id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17455 Crash on Mac waking from sleep fry@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.3.1-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 0x0000000201930840 (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, 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, openmm._openmm, openmm.app.internal.compiled, chimerax.map._map, chimerax.surface._surface, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, 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, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, psutil._psutil_osx, psutil._psutil_posix, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath, cython.cimports.libc.math, scipy._lib._ccallback_c, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct (total: 120) 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""\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation"", ""name"" : ""Foundation"", ""CFBundleVersion"" : ""3302.1.400"" } ], ""sharedCache"" : { ""base"" : 6840336384, ""size"" : 4865835008, ""uuid"" : ""d272b91e-f9f0-3854-b5b9-508b21c25dcc"" }, ""vmSummary"" : ""ReadOnly portion of Libraries: Total=2.0G resident=0K(0%) swapped_out_or_unallocated=2.0G(100%)\nWritable regions: Total=12.4G written=6906K(0%) resident=6906K(0%) swapped_out=0K(0%) unallocated=12.4G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG image 1120K 53 \nColorSync 656K 33 \nCoreAnimation 2784K 139 \nCoreGraphics 80K 5 \nCoreServices 624K 2 \nCoreUI image data 5936K 49 \nFoundation 32K 2 \nKernel Alloc Once 32K 1 \nMALLOC 10.5G 198 \nMALLOC guard page 288K 18 \nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 56.9M 60 \nStack 204.0M 60 \nVM_ALLOCATE 635.0M 280 \nVM_ALLOCATE (reserved) 640.0M 6 reserved VM address space (unallocated)\n__AUTH 5288K 672 \n__AUTH_CONST 70.9M 920 \n__CTF 824 1 \n__DATA 36.6M 1166 \n__DATA_CONST 35.8M 1174 \n__DATA_DIRTY 2763K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 650.9M 249 \n__OBJC_RW 2374K 1 \n__TEXT 1.3G 1195 \n__TPRO_CONST 272K 2 \ndyld private memory 304K 5 \nmapped file 334.8M 78 \nowned unmapped memory 411.7M 1 \npage table in kernel 6906K 1 \nshared memory 3152K 20 \n=========== ======= ======= \nTOTAL 14.9G 6747 \nTOTAL, minus reserved VM space 14.3G 6747 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""d433786abb8cb197a80310973d7e14fb5333d889"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""64b21a7351cbb02ce3442e4e"", ""factorPackIds"" : { ""REMINDERS_GROCERY"" : ""6647f0f7b6a75d3dc32993e7"" }, ""deploymentId"" : 240000042 }, { ""rolloutId"" : ""64c17a9925d75a7281053d4c"", ""factorPackIds"" : { ""SIRI_AUDIO_DISABLE_MEDIA_ENTITY_SYNC"" : ""64d29746ad29a465b3bbeace"" }, ""deploymentId"" : 240000002 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/michellefry/Partners HealthCare Dropbox/Michelle > Fry/ChaoLab/parasites/symposium/HHMI_sym_Apr_2025/20250417_J1286_images.cxs"" Opened J1259_flip.mrc as #2, grid size 480,480,480, pixel 0.822, shown at level 0.0773, step 1, values float32 opened ChimeraX session > hide #!10 models > open ""/Users/michellefry/Partners HealthCare Dropbox/Michelle > Fry/ChaoLab/parasites/acanthamoeba/mito_lysate/ATPsynthase/chimera_sessions/coot/20250418_all.pdb"" Chain information for 20250418_all.pdb #13 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H I J K L M N O P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available > hide #!13 atoms > show #!13 cartoons Computing secondary structure > select clear > hide sele Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide sel > select clear > color #13 #009193ff > close #13 > open ""/Users/michellefry/Partners HealthCare Dropbox/Michelle > Fry/ChaoLab/parasites/acanthamoeba/mito_lysate/ATPsynthase/chimera_sessions/coot/20250418_all- > coot-13.pdb"" Chain information for 20250418_all-coot-13.pdb #13 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H I J K L M N O P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available > hide #!13 atoms > show #!13 cartoons Computing secondary structure > select clear Drag select of 2 J1259_flip.mrc > select clear > select #2 4 models selected > select clear > hide sel > color #14 red > color #13 red > color #13 #009193ff > select down 1 pseudobond, 1 model selected > select up 4 pseudobonds, 1 model selected > select up 40161 atoms, 40883 bonds, 4 pseudobonds, 5180 residues, 2 models selected > select up 309687 atoms, 315119 bonds, 4 pseudobonds, 40140 residues, 15 models selected > select up 309687 atoms, 315119 bonds, 4 pseudobonds, 40140 residues, 15 models selected > select up 309687 atoms, 315119 bonds, 4 pseudobonds, 40140 residues, 15 models selected > select down 40161 atoms, 40883 bonds, 4 pseudobonds, 5180 residues, 2 models selected > select down 4 pseudobonds, 1 model selected > color #9/R light blue > color #13/R light blue > color #13/V teal > color #13/T light blue > color #13/S light blue > color #13/R light blue > select clear > color #13/C sea green > color #13/B hot pink > color #13/R light blue > color #13/Q navy > color #13/G dodger blue > color #13/F lightblue purple Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color #13/F purple > color #13/F orchid > color #13/F medium purple > color #13/A magenta > select #13/B 1955 atoms, 1994 bonds, 244 residues, 1 model selected > select #13/C 1155 atoms, 1176 bonds, 154 residues, 1 model selected > select #13/D 350 atoms, 354 bonds, 45 residues, 1 model selected > color #13/D light pink > select clear > color #13/D salmon > color #13/E tan > color #9/N purple > color #13/N purple > color #13/N dark slate blue > color #13/H dark slate blue > color #13/I dark slate blue > color #13/J dark slate blue > color #13/K dark slate blue > color #13/L dark slate blue > color #13/M dark slate blue > color #13/N dark slate blue > color #13/O dark slate blue > color #13/P dark slate blue > color #13/X aquamarine > color #13/X olive drab > select clear > hide #!13 models > color #2 darkgrey models > color #2 #919191ff models > ui tool show ""Hide Dust"" > surface dust #2 size 5.81 > surface dust #2 size 5.34 > surface dust #2 size 10.37 > surface dust #2 size 11.08 > surface dust #2 size 10.71 > save J1286_map.png transparentBackground true > hide #!2 models > show #!13 models > show #!2 models > color #2 #5e5e5eff models > color #2 #5e5e5ea1 models > color #2 #5e5e5e6f models > color #2 #5e5e5e64 models > color #2 #5e5e5e63 models > hide #!13 models > show #!13 models > hide #!2 models > save J1286_model.png transparentBackground true > show #!2 models > show #7 models > open ""/Users/michellefry/Partners HealthCare Dropbox/Michelle > Fry/ChaoLab/parasites/acanthamoeba/mito_lysate/ATPsynthase/chimera_sessions/coot/20250418_all- > coot-13.pdb"" Chain information for 20250418_all-coot-13.pdb #14 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H I J K L M N O P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available > color #14 darkgrey > color #14 #ebebebff > hide #7#!13-14 atoms > show #7#!13-14 cartoons Computing secondary structure > hide #!13 models > select clear > ui mousemode right select > select clear > select up 4 pseudobonds, 1 model selected > select down 1 pseudobond, 1 model selected > hide sel > color #14/B pink > color #14/B hot pink > color #14 silver > color #2 #424242ff models > color #2 #4242424c models > color #2 #4242424d models > color #14/B hot pink > color #14/W teal > select #14/s 3748 atoms, 3806 bonds, 487 residues, 1 model selected > select #14/T 3764 atoms, 3823 bonds, 490 residues, 1 model selected > color #14/T light blue > select clear > color #14 #d6d6d6ff > color #14/B hot pink > open ""/Users/michellefry/Partners HealthCare Dropbox/Michelle > Fry/ChaoLab/parasites/acanthamoeba/mito_lysate/ATPsynthase/chimera_sessions/coot/20250418_all- > coot-13.pdb"" Chain information for 20250418_all-coot-13.pdb #15 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H I J K L M N O P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available > color #15 #d6d6d6ff > hide #7#!14-15 surfaces > hide #7#!14-15 atoms > show #7#!14-15 cartoons Computing secondary structure > color #14 silver > color #14 #d6d6d6ff > color #14/B hot pink > color #15/W teal > color #15/T light blue > hide #!15 models > save J1286_mdh.png transparentBackground true > show #!15 models > hide #!14 models > select clear Drag select of 1 pseudobonds > hide sel > ui tool show ""Side View"" > save J1286_stalk.png transparentBackground true > save ""/Users/michellefry/Partners HealthCare Dropbox/Michelle > Fry/ChaoLab/parasites/acanthamoeba/mito_lysate/ATPsynthase/chimera_sessions/20250418_J1259.cxs"" > hide target m > select add #15 40161 atoms, 40883 bonds, 4 pseudobonds, 5180 residues, 2 models selected > select subtract #15 Nothing selected > open ""/Users/michellefry/Partners HealthCare Dropbox/Michelle > Fry/ChaoLab/parasites/acanthamoeba/mito_lysate/ATPsynthase/chimera_sessions/model_angelo/j1474_AcCV_TM.pdb"" Chain information for j1474_AcCV_TM.pdb #16 --- Chain | Description H | No description available I | No description available J | No description available K | No description available Computing secondary structure > open ""/Users/michellefry/Partners HealthCare Dropbox/Michelle > Fry/ChaoLab/parasites/acanthamoeba/mito_lysate/ATPsynthase/chimera_sessions/maps/J1474_flip.mrc"" Opened J1474_flip.mrc as #17, grid size 200,200,200, pixel 1.64, shown at level 0.168, step 1, values float32 > view > volume #17 level 0.2834 > hide #!17 models > color #16/H turquiose Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #16/H turquooise Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #16/H turquoise > color #16/H:46-64 blue > color #16/H:20-64 blue > color #16/H:1-15 turquoise > color #16/H:20-25 turquoise > color #16/H:26-37 turquoise > color #16/H turquoise > select #16/H:12 31 atoms, 28 bonds, 4 residues, 1 model selected > select up 789 atoms, 802 bonds, 97 residues, 1 model selected > select up 1486 atoms, 1518 bonds, 182 residues, 1 model selected > color sele blyue Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color sele blue Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > select down 789 atoms, 802 bonds, 97 residues, 1 model selected > select down 31 atoms, 28 bonds, 4 residues, 1 model selected > select up 789 atoms, 802 bonds, 97 residues, 1 model selected > select down 31 atoms, 28 bonds, 4 residues, 1 model selected > select down 31 atoms, 28 bonds, 4 residues, 1 model selected > select down 31 atoms, 28 bonds, 4 residues, 1 model selected > select down 31 atoms, 28 bonds, 4 residues, 1 model selected > select clear > close #16 > open ""/Users/michellefry/Partners HealthCare Dropbox/Michelle > Fry/ChaoLab/parasites/acanthamoeba/mito_lysate/ATPsynthase/chimera_sessions/model_angelo/j1474_AcCV_TM.pdb"" Chain information for j1474_AcCV_TM.pdb #16 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available > hide #!16 atoms > show #!16 cartoons Computing secondary structure > select clear Drag select of 4 residues > select clear Drag select of 2 residues > select clear > hide sel > select clear Drag select of 5 residues > select clear Drag select of 2 residues > select clear > hide sel > select clear > ui mousemode right ""rotate selected models"" > ui mousemode right translate > show #!17 models > view > select clear > hide #!17 models > show #!17 models > hide #!17 models > show #!17 models > hide #!17 models > color #16/A teal > color #16/B light blue > color #16/B tan > color #16/C violet red Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color #16/C violet red Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color #16/C dark magenta > color #16/C blue > color #16/D dark magenta > color #16/D orchid > color #16/E medium purple > color #16/H teal > color #16/H blue > color #16/C dodger blue > color #16/A blue > color #16/F olive sludge Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color #16/F olive drab > color #16/F medium purple > color #16/G olive drab > color #16/E plum > select clear > hide sel > color #16/E pink > select clear > turn y 90 > turn x 90 > save J1474_dimer.png transparentBackground true > hide #!16 models > show #!17 models > save J1474_model.png transparentBackground true > open > /Users/michellefry/Downloads/cryosparc_P142_J1493_class_03_00042_volume_sharp.mrc Opened cryosparc_P142_J1493_class_03_00042_volume_sharp.mrc as #18, grid size 128,128,128, pixel 3.39, shown at level 0.305, step 1, values float32 > volume #18 level 0.3154 > close #18 > open > /Users/michellefry/Downloads/cryosparc_P142_J1493_class_02_00042_volume_sharp.mrc Opened cryosparc_P142_J1493_class_02_00042_volume_sharp.mrc as #18, grid size 128,128,128, pixel 3.39, shown at level 0.39, step 1, values float32 > lighting full > open > /Users/michellefry/Downloads/cryosparc_P142_J1496_003_volume_map_sharp.mrc Opened cryosparc_P142_J1496_003_volume_map_sharp.mrc as #19, grid size 132,132,132, pixel 3.29, shown at level 0.355, step 1, values float32 > volume #19 level 0.6828 > close #19 > open > /Users/michellefry/Downloads/cryosparc_P142_J1497_003_volume_map_sharp.mrc Opened cryosparc_P142_J1497_003_volume_map_sharp.mrc as #19, grid size 132,132,132, pixel 3.29, shown at level 0.355, step 1, values float32 > volume #19 level 0.6455 > close #19 > open > /Users/michellefry/Downloads/cryosparc_P142_J1503_003_volume_map_sharp.mrc Opened cryosparc_P142_J1503_003_volume_map_sharp.mrc as #19, grid size 220,220,220, pixel 1.64, shown at level 0.171, step 1, values float32 > open > /Users/michellefry/Downloads/fold_acciii_dimer/fold_acciii_dimer_model_0.cif Chain information for fold_acciii_dimer_model_0.cif #20 --- Chain | Description A B | . C D | . E F | . G H | . I J | . K L | . M N | . O P | . Q R | . S T | . > hide #20 atoms > show #20 cartoons Computing secondary structure > color #20 #919191ff > color #20 bychain > select add #20 34786 atoms, 35678 bonds, 4418 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models #20,1,0,0,175.51,0,1,0,0.42495,0,0,1,161.71 > view matrix models #20,1,0,0,213.19,0,1,0,160.28,0,0,1,152.8 > view matrix models #20,1,0,0,185.91,0,1,0,172.8,0,0,1,177.86 > ui mousemode right ""rotate selected models"" > view matrix models > #20,0.73693,-0.30146,-0.60502,190.99,-0.17742,0.77741,-0.60345,176.55,0.65227,0.55204,0.51942,168.56 > view matrix models > #20,0.61734,-0.37719,-0.69037,192.88,-0.12316,0.8204,-0.55836,175.67,0.777,0.42972,0.46002,167.31 > ui mousemode right ""translate selected models"" > view matrix models > #20,0.61734,-0.37719,-0.69037,179.92,-0.12316,0.8204,-0.55836,182.46,0.777,0.42972,0.46002,159.58 > ui tool show ""Fit in Map"" > fitmap #20 inMap #19 Fit molecule fold_acciii_dimer_model_0.cif (#20) to map cryosparc_P142_J1503_003_volume_map_sharp.mrc (#19) using 34786 atoms average map value = 0.1505, steps = 92 shifted from previous position = 2 rotated from previous position = 7.25 degrees atoms outside contour = 20315, contour level = 0.17104 Position of fold_acciii_dimer_model_0.cif (#20) relative to cryosparc_P142_J1503_003_volume_map_sharp.mrc (#19) coordinates: Matrix rotation and translation 0.57804038 -0.28567928 -0.76436684 180.67289760 -0.21494950 0.85032515 -0.48035806 181.50838321 0.78718869 0.44196662 0.43011565 161.18688777 Axis 0.51059272 -0.85893068 0.03915553 Axis point -6.26273325 0.00000000 278.13041658 Rotation angle (degrees) 64.58062447 Shift along axis -57.34149439 > volume #19 level 0.1771 > volume #19 level 0.2487 > fitmap #20 inMap #19 Fit molecule fold_acciii_dimer_model_0.cif (#20) to map cryosparc_P142_J1503_003_volume_map_sharp.mrc (#19) using 34786 atoms average map value = 0.1505, steps = 48 shifted from previous position = 0.0417 rotated from previous position = 0.0206 degrees atoms outside contour = 27824, contour level = 0.2487 Position of fold_acciii_dimer_model_0.cif (#20) relative to cryosparc_P142_J1503_003_volume_map_sharp.mrc (#19) coordinates: Matrix rotation and translation 0.57812353 -0.28556355 -0.76434720 180.66973912 -0.21473094 0.85049121 -0.48016177 181.49657825 0.78718728 0.44172181 0.43036965 161.14659133 Axis 0.51041613 -0.85903280 0.03921765 Axis point -6.28880036 0.00000000 278.15624680 Rotation angle (degrees) 64.56466185 Shift along axis -57.37497342 > select clear > select add #20 34786 atoms, 35678 bonds, 4418 residues, 1 model selected > ui mousemode right ""rotate selected models"" > view matrix models > #20,-0.23295,0.52031,0.82159,187.08,-0.012296,-0.84634,0.53249,181.66,0.97241,0.11394,0.20356,159.85 > fitmap #20 inMap #19 Fit molecule fold_acciii_dimer_model_0.cif (#20) to map cryosparc_P142_J1503_003_volume_map_sharp.mrc (#19) using 34786 atoms average map value = 0.1505, steps = 160 shifted from previous position = 7.2 rotated from previous position = 26.7 degrees atoms outside contour = 27814, contour level = 0.2487 Position of fold_acciii_dimer_model_0.cif (#20) relative to cryosparc_P142_J1503_003_volume_map_sharp.mrc (#19) coordinates: Matrix rotation and translation -0.57801079 0.28563452 0.76440595 181.00820440 0.21504287 -0.85031129 0.48034079 180.17385482 0.78718492 0.44202221 0.43006543 161.15331913 Axis -0.45896686 -0.27283869 -0.84552260 Axis point 48.08569748 63.37247405 0.00000000 Rotation angle (degrees) 177.60752748 Shift along axis -268.49393963 > volume flip #19 Opened cryosparc_P142_J1503_003_volume_map_sharp.mrc z flip as #21, grid size 220,220,220, pixel 1.64, shown at step 1, values float32 > view matrix models > #20,0.40573,-0.91123,-0.071066,172.24,-0.27886,-0.19746,0.93981,184.39,-0.87041,-0.36149,-0.33422,186.09 > fitmap #20 inMap #21 Fit molecule fold_acciii_dimer_model_0.cif (#20) to map cryosparc_P142_J1503_003_volume_map_sharp.mrc z flip (#21) using 34786 atoms average map value = 0.2025, steps = 112 shifted from previous position = 15.7 rotated from previous position = 12.8 degrees atoms outside contour = 22657, contour level = 0.2487 Position of fold_acciii_dimer_model_0.cif (#20) relative to cryosparc_P142_J1503_003_volume_map_sharp.mrc z flip (#21) coordinates: Matrix rotation and translation 0.55289423 -0.81459960 -0.17531540 180.24550430 -0.27387795 -0.37636984 0.88506306 180.47122902 -0.78695543 -0.44133123 -0.43119357 198.79691613 Axis -0.85161770 0.39270636 0.34717288 Axis point 0.00000000 188.97580159 83.93093861 Rotation angle (degrees) 128.85374616 Shift along axis -13.61116443 > select clear > lighting shadows false > hide #!21 models > color #20 darkgrey > color #20 #d783ffff > color #20 #7a81ffff > color #20/Q dodger blue > color #20/C dodger blue > color #20/E dodger blue > color #20/G dodger blue > color #20/K dodger blue > color #20/O dodger blue > color #20/T dodger blue > color #20/M dodger blue > select #20/M:95 6 atoms, 5 bonds, 1 residue, 1 model selected > select up 121 atoms, 121 bonds, 14 residues, 1 model selected > select up 1011 atoms, 1032 bonds, 122 residues, 1 model selected > select clear > color #20/B dodger blue > color #20/J dodger blue > turn x, 90 Expected an axis vector or a keyword > turn x 90 > show #!21 models > color #21 #ffb2b29f models > color #21 #ffb2b29e models > select clear > volume #19 level 0.2534 > volume #21 level 0.2049 > volume #21 level 0.2191 > volume #21 level 0.2274 > save ""/Users/michellefry/Partners HealthCare Dropbox/Michelle > Fry/ChaoLab/parasites/acanthamoeba/mito_lysate/ComplexIII/maps/J1503_flip.mrc"" > models #21 > save ""/Users/michellefry/Partners HealthCare Dropbox/Michelle > Fry/ChaoLab/parasites/acanthamoeba/mito_lysate/ComplexIII/AcCIII_dimer_model0.pdb"" > models #20 > open > /Users/michellefry/Downloads/cryosparc_P142_J1524_006_volume_map_sharp.mrc Opened cryosparc_P142_J1524_006_volume_map_sharp.mrc as #22, grid size 220,220,220, pixel 1.64, shown at level 0.188, step 1, values float32 > hide #20 models > volume #22 level 0.2179 > close #22 > open ""/Users/michellefry/Partners HealthCare Dropbox/Michelle > Fry/ChaoLab/parasites/acanthamoeba/mito_lysate/ATPsynthase/chimera_sessions/20250418_J1259.cxs"" Opened J1259_flip.mrc as #2, grid size 480,480,480, pixel 0.822, shown at level 0.0773, step 1, values float32 opened ChimeraX session > open ""/Users/michellefry/Partners HealthCare Dropbox/Michelle > Fry/ChaoLab/parasites/acanthamoeba/mito_lysate/ComplexIII/maps/J1503_flip.mrc"" Opened J1503_flip.mrc as #16, grid size 220,220,220, pixel 1.64, shown at level 0.171, step 1, values float32 > open ""/Users/michellefry/Partners HealthCare Dropbox/Michelle > Fry/ChaoLab/parasites/acanthamoeba/mito_lystae/ComplexIII/ccpem/Flex- > EM_1/1_MD/final1_mdcg.pdb"" Chain information for final1_mdcg.pdb #17 --- Chain | Description A B | No description available C D | No description available E F | No description available G H | No description available I J | No description available K L | No description available M N | No description available O P | No description available Q R | No description available S T | No description available > hide #!2 models > hide #7 models > hide #!15 models > hide #17 atoms > show #17 cartoons Computing secondary structure > lighting full > ui tool show ""Side View"" > color #16 #99bfe5be models > color #16 #99bfe5bd models > graphics silhouettes false > lighting flat > lighting full > volume #16 level 0.2162 > graphics silhouettes false > view sel No displayed objects specified. > view sel No displayed objects specified. > view > view orient > view sel No displayed objects specified. > view > view orient > turn x 90 > color #17 #005493ff > color #16 #929292ff models > volume #16 level 0.2336 > color #16 #929292b7 models > color #16 #929292b8 models > cartoon style #16-17 modeHelix tube sides 20 > color #16 #929292c8 models > color #16 #929292cf models > lighting simple > close #16 > close #17 > show #!15 models > show #!14 models > hide #!15 models > show #!15 models > show #!13 models > show #!2 models > open > /Users/michellefry/Downloads/cryosparc_P142_J1561_006_volume_map_sharp.mrc Opened cryosparc_P142_J1561_006_volume_map_sharp.mrc as #16, grid size 440,440,440, pixel 0.822, shown at level 0.0764, step 2, values float32 > volume flip #16 Opened cryosparc_P142_J1561_006_volume_map_sharp.mrc z flip as #17, grid size 440,440,440, pixel 0.822, shown at step 1, values float32 > volume #17 color #929292 > volume #17 level 0.09467 > ui tool show ""Fit in Map"" > fitmap #17 inMap #2 Fit map cryosparc_P142_J1561_006_volume_map_sharp.mrc z flip in map J1259_flip.mrc using 506557 points correlation = 0.647, correlation about mean = 0.2172, overlap = 2840 steps = 724, shift = 22.4, angle = 38.2 degrees Position of cryosparc_P142_J1561_006_volume_map_sharp.mrc z flip (#17) relative to J1259_flip.mrc (#2) coordinates: Matrix rotation and translation 0.97150458 0.19031122 -0.14128157 -14.01432094 -0.07195988 0.80476203 0.58921970 -77.03624534 0.22583316 -0.56226303 0.79552477 123.38532463 Axis -0.93107933 -0.29684592 -0.21207022 Axis point 0.00000000 158.28762105 178.27943650 Rotation angle (degrees) 38.19640510 Shift along axis 9.74998611 > volume #17 color #00fdff > select add #17 1 pseudobond, 3 models selected > view matrix models > #15.1,1,0,0,0,0,1,0,0,0,0,1,0,#17,0.42795,0.85249,-0.30021,-8.106,-0.69091,0.52271,0.49942,100.26,0.58267,-0.0063061,0.81268,-43.589 > view matrix models > #15.1,1,0,0,0,0,1,0,0,0,0,1,0,#17,0.70253,0.66976,-0.24057,-34.78,-0.47998,0.69552,0.53467,25.187,0.52542,-0.26015,0.8101,12.859 > view matrix models > #15.1,1,0,0,0,0,1,0,0,0,0,1,0,#17,0.060194,-0.97819,-0.19882,369.54,0.62073,-0.1193,0.7749,-67.1,-0.78171,-0.17005,0.6,267.28 > view matrix models > #15.1,1,0,0,0,0,1,0,0,0,0,1,0,#17,-0.15043,-0.9672,-0.20467,406.19,0.65858,-0.25244,0.70891,-38.093,-0.73732,-0.028146,0.67495,220.42 > fitmap #17 inMap #2 Fit map cryosparc_P142_J1561_006_volume_map_sharp.mrc z flip in map J1259_flip.mrc using 506557 points correlation = 0.7096, correlation about mean = 0.1301, overlap = 3407 steps = 376, shift = 40.5, angle = 12.3 degrees Position of cryosparc_P142_J1561_006_volume_map_sharp.mrc z flip (#17) relative to J1259_flip.mrc (#2) coordinates: Matrix rotation and translation -0.33963039 -0.93395072 -0.11129811 453.03457551 0.63806108 -0.31572059 0.70228099 -4.46979580 -0.69103493 0.16750097 0.70314590 164.69579352 Axis -0.30406313 0.32962450 0.89380832 Axis point 256.89755103 119.18599461 0.00000000 Rotation angle (degrees) 118.43116029 Shift along axis 7.98200503 > hide #!17 models > select subtract #17 1 pseudobond, 1 model selected > show #!16 models > fitmap #16 inMap #2 Fit map cryosparc_P142_J1561_006_volume_map_sharp.mrc in map J1259_flip.mrc using 106403 points correlation = 0.4643, correlation about mean = -0.04888, overlap = 243.3 steps = 200, shift = 17.5, angle = 5.04 degrees Position of cryosparc_P142_J1561_006_volume_map_sharp.mrc (#16) relative to J1259_flip.mrc (#2) coordinates: Matrix rotation and translation 0.99673448 0.03918325 -0.07060483 15.87971192 -0.03670737 0.99867633 0.03602997 -12.60962791 0.07192314 -0.03332060 0.99685345 -3.02430258 Axis -0.39462949 -0.81103497 -0.43184469 Axis point 21.51277133 0.00000000 253.34937935 Rotation angle (degrees) 5.04096394 Shift along axis 5.26627556 > hide #!16 models > show #!17 models > hide #!2 models > color #17 #919191ff models > close #17 > show #!16 models > select add #16 1 pseudobond, 3 models selected > view matrix models > #15.1,1,0,0,0,0,1,0,0,0,0,1,0,#16,0.76684,0.61139,0.19535,-96.493,0.47781,-0.34056,-0.80977,295.49,-0.42855,0.7143,-0.55328,233.3 > show #!2 models > fitmap #16 inMap #2 Fit map cryosparc_P142_J1561_006_volume_map_sharp.mrc in map J1259_flip.mrc using 106403 points correlation = 0.8066, correlation about mean = 0.5911, overlap = 781.9 steps = 452, shift = 29.7, angle = 21.2 degrees Position of cryosparc_P142_J1561_006_volume_map_sharp.mrc (#16) relative to J1259_flip.mrc (#2) coordinates: Matrix rotation and translation 0.51259695 0.84050978 0.17546417 -117.91762644 0.67738015 -0.27028079 -0.68418158 230.08585808 -0.52763671 0.46956533 -0.70788975 326.61605501 Axis 0.84777193 0.51663774 -0.11986747 Axis point 0.00000000 75.88909107 210.68339010 Rotation angle (degrees) 137.12053232 Shift along axis -20.24685693 > view matrix models > #15.1,1,0,0,0,0,1,0,0,0,0,1,0,#16,0.066307,0.96739,0.24447,-74.507,0.67992,0.13551,-0.72065,162.24,-0.73028,0.214,-0.64876,398.41 > view matrix models > #15.1,1,0,0,0,0,1,0,0,0,0,1,0,#16,-0.1589,-0.97426,0.15991,335.4,-0.81091,0.036397,-0.58404,419.92,0.56319,-0.22247,-0.79582,275.44 > fitmap #16 inMap #2 Fit map cryosparc_P142_J1561_006_volume_map_sharp.mrc in map J1259_flip.mrc using 106403 points correlation = 0.9789, correlation about mean = 0.813, overlap = 1196 steps = 704, shift = 43.1, angle = 39.5 degrees Position of cryosparc_P142_J1561_006_volume_map_sharp.mrc (#16) relative to J1259_flip.mrc (#2) coordinates: Matrix rotation and translation 0.48477512 -0.87068476 0.08307312 250.77233249 -0.62997429 -0.41347663 -0.65739598 498.29948662 0.60673345 0.26635528 -0.74895219 163.51542974 Axis 0.84841489 -0.48095330 0.22107937 Axis point 0.00000000 292.05638439 136.80258860 Rotation angle (degrees) 147.01644455 Shift along axis 9.25008473 > hide #!2 models > color #16 #929292ff models > volume #16 level 0.08552 > volume #16 step 1 > volume #16 level 0.09746 > volume #16 level 0.1046 > save ""/Users/michellefry/Partners HealthCare Dropbox/Michelle > Fry/ChaoLab/parasites/acanthamoeba/mito_lysate/ATPsynthase/chimera_sessions/maps/J1561.mrc"" > models #16 > close #16 > open > /Users/michellefry/Downloads/cryosparc_P142_J1561_006_volume_map_sharp.mrc Opened cryosparc_P142_J1561_006_volume_map_sharp.mrc as #16, grid size 440,440,440, pixel 0.822, shown at level 0.0764, step 2, values float32 > fitmap #13 inMap #16 Fit molecule 20250418_all-coot-13.pdb (#13) to map cryosparc_P142_J1561_006_volume_map_sharp.mrc (#16) using 40161 atoms average map value = 0.03576, steps = 512 shifted from previous position = 33.5 rotated from previous position = 39.1 degrees atoms outside contour = 34821, contour level = 0.07637 Position of 20250418_all-coot-13.pdb (#13) relative to cryosparc_P142_J1561_006_volume_map_sharp.mrc (#16) coordinates: Matrix rotation and translation 0.79785189 -0.31209716 0.51577876 -1.28097353 0.41760262 0.90316779 -0.09947858 -54.93757472 -0.43478778 0.29475973 0.85092672 84.29054156 Axis 0.31250764 0.75350187 0.57842364 Axis point 160.71325953 0.00000000 69.68847369 Rotation angle (degrees) 39.10665016 Shift along axis 6.95976218 > select add #13 40161 atoms, 40883 bonds, 5 pseudobonds, 5180 residues, 3 models selected > view matrix models > #13,-0.84642,-0.37601,0.37708,338.96,-0.49522,0.29548,-0.81697,355.27,0.19577,-0.87824,-0.43631,417,#15.1,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix models > #13,-0.52195,0.33172,-0.78583,377.35,0.85198,0.15815,-0.49913,70.647,-0.041295,-0.93003,-0.36516,456.12,#15.1,1,0,0,0,0,1,0,0,0,0,1,0 > fitmap #13 inMap #16 Fit molecule 20250418_all-coot-13.pdb (#13) to map cryosparc_P142_J1561_006_volume_map_sharp.mrc (#16) using 40161 atoms average map value = 0.02941, steps = 172 shifted from previous position = 18.9 rotated from previous position = 7.54 degrees atoms outside contour = 34555, contour level = 0.07637 Position of 20250418_all-coot-13.pdb (#13) relative to cryosparc_P142_J1561_006_volume_map_sharp.mrc (#16) coordinates: Matrix rotation and translation -0.56992843 0.41788042 -0.70750091 362.14714794 0.81879824 0.21659380 -0.53165456 77.34021594 -0.06892772 -0.88230555 -0.46560271 455.79780528 Axis -0.42168617 -0.76793590 0.48213610 Axis point 95.74317888 0.00000000 303.97680846 Rotation angle (degrees) 155.43202904 Shift along axis 7.65180354 > hide #!14 models > hide #!15 models > select add #15 80322 atoms, 81766 bonds, 8 pseudobonds, 10360 residues, 4 models selected > select subtract #15 40161 atoms, 40883 bonds, 4 pseudobonds, 5180 residues, 2 models selected > view matrix models > #13,0.52186,0.45716,-0.72019,156.71,0.84332,-0.14947,0.5162,-62.832,0.12834,-0.87673,-0.46354,418.12 > ui mousemode right ""translate selected models"" > view matrix models > #13,0.52186,0.45716,-0.72019,134.24,0.84332,-0.14947,0.5162,-31.608,0.12834,-0.87673,-0.46354,389.66 > fitmap #13 inMap #16 Fit molecule 20250418_all-coot-13.pdb (#13) to map cryosparc_P142_J1561_006_volume_map_sharp.mrc (#16) using 40161 atoms average map value = 0.08064, steps = 332 shifted from previous position = 25.7 rotated from previous position = 18.3 degrees atoms outside contour = 22205, contour level = 0.07637 Position of 20250418_all-coot-13.pdb (#13) relative to cryosparc_P142_J1561_006_volume_map_sharp.mrc (#16) coordinates: Matrix rotation and translation 0.51197893 0.67855795 -0.52672259 76.64056008 0.84075847 -0.27015656 0.46919146 8.06695149 0.17607604 -0.68306262 -0.70881781 409.13555887 Axis -0.84762968 -0.51699793 0.11931915 Axis point 0.00000000 75.84935051 210.52551842 Rotation angle (degrees) 137.18042738 Shift along axis -20.31570491 > view matrix models > #13,0.51198,0.67856,-0.52672,78.341,0.84076,-0.27016,0.46919,9.1109,0.17608,-0.68306,-0.70882,409.54 > ui mousemode right ""rotate selected models"" > view matrix models > #13,0.88169,-0.4016,0.24769,50.791,-0.44513,-0.88206,0.15435,412.16,0.15649,-0.24634,-0.95647,384.31 > view matrix models > #13,0.89093,-0.43042,0.14483,73.665,-0.45401,-0.8515,0.26234,387.94,0.010405,-0.29948,-0.95404,419.99 > view matrix models > #13,0.82496,-0.38309,0.41555,26.091,-0.54481,-0.73466,0.4043,357.34,0.1504,-0.55993,-0.81478,413.01 > fitmap #13 inMap #16 Fit molecule 20250418_all-coot-13.pdb (#13) to map cryosparc_P142_J1561_006_volume_map_sharp.mrc (#16) using 40161 atoms average map value = 0.1051, steps = 328 shifted from previous position = 5.84 rotated from previous position = 27.8 degrees atoms outside contour = 14960, contour level = 0.07637 Position of 20250418_all-coot-13.pdb (#13) relative to cryosparc_P142_J1561_006_volume_map_sharp.mrc (#16) coordinates: Matrix rotation and translation 0.48470298 -0.63059909 0.60614173 93.50270142 -0.87077633 -0.41327567 0.26636778 380.66009583 0.08253235 -0.65692313 -0.74942672 429.26530151 Axis -0.84840730 0.48114198 -0.22069764 Axis point 0.00000000 292.04675495 136.85520103 Rotation angle (degrees) 147.03464088 Shift along axis 9.08534085 > save ""/Users/michellefry/Partners HealthCare Dropbox/Michelle > Fry/ChaoLab/parasites/acanthamoeba/mito_lysate/ATPsynthase/chimera_sessions/20250421_J1561_all_fit.pdb"" > models #13 > open ""/Users/michellefry/Partners HealthCare Dropbox/Michelle > Fry/ChaoLab/parasites/acanthamoeba/mito_lysate/ATPsynthase/chimera_sessions/coot/20250417_nucleotides.pdb"" > close #17 > hide #!13 models > show #!14 models > show #!13 models > hide #!13 models > select subtract #13 Nothing selected > hide #!16 models > open ""/Users/michellefry/Partners HealthCare Dropbox/Michelle > Fry/ChaoLab/parasites/acanthamoeba/mito_lysate/ATPsynthase/chimera_sessions/coot/20250417_nucleotides.pdb"" > combine #16 #17 Computing secondary structure > hide #17 models > hide #!14 models > hide #18 models > show #18 models > select ~sel & ##selected Nothing selected > select ~sel & ##selected Nothing selected > combine #13 #17 > hide #!19 models > show #!19 models > hide #!19 models > show #!19 models > close #19 > close #18 > combine #14 #17 > fitmap #18 inMap #16 Fit molecule combination (#18) to map cryosparc_P142_J1561_006_volume_map_sharp.mrc (#16) using 40324 atoms average map value = 0.03584, steps = 468 shifted from previous position = 33.6 rotated from previous position = 39 degrees atoms outside contour = 34891, contour level = 0.07637 Position of combination (#18) relative to cryosparc_P142_J1561_006_volume_map_sharp.mrc (#16) coordinates: Matrix rotation and translation 0.79940555 -0.30981553 0.51474761 -1.81661354 0.41528203 0.90409294 -0.10078089 -54.58193448 -0.43415620 0.29433024 0.85139774 84.15697569 Axis 0.31410523 0.75435902 0.57643765 Axis point 160.78878564 0.00000000 70.31654057 Rotation angle (degrees) 38.97248249 Shift along axis 6.76626705 > show #!16 models > select add #18 40324 atoms, 41056 bonds, 4 pseudobonds, 5185 residues, 2 models selected > view matrix models > #18,0.68217,-0.69696,0.2211,142.94,0.72526,0.60651,-0.32581,-17.108,0.09298,0.38261,0.91922,-41.152 > view matrix models > #18,-0.16948,-0.93176,-0.3211,443.71,0.38112,0.2385,-0.89323,218.17,0.90886,-0.27376,0.31469,37.743 > view matrix models > #18,-0.51114,-0.45752,0.72761,224.68,-0.26855,-0.71916,-0.64085,456.31,0.81647,-0.52296,0.24472,111.39 > view matrix models > #18,-0.35925,0.28744,0.88787,36.696,-0.18936,-0.95405,0.23225,316.5,0.91383,-0.084693,0.39717,-11.736 > view matrix models > #18,0.94591,0.18606,0.26577,-67.66,0.16337,-0.98093,0.10528,280.38,0.28029,-0.056167,-0.95827,357.77 > fitmap #18 inMap #16 Fit molecule combination (#18) to map cryosparc_P142_J1561_006_volume_map_sharp.mrc (#16) using 40324 atoms average map value = 0.03099, steps = 260 shifted from previous position = 27.1 rotated from previous position = 15.8 degrees atoms outside contour = 34396, contour level = 0.07637 Position of combination (#18) relative to cryosparc_P142_J1561_006_volume_map_sharp.mrc (#16) coordinates: Matrix rotation and translation 0.96357702 -0.04682254 0.26330017 -23.75888807 -0.09719202 -0.97854447 0.18167121 327.86998873 0.24914462 -0.20064488 -0.94745374 365.72259547 Axis -0.99076526 0.03668386 -0.13053160 Axis point 0.00000000 181.39096280 168.29086927 Rotation angle (degrees) 168.87560279 Shift along axis -12.17133962 > ui mousemode right ""translate selected models"" > view matrix models > #18,0.96358,-0.046823,0.2633,-51.298,-0.097192,-0.97854,0.18167,368.44,0.24914,-0.20064,-0.94745,367.46 > view matrix models > #18,0.96358,-0.046823,0.2633,-55.929,-0.097192,-0.97854,0.18167,370.48,0.24914,-0.20064,-0.94745,358.28 > ui mousemode right ""rotate selected models"" > view matrix models > #18,0.8677,-0.28323,0.40851,-24.788,-0.3298,-0.94289,0.046788,432.76,0.37193,-0.17532,-0.91156,324.44 > view matrix models > #18,0.87908,-0.35588,0.31713,3.1294,-0.42124,-0.89136,0.16741,417.7,0.2231,-0.28076,-0.93349,374.35 > view matrix models > #18,0.97365,-0.14482,0.17619,-24.173,-0.18672,-0.94976,0.25118,368.74,0.13096,-0.27745,-0.95177,394.22 > view matrix models > #18,0.96076,-0.27054,0.061238,21.925,-0.26877,-0.85337,0.44667,329.9,-0.068584,-0.4456,-0.8926,448.94 > ui mousemode right ""translate selected models"" > view matrix models > #18,0.96076,-0.27054,0.061238,36.481,-0.26877,-0.85337,0.44667,309.29,-0.068584,-0.4456,-0.8926,449.68 > fitmap #18 inMap #16 Fit molecule combination (#18) to map cryosparc_P142_J1561_006_volume_map_sharp.mrc (#16) using 40324 atoms average map value = 0.1053, steps = 548 shifted from previous position = 13.9 rotated from previous position = 48.1 degrees atoms outside contour = 14979, contour level = 0.07637 Position of combination (#18) relative to cryosparc_P142_J1561_006_volume_map_sharp.mrc (#16) coordinates: Matrix rotation and translation 0.48475687 -0.63062504 0.60607165 93.51522437 -0.87075267 -0.41328690 0.26642769 380.64244888 0.08246550 -0.65689116 -0.74946210 429.27857014 Axis -0.84842424 0.48113406 -0.22064979 Axis point 0.00000000 292.04194010 136.86614437 Rotation angle (degrees) 147.03425834 Shift along axis 9.07923733 > save ""/Users/michellefry/Partners HealthCare Dropbox/Michelle > Fry/ChaoLab/parasites/acanthamoeba/mito_lysate/ATPsynthase/chimera_sessions/20250421_J1561_all_fit.pdb"" > models #18 ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/michellefry/Downloads/cryosparc_P142_J1503_003_volume_map_sharp.mrc Opened cryosparc_P142_J1503_003_volume_map_sharp.mrc as #1, grid size 220,220,220, pixel 1.64, shown at level 0.171, step 1, values float32 > ui tool show Registration OpenGL version: 4.1 Metal - 89.3 OpenGL renderer: Apple M4 Pro 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: Mac16,8 Model Number: Z1FE000M3LL/A Chip: Apple M4 Pro Total Number of Cores: 12 (8 performance and 4 efficiency) Memory: 24 GB System Firmware Version: 11881.81.4 OS Loader Version: 11881.81.4 Software: System Software Overview: System Version: macOS 15.3.1 (24D70) Kernel Version: Darwin 24.3.0 Time since boot: 10 days, 16 hours, 56 minutes Graphics/Displays: Apple M4 Pro: Chipset Model: Apple M4 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: DELL U2720Q: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 autocommand: 2.2.2 babel: 2.16.0 backports.tarfile: 1.2.0 beautifulsoup4: 4.12.3 biopython: 1.83 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-ArtiaX: 0.6.0 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-Clipper: 0.24.0 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-EMalign: 0.1.3 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-ISOLDE: 1.9 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-LigandRecognizer: 0.2 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-NIHPresets: 1.2.7 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-QScore: 1.1 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 DiffFit: 0.7.0 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 finufft: 2.3.1 fonttools: 4.55.3 fsspec: 2025.3.2 funcparserlib: 2.0.0a0 geomdl: 5.3.1 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 importlib_metadata: 8.0.0 importlib_resources: 6.4.0 inflect: 7.3.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jaraco.context: 5.3.0 jaraco.functools: 4.0.1 jaraco.text: 3.12.1 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 more-itertools: 10.3.0 mpmath: 1.3.0 mrcfile: 1.5.0 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 ordered-set: 4.1.0 packaging: 23.2 packaging: 24.1 pandas: 2.2.3 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 platformdirs: 4.2.2 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pyarrow: 19.0.1 pycollada: 0.8 pydantic: 2.11.3 pydantic_core: 2.33.1 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 starfile: 0.5.12 superqt: 0.6.3 sympy: 1.13.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tomli: 2.0.1 torch: 2.2.1 tornado: 6.4.2 traitlets: 5.14.3 typeguard: 4.3.0 typing-inspection: 0.4.0 typing_extensions: 4.12.2 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: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 zipp: 3.19.2 }}} " defect closed normal Window Toolkit duplicate all ChimeraX