add #2/B:25 164 atoms, 155 bonds, 11 residues, 1 model selected > select add #2/B:24 181 atoms, 171 bonds, 12 residues, 1 model selected > select add #2/B:23 200 atoms, 189 bonds, 13 residues, 1 model selected > select add #2/B:22 224 atoms, 214 bonds, 14 residues, 1 model selected > select add #2/B:21 244 atoms, 234 bonds, 15 residues, 1 model selected > select add #2/B:20 251 atoms, 240 bonds, 16 residues, 1 model selected > select add #2/B:19 258 atoms, 246 bonds, 17 residues, 1 model selected > select subtract #2/B:19 251 atoms, 240 bonds, 16 residues, 1 model selected > select add #2/B:19 258 atoms, 246 bonds, 17 residues, 1 model selected > select add #2/B:18 272 atoms, 259 bonds, 18 residues, 1 model selected > select add #2/B:17 279 atoms, 265 bonds, 19 residues, 1 model selected > select add #2/B:16 289 atoms, 274 bonds, 20 residues, 1 model selected > select add #2/B:15 310 atoms, 295 bonds, 21 residues, 1 model selected > select add #2/B:13 317 atoms, 301 bonds, 22 residues, 1 model selected > select add #2/B:14 336 atoms, 319 bonds, 23 residues, 1 model selected > select add #2/B:12 343 atoms, 325 bonds, 24 residues, 1 model selected > select add #2/B:11 367 atoms, 348 bonds, 25 residues, 1 model selected > select add #2/B:9 377 atoms, 357 bonds, 26 residues, 1 model selected > select add #2/B:10 384 atoms, 363 bonds, 27 residues, 1 model selected > color sel blue > select clear [Repeated 3 time(s)] > select add #2/B:90 19 atoms, 18 bonds, 1 residue, 1 model selected > select add #2/B:89 33 atoms, 31 bonds, 2 residues, 1 model selected > select add #2/B:88 57 atoms, 54 bonds, 3 residues, 1 model selected > select add #2/B:87 79 atoms, 75 bonds, 4 residues, 1 model selected > select clear > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 17736 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > preset cartoons/nucleotides cylinders/stubs Using preset: Cartoons/Nucleotides / Cylinders/Stubs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh tube rad 2 sides 24 thick 0.6 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides stubs > preset cartoons/nucleotides licorice/ovals Using preset: Cartoons/Nucleotides / Licorice/Ovals Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh default arrows f x round width 1 thick 1 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides tube/slab shape ellipsoid > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > undo [Repeated 3 time(s)] > toolshed show > save /Users/payalpratap/Desktop/image96.png supersample 3 > save > /Users/payalpratap/Desktop/Structural_Biology/UCSF_Local_Directory/Fusion4_Tspan12_Bril/Chimera/images/Tspan12_1.bmp > width 878 height 739 supersample 3 > save > /Users/payalpratap/Desktop/Structural_Biology/UCSF_Local_Directory/Fusion4_Tspan12_Bril/Chimera/images/Tspan12_1.gif > width 878 height 739 supersample 3 > save > /Users/payalpratap/Desktop/Structural_Biology/UCSF_Local_Directory/Fusion4_Tspan12_Bril/Chimera/images/Tspan12_1.tif > width 878 height 739 supersample 3 > save /Users/payalpratap/Desktop/picture.png supersample 3 > transparentBackground true > lighting flat > lighting full > lighting soft > lighting simple > graphics silhouettes false > graphics silhouettes true > save /Users/payalpratap/Desktop/picture.png supersample 3 > transparentBackground true [Repeated 1 time(s)] > graphics silhouettes false > save /Users/payalpratap/Desktop/picture1.png supersample 3 > transparentBackground true > open > /Users/payalpratap/Desktop/Structural_Biology/UCSF_Local_Directory/Fusion4_Tspan12_Bril/cryosparc/DeepEMhancer/cryosparc_P9_J329_006_volume_map_sharp_deepEMhancer_resampled.mrc Opened cryosparc_P9_J329_006_volume_map_sharp_deepEMhancer_resampled.mrc as #3, grid size 480,480,480, pixel 0.819, shown at level 0.000616, step 2, values float32 > volume #3 step 1 > volume #3 level 0.9935 > hide #!3 models > molmap #2 5 Opened Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 as #4, grid size 52,75,114, pixel 1.67, shown at level 0.114, step 1, values float32 > undo [Repeated 1 time(s)] > close #4 > close #3 > show sel cartoons [Repeated 3 time(s)] > hide #!2 models > show #!2 models > show sel cartoons [Repeated 2 time(s)] > select up 675 atoms, 682 bonds, 42 residues, 1 model selected Drag select of 106 residues, 1 pseudobonds > select up 1656 atoms, 1672 bonds, 1 pseudobond, 115 residues, 2 models selected > select up 3081 atoms, 3125 bonds, 1 pseudobond, 208 residues, 2 models selected > select up 17736 atoms, 17959 bonds, 5 pseudobonds, 1163 residues, 2 models selected > select up 17736 atoms, 17959 bonds, 5 pseudobonds, 1163 residues, 2 models selected > select up 35472 atoms, 35918 bonds, 5 pseudobonds, 2326 residues, 3 models selected > select up 35472 atoms, 35918 bonds, 5 pseudobonds, 2326 residues, 3 models selected > select up 35472 atoms, 35918 bonds, 5 pseudobonds, 2326 residues, 3 models selected > show sel & #!2 cartoons Drag select of 391 residues, 1 pseudobonds > select up 9198 atoms, 9296 bonds, 1 pseudobond, 601 residues, 2 models selected > select up 14655 atoms, 14834 bonds, 1 pseudobond, 955 residues, 2 models selected > select up 17736 atoms, 17959 bonds, 5 pseudobonds, 1163 residues, 2 models selected > select down 14655 atoms, 14834 bonds, 1 pseudobond, 955 residues, 2 models selected > combine #2 > hide #!2 models > hide #!3 models > show #!3 models Drag select of 533 residues, 2 pseudobonds > select up 10789 atoms, 10908 bonds, 2 pseudobonds, 705 residues, 2 models selected > select up 14655 atoms, 14834 bonds, 2 pseudobonds, 955 residues, 2 models selected > select up 17736 atoms, 17959 bonds, 5 pseudobonds, 1163 residues, 2 models selected > select down 14655 atoms, 14834 bonds, 2 pseudobonds, 955 residues, 2 models selected > delete atoms (#!3 & sel) > delete bonds (#!3 & sel) > molmap #2 5 Opened Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 as #4, grid size 52,75,114, pixel 1.67, shown at level 0.114, step 1, values float32 > close #4 > molmap #3 5 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 as #4, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 > color #4 #b2b2b26f models > ui tool show ""Surface Color"" > color radial #4.1 palette #ff0000:#ffffff:#0000ff > color single #4.1 > ui tool show ""Color Zone"" > color zone #4 near #3 distance 10 > color #4 #b2b2b280 models [Repeated 1 time(s)] > color zone #4 near #3 distance 10 > volume splitbyzone #4 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 0 as #5.1, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 1 as #5.2, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 2 as #5.3, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 3 as #5.4, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 4 as #5.5, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 5 as #5.6, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 6 as #5.7, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 7 as #5.8, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 > volume #5.1 level 0.2545 > hide #!5.7 models > show #!5.7 models > color #5 #b2b2b2b3 models > color #5.1 #b2b2b287 models > ui tool show ""Color Zone"" > color zone #5.1 near #3 distance 10 > close #4 > color zone #5.1 near #3 distance 10 [Repeated 1 time(s)] > close #5 > molmap #3 5 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 as #4, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 > color zone #4 near #3 distance 10 > color #4.1 #b2b2b25b > color zone #4 near #3 distance 10 [Repeated 1 time(s)] > volume splitbyzone #4 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 0 as #5.1, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 1 as #5.2, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 2 as #5.3, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 3 as #5.4, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 4 as #5.5, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 5 as #5.6, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 6 as #5.7, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 Opened copy of Fusion_BRIL4_real_space_refined_140_edit.pdb map 5 7 as #5.8, grid size 44,66,44, pixel 1.67, shown at level 0.097, step 1, values float32 > color #5.2 #0000ff32 models > color #5.3 #ffff0020 models > color #5.3 #ffff0034 models > color #5.4 #00fdff33 models > color #5.5 #8d81a933 models > color #5.6 #00ff0033 models > color #5.7 #ff000033 models > color #5.7 #fffb00ff models > undo [Repeated 1 time(s)] > color #5.7 #ff2600ff models > color #5.7 #ff260033 models > color #5.8 #ff00ff33 models > select clear > save /Users/payalpratap/Desktop/picture2.png supersample 3 > transparentBackground true > color #5.2 #0000ff80 models > color #5.2 #0000ff66 models > color #5.1 #b2b2b266 models > color #5.3 #ffff0066 models > color #5.4 #00fdff66 models > color #5.5 #8d81a966 models > color #5.6 #00ff0066 models > color #5.7 #ff260066 models > color #5.8 #ff00ff66 models > save /Users/payalpratap/Desktop/picture2.png supersample 3 > transparentBackground true > color #5.2 #0000ff99 models > color #5.3 #ffff0099 models > color #5.4 #00fdff99 models > color #5.5 #8d81a999 models > color #5.6 #00ff0099 models > color #5.7 #ff260099 models > color #5.8 #ff00ff99 models > save /Users/payalpratap/Desktop/picture2.png supersample 3 > transparentBackground true [Repeated 1 time(s)] > save > /Users/payalpratap/Desktop/Structural_Biology/UCSF_Local_Directory/Fusion4_Tspan12_Bril/Chimera/Tspan12_Fzd4_Figure4.cxs > includeMaps true ——— End of log from Mon Jul 20 00:02:01 2026 ——— > view name session-start opened ChimeraX session > open 8WM9 8wm9 title: Fzd4/DEP complex [more info...] Chain information for 8wm9 #6 --- Chain | Description | UniProt A B | Frizzled-4 | FZD4_HUMAN 1-537 C | Segment polarity protein dishevelled homolog DVL-2 | DVL2_HUMAN 1-736 Non-standard residues in 8wm9 #6 --- Y01 — cholesterol hemisuccinate > matchmaker #6/A to #3/A No 'to' model specified > matchmaker #6/A to #1/A 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 Fusion_BRIL4_real_space_refined_140.pdb, chain A (#1) with 8wm9, chain A (#6), sequence alignment score = 1322.9 RMSD between 244 pruned atom pairs is 1.063 angstroms; (across all 297 pairs: 5.248) > hide #!5 models Drag select of 59 residues > select up 1284 atoms, 1319 bonds, 161 residues, 1 model selected > select up 2492 atoms, 2560 bonds, 320 residues, 1 model selected > select up 2667 atoms, 2750 bonds, 325 residues, 1 model selected > select up 5879 atoms, 6055 bonds, 729 residues, 1 model selected > select down 2667 atoms, 2750 bonds, 325 residues, 1 model selected > select down 2492 atoms, 2560 bonds, 320 residues, 1 model selected > color sel purple > select clear Drag select of 13 residues > select up 376 atoms, 381 bonds, 49 residues, 1 model selected > select up 646 atoms, 661 bonds, 84 residues, 1 model selected > select up 667 atoms, 681 bonds, 87 residues, 1 model selected > select up 1646 atoms, 1689 bonds, 217 residues, 1 model selected > select up 1671 atoms, 1714 bonds, 220 residues, 1 model selected > select up 2283 atoms, 2344 bonds, 298 residues, 1 model selected > select up 2377 atoms, 2440 bonds, 310 residues, 1 model selected > select up 2552 atoms, 2630 bonds, 315 residues, 1 model selected > select up 5879 atoms, 6055 bonds, 729 residues, 1 model selected > select down 2552 atoms, 2630 bonds, 315 residues, 1 model selected > select up 5879 atoms, 6055 bonds, 729 residues, 1 model selected > select down 2552 atoms, 2630 bonds, 315 residues, 1 model selected > color sel hot pink > color sel #942193ff > color sel #531b93ff > color sel #941751ff > color sel #942193ff > color sel #531b93ff > hide #!3 models > select ::name=""Y01"" 350 atoms, 380 bonds, 10 residues, 1 model selected > color sel #929000ff > color sel #73fdffff > color sel #7a81ffff > color sel #d4fb79ff > color sel #fffc79ff > show #!5 models > hide #!5 models > show #!3 models > color sel #8efa00ff > color sel #00fdffff > color sel #7a81ffff > color sel #76d6ffff > color sel #ff2600ff > color sel #797979ff > color sel #5e5e5eff > color sel #424242ff > color sel #212121ff > color sel #4f8f00ff > show #!4 models > hide #!4 models > open > /Users/payalpratap/Desktop/Structural_Biology/UCSF_Local_Directory/Fusion4_Tspan12_Bril/cryosparc/DeepEMhancer/cryosparc_P9_J329_006_volume_map_sharp_deepEMhancer_resampled.mrc Opened cryosparc_P9_J329_006_volume_map_sharp_deepEMhancer_resampled.mrc as #7, grid size 480,480,480, pixel 0.819, shown at level 0.000616, step 2, values float32 > volume #7 step 1 > volume #7 level 2.117 > volume #7 level 0.8984 > select #6/B:505 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 137 atoms, 140 bonds, 17 residues, 1 model selected > select up 646 atoms, 661 bonds, 84 residues, 1 model selected > select up 667 atoms, 681 bonds, 87 residues, 1 model selected > select up 1646 atoms, 1689 bonds, 217 residues, 1 model selected > select up 1671 atoms, 1714 bonds, 220 residues, 1 model selected > select up 2283 atoms, 2344 bonds, 298 residues, 1 model selected > select up 2377 atoms, 2440 bonds, 310 residues, 1 model selected > select up 2552 atoms, 2630 bonds, 315 residues, 1 model selected > select down 2377 atoms, 2440 bonds, 310 residues, 1 model selected > hide sel cartoons > color #7 #b2b2b298 models > hide #!7 models > show #!7 models > hide sel atoms > hide #!3 models > show #!3 models > save > /Users/payalpratap/Desktop/Structural_Biology/UCSF_Local_Directory/Fusion4_Tspan12_Bril/Chimera/Tspan12_Fzd4_Figure4.cxs > includeMaps true ——— End of log from Fri Jul 24 01:26:39 2026 ——— > view name session-start opened ChimeraX session > hide #!6 models > hide #!7 models > ui tool show ""Show Sequence Viewer"" [Repeated 1 time(s)] > sequence chain #3/B Alignment identifier is 3/B > select #3/B:65 14 atoms, 14 bonds, 1 residue, 1 model selected > select #3/B:64-65 31 atoms, 32 bonds, 2 residues, 1 model selected > select #3/B:66 16 atoms, 15 bonds, 1 residue, 1 model selected > select #3/B:65-66 30 atoms, 30 bonds, 2 residues, 1 model selected > select #3/B:65-66 30 atoms, 30 bonds, 2 residues, 1 model selected > select #3/B:65-66 30 atoms, 30 bonds, 2 residues, 1 model selected > select #3/B:65 14 atoms, 14 bonds, 1 residue, 1 model selected > select #3/B:65 14 atoms, 14 bonds, 1 residue, 1 model selected > show sel atoms > show #!2 models > style sel stick Changed 14 atom styles > select #2/A:300 14 atoms, 13 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 14 atom styles > style sel stick Changed 14 atom styles > color sel byhetero > select up 502 atoms, 512 bonds, 30 residues, 1 model selected > show sel atoms > style sel stick Changed 502 atom styles > color sel byhetero > select H 19035 atoms, 2534 residues, 3 models selected > delete atoms (#!2-3 & sel) > delete bonds (#!2-3 & sel) > select zone #2/B:65 4 #2/A Selected 3 atoms > select #3/B:64 10 atoms, 10 bonds, 1 residue, 1 model selected > select #3/B:64 10 atoms, 10 bonds, 1 residue, 1 model selected > select #3/B:81 4 atoms, 3 bonds, 1 residue, 1 model selected > select #3/B:81 4 atoms, 3 bonds, 1 residue, 1 model selected > select #3/B:84-85 11 atoms, 10 bonds, 2 residues, 1 model selected > select #3/B:84-85 11 atoms, 10 bonds, 2 residues, 1 model selected > select #3/B:84-85 11 atoms, 10 bonds, 2 residues, 1 model selected > select #3/B:84-85 11 atoms, 10 bonds, 2 residues, 1 model selected > select #3/B:84 4 atoms, 3 bonds, 1 residue, 1 model selected > select #3/B:84 4 atoms, 3 bonds, 1 residue, 1 model selected > select #3/B:101 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/B:101 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 8 atom styles > show #!7 models > volume #7 level 0.2571 > volume #7 level 0.706 > volume #7 level 1.54 > ui tool show ""Show Sequence Viewer"" > sequence chain #2/A Alignment identifier is 2/A > select #2/A:326 7 atoms, 6 bonds, 1 residue, 1 model selected > hide #!7 models > select #3/B:190 6 atoms, 5 bonds, 1 residue, 1 model selected > select #3/B:190 6 atoms, 5 bonds, 1 residue, 1 model selected > style sel stick Changed 6 atom styles > style sel stick Changed 6 atom styles > show sel atoms > select #2/A:326 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/A:223 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:223 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:256 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 8 atom styles > select #2/A:347 11 atoms, 11 bonds, 1 residue, 1 model selected > select #2/A:347 11 atoms, 11 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > show sel atoms > style sel stick Changed 11 atom styles > color sel red > select #3/B:26 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/B:26 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 8 atom styles > show #!7 models > volume #7 level 0.6419 > hide #!7 models > color sel red > select #3/B:49 7 atoms, 6 bonds, 1 residue, 1 model selected > select #3/B:49 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 7 atom styles > color sel red > select up 41 atoms, 40 bonds, 7 residues, 1 model selected > select down 7 atoms, 6 bonds, 1 residue, 1 model selected > hide #!3 models > show #!3 models > hide #!2 models > hide #!3 models > show #!3 models > show #!2 models > hide #!2 models > hide #!3 models > show #!3 models > show #!2 models > select #3/B:101 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/B:101 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > color sel red > show #!7 models > hide #!7 models > select #3/B:138 12 atoms, 12 bonds, 1 residue, 1 model selected > select #3/B:138 12 atoms, 12 bonds, 1 residue, 1 model selected > select #3/B:138 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 12 atom styles > color sel yellow > select #3/B:188 4 atoms, 3 bonds, 1 residue, 1 model selected > select #3/B:188 4 atoms, 3 bonds, 1 residue, 1 model selected > color sel yellow > hide #!3 models > show #!3 models > hide #!2 models > select #3/B:210 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/B:210 8 atoms, 7 bonds, 1 residue, 1 model selected > show #!2 models > select #2/A:223 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:223 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel red > style sel stick Changed 8 atom styles > show sel atoms > color sel byhetero > select #2/A:256 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:256 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel red > select > #2/A:188-190,213-243,250-275,296-298,300-329,341-365,384-390,392-437,445-461,482-499,504-521,523-542,544-566,568-572,578-602 2369 atoms, 2414 bonds, 297 residues, 1 model selected > select #2/A:342 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:342 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms [Repeated 1 time(s)] > color sel lime > style sel stick Changed 8 atom styles > color sel red > color sel byhetero > show #!7 models > select #2/A:417 11 atoms, 10 bonds, 1 residue, 1 model selected > select #2/A:417 11 atoms, 10 bonds, 1 residue, 1 model selected > hide #!7 models > show sel atoms > style sel stick Changed 11 atom styles > color sel red > show #!6 models > hide #!3 models > hide #!2 models > ui tool show ""Show Sequence Viewer"" > sequence chain #6/A Alignment identifier is 6/A > select #6/A:233 6 atoms, 5 bonds, 1 residue, 1 model selected > select #6/A:233 6 atoms, 5 bonds, 1 residue, 1 model selected > select #6/A:335 14 atoms, 15 bonds, 1 residue, 1 model selected > select #6/A:335 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > select zone #7/A:335 4 #2/A No atoms or surfaces specified > select zone #7/A:335 4 #6/C No atoms or surfaces specified > select zone #6/A:335 4 #6/C Selected 2 atoms > select #6/A:342 8 atoms, 7 bonds, 1 residue, 1 model selected > select #6/A:342 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select #6/A:417 11 atoms, 10 bonds, 1 residue, 1 model selected > select #6/A:417 11 atoms, 10 bonds, 1 residue, 1 model selected > select #6/A:445 7 atoms, 6 bonds, 1 residue, 1 model selected > select #6/A:445 7 atoms, 6 bonds, 1 residue, 1 model selected > select #6/A:488 4 atoms, 3 bonds, 1 residue, 1 model selected > select #6/A:488 4 atoms, 3 bonds, 1 residue, 1 model selected > select #6/A:497 6 atoms, 5 bonds, 1 residue, 1 model selected > select #6/A:497 6 atoms, 5 bonds, 1 residue, 1 model selected > select ::name=""Y01"" 350 atoms, 380 bonds, 10 residues, 1 model selected > select zone #6/Y01 4 #6/A No atoms or surfaces specified > select zone Y01 4 #6/A Missing or invalid ""near"" argument: invalid objects specifier > name frozen cholesterol sel > select zone cholesterol 4 #6/A Selected 32 atoms > info selection level residue residue id #6/A:253 name ARG index 252 residue id #6/A:257 name PHE index 256 residue id #6/A:264 name ILE index 263 residue id #6/A:267 name ILE index 266 residue id #6/A:274 name THR index 273 residue id #6/A:300 name THR index 299 residue id #6/A:304 name ILE index 303 residue id #6/A:307 name LEU index 306 residue id #6/A:311 name PHE index 310 residue id #6/A:312 name PHE index 311 residue id #6/A:344 name SER index 343 residue id #6/A:345 name SER index 344 residue id #6/A:349 name ILE index 348 residue id #6/A:352 name TRP index 351 residue id #6/A:363 name LEU index 362 residue id #6/A:366 name ARG index 365 residue id #6/A:507 name PHE index 506 > ui tool show Log > select up 154 atoms, 145 bonds, 17 residues, 1 model selected > color sel yellow > color sel byhetero > select ::name=""Y01"" 350 atoms, 380 bonds, 10 residues, 1 model selected > color sel byhetero > select zone cholesterol 5 #6/A Selected 133 atoms > show sel atoms > select up 291 atoms, 276 bonds, 35 residues, 1 model selected > show sel atoms > color sel byhetero > select #6/A:253 11 atoms, 10 bonds, 1 residue, 1 model selected > select #6/A:253 11 atoms, 10 bonds, 1 residue, 1 model selected > select > #3/B:10-45,53-58,65-87,90-106,127-135,145-157,165-171,179-181,189-194,206-213,218-239 1117 atoms, 1134 bonds, 150 residues, 1 model selected > show #!3 models > select #3/B:174 5 atoms, 4 bonds, 1 residue, 1 model selected > select #3/B:174-175 13 atoms, 12 bonds, 2 residues, 1 model selected > select #3/B:125 14 atoms, 15 bonds, 1 residue, 1 model selected > select #3/B:107-125 19 atoms, 19 bonds, 1 pseudobond, 2 residues, 2 models selected > show #!7 models > ui tool show ""Volume Viewer"" > volume #7 level 2.373 > volume #7 level 1.283 > select #3/B:134 11 atoms, 10 bonds, 1 residue, 1 model selected > select #3/B:134 11 atoms, 10 bonds, 1 residue, 1 model selected > hide #!6 models > hide #!7 models > show #!2 models > show sel atoms > style sel stick Changed 11 atom styles > select zone #2/B:134 5 #2/A Selected 1 atoms > select up 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 159 atoms, 160 bonds, 20 residues, 1 model selected > select up 2125 atoms, 2175 bonds, 269 residues, 1 model selected > select down 159 atoms, 160 bonds, 20 residues, 1 model selected > select down 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 159 atoms, 160 bonds, 20 residues, 1 model selected > show sel atoms > style sel stick Changed 159 atom styles > color sel byhetero > select #3/B:22 14 atoms, 15 bonds, 1 residue, 1 model selected > select #3/B:22 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 14 atom styles > show #!7 models > volume #7 level 1.027 > show #!6 models > hide #!2 models > hide #!7 models > select #6/C:444 14 atoms, 15 bonds, 1 residue, 1 model selected > select up 49 atoms, 50 bonds, 5 residues, 1 model selected > select up 660 atoms, 675 bonds, 89 residues, 1 model selected > show sel atoms > ui tool show ""Show Sequence Viewer"" > sequence chain #6/A Alignment identifier is 6/A > select #6/A:267 8 atoms, 7 bonds, 1 residue, 1 model selected > select #6/A:267 8 atoms, 7 bonds, 1 residue, 1 model selected > select #6/A:267 8 atoms, 7 bonds, 1 residue, 1 model selected > select #6/A:267 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel cyan > undo > show #!2 models > hide #!6 models > ui tool show ""Show Sequence Viewer"" > sequence chain #2/A Alignment identifier is 2/A > select #3/B:73 11 atoms, 11 bonds, 1 residue, 1 model selected > select #3/B:73 11 atoms, 11 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 11 atom styles > select #2/A:231 11 atoms, 11 bonds, 1 residue, 1 model selected > select #2/A:231 11 atoms, 11 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 11 atom styles > select #2/A:267 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:267 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 8 atom styles > select #2/A:264 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:264 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 8 atom styles > select #3/B:22 14 atoms, 15 bonds, 1 residue, 1 model selected > select #3/B:22 14 atoms, 15 bonds, 1 residue, 1 model selected > select #2/A:231 11 atoms, 11 bonds, 1 residue, 1 model selected > show #!7 models > hide #!7 models > select #3/B:75 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/B:75-76 16 atoms, 15 bonds, 2 residues, 1 model selected > show sel atoms > style sel stick Changed 16 atom styles > show #!7 models > hide #!7 models > select #2/A:267 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:267 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:250 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 12 atom styles > show #!6 models > show #!5 models > show #!4 models > hide #!4 models > hide #!5 models > hide #!2 models > hide #!6 models > combine #3 > hide #!3 models > show #!8 cartoons [Repeated 4 time(s)] > close #8 > combine #2 > hide #!8 models > show #!8 models Drag select of 56 residues > select up 761 atoms, 772 bonds, 101 residues, 1 model selected > select up 921 atoms, 941 bonds, 120 residues, 1 model selected > select down 761 atoms, 772 bonds, 101 residues, 1 model selected > select up 921 atoms, 941 bonds, 120 residues, 1 model selected > select down 761 atoms, 772 bonds, 101 residues, 1 model selected > select up 921 atoms, 941 bonds, 120 residues, 1 model selected > select up 8974 atoms, 9197 bonds, 1163 residues, 1 model selected > select down 921 atoms, 941 bonds, 120 residues, 1 model selected > color sel #ff2600ff > color sel #ff7e79ff Drag select of 35 residues > select up 340 atoms, 345 bonds, 44 residues, 1 model selected > select up 1655 atoms, 1692 bonds, 215 residues, 1 model selected > select up 8974 atoms, 9197 bonds, 1163 residues, 1 model selected > select down 1655 atoms, 1692 bonds, 215 residues, 1 model selected > color sel dark gray Drag select of 16 residues > select up 363 atoms, 363 bonds, 50 residues, 1 model selected > select up 1719 atoms, 1770 bonds, 228 residues, 1 model selected > select up 8974 atoms, 9197 bonds, 1163 residues, 1 model selected > select down 1719 atoms, 1770 bonds, 228 residues, 1 model selected > color sel dark gray > color sel gray > select clear Drag select of 46 residues > select up 555 atoms, 559 bonds, 74 residues, 1 model selected > select up 1719 atoms, 1770 bonds, 228 residues, 1 model selected > select up 8974 atoms, 9197 bonds, 1163 residues, 1 model selected > select down 1719 atoms, 1770 bonds, 228 residues, 1 model selected > select up 8974 atoms, 9197 bonds, 1163 residues, 1 model selected > select down 1719 atoms, 1770 bonds, 228 residues, 1 model selected > color sel #797979ff > color sel #5e5e5eff > color sel #424242ff > color sel #5e5e5eff > select clear Drag select of 6 atoms, 6 bonds, 21 residues, 1 pseudobonds > select up 553 atoms, 557 bonds, 1 pseudobond, 70 residues, 2 models selected > select up 3109 atoms, 3179 bonds, 1 pseudobond, 392 residues, 2 models selected > select up 8974 atoms, 9197 bonds, 5 pseudobonds, 1163 residues, 2 models selected > select up 8974 atoms, 9197 bonds, 5 pseudobonds, 1163 residues, 2 models selected > select up 43133 atoms, 44022 bonds, 5 pseudobonds, 4426 residues, 11 models selected > select up 43133 atoms, 44022 bonds, 5 pseudobonds, 4426 residues, 11 models selected > select down 8974 atoms, 9197 bonds, 5 pseudobonds, 1163 residues, 2 models selected > select down 5 pseudobonds, 1 model selected > select down 3109 atoms, 3179 bonds, 1 pseudobond, 392 residues, 2 models selected > color (#!8 & sel) lime > select clear Drag select of 7 residues > select up 110 atoms, 109 bonds, 22 residues, 1 model selected > select up 120 atoms, 119 bonds, 24 residues, 1 model selected > select up 128 atoms, 126 bonds, 25 residues, 1 model selected > select up 821 atoms, 847 bonds, 109 residues, 1 model selected > select up 826 atoms, 851 bonds, 110 residues, 1 model selected > select up 1570 atoms, 1614 bonds, 208 residues, 1 model selected > select up 8974 atoms, 9197 bonds, 1163 residues, 1 model selected > select down 1570 atoms, 1614 bonds, 208 residues, 1 model selected > color sel blue > select clear > hide #!8 atoms > select #3/B:49 7 atoms, 6 bonds, 1 residue, 1 model selected > select #3/B:49 7 atoms, 6 bonds, 1 residue, 1 model selected > color #8 red > undo > ui tool show ""Show Sequence Viewer"" > sequence chain #8/B Alignment identifier is 8/B > select #8/B:49 7 atoms, 6 bonds, 1 residue, 1 model selected > select #8/B:49 7 atoms, 6 bonds, 1 residue, 1 model selected > color sel red > select #8/B:65 7 atoms, 7 bonds, 1 residue, 1 model selected > select #8/B:65 7 atoms, 7 bonds, 1 residue, 1 model selected > color sel red > show sel atoms > style sel stick Changed 7 atom styles > color sel byhetero > color sel orange > color sel byhetero > color sel #ff9300ff > color sel #ff7e79ff > color sel #ff2600ff > color sel #d783ffff > color sel byhetero > select zone #8/B:64 5 #2/A Selected 4 atoms > select zone #8/B:64 5 #8/A Selected 4 atoms > show sel atoms > style sel sphere Changed 4 atom styles > show sel atoms > style sel stick Changed 4 atom styles > select up 18 atoms, 16 bonds, 2 residues, 1 model selected > show sel atoms > color sel byhetero > select zone #8/B:64 4 #8/A Selected 1 atoms > hide sel atoms > select up 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 250 atoms, 260 bonds, 30 residues, 1 model selected > select up 2125 atoms, 2175 bonds, 269 residues, 1 model selected > hide sel atoms Drag select of 3 atoms, 4 bonds, 5 residues > select up 439 atoms, 451 bonds, 55 residues, 1 model selected > select up 2874 atoms, 2942 bonds, 368 residues, 1 model selected > select up 2905 atoms, 2974 bonds, 371 residues, 1 model selected > hide sel atoms > select #8/B:49 7 atoms, 6 bonds, 1 residue, 1 model selected > color sel #d783ffff [Repeated 2 time(s)] > select #8/B:85 7 atoms, 6 bonds, 1 residue, 1 model selected > select #8/B:85 7 atoms, 6 bonds, 1 residue, 1 model selected > color sel #d783ffff [Repeated 1 time(s)] > select clear > select #8/B:101 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/B:101 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel #d783ffff [Repeated 1 time(s)] > show #!7 models > volume #7 level 0.7702 > hide #!7 models > select #8/B:104 11 atoms, 11 bonds, 1 residue, 1 model selected > select #8/B:138 12 atoms, 12 bonds, 1 residue, 1 model selected > select #8/B:138 12 atoms, 12 bonds, 1 residue, 1 model selected > color sel #d783ffff [Repeated 1 time(s)] > select > #8/B:10-45,53-58,65-87,90-106,127-135,145-157,165-171,179-181,189-194,206-213,218-239 1117 atoms, 1134 bonds, 150 residues, 1 model selected > select #8/B:188 4 atoms, 3 bonds, 1 residue, 1 model selected > select #8/B:188 4 atoms, 3 bonds, 1 residue, 1 model selected > color sel #d783ffff [Repeated 1 time(s)] > select > #8/B:10-45,53-58,65-87,90-106,127-135,145-157,165-171,179-181,189-194,206-213,218-239 1117 atoms, 1134 bonds, 150 residues, 1 model selected > select #8/B:80 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/B:79-80 16 atoms, 15 bonds, 2 residues, 1 model selected > select #8/B:79 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/B:79 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel #d783ffff [Repeated 1 time(s)] > select #8/B:78 4 atoms, 3 bonds, 1 residue, 1 model selected > select #8/B:78 4 atoms, 3 bonds, 1 residue, 1 model selected > color sel #d783ffff [Repeated 1 time(s)] > select clear > select #8/B:210 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/B:210 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/B:210 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel #d783ffff [Repeated 1 time(s)] > select #8/B:134 11 atoms, 10 bonds, 1 residue, 1 model selected > select #8/B:134 11 atoms, 10 bonds, 1 residue, 1 model selected > color sel #d783ffff [Repeated 1 time(s)] > style sel stick Changed 11 atom styles > show sel atoms > color sel byhetero > select zone #8/B:134 4 #8/A Nothing selected > select zone #8/B:134 5 #8/A Selected 1 atoms > show sel atoms [Repeated 1 time(s)] > style sel stick Changed 1 atom style > show sel atoms > style sel stick Changed 1 atom style > select zone #8/B:134 6 #8/A Selected 3 atoms > show sel atoms > select zone #8/B:134 10#8/A Missing or invalid ""range"" argument: Expected a number > show sel atoms [Repeated 1 time(s)] > select up 16 atoms, 15 bonds, 2 residues, 1 model selected > show sel atoms > hide sel atoms > select zone #8/B:134 4#8/A Missing or invalid ""range"" argument: Expected a number > select up 159 atoms, 160 bonds, 20 residues, 1 model selected > select down 16 atoms, 15 bonds, 2 residues, 1 model selected > select zone #8/B:134 4 #8/A Nothing selected > show #!8 atoms > hide #!8 atoms > select zone #8/B:134 5 #8/A Selected 1 atoms > select up 5 atoms, 4 bonds, 1 residue, 1 model selected > show sel atoms > select #8/B:134 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > open 9MAN 9man title: Structure of Norrin in complex with human Tspan12 large extracellular loop (Tspan12 LEL) [more info...] Chain information for 9man #9 --- Chain | Description | UniProt A B | Maltose/maltodextrin-binding periplasmic protein,Norrin | MALE_ECO57 -355-11, NDP_HUMAN 25-133 C D | Maltose/maltodextrin-binding periplasmic protein,Tetraspanin-12 | MALE_ECO57 -265-101, TSN12_HUMAN 115-224 > matchmaker #9/C to #8/B 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 copy of Fusion_BRIL4_real_space_refined_140_edit.pdb, chain B (#8) with 9man, chain C (#9), sequence alignment score = 387.9 RMSD between 76 pruned atom pairs is 0.920 angstroms; (across all 85 pairs: 1.671) > select #8/A:288 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 159 atoms, 160 bonds, 20 residues, 1 model selected > show sel atoms > color sel byhetero > select #8/B:78 4 atoms, 3 bonds, 1 residue, 1 model selected > select #8/B:78 4 atoms, 3 bonds, 1 residue, 1 model selected > color sel orange red > hide #9 models > select #8/A:253 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 11 atom styles > color sel byhetero > show #!7 models > volume #7 level 1.091 > show #!6 models > select add #6 5890 atoms, 6065 bonds, 4 pseudobonds, 730 residues, 4 models selected > hide sel atoms > select add #7 5890 atoms, 6065 bonds, 4 pseudobonds, 730 residues, 6 models selected > hide #!6 models > hide #!7 models > select #8/A:253 11 atoms, 10 bonds, 1 residue, 1 model selected > select #8/A:253 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > show #!6 models > show #!7 models > select #8/B:18 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/B:18 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/B:23 8 atoms, 7 bonds, 1 residue, 1 model selected > hide #!7 models > select #8/B:22 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 14 atom styles > show #!7 models > hide #!8 models > show #!8 models > hide #!7 models > select #8/B:147 7 atoms, 6 bonds, 1 residue, 1 model selected > select #8/B:147 7 atoms, 6 bonds, 1 residue, 1 model selected > color sel lime > select clear > select #8/A:289 9 atoms, 8 bonds, 1 residue, 1 model selected > select #8/B:142 11 atoms, 10 bonds, 1 residue, 1 model selected > style sel stick Changed 11 atom styles > show sel atoms > color sel byhetero > hide #!6 models > select #8/A:239 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 8 atom styles > select #8/B:79 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 8 atom styles > select > #8/B:10-45,53-58,65-87,90-106,127-135,145-157,165-171,179-181,189-194,206-213,218-239 1117 atoms, 1134 bonds, 150 residues, 1 model selected > select #8/B:148-149 15 atoms, 15 bonds, 2 residues, 1 model selected > select #8/B:148-149 15 atoms, 15 bonds, 2 residues, 1 model selected > select #8/B:148 10 atoms, 10 bonds, 1 residue, 1 model selected > select #8/B:148 10 atoms, 10 bonds, 1 residue, 1 model selected > select #8/B:147 7 atoms, 6 bonds, 1 residue, 1 model selected > select #8/B:147 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 7 atom styles > select #8/B:85 7 atoms, 6 bonds, 1 residue, 1 model selected > style sel stick Changed 7 atom styles > show sel atoms > select #8/B:95 14 atoms, 15 bonds, 1 residue, 1 model selected > select #8/B:95 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 14 atom styles > show #!7 models > hide #!8 models > show #!8 models > hide #!7 models > ui tool show ""Show Sequence Viewer"" > sequence chain #8/A Alignment identifier is 8/A > select #8/A:293 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/A:293 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel red > color sel byhetero > select #8/A:298-299 17 atoms, 16 bonds, 2 residues, 1 model selected > select #8/A:298-299 17 atoms, 16 bonds, 2 residues, 1 model selected > select #8/A:298 9 atoms, 8 bonds, 1 residue, 1 model selected > select #8/A:298 9 atoms, 8 bonds, 1 residue, 1 model selected > color sel red > show sel atoms > style sel stick Changed 9 atom styles > select #8/B:65 7 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > show #!1 models > hide #!8 models > select #8/B:26 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/B:26 8 atoms, 7 bonds, 1 residue, 1 model selected > hide #!1 models > show #!8 models > show sel atoms > style sel stick Changed 8 atom styles > select #8/A:232 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 8 atom styles > select zone #8/B:26 5 #8/A Nothing selected > select zone #8/B:26 10 #8/A Selected 12 atoms > select zone #8/B:26 5 #8/A Nothing selected > show #!8 atoms > hide #!8 atoms > select zone #8/B:26 7 #8/A Nothing selected > undo [Repeated 1 time(s)] > select zone #8/B:26 7 #8/A Nothing selected > select zone #8/B:26 8 #8/A Selected 3 atoms > show #!7 models > select #8/B:187 7 atoms, 7 bonds, 1 residue, 1 model selected > select #8/B:187 7 atoms, 7 bonds, 1 residue, 1 model selected > select #8/B:190 6 atoms, 5 bonds, 1 residue, 1 model selected > select #8/B:190 6 atoms, 5 bonds, 1 residue, 1 model selected > hide #!7 models > color sel red > show #9 models > hide #9 models > select #8/B:81 4 atoms, 3 bonds, 1 residue, 1 model selected > select #8/B:81 4 atoms, 3 bonds, 1 residue, 1 model selected > select #8/B:101 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/B:101 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/B:161 4 atoms, 3 bonds, 1 residue, 1 model selected > select #8/B:161 4 atoms, 3 bonds, 1 residue, 1 model selected > color sel cyan > select #8/B:27 6 atoms, 5 bonds, 1 residue, 1 model selected > select #8/B:27 6 atoms, 5 bonds, 1 residue, 1 model selected > color sel cyan > save > /Users/payalpratap/Desktop/Structural_Biology/UCSF_Local_Directory/Fusion4_Tspan12_Bril/Chimera/Tspan12_Fzd4_FEVR_mutants.cxs > includeMaps true ——— End of log from Mon Jul 27 21:06:11 2026 ——— > view name session-start opened ChimeraX session > select #8/B:101 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/B:101 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/B:210 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/B:210 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/B:44 7 atoms, 6 bonds, 1 residue, 1 model selected > select #8/B:44 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 7 atom styles > color sel #ebade7ff > color sel #fd5af1ff > color sel #f3d5f3ff > color sel #ffc2c2ff > color sel #ebade7ff > select clear > color #!8 byhetero > select #8/B:81 4 atoms, 3 bonds, 1 residue, 1 model selected > select #8/B:81 4 atoms, 3 bonds, 1 residue, 1 model selected > color sel hot pink > color sel magenta > color sel #ebade7ff [Repeated 1 time(s)] > color sel #ff8ad8ff > select #8/B:44 7 atoms, 6 bonds, 1 residue, 1 model selected > color sel #ff8ad8ff [Repeated 1 time(s)] > select clear > color #!8 byhetero > select #8/A:347 11 atoms, 11 bonds, 1 residue, 1 model selected > select #8/A:347 11 atoms, 11 bonds, 1 residue, 1 model selected > color sel blue > color sel hot pink > select > #8/B:10-45,53-58,65-87,90-106,127-135,145-157,165-171,179-181,189-194,206-213,218-239 1117 atoms, 1134 bonds, 150 residues, 1 model selected > select #8/B:26 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/B:26 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel #ff8ad8ff [Repeated 1 time(s)] > select #8/B:96 12 atoms, 12 bonds, 1 residue, 1 model selected > select #8/B:96 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 12 atom styles > color sel #ff8ad8ff [Repeated 1 time(s)] > color sel byhetero > select #8/B:125 14 atoms, 15 bonds, 1 residue, 1 model selected > select #8/B:125 14 atoms, 15 bonds, 1 residue, 1 model selected > select #8/B:188 4 atoms, 3 bonds, 1 residue, 1 model selected > select #8/B:188 4 atoms, 3 bonds, 1 residue, 1 model selected > color sel yellow > color sel #ff8ad8ff [Repeated 1 time(s)] > select #8/B:146 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/B:146 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 8 atom styles > select #8/B:201 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/B:201 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel #ff8ad8ff [Repeated 1 time(s)] > select clear > select #8/B:49 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 7 atom styles > select #8/B:44 7 atoms, 6 bonds, 1 residue, 1 model selected > color sel #0433ffff > color sel byhetero > select clear > select #8/B:44 7 atoms, 6 bonds, 1 residue, 1 model selected > select #8/B:146 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/B:146 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel #ff8ad8ff > select #8/B:19 5 atoms, 4 bonds, 1 residue, 1 model selected > select #8/B:19 5 atoms, 4 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 5 atom styles > color sel #ff8ad8ff [Repeated 1 time(s)] > hide sel atoms > select clear > select > #8/B:10-45,53-58,65-87,90-106,127-135,145-157,165-171,179-181,189-194,206-213,218-239 1117 atoms, 1134 bonds, 150 residues, 1 model selected > select > #8/A:188-190,213-243,250-275,296-298,300-329,341-365,384-390,392-437,445-461,482-499,504-521,523-542,544-566,568-572,578-602 2369 atoms, 2414 bonds, 297 residues, 1 model selected > select #8/A:226-227 19 atoms, 20 bonds, 2 residues, 1 model selected > select #8/A:226-227 19 atoms, 20 bonds, 2 residues, 1 model selected > select #8/A:226 14 atoms, 15 bonds, 1 residue, 1 model selected > select #8/A:226 14 atoms, 15 bonds, 1 residue, 1 model selected > color sel #ff8ad8ff [Repeated 1 time(s)] > select #8/B:205 4 atoms, 3 bonds, 1 residue, 1 model selected > select #8/B:205 4 atoms, 3 bonds, 1 residue, 1 model selected > color sel #ff8ad8ff [Repeated 1 time(s)] > select #8/B:181 6 atoms, 5 bonds, 1 residue, 1 model selected > select #8/B:181 6 atoms, 5 bonds, 1 residue, 1 model selected > color sel #ff8ad8ff [Repeated 2 time(s)] > select #8/B:189 6 atoms, 5 bonds, 1 residue, 1 model selected > select #8/B:189 6 atoms, 5 bonds, 1 residue, 1 model selected > color sel #ff8ad8ff [Repeated 1 time(s)] > select > #8/A:188-190,213-243,250-275,296-298,300-329,341-365,384-390,392-437,445-461,482-499,504-521,523-542,544-566,568-572,578-602 2369 atoms, 2414 bonds, 297 residues, 1 model selected > select > #8/A:188-190,213-243,250-275,296-298,300-329,341-365,384-390,392-437,445-461,482-499,504-521,523-542,544-566,568-572,578-602 2369 atoms, 2414 bonds, 297 residues, 1 model selected > select > #8/A:188-190,213-243,250-275,296-298,300-329,341-365,384-390,392-437,445-461,482-499,504-521,523-542,544-566,568-572,578-602 2369 atoms, 2414 bonds, 297 residues, 1 model selected > select #8/A:342 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/A:342 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel #ff8ad8ff [Repeated 1 time(s)] > select #8/A:256 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/A:256-257 19 atoms, 19 bonds, 2 residues, 1 model selected > select #8/A:256 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/A:256 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel #ff8ad8ff [Repeated 1 time(s)] > undo [Repeated 6 time(s)] > select #8/A:256 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/A:256 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel #ff8ad8ff [Repeated 1 time(s)] > show sel atoms > select zone #8/A:256 5 #8 Selected 56 atoms > select #8/A:326 7 atoms, 6 bonds, 1 residue, 1 model selected > select #8/A:326 7 atoms, 6 bonds, 1 residue, 1 model selected > color sel #ff8ad8ff [Repeated 1 time(s)] > select #8/A:273 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/A:273 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel #ff8ad8ff [Repeated 3 time(s)] > color sel #76d6ffff > show sel atoms > style sel stick Changed 8 atom styles > color sel #ff8ad8ff > select #8/A:211 12 atoms, 12 bonds, 1 residue, 1 model selected > select #8/A:211 12 atoms, 12 bonds, 1 residue, 1 model selected > color sel #ff8ad8ff [Repeated 3 time(s)] > color sel #ff40ffff > color sel #ff2600ff > color sel #009051ff > color sel #000000ff > color sel #ff8ad8ff > show sel atoms > style sel stick Changed 12 atom styles > select #8/A:293 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel #ff8ad8ff > select #8/A:298 9 atoms, 8 bonds, 1 residue, 1 model selected > color sel #ff8ad8ff > color sel byhetero > select #8/A:223 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/A:223 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/A:223 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel #000000ff > style sel stick Changed 8 atom styles > show sel atoms > color sel #ff8ad8ff [Repeated 1 time(s)] > color sel byhetero > select #8/A:226 14 atoms, 15 bonds, 1 residue, 1 model selected > select #8/A:226-227 19 atoms, 20 bonds, 2 residues, 1 model selected > select #8/A:226-227 19 atoms, 20 bonds, 2 residues, 1 model selected > select #8/A:226 14 atoms, 15 bonds, 1 residue, 1 model selected > select #8/A:226 14 atoms, 15 bonds, 1 residue, 1 model selected > color sel #000000ff > style sel stick Changed 14 atom styles > show sel atoms > color sel #fd5af1ff > color sel byhetero > select #8/A:228 6 atoms, 5 bonds, 1 residue, 1 model selected > select #8/A:228 6 atoms, 5 bonds, 1 residue, 1 model selected > color sel #fd5af1ff [Repeated 1 time(s)] > color sel #f3d5f3ff > color sel #ebade7ff > select #8/A:226 14 atoms, 15 bonds, 1 residue, 1 model selected > select up 251 atoms, 258 bonds, 31 residues, 1 model selected > select down 14 atoms, 15 bonds, 1 residue, 1 model selected > color sel #f3d5f3ff > color sel #ebade7ff > show sel atoms [Repeated 3 time(s)] > style sel stick Changed 14 atom styles > select #8/A:228 6 atoms, 5 bonds, 1 residue, 1 model selected > style sel stick Changed 6 atom styles > show sel cartoons > style sel stick Changed 6 atom styles > hide sel atoms > style sel stick Changed 6 atom styles > style sel stick Changed 6 atom styles > select #8/A:228 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel cartoons [Repeated 4 time(s)] > style sel stick Changed 6 atom styles > style sel stick Changed 6 atom styles > select up 251 atoms, 258 bonds, 31 residues, 1 model selected > select down 6 atoms, 5 bonds, 1 residue, 1 model selected > select #8/A:228 6 atoms, 5 bonds, 1 residue, 1 model selected > select #8/A:228 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select #8/A:229 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/A:229 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel #ebade7ff [Repeated 1 time(s)] > show sel atoms > style sel stick Changed 8 atom styles > select #8/A:232-233 14 atoms, 13 bonds, 2 residues, 1 model selected > select #8/A:232-233 14 atoms, 13 bonds, 2 residues, 1 model selected > select #8/A:232 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/A:232 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel #ebade7ff [Repeated 2 time(s)] > color sel #fd5af1ff > color sel #ebade7ff > select #8/A:234 7 atoms, 6 bonds, 1 residue, 1 model selected > select #8/A:234 7 atoms, 6 bonds, 1 residue, 1 model selected > color sel #ebade7ff [Repeated 1 time(s)] > style sel stick Changed 7 atom styles > show sel atoms > color sel byhetero > select #8/A:237 7 atoms, 6 bonds, 1 residue, 1 model selected > select #8/A:237 7 atoms, 6 bonds, 1 residue, 1 model selected > color sel #ebade7ff [Repeated 1 time(s)] > show sel atoms > style sel stick Changed 7 atom styles > color sel byhetero > select #8/A:239 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel #ebade7ff > color sel byhetero > select #8/A:245 6 atoms, 5 bonds, 1 residue, 1 model selected > select #8/A:245-246 12 atoms, 11 bonds, 2 residues, 1 model selected > color sel #ebade7ff [Repeated 1 time(s)] > show sel atoms > style sel stick Changed 12 atom styles > undo [Repeated 4 time(s)] > redo > select #8/A:245 6 atoms, 5 bonds, 1 residue, 1 model selected > select #8/A:245 6 atoms, 5 bonds, 1 residue, 1 model selected > select #8/A:245 6 atoms, 5 bonds, 1 residue, 1 model selected > color sel #ebade7ff [Repeated 1 time(s)] > show sel cartoons > show sel atoms > style sel stick Changed 6 atom styles > color sel byhetero > select zone #8/A:245 5 #8 Selected 40 atoms > select zone #8/A:245 5 #8/B Nothing selected > select #8/A:293 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/A:293 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/A:253 11 atoms, 10 bonds, 1 residue, 1 model selected > select #8/A:253 11 atoms, 10 bonds, 1 residue, 1 model selected > color sel #000000ff > color sel #ff8ad8ff > color sel #fd5af1ff > color sel #ebade7ff > color sel byhetero > select #8/A:293 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/A:293 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/A:298 9 atoms, 8 bonds, 1 residue, 1 model selected > select #8/A:298 9 atoms, 8 bonds, 1 residue, 1 model selected > select #8/A:302 6 atoms, 5 bonds, 1 residue, 1 model selected > select #8/A:302 6 atoms, 5 bonds, 1 residue, 1 model selected > color sel #ebade7ff [Repeated 1 time(s)] > select #8/A:322 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/A:322 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel #ebade7ff [Repeated 1 time(s)] > show sel atoms > select #8/A:347 11 atoms, 11 bonds, 1 residue, 1 model selected > color sel #ebade7ff [Repeated 1 time(s)] > show sel atoms > select #8/A:342 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel #ebade7ff [Repeated 1 time(s)] > show sel atoms > color sel byhetero > select #8/A:326 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 7 atom styles > color sel #ebade7ff [Repeated 1 time(s)] > select #8/A:256 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel #ebade7ff [Repeated 1 time(s)] > select #8/B:96 12 atoms, 12 bonds, 1 residue, 1 model selected > color sel #ebade7ff [Repeated 1 time(s)] > select #8/B:101 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel #ebade7ff [Repeated 1 time(s)] > show sel atoms > style sel stick Changed 8 atom styles > select clear > select #8/B:85 7 atoms, 6 bonds, 1 residue, 1 model selected > color sel #ebade7ff [Repeated 1 time(s)] > color sel byhetero > select #8/B:81 4 atoms, 3 bonds, 1 residue, 1 model selected > color sel #ebade7ff [Repeated 1 time(s)] > style sel stick Changed 4 atom styles > style sel stick Changed 4 atom styles > show sel atoms [Repeated 3 time(s)] > select #8/B:78 4 atoms, 3 bonds, 1 residue, 1 model selected > color sel #ebade7ff [Repeated 1 time(s)] > select #8/B:79 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel #ebade7ff [Repeated 1 time(s)] > color sel byhetero > select #8/B:65 7 atoms, 7 bonds, 1 residue, 1 model selected > color sel #ebade7ff > color sel byhetero > select #8/B:26 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel #ebade7ff > color sel byhetero > select #8/B:27 6 atoms, 5 bonds, 1 residue, 1 model selected > select #8/A:325 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/A:325 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel #929000ff > color sel #ebade7ff > show sel atoms > select #8/A:328 11 atoms, 11 bonds, 1 residue, 1 model selected > select #8/A:328 11 atoms, 11 bonds, 1 residue, 1 model selected > color sel #ebade7ff [Repeated 1 time(s)] > show sel atoms > style sel stick Changed 11 atom styles > select #8/A:339 5 atoms, 4 bonds, 1 residue, 1 model selected > select #8/A:339 5 atoms, 4 bonds, 1 residue, 1 model selected > color sel #ebade7ff [Repeated 1 time(s)] > show sel atoms > style sel stick Changed 5 atom styles > select #8/A:342 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/A:342 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel #ebade7ff [Repeated 1 time(s)] > show sel atoms > color sel byhetero > select #8/A:344 6 atoms, 5 bonds, 1 residue, 1 model selected > select #8/A:344 6 atoms, 5 bonds, 1 residue, 1 model selected > color sel #ebade7ff [Repeated 1 time(s)] > show sel atoms > style sel stick Changed 6 atom styles > select #8/A:347 11 atoms, 11 bonds, 1 residue, 1 model selected > select #8/A:347 11 atoms, 11 bonds, 1 residue, 1 model selected > color sel #ebade7ff [Repeated 2 time(s)] > show sel atoms [Repeated 1 time(s)] > color sel byhetero > select #8/A:348 10 atoms, 10 bonds, 1 residue, 1 model selected > select #8/A:348 10 atoms, 10 bonds, 1 residue, 1 model selected > color sel #ebade7ff [Repeated 1 time(s)] > show sel atoms > show sel cartoons > style sel stick Changed 10 atom styles > color sel byhetero > select zone #8/A:348 5 #8/B Nothing selected > select #8/A:358 9 atoms, 8 bonds, 1 residue, 1 model selected > select #8/A:358 9 atoms, 8 bonds, 1 residue, 1 model selected > color sel #ebade7ff > show sel atoms > style sel stick Changed 9 atom styles > color sel byhetero > select #8/A:377 6 atoms, 5 bonds, 1 residue, 1 model selected > select #8/A:377 6 atoms, 5 bonds, 1 residue, 1 model selected > color sel #ebade7ff [Repeated 1 time(s)] > show sel atoms > style sel stick Changed 6 atom styles > color sel byhetero > select #8/A:302 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > select #8/A:394 7 atoms, 7 bonds, 1 residue, 1 model selected > select #8/A:394 7 atoms, 7 bonds, 1 residue, 1 model selected > color sel #ebade7ff [Repeated 1 time(s)] > show sel atoms > style sel stick Changed 7 atom styles > color sel byhetero [Repeated 2 time(s)] > select #8/A:417 11 atoms, 10 bonds, 1 residue, 1 model selected > select #8/A:417 11 atoms, 10 bonds, 1 residue, 1 model selected > color sel #000000ff > color sel #ebade7ff > style sel stick Changed 11 atom styles > show sel atoms > color sel byhetero > select #8/A:420 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/A:420 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel #ebade7ff [Repeated 1 time(s)] > show sel atoms > style sel stick Changed 8 atom styles > select #8/A:540 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/A:540 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel #000000ff > color sel #ebade7ff > style sel stick Changed 8 atom styles > show sel atoms > color sel byhetero > select #8/A:543 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/A:543 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel #ebade7ff [Repeated 1 time(s)] > style sel stick Changed 8 atom styles > show sel atoms > color sel byhetero > select #8/A:548 7 atoms, 6 bonds, 1 residue, 1 model selected > select #8/A:548-549 15 atoms, 14 bonds, 2 residues, 1 model selected > color sel #ebade7ff [Repeated 1 time(s)] > show sel atoms > style sel stick Changed 15 atom styles > color sel byhetero > select #8/A:551 7 atoms, 6 bonds, 1 residue, 1 model selected > select #8/A:551 7 atoms, 6 bonds, 1 residue, 1 model selected > color sel #ebade7ff [Repeated 1 time(s)] > style sel stick Changed 7 atom styles > hide sel atoms > color sel byhetero > show sel atoms > select #8/A:576 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/A:576 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel #ebade7ff [Repeated 1 time(s)] > show sel atoms > style sel stick Changed 8 atom styles > color sel byhetero > select #8/A:595 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/A:594-595 12 atoms, 11 bonds, 2 residues, 1 model selected > select #8/A:594 4 atoms, 3 bonds, 1 residue, 1 model selected > select #8/A:594 4 atoms, 3 bonds, 1 residue, 1 model selected > color sel #ebade7ff [Repeated 1 time(s)] > select #8/A:598 4 atoms, 3 bonds, 1 residue, 1 model selected > select #8/A:598 4 atoms, 3 bonds, 1 residue, 1 model selected > color sel #ebade7ff [Repeated 1 time(s)] > select #8/A:603 6 atoms, 5 bonds, 1 residue, 1 model selected > select #8/A:603 6 atoms, 5 bonds, 1 residue, 1 model selected > color sel #ebade7ff [Repeated 2 time(s)] > style sel stick Changed 6 atom styles > show sel atoms > color sel byhetero > save > /Users/payalpratap/Desktop/Structural_Biology/UCSF_Local_Directory/Fusion4_Tspan12_Bril/Chimera/Tspan12_Fzd4_FEVR_mutants.cxs > includeMaps true > hide sel atoms [Repeated 1 time(s)] > select up 984 atoms, 1004 bonds, 123 residues, 1 model selected > select up 993 atoms, 1012 bonds, 124 residues, 1 model selected > select up 3109 atoms, 3179 bonds, 392 residues, 1 model selected > select up 8974 atoms, 9197 bonds, 1163 residues, 1 model selected > select up 46199 atoms, 47185 bonds, 4803 residues, 11 models selected > select up 46199 atoms, 47185 bonds, 4803 residues, 11 models selected > select up 46199 atoms, 47185 bonds, 4803 residues, 11 models selected > select up 46199 atoms, 47185 bonds, 4803 residues, 11 models selected > hide sel & #!8 atoms > undo > select clear > select #8/B:146 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/B:146 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/B:81 4 atoms, 3 bonds, 1 residue, 1 model selected > select #8/B:81 4 atoms, 3 bonds, 1 residue, 1 model selected > color sel #ebade7ff [Repeated 2 time(s)] > select > #8/B:10-45,53-58,65-87,90-106,127-135,145-157,165-171,179-181,189-194,206-213,218-239 1117 atoms, 1134 bonds, 150 residues, 1 model selected > select #8/B:39 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/B:39 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/B:42 7 atoms, 6 bonds, 1 residue, 1 model selected > select #8/B:42 7 atoms, 6 bonds, 1 residue, 1 model selected > select #8/B:84 4 atoms, 3 bonds, 1 residue, 1 model selected > select #8/B:84 4 atoms, 3 bonds, 1 residue, 1 model selected > color sel #ebade7ff [Repeated 1 time(s)] > style sel stick Changed 4 atom styles > show sel atoms [Repeated 2 time(s)] > style sel stick Changed 4 atom styles > style sel stick Changed 4 atom styles > show sel atoms > hide sel atoms [Repeated 2 time(s)] > select #8/B:19 5 atoms, 4 bonds, 1 residue, 1 model selected > color sel #ebade7ff [Repeated 1 time(s)] > select #8/A:273 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel #ebade7ff > select #8/A:223 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel #ebade7ff > color sel byhetero > select #8/A:273 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel byhetero > select #8/B:146 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel #ebade7ff > color sel byhetero > select #8/B:210 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel #ebade7ff > select #8/B:189 6 atoms, 5 bonds, 1 residue, 1 model selected > color sel #ebade7ff > select add #8/B:188 10 atoms, 8 bonds, 2 residues, 1 model selected > select add #8/B:181 16 atoms, 13 bonds, 3 residues, 1 model selected > select add #8/B:201 24 atoms, 20 bonds, 4 residues, 1 model selected > color sel #ebade7ff > select add #8/B:205 28 atoms, 23 bonds, 5 residues, 1 model selected > color sel #ebade7ff > select clear > select #8/B:190 6 atoms, 5 bonds, 1 residue, 1 model selected > color sel #256af7ff > color sel blue > select clear > select #8/B:134 11 atoms, 10 bonds, 1 residue, 1 model selected > color sel #ebade7ff > select add #8/B:49 18 atoms, 16 bonds, 2 residues, 1 model selected > color sel #ebade7ff > select add #8/B:210 26 atoms, 23 bonds, 3 residues, 1 model selected > color sel #ebade7ff > color sel byhetero > select clear > select #8/A:298 9 atoms, 8 bonds, 1 residue, 1 model selected > color sel #ebade7ff > color sel byhetero > select add #8/A:293 17 atoms, 15 bonds, 2 residues, 1 model selected > select add #8/A:214 23 atoms, 20 bonds, 3 residues, 1 model selected > select subtract #8/A:293 15 atoms, 13 bonds, 2 residues, 1 model selected > select down 15 atoms, 13 bonds, 2 residues, 1 model selected > select up 272 atoms, 278 bonds, 34 residues, 1 model selected > select up 2125 atoms, 2175 bonds, 269 residues, 1 model selected > select up 2136 atoms, 2186 bonds, 270 residues, 1 model selected > select clear > select #8/A:226 14 atoms, 15 bonds, 1 residue, 1 model selected > color sel byhetero > select clear > save > /Users/payalpratap/Desktop/Structural_Biology/UCSF_Local_Directory/Fusion4_Tspan12_Bril/Chimera/Tspan12_Fzd4_FEVR_mutants.cxs > includeMaps true > hide #!8 atoms > show #!8 atoms > undo [Repeated 1 time(s)] > save > /Users/payalpratap/Desktop/Structural_Biology/UCSF_Local_Directory/Fusion4_Tspan12_Bril/Chimera/Tspan12_Fzd4_FEVR_mutants.cxs > includeMaps true ——— End of log from Tue Aug 4 09:23:10 2026 ——— > view name session-start opened ChimeraX session > select #8/B:184 11 atoms, 10 bonds, 1 residue, 1 model selected > select #8/B:184 11 atoms, 10 bonds, 1 residue, 1 model selected > color sel #ebade7ff > undo > select #8/B:26 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/B:26 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/A:279 11 atoms, 10 bonds, 1 residue, 1 model selected > select #8/A:273-274 15 atoms, 14 bonds, 2 residues, 1 model selected > select #8/A:273-274 15 atoms, 14 bonds, 2 residues, 1 model selected > select #8/A:273 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/A:273 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/A:253 11 atoms, 10 bonds, 1 residue, 1 model selected > select #8/A:253 11 atoms, 10 bonds, 1 residue, 1 model selected > color sel cyan > undo > select #8/B:71 6 atoms, 5 bonds, 1 residue, 1 model selected > select #8/B:71 6 atoms, 5 bonds, 1 residue, 1 model selected > color sel orange > show sel atoms > style sel stick Changed 6 atom styles > select #8/B:72 6 atoms, 5 bonds, 1 residue, 1 model selected > select #8/B:72 6 atoms, 5 bonds, 1 residue, 1 model selected > style sel stick Changed 6 atom styles > show sel atoms > color sel byhetero > select up 165 atoms, 167 bonds, 23 residues, 1 model selected > color sel byhetero > select #8/B:144 11 atoms, 10 bonds, 1 residue, 1 model selected > select #8/B:145 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 14 atom styles > select up 128 atoms, 135 bonds, 13 residues, 1 model selected > select add #8/B:143 140 atoms, 147 bonds, 14 residues, 1 model selected > select add #8/B:144 151 atoms, 157 bonds, 15 residues, 1 model selected > select add #8/B:141 158 atoms, 164 bonds, 16 residues, 1 model selected > show sel atoms > style sel stick Changed 158 atom styles > select #8/A:289 9 atoms, 8 bonds, 1 residue, 1 model selected > color sel #ebade7ff [Repeated 1 time(s)] > color sel byhetero > show #!7 models > hide #!7 models > hide sel atoms [Repeated 3 time(s)] > select add #8 8974 atoms, 9197 bonds, 5 pseudobonds, 1163 residues, 2 models selected > hide sel atoms > select #8/B:71 6 atoms, 5 bonds, 1 residue, 1 model selected > color sel blue > select #8/B:27 6 atoms, 5 bonds, 1 residue, 1 model selected > color sel blue > select #8/B:161 4 atoms, 3 bonds, 1 residue, 1 model selected > color sel blue > select clear > select #8/A:293 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel #ebade7ff [Repeated 1 time(s)] > select #8/A:211 12 atoms, 12 bonds, 1 residue, 1 model selected > color sel #ebade7ff [Repeated 1 time(s)] > select #8/B:147 7 atoms, 6 bonds, 1 residue, 1 model selected > color sel #0433ffff > select clear > select #8/B:147 7 atoms, 6 bonds, 1 residue, 1 model selected > color sel blue > select clear > undo [Repeated 7 time(s)] > redo > undo [Repeated 3 time(s)]No undo action is available > redo [Repeated 10 time(s)]No redo action is available > save > /Users/payalpratap/Desktop/Structural_Biology/UCSF_Local_Directory/Fusion4_Tspan12_Bril/Chimera/Tspan12_Fzd4_FEVR_mutants.cxs > includeMaps true ——— End of log from Tue Aug 4 16:40:37 2026 ——— > view name session-start opened ChimeraX session > lighting flat Drag select of 447 residues > select up 3967 atoms, 4054 bonds, 521 residues, 1 model selected > select up 4295 atoms, 4404 bonds, 563 residues, 1 model selected > select up 8974 atoms, 9197 bonds, 1163 residues, 1 model selected > select down 4295 atoms, 4404 bonds, 563 residues, 1 model selected > hide sel cartoons > save /Users/payalpratap/Desktop/mutants.png supersample 3 > transparentBackground true > select #8/A:417 11 atoms, 10 bonds, 1 residue, 1 model selected > select add #8/A:420 19 atoms, 17 bonds, 2 residues, 1 model selected > select add #8/A:328 30 atoms, 28 bonds, 3 residues, 1 model selected > select add #8/A:326 37 atoms, 34 bonds, 4 residues, 1 model selected > select add #8/A:325 45 atoms, 41 bonds, 5 residues, 1 model selected > select add #8/A:339 50 atoms, 45 bonds, 6 residues, 1 model selected > select add #8/A:540 58 atoms, 52 bonds, 7 residues, 1 model selected > select add #8/A:543 66 atoms, 59 bonds, 8 residues, 1 model selected > select add #8/A:549 74 atoms, 66 bonds, 9 residues, 1 model selected > select add #8/A:548 81 atoms, 72 bonds, 10 residues, 1 model selected > select add #8/A:551 88 atoms, 78 bonds, 11 residues, 1 model selected > select add #8/A:394 95 atoms, 85 bonds, 12 residues, 1 model selected > select add #8/A:358 104 atoms, 93 bonds, 13 residues, 1 model selected > select add #8/A:226 118 atoms, 108 bonds, 14 residues, 1 model selected > select add #8/A:223 126 atoms, 115 bonds, 15 residues, 1 model selected > select subtract #8/A:325 118 atoms, 108 bonds, 14 residues, 1 model selected > select add #8/A:325 126 atoms, 115 bonds, 15 residues, 1 model selected > select add #8/A:322 134 atoms, 122 bonds, 16 residues, 1 model selected > select add #8/A:342 142 atoms, 129 bonds, 17 residues, 1 model selected > select add #8/A:344 148 atoms, 134 bonds, 18 residues, 1 model selected > select add #8/A:347 159 atoms, 145 bonds, 19 residues, 1 model selected > select add #8/A:348 169 atoms, 155 bonds, 20 residues, 1 model selected > select add #8/A:234 176 atoms, 161 bonds, 21 residues, 1 model selected > select add #8/A:232 184 atoms, 168 bonds, 22 residues, 1 model selected > select add #8/A:229 192 atoms, 175 bonds, 23 residues, 1 model selected > select add #8/A:228 198 atoms, 180 bonds, 24 residues, 1 model selected > select add #8/A:598 202 atoms, 183 bonds, 25 residues, 1 model selected > select add #8/A:256 210 atoms, 190 bonds, 26 residues, 1 model selected > select add #8/A:253 221 atoms, 200 bonds, 27 residues, 1 model selected > select add #8/A:603 227 atoms, 205 bonds, 28 residues, 1 model selected > select add #8/A:245 233 atoms, 210 bonds, 29 residues, 1 model selected > select add #8/A:298 242 atoms, 218 bonds, 30 residues, 1 model selected > select add #8/A:302 248 atoms, 223 bonds, 31 residues, 1 model selected > select add #8/A:289 257 atoms, 231 bonds, 32 residues, 1 model selected > select add #8/A:293 265 atoms, 238 bonds, 33 residues, 1 model selected > select add #8/A:211 277 atoms, 250 bonds, 34 residues, 1 model selected > select add #8/A:576 285 atoms, 257 bonds, 35 residues, 1 model selected > color sel hot pink > select add #8/A:273 293 atoms, 264 bonds, 36 residues, 1 model selected > select add #8/A:594 297 atoms, 267 bonds, 37 residues, 1 model selected > select add #8/A:239 305 atoms, 274 bonds, 38 residues, 1 model selected > select add #8/A:237 312 atoms, 280 bonds, 39 residues, 1 model selected > select subtract #8/A:594 308 atoms, 277 bonds, 38 residues, 1 model selected > color sel hot pink > select clear > select #8/A:594 4 atoms, 3 bonds, 1 residue, 1 model selected > color sel magenta > color sel hot pink > select clear > select #8/A:377 6 atoms, 5 bonds, 1 residue, 1 model selected > select add #8/B:79 14 atoms, 12 bonds, 2 residues, 1 model selected > select add #8/B:78 18 atoms, 15 bonds, 3 residues, 1 model selected > select add #8/B:81 22 atoms, 18 bonds, 4 residues, 1 model selected > select add #8/B:85 29 atoms, 24 bonds, 5 residues, 1 model selected > select add #8/B:84 33 atoms, 27 bonds, 6 residues, 1 model selected > select add #8/B:19 38 atoms, 31 bonds, 7 residues, 1 model selected > select add #8/B:26 46 atoms, 38 bonds, 8 residues, 1 model selected > select add #8/B:101 54 atoms, 45 bonds, 9 residues, 1 model selected > select add #8/B:65 61 atoms, 52 bonds, 10 residues, 1 model selected > select add #8/B:188 65 atoms, 55 bonds, 11 residues, 1 model selected > select add #8/B:189 71 atoms, 60 bonds, 12 residues, 1 model selected > select add #8/B:138 83 atoms, 72 bonds, 13 residues, 1 model selected > select add #8/B:146 91 atoms, 79 bonds, 14 residues, 1 model selected > select add #8/B:134 102 atoms, 89 bonds, 15 residues, 1 model selected > select add #8/B:49 109 atoms, 95 bonds, 16 residues, 1 model selected > select add #8/B:201 117 atoms, 102 bonds, 17 residues, 1 model selected > select add #8/B:205 121 atoms, 105 bonds, 18 residues, 1 model selected > select add #8/B:210 129 atoms, 112 bonds, 19 residues, 1 model selected > color sel hot pink > select add #8/B:181 135 atoms, 117 bonds, 20 residues, 1 model selected > select add #8/B:96 147 atoms, 129 bonds, 21 residues, 1 model selected > color sel hot pink > select clear > save /Users/payalpratap/Desktop/mutants.png supersample 3 > transparentBackground true > save > /Users/payalpratap/Desktop/Structural_Biology/UCSF_Local_Directory/Fusion4_Tspan12_Bril/Chimera/Tspan12_Fzd4_FEVR_mutants.cxs ——— End of log from Wed Aug 12 15:30:28 2026 ——— > view name session-start opened ChimeraX session > lighting simple > lighting soft > save /Users/payalpratap/Desktop/mutants_left-view_soft.png supersample 3 > transparentBackground true > lighting flat > lighting full > save /Users/payalpratap/Desktop/mutants_left-view_full.png supersample 3 > transparentBackground true > lighting simple > save /Users/payalpratap/Desktop/mutants_left-view_simple.png supersample 3 > transparentBackground true > lighting shadows true > lighting full > lighting flat > lighting full > lighting shadows false > graphics silhouettes false > lighting simple > lighting soft > lighting full > lighting flat > graphics silhouettes false > graphics silhouettes true > lighting flat > save /Users/payalpratap/Desktop/mutants_left-view_flat.png supersample 3 > transparentBackground true > lighting soft > ui tool show H-Bonds > hide #8 target a > ~hbonds > show #!8 cartoons > hide #!8 cartoons > undo > ui tool show Meeting > hide #8.1 models > show #8.1 models > hide #8.1 models > show #8.1 models > hide #8.1 models > show #8.1 models > hide #8.1 models > show #8.1 models > lighting flat > lighting full > lighting soft > lighting simple > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > save /Users/payalpratap/Desktop/mutants_right-view_soft.png supersample 3 > transparentBackground true > select #8/B:65 7 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select clear > lighting soft > select #8/A:301 4 atoms, 3 bonds, 1 residue, 1 model selected > select clear > ui tool show ""Side View"" > select clear > select #8/B:36 11 atoms, 10 bonds, 1 residue, 1 model selected > select #8/B:36 11 atoms, 10 bonds, 1 residue, 1 model selected > select clear > select #8/A:300 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > select #8/A:300 7 atoms, 6 bonds, 1 residue, 1 model selected > select #8/A:300 7 atoms, 6 bonds, 1 residue, 1 model selected > select zone 5 #7/B:65 Missing or invalid ""near"" argument: invalid objects specifier > select zone 5 #7/B:65 #7/A Missing or invalid ""near"" argument: invalid objects specifier > select zone 5 #8/B:65 #8/A Missing or invalid ""near"" argument: invalid objects specifier > select clear > select zone 5 #8/B:65 #8/A Missing or invalid ""near"" argument: invalid objects specifier > select zone #8/B:65 5 #8/A Selected 14 atoms > show sel atoms > style sel stick Changed 14 atom styles > select up 44 atoms, 39 bonds, 6 residues, 1 model selected > style sel stick Changed 44 atom styles > show sel atoms > style sel stick Changed 44 atom styles > select clear > hide #8.1 models > select clear > select zone #8/B:65 4#8/A Missing or invalid ""range"" argument: Expected a number > select zone #8/B:65 4 #8/A Selected 3 atoms > undo No undo action is available > hide sel atoms > select up 44 atoms, 39 bonds, 6 residues, 1 model selected > hide sel atoms > hide #8.1 models > select zone #8/B:65 4 #8/A Selected 3 atoms > show sel atoms > select up 15 atoms, 13 bonds, 2 residues, 1 model selected > show sel atoms > select clear > select zone #8/B:65 5 #8/A Selected 14 atoms > show sel atoms > style sel stick Changed 14 atom styles > show sel atoms > select up 44 atoms, 39 bonds, 6 residues, 1 model selected > show sel atoms > style sel stick Changed 44 atom styles > select #8/A:279@CZ 1 atom, 1 residue, 1 model selected > select #8/B:64 10 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 10 atom styles > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > hide sel atoms > select #8/B:65 7 atoms, 7 bonds, 1 residue, 1 model selected > select clear > lighting flat > lighting shadows true intensity 0.5 > lighting flat > lighting soft > lighting simple > graphics silhouettes false > graphics silhouettes true > lighting shadows true > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting full > lighting shadows false > lighting shadows true > lighting flat > lighting shadows true intensity 0.5 > lighting shadows false > save /Users/payalpratap/Desktop/mutants_P65A_flat.png supersample 3 > transparentBackground true > lighting soft > save /Users/payalpratap/Desktop/mutants_P65A_soft.png supersample 3 > transparentBackground true > lighting soft > graphics silhouettes false > graphics silhouettes true > hide #!8 atoms > select #8/A:289 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > color sel bychain > undo > color sel byhetero > select clear > select zone #8/A:289 5 #8/A,B Selected 52 atoms > select zone #8/A:289 5 #8/B Selected 19 atoms > show sel atoms > select up 37 atoms, 38 bonds, 3 residues, 1 model selected > show sel atoms > select clear > lighting soft > save /Users/payalpratap/Desktop/mutants_E289R_soft.png supersample 3 > transparentBackground true > lighting flat > save /Users/payalpratap/Desktop/mutants_E289R_flat.png supersample 3 > transparentBackground true > hide #!8 atoms > select clear > select #8/B:79 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select clear > select #8/A:239 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select clear > select zone #8/A:239 5 #8/B Selected 4 atoms > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select zone #8/B:M79 5 #8/A No atoms or surfaces specified > select zone #8/B:79 5 #8/A Selected 15 atoms > show sel atoms > style sel stick Changed 15 atom styles > select up 28 atoms, 25 bonds, 4 residues, 1 model selected > show sel atoms > style sel stick Changed 28 atom styles > color sel byhetero > select clear > undo > select clear > select zone #8/B:79 5 #8/B Selected 38 atoms > show sel atoms > style sel stick Changed 38 atom styles > select up 83 atoms, 83 bonds, 11 residues, 1 model selected > show sel cartoons > show sel atoms > show sel cartoons > style sel stick Changed 83 atom styles > hide sel atoms > select zone #8/B:79 4 #8/B Selected 20 atoms > show sel atoms > select up 71 atoms, 71 bonds, 9 residues, 1 model selected > show sel atoms > select #8/B:82 12 atoms, 12 bonds, 1 residue, 1 model selected > select add #8/B:83 18 atoms, 17 bonds, 2 residues, 1 model selected > hide sel atoms > select #8/B:79 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/B:80 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #8/B:77 15 atoms, 13 bonds, 2 residues, 1 model selected > hide sel atoms > select #8/B:96 12 atoms, 12 bonds, 1 residue, 1 model selected > select clear > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting flat > lighting soft > graphics silhouettes false > graphics silhouettes true > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting flat > save /Users/payalpratap/Desktop/mutants_L239P_M79R_flat.png supersample 3 > transparentBackground true > lighting soft > lighting shadows true intensity 0.5 > save /Users/payalpratap/Desktop/mutants_L239P_M79R_soft.png supersample 3 > transparentBackground true > lighting flat > lighting shadows true intensity 0.5 > lighting shadows false > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > save /Users/payalpratap/Desktop/mutants_L239P_M79R_soft2.png supersample 3 > transparentBackground true > lighting shadows true > save /Users/payalpratap/Desktop/mutants_L239P_M79R_soft.png supersample 3 > transparentBackground true > lighting flat > save /Users/payalpratap/Desktop/mutants_L239P_M79R_soft.png supersample 3 > transparentBackground true > save /Users/payalpratap/Desktop/mutants_L239P_M79R_flat.png supersample 3 > transparentBackground true > lighting soft > save /Users/payalpratap/Desktop/mutants_L239P_M79R_soft.png supersample 3 > transparentBackground true > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > save /Users/payalpratap/Desktop/mutants_L239P_M79R_soft.png supersample 3 > transparentBackground true > lighting shadows true > save /Users/payalpratap/Desktop/mutants_L239P_M79R_soft.png supersample 3 > transparentBackground true > select #8/B:134 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select zone #8/B:134 4 #8/A Nothing selected > select zone #8/B:134 5 #8/A Selected 1 atoms > show sel atoms > select zone #8/B:134 5 #8/B Selected 58 atoms > show sel atoms > style sel stick Changed 58 atom styles > show sel atoms > select up 119 atoms, 118 bonds, 15 residues, 1 model selected > show sel atoms > style sel stick Changed 119 atom styles > undo No undo action is available > hide sel atoms > select clear > select #8/B:134 11 atoms, 10 bonds, 1 residue, 1 model selected > hide sel atoms > select clear > select add #8/B:22 14 atoms, 15 bonds, 1 residue, 1 model selected > select add #8/B:75 22 atoms, 22 bonds, 2 residues, 1 model selected > select add #8/B:76 30 atoms, 29 bonds, 3 residues, 1 model selected > hide sel atoms > select clear > lighting flat > save /Users/payalpratap/Desktop/mutants_L239P_M79R_G78R_flat.png supersample > 3 transparentBackground true > lighting soft > save /Users/payalpratap/Desktop/mutants_L239P_M79R_G78R_soft.png supersample > 3 transparentBackground true > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > save /Users/payalpratap/Desktop/mutants_L239P_M79R_G78R_soft2.png > supersample 3 transparentBackground true > lighting shadows true > lighting shadows false > lighting shadows true > save /Users/payalpratap/Desktop/mutants_L239P_M79R_G78R_soft.png supersample > 3 transparentBackground true > lighting flat > save /Users/payalpratap/Desktop/mutants_L239P_M79R_G78R_flat.png supersample > 3 transparentBackground true > lighting soft > save /Users/payalpratap/Desktop/mutants_L239P_M79R_G78R_soft.png supersample > 3 transparentBackground true > lighting shadows true intensity 0.5 > save /Users/payalpratap/Desktop/mutants_L239P_M79R_G78R_flat.png supersample > 3 transparentBackground true > lighting flat > save /Users/payalpratap/Desktop/mutants_L239P_M79R_G78R_flat.png supersample > 3 transparentBackground true > lighting soft > save /Users/payalpratap/Desktop/mutants_L239P_M79R_G78R_soft.png supersample > 3 transparentBackground true > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > save /Users/payalpratap/Desktop/mutants_L239P_M79R_G78R_soft2.png > supersample 3 transparentBackground true > select #8/B:73 11 atoms, 11 bonds, 1 residue, 1 model selected > style sel stick Changed 11 atom styles > show sel atoms > select add #8/B:76 19 atoms, 18 bonds, 2 residues, 1 model selected > show sel atoms Drag select of 1 residues > select #8/B:79 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #8/A:239 16 atoms, 14 bonds, 2 residues, 1 model selected > hide sel atoms > select #8/B:98 4 atoms, 3 bonds, 1 residue, 1 model selected > select clear > select #8/A:287 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 159 atoms, 160 bonds, 20 residues, 1 model selected > select up 2125 atoms, 2175 bonds, 269 residues, 1 model selected > show sel atoms > style sel stick Changed 2125 atom styles > select #8/B:145 14 atoms, 15 bonds, 1 residue, 1 model selected > select down 14 atoms, 15 bonds, 1 residue, 1 model selected > select up 128 atoms, 135 bonds, 13 residues, 1 model selected > style sel stick Changed 128 atom styles > show sel atoms > combine #8 > hide #!8 models > hide #!10 models > show #!10 models > select add #8 8974 atoms, 9197 bonds, 5 pseudobonds, 1163 residues, 2 models selected > select subtract #8 Nothing selected > select clear > hide #!10 atoms > select #10/B:102 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 139 atoms, 143 bonds, 17 residues, 1 model selected > select up 749 atoms, 767 bonds, 99 residues, 1 model selected > show #!3 models > hide #!10 models > show #!2 models > hide #!3 models > show #!4 models > hide #!4 models > show #!3 models > hide #!2 models > hide #!3 models > show #!4 models > show #!5 models > hide #!5 models > hide #!4 models > show #!5 models > hide #!5 models > show #!6 models > hide #!6 models > show #!7 models > hide #!7 models > show #!8 models > hide #!8 models > show #8.1 models > hide #8.1 models > hide #!8 models > show #9 models > hide #9 models > show #!10 models > select up 769 atoms, 788 bonds, 101 residues, 1 model selected > select up 1450 atoms, 1495 bonds, 184 residues, 1 model selected > select up 1455 atoms, 1499 bonds, 185 residues, 1 model selected > select up 1570 atoms, 1614 bonds, 208 residues, 1 model selected > select up 8974 atoms, 9197 bonds, 1163 residues, 1 model selected > select down 1570 atoms, 1614 bonds, 208 residues, 1 model selected > color sel blue > select #10/A:364 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 199 atoms, 205 bonds, 25 residues, 1 model selected > select up 2125 atoms, 2175 bonds, 269 residues, 1 model selected > color sel lime > select up 2136 atoms, 2186 bonds, 270 residues, 1 model selected > select up 3109 atoms, 3179 bonds, 392 residues, 1 model selected > select up 8974 atoms, 9197 bonds, 1163 residues, 1 model selected > select down 3109 atoms, 3179 bonds, 392 residues, 1 model selected > color sel lime > select clear > select #10/B:75 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #10/B:76 16 atoms, 14 bonds, 2 residues, 1 model selected > select add #10/B:22 30 atoms, 29 bonds, 3 residues, 1 model selected > show sel atoms > color sel byhetero > select #10/B:233 5 atoms, 4 bonds, 1 residue, 1 model selected > select #10/B:79 8 atoms, 7 bonds, 1 residue, 1 model selected > style sel stick Changed 8 atom styles > show sel atoms > color sel byhetero > select #10/B:19 5 atoms, 4 bonds, 1 residue, 1 model selected > select clear > select #10/A:239 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select clear > lighting flat > save /Users/payalpratap/Desktop/mutants_W22A_I75A_I76A_flat.png supersample > 3 transparentBackground true > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting full > lighting shadows false > lighting shadows true > lighting shadows false > lighting soft > save /Users/payalpratap/Desktop/mutants_W22A_I75A_I76A_soft.png supersample > 3 transparentBackground true > lighting shadows true intensity 0.5 > save /Users/payalpratap/Desktop/mutants_W22A_I75A_I76A_soft2.png supersample > 3 transparentBackground true > lighting shadows false > lighting shadows true > lighting shadows false > save /Users/payalpratap/Desktop/mutants_W22A_I75A_I76A_soft3.png supersample > 3 transparentBackground true > select #8/B:95 14 atoms, 15 bonds, 1 residue, 1 model selected > select #8/B:95 14 atoms, 15 bonds, 1 residue, 1 model selected > show #!10 atoms > hide #!10 atoms > hide #!10 models > show #!7 models > show #!8 models > hide #!7 models > show sel atoms > hide sel atoms > select up 139 atoms, 143 bonds, 17 residues, 1 model selected > select up 749 atoms, 767 bonds, 99 residues, 1 model selected > select up 769 atoms, 788 bonds, 101 residues, 1 model selected > select up 1450 atoms, 1495 bonds, 184 residues, 1 model selected > select up 1455 atoms, 1499 bonds, 185 residues, 1 model selected > select up 1570 atoms, 1614 bonds, 208 residues, 1 model selected > select up 8974 atoms, 9197 bonds, 1163 residues, 1 model selected > select up 55173 atoms, 56382 bonds, 5966 residues, 12 models selected > select up 55173 atoms, 56382 bonds, 5966 residues, 12 models selected > select up 55173 atoms, 56382 bonds, 5966 residues, 12 models selected > hide sel & #!8 atoms > select #8/B:95 14 atoms, 15 bonds, 1 residue, 1 model selected > select #8/B:95 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > ui tool show ""Side View"" > select up 139 atoms, 143 bonds, 17 residues, 1 model selected > select up 749 atoms, 767 bonds, 99 residues, 1 model selected > select up 769 atoms, 788 bonds, 101 residues, 1 model selected > select up 1450 atoms, 1495 bonds, 184 residues, 1 model selected > select up 1455 atoms, 1499 bonds, 185 residues, 1 model selected > select clear > select zone #8/B:134 5 #8/B Selected 58 atoms > select zone #8/B:134 4 #8/B Selected 28 atoms > show sel atoms > style sel stick Changed 28 atom styles > select up 104 atoms, 102 bonds, 13 residues, 1 model selected > show sel atoms > style sel stick Changed 104 atom styles > select #8/B:134 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select clear > show #!10 models > hide #!8 models > select #10/B:146 8 atoms, 7 bonds, 1 residue, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain #10/B Alignment identifier is 10/B > select #10/B:95 14 atoms, 15 bonds, 1 residue, 1 model selected > select #10/B:95 14 atoms, 15 bonds, 1 residue, 1 model selected > style sel stick Changed 14 atom styles > show sel atoms > hide sel atoms > select #10/B:145-146 22 atoms, 23 bonds, 2 residues, 1 model selected > select #10/B:145-146 22 atoms, 23 bonds, 2 residues, 1 model selected > select #10/B:145 14 atoms, 15 bonds, 1 residue, 1 model selected > select #10/B:145 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select zone #8/B:145 4 #8/B Selected 24 atoms > select #10/B:145 14 atoms, 15 bonds, 1 residue, 1 model selected > select zone #10/B:145 4 #10/A Selected 6 atoms > show sel atoms > select up 21 atoms, 20 bonds, 3 residues, 1 model selected > show sel atoms > style sel stick Changed 21 atom styles > color sel byhetero > select clear > select #10/A:208 5 atoms, 4 bonds, 1 residue, 1 model selected > hide sel atoms > select clear > lighting flat > save /Users/payalpratap/Desktop/mutants_W145KE_flat.png supersample 3 > transparentBackground true > lighting soft > save /Users/payalpratap/Desktop/mutants_W145KE_soft.png supersample 3 > transparentBackground true > lighting shadows true intensity 0.5 > save /Users/payalpratap/Desktop/mutants_W145KE_soft2.png supersample 3 > transparentBackground true > lighting shadows false > save /Users/payalpratap/Desktop/mutants_W145KE_soft3.png supersample 3 > transparentBackground true > select #10/B:95 14 atoms, 15 bonds, 1 residue, 1 model selected > select #10/B:95 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms Drag select of 22 atoms, 22 bonds, 17 residues > hide sel atoms > select clear > select #10/B:95 14 atoms, 15 bonds, 1 residue, 1 model selected > select up 139 atoms, 143 bonds, 17 residues, 1 model selected > select up 749 atoms, 767 bonds, 99 residues, 1 model selected > select zone #10/B:95 4 #10/A Selected 2 atoms > show sel atoms > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 8 atom styles > color sel byhetero > select clear > select zone #10/B:95 4 #10/B Selected 21 atoms > show sel atoms > style sel stick Changed 21 atom styles > select up 66 atoms, 64 bonds, 8 residues, 1 model selected > style sel stick Changed 66 atom styles > show sel atoms > hide sel atoms > select clear > lighting flat > save /Users/payalpratap/Desktop/mutants_W95K_flat.png supersample 3 > transparentBackground true > lighting soft > save /Users/payalpratap/Desktop/mutants_W95K_soft.png supersample 3 > transparentBackground true > lighting shadows true intensity 0.5 > save /Users/payalpratap/Desktop/mutants_W95K_soft2.png supersample 3 > transparentBackground true > lighting shadows false > save /Users/payalpratap/Desktop/mutants_W95K_soft3.png supersample 3 > transparentBackground true > select #10/B:91 8 atoms, 7 bonds, 1 residue, 1 model selected > select #10/B:91-95 43 atoms, 44 bonds, 5 residues, 1 model selected > lighting flat > hide sel atoms > select up 139 atoms, 143 bonds, 17 residues, 1 model selected > select up 749 atoms, 767 bonds, 99 residues, 1 model selected > select up 769 atoms, 788 bonds, 101 residues, 1 model selected > select up 1450 atoms, 1495 bonds, 184 residues, 1 model selected > select up 1455 atoms, 1499 bonds, 185 residues, 1 model selected > select up 1570 atoms, 1614 bonds, 208 residues, 1 model selected > select up 8974 atoms, 9197 bonds, 1163 residues, 1 model selected > select up 55173 atoms, 56382 bonds, 5966 residues, 12 models selected > select up 55173 atoms, 56382 bonds, 5966 residues, 12 models selected > hide sel & #!10 atoms > select clear > select #10/B:79 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #10/B:78 12 atoms, 10 bonds, 2 residues, 1 model selected > show #!8 models > hide #!8 models > color sel hot pink > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!8 models > select #10/A:239 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel hot pink > select clear > select #10/B:65 7 atoms, 7 bonds, 1 residue, 1 model selected > color sel hot pink > select clear > select #10/A:289 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > color sel hot pink > select clear > hide #10.1 models > show #10.1 models > save /Users/payalpratap/Desktop/mutants_FEVR_interface_left_flat.png > supersample 3 transparentBackground true > lighting soft > save /Users/payalpratap/Desktop/mutants_FEVR_interface_left_soft.png > supersample 3 transparentBackground true > lighting shadows true intensity 0.5 > save /Users/payalpratap/Desktop/mutants_FEVR_interface_left_soft2.png > supersample 3 transparentBackground true > lighting shadows false > save /Users/payalpratap/Desktop/mutants_FEVR_interface_left_soft3.png > supersample 3 transparentBackground true > lighting shadows true > lighting shadows false > turn -y 180 > lighting flat > save /Users/payalpratap/Desktop/mutants_FEVR_interface_right_flat.png > supersample 3 transparentBackground true > lighting soft > save /Users/payalpratap/Desktop/mutants_FEVR_interface_right_soft.png > supersample 3 transparentBackground true > lighting shadows true intensity 0.5 > save /Users/payalpratap/Desktop/mutants_FEVR_interface_right_soft2.png > supersample 3 transparentBackground true > lighting shadows false > save /Users/payalpratap/Desktop/mutants_FEVR_interface_right_soft3.png > supersample 3 transparentBackground true ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.10 (2025-06-26) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX 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: MW2U3LL/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: 49 days, 20 hours, 55 minutes 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 Acer ET322QU: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 75.00Hz 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: 6.4.0 babel: 2.17.0 beautifulsoup4: 4.13.3 blockdiag: 3.0.0 blosc2: 3.5.0 build: 1.2.2.post1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.2 ChimeraX-AddCharge: 1.5.19 ChimeraX-AddH: 2.2.7 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.20.2 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Aniso: 1.1.4 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.60.7 ChimeraX-AtomicLibrary: 14.1.18 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.5.1 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.10 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5.1 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.6.2 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.10.1 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.19 ChimeraX-ModelPanel: 1.5.1 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14.1 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.10 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.3 ChimeraX-ProfileGrids: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.3 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.7 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.1 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.45.2 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.5 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.2 coverage: 7.9.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.12 debugpy: 1.8.14 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.0 filelock: 3.18.0 fonttools: 4.58.4 funcparserlib: 2.0.0a0 glfw: 2.9.0 grako: 3.16.5 h5py: 3.14.0 html2text: 2024.2.26 idna: 3.10 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.1.0 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.7 jedi: 0.19.1 Jinja2: 3.1.6 jupyter_client: 8.6.3 jupyter_core: 5.8.1 jupyterlab_widgets: 3.0.15 kiwisolver: 1.4.8 line_profiler: 4.2.0 lxml: 5.3.1 lz4: 4.4.4 MarkupSafe: 3.0.2 matplotlib: 3.10.1 matplotlib-inline: 0.1.7 msgpack: 1.1.0 ndindex: 1.10.0 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.11.0 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 24.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.4.0 pip: 25.0.1 pkginfo: 1.11.1 platformdirs: 4.3.8 pluggy: 1.6.0 prompt_toolkit: 3.0.51 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.32 Pygments: 2.18.0 pynmrstar: 3.3.5 pynrrd: 1.0.0 PyOpenGL: 3.1.9 PyOpenGL-accelerate: 3.1.9 pyopenxr: 1.1.4501 pyparsing: 3.2.3 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.8.1 PyQt6-Qt6: 6.8.2 PyQt6-WebEngine-commercial: 6.8.0 PyQt6-WebEngine-Qt6: 6.8.2 PyQt6_sip: 13.10.0 pytest: 8.4.1 pytest-cov: 6.2.1 python-dateutil: 2.9.0.post0 pytz: 2025.2 pyzmq: 27.0.0 qtconsole: 5.5.2 QtPy: 2.4.3 qtshim: 1.1 RandomWords: 0.4.0 requests: 2.32.3 roman-numerals-py: 3.1.0 scipy: 1.14.0 setuptools: 78.1.0 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.7 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.1.0 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.7.1 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.4 tornado: 6.5.1 traitlets: 5.14.3 typing_extensions: 4.14.0 tzdata: 2025.2 urllib3: 2.5.0 wcwidth: 0.2.13 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.14 }}} " defect new normal Unassigned