id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19298 Crash on Mac waking from sleep hrishikesh.das@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.7.1-x86_64-i386-64bit 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 Thread 0x0000700023210000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070002220d000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070002120a000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000700020207000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070001f204000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070001e201000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070001d1fe000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070001c1fb000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070001b1f8000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070001a1f5000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00007000191f2000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00007000181ef000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00007000171ec000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00007000161e9000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00007000151e6000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00007ff85d1f1000 (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, chimerax.map._map, chimerax.surface._surface, chimerax.pdb_lib._load_libs, 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, PIL._imagingmath, chimerax.core._mac_util, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, chimerax.atom_search.ast, chimerax.chem_group._chem_group, psutil._psutil_osx, psutil._psutil_posix (total: 62) 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Bytes before following region: 4553969303\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10f701000-10f705000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX"", ""exception"" : {""codes"":""0x0000000000000001, 0x0000000000000169"",""rawCodes"":[1,361],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGSEGV"",""subtype"":""KERN_INVALID_ADDRESS at 0x0000000000000169""}, ""termination"" : {""flags"":0,""code"":11,""namespace"":""SIGNAL"",""indicator"":""Segmentation fault: 11"",""byProc"":""ChimeraX"",""byPid"":61487}, ""ktriageinfo"" : ""VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n"", ""vmregioninfo"" : ""0x169 is not in any region. 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240000005 }, { ""rolloutId"" : ""5ffde50ce2aacd000d47a95f"", ""factorPackIds"" : { }, ""deploymentId"" : 240000500 } ], ""experiments"" : [ { ""treatmentId"" : ""28060e10-d4e5-4163-aa2b-d8bd088d5cbf"", ""experimentId"" : ""6685b283afc7c17197d69eec"", ""deploymentId"" : 400000012 } ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet > ui tool hide ""command line interface"" > ui tool show clix 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/hrishikeshdas/Documents/Projects/FASTKD/FASTKD5/Structures_FAST5/FAST5-trimer/F5_ATP6Cox3_RNA_trimer/F5_ATP6cox3_trimer_RNA_41/ATP6Cox3_41NtTrimer1.cxs opened ChimeraX session > hide #!2 models > show #!3 models > show #!2 models > hide #!2 models > hide #!3 models > show #!4 models > show #!4 cartoons > ~label #4 residues > hide #!4 atoms > select #4/G:30 23 atoms, 25 bonds, 1 residue, 1 model selected > show sel atoms > show #!3 models > hide #!4 models > select #3/G:31 20 atoms, 21 bonds, 1 residue, 1 model selected > select #3/G:31 20 atoms, 21 bonds, 1 residue, 1 model selected > select #3/G:30 22 atoms, 24 bonds, 1 residue, 1 model selected > show sel atoms > show #!4 models > hide #!3 models > show #!3 models > hide #!4 models > hide #!3 models > show #!3 models > show #!4 models > select clear > view > hide #!3-4 atoms > hide #!4 models > hide #!3 models > show #!2 models > hide #!2 surfaces > hide #!2 atoms > ui tool show CliX > select #2/g:13-24 253 atoms, 282 bonds, 12 residues, 1 model selected > show sel atoms > view sel > select #2/G 862 atoms, 962 bonds, 41 residues, 1 model selected > color (#!2 & sel) cornflower blue > color sel byhetero > color (#!2 & sel) medium blue > color (#!2 & sel) blue > color (#!2 & sel) cyan > color sel byhetero > select clear > select #2/g:13-24 253 atoms, 282 bonds, 12 residues, 1 model selected > hbonds sel reveal true 191 hydrogen bonds found > show #1 models > color #1 #0032ffff models > color #1 #000dffff models > color #1 #0098ffff models > color #1 #009856ff models > color #1 #009878ff models > color #1 #e29878ff models > color #1 #fb9878ff models > color #1 #e5f378ff models > color #1 #e5d278ff models > color #1 #e57c78ff models > color #1 #e54b78ff models > color #1 #e55b78ff models > color #1 #e58d78ff models > color #1 #e5a278ff models > color #1 #e5a2ffff models > color #1 #e545ffff models > color #1 #e523ffff models > color #1 #e507ffff models > select clear > select #2/g:13-24 253 atoms, 282 bonds, 11 pseudobonds, 12 residues, 2 models selected > ui tool show Contacts > contacts sel restrict cross overlapCutoff -0.3 resSeparation 5 intraRes true > ignoreHiddenModels true select true color #220422 showDist true reveal true 81 contacts > show #!5 models > select clear > label #1-2#!5 text ""{0.name} {0.number}{0.insertion_code}"" > save > /Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD5/Structures_FAST5/FAST5-trimer/F5_ATP6Cox3_RNA_trimer/F5_ATP6cox3_trimer_RNA_41/human_ATP6Cox3_41.cxs > hide #!5 models > show #!5 models > hide #1 models > hide #!2 models > show #1 models > show #!4 models > hide #!4 atoms > view > hide #!4 cartoons > select #4/g:13-24 254 atoms, 283 bonds, 12 residues, 1 model selected > show sel atoms > label sel text ""{0.name} {0.number}{0.insertion_code}"" > hbonds sel reveal true 187 hydrogen bonds found > view sel > select #4/g:13-24 254 atoms, 283 bonds, 8 pseudobonds, 12 residues, 2 models selected > ui tool show Contacts > contacts sel restrict cross overlapCutoff -0.3 resSeparation 5 intraRes true > ignoreHiddenModels true select true color #220422 showDist true reveal true 75 contacts > contacts sel restrict cross overlapCutoff -0.3 resSeparation 5 intraRes true > ignoreHiddenModels true select true color #220422 showDist true reveal true 18 contacts > select #4/g:13-24 254 atoms, 283 bonds, 9 pseudobonds, 12 residues, 3 models selected > label (#!4 & sel) text ""{0.name} {0.number}{0.insertion_code}"" > show #5.1 models > hbonds sel reveal true 187 hydrogen bonds found > color sel byhetero > select #4/g:13-24 254 atoms, 283 bonds, 9 pseudobonds, 12 residues, 3 models selected > ui tool show Contacts > contacts sel restrict cross overlapCutoff -0.3 resSeparation 5 intraRes true > ignoreHiddenModels true select true color #220422 showDist true reveal true 75 contacts > select clear > color #!4 byhetero > hide #5.1 models > label #1,4#!5 text ""{0.name} {0.number}{0.insertion_code}"" > hide #!5 models > show #!5 models > show #5.1 models > hide #5.1 models > hide #!5 models > hide #!4 models > show #!3 models > hide #!3 models > show #!4 models > hide #!4 atoms > select #4/g:13-24 254 atoms, 283 bonds, 8 pseudobonds, 12 residues, 2 models selected > show sel atoms > select clear > select #2/g:13-24 253 atoms, 282 bonds, 12 residues, 1 model selected > show #!4 atoms > show #!2 models > hide sel atoms > undo > ~label (#!2 & sel) residues > hide sel atoms > hide #!2 models > show #!2 models > select clear > hide #!2,4 atoms > select #2/g:13-24 253 atoms, 282 bonds, 12 residues, 1 model selected > show sel atoms > hbonds sel reveal true 191 hydrogen bonds found > select clear > label #1-2,4 text ""{0.name} {0.number}{0.insertion_code}"" > show #!5 models > hide #!2 models > show #!2 models > hide #!2 models > select #4/g:13-24 254 atoms, 283 bonds, 12 residues, 1 model selected > show sel atoms > select clear > show #!2 models > hide #!2 models > show #!2 models > hide #!4 models > show #!4 models > select #4/g:20 23 atoms, 25 bonds, 1 residue, 1 model selected > view sel > hide #!2 models > select #4/g:13-24 254 atoms, 283 bonds, 12 residues, 1 model selected > hbonds sel reveal true 187 hydrogen bonds found > select clear > select #4/g:20 23 atoms, 25 bonds, 1 residue, 1 model selected > select #4/g:20 23 atoms, 25 bonds, 1 residue, 1 model selected > view sel > view > view sel > select clear > ui tool show ""Side View"" > save > ""/Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD5/Structures_FAST5/FAST5-trimer/F5_ATP6Cox3_RNA_trimer/F5_ATP6cox3_trimer_RNA_41/New > Folder With Items/Ch_G20_region.png"" width 1161 height 847 supersample 3 > show #!2 models > hide #!4 models > hide #!5 models > show #!5 models > hide #!2 models > show #!4 models > save > ""/Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD5/Structures_FAST5/FAST5-trimer/F5_ATP6Cox3_RNA_trimer/F5_ATP6cox3_trimer_RNA_41/New > Folder With Items/Ch_A23_region.png"" width 1161 height 847 supersample 3 > hide #!4 models > show #!2 models > select #2/g:23 20 atoms, 21 bonds, 1 residue, 1 model selected > view sel > select #2/g:13-24 253 atoms, 282 bonds, 12 residues, 1 model selected > hbonds sel reveal true 191 hydrogen bonds found > select #2/g:13-24 253 atoms, 282 bonds, 11 pseudobonds, 12 residues, 2 models selected > ui tool show Contacts > contacts sel restrict cross overlapCutoff -0.3 resSeparation 5 intraRes true > ignoreHiddenModels true select true color #220422 showDist true reveal true 81 contacts > select clear > select #2/g:23 20 atoms, 21 bonds, 1 residue, 1 model selected > view sel > select clear > save > ""/Users/hrishikeshdas/Documents/Projects/FASTKD/FASTKD5/Structures_FAST5/FAST5-trimer/F5_ATP6Cox3_RNA_trimer/F5_ATP6cox3_trimer_RNA_41/New > Folder With Items/Hu_C23_region.png"" width 1161 height 847 supersample 3 > hide #!2 models > hide #1 models > show #1 models > show #!3 models > hide #!3 atoms > hide #!3 cartoons > select #3/g:13-24 249 atoms, 276 bonds, 12 residues, 1 model selected > show sel atoms > label sel text ""{0.name} {0.number}{0.insertion_code}"" > show #!2 models > hide #1 models > show #1 models > hide #!3 models > show #!3 models > hide #!2 models > show #!2 models > hide #!2 models > hide #!3 models > show #!2 models > hide #!2 models > show #!2 models > hide #!5 models > view > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > hide #!2 models > hide #1 models > show #!2 models > hide #!2 atoms > show #!2 cartoons > ~label #2 residues > view sel > select clear > view > open /Users/hrishikeshdas/Library/CloudStorage/OneDrive- > KarolinskaInstitutet/FASTKD5/cryosparc_P34_J388_class_01_00142_volume_sharp_fliped.mrc Opened cryosparc_P34_J388_class_01_00142_volume_sharp_fliped.mrc as #8, grid size 128,128,128, pixel 2.03, shown at level 0.0754, step 1, values float32 > volume #8 level 0.2911 > close #8 > view > select #2/B#3/B#4/B#6/B#7/B#9/B 28482 atoms, 29130 bonds, 6 pseudobonds, 3504 residues, 12 models selected > color (#!2 & sel) #c7eae5ff > select clear > select #2/G#3/G#4/G#6/G#7/G#9/G 5182 atoms, 5786 bonds, 124 pseudobonds, 246 residues, 7 models selected > color (#!2 & sel) #e6f5d0ff > select clear > color #2 #a1d76aff > undo > select #2/G#3/G#4/G#6/G#7/G#9/G 5182 atoms, 5786 bonds, 124 pseudobonds, 246 residues, 7 models selected > select clear > select #2/G#3/G#4/G#6/G#7/G#9/G 5182 atoms, 5786 bonds, 124 pseudobonds, 246 residues, 7 models selected > color (#!2 & sel) #a1d76aff > select clear > open /Users/hrishikeshdas/Downloads/cryosparc_P102_J452_009_volume_map.mrc Opened cryosparc_P102_J452_009_volume_map.mrc as #8, grid size 256,256,256, pixel 1.02, shown at level 0.0431, step 1, values float32 > hide #!8 models > hide #!2 models > show #!8 models > view > volume #8 level 0.05443 > volume #8 level 0.1434 > open > /Users/hrishikeshdas/Documents/Projects/PAP_SUV3-PNPase/hSUV3/SUV3_alphafold.pdb SUV3_alphafold.pdb title: Alphafold monomer V2.0 prediction for atp-dependent RNA helicase SUPV3L1, mitochondrial (Q8IYB8) [more info...] Chain information for SUV3_alphafold.pdb #10 --- Chain | Description | UniProt A | atp-dependent RNA helicase SUPV3L1, mitochondrial | SUV3_HUMAN 1-786 > select add #10 6190 atoms, 6329 bonds, 786 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models #10,1,0,0,3.6477,0,1,0,9.1054,0,0,1,225.41 > view matrix models #10,1,0,0,57.692,0,1,0,140.75,0,0,1,195.77 > view matrix models #10,1,0,0,97.718,0,1,0,124.03,0,0,1,159.75 > ui mousemode right ""rotate selected models"" > view matrix models > #10,0.612,0.2858,0.73741,106.79,-0.67244,0.67882,0.29499,123.92,-0.41626,-0.6764,0.60763,150.42 > ui mousemode right ""translate selected models"" > view matrix models > #10,0.612,0.2858,0.73741,119.49,-0.67244,0.67882,0.29499,127.65,-0.41626,-0.6764,0.60763,162.83 > view matrix models > #10,0.612,0.2858,0.73741,122,-0.67244,0.67882,0.29499,133.45,-0.41626,-0.6764,0.60763,164.03 > ui mousemode right ""rotate selected models"" > view matrix models > #10,0.34987,0.68881,0.63492,115.56,-0.84264,0.52753,-0.10797,124.4,-0.40932,-0.49724,0.76499,166.44 > ui tool show ""Fit in Map"" > fitmap #10 inMap #8 Fit molecule SUV3_alphafold.pdb (#10) to map cryosparc_P102_J452_009_volume_map.mrc (#8) using 6190 atoms average map value = 0.05432, steps = 84 shifted from previous position = 2.86 rotated from previous position = 3.83 degrees atoms outside contour = 5260, contour level = 0.14339 Position of SUV3_alphafold.pdb (#10) relative to cryosparc_P102_J452_009_volume_map.mrc (#8) coordinates: Matrix rotation and translation 0.40704602 0.65440396 0.63723543 118.73414367 -0.81680934 0.57303626 -0.06672292 125.40368243 -0.40882275 -0.49334055 0.76777540 165.75977715 Axis -0.22999311 0.56393867 -0.79314333 Axis point 198.82141921 29.66186707 0.00000000 Rotation angle (degrees) 68.04187599 Shift along axis -88.05931111 > vop flip #8 Opened cryosparc_P102_J452_009_volume_map.mrc z flip as #11, grid size 256,256,256, pixel 1.02, shown at step 1, values float32 > view matrix models > #10,0.20212,0.78026,0.5919,115.15,-0.91943,0.35935,-0.15974,123.37,-0.33734,-0.51192,0.79002,167.03 > view matrix models > #10,0.046828,0.35652,0.93311,121.88,-0.86027,0.48916,-0.14373,123.78,-0.50768,-0.796,0.32961,157.4 > fitmap #10 inMap #11 Fit molecule SUV3_alphafold.pdb (#10) to map cryosparc_P102_J452_009_volume_map.mrc z flip (#11) using 6190 atoms average map value = 0.07074, steps = 88 shifted from previous position = 4.22 rotated from previous position = 3.64 degrees atoms outside contour = 4968, contour level = 0.14339 Position of SUV3_alphafold.pdb (#10) relative to cryosparc_P102_J452_009_volume_map.mrc z flip (#11) coordinates: Matrix rotation and translation 0.06263843 0.32236966 0.94453916 126.13564132 -0.88284533 0.45928194 -0.09820506 122.40607542 -0.46546811 -0.82773057 0.31337125 157.98356204 Axis -0.36600604 0.70740661 -0.60466145 Axis point 175.86716568 0.00000000 62.34065104 Rotation angle (degrees) 94.72389760 Shift along axis -55.10211011 > view sel > view matrix models > #10,-0.10907,0.29831,0.94822,124.47,-0.94096,0.27654,-0.19523,120.64,-0.32046,-0.91353,0.25054,158.66 > view matrix models > #10,0.46593,-0.80847,0.35956,123.65,0.46304,0.56907,0.67952,151.47,-0.75399,-0.15012,0.63951,158.5 > ui mousemode right ""translate selected models"" > view matrix models > #10,0.46593,-0.80847,0.35956,157.55,0.46304,0.56907,0.67952,139.62,-0.75399,-0.15012,0.63951,147.85 > view matrix models > #10,0.46593,-0.80847,0.35956,145.93,0.46304,0.56907,0.67952,128.29,-0.75399,-0.15012,0.63951,152.96 > view matrix models > #10,0.46593,-0.80847,0.35956,144.95,0.46304,0.56907,0.67952,122.15,-0.75399,-0.15012,0.63951,152.23 > fitmap #10 inMap #11 Fit molecule SUV3_alphafold.pdb (#10) to map cryosparc_P102_J452_009_volume_map.mrc z flip (#11) using 6190 atoms average map value = 0.06887, steps = 104 shifted from previous position = 4.55 rotated from previous position = 4.1 degrees atoms outside contour = 5007, contour level = 0.14339 Position of SUV3_alphafold.pdb (#10) relative to cryosparc_P102_J452_009_volume_map.mrc z flip (#11) coordinates: Matrix rotation and translation 0.46839522 -0.82097326 0.32651009 148.16847030 0.52158902 0.55522912 0.64781598 122.68317428 -0.71312750 -0.13312984 0.68827730 149.46991463 Axis -0.41783943 0.55625059 0.71832826 Axis point 57.52632082 201.09756683 0.00000000 Rotation angle (degrees) 69.14827117 Shift along axis 113.70042366 > view matrix models > #10,0.4684,-0.82097,0.32651,149.61,0.52159,0.55523,0.64782,124.52,-0.71313,-0.13313,0.68828,153.07 > ui mousemode right ""rotate selected models"" > view matrix models > #10,-0.80544,0.58411,-0.10039,121.96,-0.54093,-0.65528,0.52726,115.78,0.2422,0.47898,0.84375,163.79 > ui mousemode right ""translate selected models"" > view matrix models > #10,-0.80544,0.58411,-0.10039,121.58,-0.54093,-0.65528,0.52726,126.74,0.2422,0.47898,0.84375,158.82 > ui mousemode right ""rotate selected models"" > view matrix models > #10,-0.71216,0.6882,-0.1386,121.41,-0.66062,-0.59017,0.46398,123.96,0.23751,0.42198,0.87494,159.61 > ui mousemode right ""translate selected models"" > view matrix models > #10,-0.71216,0.6882,-0.1386,121.4,-0.66062,-0.59017,0.46398,130.63,0.23751,0.42198,0.87494,157.26 > fitmap #10 inMap #11 Fit molecule SUV3_alphafold.pdb (#10) to map cryosparc_P102_J452_009_volume_map.mrc z flip (#11) using 6190 atoms average map value = 0.07775, steps = 192 shifted from previous position = 11.2 rotated from previous position = 16.5 degrees atoms outside contour = 4794, contour level = 0.14339 Position of SUV3_alphafold.pdb (#10) relative to cryosparc_P102_J452_009_volume_map.mrc z flip (#11) coordinates: Matrix rotation and translation -0.52897305 0.77826941 -0.33835522 123.84394212 -0.83530274 -0.40708256 0.36953098 129.89484165 0.14985615 0.47810097 0.86542627 146.32351797 Axis 0.06426901 -0.28900124 -0.95516898 Axis point 90.15832259 4.01162330 0.00000000 Rotation angle (degrees) 122.36525401 Shift along axis -169.34412840 > ui mousemode right ""rotate selected models"" > view matrix models > #10,-0.30809,0.85687,-0.41336,124.42,-0.93449,-0.19112,0.30033,126.61,0.17834,0.47881,0.85962,146.51 > fitmap #10 inMap #11 Fit molecule SUV3_alphafold.pdb (#10) to map cryosparc_P102_J452_009_volume_map.mrc z flip (#11) using 6190 atoms average map value = 0.07968, steps = 56 shifted from previous position = 2.8 rotated from previous position = 1.95 degrees atoms outside contour = 4743, contour level = 0.14339 Position of SUV3_alphafold.pdb (#10) relative to cryosparc_P102_J452_009_volume_map.mrc z flip (#11) coordinates: Matrix rotation and translation -0.29579411 0.86579191 -0.40362141 121.71129708 -0.94248617 -0.19566450 0.27098940 126.93794586 0.15564605 0.46056465 0.87387329 147.14695860 Axis 0.09965797 -0.29400177 -0.95059521 Axis point 98.53996828 -12.09770737 0.00000000 Rotation angle (degrees) 107.98648529 Shift along axis -165.06767354 > select clear > fitmap #10 inMap #11 Fit molecule SUV3_alphafold.pdb (#10) to map cryosparc_P102_J452_009_volume_map.mrc z flip (#11) using 6190 atoms average map value = 0.07968, steps = 44 shifted from previous position = 0.00763 rotated from previous position = 0.0111 degrees atoms outside contour = 4741, contour level = 0.14339 Position of SUV3_alphafold.pdb (#10) relative to cryosparc_P102_J452_009_volume_map.mrc z flip (#11) coordinates: Matrix rotation and translation -0.29584858 0.86581440 -0.40353323 121.70961571 -0.94243990 -0.19565097 0.27116004 126.93391951 0.15582260 0.46052812 0.87386108 147.14283521 Axis 0.09954997 -0.29405090 -0.95059133 Axis point 98.52362778 -12.09471199 0.00000000 Rotation angle (degrees) 107.98808636 Shift along axis -165.08154763 > rainbow #10 > select clear > select #10:691-786 742 atoms, 753 bonds, 96 residues, 1 model selected > delete atoms sel > delete bonds sel > select add #10 5448 atoms, 5575 bonds, 690 residues, 1 model selected > view matrix models > #10,-0.85854,0.11702,-0.49921,122.29,-0.48252,-0.51373,0.70941,133.48,-0.17344,0.84994,0.49752,141.24 > view matrix models > #10,0.13727,0.98091,-0.13777,124.94,-0.98863,0.14429,0.042268,122.98,0.06134,0.1304,0.98956,149.57 > view matrix models > #10,-0.32729,-0.93001,0.16724,133.46,0.67445,-0.10596,0.73068,131.71,-0.66182,0.35194,0.66192,145.14 > view matrix models > #10,0.33394,0.65122,0.68146,137.48,-0.60512,0.70243,-0.37473,115.33,-0.72271,-0.28723,0.62864,145.87 > view matrix models > #10,0.45178,-0.89151,-0.033329,129.5,0.23869,0.084795,0.96739,135.39,-0.8596,-0.445,0.25111,140.71 > view matrix models > #10,0.28787,-0.95634,-0.05052,129.55,0.09031,-0.025409,0.99559,136.18,-0.9534,-0.29116,0.079052,137.98 > ui mousemode right ""translate selected models"" > view matrix models > #10,0.28787,-0.95634,-0.05052,142.18,0.09031,-0.025409,0.99559,128.28,-0.9534,-0.29116,0.079052,148.4 > view matrix models > #10,0.28787,-0.95634,-0.05052,135.95,0.09031,-0.025409,0.99559,131.85,-0.9534,-0.29116,0.079052,141.93 > ui mousemode right ""rotate selected models"" > view matrix models > #10,0.63532,-0.76234,0.1233,137.78,0.43161,0.48293,0.7619,127.06,-0.64038,-0.43083,0.63585,150.09 > fitmap #10 inMap #11 Fit molecule SUV3_alphafold.pdb (#10) to map cryosparc_P102_J452_009_volume_map.mrc z flip (#11) using 5448 atoms average map value = 0.07307, steps = 156 shifted from previous position = 3.39 rotated from previous position = 7.28 degrees atoms outside contour = 4308, contour level = 0.14339 Position of SUV3_alphafold.pdb (#10) relative to cryosparc_P102_J452_009_volume_map.mrc z flip (#11) coordinates: Matrix rotation and translation 0.68411349 -0.72890993 0.02605898 140.42389874 0.48741729 0.48345695 0.72711332 127.46618466 -0.54259851 -0.48472644 0.68602272 150.00358016 Axis -0.67000767 0.31440203 0.67248872 Axis point 12.69902113 230.22488041 0.00000000 Rotation angle (degrees) 64.73556626 Shift along axis 46.86625356 > view matrix models > #10,0.5984,-0.60946,0.52008,147.65,0.55837,0.78275,0.27482,120.13,-0.57458,0.12594,0.8087,150.76 > fitmap #10 inMap #11 Fit molecule SUV3_alphafold.pdb (#10) to map cryosparc_P102_J452_009_volume_map.mrc z flip (#11) using 5448 atoms average map value = 0.07477, steps = 120 shifted from previous position = 3.41 rotated from previous position = 12 degrees atoms outside contour = 4307, contour level = 0.14339 Position of SUV3_alphafold.pdb (#10) relative to cryosparc_P102_J452_009_volume_map.mrc z flip (#11) coordinates: Matrix rotation and translation 0.68137099 -0.62831984 0.37543015 145.53679807 0.50163979 0.77438953 0.38558838 120.51852373 -0.53300200 -0.07439804 0.84283678 149.88395797 Axis -0.30241034 0.59723343 0.74287295 Axis point 48.80688919 273.92812562 0.00000000 Rotation angle (degrees) 49.51125728 Shift along axis 139.31059687 > view matrix models > #10,-0.72436,-0.65635,-0.21096,138.52,0.089167,-0.39262,0.91537,130.97,-0.68363,0.64425,0.34292,141.34 > fitmap #10 inMap #11 Fit molecule SUV3_alphafold.pdb (#10) to map cryosparc_P102_J452_009_volume_map.mrc z flip (#11) using 5448 atoms average map value = 0.08795, steps = 124 shifted from previous position = 4.14 rotated from previous position = 13.6 degrees atoms outside contour = 4055, contour level = 0.14339 Position of SUV3_alphafold.pdb (#10) relative to cryosparc_P102_J452_009_volume_map.mrc z flip (#11) coordinates: Matrix rotation and translation -0.77405891 -0.54864142 -0.31595165 137.24004233 0.09315772 -0.59231247 0.80030470 136.29387952 -0.62622239 0.59004963 0.50959492 141.72708850 Axis -0.28289613 0.41746624 0.86353444 Axis point 83.17018573 53.63562102 0.00000000 Rotation angle (degrees) 158.18494596 Shift along axis 140.45963808 > view matrix models > #10,-0.29091,0.76451,-0.57523,130.46,-0.95361,-0.28035,0.10967,126.7,-0.077426,0.58045,0.8106,145.58 > view matrix models > #10,0.34783,-0.68454,0.64064,150.38,0.4823,0.7166,0.50386,129.08,-0.80399,0.13372,0.57941,143.79 > ui mousemode right zoom > ui mousemode right ""translate selected models"" > view matrix models > #10,0.34783,-0.68454,0.64064,149.97,0.4823,0.7166,0.50386,138.29,-0.80399,0.13372,0.57941,143.01 > view matrix models > #10,0.34783,-0.68454,0.64064,142.7,0.4823,0.7166,0.50386,144.28,-0.80399,0.13372,0.57941,144.25 > fitmap #10 inMap #8 Fit molecule SUV3_alphafold.pdb (#10) to map cryosparc_P102_J452_009_volume_map.mrc (#8) using 5448 atoms average map value = 0.07237, steps = 100 shifted from previous position = 8.92 rotated from previous position = 6.69 degrees atoms outside contour = 4283, contour level = 0.14339 Position of SUV3_alphafold.pdb (#10) relative to cryosparc_P102_J452_009_volume_map.mrc (#8) coordinates: Matrix rotation and translation 0.43614312 -0.61124021 0.66042760 145.46605914 0.43437206 0.78574610 0.44036805 135.06497621 -0.78809906 0.09480779 0.60820341 146.03973804 Axis -0.18990995 0.79606846 0.57463833 Axis point 139.54891256 0.00000000 -148.22313504 Rotation angle (degrees) 65.47776729 Shift along axis 163.81554746 > view matrix models > #10,0.43614,-0.61124,0.66043,142.34,0.43437,0.78575,0.44037,133.07,-0.7881,0.094808,0.6082,151.65 > view matrix models > #10,0.43614,-0.61124,0.66043,130.24,0.43437,0.78575,0.44037,124.04,-0.7881,0.094808,0.6082,155.18 > ui mousemode right ""rotate selected models"" > view matrix models > #10,0.3073,-0.36966,0.87688,133.17,0.38096,0.8922,0.24261,120.97,-0.87203,0.2595,0.41499,152.11 > ui mousemode right ""translate selected models"" > view matrix models > #10,0.3073,-0.36966,0.87688,137.16,0.38096,0.8922,0.24261,124.14,-0.87203,0.2595,0.41499,151.6 > view matrix models > #10,0.3073,-0.36966,0.87688,132.03,0.38096,0.8922,0.24261,122.02,-0.87203,0.2595,0.41499,158.52 > ui mousemode right ""rotate selected models"" > view matrix models > #10,0.078111,-0.64077,0.76375,131.1,0.2474,0.75459,0.60778,127.84,-0.96576,0.14148,0.21747,155.91 > ui mousemode right ""translate selected models"" > view matrix models > #10,0.078111,-0.64077,0.76375,138.1,0.2474,0.75459,0.60778,132.11,-0.96576,0.14148,0.21747,150.82 > fitmap #10 inMap #8 Fit molecule SUV3_alphafold.pdb (#10) to map cryosparc_P102_J452_009_volume_map.mrc (#8) using 5448 atoms average map value = 0.2012, steps = 224 shifted from previous position = 7.91 rotated from previous position = 38.9 degrees atoms outside contour = 1970, contour level = 0.14339 Position of SUV3_alphafold.pdb (#10) relative to cryosparc_P102_J452_009_volume_map.mrc (#8) coordinates: Matrix rotation and translation 0.37453509 -0.08115610 0.92365426 129.86010587 -0.02718999 0.99477246 0.09843019 126.62706393 -0.92681401 -0.06197972 0.37037055 146.95730251 Axis -0.08632581 0.99584356 0.02904227 Axis point 176.64418900 0.00000000 -32.11354661 Rotation angle (degrees) 68.29430904 Shift along axis 119.15844182 > select clear > volume #8 style mesh > volume #8 level 0.1327 > close #11 > show #10 atoms > color #10 byhetero > open > /Users/hrishikeshdas/Documents/Projects/PAP_SUV3-PNPase/hSUV3/SUV3_alphafold_dIDP_684.pdb SUV3_alphafold_dIDP_684.pdb title: Alphafold monomer V2.0 prediction for atp-dependent RNA helicase SUPV3L1, mitochondrial (Q8IYB8) [more info...] Chain information for SUV3_alphafold_dIDP_684.pdb #11 --- Chain | Description | UniProt A | atp-dependent RNA helicase SUPV3L1, mitochondrial | SUV3_HUMAN 1-786 > hide #!8 models > show #!8 models Error processing trigger ""graphics update"": You deleted or moved a volume file that is still open in ChimeraX. /Users/hrishikeshdas/Downloads/cryosparc_P102_J452_009_volume_map.mrc To allow fast initial display of volume data ChimeraX does not read all data from the file when it is first opened, and will later read more data when needed. ChimeraX got an error trying to read the above file. > hide #10-11 atoms > hide #!8 models > show #!8 models > hide #10 models > show #10 models > hide #!8 models > show #!8 models > hide #11 models > show #11 models > select add #11 6190 atoms, 6329 bonds, 786 residues, 1 model selected > view matrix models #11,1,0,0,63.85,0,1,0,159.69,0,0,1,126.23 > view matrix models #11,1,0,0,103.36,0,1,0,120.45,0,0,1,140.39 > ui mousemode right ""rotate selected models"" > view matrix models > #11,-0.96375,-0.26623,0.017402,83.842,-0.11442,0.47137,0.87448,138.44,-0.24102,0.84079,-0.48474,105.44 > ui mousemode right ""translate selected models"" > view matrix models > #11,-0.96375,-0.26623,0.017402,162.85,-0.11442,0.47137,0.87448,137.76,-0.24102,0.84079,-0.48474,120.84 > view matrix models > #11,-0.96375,-0.26623,0.017402,119.39,-0.11442,0.47137,0.87448,122.56,-0.24102,0.84079,-0.48474,99.193 > ui mousemode right ""rotate selected models"" > view matrix models > #11,-0.42042,-0.87145,-0.25264,122.4,-0.88223,0.32758,0.33819,104.5,-0.21196,0.36506,-0.90653,93.224 > ui mousemode right ""translate selected models"" > view matrix models > #11,-0.42042,-0.87145,-0.25264,146.34,-0.88223,0.32758,0.33819,116.24,-0.21196,0.36506,-0.90653,95.876 > view matrix models > #11,-0.42042,-0.87145,-0.25264,136.74,-0.88223,0.32758,0.33819,120.13,-0.21196,0.36506,-0.90653,103.54 > fitmap #11 inMap #8 You deleted or moved a volume file that is still open in ChimeraX. /Users/hrishikeshdas/Downloads/cryosparc_P102_J452_009_volume_map.mrc To allow fast initial display of volume data ChimeraX does not read all data from the file when it is first opened, and will later read more data when needed. ChimeraX got an error trying to read the above file. > fitmap #11 inMap #8 You deleted or moved a volume file that is still open in ChimeraX. /Users/hrishikeshdas/Downloads/cryosparc_P102_J452_009_volume_map.mrc To allow fast initial display of volume data ChimeraX does not read all data from the file when it is first opened, and will later read more data when needed. ChimeraX got an error trying to read the above file. > close #8 > open > /Users/hrishikeshdas/Documents/Projects/PAP_SUV3-PNPase/hSUV3/cryosparc_P102_J452_009_volume_map.mrc Opened cryosparc_P102_J452_009_volume_map.mrc as #8, grid size 256,256,256, pixel 1.02, shown at level 0.0431, step 1, values float32 > open > /Users/hrishikeshdas/Documents/Projects/PAP_SUV3-PNPase/hSUV3/cryosparc_P102_J452_009_volume_map.mrc Opened cryosparc_P102_J452_009_volume_map.mrc as #12, grid size 256,256,256, pixel 1.02, shown at level 0.0431, step 1, values float32 > volume #12 level 0.06798 > close #8 > volume #12 level 0.1142 > volume #12 style mesh > volume #12 color #ffb2b2 > volume #12 color #b2b2b2 > volume #12 level 0.1249 > volume #12 level 0.164 > select clear > volume #12 level 0.2127 > volume #12 style surface > volume #12 level 0.3312 > fitmap #11 inMap #12 Fit molecule SUV3_alphafold_dIDP_684.pdb (#11) to map cryosparc_P102_J452_009_volume_map.mrc (#12) using 6190 atoms average map value = 0.1883, steps = 96 shifted from previous position = 5.23 rotated from previous position = 7.31 degrees atoms outside contour = 5111, contour level = 0.33124 Position of SUV3_alphafold_dIDP_684.pdb (#11) relative to cryosparc_P102_J452_009_volume_map.mrc (#12) coordinates: Matrix rotation and translation -0.46318807 -0.87322017 -0.15147058 142.13344203 -0.86496383 0.40816518 0.29195678 121.03459743 -0.19311754 0.26624748 -0.94436111 104.00057249 Axis -0.51797034 0.83906913 0.16634220 Axis point 109.13846857 0.00000000 38.77854707 Rotation angle (degrees) 178.57792433 Shift along axis 45.23517059 > volume #12 style mesh > volume #12 level 0.3585 > volume #12 style surface > volume #12 level 0.1427 ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet > ui tool hide ""command line interface"" > ui tool show clix UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 ATI-7.0.24 OpenGL renderer: AMD Radeon Pro 5300M OpenGL Engine OpenGL vendor: ATI Technologies Inc. Python: 3.11.4 Locale: en_US.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: MacBookPro16,1 Processor Name: 6-Core Intel Core i7 Processor Speed: 2,6 GHz Number of Processors: 1 Total Number of Cores: 6 L2 Cache (per Core): 256 KB L3 Cache: 12 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 2092.0.0.0.0 (iBridge: 23.16.10350.0.0,0) OS Loader Version: 583~2317 Software: System Software Overview: System Version: macOS 15.7.1 (24G231) Kernel Version: Darwin 24.6.0 Time since boot: 22 days, 11 hours, 31 minutes Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0000 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 AMD Radeon Pro 5300M: Chipset Model: AMD Radeon Pro 5300M Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0043 ROM Revision: 113-D3220E-190 VBIOS Version: 113-D32207P1-019 Option ROM Version: 113-D32207P1-019 EFI Driver Version: 01.A1.190 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 3072 x 1920 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-clix: 0.2.0 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-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Window Toolkit duplicate all ChimeraX