id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16021 Crash on Mac waking from sleep sean@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.6.1-x86_64-i386-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x0000000204a8e240 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 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, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, chimerax.chem_group._chem_group, chimerax.atom_search.ast, chimerax.coulombic._esp, chimerax.mlp._mlp, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, lxml._elementpath, lxml.etree (total: 63) {""app_name"":""ChimeraX"",""timestamp"":""2024-09-25 20:23:17.00 +0100"",""app_version"":""1.8.0"",""slice_uuid"":""194a3167-3db5-3029-8d22-1d742b826bb9"",""build_version"":""1.8.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 14.6.1 (23G93)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""8CDB7D00-EED0-41DA-A6B2-781A24C4B2F8""} { ""uptime"" : 1000000, ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 502, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro18,1"", ""coalitionID"" : 166650, ""osVersion"" : { ""train"" : ""macOS 14.6.1"", ""build"" : ""23G93"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2024-09-25 20:22:03.7500 +0100"", ""codeSigningMonitor"" : 1, ""incident"" : ""8CDB7D00-EED0-41DA-A6B2-781A24C4B2F8"", ""pid"" : 88455, ""translated"" : true, ""cpuType"" : ""X86-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2024-09-25 11:29:54.5205 +0100"", ""procStartAbsTime"" : 24079284145589, ""procExitAbsTime"" : 24577915846215, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.8.0"",""CFBundleVersion"":""1.8.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""EDD8B610-D200-5890-8C1B-29D609195B52"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""ECED8795-F73E-B1B9-01B1-947CFD465E40"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""wakeTime"" : 1, ""sleepWakeUUID"" : ""86C7C461-B75B-4121-A4E7-A7DC84BC428A"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x3deb4ade88f8 is not in any region. 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All rights reserved. How to cite UCSF ChimeraX > open ""/Users/sean/Documents/Projects/GOLPH3 paper/Briggs Kat > Collaboration/GOLPH3 3kn1.pdb"" GOLPH3 3kn1.pdb title: Crystal structure of golgi phosphoprotein 3 N-term truncation variant [more info...] Chain information for GOLPH3 3kn1.pdb #1 --- Chain | Description | UniProt A | golgi phosphoprotein 3 | GOLP3_HUMAN 52-298 Non-standard residues in GOLPH3 3kn1.pdb #1 --- SO4 — sulfate ion 5 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > select sulfate 30 atoms, 24 bonds, 6 residues, 1 model selected > hide sel atoms > select clear Alignment identifier is 1/A > select clear > select /A:59-297 1895 atoms, 1926 bonds, 239 residues, 1 model selected > hide sel atoms > coulombic sel The following residues are missing heavy (non-hydrogen) atoms, which may result in inaccurate electrostatics: /A ARG 59 /A ARG 112 /A GLN 211 /A ARG 231 /A LYS 266 /A LYS 282 /A ASN 284 /A THR 297 Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for GOLPH3 3kn1.pdb_A SES surface #1.1: minimum, -23.22, mean -2.15, maximum 13.32 To also show corresponding color key, enter the above coulombic command and add key true > select clear > select ::name=""HOH"" 9 atoms, 9 residues, 1 model selected > hide sel atoms > select clear > set bgColor white > set bgColor black > save /Users/sean/Desktop/image1.png supersample 3 > set bgColor white > save /Users/sean/Desktop/image2.png supersample 3 > lighting simple > lighting soft > lighting full > lighting simple > lighting full > save /Users/sean/Desktop/image3.png supersample 3 > lighting soft > save /Users/sean/Desktop/image4.png supersample 3 > lighting simple > save /Users/sean/Desktop/image5.png supersample 3 > lighting flat > save /Users/sean/Desktop/image6.png supersample 3 > lighting shadows true intensity 0.5 > lighting shadows false > graphics silhouettes false > graphics silhouettes true > lighting flat > lighting full > lighting shadows false > lighting shadows true > lighting shadows false > lighting soft > 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 simple > lighting shadows true > lighting shadows false > graphics silhouettes false > graphics silhouettes true > save /Users/sean/Desktop/image7.png supersample 3 > lighting soft > save /Users/sean/Desktop/image8.png supersample 3 > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting full > lighting shadows false > save /Users/sean/Desktop/image9.png supersample 3 > lighting shadows true > lighting shadows false > lighting flat > lighting shadows true intensity 0.5 > lighting shadows false > graphics silhouettes false > graphics silhouettes true > lighting simple > lighting shadows true > lighting shadows false > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting full > lighting shadows false > lighting shadows true > lighting shadows false > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > mlp Map values for surface ""GOLPH3 3kn1.pdb_A SES surface"": minimum -27.57, mean -4.444, maximum 36.64 To also show corresponding color key, enter the above mlp command and add key true > save /Users/sean/Desktop/image10.png supersample 3 > lighting simple > save /Users/sean/Desktop/image11.png supersample 3 > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting simple > lighting shadows true > lighting shadows false > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting full > lighting shadows false > save /Users/sean/Desktop/image12.png supersample 3 > lighting flat > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting simple > lighting soft > lighting full > lighting flat > coulombic Coulombic values for GOLPH3 3kn1.pdb_A SES surface #1.1: minimum, -23.22, mean -2.15, maximum 13.32 To also show corresponding color key, enter the above coulombic command and add key true > lighting simple > lighting shadows true > lighting shadows false > graphics silhouettes false > graphics silhouettes true The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. Unsupported scale factor (0.000000) detected on Display1 > hide surfaces > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > lighting soft > lighting full > lighting simple > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > save /Users/sean/Desktop/image1.png supersample 3 > graphics silhouettes true > save /Users/sean/Desktop/image2.png supersample 3 > select ::name=""GLN"" 77 atoms, 68 bonds, 9 residues, 1 model selected > show sel atoms > undo > show sel atoms > hide sel atoms > select ::name=""GLU"" 171 atoms, 153 bonds, 19 residues, 1 model selected > show sel atoms > select ::name=""ASP"" 112 atoms, 98 bonds, 14 residues, 1 model selected > show sel atoms > select clear > save /Users/sean/Desktop/image3.png supersample 3 > graphics silhouettes false > save /Users/sean/Desktop/image4.png supersample 3 > select /A:154 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:154 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:154,159 18 atoms, 16 bonds, 2 residues, 1 model selected > select /A:83,154,159 26 atoms, 23 bonds, 3 residues, 1 model selected > select /A:83,154,159,273 34 atoms, 30 bonds, 4 residues, 1 model selected > select /A:83,154,159,273,275 42 atoms, 37 bonds, 5 residues, 1 model selected > select /A:83,154,159,273,275,277 51 atoms, 45 bonds, 6 residues, 1 model selected > select /A:83,154,159,273,275,277,279 60 atoms, 53 bonds, 7 residues, 1 model selected > select /A:73,83,154,159,273,275,277,279 68 atoms, 60 bonds, 8 residues, 1 model selected > select /A:73,75,83,154,159,273,275,277,279 77 atoms, 68 bonds, 9 residues, 1 model selected > select /A:73,75,83,154,159,250,273,275,277,279 86 atoms, 76 bonds, 10 residues, 1 model selected > select /A:73,75,83,154,159,247,250,273,275,277,279 94 atoms, 83 bonds, 11 residues, 1 model selected > select /A:73,75,83,154,159,247,250,258-259,273,275,277,279 111 atoms, 99 bonds, 13 residues, 1 model selected > select /A:73,75,83,154,159,247,250,258-259,262,273,275,277,279 119 atoms, 106 bonds, 14 residues, 1 model selected > select ~sel 1815 atoms, 1818 bonds, 240 residues, 1 model selected > hide sel atoms > select clear > save /Users/sean/Desktop/image5.png supersample 3 > graphics silhouettes true > save /Users/sean/Desktop/image6.png supersample 3 > close #1 > open ""/Users/sean/Documents/Projects/GOLPH3 paper/Briggs Kat > Collaboration/20240406_leaf_fitting_v26.cxs"" format session 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 opened ChimeraX session > hide #!25 models > show #!25 models > hide #!34 models > show #!33 models > hide #!32 models > show #!32 models > hide #!33 models > ui tool show ""Side View"" > show #!31 models > hide #!31 models > show #!31 models > hide #!31 models > hide #32.1 models > show #32.1 models > hide #32.2 models > show #32.2 models > hide #!25 models > show #!25 models > show #!33 models > hide #!33 models > show #!34 models The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > hide #!34 models > set bgColor white > hide #39 models > show #39 models > hide #39 models > hide #28 models > show #28 models > hide #26.3 models > hide #!29 models > show #!29 models > hide #28 models > show #28 models > hide #!26.2 models > show #!26.2 models > hide #!26.2 models > save /Users/sean/Desktop/image1.png supersample 3 > hide #!30 models > show #!30 models > hide #27.2 models > show #27.2 models > hide #27.2 models > show #27.2 models > hide #32.1 models > show #32.1 models > hide #32.2 models > show #32.2 models > hide #38 models > show #38 models > hide #38 models > show #38 models > hide #38 models > show #38 models > ui tool show ""Side View"" > view > close > open ""/Users/sean/Documents/Projects/GOLPH3 paper/Briggs Kat > Collaboration/20240406_leaf_fitting_v26.cxs"" format session 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 opened ChimeraX session > show #!3 models > hide #!3 models > show #!3 models Unsupported scale factor (0.000000) detected on Display1 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/sean/Documents/Projects/GOLPH3 paper/Briggs Kat > Collaboration/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. > open ""/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3 > dataset/Chimera sessions/20240328_leaf_fitting_v17.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 Opened cryosparc_P126_J1413_005_volume_map.mrc as #35, grid size 480,480,480, pixel 0.953, shown at level 0.136, step 1, values float32 Opened cryosparc_P126_J1449_008_volume_map_sharp.mrc as #36, grid size 480,480,480, pixel 0.953, shown at level 0.227, step 1, values float32 Log from Fri Mar 29 15:25:34 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/20240326_leaf_fitting_v13.cxs"" Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level 0.153, 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 0.00747, step 1, values float32 Log from Tue Mar 26 13:48:19 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] > ui tool show ""Color Zone"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. [Repeated 1 time(s)] > color zone #58 near #38 distance 10.26 > hide #!1 models > select subtract #58 Nothing selected > color zone #58 near #38 distance 10.93 > color zone #58 near #38 distance 4.35 > color zone #58 near #38 distance 5.21 > color zone #58 near #38 distance 5.14 > color zone #58 near #39 distance 5.14 > volume splitbyzone #58 Opened relion_locres_filtered_20240326_GT.mrc 0 as #59.1, grid size 292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32 Opened relion_locres_filtered_20240326_GT.mrc 1 as #59.2, grid size 292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32 > hide #!59.2 models > show #!59.2 models > hide #!59.1 models > show #!59.1 models > hide #!59.2 models > show #!59.2 models > color zone #58 near #38 distance 5.14 [Repeated 1 time(s)] > color zone #59.1 near #38 distance 10.26 [Repeated 1 time(s)] > color zone #59.1 near #41 distance 9.26 > color zone #59.1 near #41 distance 9.16 > color zone #59.1 near #41 distance 9.06 > color zone #59.1 near #41 distance 8.96 > color zone #59.1 near #41 distance 8.86 > color zone #59.1 near #41 distance 8.76 > color zone #59.1 near #41 distance 8.66 > color zone #59.1 near #41 distance 8.56 > color zone #59.1 near #41 distance 8.46 > color zone #59.1 near #41 distance 8.36 > color zone #59.1 near #41 distance 8.26 > color zone #59.1 near #41 distance 8.16 > color zone #59.1 near #41 distance 8.06 > color zone #59.1 near #41 distance 7.96 > color zone #59.1 near #38 distance 7.96 > help help:user/tools/colorzone.html > close #59.1 > close #59 > show #!58 models > color zone #58 near #38 distance 5.14 > color zone #58 near #39 distance 5.14 > combine #38 #39 #41 #42 #43 #44 #45 #46 #47 #48 #49 #50 #51 #52 #53 #54 #55 Remapping chain ID 'D' in 20240711_copi_golph3_alpha_I592-G900.cif #39 to 'E' Remapping chain ID 'F' in 20240711_copi_golph3_betaprime_L587-D905.cif #42 to 'G' Remapping chain ID 'E' in 20240711_copi_golph3_beta_S711-L953.cif #43 to 'H' Remapping chain ID 'E' in 20240711_copi_golph3_beta_H311-E659.cif #44 to 'I' Remapping chain ID 'E' in 20240711_copi_golph3_beta_M1-H311_K660-A710.cif #45 to 'J' Remapping chain ID 'G' in 20240711_copi_golph3_delta_M1-S273.cif #46 to 'K' Remapping chain ID 'H' in 20240711_copi_golph3_gamma1_K300-F448.cif #47 to 'L' Remapping chain ID 'H' in 20240711_copi_golph3_gamma1_M1-P299.cif #48 to 'M' Remapping chain ID 'H' in 20240711_copi_golph3_gammm1_T449-R609.cif #49 to 'N' Remapping chain ID 'I' in 20240711_copi_golph3_zeta1.cif #50 to 'O' Remapping chain ID 'B' in 20240711_copi_golph3_third_Arf1.cif #53 to 'P' Remapping chain ID 'A' in 20240711_copi_golph3_golph3_.cif #55 to 'Q' > hide #!59 models > show #!59 models > hide #55 models > hide #!54 models > hide #53 models > hide #52 models > hide #51 models > hide #50 models > hide #!49 models > hide #48 models > hide #47 models > hide #!46 models > hide #!45 models > hide #!44 models > hide #!43 models > hide #42 models > hide #41 models > hide #39 models > hide #38 models > hide #!58 models > color zone #58 near #59 distance 5.14 > show #!58 models > hide #!59 models > color zone #58 near #59 distance 4.97 > color zone #58 near #59 distance 4.45 > surface dust #58 size 17.1 > color zone #58 near #59 distance 4.31 > color zone #58 near #59 distance 4.7 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #58 step 1 > volume #58 level 0.005 > color zone #58 near #59 distance 5.19 > set bgColor white > save /Users/becca/Desktop/image1.png supersample 3 > lighting simple > graphics silhouettes false > graphics silhouettes true > volume #58 level 0.008 > save /Users/becca/Desktop/image1.png supersample 3 > volume #58 level 0.005 > color zone #58 near #59 distance 5.43 > color zone #58 near #59 distance 6.99 > save /Users/becca/Desktop/image1.png supersample 3 > volume #58 level 0.008 > save /Users/becca/Desktop/image1.png supersample 3 > hide #!58 models > show #!59 models > rename #59 combined_model_COPI_GOLPH3 > save ""/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3 > paper/Chimera sessions/20240806_COPI_leaf_AF3_for_figs_v1.cxs"" > show #!1 models > save ""/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3 > paper/Chimera sessions/20240806_COPI_leaf_AF3_for_figs_v1.cxs"" > hide #!59 models > show #!58 models > hide #!1 models > volume #58 level 0.005 > ui mousemode right ""map eraser"" > volume erase #58 center 281.84,261.87,305.71 radius 22.725 Opened relion_locres_filtered_20240326_GT.mrc copy as #61, grid size 292,292,292, pixel 1.71, shown at step 1, values float32 > surface dust #61 size 17.1 > color zone #61 near #59 distance 10.26 > color zone #61 near #59 distance 10.16 > color zone #61 near #59 distance 6.84 > save /Users/becca/Desktop/image1.png supersample 3 > volume #61 level 0.008 > save /Users/becca/Desktop/image2.png supersample 3 > volume #61 level 0.005 > save /Users/becca/Desktop/image3.png supersample 3 > volume #61 level 0.008 > save /Users/becca/Desktop/image4.png supersample 3 > color zone #61 near #59 distance 4.76 > color zone #61 near #59 distance 4.4 > color zone #61 near #59 distance 5.99 > save /Users/becca/Desktop/image5.png supersample 3 > hide #!61 models > show #!1 models > color #1 #a9a9a9a0 models > hide #!1 models > color #1 #a9a9a9a1 models > show #!1 models > show #!57 models > hide #!57 models > show #!59 models > hide #!1 models > show #!1 models > hide #!1 models > ui mousemode right select > select #59/O:73 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 8 atom styles > select #59/O:74 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 8 atom styles > select #59/O:72 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > show sel cartoons > style sel stick Changed 6 atom styles > show #!1 models > hide #!1 models > select #59/O:108 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 8 atom styles > select #59/O:107 9 atoms, 8 bonds, 1 residue, 1 model selected > style sel stick Changed 9 atom styles > show sel atoms > select #59/O:109 7 atoms, 6 bonds, 1 residue, 1 model selected > select #59/O:108 8 atoms, 7 bonds, 1 residue, 1 model selected > select #59/O:108 8 atoms, 7 bonds, 1 residue, 1 model selected > select #59/O:109 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 7 atom styles > select #59/O:106 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 11 atom styles > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > select #59/Q:223 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 8 atom styles > select clear > select #59/Q:224 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 9 atom styles > select #59/Q:225 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 14 atom styles > select #59/Q:259 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 9 atom styles > select #59/Q:263 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 8 atom styles > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > select #59/Q:225 14 atoms, 15 bonds, 1 residue, 1 model selected > select #59/Q:226 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 7 atom styles > select clear > select #59/Q:225 14 atoms, 15 bonds, 1 residue, 1 model selected > select #59/Q:226@CB 1 atom, 1 residue, 1 model selected > select #59/Q:226@CA 1 atom, 1 residue, 1 model selected > select #59/Q:226 7 atoms, 6 bonds, 1 residue, 1 model selected > select #59/O:107@NZ 1 atom, 1 residue, 1 model selected > select #59/Q:259 9 atoms, 8 bonds, 1 residue, 1 model selected > select #59/O:106@CG 1 atom, 1 residue, 1 model selected > select clear [Repeated 1 time(s)] > select #59/O:106 11 atoms, 10 bonds, 1 residue, 1 model selected > hide sel atoms > select #59/O:108@CB 1 atom, 1 residue, 1 model selected > hide sel atoms > undo > select #59/O:107 9 atoms, 8 bonds, 1 residue, 1 model selected > select #59/O:108 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select clear > select #59/Q:263 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > show #!1 models > select #59/M:12 6 atoms, 5 bonds, 1 residue, 1 model selected > select #59/M:1 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel cartoons > select #59/M:3 9 atoms, 8 bonds, 1 residue, 1 model selected > select #59/M:2 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms [Repeated 1 time(s)] > select #59/M:3 9 atoms, 8 bonds, 1 residue, 1 model selected > select #59/M:2 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel cartoons > select clear > select #59/M:3 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel cartoons > select clear > select #59/M:4 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel cartoons > select clear > select #59/M:5 11 atoms, 11 bonds, 1 residue, 1 model selected > hide sel cartoons > select #59/M:16 6 atoms, 5 bonds, 1 residue, 1 model selected > select #59/M:6 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > hide sel cartoons > select #59/M:7 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel cartoons > select #59/M:8 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel cartoons > select #1 2 models selected > select #59/M:9 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel cartoons > select #1 2 models selected > select #1 2 models selected > select clear > select #1 2 models selected > select clear > select #59/M:10 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel cartoons > select clear > select #59/M:11 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel cartoons > select #59/M:12 6 atoms, 5 bonds, 1 residue, 1 model selected > hide sel cartoons > select #59/M:13 4 atoms, 3 bonds, 1 residue, 1 model selected > hide sel cartoons > select #59/M:14 4 atoms, 3 bonds, 1 residue, 1 model selected > hide sel cartoons > select #59/M:15 4 atoms, 3 bonds, 1 residue, 1 model selected > hide sel cartoons > select #59/M:16 6 atoms, 5 bonds, 1 residue, 1 model selected > hide sel cartoons > select #59/K:255 4 atoms, 3 bonds, 1 residue, 1 model selected > delete sel > select #59/K:254 8 atoms, 7 bonds, 1 residue, 1 model selected > delete sel > select #59/K:253 8 atoms, 7 bonds, 1 residue, 1 model selected > delete sel > select #59/K:252 6 atoms, 5 bonds, 1 residue, 1 model selected > delete sel > select #59/K:251 6 atoms, 5 bonds, 1 residue, 1 model selected > delete sel > select #59/K:250 8 atoms, 7 bonds, 1 residue, 1 model selected > delete sel > select #59/K:249 8 atoms, 7 bonds, 1 residue, 1 model selected > delete sel > select #59/K:248 7 atoms, 6 bonds, 1 residue, 1 model selected > delete sel > select #59/K:247 9 atoms, 8 bonds, 1 residue, 1 model selected > delete sel > save ""/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3 > paper/Chimera sessions/20240806_COPI_leaf_AF3_for_figs_v2.cxs"" > show #!61 models > hide #!1 models > color zone #61 near #59 distance 5.86 > color zone #61 near #59 distance 5.55 > save ""/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3 > paper/Chimera sessions/20240806_COPI_leaf_AF3_for_figs_v2.cxs"" ——— End of log from Tue Aug 6 15:17:45 2024 ——— opened ChimeraX session > hide #!61 models > show #!61 models > hide #!59 models > show #!59 models > hide #!61 models > show #!58 models > hide #!58 models > show #!58 models > show #!61 models > hide #!61 models > show #!61 models > hide #!61 models > show #!56 models > hide #!56 models > show #!57 models > close #61 > combine #1 No structures specified > open ""/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3 > dataset/Structure files/relion_locres_filtered_20240326_GT.mrc"" Opened relion_locres_filtered_20240326_GT.mrc as #60, grid size 292,292,292, pixel 1.71, shown at level 0.00473, step 2, values float32 > select add #60 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #60,1,0,0,94.293,0,1,0,59.794,0,0,1,17.203 > view matrix models #60,1,0,0,87.011,0,1,0,46.591,0,0,1,75.712 > view matrix models #60,1,0,0,62.484,0,1,0,72.607,0,0,1,72.836 > ui tool show ""Fit in Map"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. [Repeated 1 time(s)] > fitmap #60 inMap #1 Fit map relion_locres_filtered_20240326_GT.mrc in map relion_locres_filtered_20240326_GT.mrc using 30918 points correlation = 1, correlation about mean = 1, overlap = 3.365 steps = 92, shift = 5.1, angle = 0.971 degrees Position of relion_locres_filtered_20240326_GT.mrc (#60) relative to relion_locres_filtered_20240326_GT.mrc (#1) coordinates: Matrix rotation and translation 0.99999999 0.00004012 -0.00014956 0.04461249 -0.00004012 1.00000000 0.00001176 -0.00027160 0.00014956 -0.00001176 0.99999999 -0.04335390 Axis -0.07572659 -0.96307673 -0.25835770 Axis point 275.92599265 0.00000000 302.35452588 Rotation angle (degrees) 0.00889794 Shift along axis 0.00808403 > select subtract #60 Nothing selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #60 step 1 > volume #60 level 0.005 > save ""/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3 > paper/Chimera sessions/20240808_COPI_leaf_AF3_for_figs_v5.cxs"" > color #24 #98fcffff > color #24 label_red Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #24 alphav1 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color name label_red #E32723 Color 'label_red' is opaque: rgb(89%, 15.3%, 13.7%) hex: #e32723 > color name label_purple #6C4896 Color 'label_purple' is opaque: rgb(42.4%, 28.2%, 58.8%) hex: #6c4896 > color name arf1v2 #EB70A8 Color 'arf1v2' is opaque: rgb(92.2%, 43.9%, 65.9%) hex: #eb70a8 > color name alphav1 #5786F5 Color 'alphav1' is opaque: rgb(34.1%, 52.5%, 96.1%) hex: #5786f5 > color name alphav2 #2A4B9B Color 'alphav2' is opaque: rgb(16.5%, 29.4%, 60.8%) hex: #2a4b9b > color name betapv1 #53EAF3 Color 'betapv1' is opaque: rgb(32.5%, 91.8%, 95.3%) hex: #53eaf3 > color name betapv2 #759ED9 Color 'betapv2' is opaque: rgb(45.9%, 62%, 85.1%) hex: #759ed9 > color name betav1 #37863D Color 'betav1' is opaque: rgb(21.6%, 52.5%, 23.9%) hex: #37863d > color name betav2 #207B35 Color 'betav2' is opaque: rgb(12.5%, 48.2%, 20.8%) hex: #207b35 > color name deltav1 #CE8041 Color 'deltav1' is opaque: rgb(80.8%, 50.2%, 25.5%) hex: #ce8041 > color name deltav2 #E97408 Color 'deltav2' is opaque: rgb(91.4%, 45.5%, 3.14%) hex: #e97408 > color name epsilonv1 #F06969 Color 'epsilonv1' is opaque: rgb(94.1%, 41.2%, 41.2%) hex: #f06969 > color name gammav1 #2AFF3C Color 'gammav1' is opaque: rgb(16.5%, 100%, 23.5%) hex: #2aff3c > color name gammav2 #61B230 Color 'gammav2' is opaque: rgb(38%, 69.8%, 18.8%) hex: #61b230 > color name zetav1 #E0C819 Color 'zetav1' is opaque: rgb(87.8%, 78.4%, 9.8%) hex: #e0c819 > color name zetav2 #EFE30C Color 'zetav2' is opaque: rgb(93.7%, 89%, 4.71%) hex: #efe30c > color name arf1v1 #FF76AF Color 'arf1v1' is opaque: rgb(100%, 46.3%, 68.6%) hex: #ff76af > color #24 label_red > color #60 white models > color #56 white models > hide #!57 models > hide #!58 models > hide #!59 models > color #38 alphav1 > show #38 models > hide #!60 models > show #39 models > show #41 models > show #42 models > show #!43 models > show #!44 models > show #!45 models > show #!46 models > show #48 models > show #47 models > show #!49 models > show #50 models > show #51 models > show #52 models > show #53 models > show #!54 models > color #39 alphav1 > color #41 betapv1 > color #42 betapv1 > color #43 betav1 > color #44 betav1 > color #45 betav1 > color #46 deltav1 > color #47 gammav1 > color #47 gammav2 > color #48 gammav2 > color #49 gammav2 > color #43 betav2 > color #44 betav2 > color #45 betav2 > color #50 zetav1 > color #51 arf1v1 > color #52 arf1v1 > color #53 arf1v1 > color #47 #acacacff > color #47 gammav2 > color #47 #61db30ff > color #47 #61c730ff > color #47 #58c730ff > color #47 #58de30ff > color name gammav3 #58DE30 Color 'gammav3' is opaque: rgb(34.5%, 87.1%, 18.8%) hex: #58de30 > color #48 gammav3 > color #49 gammav3 > color #51 arf1v2 > color #52 arf1v2 > color #53 arf1v2 > color #38 alphav1 > color #38 alphav2 > color #39 alphav2 > color #54 label_purple > color #55 label_purple > show #55 models > color #11 #801effff > color #11 #801ed1ff > color name label_purplev2 #7F1ED1 Color 'label_purplev2' is opaque: rgb(49.8%, 11.8%, 82%) hex: #7f1ed1 > color #54 label_purplev2 > color #55 label_purplev2 > combine #38 #39 #40 #41 #42 #43 #44 #45 #46 #47 #48 #49 #50 #51 #52 #53 #54 > #55 Remapping chain ID 'D' in 20240711_copi_golph3_alpha_I592-G900.cif #39 to 'E' Remapping chain ID 'D' in fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif #40 to 'I' Remapping chain ID 'E' in fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif #40 to 'J' Remapping chain ID 'F' in 20240711_copi_golph3_betaprime_M1-S586.cif #41 to 'K' Remapping chain ID 'F' in 20240711_copi_golph3_betaprime_L587-D905.cif #42 to 'L' Remapping chain ID 'E' in 20240711_copi_golph3_beta_S711-L953.cif #43 to 'M' Remapping chain ID 'E' in 20240711_copi_golph3_beta_H311-E659.cif #44 to 'N' Remapping chain ID 'E' in 20240711_copi_golph3_beta_M1-H311_K660-A710.cif #45 to 'O' Remapping chain ID 'G' in 20240711_copi_golph3_delta_M1-S273.cif #46 to 'P' Remapping chain ID 'H' in 20240711_copi_golph3_gamma1_K300-F448.cif #47 to 'Q' Remapping chain ID 'H' in 20240711_copi_golph3_gamma1_M1-P299.cif #48 to 'R' Remapping chain ID 'H' in 20240711_copi_golph3_gammm1_T449-R609.cif #49 to 'S' Remapping chain ID 'I' in 20240711_copi_golph3_zeta1.cif #50 to 'T' Remapping chain ID 'B' in 20240711_copi_golph3_beta_Arf1_.cif #51 to 'U' Remapping chain ID 'C' in 20240711_copi_golph3_gamma_Arf1_.cif #52 to 'V' Remapping chain ID 'B' in 20240711_copi_golph3_third_Arf1.cif #53 to 'W' Remapping chain ID 'A' in 20240711_copi_golph3_golph3_M1-.cif #54 to 'X' Remapping chain ID 'A' in 20240711_copi_golph3_golph3_.cif #55 to 'Y' > hide #38 models > hide #39 models > hide #41 models > hide #42 models > hide #!43 models > hide #!44 models > hide #!45 models > hide #!46 models > hide #47 models > hide #48 models > hide #!49 models > hide #50 models > hide #51 models > hide #52 models > hide #53 models > hide #!54 models > hide #55 models > rename #59 combined_model_COPI_GOLPH3_colorset1 > rename #58 relion_locres_filtered_20240326_GT_colorset1.mrc > ui tool show ""Color Zone"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > show #!60 models > color zone #60 near #61 distance 10.26 > color zone #60 near #61 distance 10.73 > color zone #60 near #61 distance 4.91 > volume #60 level 0.01316 > close #61 > combine #38 #39 #41 #42 #43 #44 #45 #46 #47 #48 #49 #50 #51 #52 #53 #54 #55 Remapping chain ID 'D' in 20240711_copi_golph3_alpha_I592-G900.cif #39 to 'E' Remapping chain ID 'F' in 20240711_copi_golph3_betaprime_L587-D905.cif #42 to 'G' Remapping chain ID 'E' in 20240711_copi_golph3_beta_S711-L953.cif #43 to 'H' Remapping chain ID 'E' in 20240711_copi_golph3_beta_H311-E659.cif #44 to 'I' Remapping chain ID 'E' in 20240711_copi_golph3_beta_M1-H311_K660-A710.cif #45 to 'J' Remapping chain ID 'G' in 20240711_copi_golph3_delta_M1-S273.cif #46 to 'K' Remapping chain ID 'H' in 20240711_copi_golph3_gamma1_K300-F448.cif #47 to 'L' Remapping chain ID 'H' in 20240711_copi_golph3_gamma1_M1-P299.cif #48 to 'M' Remapping chain ID 'H' in 20240711_copi_golph3_gammm1_T449-R609.cif #49 to 'N' Remapping chain ID 'I' in 20240711_copi_golph3_zeta1.cif #50 to 'O' Remapping chain ID 'B' in 20240711_copi_golph3_third_Arf1.cif #53 to 'P' Remapping chain ID 'A' in 20240711_copi_golph3_golph3_.cif #55 to 'Q' The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > color zone #60 near #61 distance 4.91 > hide #!60 models > ui mousemode right select > select #61/K:255 4 atoms, 3 bonds, 1 residue, 1 model selected > delete sel > select #61/K:254 8 atoms, 7 bonds, 1 residue, 1 model selected > delete sel > select #61/K:252 6 atoms, 5 bonds, 1 residue, 1 model selected > select #61/K:253 8 atoms, 7 bonds, 1 residue, 1 model selected > delete sel > select clear > select #61/K:252 6 atoms, 5 bonds, 1 residue, 1 model selected > delete sel > select #61/K:251 6 atoms, 5 bonds, 1 residue, 1 model selected > delete sel > select #61/K:250 8 atoms, 7 bonds, 1 residue, 1 model selected > delete sel > select #61/K:249 8 atoms, 7 bonds, 1 residue, 1 model selected > delete sel > select #61/K:248 7 atoms, 6 bonds, 1 residue, 1 model selected > delete sel > show #!60 models > color single #60 > color zone #60 near #61 distance 4.91 > volume #60 level 0.008979 > color zone #60 near #61 distance 4.85 > color zone #60 near #61 distance 6.64 > color #1 #ebebebff models > color #1 #d6d6d6ff models > volume #60 level 0.008 > hide #!61 models > rename #61 combine_model_COPI_GOLPH3_colorset2 > rename #60 relion_locres_filtered_20240326_GT_colorset2.mrc > save /Users/becca/Desktop/image1.png supersample 3 > color #1 #d6d6d6cc models > color #1 #d6d6d69a models > color #1 #d6d6d699 models > show #!1 models > hide #!60 models > show #!61 models > save /Users/becca/Desktop/image2.png supersample 3 > save /Users/becca/Desktop/image3.png supersample 3 > hide #!61 models > show #!60 models > hide #!1 models > save /Users/becca/Desktop/image4.png supersample 3 > color #60 #ffffffb9 models > color #60 #ffffffb7 models > color zone #60 near #61 distance 6.64 > color #60 #ffffffb8 models > save ""/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3 > paper/Chimera sessions/20240808_COPI_leaf_AF3_for_figs_v6.cxs"" > hide #!60 models > show #!61 models > color #61/chain Q label_purple Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #61/chainQ label_purple > color #61/chainP label_purple > color #61/chainP blue > color #61/P blue > undo > color #61/Q label_purple > color #61/R label_purple > color #61/p label_purple > undo > color #61/o label_purple > undo > color #61/a label_purple > open ""/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3 > dataset/Structure files/relion_locres_filtered_20240326_GT.mrc"" Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #62, grid size 292,292,292, pixel 1.71, shown at level 0.00473, step 2, values float32 > color #62 white models The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #62 step 1 > volume #62 level 0.008 > select add #62 2 models selected > show #!60 models > ui mousemode right ""translate selected models"" > view matrix models #62,1,0,0,82.731,0,1,0,56.524,0,0,1,33.509 > view matrix models #62,1,0,0,79.094,0,1,0,68.742,0,0,1,76.061 > view matrix models #62,1,0,0,75.329,0,1,0,66.28,0,0,1,82.958 > view matrix models #62,1,0,0,62.569,0,1,0,73.325,0,0,1,77.393 > fitmap #62 inMap #1 Fit map relion_locres_filtered_20240326_GT_colorset2.mrc in map relion_locres_filtered_20240326_GT.mrc using 67258 points correlation = 1, correlation about mean = 1, overlap = 21.45 steps = 52, shift = 2.4, angle = 0.977 degrees Position of relion_locres_filtered_20240326_GT_colorset2.mrc (#62) relative to relion_locres_filtered_20240326_GT.mrc (#1) coordinates: Matrix rotation and translation 1.00000000 -0.00001875 -0.00002627 0.01893074 0.00001875 1.00000000 -0.00002003 -0.00224731 0.00002628 0.00002003 1.00000000 0.00132667 Axis 0.52718994 -0.69167549 0.49361502 Axis point 178.51353821 0.00000000 475.91658522 Rotation angle (degrees) 0.00217651 Shift along axis 0.01218937 > select subtract #62 Nothing selected > color zone #62 near #61 distance 10.26 > hide #!60 models > hide #!61 models > surface dust #62 size 17.1 > show #!60 models > surface dust #60 size 17.1 > surface dust #62 size 17.1 > hide #!62 models > hide #!60 models > show #!62 models > save /Users/becca/Desktop/image5.png supersample 3 > hide #!62 models > show #!61 models > show #!1 models > save /Users/becca/Desktop/image6.png supersample 3 > hide #!1 models > show #!1 models > save /Users/becca/Desktop/image7.png supersample 3 > hide #!1 models > hide #!61 models > show #!62 models > save /Users/becca/Desktop/image8.png supersample 3 > save /Users/becca/Desktop/image9.png supersample 3 > hide #!62 models > show #!61 models > show #!1 models > save /Users/becca/Desktop/image10.png supersample 3 > hide #!1 models > color #61/b gammav2 > color #61/c gammav2 > color #61/d gammav2 > color #61/e gammav2 > color #61/f gammav2 > color #61/g gammav2 > color #61/f betapv2 > color #61/g betapv2 > color #61/h gammav2 > color #61/i gammav2 > color #61/j gammav2 > color #61/k gammav2 > color #61/l gammav2 > color #61/m gammav2 > color #61/n gammav2 > open ""/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3 > dataset/Structure files/relion_locres_filtered_20240326_GT.mrc"" Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #63, grid size 292,292,292, pixel 1.71, shown at level 0.00473, step 2, values float32 > color #63 white models > select add #63 2 models selected > view matrix models #63,1,0,0,75.253,0,1,0,55.49,0,0,1,11.12 > view matrix models #63,1,0,0,90.631,0,1,0,59.745,0,0,1,63.045 > view matrix models #63,1,0,0,68.515,0,1,0,55.118,0,0,1,78.162 > view matrix models #63,1,0,0,66.634,0,1,0,67.567,0,0,1,67.24 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #63 step 1 > volume #63 level 0.008 > fitmap #63 inMap #1 Fit map relion_locres_filtered_20240326_GT_colorset2.mrc in map relion_locres_filtered_20240326_GT.mrc using 67258 points correlation = 0.5415, correlation about mean = 0.1363, overlap = 7.061 steps = 116, shift = 7.07, angle = 5.74 degrees Position of relion_locres_filtered_20240326_GT_colorset2.mrc (#63) relative to relion_locres_filtered_20240326_GT.mrc (#1) coordinates: Matrix rotation and translation 0.99362306 0.08167924 -0.07772850 -0.92565197 -0.08058175 0.99660031 0.01715800 10.92285128 0.07886570 -0.01078508 0.99682691 -23.17442071 Axis -0.12297538 -0.68915930 -0.71409839 Axis point 213.07603457 14.21459699 0.00000000 Rotation angle (degrees) 6.52360209 Shift along axis 9.13506435 > show #!1 models > view matrix models > #63,0.99499,0.069158,-0.072244,60.427,-0.06889,0.99761,0.0061881,84.855,0.072498,-0.0011802,0.99737,52.494 > view matrix models > #63,0.99499,0.069158,-0.072244,61.276,-0.06889,0.99761,0.0061881,84.838,0.072498,-0.0011802,0.99737,55.066 > show #!60 models > hide #!60 models > show #!60 models > hide #!60 models > show #!60 models > hide #!60 models > hide #!61 models > fitmap #63 inMap #1 Fit map relion_locres_filtered_20240326_GT_colorset2.mrc in map relion_locres_filtered_20240326_GT.mrc using 67258 points correlation = 0.5415, correlation about mean = 0.1362, overlap = 7.06 steps = 64, shift = 3.65, angle = 0.0144 degrees Position of relion_locres_filtered_20240326_GT_colorset2.mrc (#63) relative to relion_locres_filtered_20240326_GT.mrc (#1) coordinates: Matrix rotation and translation 0.99360075 0.08181777 -0.07786785 -0.90541724 -0.08073064 0.99659074 0.01701358 11.00212074 0.07899439 -0.01061838 0.99681851 -23.23121300 Axis -0.12141808 -0.68927119 -0.71425687 Axis point 213.54257878 14.23471065 0.00000000 Rotation angle (degrees) 6.53375156 Shift along axis 9.11954274 > view matrix models > #63,0.99497,0.069297,-0.072381,72.42,-0.069041,0.9976,0.006042,87.797,0.072626,-0.0010144,0.99736,54.674 > fitmap #63 inMap #1 Fit map relion_locres_filtered_20240326_GT_colorset2.mrc in map relion_locres_filtered_20240326_GT.mrc using 67258 points correlation = 1, correlation about mean = 1, overlap = 21.46 steps = 152, shift = 9.34, angle = 6.54 degrees Position of relion_locres_filtered_20240326_GT_colorset2.mrc (#63) relative to relion_locres_filtered_20240326_GT.mrc (#1) coordinates: Matrix rotation and translation 1.00000000 -0.00003458 0.00000150 0.00697228 0.00003458 1.00000000 -0.00002441 0.00466924 -0.00000150 0.00002441 1.00000000 -0.01150830 Axis 0.57631042 0.03541164 0.81646330 Axis point -140.35346721 288.49393815 0.00000000 Rotation angle (degrees) 0.00242674 Shift along axis -0.00521256 > select subtract #63 Nothing selected > hide #!1 models > show #!62 models > hide #!62 models > show #!60 models > hide #!60 models > show #!61 models > hide #!61 models > color zone #63 near #61 distance 10.26 > color zone #63 near #61 distance 10.66 > color zone #63 near #61 distance 8.31 > surface dust #63 size 17.1 > show #!62 models > hide #!62 models > show #!62 models > hide #!62 models > show #!62 models > hide #!62 models > save /Users/becca/Desktop/image1.png supersample 3 > hide #!63 models > show #!61 models > show #!1 models > save /Users/becca/Desktop/image2.png supersample 3 > save /Users/becca/Desktop/image3.png supersample 3 > hide #!1 models The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > hide #!61 models > show #!63 models > save /Users/becca/Desktop/image4.png supersample 3 > save /Users/becca/Desktop/image5.png supersample 3 > hide #!63 models > show #!62 models > hide #!62 models > show #!62 models > hide #!62 models > show #!61 models > show #!1 models > save /Users/becca/Desktop/image6.png supersample 3 > open ""/Users/becca/Desktop/Postdoc/COPI notebooks and > resources/Processing/Files from > csparc/cryosparc_P126_J2191_class_02_final_volume.mrc"" Opened cryosparc_P126_J2191_class_02_final_volume.mrc as #64, grid size 180,180,180, pixel 2.42, shown at level 0.333, step 1, values float32 > open ""/Users/becca/Desktop/Postdoc/COPI notebooks and > resources/Processing/Files from > csparc/cryosparc_P126_J2191_class_01_final_volume.mrc"" Opened cryosparc_P126_J2191_class_01_final_volume.mrc as #65, grid size 180,180,180, pixel 2.42, shown at level 0.333, step 1, values float32 > open ""/Users/becca/Desktop/Postdoc/COPI notebooks and > resources/Processing/Files from > csparc/cryosparc_P126_J2191_class_00_final_volume.mrc"" Opened cryosparc_P126_J2191_class_00_final_volume.mrc as #66, grid size 180,180,180, pixel 2.42, shown at level 0.337, step 1, values float32 > close #66 > close #65 > close #64 > save ""/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3 > paper/Chimera sessions/20240808_COPI_leaf_AF3_for_figs_v7.cxs"" ——— End of log from Fri Aug 9 13:21:55 2024 ——— opened ChimeraX session > save ""/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3 > paper/Chimera sessions/20240808_COPI_leaf_AF3_for_figs_v7_with_files.cxs"" > includeMaps true ——— End of log from Wed Sep 25 22:56:27 2024 ——— opened ChimeraX session OpenGL version: 4.1 Metal - 88.1 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,1 Model Number: Z14V000GPB/A Chip: Unknown Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 32 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: 29 days, 9 hours, 10 minutes Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 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: 2.2.4 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: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 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: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 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: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 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-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 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: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 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: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 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: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 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: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 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: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect assigned normal Window Toolkit all ChimeraX