id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16851 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.6.1-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 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 Current thread 0x00000001ef3a8f40 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 330 in event_loop File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, 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Thunderbolt Bus: MacBook Pro, Apple Inc. Boot Volume File System Type: apfs Memory Module: LPDDR5, Micron USB Device: USB31Bus USB Device: USB31Bus Display: Color LCD, 2560 x 1600 Retina, Main, MirrorOff, Online Model: Mac14,7, BootROM 10151.140.19, proc 8:4:4 processors, 16 GB, SMC Graphics: Apple M2, Apple M2, Built-In AirPort: spairport_wireless_card_type_wifi (0x14E4, 0x4378), wl0: Jan 13 2024 02:32:45 version 18.20.440.9.7.8.167 FWID 01-9a7f6652 AirPort: Bluetooth: Version (null), 0 services, 0 devices, 0 incoming serial ports ===== Log before crash start ===== UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3 > paper/Chimera sessions/20250212_chimera_for_figures_v2.cxs"" Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292, pixel 1.71, shown at level 0.0066, step 1, values float32 Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown at level 0.124, step 1, values float32 Opened postprocess_job007.mrc as #2, grid size 168,168,168, pixel 3.4, shown at level 0.36, step 1, values float32 Opened postprocess_job020.mrc as #3, grid size 192,192,192, pixel 2.55, shown at level 0.3, step 1, values float32 Opened copi_triad_bin15_filt.mrc as #4, grid size 236,236,236, pixel 2.55, shown at level 0.0057, step 1, values float32 Opened relion_locres_filtered_job073.mrc as #5, grid size 292,292,292, pixel 1.71, shown at level 0.0053, step 1, values float32 Opened relion_locres_filtered_job076.mrc as #6, grid size 292,292,292, pixel 1.71, shown at level 0.0054, step 1, values float32 Opened relion_locres_filtered_job092.mrc as #7, grid size 292,292,292, pixel 1.71, shown at level 0.0065, step 1, values float32 Opened relion_locres_filtered_20240325_GT.mrc as #8, grid size 292,292,292, pixel 1.71, shown at level 0.0065, step 1, values float32 Opened relion_locres_filtered_job073.mrc gaussian 3.00 as #9, grid size 292,292,292, pixel 1.71, shown at level 0.00478, step 1, values float32 Opened postprocess_job020.mrc gaussian 3.50 as #12, grid size 192,192,192, pixel 2.55, shown at level 0.299, step 1, values float32 Opened relion_locres_filtered_job073_lp15.mrc as #11, grid size 292,292,292, pixel 1.71, shown at level 0.0045, step 1, values float32 Opened relion_locres_filtered_job073_lp18.mrc as #10, grid size 292,292,292, pixel 1.71, shown at level 0.00422, step 1, values float32 Opened postprocess_job020_lp20.mrc as #13, grid size 192,192,192, pixel 2.55, shown at level 0.289, step 1, values float32 Opened postprocess_job020_lp25.mrc as #14, grid size 192,192,192, pixel 2.55, shown at level 0.278, step 1, values float32 Log from Wed Feb 12 11:24:19 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3 > paper/Chimera sessions/20250130_chimera_for_figures.cxs"" Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292, pixel 1.71, shown at level 0.0066, step 1, values float32 Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown at level 0.124, step 1, values float32 Opened postprocess_job007.mrc as #2, grid size 168,168,168, pixel 3.4, shown at level 0.36, step 1, values float32 Opened postprocess_job020.mrc as #3, grid size 192,192,192, pixel 2.55, shown at level 0.3, step 1, values float32 Opened copi_triad_bin15_filt.mrc as #4, grid size 236,236,236, pixel 2.55, shown at level 0.0057, step 1, values float32 Opened relion_locres_filtered_job073.mrc as #5, grid size 292,292,292, pixel 1.71, shown at level 0.0053, step 1, values float32 Opened relion_locres_filtered_job076.mrc as #6, grid size 292,292,292, pixel 1.71, shown at level 0.0054, step 1, values float32 Opened relion_locres_filtered_job092.mrc as #7, grid size 292,292,292, pixel 1.71, shown at level 0.0065, step 1, values float32 Opened relion_locres_filtered_20240325_GT.mrc as #8, grid size 292,292,292, pixel 1.71, shown at level 0.0065, step 1, values float32 Opened relion_locres_filtered_job073.mrc gaussian 3.00 as #9, grid size 292,292,292, pixel 1.71, shown at level 0.00478, step 1, values float32 Opened postprocess_job020.mrc gaussian 3.50 as #12, grid size 192,192,192, pixel 2.55, shown at level 0.299, step 1, values float32 Opened relion_locres_filtered_job073_lp15.mrc as #11, grid size 292,292,292, pixel 1.71, shown at level 0.0047, step 1, values float32 Opened relion_locres_filtered_job073_lp18.mrc as #10, grid size 292,292,292, pixel 1.71, shown at level 0.00422, step 1, values float32 Opened postprocess_job020_lp20.mrc as #13, grid size 192,192,192, pixel 2.55, shown at level 0.289, step 1, values float32 Opened postprocess_job020_lp25.mrc as #14, grid size 192,192,192, pixel 2.55, shown at level 0.278, step 1, values float32 Log from Thu Jan 30 11:29:53 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3 > paper/Chimera sessions/20250101_chimera_for_figures.cxs"" Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292, pixel 1.71, shown at level 0.0066, step 1, values float32 Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown at level 0.124, step 1, values float32 Opened postprocess_job007.mrc as #2, grid size 168,168,168, pixel 3.4, shown at level 0.36, step 1, values float32 Opened postprocess_job020.mrc as #3, grid size 192,192,192, pixel 2.55, shown at level 0.3, step 1, values float32 Opened copi_triad_bin15_filt.mrc as #4, grid size 236,236,236, pixel 2.55, shown at level 0.0057, step 1, values float32 Opened relion_locres_filtered_job073.mrc as #5, grid size 292,292,292, pixel 1.71, shown at level 0.0053, step 1, values float32 Opened relion_locres_filtered_job076.mrc as #6, grid size 292,292,292, pixel 1.71, shown at level 0.0054, step 1, values float32 Opened relion_locres_filtered_job092.mrc as #7, grid size 292,292,292, pixel 1.71, shown at level 0.0065, step 1, values float32 Opened relion_locres_filtered_20240325_GT.mrc as #8, grid size 292,292,292, pixel 1.71, shown at level 0.0065, step 1, values float32 Opened relion_locres_filtered_job073.mrc gaussian 3.00 as #9, grid size 292,292,292, pixel 1.71, shown at level 0.00478, step 1, values float32 Opened postprocess_job020.mrc gaussian 3.50 as #12, grid size 192,192,192, pixel 2.55, shown at level 0.299, step 1, values float32 Opened relion_locres_filtered_job073_lp15.mrc as #11, grid size 292,292,292, pixel 1.71, shown at level 0.0047, step 1, values float32 Opened relion_locres_filtered_job073_lp18.mrc as #10, grid size 292,292,292, pixel 1.71, shown at level 0.00422, step 1, values float32 Opened postprocess_job020_lp20.mrc as #13, grid size 192,192,192, pixel 2.55, shown at level 0.289, step 1, values float32 Opened postprocess_job020_lp25.mrc as #14, grid size 192,192,192, pixel 2.55, shown at level 0.278, step 1, values float32 Log from Thu Jan 9 16:57:06 2025UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3 > paper/Chimera sessions/20241218_chimera_for_figures.cxs"" Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292, pixel 1.71, shown at level 0.0066, step 1, values float32 Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown at level 0.124, step 1, values float32 Opened postprocess_job007.mrc as #2, grid size 168,168,168, pixel 3.4, shown at level 0.36, step 1, values float32 Opened postprocess_job020.mrc as #3, grid size 192,192,192, pixel 2.55, shown at level 0.3, step 1, values float32 Opened copi_triad_bin15_filt.mrc as #4, grid size 236,236,236, pixel 2.55, shown at level 0.0057, step 1, values float32 Opened relion_locres_filtered_job073.mrc as #5, grid size 292,292,292, pixel 1.71, shown at level 0.0053, step 1, values float32 Opened relion_locres_filtered_job076.mrc as #6, grid size 292,292,292, pixel 1.71, shown at level 0.0054, step 1, values float32 Opened relion_locres_filtered_job092.mrc as #7, grid size 292,292,292, pixel 1.71, shown at level 0.0065, step 1, values float32 Opened relion_locres_filtered_20240325_GT.mrc as #8, grid size 292,292,292, pixel 1.71, shown at level 0.0065, step 1, values float32 Opened relion_locres_filtered_job073.mrc gaussian 3.00 as #9, grid size 292,292,292, pixel 1.71, shown at level 0.00478, step 1, values float32 Opened relion_locres_filtered_job076.mrc gaussian 3.00 as #10, grid size 292,292,292, pixel 1.71, shown at level 0.00477, step 1, values float32 Opened relion_locres_filtered_20240325_GT.mrc gaussian 3.50 as #11, grid size 292,292,292, pixel 1.71, shown at level 0.00468, step 1, values float32 Opened postprocess_job020.mrc gaussian 3.50 as #12, grid size 192,192,192, pixel 2.55, shown at level 0.299, step 1, values float32 Opened copi_triad_bin15_filt.mrc gaussian 1.5 as #13, grid size 236,236,236, pixel 2.55, shown at level 0.00478, step 1, values float32 Opened relion_locres_filtered_job073_coloredbymodel.mrc as #14, grid size 292,292,292, pixel 1.71, shown at level 0.006, step 1, values float32 Log from Wed Dec 18 14:00:13 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3 > paper/Chimera sessions/20241212_chimera_for_figures.cxs"" Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292, pixel 1.71, shown at level 0.00851, step 1, values float32 Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown at level 0.179, step 1, values float32 Opened postprocess_job007.mrc as #2, grid size 168,168,168, pixel 3.4, shown at level 0.36, step 1, values float32 Opened postprocess_job020.mrc as #3, grid size 192,192,192, pixel 2.55, shown at level 0.3, step 1, values float32 Opened copi_triad_bin15_filt.mrc as #4, grid size 236,236,236, pixel 2.55, shown at level 0.0057, step 1, values float32 Opened relion_locres_filtered_job073.mrc as #5, grid size 292,292,292, pixel 1.71, shown at level 0.0053, step 1, values float32 Opened relion_locres_filtered_job076.mrc as #6, grid size 292,292,292, pixel 1.71, shown at level 0.0049, step 1, values float32 Opened relion_locres_filtered_job092.mrc as #7, grid size 292,292,292, pixel 1.71, shown at level 0.0065, step 1, values float32 Opened relion_locres_filtered_20240325_GT.mrc as #8, grid size 292,292,292, pixel 1.71, shown at level 0.0065, step 1, values float32 Opened relion_locres_filtered_job073.mrc gaussian 3.00 as #9, grid size 292,292,292, pixel 1.71, shown at level 0.00478, step 1, values float32 Opened relion_locres_filtered_job076.mrc gaussian 3.00 as #10, grid size 292,292,292, pixel 1.71, shown at level 0.00477, step 1, values float32 Opened relion_locres_filtered_20240325_GT.mrc gaussian 3.50 as #11, grid size 292,292,292, pixel 1.71, shown at level 0.00468, step 1, values float32 Opened postprocess_job020.mrc gaussian 3.50 as #12, grid size 192,192,192, pixel 2.55, shown at level 0.299, step 1, values float32 Opened copi_triad_bin15_filt.mrc gaussian 1.5 as #13, grid size 236,236,236, pixel 2.55, shown at level 0.00478, step 1, values float32 Opened relion_locres_filtered_job073_coloredbymodel.mrc as #14, grid size 292,292,292, pixel 1.71, shown at level 0.006, step 1, values float32 Log from Thu Dec 12 11:04:26 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3 > paper/Chimera sessions/20241210_chimera_for_figures_v5.cxs"" Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292, pixel 1.71, shown at level 0.00851, step 1, values float32 Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown at level 0.179, step 1, values float32 Opened postprocess_job007.mrc as #2, grid size 168,168,168, pixel 3.4, shown at level 0.36, step 1, values float32 Opened postprocess_job020.mrc as #3, grid size 192,192,192, pixel 2.55, shown at level 0.3, step 1, values float32 Opened copi_triad_bin15_filt.mrc as #4, grid size 236,236,236, pixel 2.55, shown at level 0.0057, step 1, values float32 Opened relion_locres_filtered_job073.mrc as #5, grid size 292,292,292, pixel 1.71, shown at level 0.0055, step 1, values float32 Opened relion_locres_filtered_job076.mrc as #6, grid size 292,292,292, pixel 1.71, shown at level 0.0049, step 1, values float32 Opened relion_locres_filtered_job092.mrc as #7, grid size 292,292,292, pixel 1.71, shown at level 0.0065, step 1, values float32 Opened relion_locres_filtered_20240325_GT.mrc as #8, grid size 292,292,292, pixel 1.71, shown at level 0.0065, step 1, values float32 Opened relion_locres_filtered_job073.mrc gaussian 3.00 as #9, grid size 292,292,292, pixel 1.71, shown at level 0.00478, step 1, values float32 Opened relion_locres_filtered_job076.mrc gaussian 3.00 as #10, grid size 292,292,292, pixel 1.71, shown at level 0.00477, step 1, values float32 Opened relion_locres_filtered_20240325_GT.mrc gaussian 3.50 as #11, grid size 292,292,292, pixel 1.71, shown at level 0.00468, step 1, values float32 Opened postprocess_job020.mrc gaussian 3.50 as #12, grid size 192,192,192, pixel 2.55, shown at level 0.299, step 1, values float32 Opened copi_triad_bin15_filt.mrc gaussian 1.5 as #13, grid size 236,236,236, pixel 2.55, shown at level 0.00478, step 1, values float32 Opened relion_locres_filtered_job073_coloredbymodel.mrc as #14, grid size 292,292,292, pixel 1.71, shown at level 0.006, step 1, values float32 Log from Tue Dec 10 13:42:08 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3 > paper/Chimera sessions/20241207_chimera_for_figures.cxs"" Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292, pixel 1.71, shown at level 0.006, step 1, values float32 Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown at level 0.179, step 1, values float32 Opened postprocess_job007.mrc as #2, grid size 168,168,168, pixel 3.4, shown at level 0.36, step 1, values float32 Opened postprocess_job020.mrc as #3, grid size 192,192,192, pixel 2.55, shown at level 0.3, step 1, values float32 Opened copi_triad_bin15_filt.mrc as #4, grid size 236,236,236, pixel 2.55, shown at level 0.0057, step 1, values float32 Opened relion_locres_filtered_job073.mrc as #5, grid size 292,292,292, pixel 1.71, shown at level 0.0055, step 1, values float32 Opened relion_locres_filtered_job076.mrc as #6, grid size 292,292,292, pixel 1.71, shown at level 0.0049, step 1, values float32 Opened relion_locres_filtered_job092.mrc as #7, grid size 292,292,292, pixel 1.71, shown at level 0.0065, step 1, values float32 Opened relion_locres_filtered_20240325_GT.mrc as #8, grid size 292,292,292, pixel 1.71, shown at level 0.0065, step 1, values float32 Opened relion_locres_filtered_job073.mrc gaussian 3.00 as #9, grid size 292,292,292, pixel 1.71, shown at level 0.00478, step 1, values float32 Opened relion_locres_filtered_job076.mrc gaussian 3.00 as #10, grid size 292,292,292, pixel 1.71, shown at level 0.00477, step 1, values float32 Opened relion_locres_filtered_20240325_GT.mrc gaussian 3.50 as #11, grid size 292,292,292, pixel 1.71, shown at level 0.00468, step 1, values float32 Opened postprocess_job020.mrc gaussian 3.50 as #12, grid size 192,192,192, pixel 2.55, shown at level 0.323, step 1, values float32 Opened copi_triad_bin15_filt.mrc gaussian 1.5 as #13, grid size 236,236,236, pixel 2.55, shown at level 0.00472, step 1, values float32 Log from Sat Dec 7 12:37:17 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3 > paper/Chimera sessions/20241125_chimera_for_figures.cxs"" Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292, pixel 1.71, shown at level 0.005, step 1, values float32 Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown at level 0.155, step 1, values float32 Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #63, grid size 292,292,292, pixel 1.71, shown at level 0.0053, step 1, values float32 Log from Tue Nov 26 17:24:46 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3 > paper/Figures/2024_Nov/20241122_chimera_for_figures.cxs"" Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32 Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown at level 0.155, step 1, values float32 Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #63, grid size 292,292,292, pixel 1.71, shown at level 0.0053, step 1, values float32 Log from Fri Nov 22 15:12:25 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3 > paper/Figures/2024_Nov/Figure1/20241114_v2.cxs"" Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32 Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown at level 0.155, step 1, values float32 Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #63, grid size 292,292,292, pixel 1.71, shown at level 0.0053, step 1, values float32 Log from Thu Nov 14 15:28:36 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3 > paper/Chimera sessions/20241017_COPI_leaf_all_AF3_results_aligned.cxs"" Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32 Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown at level 0.155, step 1, values float32 Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #63, grid size 292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32 Log from Thu Oct 17 14:08:25 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3 > paper/Chimera sessions/20241009_COPI_leaf_AF3_for_figs_v8.cxs"" Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32 Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown at level 0.155, step 1, values float32 Opened relion_locres_filtered_20240326_GT_colorset1.mrc as #58, grid size 292,292,292, pixel 1.71, shown at level 0.005, step 1, values float32 Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #60, grid size 292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32 Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #62, grid size 292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32 Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #63, grid size 292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32 Log from Wed Oct 9 16:21:15 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3 > paper/Chimera sessions/20240808_COPI_leaf_AF3_for_figs_v7_with_files.cxs"" Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32 Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown at level 0.155, step 1, values float32 Opened relion_locres_filtered_20240326_GT_colorset1.mrc as #58, grid size 292,292,292, pixel 1.71, shown at level 0.005, step 1, values float32 Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #60, grid size 292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32 Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #62, grid size 292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32 Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #63, grid size 292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32 Log from Wed Sep 25 22:56:27 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3 > paper/Chimera sessions/20240808_COPI_leaf_AF3_for_figs_v7.cxs"" Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32 Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown at level 0.155, step 1, values float32 Opened relion_locres_filtered_20240326_GT_colorset1.mrc as #58, grid size 292,292,292, pixel 1.71, shown at level 0.005, step 1, values float32 Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #60, grid size 292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32 Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #62, grid size 292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32 Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #63, grid size 292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32 Log from Fri Aug 9 13:21:55 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3 > paper/Chimera sessions/20240806_COPI_leaf_AF3_for_figs_v2.cxs"" Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32 Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown at level 0.155, step 1, values float32 Opened relion_locres_filtered_20240326_GT.mrc as #58, grid size 292,292,292, pixel 1.71, shown at level 0.005, step 1, values float32 Opened relion_locres_filtered_20240326_GT.mrc copy as #61, grid size 292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32 Log from Tue Aug 6 15:17:45 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3 > dataset/Chimera sessions/20240715_leaf_fitting_AF3_only_v4.cxs"" Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292, pixel 1.71, shown at level 0.00585, step 1, values float32 Log from Wed Jul 24 16:40:43 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3 > dataset/Structure files/alphafold 3 > /fold_20240711_copi_golph3/20240711_leaf_fitting_alphafold_withGolph3AF3_v2.cxs"" Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292, pixel 1.71, shown at level 0.00736, step 1, values float32 Log from Sat Jul 13 09:14:12 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3 > dataset/Structure files/alphafold 3 /GT 20240604 > /fold_2024_06_04_12_31/20240710_leaf_fitting_alphafold_only_withAF3_v5.cxs"" Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292, pixel 1.71, shown at level 0.00736, step 1, values float32 Log from Fri Jul 12 14:16:12 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3 > dataset/Structure files/alphafold 3 /GT 20240604 > /fold_2024_06_04_12_31/20240710_leaf_fitting_alphafold_only_withAF3_v4.cxs"" Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292, pixel 1.71, shown at level 0.00465, step 1, values float32 Log from Wed Jul 10 18:08:13 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3 > dataset/Structure files/alphafold 3 /GT 20240604 > /fold_2024_06_04_12_31/20240710_leaf_fitting_alphafold_only_withAF3_v2.cxs"" Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292, pixel 1.71, shown at level 0.00465, step 1, values float32 Log from Wed Jul 10 17:31:38 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3 > dataset/Chimera sessions/20240710_leaf_fitting_alphafold_only_fitting.cxs"" Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292, pixel 1.71, shown at level 0.00404, step 1, values float32 Log from Wed Jul 10 16:36:09 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3 > dataset/Chimera sessions/20240710_leaf_fitting_alphafold_only_fitting.cxs"" Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292, pixel 1.71, shown at level 0.00404, step 1, values float32 Log from Wed Jul 10 16:07:37 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3 > dataset/Chimera sessions/20240709_leaf_fitting_v39_labelled.cxs"" Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292, pixel 1.71, shown at level 0.00473, step 1, values float32 Log from Tue Jul 9 17:02:08 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3 > dataset/Chimera sessions/20240708_leaf_fitting_v36_labelled.cxs"" Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level 0.12, step 1, values float32 Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128, pixel 3.4, shown at level 0.368, step 1, values float32 Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02, shown at level 2.05, step 1, values float32 Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78, shown at level 0.0358, step 1, values float32 Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150, pixel 3.4, shown at level 0.475, step 1, values float32 Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02, shown at level 1.91, step 1, values float32 Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78, shown at level 0.0556, step 1, values float32 Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160, pixel 3.4, shown at level 0.54, step 1, values float32 Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02, shown at level 1.01, step 1, values float32 Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160, pixel 3.4, shown at level 0.5, step 1, values float32 Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02, shown at level 1.74, step 1, values float32 Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78, shown at level 0.0393, step 1, values float32 Opened relion_locres_filtered_20240325_GT.mrc as #33, grid size 292,292,292, pixel 1.71, shown at level 0.0083, step 1, values float32 Opened relion_locres_filtered_20240326_GT.mrc as #34, grid size 292,292,292, pixel 1.71, shown at level 0.00463, step 1, values float32 Log from Mon Jul 8 16:31:05 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3 > dataset/Chimera sessions/20240522_leaf_fitting_v32_labelled.cxs"" Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level 0.12, step 1, values float32 Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55, shown at level 0.0037, step 1, values float32 Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128, pixel 3.4, shown at level 0.368, step 1, values float32 Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02, shown at level 2.05, step 1, values float32 Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78, shown at level 0.0358, step 1, values float32 Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150, pixel 3.4, shown at level 0.475, step 1, values float32 Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02, shown at level 1.91, step 1, values float32 Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78, shown at level 0.0556, step 1, values float32 Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160, pixel 3.4, shown at level 0.54, step 1, values float32 Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02, shown at level 1.01, step 1, values float32 Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160, pixel 3.4, shown at level 0.5, step 1, values float32 Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02, shown at level 1.74, step 1, values float32 Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78, shown at level 0.0393, step 1, values float32 Opened relion_locres_filtered_20240325_GT.mrc as #33, grid size 292,292,292, pixel 1.71, shown at level 0.0083, step 1, values float32 Opened relion_locres_filtered_20240326_GT.mrc as #34, grid size 292,292,292, pixel 1.71, shown at level 0.00733, step 1, values float32 Log from Mon Jun 3 13:56:09 2024UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3 > dataset/Chimera > sessions/20240521_leaf_fitting_v31_mutations_interactions_labeled.cxs"" Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level 0.12, step 1, values float32 Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55, shown at level 0.0037, step 1, values float32 Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128, pixel 3.4, shown at level 0.368, step 1, values float32 Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02, shown at level 2.05, step 1, values float32 Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78, shown at level 0.0358, step 1, values float32 Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150, pixel 3.4, shown at level 0.475, step 1, values float32 Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02, shown at level 1.91, step 1, values float32 Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78, shown at level 0.0556, step 1, values float32 Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160, pixel 3.4, shown at level 0.54, step 1, values float32 Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02, shown at level 1.01, step 1, values float32 Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160, pixel 3.4, shown at level 0.5, step 1, values float32 Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02, shown at level 1.74, step 1, values float32 Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78, shown at level 0.0393, step 1, values float32 Opened relion_locres_filtered_20240325_GT.mrc as #33, grid size 292,292,292, pixel 1.71, shown at level 0.0083, step 1, values float32 Opened relion_locres_filtered_20240326_GT.mrc as #34, grid size 292,292,292, pixel 1.71, shown at level 0.00733, step 1, values float32 Log from Tue May 21 23:56:29 2024UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3 > dataset/Chimera sessions/20240406_leaf_fitting_v25.cxs"" Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level 0.187, step 1, values float32 Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55, shown at level 0.0037, step 1, values float32 Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128, pixel 3.4, shown at level 0.368, step 1, values float32 Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02, shown at level 2.05, step 1, values float32 Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78, shown at level 0.0358, step 1, values float32 Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150, pixel 3.4, shown at level 0.475, step 1, values float32 Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02, shown at level 1.91, step 1, values float32 Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78, shown at level 0.0556, step 1, values float32 Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160, pixel 3.4, shown at level 0.54, step 1, values float32 Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02, shown at level 1.01, step 1, values float32 Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160, pixel 3.4, shown at level 0.5, step 1, values float32 Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02, shown at level 1.74, step 1, values float32 Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78, shown at level 0.0393, step 1, values float32 Opened relion_locres_filtered_20240325_GT.mrc as #33, grid size 292,292,292, pixel 1.71, shown at level 0.0083, step 1, values float32 Opened relion_locres_filtered_20240326_GT.mrc as #34, grid size 292,292,292, pixel 1.71, shown at level 0.00645, step 1, values float32 Log from Mon Apr 15 16:36:47 2024UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3 > dataset/Chimera sessions/20240406_leaf_fitting_v21.cxs"" Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level 0.187, step 1, values float32 Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55, shown at level 0.0037, step 1, values float32 Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128, pixel 3.4, shown at level 0.368, step 1, values float32 Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02, shown at level 2.05, step 1, values float32 Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78, shown at level 0.0358, step 1, values float32 Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150, pixel 3.4, shown at level 0.475, step 1, values float32 Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02, shown at level 1.91, step 1, values float32 Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78, shown at level 0.0556, step 1, values float32 Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160, pixel 3.4, shown at level 0.54, step 1, values float32 Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02, shown at level 1.01, step 1, values float32 Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160, pixel 3.4, shown at level 0.5, step 1, values float32 Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02, shown at level 1.74, step 1, values float32 Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78, shown at level 0.0393, step 1, values float32 Opened relion_locres_filtered_20240325_GT.mrc as #33, grid size 292,292,292, pixel 1.71, shown at level 0.0083, step 1, values float32 Opened relion_locres_filtered_20240326_GT.mrc as #34, grid size 292,292,292, pixel 1.71, shown at level 0.00645, step 1, values float32 Log from Mon Apr 15 15:35:58 2024UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. [deleted to fit within ticket limits] > hide #14 models > show #15 models > hide #15 models > show #15 models > show #14 models > show #13 models > show #12 models > show #11 models > hide #15 models > hide #14 models > hide #13 models > hide #12 models > hide #11 models > show #12 models > hide #12 models > show #13 models > hide #13 models > show #14 models > hide #14 models > show #15 models > hide #15 models > close #11-15 > ui tool show Matchmaker > matchmaker #16-20 to #1 Computing secondary structure [Repeated 5 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241017_copi_golph3_man1b1_37_160_model_0.cif, chain B (#16), sequence alignment score = 4867.7 RMSD between 886 pruned atom pairs is 0.833 angstroms; (across all 953 pairs: 1.913) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241017_copi_golph3_man1b1_37_160_model_1.cif, chain B (#17), sequence alignment score = 4837.1 RMSD between 760 pruned atom pairs is 0.848 angstroms; (across all 953 pairs: 2.809) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241017_copi_golph3_man1b1_37_160_model_2.cif, chain B (#18), sequence alignment score = 4849.7 RMSD between 755 pruned atom pairs is 0.945 angstroms; (across all 953 pairs: 2.826) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241017_copi_golph3_man1b1_37_160_model_3.cif, chain B (#19), sequence alignment score = 4858.7 RMSD between 733 pruned atom pairs is 1.041 angstroms; (across all 953 pairs: 3.784) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241017_copi_golph3_man1b1_37_160_model_4.cif, chain B (#20), sequence alignment score = 4843.1 RMSD between 767 pruned atom pairs is 0.737 angstroms; (across all 953 pairs: 4.033) > select add #16 37356 atoms, 38057 bonds, 4699 residues, 1 model selected > select add #17 74712 atoms, 76114 bonds, 9398 residues, 2 models selected > select add #18 112068 atoms, 114171 bonds, 14097 residues, 3 models selected > select add #19 149424 atoms, 152228 bonds, 18796 residues, 4 models selected > select add #20 186780 atoms, 190285 bonds, 23495 residues, 5 models selected > show sel cartoons > select subtract #20 149424 atoms, 152228 bonds, 18796 residues, 4 models selected > select subtract #19 112068 atoms, 114171 bonds, 14097 residues, 3 models selected > select subtract #18 74712 atoms, 76114 bonds, 9398 residues, 2 models selected > select subtract #17 37356 atoms, 38057 bonds, 4699 residues, 1 model selected > select subtract #16 Nothing selected > hide #20 models > hide #19 models > hide #18 models > hide #17 models > hide #16 models > show #17 models > hide #17 models > show #18 models > hide #18 models > show #19 models > hide #19 models > show #20 models > hide #20 models > close #17-20 > ui tool show Matchmaker > matchmaker #21-30 to #1 Computing secondary structure [Repeated 10 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241017_copi_golph3_man1b1_1_160_model_0.cif, chain B (#21), sequence alignment score = 4853.9 RMSD between 848 pruned atom pairs is 0.740 angstroms; (across all 953 pairs: 1.552) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241017_copi_golph3_man1b1_1_160_model_1.cif, chain B (#22), sequence alignment score = 4829.9 RMSD between 816 pruned atom pairs is 0.748 angstroms; (across all 953 pairs: 1.465) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241017_copi_golph3_man1b1_1_160_model_2.cif, chain B (#23), sequence alignment score = 4843.7 RMSD between 860 pruned atom pairs is 0.927 angstroms; (across all 953 pairs: 1.398) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241017_copi_golph3_man1b1_1_160_model_3.cif, chain B (#24), sequence alignment score = 4852.7 RMSD between 825 pruned atom pairs is 0.786 angstroms; (across all 953 pairs: 1.400) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241017_copi_golph3_man1b1_1_160_model_4.cif, chain B (#25), sequence alignment score = 4874.3 RMSD between 675 pruned atom pairs is 0.979 angstroms; (across all 953 pairs: 2.784) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241017_copi_golph3_3gtp_model_0.cif, chain B (#26), sequence alignment score = 4851.5 RMSD between 839 pruned atom pairs is 0.974 angstroms; (across all 953 pairs: 3.156) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241017_copi_golph3_3gtp_model_1.cif, chain B (#27), sequence alignment score = 4834.1 RMSD between 533 pruned atom pairs is 1.124 angstroms; (across all 953 pairs: 3.328) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241017_copi_golph3_3gtp_model_2.cif, chain B (#28), sequence alignment score = 4817.9 RMSD between 885 pruned atom pairs is 0.895 angstroms; (across all 953 pairs: 3.409) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241017_copi_golph3_3gtp_model_3.cif, chain B (#29), sequence alignment score = 4861.7 RMSD between 710 pruned atom pairs is 1.062 angstroms; (across all 953 pairs: 2.629) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241017_copi_golph3_3gtp_model_4.cif, chain B (#30), sequence alignment score = 4833.5 RMSD between 810 pruned atom pairs is 0.780 angstroms; (across all 953 pairs: 2.106) > ui tool show Matchmaker > matchmaker #31-40 to #1 Computing secondary structure [Repeated 10 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241017_copi_golph3_3gtp_24_pa_model_0.cif, chain B (#31), sequence alignment score = 4869.5 RMSD between 532 pruned atom pairs is 1.010 angstroms; (across all 953 pairs: 3.106) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241017_copi_golph3_3gtp_24_pa_model_1.cif, chain B (#32), sequence alignment score = 4859.9 RMSD between 586 pruned atom pairs is 0.894 angstroms; (across all 953 pairs: 2.805) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241017_copi_golph3_3gtp_24_pa_model_2.cif, chain B (#33), sequence alignment score = 4876.7 RMSD between 583 pruned atom pairs is 1.037 angstroms; (across all 953 pairs: 2.347) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241017_copi_golph3_3gtp_24_pa_model_3.cif, chain B (#34), sequence alignment score = 4859.3 RMSD between 701 pruned atom pairs is 1.064 angstroms; (across all 953 pairs: 2.203) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241017_copi_golph3_3gtp_24_pa_model_4.cif, chain B (#35), sequence alignment score = 4844.3 RMSD between 705 pruned atom pairs is 1.081 angstroms; (across all 953 pairs: 2.238) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241017_copi_golph3_2arf_model_0.cif, chain B (#36), sequence alignment score = 4873.1 RMSD between 775 pruned atom pairs is 0.769 angstroms; (across all 953 pairs: 2.621) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241017_copi_golph3_2arf_model_1.cif, chain B (#37), sequence alignment score = 4840.1 RMSD between 874 pruned atom pairs is 1.023 angstroms; (across all 953 pairs: 3.184) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241017_copi_golph3_2arf_model_2.cif, chain B (#38), sequence alignment score = 4855.1 RMSD between 760 pruned atom pairs is 0.747 angstroms; (across all 953 pairs: 3.283) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241017_copi_golph3_2arf_model_3.cif, chain B (#39), sequence alignment score = 4835.3 RMSD between 872 pruned atom pairs is 0.686 angstroms; (across all 953 pairs: 1.722) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241017_copi_golph3_2arf_model_4.cif, chain B (#40), sequence alignment score = 4864.7 RMSD between 718 pruned atom pairs is 0.787 angstroms; (across all 953 pairs: 2.790) > ui tool show Matchmaker > matchmaker #41-80 to #1 Computing secondary structure [Repeated 40 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241017_copi_deltatrunc_golph3_fl_model_0.cif, chain B (#41), sequence alignment score = 4862.9 RMSD between 789 pruned atom pairs is 0.655 angstroms; (across all 953 pairs: 2.194) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241017_copi_deltatrunc_golph3_fl_model_1.cif, chain B (#42), sequence alignment score = 4859.3 RMSD between 721 pruned atom pairs is 0.941 angstroms; (across all 953 pairs: 2.830) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241017_copi_deltatrunc_golph3_fl_model_2.cif, chain B (#43), sequence alignment score = 4859.9 RMSD between 758 pruned atom pairs is 0.784 angstroms; (across all 953 pairs: 2.695) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241017_copi_deltatrunc_golph3_fl_model_3.cif, chain B (#44), sequence alignment score = 4853.9 RMSD between 760 pruned atom pairs is 0.870 angstroms; (across all 953 pairs: 2.928) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241017_copi_deltatrunc_golph3_fl_model_4.cif, chain B (#45), sequence alignment score = 4850.3 RMSD between 773 pruned atom pairs is 0.728 angstroms; (across all 953 pairs: 2.378) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241017_copi_golph3_2arf_2gtp_17oa_17_pa_model_0.cif, chain B (#46), sequence alignment score = 4879.1 RMSD between 776 pruned atom pairs is 0.758 angstroms; (across all 953 pairs: 3.074) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241017_copi_golph3_2arf_2gtp_17oa_17_pa_model_1.cif, chain B (#47), sequence alignment score = 4864.7 RMSD between 713 pruned atom pairs is 0.826 angstroms; (across all 953 pairs: 2.786) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241017_copi_golph3_2arf_2gtp_17oa_17_pa_model_2.cif, chain B (#48), sequence alignment score = 4858.7 RMSD between 767 pruned atom pairs is 0.724 angstroms; (across all 953 pairs: 2.681) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241017_copi_golph3_2arf_2gtp_17oa_17_pa_model_3.cif, chain B (#49), sequence alignment score = 4859.3 RMSD between 788 pruned atom pairs is 0.696 angstroms; (across all 953 pairs: 2.331) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241017_copi_golph3_2arf_2gtp_17oa_17_pa_model_4.cif, chain B (#50), sequence alignment score = 4853.3 RMSD between 790 pruned atom pairs is 0.889 angstroms; (across all 953 pairs: 2.298) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241015_copi_golph3_lipids_man1b1_model_0.cif, chain E (#51), sequence alignment score = 4862.3 RMSD between 745 pruned atom pairs is 0.764 angstroms; (across all 953 pairs: 2.927) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241015_copi_golph3_lipids_man1b1_model_1.cif, chain E (#52), sequence alignment score = 4852.7 RMSD between 786 pruned atom pairs is 0.865 angstroms; (across all 953 pairs: 2.722) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241015_copi_golph3_lipids_man1b1_model_2.cif, chain E (#53), sequence alignment score = 4846.1 RMSD between 789 pruned atom pairs is 0.888 angstroms; (across all 953 pairs: 2.508) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241015_copi_golph3_lipids_man1b1_model_3.cif, chain E (#54), sequence alignment score = 4843.1 RMSD between 769 pruned atom pairs is 0.721 angstroms; (across all 953 pairs: 2.945) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241015_copi_golph3_lipids_man1b1_model_4.cif, chain E (#55), sequence alignment score = 4833.5 RMSD between 744 pruned atom pairs is 0.804 angstroms; (across all 953 pairs: 2.757) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241015_copi_golph3_lipids_galnt7_model_0.cif, chain E (#56), sequence alignment score = 4850.3 RMSD between 768 pruned atom pairs is 0.753 angstroms; (across all 953 pairs: 2.885) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241015_copi_golph3_lipids_galnt7_model_1.cif, chain E (#57), sequence alignment score = 4852.1 RMSD between 720 pruned atom pairs is 0.792 angstroms; (across all 953 pairs: 2.881) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241015_copi_golph3_lipids_galnt7_model_2.cif, chain E (#58), sequence alignment score = 4837.1 RMSD between 889 pruned atom pairs is 0.711 angstroms; (across all 953 pairs: 2.128) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241015_copi_golph3_lipids_galnt7_model_3.cif, chain E (#59), sequence alignment score = 4841.3 RMSD between 749 pruned atom pairs is 0.804 angstroms; (across all 953 pairs: 3.211) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241015_copi_golph3_lipids_galnt7_model_4.cif, chain E (#60), sequence alignment score = 4828.7 RMSD between 712 pruned atom pairs is 0.875 angstroms; (across all 953 pairs: 2.880) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241015_copi_golph3_lipids_galnt2_model_0.cif, chain E (#61), sequence alignment score = 4841.9 RMSD between 772 pruned atom pairs is 0.832 angstroms; (across all 953 pairs: 2.917) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241015_copi_golph3_lipids_galnt2_model_1.cif, chain E (#62), sequence alignment score = 4830.5 RMSD between 767 pruned atom pairs is 1.024 angstroms; (across all 953 pairs: 2.805) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241015_copi_golph3_lipids_galnt2_model_2.cif, chain E (#63), sequence alignment score = 4823.3 RMSD between 767 pruned atom pairs is 0.852 angstroms; (across all 953 pairs: 3.765) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241015_copi_golph3_lipids_galnt2_model_3.cif, chain E (#64), sequence alignment score = 4799.9 RMSD between 781 pruned atom pairs is 0.886 angstroms; (across all 953 pairs: 2.678) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241015_copi_golph3_lipids_galnt2_model_4.cif, chain E (#65), sequence alignment score = 4855.1 RMSD between 649 pruned atom pairs is 0.917 angstroms; (across all 953 pairs: 2.733) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241015_copi_golph3_lipids_fam3c_model_0.cif, chain E (#66), sequence alignment score = 4826.3 RMSD between 757 pruned atom pairs is 0.870 angstroms; (across all 953 pairs: 4.009) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241015_copi_golph3_lipids_fam3c_model_1.cif, chain E (#67), sequence alignment score = 4823.3 RMSD between 791 pruned atom pairs is 0.692 angstroms; (across all 953 pairs: 1.847) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241015_copi_golph3_lipids_fam3c_model_2.cif, chain E (#68), sequence alignment score = 4846.7 RMSD between 738 pruned atom pairs is 0.788 angstroms; (across all 953 pairs: 4.195) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241015_copi_golph3_lipids_fam3c_model_3.cif, chain E (#69), sequence alignment score = 4850.3 RMSD between 764 pruned atom pairs is 0.688 angstroms; (across all 953 pairs: 3.004) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241015_copi_golph3_lipids_fam3c_model_4.cif, chain E (#70), sequence alignment score = 4850.3 RMSD between 748 pruned atom pairs is 0.913 angstroms; (across all 953 pairs: 2.788) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241015_copi_golph3_lipid_lcs_model_0.cif, chain E (#71), sequence alignment score = 4846.1 RMSD between 764 pruned atom pairs is 0.815 angstroms; (across all 953 pairs: 2.852) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241015_copi_golph3_lipid_lcs_model_1.cif, chain E (#72), sequence alignment score = 4843.7 RMSD between 740 pruned atom pairs is 0.878 angstroms; (across all 953 pairs: 3.021) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241015_copi_golph3_lipid_lcs_model_2.cif, chain E (#73), sequence alignment score = 4844.3 RMSD between 768 pruned atom pairs is 0.842 angstroms; (across all 953 pairs: 2.822) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241015_copi_golph3_lipid_lcs_model_3.cif, chain E (#74), sequence alignment score = 4838.3 RMSD between 762 pruned atom pairs is 0.904 angstroms; (across all 953 pairs: 3.114) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241015_copi_golph3_lipid_lcs_model_4.cif, chain E (#75), sequence alignment score = 4834.1 RMSD between 767 pruned atom pairs is 1.170 angstroms; (across all 953 pairs: 2.629) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241015_copi_golph3_lipid_gpp130_model_0.cif, chain E (#76), sequence alignment score = 4843.1 RMSD between 777 pruned atom pairs is 0.739 angstroms; (across all 953 pairs: 3.690) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241015_copi_golph3_lipid_gpp130_model_1.cif, chain E (#77), sequence alignment score = 4828.7 RMSD between 773 pruned atom pairs is 0.885 angstroms; (across all 953 pairs: 2.109) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241015_copi_golph3_lipid_gpp130_model_2.cif, chain E (#78), sequence alignment score = 4847.9 RMSD between 757 pruned atom pairs is 0.838 angstroms; (across all 953 pairs: 2.411) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241015_copi_golph3_lipid_gpp130_model_3.cif, chain E (#79), sequence alignment score = 4826.9 RMSD between 775 pruned atom pairs is 0.920 angstroms; (across all 953 pairs: 2.422) Matchmaker fold_20240711_copi_golph3_model_0.cif, chain E (#1) with fold_20241015_copi_golph3_lipid_gpp130_model_4.cif, chain E (#80), sequence alignment score = 4829.3 RMSD between 750 pruned atom pairs is 0.629 angstroms; (across all 953 pairs: 2.904) > select add #21 37603 atoms, 38310 bonds, 4735 residues, 1 model selected > select add #22 75206 atoms, 76620 bonds, 9470 residues, 2 models selected > select add #23 112809 atoms, 114930 bonds, 14205 residues, 3 models selected > select add #24 150412 atoms, 153240 bonds, 18940 residues, 4 models selected > select add #25 188015 atoms, 191550 bonds, 23675 residues, 5 models selected > show sel cartoons > select subtract #25 150412 atoms, 153240 bonds, 18940 residues, 4 models selected > select subtract #24 112809 atoms, 114930 bonds, 14205 residues, 3 models selected > select subtract #23 75206 atoms, 76620 bonds, 9470 residues, 2 models selected > select subtract #22 37603 atoms, 38310 bonds, 4735 residues, 1 model selected > select subtract #21 Nothing selected > hide #24 models > hide #25 models > hide #23 models > hide #22 models > hide #21 models > save ""/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3 > paper/Chimera sessions/20250212_AF3_all_results_aligned.cxs"" > show #21 models > show #1 models > hide #21 models > show #21 models > hide #21 models > show #21 models > hide #21 models > show #21 models > hide #21 models > show #22 models > hide #22 models > show #23 models > hide #23 models > show #24 models > hide #24 models > show #25 models > hide #25 models > show #25 models > hide #1 models > hide #25 models > show #24 models > hide #24 models > show #21 models > hide #21 models > show #22 models > hide #22 models > show #23 models > hide #23 models > show #24 models > hide #24 models > show #25 models > hide #25 models > close #25 > select add #26 36421 atoms, 37093 bonds, 4578 residues, 1 model selected > select add #27 72842 atoms, 74186 bonds, 9156 residues, 2 models selected > select add #28 109263 atoms, 111279 bonds, 13734 residues, 3 models selected > select add #29 145684 atoms, 148372 bonds, 18312 residues, 4 models selected > select add #30 182105 atoms, 185465 bonds, 22890 residues, 5 models selected > show sel cartoons > select subtract #30 145684 atoms, 148372 bonds, 18312 residues, 4 models selected > select subtract #29 109263 atoms, 111279 bonds, 13734 residues, 3 models selected > select subtract #28 72842 atoms, 74186 bonds, 9156 residues, 2 models selected > select subtract #27 36421 atoms, 37093 bonds, 4578 residues, 1 model selected > select subtract #26 Nothing selected > hide #30 models > hide #29 models > hide #28 models > hide #27 models > show #1 models > hide #1 models > hide #26 models > show #27 models > hide #27 models > show #28 models > show #26 models > hide #26 models > hide #28 models > show #29 models > hide #29 models > show #30 models > show #28 models > show #26 models > hide #26 models > hide #28 models > hide #30 models > show #27 models > close #27 > close #29 > select add #31 36853 atoms, 37501 bonds, 4602 residues, 1 model selected > select add #32 73706 atoms, 75002 bonds, 9204 residues, 2 models selected > select add #33 110559 atoms, 112503 bonds, 13806 residues, 3 models selected > select add #34 147412 atoms, 150004 bonds, 18408 residues, 4 models selected > select add #35 184265 atoms, 187505 bonds, 23010 residues, 5 models selected > show sel cartoons > select subtract #35 147412 atoms, 150004 bonds, 18408 residues, 4 models selected > select subtract #34 110559 atoms, 112503 bonds, 13806 residues, 3 models selected > select subtract #33 73706 atoms, 75002 bonds, 9204 residues, 2 models selected > select subtract #32 36853 atoms, 37501 bonds, 4602 residues, 1 model selected > select subtract #31 Nothing selected > hide #35 models > hide #34 models > hide #33 models > hide #32 models > hide #31 models > show #31 models > hide #31 models > show #32 models > hide #32 models > show #33 models > hide #33 models > show #34 models > hide #34 models > show #35 models > hide #35 models > show #31 models > show #32 models > show #33 models > hide #33 models > hide #32 models > show #32 models > show #33 models > hide #32 models > hide #31 models > hide #33 models > show #34 models > hide #34 models > show #35 models > close #31-35 > select add #36 34868 atoms, 35508 bonds, 4394 residues, 1 model selected > select add #37 69736 atoms, 71016 bonds, 8788 residues, 2 models selected > select add #38 104604 atoms, 106524 bonds, 13182 residues, 3 models selected > select add #39 139472 atoms, 142032 bonds, 17576 residues, 4 models selected > select add #40 174340 atoms, 177540 bonds, 21970 residues, 5 models selected > show sel cartoons > select subtract #40 139472 atoms, 142032 bonds, 17576 residues, 4 models selected > select subtract #39 104604 atoms, 106524 bonds, 13182 residues, 3 models selected > select subtract #38 69736 atoms, 71016 bonds, 8788 residues, 2 models selected > select subtract #37 34868 atoms, 35508 bonds, 4394 residues, 1 model selected > select subtract #36 Nothing selected > hide #40 models > hide #39 models > hide #38 models > hide #37 models > hide #36 models > show #37 models > show #1 models > hide #1 models > show #38 models > hide #38 models > hide #37 models > show #38 models > hide #38 models > show #39 models > show #37 models > hide #37 models > hide #39 models > show #40 models > hide #40 models > save ""/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3 > paper/Chimera sessions/20250212_AF3_all_results_aligned_v2.cxs"" [Repeated 1 time(s)] ——— End of log from Wed Feb 12 13:50:37 2025 ——— opened ChimeraX session > select add #41 39522 atoms, 40261 bonds, 4983 residues, 1 model selected > select add #42 79044 atoms, 80522 bonds, 9966 residues, 2 models selected > select add #43 118566 atoms, 120783 bonds, 14949 residues, 3 models selected > select add #44 158088 atoms, 161044 bonds, 19932 residues, 4 models selected > select add #45 197610 atoms, 201305 bonds, 24915 residues, 5 models selected > show sel cartoons > select subtract #45 158088 atoms, 161044 bonds, 19932 residues, 4 models selected > select subtract #44 118566 atoms, 120783 bonds, 14949 residues, 3 models selected > select subtract #43 79044 atoms, 80522 bonds, 9966 residues, 2 models selected > select subtract #42 39522 atoms, 40261 bonds, 4983 residues, 1 model selected > select subtract #41 Nothing selected > hide #45 models > hide #44 models > hide #43 models > hide #42 models > hide #41 models > select add #36 34868 atoms, 35508 bonds, 4394 residues, 1 model selected > select add #37 69736 atoms, 71016 bonds, 8788 residues, 2 models selected > select add #38 104604 atoms, 106524 bonds, 13182 residues, 3 models selected > select add #39 139472 atoms, 142032 bonds, 17576 residues, 4 models selected > select add #40 174340 atoms, 177540 bonds, 21970 residues, 5 models selected > select add #41 213862 atoms, 217801 bonds, 26953 residues, 6 models selected > show #46-80 cartoons > select subtract #36 178994 atoms, 182293 bonds, 22559 residues, 5 models selected > select subtract #37 144126 atoms, 146785 bonds, 18165 residues, 4 models selected > select subtract #38 109258 atoms, 111277 bonds, 13771 residues, 3 models selected > select subtract #39 74390 atoms, 75769 bonds, 9377 residues, 2 models selected > select subtract #40 39522 atoms, 40261 bonds, 4983 residues, 1 model selected > select subtract #41 Nothing selected > show #40 models > show #39 models > show #38 models > show #37 models > show #36 models > hide #36 models > hide #37 models > hide #38 models > hide #39 models > hide #40 models > show #40 models > hide #46 models > hide #40 models > hide #47 models > hide #48 models > hide #49 models > hide #50 models > show #49 models > show #50 models > hide #51 models > hide #52 models > show #51 models > hide #53 models > hide #49 models > hide #50 models > hide #51 models > hide #54 models > hide #55 models > hide #56 models > hide #57 models > hide #58 models > hide #59 models > hide #60 models > hide #80 models > hide #79 models > hide #78 models > hide #77 models > hide #76 models > hide #75 models > hide #74 models > hide #73 models > hide #72 models > hide #71 models > hide #70 models > hide #69 models > hide #68 models > hide #67 models > hide #66 models > hide #65 models > hide #64 models > hide #63 models > hide #62 models > hide #61 models > show #36 models > show #37 models > hide #37 models > hide #36 models > show #36 models > show #38 models > show #40 models > hide #40 models > hide #38 models > hide #36 models > show #41 models > show #36 models > hide #36 models > show #36 models > hide #36 models > show #42 models > show #43 models > show #44 models > hide #44 models > show #44 models > hide #44 models > show #44 models > show #45 models > close #41-45 > show #46 models > show #47 models > show #48 models > show #49 models > show #50 models > hide #50 models > hide #49 models > hide #48 models > hide #47 models > show #47 models > hide #47 models > show #47 models > hide #47 models > hide #46 models > show #48 models > hide #48 models > show #49 models > hide #49 models > show #50 models > hide #50 models > close #46-50 > show #51 models > show #52 models > show #53 models > show #54 models > show #55 models > hide #55 models > hide #54 models > hide #53 models > hide #52 models > hide #51 models > show #52 models > hide #52 models > show #53 models > hide #53 models > show #54 models > hide #54 models > show #55 models > hide #55 models > show #54 models > hide #54 models > show #53 models > hide #53 models > show #52 models > hide #52 models > show #51 models > hide #51 models > close #51-55 > show #56 models > show #57 models > hide #57 models > hide #56 models > show #57 models > hide #57 models > show #58 models > show #57 models > hide #57 models > show #1 models > hide #1 models > hide #58 models > show #59 models > hide #59 models > show #60 models > hide #60 models > show #58 models > hide #58 models > show #56 models > hide #56 models > show #57 models > hide #57 models > show #59 models > hide #59 models > show #60 models > hide #60 models > show #58 models > show #1 models > hide #1 models > hide #58 models > show #61 models > show #62 models > hide #62 models > hide #61 models > show #62 models > hide #62 models > show #63 models > hide #63 models > show #63 models > hide #63 models > show #64 models > hide #64 models > show #65 models > hide #65 models > show #62 models > show #61 models > show #63 models > show #64 models > show #65 models > close #61-65 > show #66 models > show #67 models > hide #67 models > hide #66 models > show #67 models > hide #67 models > show #68 models > hide #68 models > show #69 models > hide #69 models > show #70 models > show #69 models > show #68 models > show #67 models > show #66 models > hide #70 models > hide #69 models > hide #68 models > hide #67 models > hide #66 models > show #66 models > close #66-70 > show #71 models > show #72 models > hide #72 models > hide #71 models > show #1 models > show #71 models > hide #71 models > show #71 models > hide #71 models > hide #1 models > show #71 models > show #1 models > hide #1 models > hide #71 models > show #72 models > hide #72 models > show #73 models > show #72 models > show #71 models > hide #71 models > hide #72 models > hide #73 models > show #74 models > hide #74 models > show #74 models > show #75 models > hide #75 models > hide #74 models > show #71 models > hide #71 models > show #72 models > hide #72 models > show #73 models > hide #73 models > show #74 models > hide #74 models > show #75 models > hide #75 models > close #71-75 > show #76 models > show #77 models > show #78 models > hide #78 models > hide #77 models > show #1 models > hide #1 models > show #1 models > hide #1 models > hide #76 models > show #77 models > show #76 models > hide #76 models > hide #77 models > show #78 models > hide #78 models > show #79 models > hide #79 models > show #80 models > hide #80 models > close #76-80 > show #1 models > hide #1 models > show #16 models > hide #16 models > save ""/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3 > paper/Chimera sessions/20250212_AF3_all_results_aligned_v3.cxs"" ——— End of log from Wed Feb 12 15:48:26 2025 ——— opened ChimeraX session OpenGL version: 4.1 Metal - 88.1 OpenGL renderer: Apple M2 OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac14,7 Model Number: Z16S000N6D/A Chip: Apple M2 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 10151.140.19 OS Loader Version: 10151.140.19 Software: System Software Overview: System Version: macOS 14.6.1 (23G93) Kernel Version: Darwin 23.6.0 Time since boot: 2 days, 3 hours, 59 minutes Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL P2422H: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 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 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: 1.2.1 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: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 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 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 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: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 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: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 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: 1.18.1 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 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: 1.41 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: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 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: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Window Toolkit duplicate all ChimeraX